{ "generated": "2026-10-16", "schema_version": "1.0", "provenance": "Prepared by the Department of Neurophysiology, Kobe University Graduate School of Medicine. Quantitative statements were checked against the published articles.", "count": 62, "papers": [ { "id": "yamauchi-2026-acm-trans-comput-healthc", "doi": "10.1145/3723048", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1145/3723048", "title": "Development and Evaluation of an Auditory VR Generative System via Natural Language Interaction to Aid Exposure Therapy for PTSD Patients", "authors": [ "Yamauchi Y", "Ino K", "Sakaguchi M", "Zempo K" ], "pi_role": "co_author", "year": 2026, "published_date": "2026-06-22", "journal": "ACM Transactions on Computing for Healthcare", "volume": "7", "issue": "3", "pages": "1-28", "type": "research_article", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "other" ], "tldr": "An LLM-driven tool lets clinicians build spatial-audio scenes for PTSD exposure work by typing plain language, cutting scenario-building time, with usability rated above the SUS benchmark.", "summary": "Producing personalised auditory virtual-reality scenes for exposure-based PTSD therapy normally needs an audio expert and hours of work. The authors built a system in which GPT-4, linked to a labelled sound library, proposes the sounds, their timing and their positions from a typed theme, accepts natural-language edits, and renders the result with HRTF-based spatial audio. A preliminary study compared human-only, human-edited and system-only scenario building, and a user study had three clinicians create scenes for three themes and rate usability and output quality. The tool was usable and fast, but scenes needing tightly timed, overlapping sounds (such as a car crash) were rendered poorly and users often missed the timing errors in the text proposals. This is an engineering and usability study with clinicians only and no patients were exposed to the stimuli; it is exploratory, not a treatment, gives no medical advice, and is not recruiting participants.", "research_question": "Can clinicians without audio-production skills use a natural-language, LLM-based system to create auditory VR stimuli of clinically usable quality, and is the system user-friendly?", "approach": "A GPT-4 system linked to a CSV-indexed sound dataset generates sound queries, scenarios and source coordinates that are rendered with HRTF convolution. It was tested in a preliminary time/validity comparison of 36 scenarios and in a user study where three clinicians each completed three themed trials, followed by the SUS, an anchored 7-point output-quality questionnaire and interviews.", "key_findings": [ { "finding": "Scenario-building time differed across the three conditions (p = 1.7e-7), averaging 1,317 s when humans worked alone, 325 s when humans edited system proposals and 50 s when the system worked alone.", "evidence": "Section 5.5, Fig. 3", "species": "human (clinician raters)", "n": "n = 36 scenarios", "stats": "Kruskal-Wallis p = 1.7e-7; Tukey-HSD A vs B p = 0.015, A vs C p = 7.2e-8, B vs C p = 0.015" }, { "finding": "Clinician-rated scenario validity was lower for system-only scenarios than for human-only ones (p = 0.0084), whereas human-edited system scenarios did not differ from human-only ones (p = 0.21), suggesting the system works best as a draft that humans adjust.", "evidence": "Section 5.5, Fig. 3", "species": "human (clinician raters)", "n": "n = 108 ratings from three clinicians", "stats": "Friedman p = 0.012; A vs C p = 0.0084; A vs B p = 0.21; B vs C p = 0.40" }, { "finding": "All three clinicians obtained audio output in all nine trials without problems, making on average 1.7 modifications per trial, mostly to the scenario rather than to sound positions.", "evidence": "Section 7.1, Table 1", "species": "human (clinicians)", "n": "three participants, nine trials", "stats": "descriptive" }, { "finding": "Clinicians rated spatial grounding at an average of 6.2 and audio clarity at an average of 6.7 on 7-point scales.", "evidence": "Section 7.2, Fig. 8", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive means" }, { "finding": "The mean SUS score was 72.7, above the benchmark of 68, but individual scores ranged from 55 to 82.5.", "evidence": "Section 7.3", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive" }, { "finding": "Scenes requiring several closely related sounds to overlap, such as a car accident, were the weakest, with an average consistency score of 4.3, because the system played such sounds sequentially and users rarely noticed timing errors in text proposals.", "evidence": "Sections 7.2 and 8", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive" } ], "methods": [ "large language model (GPT-4) for sound query, scenario planning and sound-source placement", "dataset linking via llamaindex and langchain", "HRTF convolution for spatial audio rendering", "System Usability Scale", "anchored 7-point Likert output-quality questionnaire", "Kruskal-Wallis, Friedman and Tukey-HSD tests", "post-session interviews" ], "models": [ "clinicians and clinical psychologists experienced in treating PTSD and anxiety disorders" ], "brain_regions": [], "data_code_availability": [], "limitations": [ "Only three clinicians took part and no patients were exposed to the generated stimuli, so clinical feasibility remains untested.", "The sound library had to be kept small because of the LLM token limit.", "Text-only proposals make timing errors hard to notice, and the system cannot render moving sound sources or distance attenuation.", "Outputs that need refinement still require an audio expert, which undercuts independent use by clinicians." ], "keywords": [ "PTSD", "exposure therapy", "auditory VR", "spatial audio", "large language model", "natural language interaction", "usability" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md" }, { "id": "ino-2026-medrxiv", "doi": "10.64898/2026.05.02.26352243", "pmid": null, "pmcid": null, "url": "https://medrxiv.org/cgi/content/short/2026.05.02.26352243v1", "title": "Sound Exposure During Sleep (SES) in PTSD Patients: An Open-Label Feasibility Study", "authors": [ "Ino K", "Zempo K", "Hori A", "Maruyama T", "Tominaga M", "Sugaya Y", "Oba M", "Yamauchi Y", "Sato L", "Sekiba H", "Kawakami C", "Bachman G", "Waki I", "Kitagawa H", "Yanagisawa M", "Kim Y", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2026, "published_date": "2026-05-04", "journal": "medRxiv", "volume": null, "issue": null, "pages": null, "type": "preprint", "peer_reviewed": false, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "sound_exposure_during_sleep", "human_sleep_clinical", "fear_memory_ptsd" ], "tldr": "A single-arm, open-label study tested whether personalized trauma-linked sounds can be delivered during NREM sleep to people with PTSD; all six who reached the overnight session completed it.", "summary": "This preprint reports an exploratory, single-arm, open-label feasibility study of Sound Exposure during Sleep (SES), in which each participant with PTSD helped create a short personal sound linked to their own trauma memory that was then played back during NREM sleep. The primary question was procedural: could the personalized sound be built while awake and then delivered overnight under technician monitoring, and would participants tolerate the night. Of 13 consenting patients, 8 entered sound development and 6 received and completed the overnight session, with all recorded adverse events at the mildest grade and none attributed to the sounds during sleep. Three device problems occurred overnight but none stopped a session, and the authors stress that sham-controlled, blinded trials are needed before any conclusions beyond feasibility. SES is at an exploratory stage and is not a treatment; this page gives no medical advice, and the study is not enrolling participants.", "research_question": "Is it feasible to create a personalized trauma-linked sound with each PTSD patient and deliver it repeatedly during NREM sleep in a monitored overnight session?", "approach": "Patients built and rated a 30-second personal sound across clinic visits, then spent one monitored night in a hospital research unit where a sleep technician started sound playback only after sustained deep NREM sleep; feasibility, adverse events, device events and sleep architecture were recorded, with a follow-up visit 1-4 weeks later.", "key_findings": [ { "finding": "Of 13 patients who gave written consent, 8 entered the sound-development phase and 6 of those 8 (75%) went on to the overnight session.", "evidence": "Fig. 2", "species": "human", "n": "13 consented; 8 entered sound development; 6 reached Visit 4", "stats": null }, { "finding": "All 6 participants who reached the overnight session completed it (completion rate 100%), none asked to stop early, and all attended the follow-up visit.", "evidence": "Results, Primary Outcome", "species": "human", "n": "n = 6", "stats": null }, { "finding": "All recorded adverse events were CTCAE grade 1, none were judged attributable to sound delivered during sleep, and no confusion, delirium or suicidal ideation was observed.", "evidence": "Results, Safety and Adverse Events", "species": "human", "n": "n = 6", "stats": null }, { "finding": "Device-related events occurred in three participants overnight (an unresponsive tagging button, a recording-PC power shortfall after sound delivery, and a wrong earphone), but none prevented completion of the session.", "evidence": "Results; Methods, Equipment and Data Handling", "species": "human", "n": "3 of 6 participants", "stats": null } ], "methods": [ "single-arm open-label feasibility design with prospective trial registration", "home portable EEG screening for slow-wave sleep duration", "personalized 30-second trauma-linked sound development rated with subjective distress scales", "overnight sleep-stage-timed sound delivery operated manually by an on-site sleep technician", "CTCAE v5.0 adverse-event monitoring", "Welch t-tests and permutation-based sensitivity analyses (exploratory)" ], "models": [ "adult patients with PTSD (n = 6 completing; all female)" ], "brain_regions": [], "data_code_availability": [ { "type": "data", "url": null, "as_stated": "Source data underlying main and supplementary figures are provided as Source Data files, excluding direct personal identifiers" }, { "type": "code", "url": null, "as_stated": "no custom analytical code beyond standard library function calls was required" } ], "limitations": [ "There was no sham comparator, so nonspecific and expectancy contributions cannot be separated from the sound itself.", "The sample was small (n = 6), all female, and selected by physician judgement, limiting generalizability.", "The two protocol versions were run sequentially and are nearly collinear with enrollment time, so their comparison is confounded.", "Half of the participants were on stable memantine, a possible mechanistic confounder.", "Sleep staging, stimulation and outcome ratings were not blinded." ], "keywords": [ "PTSD", "sleep", "targeted memory reactivation", "NREM sleep", "feasibility", "auditory cues" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md" }, { "id": "nagai-2026-jove", "doi": "10.3791/69042", "pmid": "42113802", "pmcid": null, "url": "https://doi.org/10.3791/69042", "title": "Method for Selective REM Sleep Deprivation using The Selective Nose Flicking for Forgetting REM (SNiFFer)", "authors": [ "Nagai K", "Koyanagi I", "Kawakami C", "Chavan P", "Wang Y", "Naoi T", "Tezuka T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2026, "published_date": "2026-04-21", "journal": "Journal of Visualized Experiments", "volume": null, "issue": "230", "pages": null, "type": "methods_protocol", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "rem_sleep_memory", "sleep_staging_closed_loop_tools", "fear_memory_ptsd" ], "tldr": "A protocol that interrupts REM sleep in mice by brushing the nose whenever a real-time EEG classifier detects REM, with stimulation-matched yoked controls; 6 h of deprivation after trace fear conditioning left recall unchanged.", "summary": "This methods article describes SNiFFer, a way to selectively deprive mice of REM sleep by lightly brushing the top of the nose with a soft paintbrush, which wakes the animal within about a second. A real-time, single-channel EEG sleep-stage classifier flags REM onset so the experimenter can stimulate only during REM, while a paired yoked mouse receives brushing at the same times regardless of its own state. The protocol covers EEG electrode surgery, handling and habituation, baseline recording, trace fear conditioning, 6 h of post-training deprivation, recall tests and analysis. In 12 deprived and 12 yoked mice, stimuli fell mostly in REM for the deprived group, total REM time and REM episode duration fell, and NREM sleep rose, which the authors suggest reflects homeostatic compensation. Contextual and cued fear recall did not differ between groups, indicating no measurable effect of this 6 h REM loss on trace fear memory consolidation in this paradigm.", "research_question": "Can REM sleep be removed selectively in mice with a mild, localized tactile stimulus and a stimulation-matched control, and does REM loss in the 6 h after trace fear conditioning affect memory consolidation?", "approach": "Manual nasal brushing triggered by an automatic real-time single-channel EEG REM detector (4-s epochs), compared against yoked mice receiving identical stimulation timing, with expert-scored sleep architecture and freezing-based contextual and cued recall tests after trace fear conditioning.", "key_findings": [ { "finding": "Brushing the nose during REM sleep produced arousal with a mean latency of 0.89 ± 0.063 s from stimulus onset, judged by whisker movement.", "evidence": "Protocol step 5.1.1", "species": "mouse", "n": null, "stats": "mean ± SEM" }, { "finding": "In the deprived group over 85% of brushing events fell in REM sleep, whereas in the yoked group more than 90% fell in wakefulness or NREM sleep, confirming REM-targeted delivery.", "evidence": "Fig. 1B", "species": "mouse", "n": "n = 12 REM-deprived mice (6 males and 6 females) and n = 12 yoked mice (6 males and 6 females)", "stats": null }, { "finding": "Over the 6-hour deprivation period, deprived mice had significantly less total REM sleep, less wake and more NREM sleep than yoked controls, which the authors suggest reflects homeostatic compensation of lost REM by NREM sleep.", "evidence": "Fig. 1C", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "p < 0.01 or p < 0.05, two-tailed unpaired t test with Welch's correction" }, { "finding": "The protocol shortened individual REM episodes but did not change the number of REM episodes or overall sleep-stage transitions.", "evidence": "Fig. 1D–F", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "p < 0.05, two-way ANOVA (sleep stage x group) with post hoc bootstrap and Fisher's LSD test (episode duration)" }, { "finding": "The relationship between REM amount and NREM-to-REM transitions differed between groups, with a significantly different regression slope, and some deprived mice showed REM episode counts beyond the mean ± 2 SD range because of increased REM transitions.", "evidence": "Fig. 1C, 1G", "species": "mouse", "n": "n = 12 mice per group", "stats": "p < 0.0001, linear regression slope comparison" }, { "finding": "After comparable conditioning in both groups, 6 h of REM deprivation following trace fear conditioning produced no significant group differences in contextual or sound-cued freezing or in the discrimination index, and REM amount did not correlate significantly with freezing.", "evidence": "Fig. 1H–M", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "not significant; two-tailed unpaired t test with Welch's correction (contextual freezing, discrimination index); Pearson correlation" } ], "methods": [ "EEG screw electrode implantation under isoflurane anesthesia", "automatic real-time single-channel EEG sleep-stage classification using the last 4-s epoch", "closed-loop manual nose brushing with a soft paintbrush at REM onset", "yoked control mice receiving stimulation matched in onset and duration", "handling and habituation over four days", "trace fear conditioning with five tone–footshock pairings", "contextual and sound-cued recall tests with automated freezing scoring", "expert manual sleep-stage scoring of EEG", "discrimination index and shock reactivity index", "unpaired t tests with Welch's correction, two-way ANOVA, linear regression and Pearson correlation" ], "models": [ "C57BL/6J mice, male and female, 11–13 weeks old" ], "brain_regions": [], "data_code_availability": [], "limitations": [ "Because brushing is done by hand, the protocol is not suited to long-term REM sleep deprivation.", "The real-time REM detector needs more than 4 s of EEG, so the operator must also watch the EEG signal.", "Physiological or biochemical stress markers such as corticosterone were not measured, so the authors cannot conclude the method is less stressful than other approaches.", "Some mice had relatively high or low REM amounts, a source of within-group variability that may confound group comparisons.", "Deprivation covered only 6 h after learning; whether REM after the session compensated for the loss would require longer deprivation to test.", "Excess bedding or the animal's posture can block access to the nose and must be managed during the session." ], "keywords": [ "REM sleep deprivation", "SNiFFer", "closed-loop", "real-time sleep staging", "EEG", "yoked control", "nasal tactile stimulation", "trace fear conditioning", "memory consolidation", "mouse" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md" }, { "id": "srinivasan-2025-nat-commun", "doi": "10.1038/s41467-025-62554-8", "pmid": "40764488", "pmcid": "PMC12325634", "url": "https://doi.org/10.1038/s41467-025-62554-8", "title": "Transient reactivation of small ensembles of adult-born neurons during REM sleep supports memory consolidation in mice", "authors": [ "Srinivasan S", "Koyanagi I", "Vergara P", "Wang Y", "Ohba A", "Naoi T", "Vogt KE", "Chérasse Y", "Kutsumura N", "Sakurai T", "Tezuka T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2025, "published_date": "2025-08-05", "journal": "Nature Communications", "volume": "16", "issue": "1", "pages": "7210", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory", "fear_memory_ptsd" ], "tldr": "In mice, a handful of young adult-born dentate gyrus neurons active during fear learning reactivate in REM sleep, and silencing them then, or at one theta phase, disrupts memory consolidation.", "summary": "The study asked whether the specific information carried by young adult-born neurons in the dentate gyrus must be replayed during REM sleep for fear memory to be consolidated. Calcium imaging in freely moving mice showed that adult-born neuron population activity was more stable across sessions than that of developmentally born granule neurons and correlated more strongly between the conditioning context and later REM sleep. Using activity-dependent genetic tagging with a light-gated silencer, the authors found that inhibiting only the few context-tagged young adult-born neurons during REM sleep after conditioning reduced later fear memory, whereas silencing them during retrieval, silencing neurons tagged in a different context, or silencing older adult-born or developmentally born neurons did not. A closed-loop system further showed that silencing adult-born neuron activity at only one of four theta phases during REM sleep reduced both contextual and trace fear memory, suggesting that timing within the theta cycle matters for consolidation.", "research_question": "Is REM sleep reactivation of specific adult-born neuron memory ensembles, and their timing relative to theta oscillations, causally required for fear memory consolidation?", "approach": "The authors combined miniature-microscope calcium imaging of adult-born and developmentally born granule neurons across fear conditioning and sleep with activity-dependent optogenetic silencing of tagged ensembles restricted to REM sleep or to retrieval. They also used closed-loop, theta phase-specific optogenetic silencing of adult-born neurons during REM sleep after trace fear conditioning.", "key_findings": [ { "finding": "Activity-dependent tagging labelled only a few young adult-born neurons per mouse, and the authors report that REM sleep reactivation of ensembles of as few as ~3 such neurons is necessary for fear memory consolidation.", "evidence": "Fig. 2b-d; Fig. 3a-b", "species": "mouse", "n": "n = 8 mice", "stats": "mean (standard deviation) of 2.4 (3.2) tagged neurons per mouse" }, { "finding": "Population activity of adult-born neurons was more stable over time than that of granule neurons and showed stronger correlations between the conditioning context and subsequent REM sleep.", "evidence": "Fig. 1i-k; Supplementary Table 2", "species": "mouse", "n": "GNs, n = 363 neurons in 3 mice; ABNs, n = 136 neurons in 3 mice", "stats": "linear model of population vector correlations" }, { "finding": "Optogenetically silencing context A-tagged young adult-born neurons only during REM sleep after conditioning reduced later contextual freezing compared with controls, with light delivery in REM sleep reaching a mean sensitivity of 0.83 and precision of 0.82.", "evidence": "Fig. 3a-b; Supplementary Fig. 4d, 5a-b", "species": "mouse", "n": "cfos-, n = 15 mice; cfos+, n = 14", "stats": "p = 0.002, two-tailed unpaired t-test" }, { "finding": "REM sleep silencing had no detectable effect on memory when the tagged ensembles came from a different context (p = 0.69), from 10-week-old adult-born neurons (p = 0.38), or from developmentally born granule neurons (p = 0.77).", "evidence": "Fig. 3c-h", "species": "mouse", "n": "context C: cfos-, n = 10, cfos+, n = 11; 10-week-old ABNs: cfos-, n = 10, cfos+, n = 12; GNs: cfos-, n = 13, cfos+, n = 14 mice", "stats": "p = 0.69, p = 0.38, p = 0.77, two-tailed unpaired t-test" }, { "finding": "Silencing tagged adult-born neurons during memory retrieval tests in wakefulness did not change freezing.", "evidence": "Fig. 2i-l", "species": "mouse", "n": "n = 14 mice; n = 10", "stats": "p = 0.21 and p = 0.056, two-tailed paired t-test" }, { "finding": "Closed-loop silencing of adult-born neurons at Phase 1 of the local theta cycle during REM sleep, but not at the other three phases, reduced freezing in both context and trace fear tests versus yoked controls.", "evidence": "Fig. 4c-e", "species": "mouse", "n": "Yoked control, n = 12 mice; Phase 1, n = 7; Phase 2, n = 9; Phase 3, n = 10; Phase 4, n = 9 mice", "stats": "Context test: p = 0.042; Trace test: p = 0.013; one-way ANOVA with Dunnett's multiple comparisons" } ], "methods": [ "in vivo calcium imaging with a miniaturised microendoscope in freely moving, naturally sleeping mice", "activity-dependent genetic tagging with doxycycline-controlled cfos-tTA expression", "optogenetic silencing with Jaws and halorhodopsin restricted to REM sleep", "closed-loop theta phase-specific light delivery based on local field potential recordings", "acute brain slice electrophysiology", "contextual and trace fear conditioning", "linear mixed models of neuronal activity and population vector correlations" ], "models": [ "pNestin-CreERT2/cfos-tTA/TRE-LSL-GCaMP6s triple-transgenic mice", "nestin/cfos/TRE-LSL-JawsGFP mice", "nestin/pCAG-LSL-Halorhodopsin-YFP mice", "C57BL/6J mice" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/2xfktwhj8x.1", "as_stated": "Data for LFP and phase-specific silencing study is available at Mendeley Data" }, { "type": "code", "url": "https://github.com/vergaloy/Srinivasan_Koyanagi_2025", "as_stated": "The datasets and custom code used to perform the non-trivial quantitative analyses are available on GitHub" }, { "type": "code", "url": "https://zenodo.org/records/15803872", "as_stated": "A preserved snapshot of the code at the time of publication has also been archived on Zenodo" } ], "limitations": [ "Some mice showed no detectable tagged cells, which the authors attribute to individual variability or technical limits of the cfos promoter-driven expression system.", "Technical challenges prevented reliable correlation analyses at the level of individual mice, so the authors relied on larger groups, a blinded and randomized replication, and control experiments.", "Labelling relies on cfos promoter activation, which could in principle bias which neuron subsets are tagged, although the authors argue this does not substantially affect their interpretation." ], "keywords": [ "adult neurogenesis", "adult-born neurons", "REM sleep", "memory consolidation", "memory reactivation", "theta oscillation", "fear conditioning", "optogenetics", "calcium imaging", "dentate gyrus" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md" }, { "id": "chen-2025-embc", "doi": "10.1109/EMBC58623.2025.11253414", "pmid": "41336586", "pmcid": null, "url": "https://doi.org/10.1109/EMBC58623.2025.11253414", "title": "Classification of Global Brain States by Resampling and Data Augmentation of EEG", "authors": [ "Chen J", "Koyanagi I", "Sakaguchi M", "Tezuka T" ], "pi_role": "co_author", "year": 2025, "published_date": "2025-07-14", "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "volume": null, "issue": null, "pages": "1-7", "type": "conference_paper", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "sleep_staging_closed_loop_tools" ], "tldr": "Comparing resampling and SMOTE on training and validation sets, a ResNet classifier of four mouse EEG brain states scored best when only the validation data were undersampled.", "summary": "Some brain states, such as a high-theta form of wakefulness, occur in a small fraction of EEG epochs, so classifiers trained on imbalanced data tend to ignore them. The authors trained a one-dimensional ResNet on single-channel mouse EEG labelled by experts into four states (REM, NREM, high-theta wake and low-theta wake). They tested raw data, random oversampling, random undersampling and SMOTE on both the training and the validation (early-stopping) sets, giving 16 combinations, while keeping the test set at its original distribution. Undersampling only the validation data while leaving training data unchanged gave the highest overall F1 score, which the authors take to suggest that balancing the data used for model selection can matter on its own. The work is intended to support a closed-loop optogenetic framework that acts when a given brain state is detected.", "research_question": "Does applying resampling or SMOTE to the training and/or validation data improve automatic classification of rare global brain states, including wake substates, from single-channel mouse EEG?", "approach": "A ResNet was trained on expert-labelled four-second EEG epochs from mice, and all 16 combinations of raw, oversampled, undersampled and SMOTE-augmented training and validation sets were compared on an untouched test set using class-weighted and per-class accuracy, precision, recall and F1.", "key_findings": [ { "finding": "The dataset comprised 549,595 four-second epochs from 610 hours of single-channel mouse EEG, each labelled by experts as REM, NREM, high-theta wake or low-theta wake.", "evidence": "Section III (Dataset)", "species": "mouse", "n": "549,595 epochs from 610 hours of recording", "stats": null }, { "finding": "With no resampling of either training or validation data, the overall F1 score on the test data was 85.00%, whereas undersampling only the validation data raised it to 86.04%, the highest of the 16 combinations tested.", "evidence": "Table IV; Section VII", "species": "mouse", "n": "16 training/validation combinations; 60% training, 20% validation, 20% test", "stats": "overall F1 85.00% (raw/raw) vs 86.04% (raw train, undersampled validation); class-size-weighted averages" }, { "finding": "The raw-training, undersampled-validation combination also gave the highest per-class F1 for low-theta wake, high-theta wake and NREM, but not for REM, where it was only slightly below the raw/raw combination.", "evidence": "Table IV; Section VII", "species": "mouse", "n": null, "stats": "per-class F1 scores" }, { "finding": "During training, undersampling started with low accuracy but caught up with the other methods after many iterations, while oversampling reached the highest training accuracy; test accuracy fluctuated more but stayed close to training accuracy.", "evidence": "Fig. 5; Fig. 6", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors suggest that adjusting the class distribution of the validation data alone, without preprocessing the training data, can improve overall accuracy and precision.", "evidence": "Section VII", "species": "mouse", "n": null, "stats": null } ], "methods": [ "EEG and EMG electrode implantation in mice under isoflurane anesthesia", "single-channel EEG segmented into four-second epochs and downsampled to 128 Hz", "expert labelling of four brain states (REM, NREM, high-theta wake, low-theta wake)", "one-dimensional ResNet classifier with residual blocks", "random oversampling, random undersampling and SMOTE applied to training and validation sets", "early stopping on validation data; test set kept at original class distribution", "class-weighted and per-class accuracy, precision, recall and F1 score" ], "models": [ "mice (9 weeks old at surgery)" ], "brain_regions": [], "data_code_availability": [], "limitations": [ "Only a single dataset collected in one laboratory was used.", "All recordings were mouse EEG from skull-fixed electrodes, so applying the method to human scalp EEG would need to account for larger noise.", "Other network architectures and further data augmentation types were not evaluated and are left for future work.", "For REM, the best-performing resampling combination was not the best, so gains were not uniform across classes." ], "keywords": [ "EEG", "global brain states", "high-theta wake", "class imbalance", "resampling", "SMOTE", "data augmentation", "ResNet", "validation set balancing", "mouse", "closed-loop optogenetics" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md" }, { "id": "sekiba-2025-medrxiv", "doi": "10.1101/2025.07.02.25330609", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1101/2025.07.02.25330609", "title": "REM sleep rhythm impairment in people with PTSD", "authors": [ "Sekiba H", "Hirohata S", "Hori A", "Suga Y", "Toshishige Y", "Vergara P", "Masaki M", "Tominaga M", "Yanagisawa M", "Kim Y", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2025, "published_date": "2025-07-05", "journal": "medRxiv", "volume": null, "issue": null, "pages": null, "type": "preprint", "peer_reviewed": false, "open_access": false, "license": "All rights reserved (medRxiv; no reuse without permission)", "related_versions": [], "themes": [ "human_sleep_clinical" ], "tldr": "Multi-night home polysomnography shows that people with PTSD sleep about as long as matched controls but have delayed, short, fragmented REM sleep and a weakened rhythm of REM recurrence across the night.", "summary": "Laboratory sleep studies of PTSD give conflicting results, possibly because a single night in an unfamiliar room distorts sleep in hypervigilant people. This observational study recorded sleep at home over several nights with a portable five-electrode polysomnography device in 29 people with PTSD and 29 healthy controls matched by propensity score on age, sex and BMI, with stages scored by trained technologists. Total sleep time did not differ, but the PTSD group had less regular sleep timing, longer sleep onset, lower sleep efficiency, more arousals and a set of REM sleep abnormalities. Autocorrelation analyses against shuffled data showed that the periodic recurrence of REM sleep, and of deep N3 sleep, was weaker in PTSD, leading the authors to suggest that REM sleep is a core domain of sleep disruption in the disorder. This is an observational research study, not a treatment; it gives no medical advice and is not recruiting participants.", "research_question": "What does naturalistic sleep architecture look like in people with PTSD when it is recorded at home over multiple nights rather than in a laboratory?", "approach": "Participants self-applied a five-electrode portable PSG harness at home for several nights; technologist-scored 30-second epochs were compared between PTSD and propensity-matched controls for sleep regularity, macro-architecture, stage-specific latency, episode and fragmentation measures, and for stage rhythmicity using autocorrelation compared with shuffled episode sequences.", "key_findings": [ { "finding": "People with PTSD had a lower sleep regularity index than controls, while the within-group variation of midsleep time was similar (p = 0.22).", "evidence": "Fig. 2b-c", "species": "human", "n": "Healthy (n = 28) versus PTSD (n = 29)", "stats": "Mann-Whitney test, U = 252, p = 0.014" }, { "finding": "Total sleep time did not differ (p = 0.70), but people with PTSD took longer to fall asleep (p = 0.018), had lower sleep efficiency (p = 0.0096) and a higher arousal index (p = 0.020).", "evidence": "Fig. 3a-d", "species": "human", "n": "Healthy (n = 29) versus PTSD (n = 29)", "stats": "Welch's t-test for total sleep time; Mann-Whitney tests for latency, efficiency and arousal index" }, { "finding": "People with PTSD had less REM sleep (p = 0.045) and more N2 (p = 0.042), a longer latency to REM sleep (p < 0.001), shorter REM episodes (p = 0.0042) and a higher REM fragmentation index (p = 0.0033), whereas most NREM parameters did not differ.", "evidence": "Fig. 4a-e", "species": "human", "n": "Healthy (n = 29) versus PTSD (n = 29)", "stats": "REM latency: Mann-Whitney test, U = 181, p < 0.001; REM episode duration: t(56) = 3.0, p = 0.0042; fragmentation: U = 234, p = 0.0033" }, { "finding": "Across all recorded nights, controls showed a first REM sleep peak around 75 minutes and a second N3 peak around 110 minutes after sleep onset, and both peaks were absent in people with PTSD.", "evidence": "Fig. 5, Fig. S2", "species": "human", "n": "Healthy: 130 nights; PTSD: 149 nights", "stats": "descriptive (group stacked-area probability)" }, { "finding": "REM sleep latency was more variable in PTSD, and REM rhythmicity was weaker both as deviation of the REM autocorrelation from shuffled data (p < 0.001) and as a wider spread of intervals between REM episodes within nights (p = 0.0019).", "evidence": "Fig. 6b, 6e-f", "species": "human", "n": "Healthy (n = 28) versus PTSD (n = 27) participants; interval analysis Healthy (n = 108) versus PTSD (n = 76) nights", "stats": "latency variability: F(28, 28) = 3.7, p < 0.001; rhythmicity: Mann-Whitney test, U = 180, p < 0.001; interval SD: U = 3006, p = 0.0019" }, { "finding": "N3 rhythmicity was also weaker in PTSD (p = 0.011), whereas N2 rhythmicity was similar between groups and neither group showed rhythmic N1 or WASO.", "evidence": "Fig. 7c-d, Fig. S3, Fig. S4", "species": "human", "n": "Healthy (n = 27) versus PTSD (n = 22)", "stats": "Two-tailed unpaired t-test, t(47) = 2.6, p = 0.011" } ], "methods": [ "multi-night in-home polysomnography with a portable self-applied five-electrode device", "sleep staging in 30-second epochs by trained sleep technologists according to the AASM manual", "propensity-score matching of controls on age, sex and BMI", "sleep regularity index", "autocorrelation-based rhythmicity analysis against within-night shuffled episode sequences", "two-Gaussian mixture model to set a threshold for REM episode intervals", "bias-corrected and accelerated bootstrap confidence intervals" ], "models": [ "adults with PTSD (eligibility by the Posttraumatic Diagnostic Scale, PDS-IV)", "propensity-matched healthy adult controls" ], "brain_regions": [], "data_code_availability": [ { "type": "code", "url": "https://github.com/seki-haru/PTSD_Sleep_Analysis.git", "as_stated": "Custom MATLAB scripts used for sleep parameter analysis ... are available on GitHub" }, { "type": "data", "url": null, "status": "not_publicly_resolvable_2026-10-16", "as_stated": "The data supporting the plots in this study are available on Mendeley Data" } ], "limitations": [ "Comorbid illnesses and medications, which can affect sleep, were not accounted for.", "Selective serotonin reuptake inhibitors, the first-line drug for PTSD, lengthen REM latency and shorten REM sleep, so medication may contribute to the REM pattern observed.", "Too few N3 episodes were available to analyze N3 episode intervals.", "The work is a preprint that had not been certified by peer review." ], "keywords": [ "post-traumatic stress disorder", "REM sleep", "NREM-REM cycle", "sleep rhythmicity", "home-based polysomnography", "sleep regularity" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md" }, { "id": "chavan-2025-neurobiol-learn-mem", "doi": "10.1016/j.nlm.2025.108062", "pmid": "40345378", "pmcid": "PMC13213699", "url": "https://doi.org/10.1016/j.nlm.2025.108062", "title": "Memory processing by hippocampal adult-born neurons", "authors": [ "Chavan P", "Kitamura T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2025, "published_date": "2025-07", "journal": "Neurobiology of Learning and Memory", "volume": "220", "issue": null, "pages": "108062", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory", "fear_memory_ptsd" ], "tldr": "A review that walks through each memory stage, from encoding to sleep consolidation, retrieval and forgetting, to explain what new neurons born in the adult dentate gyrus contribute.", "summary": "This review organizes the evidence on adult-born neurons of the hippocampal dentate gyrus by the order of memory stages: encoding, consolidation during sleep, retrieval and forgetting. It contrasts these young cells with granule cells born during development, stressing their brief window of high excitability and plasticity and their role in telling similar experiences apart. The authors highlight work showing that adult-born neurons reactivated during REM sleep are needed for consolidation of contextual fear memory, a role not attributed to developmentally born granule cells. They also discuss how raising neurogenesis promotes forgetting in rodents and why this has drawn interest for post-traumatic stress disorder, while noting that human evidence remains preliminary. The review closes with open questions on human neurogenesis, network-level coordination and sleep-based consolidation models.", "research_question": "What distinct roles do adult-born dentate gyrus neurons play at each stage of memory, and how might these roles matter for human memory disorders?", "approach": "Narrative review that arranges rodent and human studies chronologically along the stages of memory and compares adult-born neurons with developmentally born granule cells.", "key_findings": [ { "finding": "The review argues that adult-born neurons pass through a transient window of heightened excitability and synaptic plasticity, approximately 4 to 6 weeks after cell division, which suits them to discriminating novel or similar experiences.", "evidence": "Section 1; Abstract", "species": "mouse; rat", "n": null, "stats": null }, { "finding": "The authors emphasize that adult-born neurons reactivated during REM sleep after contextual fear conditioning are needed for memory consolidation, a function they describe as absent in developmentally born granule cells.", "evidence": "Section 2.6; Fig. 5", "species": "mouse", "n": null, "stats": null }, { "finding": "Although human adult neurogenesis is still debated, the review cites a survey in which 84% of 57 studies supported the presence of newborn neurons in the adult human hippocampus.", "evidence": "Introduction; Section 5", "species": "human", "n": "57 studies", "stats": null }, { "finding": "The review proposes that raising neurogenesis, for example with memantine, which promotes forgetting of conditioned fear in rodents, is a direction worth testing for PTSD, while stressing that human data so far lack placebo-controlled trials.", "evidence": "Sections 2.8 and 3", "species": "mouse; human", "n": null, "stats": null } ], "methods": [ "literature review" ], "models": [ "rodents", "humans (postmortem and clinical literature)" ], "brain_regions": [ "dentate gyrus", "CA3", "CA1", "entorhinal cortex", "supramammillary nucleus" ], "data_code_availability": [ { "type": "data", "url": null, "as_stated": "No data was used for the research described in the article." } ], "limitations": [ "The extent of adult neurogenesis in the human hippocampus remains debated, and humans are thought to have far fewer adult-born neurons than rodents.", "It is unclear whether forgetting mechanisms driven by increased neurogenesis in mice also operate in humans.", "Whether adult-born neurons act as core units of memory engrams or support reactivation of engrams held by other neurons is still unresolved.", "The human memantine data cited come from an open-label study without a placebo control." ], "keywords": [ "adult neurogenesis", "dentate gyrus", "pattern separation", "REM sleep", "memory consolidation", "forgetting", "engram", "PTSD", "memantine" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md" }, { "id": "arai-2025-jneurosci", "doi": "10.1523/JNEUROSCI.2365-24.2025", "pmid": "40550695", "pmcid": "PMC12244322", "url": "https://doi.org/10.1523/JNEUROSCI.2365-24.2025", "title": "Diverse Firing Profiles of Crhbp-positive Neurons in the Dorsal Pons Suggestive of Their Pleiotropic Roles in REM Sleep Regulation in Mice", "authors": [ "Arai Y", "Kashiwagi M", "Kanda T", "Koyanagi I", "Sakaguchi M", "Yanagisawa M", "Koyama Y", "Hayashi Y" ], "pi_role": "co_author", "year": 2025, "published_date": "2025-06-23", "journal": "The Journal of Neuroscience", "volume": "45", "issue": "28", "pages": "e2365242025", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-SA 4.0", "related_versions": [], "themes": [ "sleep_circuits" ], "tldr": "Opto-tagged single-unit recordings in mice show that many Crhbp-positive neurons in the dorsal pons fire selectively in REM sleep and split into several electrophysiological subtypes.", "summary": "Crhbp-positive neurons in the sublaterodorsal tegmentum of the pons were recently shown to be important for REM sleep, but how individual cells fire across sleep and wake was unknown. The authors combined opto-tagging with glass-pipette single-unit recordings in head-fixed, unanesthetized male mice, and separately recorded the subset projecting to the medulla using a retrograde viral vector. The largest group of recorded cells was REM sleep-active, followed by wake-active cells, and most medulla-projecting cells were REM sleep-active. Clustering of firing rates and spike-waveform analysis divided each class into subtypes, and a subset of REM sleep-active cells matched the classical REM-on firing criteria. The authors suggest that these neurons play diverse roles in REM sleep regulation, including possible links to EEG theta/gamma fluctuations and muscle tone.", "research_question": "How do individual Crhbp-positive neurons in the dorsal pons, including those projecting to the medulla, fire across wake, NREM sleep and REM sleep?", "approach": "Crhbp-Cre mice expressing channelrhodopsin-2 (crossed with Ai32, or injected with a Cre-dependent retrograde AAV into the medulla) were used to identify Crhbp-positive neurons by light-evoked spikes during glass-pipette unit recordings with EEG/EMG in head-fixed mice. Neurons were classified by state-dependent firing, K-means clustering and spike width, and their firing was correlated with EEG theta/gamma power and EMG.", "key_findings": [ { "finding": "Of 58 opto-tagged Crhbp-positive neurons recorded from eight mice, the largest group was REM sleep-active (41.4%, n = 24) and the next largest was wake-active (22.4%, n = 13).", "evidence": "Fig. 1H,I", "species": "mouse", "n": "n = 58 neurons from eight mice", "stats": "proportions did not differ between narrow- and broad-waveform neurons (Fisher's exact test; p = 0.725)" }, { "finding": "Among Crhbp-positive neurons projecting to the medulla, three of four recorded cells (75%) were REM sleep-active and one (25%) was wake-active.", "evidence": "Fig. 6C-E", "species": "mouse", "n": "n = 4 neurons from 3 mice", "stats": null }, { "finding": "K-means clustering split the 24 REM sleep-active neurons into four subtypes (9, 7, 3 and 5 neurons) that differed in firing rate across states, with low-rate Cluster 1 cells mostly having broad spike waveforms.", "evidence": "Fig. 2C-I", "species": "mouse", "n": "n = 24 REM sleep-active neurons", "stats": "optimal K chosen by BIC calculated 100 times" }, { "finding": "Eight of 27 REM sleep-active Crhbp-positive neurons (25.9%) met the classical REM-on criteria of continuous firing in REM sleep and increased firing before REM onset, suggesting partial overlap between the two populations.", "evidence": "Fig. 6O", "species": "mouse", "n": "N = 8 neurons; n = 8 transitions", "stats": "Dunnett's test" }, { "finding": "During REM sleep, the firing of 20 of 62 Crhbp-positive neurons (32.3%) correlated significantly with EEG theta power and 10 (16.1%) with EEG gamma power.", "evidence": "Fig. 7", "species": "mouse", "n": "n = 62 neurons", "stats": "Pearson's correlation test" }, { "finding": "During REM sleep, 14 of 62 Crhbp-positive neurons (22.6%) showed firing correlated with EMG, mostly negatively (10 neurons, 71.4%), which the authors take as further support for a role in REM sleep muscle atonia.", "evidence": "Fig. 9A-C", "species": "mouse", "n": "n = 62 neurons", "stats": "Pearson's correlation test" } ], "methods": [ "opto-tagging with channelrhodopsin-2 to identify genetically defined neurons", "glass-pipette single-unit extracellular recording in head-fixed unanesthetized mice", "EEG/EMG sleep-wake scoring", "juxtacellular labeling with Neurobiotin to validate opto-tagging", "retrograde AAV for projection-specific labeling", "K-means clustering with BIC model selection", "spike waveform analysis", "Pearson correlation of firing rate with EEG theta/gamma power and EMG" ], "models": [ "Crhbp-Cre mice", "Crhbp-Cre; Ai32 (ChR2-EYFP) mice", "adult male mice" ], "brain_regions": [ "sublaterodorsal tegmentum (SubLDT)", "laterodorsal tegmentum (LDT)", "dorsal pons", "medullary gigantocellular reticular nucleus" ], "data_code_availability": [], "limitations": [ "Glass-pipette recording captures one neuron at a time over short durations, so throughput and sample size were small, especially for medulla-projecting neurons.", "Basal forebrain-projecting Crhbp-positive neurons could not be recorded in a projection-specific way.", "Juxtacellular recordings across sleep-wake in unanesthetized mice were not possible, so the neurotransmitter identity of each class or cluster remains unresolved.", "The physiological role of wake-active medulla-projecting Crhbp-positive neurons could not be confirmed." ], "keywords": [ "REM sleep", "pons", "Crhbp", "opto-tagging", "single-unit recording", "brainstem", "mouse" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md" }, { "id": "vergara-2025-natcommun", "doi": "10.1038/s41467-025-58817-z", "pmid": "40216771", "pmcid": "PMC11992088", "url": "https://doi.org/10.1038/s41467-025-58817-z", "title": "A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging", "authors": [ "Vergara P", "Wang Y", "Srinivasan S", "Dong Z", "Feng Y", "Koyanagi I", "Kumar D", "Chérasse Y", "Naoi T", "Sugaya Y", "Sakurai T", "Kano M", "Shuman T", "Cai D", "Yanagisawa M", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2025, "published_date": "2025-04-11", "journal": "Nature Communications", "volume": "16", "issue": "1", "pages": "3443", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [ { "doi": "10.1101/2023.05.19.540935", "relation": "preprint_of_this" } ], "themes": [ "imaging_tools" ], "tldr": "CaliAli, a software suite that aligns one-photon calcium imaging sessions using blood vessels plus neurons and extracts signals from concatenated videos, lets the same mouse neurons be followed for weeks to months.", "summary": "Following the same neurons across many miniature-microscope recording sessions is hard because the brain deforms non-rigidly between sessions and the set of active neurons changes. The authors built CaliAli, a multi-session neuron signal extraction suite that first aligns sessions with a coarse-to-fine registration driven by Hessian-enhanced blood vessel images and neuron projections, then extracts calcium signals from the concatenated videos with a memory-efficient, batch-wise adaptation of CNMF-E. They benchmarked it on simulated videos with known ground truth, dual-color (GCaMP plus tdTomato) recordings, published CA1 place cell data, and new opto-tagging experiments in the mouse dentate gyrus. CaliAli aligned sessions more accurately than existing packages, tracked more neurons, improved cross-session position decoding, and kept opto-tagged neurons consistent over weeks. Dentate gyrus population activity tracked for 99 days showed a gradual, roughly linear drift that other methods did not resolve.", "research_question": "Can combining blood-vessel landmarks with neuron projections for inter-session alignment, and extracting signals from concatenated sessions, track neurons in one-photon calcium imaging more reliably over long periods than existing tools?", "approach": "The authors developed a multiscale, weighted group-wise non-rigid alignment using blood vessels and neurons plus a CNMF-E-based extraction pipeline adapted for concatenated multi-session videos, and compared it with CellReg, SCOUT and other registration methods on simulations, dual-color data, CA1 place cell data and dentate gyrus opto-tagging recordings.", "key_findings": [ { "finding": "Across seven dentate gyrus imaging sessions spanning 99 days, the blood-vessel-plus-neuron alignment gave higher spatial correlation and crispness of aligned neuron projections than registration methods from existing calcium imaging packages.", "evidence": "Fig. 2d-f", "species": "mouse", "n": "n = 7 sessions", "stats": "repeated measures one-way ANOVA with Geisser-Greenhouse correction and Dunnett's multiple comparison test; p < 0.05 to p < 0.001" }, { "finding": "Tracking performance stayed stable when a blood-vessel similarity score was above a threshold of 2.7 and dropped sharply below it; in dentate gyrus recordings the score stayed above this threshold for over 90 days with an adjusted focal plane and over 40 days with a fixed focal plane.", "evidence": "Fig. 3a, d", "species": "mouse", "n": "n = 46 session pairs (constant focal plane); n = 15 session pairs (adjusted focal plane)", "stats": "" }, { "finding": "In dual-color recordings where a stable tdTomato label defined the true neuron identities, the new alignment reduced the distance between matched neurons significantly more than the other algorithms tested.", "evidence": "Fig. 4d-e", "species": "mouse", "n": "20,708 neuron pairs", "stats": "two-sided two-sample Kolmogorov-Smirnov test with correction for multiple comparisons; p < 0.001" }, { "finding": "On published CA1 place cell data, concatenated processing did not change within-session spatial information, but it tracked more neurons and gave lower cross-session position decoding errors than CellReg or SCOUT.", "evidence": "Fig. 6b, g, k-m", "species": "mouse", "n": "n = 12 session pairs/3 mice", "stats": "spatial information F(1, 6432) = 0.109; decoding error repeated measures one-way ANOVA F(2, 70) = 18.72" }, { "finding": "In dentate gyrus opto-tagging experiments over 4 weeks, only a minority (32.4%) of extracted components responded to light, and neurons tracked with the new suite showed a higher percentage of opto-consistent responses across sessions than other methods.", "evidence": "Fig. 7f-h", "species": "mouse", "n": "n = 6 session pairs", "stats": "repeated measures one-way ANOVA with Dunnett's multiple comparisons, F(1.4, 7.0) = 16.5" }, { "finding": "Dentate gyrus neurons tracked for 99 days had lower population vector distances across sessions than with other methods and showed a linear rather than exponential drift over time, which the authors suggest reflects gradual, continuous drift in neuronal representations.", "evidence": "Fig. 8b-c; Supplementary Fig. 15", "species": "mouse", "n": "n = 21 session pairs", "stats": "repeated measures one-way ANOVA with Dunnett's multiple comparisons, F(2.4, 48.3) = 106.6" } ], "methods": [ "one-photon calcium imaging with a head-mounted miniature microscope in freely moving mice", "multiscale non-rigid inter-session registration (diffeomorphic demons) using Hessian-filtered blood vessel and neuron projections", "weighted group-wise alignment of sessions to a common atlas", "CNMF-E-based signal extraction adapted for concatenated multi-session videos", "simulated calcium imaging videos with known ground truth", "optogenetic tagging with ChrimsonR and GCaMP6s", "dual-color GCaMP/tdTomato imaging data from a previous study", "position decoding with support vector regression" ], "models": [ "mice (lines listed in Supplementary Table 2)", "simulated one-photon calcium imaging videos" ], "brain_regions": [ "dentate gyrus", "hippocampal CA1" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.5061/dryad.crjdfn3ck", "as_stated": "Ca2+ imaging videos, simulation code, and additional source data ... are available on Dryad" }, { "type": "code", "url": "https://github.com/CaliAli-PV/CaliAli", "as_stated": "The source code for CaliAli, along with demo videos and tutorials, is available on GitHub" }, { "type": "code", "url": "https://doi.org/10.5281/zenodo.14934924", "as_stated": "A preserved version of the code at the time of publication has been archived on Zenodo" } ], "limitations": [ "Each module is tuned for concatenated video processing, so combining it with other pipelines needs adjustments and data from past studies must be reprocessed from raw videos.", "The tracking advantage may show mainly under challenging conditions such as high neuron overlap, remapping of active neurons, or complex non-rigid misalignment.", "Blood vessel structure changes over time, so direct alignment may not be possible indefinitely under some recording conditions." ], "keywords": [ "CaliAli", "one-photon calcium imaging", "miniscope", "longitudinal neuron tracking", "inter-session registration", "blood vessels", "CNMF-E", "representational drift", "dentate gyrus", "place cells" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md" }, { "id": "wang-2024-biorxiv", "doi": "10.1101/2024.10.07.616920", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1101/2024.10.07.616920", "title": "T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals", "authors": [ "Wang Y", "Vergara P", "Hasegawa S", "Tomita N", "Cherasse Y", "Naoi T", "Sakurai T", "Sugaya Y", "Kano M", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2024, "published_date": "2024-10-11", "journal": "bioRxiv", "volume": null, "issue": null, "pages": null, "type": "preprint", "peer_reviewed": false, "open_access": true, "license": null, "related_versions": [], "themes": [ "imaging_tools" ], "tldr": "A laser-fed head-mounted miniature microscope built on the open-source Miniscope v4 design lets researchers image GCaMP6s activity and drive ChrimsonR-expressing neurons in freely moving mice without unwanted opsin activation.", "summary": "Broadband LED illumination in head-mounted miniature microscopes can unintentionally activate red-shifted opsins while exciting calcium sensors, confounding all-optical experiments. The authors adapted the open-source UCLA Miniscope v4 into the T-scope V4, adding an optic-fiber port so that laser light sources replace the LED and swapping the dichroic mirror. In the dentate gyrus of a mouse co-expressing GCaMP6s and ChrimsonR, a 445-nm laser was used for continuous imaging while 1-s pulses of 589-nm light were delivered, and a subset of neurons responded reliably to each pulse, whereas a GCaMP6s-only control showed no such responses. The work is a short technical report with one experimental and one control animal, and it positions the device as a tool for linking genetically defined neuronal activity to behavior.", "research_question": "Can a laser-based miniature microscope image calcium activity and optogenetically excite the same neurons in freely moving mice without blue imaging light inadvertently activating the opsin?", "approach": "The authors rebuilt the light path of the open-source Miniscope v4 to accept laser input and a replacement dichroic, then performed an optogenetic tagging test in the dentate gyrus using GCaMP6s imaging with a 445-nm laser and ChrimsonR stimulation with a 589-nm laser, comparing against a GCaMP6s-only mouse and circularly shifted surrogate data.", "key_findings": [ { "finding": "Replacing the LED with a laser input port, mirror, diffusers and a new dichroic raised the device weight to about 4 g, with no noticeable behavioral change after a 1-week habituation with a dummy scope.", "evidence": "Fig. 1a; Results", "species": "mouse", "n": null, "stats": null }, { "finding": "The tagging protocol used 10 trials, each a 29-s baseline followed by 1-s stimulation with a 589-nm laser, while a 445-nm laser imaged GCaMP6s continuously.", "evidence": "Methods; Results", "species": "mouse", "n": null, "stats": null }, { "finding": "In the mouse co-expressing GCaMP6s and ChrimsonR, a subset of dentate gyrus neurons showed prominent calcium events time-locked to each orange-light pulse, which were absent in the GCaMP6s-only control mouse.", "evidence": "Fig. 1d-g", "species": "mouse", "n": "one co-expressing mouse and one control mouse", "stats": null }, { "finding": "The distribution of average stimulus-evoked responses differed between control neurons (n = 23) and co-expressing neurons (n = 126; P = 0.0010), whereas control neurons did not differ from circularly shifted surrogate data (P = 0.18).", "evidence": "Fig. 1h", "species": "mouse", "n": "GC (n = 23) neurons; GC-Chr (n = 126) neurons", "stats": "Kolmogorov-Smirnov test with Bonferroni correction; P = 0.0010 and P = 0.18" } ], "methods": [ "head-mounted one-photon miniature microscope with laser light input", "in vivo calcium imaging with GCaMP6s", "optogenetic tagging with ChrimsonR", "AAV-mediated gene delivery", "GRIN lens implantation", "multi-session neuron signal extraction with motion correction and CNMF-E", "confocal histology" ], "models": [ "Ai94D (TIGRE-Ins-TRE-LSL-GCaMP6s) mice backcrossed to C57BL/6J" ], "brain_regions": [ "hippocampal dentate gyrus" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/5g8xf7jgwm.1", "status": "doi_not_resolving_2026-10-16", "as_stated": "Source data is available at Mendeley Data (DOI: 10.17632/5g8xf7jgwm.1)" } ], "limitations": [ "The validation used a single co-expressing mouse and a single control mouse.", "The authors note that lowering blue-light intensity to avoid opsin activation can reduce the peak-to-noise ratio of calcium signals, a trade-off that laser sources only mitigate." ], "keywords": [ "miniscope", "calcium imaging", "optogenetics", "optogenetic tagging", "hippocampus", "biological crosstalk" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md" }, { "id": "kashiwagi-2024-cell", "doi": "10.1016/j.cell.2024.08.046", "pmid": "39303715", "pmcid": null, "url": "https://doi.org/10.1016/j.cell.2024.08.046", "title": "A pontine-medullary loop crucial for REM sleep and its deficit in Parkinson’s disease", "authors": [ "Kashiwagi M", "Beck G", "Kanuka M", "Arai Y", "Tanaka K", "Tatsuzawa C", "Koga Y", "Saito YC", "Takagi M", "Oishi Y", "Sakaguchi M", "Baba K", "Ikuno M", "Yamakado H", "Takahashi R", "Yanagisawa M", "Murayama S", "Sakurai T", "Sakai K", "Nakagawa Y", "Watanabe M", "Mochizuki H", "Hayashi Y" ], "pi_role": "co_author", "year": 2024, "published_date": "2024-10", "journal": "Cell", "volume": "187", "issue": "22", "pages": "6272-6289.e21", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "sleep_circuits" ], "tldr": "In mice, two linked brainstem neuron groups in the pons and medulla drive REM sleep, and the pontine group is depleted in brains of people with Parkinson's disease and REM sleep behavior disorder.", "summary": "The authors used a Crhbp marker to gain genetic access to a subset of neurons in the mouse sublaterodorsal tegmentum (SubLDT) of the pons. Those that project to the medulla promote REM sleep and muscle atonia, whereas a separate subset projecting to the basal forebrain promotes NREM sleep. In the dorsal medulla, Nos1-expressing neurons project back to the SubLDT and onward to thalamus and medial septum, and activating them induced REM sleep strongly enough to cause direct wake-to-REM transitions, pointing to a reciprocal pons-medulla loop as a core REM sleep circuit. In post-mortem brainstem tissue, CRHBP-immunoreactive neurons in the presumed human SubLDT were fewer in Parkinson's disease patients with REM sleep behavior disorder than in controls and contained phosphorylated alpha-synuclein. In a Parkinson's disease mouse model, activating the medulla-projecting Crhbp neurons brought reduced sleep back to control levels, which the authors suggest may point to these neurons as a target.", "research_question": "Which molecularly defined brainstem neurons form the core circuit that generates REM sleep, and are they affected in Parkinson's disease with REM sleep behavior disorder?", "approach": "Projection-specific chemogenetic and optogenetic manipulation, fiber photometry, genetic ablation and rabies/AAV circuit tracing in Crhbp-Cre and Nos1-Cre mice with EEG/EMG sleep recording, combined with CRHBP immunohistochemistry of post-mortem human brainstem and sleep recording in an alpha-synuclein mouse model.", "key_findings": [ { "finding": "Ablating Crhbp+ neurons in the SubLDT and adjacent areas reduced both REM and NREM sleep, increased wakefulness and raised muscle tone during REM sleep.", "evidence": "Fig. 1I-1K", "species": "mouse", "n": "n = 8 mice in WT group, n = 7 mice in Crhbp-Cre group", "stats": "unpaired t test" }, { "finding": "Chemogenetic activation of Crhbp+ SubLDT neurons projecting to the gigantocellular nucleus (CNO 1.5 mg/kg at ZT5) increased REM sleep at the expense of wakefulness and deepened REM atonia, whereas the separate basal forebrain-projecting subset increased NREM sleep.", "evidence": "Fig. 3C-3D, Fig. 4C-4D, Fig. S2G", "species": "mouse", "n": "n = 8 mice/group (Gi-projecting); n = 5 mice/group (BF-projecting)", "stats": "two-way repeated-measures ANOVA followed by Bonferroni's test" }, { "finding": "Population calcium activity of the Gi-projecting Crhbp+ SubLDT neurons, measured by fiber photometry, was highest during REM sleep.", "evidence": "Fig. 3G-3I", "species": "mouse", "n": "n = 6 mice", "stats": "one-way ANOVA followed by Tukey's test" }, { "finding": "Activating Nos1+ neurons in the dorsal paragigantocellular/prepositus region of the medulla, which project back to the SubLDT and to thalamus and medial septum, strongly increased REM sleep and caused direct transitions from wakefulness to REM sleep.", "evidence": "Fig. 6C-6J, Fig. 6K-6M", "species": "mouse", "n": "n = 8 mice", "stats": "two-way repeated-measures ANOVA followed by Bonferroni's test; paired Student's t test" }, { "finding": "In post-mortem brains, CRHBP-immunoreactive neurons in the presumed human SubLDT were reduced in Parkinson's disease patients with REM sleep behavior disorder compared with controls, cholinergic neurons were not significantly reduced, and CRHBP-immunoreactive neurons contained phosphorylated S129 alpha-synuclein.", "evidence": "Fig. 7A-7E", "species": "human (post-mortem tissue)", "n": "control patients without neurodegenerative diseases, n = 4; PD patients with RBD symptoms, n = 4", "stats": "p < 0.01 (bootstrap)" }, { "finding": "In BAC-SNCA A53T mice tested at 5 months, REM and NREM sleep were reduced, and chemogenetic activation of the Gi-projecting Crhbp+ SubLDT neurons brought these sleep measures back to control levels; the authors suggest these neurons might be a target in Parkinson's disease.", "evidence": "Fig. S7A-S7D", "species": "mouse", "n": null, "stats": null } ], "methods": [ "projection-specific chemogenetic activation and inhibition (hM3Dq/hM4Di with CNO)", "optogenetic inhibition with a light-activated chloride channel", "fiber photometry of population calcium activity", "Cre-dependent diphtheria toxin A ablation", "rabies virus and AAV anterograde/retrograde circuit tracing", "EEG/EMG sleep recording", "in situ hybridization and immunohistochemistry", "immunohistochemistry of post-mortem human brainstem" ], "models": [ "Crhbp-Cre knockin mice", "Nos1-Cre mice", "Crh-Cre mice", "Vglut2-Cre and Vgat-Cre mice", "BAC-SNCA A53T transgenic mice", "C57BL/6J mice", "post-mortem human brains (PD with RBD and controls)" ], "brain_regions": [ "sublaterodorsal tegmentum (SubLDT)", "dorsal paragigantocellular nucleus (DPGi)", "prepositus hypoglossal nucleus (Pr)", "gigantocellular reticular nucleus (Gi)", "basal forebrain", "thalamus", "medial septum" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/46jxff7z75.1", "status": "doi_not_resolving_2026-10-16", "as_stated": "All raw data analyzed in this paper have been deposited at Mendeley" }, { "type": "code", "url": null, "as_stated": "This paper does not report original code." } ], "limitations": [ "The human post-mortem findings do not directly show that loss of CRHBP-immunoreactive neurons causes the sleep deficits in Parkinson's disease.", "Why these neurons are vulnerable in Parkinson's disease remains unknown.", "Neuron loss in patients should be confirmed by direct measurement of Crhbp mRNA, which is more specific than immunohistochemistry.", "Whether the mouse rescue results translate into ways to address sleep deficits in Parkinson's disease remains to be examined." ], "keywords": [ "REM sleep", "NREM sleep", "brainstem", "sublaterodorsal tegmentum", "Crhbp", "Nos1", "muscle atonia", "Parkinson's disease", "REM sleep behavior disorder", "alpha-synuclein" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md" }, { "id": "li-2024-natcommun", "doi": "10.1038/s41467-024-52466-4", "pmid": "39300067", "pmcid": "PMC11413373", "url": "https://doi.org/10.1038/s41467-024-52466-4", "title": "Distinct ventral hippocampal inhibitory microcircuits regulating anxiety and fear behaviors", "authors": [ "Li K", "Koukoutselos K", "Sakaguchi M", "Ciocchi S" ], "pi_role": "co_author", "year": 2024, "published_date": "2024-09-19", "journal": "Nature Communications", "volume": "15", "issue": "1", "pages": "8228", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-ND 4.0", "related_versions": [], "themes": [ "fear_memory_ptsd", "imaging_tools" ], "tldr": "In mouse ventral CA1, PV interneurons shape anxiety-related pyramidal activity, while a VIP-to-Sst disinhibitory loop gates a separate pyramidal subpopulation needed for trace fear learning.", "summary": "Anxiety and fear rely on overlapping brain areas, and it was unclear how local inhibition in the ventral hippocampus routes activity toward one emotion or the other. Using miniature-microscope calcium imaging and optogenetics in freely moving mice, the authors tracked pyramidal neurons and three interneuron classes (PV, Sst, VIP) across anxiety tasks and trace fear conditioning. Largely separate pyramidal subpopulations responded to anxiety and to the fear cue. PV interneurons were engaged in anxiety and their silencing raised anxiety, whereas VIP activation and Sst inhibition during conditioning supported fear learning, consistent with a VIP-Sst disinhibitory motif. The work suggests a division of labor between inhibitory microcircuits for these two negative emotional states.", "research_question": "Do distinct local GABAergic interneuron microcircuits in ventral CA1 differentially control anxiety-related and fear-related pyramidal neuron activity and behavior?", "approach": "Head-mounted miniscope calcium imaging of vCA1 pyramidal, PV, Sst and VIP neurons during a forced anxiety-shifting task, elevated plus maze, open field and discriminative trace fear conditioning, combined with optogenetic inhibition or activation and monosynaptic rabies tracing from Sst interneurons.", "key_findings": [ { "finding": "Largely separate subpopulations of vCA1 pyramidal neurons responded to anxiety (37.7%) and to the fear-predicting tone (39.7%).", "evidence": "Fig. 1g, p, t", "species": "mouse", "n": "n = 77 neurons, 5 mice (anxiety); n = 81 neurons, 5 mice (fear)", "stats": null }, { "finding": "Optogenetic activation of Sst interneurons during trace fear conditioning reduced fear learning and dropped the fraction of CS+-responsive pyramidal neurons at the memory test from 48.4% to 23.1%.", "evidence": "Fig. 2p-t", "species": "mouse", "n": "tdTomato n = 9 mice; ChrimsonR n = 8 mice", "stats": null }, { "finding": "Sst interneurons were mostly inhibited by the fear cue (68.4% at the cued fear test), and rabies tracing showed nearly 9% of their local presynaptic inputs came from VIP interneurons versus 3.2% from PV interneurons.", "evidence": "Fig. 2k-o; Fig. 3a, b", "species": "mouse", "n": "n = 39 neurons, 5 mice; n = 1068 tdTomato+ cells from 5 mice", "stats": null }, { "finding": "VIP interneurons were recruited by the fear cue (41.9% during conditioning, 57.6% at retrieval) but rarely by anxiety (9% in the FAST), and their optogenetic inhibition during CS+-US pairing reduced trace fear learning and impaired next-day retrieval.", "evidence": "Fig. 3c-v", "species": "mouse", "n": "tdTomato n = 8 mice; eNpHR3.0 n = 8 mice", "stats": null }, { "finding": "PV interneurons were activated in anxiogenic compartments, and silencing them disinhibited pyramidal neurons and increased anxiety-like behavior without affecting trace fear learning or retrieval.", "evidence": "Fig. 4", "species": "mouse", "n": "tdTomato n = 6 mice; eNpHR3.0 n = 6 mice", "stats": null } ], "methods": [ "in vivo one-photon calcium imaging with a head-mounted miniature microscope and GRIN lens", "dual-color miniscope imaging combined with optogenetic activation", "optogenetic inhibition (eNpHR3.0) and activation (ChrimsonR)", "monosynaptic retrograde rabies tracing", "forced anxiety-shifting task, elevated plus maze and open field test", "discriminative trace fear conditioning and cued fear memory test" ], "models": [ "C57BL/6J mice", "PV-IRES-Cre, Sst-IRES-Cre and VIP-IRES-Cre mice" ], "brain_regions": [ "ventral hippocampus CA1" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.6084/m9.figshare.26575084", "as_stated": "The original data used in this study are available in Figshare repository under open access licence CC BY 4.0." }, { "type": "code", "url": "https://doi.org/10.6084/m9.figshare.26575084", "as_stated": "The Matlab code for AUC analysis used in this study is deposited in Figshare" } ], "limitations": [ "The authors note that Cre lines give access to broad interneuron classes, so further tools are needed to resolve the roles of specific GABAergic cell types such as OLM, bistratified or basket cells.", "Assignments of the anxiety- and fear-related interneuron populations to particular anatomical cell types are presented as speculation." ], "keywords": [ "ventral hippocampus", "anxiety", "fear conditioning", "interneurons", "parvalbumin", "somatostatin", "VIP", "disinhibition", "calcium imaging", "optogenetics" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md" }, { "id": "he-2024-embc", "doi": "10.1109/EMBC53108.2024.10782461", "pmid": "40039703", "pmcid": null, "url": "https://doi.org/10.1109/EMBC53108.2024.10782461", "title": "Real-time detection of motifs from semi-synthetic calcium imaging data with various noise types", "authors": [ "He Z", "Vergara P", "Sakaguchi M", "Tezuka T" ], "pi_role": "co_author", "year": 2024, "published_date": "2024-07-15", "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "volume": null, "issue": null, "pages": "1-7", "type": "conference_paper", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "imaging_tools" ], "tldr": "Using motifs from mouse calcium imaging planted into noisy synthetic data, seqNMF with a sliding window detected most replay events in real time, with jitter and small motifs as weak points.", "summary": "Repeated sequential firing patterns (motifs) in hippocampal neurons are thought to relate to memory replay, and detecting them before they finish would allow closed-loop intervention. Because exact motif timing is hard to define in real recordings, the authors built semi-synthetic datasets by embedding spike sequences taken from calcium imaging of adult-born neurons in mice into synthetic data with four noise types (power, jitter, and two kinds of firing noise). They used seqNMF with a skewness-based significance test and AICc to identify the number and length of motifs, then detected replays online with a multi-unit-activity trigger and a sliding window. Motif number and length were recovered, detection took about 11 ms per iteration, and most replay events were found before they ended, but performance fell with timing jitter, for small motifs and with some false detections.", "research_question": "Can replayed neuronal sequences (motifs) in calcium imaging data be identified and then detected in real time, before each replay ends, under different kinds of noise?", "approach": "Spike sequences from real mouse calcium imaging were embedded into synthetic data with controlled noise to give ground-truth replay times; seqNMF was tuned (lambda, number of factors, motif length by AICc) on the first half and then used with a multi-unit-activity gate and sliding window for online detection on held-out data, scored by F1.", "key_findings": [ { "finding": "On semi-synthetic data built from three significant real spike sequences, the factorization most often selected 3 factors, matching the embedded motifs, and AICc was lowest at a motif length of 11 bins.", "evidence": "Fig. 9; Fig. 10a-b; Fig. 11", "species": "mouse (semi-synthetic data derived from recordings)", "n": "70 neurons; 20 fittings", "stats": "lambda0 = 0.019; AICc minimum at L = 11" }, { "finding": "With a 10-bin detection window and an Hfit threshold of 0.936 chosen by maximizing F1 in training, online detection on a laptop processor averaged 11.2 ms per iteration, with each bin covering 167 milliseconds.", "evidence": "Section V", "species": "mouse (semi-synthetic data derived from recordings)", "n": null, "stats": "average detection time 11.2 ms per iteration" }, { "finding": "In noise-robustness tests for one motif with 36 replay events in 10,000 bins, detection was best without noise, the F1 curve fluctuated most under Type II firing noise, and performance was sensitive to increasing jitter.", "evidence": "Fig. 12", "species": "mouse (semi-synthetic data derived from recordings)", "n": "36 replay events in 10,000 bins", "stats": "F1 score across noise probabilities" }, { "finding": "On a 2500-bin test segment with mixed noise containing seven replay events, five were detected, with two incorrect detections, and detections occurred well before the end of each event.", "evidence": "Fig. 14", "species": "mouse (semi-synthetic data derived from recordings)", "n": "seven replay events in 2500 test bins", "stats": "five of seven detected; two incorrect detections" }, { "finding": "The method performed well for large motifs of 10 neurons or more but less well for smaller motifs.", "evidence": "Section VI", "species": "mouse (semi-synthetic data derived from recordings)", "n": null, "stats": null } ], "methods": [ "calcium imaging spike data from adult-born neurons in mice used as motif templates", "semi-synthetic data generation with power noise, jitter noise and two types of firing noise", "seqNMF (convolutional non-negative matrix factorization with x-ortho penalty)", "skewness-based motif significance test with Bonferroni correction", "Corrected Akaike Information Criterion (AICc) to choose motif length", "multi-unit activity threshold from shuffled null distribution to gate detection", "sliding-window real-time motif detection scored by F1" ], "models": [ "mouse calcium imaging data (adult-born neurons), embedded in synthetic data" ], "brain_regions": [ "hippocampus" ], "data_code_availability": [], "limitations": [ "Evaluation used semi-synthetic data, whose noise was more intricate than that of the real recordings; tests in live mice are planned for the future.", "Detection degraded with increasing timing jitter, so precise recording timing is needed.", "Smaller motifs were detected less well than large ones.", "Accuracy was sensitive to the choice of detection window length.", "Some false detections occurred, and the authors note stricter metrics may be needed before use for closed-loop intervention." ], "keywords": [ "hippocampal replay", "neuronal sequences", "motif detection", "calcium imaging", "seqNMF", "convolutional NMF", "real-time detection", "semi-synthetic data", "multi-unit activity", "closed-loop" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md" }, { "id": "kawakami-2024-bbrc", "doi": "10.1016/j.bbrc.2024.150071", "pmid": "38735136", "pmcid": null, "url": "https://doi.org/10.1016/j.bbrc.2024.150071", "title": "Spaced conditioned stimulus presentation facilitates the extinction of strong fear memory in mice", "authors": [ "Kawakami C", "Naoi T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2024, "published_date": "2024-07", "journal": "Biochemical and Biophysical Research Communications", "volume": "718", "issue": null, "pages": "150071", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "fear_memory_ptsd" ], "tldr": "In mice given trace fear conditioning with a strong shock, presenting the tone in spaced bursts extinguished fear faster than one continuous tone.", "summary": "This study asked whether the temporal pattern of re-presenting a conditioned tone changes how well mice extinguish a trace fear memory. Mice were conditioned with tone and foot shock at three shock intensities and the next day received either a continuous 180-s tone or eight 20-s tones separated by 20-s gaps in a new context. Under continuous presentation, mice conditioned with the strongest shock extinguished less well, whereas spaced presentation produced similar extinction across intensities and a steeper extinction slope after the strongest shock. The degree of contextual fear generalization did not predict extinction. The authors suggest that spaced cue presentation may engage circuits beyond the amygdala to extinguish strong trace fear memories.", "research_question": "Does spaced versus continuous presentation of a conditioned auditory stimulus differ in its ability to extinguish trace fear memories of different strengths in mice?", "approach": "Male C57BL/6 mice underwent auditory trace fear conditioning at 0.5, 0.75, or 1.0 mA and were then given continuous or spaced tone presentation during extinction training in a novel context, with freezing scored in 20-s bins and compared by ANOVA, linear regression slopes, and Pearson correlation.", "key_findings": [ { "finding": "Mice responded similarly to the first extinction tone regardless of presentation pattern or shock intensity (interaction F = 0.18, p = 0.89; group effect F = 2.45, p = 0.13).", "evidence": "Fig. 1d", "species": "mouse", "n": "n = 5 mice in the 0.5 mA continuous group, n = 6 mice in all other groups", "stats": "two-way ANOVA; interaction F = 0.18, p = 0.89; group main effect F = 2.45, p = 0.13" }, { "finding": "With continuous tone presentation, the extinction time course depended on conditioning shock intensity (p = 0.0052).", "evidence": "Fig. 1e", "species": "mouse", "n": null, "stats": "two-way ANOVA, p = 0.0052" }, { "finding": "Under continuous presentation, mice shocked at 1.0 mA showed greater residual freezing than mice shocked at 0.5 or 0.75 mA, whereas spaced-group mice extinguished similarly across intensities.", "evidence": "Fig. 1f", "species": "mouse", "n": null, "stats": "one-way ANOVA, p < 0.0001" }, { "finding": "After 1.0 mA conditioning, spaced tone presentation produced a steeper extinction slope than continuous presentation (p = 0.0030), despite a shorter total tone duration; no group difference was seen at 0.5 or 0.75 mA.", "evidence": "Fig. 1g", "species": "mouse", "n": null, "stats": "simple linear regression slope comparison, p = 0.0030" }, { "finding": "Pre-tone freezing in the new context (contextual generalization) did not correlate with the extinction index for either presentation pattern (r = -0.07, p = 0.79 continuous; r = -0.27, p = 0.28 spaced).", "evidence": "Fig. 1h", "species": "mouse", "n": null, "stats": "Pearson correlation; r = -0.07, p = 0.79 (continuous); r = -0.27, p = 0.28 (spaced)" } ], "methods": [ "auditory trace fear conditioning with graded foot-shock intensities", "extinction training with continuous versus spaced tone presentation", "automated freezing scoring (FreezeFrame)", "linear regression of extinction slopes and Pearson correlation analysis" ], "models": [ "male C57BL/6 mice, 8-14 weeks old" ], "brain_regions": [], "data_code_availability": [], "limitations": [], "keywords": [ "trace fear conditioning", "extinction learning", "auditory cue", "generalization", "PTSD" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md" }, { "id": "koyama-2024-fuzzieee", "doi": "10.1109/FUZZ-IEEE60900.2024.10611847", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1109/FUZZ-IEEE60900.2024.10611847", "title": "A Noise-Robust Approach to Estimate Dimension of Sleep EEG in Mice Using Permutation Entropy", "authors": [ "Koyama K", "Sakaguchi M", "Ohnishi T" ], "pi_role": "co_author", "year": 2024, "published_date": "2024-06-30", "journal": "2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE)", "volume": null, "issue": null, "pages": "1-8", "type": "conference_paper", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "sleep_staging_closed_loop_tools" ], "tldr": "Uses permutation entropy, which tolerates noise, to choose embedding parameters for nonlinear analysis of mouse sleep EEG and finds the same values across sleep stages.", "summary": "Nonlinear analysis of EEG by state-space embedding needs an embedding dimension and a time delay, but standard estimators such as correlation integration are thrown off by noise. The authors instead used permutation entropy, an ordinal-pattern measure that is less sensitive to noise, to estimate these parameters from mouse EEG recorded across sleep stages. The estimates pointed to an embedding dimension of 5 and a time delay of 8 ms independent of stage. They also report that permutation entropy separated REM sleep from wakefulness, which a linear power-spectrum analysis did not.", "research_question": "Can embedding dimension and time delay for nonlinear analysis of mouse sleep EEG be estimated reliably despite noise, and do they differ by sleep stage?", "approach": "Permutation entropy was applied to mouse EEG from different sleep stages to estimate embedding parameters, and the resulting nonlinear description was compared with power spectrum density for separating vigilance states.", "key_findings": [ { "finding": "Permutation entropy analysis suggested an embedding dimension of 5 and a time delay of 8 ms for mouse EEG, regardless of sleep stage.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Permutation entropy distinguished REM sleep from wakefulness, whereas a linear power spectrum density approach did not.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors argue that conventional correlation integration fails to give correct embedding parameters for EEG because of noise, motivating the permutation-entropy approach.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null } ], "methods": [ "EEG recording in mice across sleep stages", "permutation entropy", "state-space (delay) embedding", "power spectrum density comparison" ], "models": [ "mice" ], "brain_regions": [], "data_code_availability": [], "limitations": [], "keywords": [ "sleep EEG", "permutation entropy", "embedding dimension", "time delay", "nonlinear dynamics", "REM sleep", "mouse" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyama-2024-fuzzieee.md" }, { "id": "vergara-2023-biorxiv", "doi": "10.1101/2023.05.19.540935", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1101/2023.05.19.540935", "title": "CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging", "authors": [ "Vergara P", "Wang Y", "Srinivasan S", "Cherasse Y", "Naoi T", "Sugaya Y", "Sakurai T", "Kano M", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2023, "published_date": "2023-05-19", "journal": "bioRxiv", "volume": null, "issue": null, "pages": null, "type": "preprint", "peer_reviewed": false, "open_access": true, "license": "CC BY-NC-ND 4.0", "related_versions": [ { "doi": "10.1038/s41467-025-58817-z", "relation": "published_version" } ], "themes": [ "imaging_tools" ], "tldr": "Preprint introducing CaliAli, which aligns one-photon calcium imaging sessions using blood vessels and neurons before extracting signals, so that more of the same neurons can be followed across weeks.", "summary": "Existing neuron-tracking tools match neuron footprints between sessions, which fails when the same neurons are not detected every time and when brain tissue shifts non-rigidly. This preprint presents CaliAli (Calcium Imaging intersession Alignment), which first aligns sessions using blood vessel shapes together with neuron projections and then extracts calcium signals from the aligned, concatenated videos. The authors tested it on simulated videos with known ground truth, on an opto-tagging experiment in the mouse dentate gyrus, and on four weeks of dentate gyrus recordings in two contexts. CaliAli tracked neurons better than CellReg and SCOUT in the simulated scenarios and gave more consistent opto-tagging responses and more neurons active in all sessions in real data. The peer-reviewed version was published in Nature Communications in 2025.", "research_question": "Can aligning calcium imaging sessions with blood vessel information before signal extraction track the same neurons more reliably over long periods than footprint-matching tools?", "approach": "The authors registered sessions with a non-rigid diffeomorphic demons method using Hessian-enhanced blood vessel and neuron projections, extracted signals with CNMF-E from concatenated videos, and compared the results with CellReg and SCOUT on simulations and mouse dentate gyrus recordings.", "key_findings": [ { "finding": "In simulated misaligned videos, using blood vessel shapes for registration gave better alignment and smaller maximum displacement errors than neuron shapes or mean-frame projections, with the gain seen when blood vessel spatial correlation between sessions was higher than 0.4.", "evidence": "Fig. 1d-i; Extended Data Figs. 3-5", "species": "simulation", "n": null, "stats": null }, { "finding": "In mouse recordings, blood vessel correlation stayed at this level for up to 40 days between sessions.", "evidence": "Fig. 1j", "species": "mouse", "n": null, "stats": null }, { "finding": "CaliAli tracked neurons better than other methods in simulations with low neuron overlap, high neuron overlap, and remapping of active populations.", "evidence": "Fig. 2d-f; Extended Data Fig. 6b-d", "species": "simulation", "n": null, "stats": null }, { "finding": "In a dentate gyrus opto-tagging experiment, 49.6% ± 2.8% of neurons were tagged by orange light, and the proportion of optogenetically consistent neurons across sessions was higher with CaliAli than with other methods.", "evidence": "Fig. 2j-m", "species": "mouse", "n": "data from one mouse", "stats": "Permutation test" }, { "finding": "When a mouse explored two contexts over 4 weeks, CaliAli detected more dentate gyrus neurons active in all sessions, and population vectors from the same context were more highly correlated than with other methods.", "evidence": "Fig. 2n-q", "species": "mouse", "n": null, "stats": "Two-way ANOVA with Sidak's multiple comparisons" } ], "methods": [ "one-photon calcium imaging with a head-mounted miniature microscope in freely moving mice", "non-rigid inter-session registration with diffeomorphic log-demons using Hessian-enhanced blood vessel and neuron projections", "CNMF-E signal extraction from concatenated multi-session videos", "simulated calcium imaging videos with known ground truth", "optogenetic tagging with ChrimsonR and GCaMP6s", "UMAP dimensionality reduction and k-means clustering" ], "models": [ "Ai94D (TIGRE-Ins-TRE-LSL-GCaMP6s) mice", "C57BL/6J mice", "simulated one-photon calcium imaging videos" ], "brain_regions": [ "dentate gyrus" ], "data_code_availability": [ { "type": "code", "url": "https://github.com/CaliAli-PV/CaliAli", "as_stated": "The codes for CaliAli, along with demo videos and tutorials, are available on GitHub" } ], "limitations": [ "Direct alignment depends on blood vessel correlation between sessions; for longer gaps the authors propose aligning through intermediate sessions recorded at short intervals.", "For the 4-week recording, extraction thresholds were set manually because combining initialization parameters across 20 sessions was not computationally feasible." ], "keywords": [ "CaliAli", "miniscope", "one-photon calcium imaging", "longitudinal neuron tracking", "inter-session registration", "blood vessels", "CNMF-E", "dentate gyrus" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md" }, { "id": "koyanagi-2023-neurosci-res", "doi": "10.1016/j.neures.2022.10.001", "pmid": "36206953", "pmcid": null, "url": "https://doi.org/10.1016/j.neures.2022.10.001", "title": "Fully automatic REM sleep stage-specific intervention systems using single EEG in mice", "authors": [ "Koyanagi I", "Tezuka T", "Yu J", "Srinivasan S", "Naoi T", "Yasugaki S", "Nakai A", "Taniguchi S", "Hayashi Y", "Nakano Y", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2023, "published_date": "2023-01", "journal": "Neuroscience Research", "volume": "186", "issue": null, "pages": "51-58", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "sleep_staging_closed_loop_tools" ], "tldr": "A deep-learning model reading a single EEG channel classified mouse sleep stages in real time and triggered REM-specific output pulses without per-mouse calibration.", "summary": "The authors adapted a previously described AI sleep-staging model so that it runs live on mice, taking one raw EEG channel and assigning wake, NREM or REM sleep as recording proceeds. Running on four mice at once with no individual tuning, its stage calls closely matched those of a blinded human scorer in both light and dark periods. When set to emit TTL pulses only during REM sleep, the kind of trigger used to drive lasers in optogenetic experiments, it delivered REM-targeted pulses with high sensitivity and precision. Variants handled EEG recorded at a higher sampling rate via online down-sampling and classified stages in 4-s instead of 10-s windows, while an attempt to separate high-theta wakefulness from REM sleep remained weak.", "research_question": "Can a fully automatic, real-time AI sleep-stage classifier using a single EEG channel drive accurate REM sleep-specific interventions in freely behaving mice without per-animal configuration?", "approach": "A convolutional plus LSTM network was integrated with a commercial home-cage EEG/EMG recording system via TCP/IP, tested in vivo against a blinded human expert, and used to generate TTL pulses during REM sleep; derived models for down-sampled 512 Hz input, 4-s windows and high-theta wakefulness were evaluated by cross-validation.", "key_findings": [ { "finding": "Driving TTL output during REM sleep, the system achieved about 90 % sensitivity and 86 % precision without prior configuration to each mouse, and REM-targeted pulses resembled those of a human scorer.", "evidence": "Abstract; Tables 2 and 3", "species": "mouse", "n": "Manual, n = 6; UTSN-L2, n = 3; UTSN-L2-DS, n = 4 (mice = recordings)", "stats": "mean (standard deviation)" }, { "finding": "Run live on four mice simultaneously, the model's stage classifications matched a blinded human expert in light and dark periods, with REM specificity and accuracy above 97 %, although it scored more and shorter REM episodes.", "evidence": "Figs. 2-3; Table 1", "species": "mouse", "n": "n = 12 recordings from 4 mice", "stats": "two-way ANOVA" }, { "finding": "EEG recorded at 512 Hz and down-sampled online to 128 Hz yielded total amounts of each stage similar to the human expert, with differences only in some episode counts and durations.", "evidence": "Figs. 3B, 4", "species": "mouse", "n": "n = 12 recordings from the same four mice", "stats": "two-way ANOVA" }, { "finding": "A variant classifying stages in 4-s rather than 10-s windows performed similarly to the original model in five-fold cross-validation on 154 recordings, and gave similar results on an independent dataset from a different laboratory.", "evidence": "Table 1; Fig. 5; Figs. S3-S4", "species": "mouse", "n": "154 recordings from 96 mice", "stats": "cross-validation" }, { "finding": "A model that additionally separated high-theta wakefulness did not improve REM classification, because high-theta wakefulness itself was detected with low sensitivity (30.4 %) and precision (70.5 %), mostly confused with low-theta wakefulness.", "evidence": "Table 1; Fig. 5", "species": "mouse", "n": "154 recordings from 96 mice", "stats": "cross-validation" } ], "methods": [ "chronic epidural EEG and neck EMG recording in freely moving mice", "real-time deep-learning sleep stage classification (convolutional neural network with LSTM) from single-channel EEG", "closed-loop TTL pulse generation during REM sleep", "blinded human expert sleep scoring and FFT power spectrum analysis", "cross-validation of model variants" ], "models": [ "C57BL/6J mice (male mice for in vivo tests)" ], "brain_regions": [], "data_code_availability": [ { "type": "data", "url": null, "as_stated": "Data will be made available on Mendeley Data." } ], "limitations": [ "High-theta wakefulness was poorly distinguished from low-theta wakefulness, limiting further gains in REM classification.", "The minimum time window for stage classification (about 2 s for NREM) is too coarse for interventions locked to individual oscillations, which would need secondary algorithms." ], "keywords": [ "REM sleep", "sleep stage classification", "deep learning", "EEG", "closed-loop intervention", "mice" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md" }, { "id": "sakaguchi-2022-jpn-j-trauma-stress", "doi": null, "pmid": null, "pmcid": null, "url": "https://cir.nii.ac.jp/crid/1520855665683704192", "title": "PTSDの恐怖記憶処理と新しい治療技術の開発", "authors": [ "坂口 昌徳", "廣幡 小百合" ], "pi_role": "first", "year": 2022, "published_date": "2022-06-30", "journal": "トラウマティック・ストレス（Japanese Journal of Traumatic Stress）", "volume": "20", "issue": "1", "pages": "20-26", "type": "commentary_japanese_review", "peer_reviewed": null, "open_access": null, "license": null, "related_versions": [], "themes": [ "fear_memory_ptsd", "sound_exposure_during_sleep" ], "tldr": "A Japanese review that reads PTSD through fear-memory research, linking prolonged exposure to fear extinction and discussing hippocampal, sleep and sound-during-sleep findings as starting points for new methods.", "summary": "This Japanese-language review (English title: Fear Memory Processing in the Hippocampus and Sleep), written for a special issue on the biological understanding of PTSD, interprets PTSD from the standpoint of fear-memory research. It argues that prolonged exposure, the established psychotherapy for PTSD, works through the same principle as fear extinction, which avoidance normally blocks, and notes its practical burdens such as session time, distress and dropout. It then surveys mouse work on synchronized brain activity, REM-sleep theta rhythm, dentate gyrus pattern separation and adult-born neurons, including the authors' finding that a small number of adult-born neuron activations during REM sleep are needed for fear memory consolidation. Finally, it reviews studies that present conditioned sounds during sleep, including the authors' mouse replication, and describes their ongoing human study, Sound Exposure during Sleep (SES), an exploratory intervention that presents personally relevant sounds during NREM sleep. This human line of research is exploratory and is not a treatment; this page gives no medical advice, and the study is not recruiting participants.", "research_question": "What can fear-memory and sleep research, from mouse circuit studies to sound presented during sleep, contribute to understanding PTSD and to designing new, less burdensome methods?", "approach": "Narrative review in Japanese with self-contained subheaded sections, moving from extinction and conditioning theory through hippocampal and sleep mechanisms in mice to studies that present sounds during sleep.", "key_findings": [ { "finding": "The review argues that prolonged exposure works through fear extinction, and that in PTSD the extreme avoidance of trauma reminders keeps normal extinction from taking place.", "evidence": "Sections 'Extinctionと持続エクスポージャー療法' and 'トラウマ記憶と条件付け恐怖記憶'; Fig. 1", "species": "human", "n": null, "stats": null }, { "finding": "The review identifies the cost of prolonged exposure (10 to 15 sessions over about 3 months, distress from deliberately recalling the trauma, the need for skilled therapists, and high dropout) as the motivation for new approaches.", "evidence": "Section '情報処理理論と持続エクスポージャー療法'", "species": "human", "n": null, "stats": null }, { "finding": "Citing the authors' mouse work, the review reports that adult-born dentate gyrus neurons aged 4 to 6 weeks that were active during learning reactivate in later REM sleep, that silencing them during REM sleep impairs fear memory consolidation, and that the activity involved may total 500 events or fewer.", "evidence": "Section '新生ニューロンと睡眠中の恐怖記憶固定化' (ref. 18)", "species": "mouse", "n": null, "stats": null }, { "finding": "The review reports the authors' mouse replication in which only a conditioned sound played during slow-wave sleep, and not during REM sleep, weakened fear responses, and suggests that presenting sounds during sleep merits further study as a new approach.", "evidence": "Section '睡眠中の音刺激を用いた新しいエクスポージャーの開発' (refs. 13, 25)", "species": "mouse", "n": null, "stats": null } ], "methods": [ "narrative literature review" ], "models": [], "brain_regions": [ "hippocampus", "dentate gyrus", "posteromedial cortex" ], "data_code_availability": [], "limitations": [ "The authors note that the brain mechanisms behind intrusive symptoms remain largely unclear.", "The authors note that adult neurogenesis in humans may be smaller in scale than in mice, which matters for translating the mouse findings.", "Most of the mechanistic evidence discussed comes from mouse studies rather than from people with PTSD." ], "keywords": [ "PTSD", "fear memory", "extinction", "prolonged exposure", "adult neurogenesis", "REM sleep", "pattern separation", "sound stimulation during sleep" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2022-jpn-j-trauma-stress.md" }, { "id": "soares-2021-cells", "doi": "10.3390/cells10113047", "pmid": "34831271", "pmcid": "PMC8618878", "url": "https://doi.org/10.3390/cells10113047", "title": "Novel Galectin-3 Roles in Neurogenesis, Inflammation and Neurological Diseases", "authors": [ "Soares LC", "Al-Dalahmah O", "Hillis J", "Young CC", "Asbed I", "Sakaguchi M", "O’Neill E", "Szele FG" ], "pi_role": "co_author", "year": 2021, "published_date": "2021-11-05", "journal": "Cells", "volume": "10", "issue": "11", "pages": "3047", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "neural_stem_cells_galectin" ], "tldr": "A review of how the lectin Galectin-3 shapes subventricular zone neurogenesis, gliogenesis and inflammation, and how it is implicated in brain diseases.", "summary": "This review gathers recent work on Galectin-3, a multifunctional carbohydrate-binding protein best known for driving inflammation. In the healthy brain it is found mainly in the subventricular zone stem cell niche, where loss-of-function studies link it to neuroblast migration in adults and to glial fate decisions in the postnatal brain via BMP and Wnt signaling. The authors also cover its upregulation in brain injury, glioma, multiple sclerosis models and Alzheimer's disease, its possible relevance to SARS-CoV-2 brain pathology, and the related lectin Galectin-1. They argue that Galectin-3 has surprisingly specific, context-dependent roles despite many binding partners, and list open questions about its regulation.", "research_question": "What roles does Galectin-3 play in adult and postnatal neurogenesis, neuroinflammation and neurological disease?", "approach": "Narrative review of published studies, including the authors' own mouse work on subventricular zone Galectin-3, with supplementary tables of binding partners and pathway changes.", "key_findings": [ { "finding": "In the healthy mouse brain Galectin-3 is expressed in subventricular zone ependymal cells, stem cells and some progenitors but not neuroblasts, and its loss disrupts neuroblast migration and reduces olfactory bulb neurogenesis.", "evidence": "Section 2", "species": "mouse", "n": null, "stats": null }, { "finding": "In the postnatal subventricular zone, Galectin-3 regulates gliogenesis rather than neurogenesis, increasing BMP signaling and reducing Wnt signaling, and the authors describe it as a switch for astrocyte generation.", "evidence": "Section 3.1", "species": "mouse", "n": null, "stats": null }, { "finding": "The review summarizes evidence that Galectin-3 is elevated in Alzheimer's disease and that reducing it in mouse models lowers inflammation and is associated with better cognition.", "evidence": "Section 5.1", "species": "human; mouse", "n": null, "stats": null }, { "finding": "The authors conclude that, despite many binding partners, Galectin-3 has specific context-dependent effects, and its cell-type expression in the subventricular zone stays stable across disease models.", "evidence": "Section 8", "species": "mouse", "n": null, "stats": null } ], "methods": [ "narrative literature review" ], "models": [ "Gal-3 knockout mice", "floxed Gal-3 conditional knockout mice", "APP/PS1 mice" ], "brain_regions": [ "subventricular zone", "rostral migratory stream", "olfactory bulb", "hippocampal dentate gyrus" ], "data_code_availability": [], "limitations": [ "The authors note that Galectin-3 function in the hippocampal subgranular zone remains largely unexplored.", "How Galectin-3 is regulated and how it coordinates multiple signaling pathways within the same cells are stated as open questions." ], "keywords": [ "galectin", "Galectin-3", "neurogenesis", "subventricular zone", "stem cells", "inflammation" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/soares-2021-cells.md" }, { "id": "taniguchi-2021-embc", "doi": "10.1109/embc46164.2021.9629611", "pmid": "34891875", "pmcid": null, "url": "https://doi.org/10.1109/embc46164.2021.9629611", "title": "Open-Source Software for Real-time Calcium Imaging and Synchronized Neuron Firing Detection", "authors": [ "Taniguchi M", "Tezuka T", "Vergara P", "Srinivasan S", "Hosokawa T", "Cherasse Y", "Naoi T", "Sakurai T", "Sakaguchi M" ], "pi_role": "last", "year": 2021, "published_date": "2021-11-01", "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "volume": null, "issue": null, "pages": "2997-3003", "type": "conference_paper", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "imaging_tools" ], "tldr": "An open-source program reads one-photon miniscope calcium video in real time, screens out non-neuronal components with a deep network, and fires an external device when a user-defined ensemble pattern appears.", "summary": "The authors built Carignan, an open-source Python application that extends an existing online matrix-factorization pipeline so that one-photon miniscope video can be analysed frame by frame while recording. A user first records a session, defines a synchronized firing pattern from the extracted neurons, and in a second session the program sends a USB signal (for example to a laser for optogenetics) whenever that pattern occurs, enabling closed-loop experiments in freely moving animals. To reduce false-positive neuron candidates, they added a classifier that combines a convolutional-recurrent branch for the temporal trace with a 2D convolutional branch for the spatial footprint. On an annotated public 1p hippocampal dataset this combined classifier scored higher accuracy and F1 than the best existing automated-curation model, while large pretrained image backbones added little. The paper reports software benchmarks only; in vivo closed-loop experiments were left for future work.", "research_question": "Can calcium imaging from a small one-photon miniscope be processed in real time accurately enough to detect specific synchronized neuronal firing patterns and trigger an external device for closed-loop experiments?", "approach": "The authors extended an open-source online CNMF-E implementation with a two-recording workflow, a pattern-file-based synchronized-firing detector driving an Arduino USB signal device, and a deep-learning false-positive classifier; they benchmarked the classifier against existing curation methods and measured whole-system processing rates on public 2p and in-house 1p videos.", "key_findings": [ { "finding": "Combining temporal-trace and spatial-footprint branches (Conv-LSTM + 2D-CNN) gave accuracy 0.894 and F1 0.920 for false-positive neuron detection, versus 0.878 and 0.910 for the TPOT model, the best existing automated-curation method.", "evidence": "Table I", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null }, { "finding": "Models using only the temporal trace (LSTM: accuracy 0.849, F1 0.888) or only the spatial footprint (2D-CNN: accuracy 0.884, F1 0.909) did not outperform TPOT, indicating both kinds of information contribute.", "evidence": "Table I", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null }, { "finding": "Replacing the spatial branch with large ImageNet-pretrained backbones changed accuracy only slightly (for example WideResNet 50: accuracy 0.903, F1 0.923), which the authors attribute possibly to limited training data or an unsuitable pretraining domain.", "evidence": "Table I; Section IV-A", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null }, { "finding": "In whole-system tests the processing rate was higher with the deep classifier, which the authors explain by fewer neurons being detected rather than faster classification.", "evidence": "Table III; Section IV-B", "species": null, "n": "two public 2p datasets and two in-house 1p videos", "stats": null }, { "finding": "When applied to 2p data from a different domain, the deep classifiers appeared less robust than TPOT given the 15% false-neuron ratio of the training data, so the authors recommend training on images from the same domain.", "evidence": "Table IV; Section IV-B", "species": null, "n": null, "stats": null }, { "finding": "The system uses the first 500 frames of the stream for initialization and then extracts and filters neuron candidates frame by frame.", "evidence": "Fig. 1; Section III-B", "species": null, "n": null, "stats": null } ], "methods": [ "one-photon miniscope calcium imaging video acquisition (UCLA Miniscope V3) via OpenCV", "online CNMF-E source extraction with motion correction", "deep-learning false-positive classifier combining 1D convolution + LSTM on temporal traces and 2D CNN on spatial footprints", "pattern-file-based detection of synchronized firing with an Arduino USB signal device for closed-loop triggering", "benchmarking against decision tree, k-nearest neighbors, TPOT and Auto-Sklearn curation models" ], "models": [ "annotated 1p hippocampal CA1 calcium imaging dataset from mice (Tran et al.)", "public neurofinder 2p datasets (01.00 and 03.00)", "two in-house 1p miniscope videos" ], "brain_regions": [ "hippocampal CA1", "primary visual cortex (V1)" ], "data_code_availability": [ { "type": "code", "url": "https://github.com/tan1p0p/carignan", "as_stated": "The entire code of the system is available as an open-source software" } ], "limitations": [ "No in vivo closed-loop experiments were performed; these are planned future work.", "Synchronized firing patterns must currently be defined manually from a separate first recording.", "Splitting the experiment into two recordings makes it prone to errors such as unintended camera position changes.", "The deep classifiers seemed less robust than TPOT when applied to neurons and camera settings different from the training data." ], "keywords": [ "real-time calcium imaging", "one-photon miniscope", "closed-loop", "optogenetics", "CNMF-E", "false-positive detection", "deep learning", "synchronized firing" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md" }, { "id": "ohba-2021-neural-regen-res", "doi": "10.4103/1673-5374.317966", "pmid": "34269194", "pmcid": "PMC8463975", "url": "https://doi.org/10.4103/1673-5374.317966", "title": "Contribution of adult-born neurons to memory consolidation during rapid eye movement sleep", "authors": [ "Ohba A", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-07-08", "journal": "Neural Regeneration Research", "volume": "17", "issue": "2", "pages": "307-308", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-ND 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory", "fear_memory_ptsd" ], "tldr": "A perspective proposing that sparse adult-born dentate neurons firing at particular hippocampal theta phases during REM sleep reshape their synapses and steer mature granule cells to consolidate fear memory.", "summary": "This short perspective builds on the authors' earlier mouse work showing that sparse activity of adult-born hippocampal neurons during REM sleep is needed for memory consolidation. It reviews how sleep oscillations, particularly REM-sleep theta, are linked to strengthening and pruning of synapses. The authors put forward a model in which a subset of adult-born neurons fires locked to the theta phase, keeps its dendritic spines, and inhibits mature granule cells so that those cells fire at the opposite phase and form a memory trace. They outline two experimental routes to test the model: phase-specific closed-loop optogenetic manipulation and recording methods with finer time resolution than calcium sensors.", "research_question": "How might plasticity of adult-born dentate gyrus neurons, timed to hippocampal theta oscillations, support memory consolidation during REM sleep?", "approach": "Perspective article that integrates the authors' prior findings in mice with published work on sleep-dependent synaptic plasticity to propose a testable circuit hypothesis.", "key_findings": [ { "finding": "The authors argue, from their prior mouse work, that sparse activity of adult-born neurons during REM sleep after contextual fear learning is necessary for memory consolidation.", "evidence": "Main text (citing Kumar et al., 2020)", "species": "mouse", "n": null, "stats": null }, { "finding": "Only adult-born neurons at an age of heightened plasticity matter: silencing 4-week-old cells, but not 2- or 10-week-old cells, during REM sleep impairs consolidation, and random activation of 4-week-old cells also impairs memory.", "evidence": "Main text (citing Kumar et al., 2020)", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors hypothesize that theta phase-locked activity stabilizes spines in a sparse subset of adult-born neurons, which then inhibit mature granule cells in a phase-specific way so that connected mature cells fire at the reciprocal theta phase and establish a memory trace.", "evidence": "Fig. 1A-D", "species": "mouse", "n": null, "stats": null }, { "finding": "Testing the hypothesis would require phase-specific closed-loop optogenetic manipulation and methods with higher time resolution than genetically encoded calcium sensors.", "evidence": "Main text", "species": null, "n": null, "stats": null } ], "methods": [ "literature synthesis and hypothesis proposal (perspective)" ], "models": [ "mice (cited prior work)" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [], "limitations": [ "The proposed model is a hypothesis; whether adult-born neurons actually fire at a particular theta phase has not yet been verified.", "Calcium imaging used in the prior work lacks the time resolution to resolve theta phase-locked firing directly." ], "keywords": [ "adult neurogenesis", "adult-born neurons", "REM sleep", "theta oscillation", "memory consolidation", "dentate gyrus", "synaptic plasticity", "contextual fear memory" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2021-neural-regen-res.md" }, { "id": "yu-2021-bbrc", "doi": "10.1016/j.bbrc.2021.04.072", "pmid": "33906108", "pmcid": null, "url": "https://doi.org/10.1016/j.bbrc.2021.04.072", "title": "Fear generalization immediately after contextual fear memory consolidation in mice", "authors": [ "Yu J", "Naoi T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-06", "journal": "Biochemical and Biophysical Research Communications", "volume": "558", "issue": null, "pages": "102-106", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "fear_memory_ptsd" ], "tldr": "In mice, brief exposure to a context resembling the fear-conditioned one, given soon after training, produced fear generalization as early as 6 h after training, once consolidation had occurred.", "summary": "Overgeneralized fear is a feature of anxiety-related conditions such as acute stress disorder and PTSD, but when generalization first emerges after learning is not well defined. Using contextual fear conditioning in mice, the authors exposed animals to a neutral context shortly after training and then tested fear responses. Mice that encountered a context similar to the conditioned one, but not a clearly different one, generalized their fear already at 6 h after training, right after consolidation of the contextual memory. The generalization showed up both as a change in how much the mice froze and in how freezing was patterned across the conditioned and generalized contexts. The work offers a rodent paradigm for studying factors that shape early fear generalization.", "research_question": "Can fear generalization arise immediately after contextual fear memory consolidation, and does post-training exposure to a neutral context influence it?", "approach": "Mice underwent contextual fear conditioning and were exposed soon after training to either a similar or a different neutral context; freezing in the conditioned and neutral contexts was then compared 6 h after training.", "key_findings": [ { "finding": "Mice exposed to a neutral context similar to the training context soon after conditioning showed fear generalization 6 h after training, immediately after contextual fear memory consolidation.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "" }, { "finding": "Exposure to a clearly different neutral context after training did not produce this early fear generalization.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "" }, { "finding": "The generalized fear was expressed as a change in both the total amount and the pattern of freezing between the conditioned and generalized contexts.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "" } ], "methods": [ "contextual fear conditioning", "post-training context exposure", "freezing behavior analysis" ], "models": [ "mice" ], "brain_regions": [], "data_code_availability": [], "limitations": [], "keywords": [ "Context exposure", "Contextual fear conditioning", "Discrimination", "Generalization", "Memory", "PTSD" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yu-2021-bbrc.md" }, { "id": "tezuka-2021-scirep", "doi": "10.1038/s41598-021-90332-1", "pmid": "34045518", "pmcid": "PMC8160151", "url": "https://doi.org/10.1038/s41598-021-90332-1", "title": "Real-time, automatic, open-source sleep stage classification system using single EEG for mice", "authors": [ "Tezuka T", "Kumar D", "Singh S", "Koyanagi I", "Naoi T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-05-27", "journal": "Scientific Reports", "volume": "11", "issue": "1", "pages": "11151", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "sleep_staging_closed_loop_tools", "rem_sleep_memory" ], "tldr": "A neural-network classifier reads a single mouse EEG channel in 10-s epochs and labels wake, NREM and REM in real time without EMG or per-animal calibration, detecting REM with high sensitivity and specificity.", "summary": "Studying what REM sleep does in mice requires catching short, sparse REM episodes as they happen, but existing real-time staging tools need manual per-animal thresholds or extra signals such as EMG. The authors built a convolutional network (UTSN) that combines the raw one-channel EEG, its frequency spectrum and the circadian time of day, and a second version (UTSN-L) that adds a recurrent memory of the preceding epochs. Trained on expert-scored recordings and tested on held-out recordings under simulated real-time conditions, UTSN-L outperformed simpler machine-learning baselines and the network without memory, and reproduced expert-derived sleep architecture and power spectra. The open-source code includes a graphical interface that can send stage decisions to an external device for closed-loop, stage-specific experiments.", "research_question": "Can sleep stages in mice be classified automatically and in real time from a single EEG channel, with REM detected accurately enough for closed-loop interventions?", "approach": "A 1D convolutional network taking raw EEG, FFT spectrum and zeitgeber time (UTSN), optionally followed by an LSTM over the last 10 epochs (UTSN-L), was trained on expert-scored 6-h mouse recordings and compared against logistic regression, random forest, AdaBoost and single-feature networks using only past data for each decision.", "key_findings": [ { "finding": "The UTSN-L system reached 90% overall accuracy and 81% multi-class Matthews Correlation Coefficient, with 91% sensitivity and 98% specificity for REM sleep.", "evidence": "Abstract; Table 1", "species": "mouse", "n": null, "stats": null }, { "finding": "The classifiers were built from 214 expert-scored recordings of 6 h each, of which 192 were used for training and validation and 22 were held out for testing.", "evidence": "Results, Training, validation, and testing", "species": "mouse", "n": "214 recordings (192 training/validation, 22 testing)", "stats": null }, { "finding": "Adding the LSTM memory of past epochs improved classification: UTSN-L performed better overall than UTSN, which tended to call more and shorter sleep episodes than the expert scoring.", "evidence": "Table 1; Fig. 3A-D", "species": "mouse", "n": "n=22 recordings", "stats": null }, { "finding": "On held-out test recordings, results were consistent with validation, total sleep amounts were almost identical to expert scoring, and power spectra of classified epochs were almost identical to ground truth.", "evidence": "Table 2; Suppl. Table 1; Figs. 3B, 4", "species": "mouse", "n": "n=22 recordings", "stats": null }, { "finding": "A graphical interface runs the classifier on a personal computer, can output decisions to an Arduino device for closed-loop control with a 10 s delay set by the epoch window, and the code is open source.", "evidence": "Fig. 5; VIDEO S1", "species": null, "n": null, "stats": null } ], "methods": [ "epidural EEG and trapezius EMG recording in freely moving mice (EMG used only for expert scoring)", "expert visual sleep scoring in 10-s epochs", "one-dimensional convolutional neural network on raw EEG combined with FFT spectrum and zeitgeber time", "long short-term memory recurrent network over preceding epochs", "comparison with logistic regression, random forest and AdaBoost", "graphical user interface with Arduino output for closed-loop experiments" ], "models": [ "C57Bl6/J mice" ], "brain_regions": [], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/5wtxz793my.1", "as_stated": "Data underlying the results described in this manuscript are available at ... https://doi.org/10.17632/5wtxz793my.1 (after acceptance)" }, { "type": "data", "url": null, "status": "not_publicly_resolvable_2026-10-16", "as_stated": "the raw EEG and EMG recording data with stage labels" }, { "type": "code", "url": "https://github.com/tarotez/sleepstages", "as_stated": "Code for UTSN and UTSN-L are available at https://github.com/tarotez/sleepstages." } ], "limitations": [ "All evaluations used previously recorded, expert-scored data replayed under simulated real-time constraints rather than live closed-loop sessions.", "REM is much rarer than the other stages, so training data are imbalanced; the authors propose imbalance-aware loss functions or attention mechanisms as future improvements.", "Decisions are made on 10-s epochs, so closed-loop output lags by one epoch window." ], "keywords": [ "sleep stage classification", "real-time", "single-channel EEG", "REM sleep", "convolutional neural network", "LSTM", "closed-loop", "mouse", "open-source" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md" }, { "id": "vergara-2021-ijms", "doi": "10.3390/ijms22062874", "pmid": "33808976", "pmcid": "PMC7999719", "url": "https://doi.org/10.3390/ijms22062874", "title": "Remapping of Adult-Born Neuron Activity during Fear Memory Consolidation in Mice", "authors": [ "Vergara P", "Kumar D", "Srinivasan S", "Koyanagi I", "Naoi T", "Singh S", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-03-12", "journal": "International Journal of Molecular Sciences", "volume": "22", "issue": "6", "pages": "2874", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "fear_memory_ptsd", "imaging_tools" ], "tldr": "A population-level reanalysis of calcium imaging in mice shows that hippocampal adult-born neurons active during fear learning differ from those active at retrieval, with activity gradually remapping over hours of consolidation.", "summary": "This study reanalyzed previously published calcium imaging recordings of roughly 4-week-old adult-born dentate gyrus neurons in freely moving mice across contextual fear learning, a home-cage consolidation period, and memory retrieval. Using deconvolved unitary calcium events, population activity vectors, cosine similarity and hierarchical clustering, the authors asked whether a fixed set of adult-born neurons carries the fear memory from learning to retrieval. Exposure to the novel conditioning context raised activity in a subset of cells, but the same population was active before and after the shock, while a different population was active at the retrieval test. During the hours of consolidation, population activity shifted gradually from a learning-like to a test-like pattern in both sleep and wakefulness, driven by small groups of neurons that lost or gained activity. The authors suggest that adult-born neurons support fear memory formation in a way other than directly holding the trace, possibly helping to separate memories formed hours apart.", "research_question": "Do hippocampal adult-born neurons hold fear memory traces at the population level, with the same cells active during learning and retrieval?", "approach": "Population-level reanalysis of miniature-microscope calcium imaging of adult-born dentate gyrus neurons (GCaMP3 expressed via tamoxifen-induced Nestin-CreERT2) recorded across contextual fear conditioning, 2.5 h of a 5.5 h home-cage consolidation period, and a retrieval test, using deconvolution, bootstrap statistics, cosine-similarity clustering and a remapping index.", "key_findings": [ { "finding": "Exposure to the novel conditioning context increased adult-born neuron activity, with ~28% of cells increasing activity in the preshock period and ~10% decreasing activity after the shock.", "evidence": "Fig. 1D-F", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "bootstrap, p < 0.05; moving block bootstrap for individual neurons" }, { "finding": "Similarity clustering of population activity vectors showed that a similar population was active before and after the shock, whereas a different population was active during the retrieval test, so learning and retrieval populations did not overlap.", "evidence": "Fig. 2B-C", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "hierarchical clustering on cosine similarity, significant clusters p < 0.05" }, { "finding": "Across 15 min bins of the consolidation period, a remapping index declined steadily with time (all data r = -0.97, p < 0.0001), and this drift was seen in both sleep (r = -0.98) and wake (r = -0.93, p = 0.008).", "evidence": "Fig. 3A-B", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "r = -0.97 p < 0.0001 (all); r = -0.98 p < 0.0001 (sleep); r = -0.93 p = 0.008 (wake)" }, { "finding": "Remapping was carried by subsets of neurons whose activity changed with time (15 decreasing, 9 increasing, 70 unchanged); decreasing cells were mainly active during learning and increasing cells mainly at the test, and significant clusters appeared only among remapping cells.", "evidence": "Fig. 3C-F", "species": "mouse", "n": "decreasing n = 15; increasing n = 9; non-remapping n = 70", "stats": "Pearson's correlation p < 0.05, FDR q < 0.05; bootstrap p < 0.05" }, { "finding": "Adult-born neurons previously shown to be reactivated during REM sleep overlapped with the cells that decreased their activity during consolidation, which the authors suggest may link REM reactivation and remapping, without demonstrating causality.", "evidence": "Fig. S1C", "species": "mouse", "n": null, "stats": null } ], "methods": [ "in vivo calcium imaging with a head-mounted miniature microendoscope in freely moving mice", "tamoxifen-inducible genetic labeling of adult-born neurons with GCaMP3", "contextual fear conditioning", "EEG/EMG recording for sleep-wake state", "CNMF-E signal extraction and deconvolution of calcium traces", "bootstrap and moving block bootstrap statistics", "cosine similarity of population activity vectors with agglomerative hierarchical clustering", "remapping index based on angular distance" ], "models": [ "pNestin-CreERT2 x Rosa26-pCAG-LSL-GCaMP3 (Ai38) male mice on a C57BL/6J background" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [ { "type": "data_and_code", "url": "https://github.com/vergaloy/Remapping_ABNs", "as_stated": "The data (raw calcium transients and activity traces) and the code supporting the finding of this study (MATLAB) are available" } ], "limitations": [ "The work is a reanalysis of calcium imaging data from an earlier study rather than new experiments.", "Remapping could not be quantified within REM sleep because REM was brief during consolidation and adult-born neurons fired very sparsely in that state.", "Whether vigilance state influences remapping could not be tested episode by episode because of the sparse firing of adult-born neurons.", "It remains open whether remapping depends on learning and whether it is specific to immature adult-born neurons.", "The link between REM reactivation and remapping is correlational; causality was not shown." ], "keywords": [ "hippocampus", "adult neurogenesis", "memory", "contextual fear conditioning", "calcium imaging", "sleep", "memory consolidation", "remapping" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md" }, { "id": "carrier-ruiz-2021-star-protocols", "doi": "10.1016/j.xpro.2020.100238", "pmid": "33458703", "pmcid": "PMC7797924", "url": "https://doi.org/10.1016/j.xpro.2020.100238", "title": "Calcium imaging of adult-born neurons in freely moving mice", "authors": [ "Carrier-Ruiz A", "Sugaya Y", "Kumar D", "Vergara P", "Koyanagi I", "Srinivasan S", "Naoi T", "Kano M", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-03", "journal": "STAR Protocols", "volume": "2", "issue": "1", "pages": "100238", "type": "methods_protocol", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [ { "doi": "10.1016/j.neuron.2020.05.008", "relation": "protocol_for" } ], "themes": [ "imaging_tools", "adult_neurogenesis_memory", "rem_sleep_memory" ], "tldr": "A step-by-step protocol for recording calcium activity of sparse adult-born dentate gyrus neurons in freely moving mice alongside sleep recordings, including an analysis pipeline for long sessions.", "summary": "This protocol describes how the lab images calcium activity of adult-born neurons in the mouse dentate gyrus with a head-mounted miniature microscope while recording sleep with EEG/EMG electrodes. It covers genetic labeling of adult-born neurons with a tamoxifen-inducible calcium indicator, implantation of a GRIN lens and electrodes, recovery, imaging, fear conditioning and histological confirmation. Because adult-born neurons are few and rarely active, the authors adapt a constrained non-negative matrix factorization method to analyze long recordings in short overlapping batches. They report that this batch approach reduces false-positive components while recovering neurons that single-batch analysis misses, and they list troubleshooting steps and limitations.", "research_question": "How can the activity of sparse, weakly labeled adult-born dentate gyrus neurons be imaged reliably over long sessions in freely moving mice together with sleep stages?", "approach": "Nestin-CreERT2 x GCaMP3 reporter mice receive tamoxifen, then a GRIN lens over the dorsal dentate gyrus and EEG/EMG electrodes for miniature-microscope imaging during sleep and behavior. Raw videos are motion-corrected and processed with a modified CNMF-E pipeline that analyzes overlapping 1,000-frame batches.", "key_findings": [ { "finding": "Adult-born neurons are scarce and sparsely active in the imaging field, which makes their activity hard to detect by eye.", "evidence": "Quantification and statistical analysis, step notes", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors report that about 50% of preparations succeed, since GCaMP3 signal from the few labeled neurons may be undetectable before post-processing.", "evidence": "Step-by-step method details, note on baseplate attachment", "species": "mouse", "n": null, "stats": null }, { "finding": "Compared with overlapping-batch analysis, an estimated 34% of components extracted by conventional whole-video CNMF-E were classified as false positives based on low circularity.", "evidence": "Figure 11E", "species": "mouse", "n": null, "stats": null }, { "finding": "On average, 61% of neurons found by the overlapping-batch method were missed when only an individual batch was analyzed, because their peak-to-noise ratio fell below the detection threshold.", "evidence": "Figure 11H", "species": "mouse", "n": null, "stats": null }, { "finding": "Components from the overlapping-batch method were spatially and temporally closer to those from individual-batch analysis, which the authors interpret as fewer false positives without loss of true detections.", "evidence": "Figure 11G", "species": "mouse", "n": null, "stats": null }, { "finding": "Newer GCaMP6 reporter lines crossed with Nestin-CreERT2 mice did not produce indicator expression in adult-born neurons in the authors' hands, so the GCaMP3 line Ai38 is recommended.", "evidence": "Before you begin, notes", "species": "mouse", "n": null, "stats": null } ], "methods": [ "tamoxifen-inducible genetic labeling of adult-born neurons with GCaMP3", "GRIN lens implantation over the dorsal dentate gyrus", "in vivo calcium imaging with a head-mounted miniature microscope in freely moving mice", "EEG/EMG recording and sleep staging in 10-s bins", "contextual fear conditioning", "constrained non-negative matrix factorization (CNMF-E) with overlapping batches", "cross-session alignment by motion correction to a shared reference frame", "perfusion, cryosectioning and confocal histology" ], "models": [ "Nestin-CreERT2 transgenic mice", "Ai38 (RCL-GCaMP3) reporter mice", "male C57BL/6 background mice" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [ { "type": "code", "url": "https://github.com/vergaloy/ABNs-Calcium-extraction", "as_stated": "Data and code underlying the results described in this manuscript are available at" }, { "type": "data", "url": "https://data.mendeley.com/datasets/gfbdv5kfrz/1", "as_stated": "the raw data from the related article (Kumar et al., 2020) are available at" } ], "limitations": [ "The miniature microscope has no optical sectioning, so one detected transient may come from two neurons stacked along the z-axis.", "Implanting the GRIN lens partially lesions the ipsilateral CA1, which may reorganize the circuit.", "Because adult-born neurons change as they mature, reusing the same mice across several tasks while keeping comparable neuron properties is difficult.", "The described hardware is costly, although open-source miniature microscopes are a cheaper option.", "Tracking the same adult-born neurons across days may not be possible given their small number; tracking was achieved within the same day." ], "keywords": [ "adult-born neurons", "adult neurogenesis", "dentate gyrus", "calcium imaging", "miniscope", "GCaMP3", "sleep recording", "CNMF-E", "protocol" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md" }, { "id": "koyanagi-2021-molbrain", "doi": "10.1186/s13041-021-00733-6", "pmid": "33568175", "pmcid": "PMC7874630", "url": "https://doi.org/10.1186/s13041-021-00733-6", "title": "Metabolic fingerprints of fear memory consolidation during sleep", "authors": [ "Koyanagi I", "Sonomura K", "Naoi T", "Ohnishi T", "Kaneko N", "Sawamoto K", "Sato T-A", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2021, "published_date": "2021-02-10", "journal": "Molecular Brain", "volume": "14", "issue": "1", "pages": "30", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "rem_sleep_memory", "fear_memory_ptsd" ], "tldr": "Metabolomic profiling of the mouse dentate gyrus shows that metabolites shift strongly between sleep and wakefulness, and purine metabolism links sleep state transitions with fear memory consolidation.", "summary": "The authors combined real-time EEG/EMG sleep-state detection with mass-spectrometry metabolomics of dentate gyrus tissue to ask which metabolites accompany fear memory processing during sleep in mice. Metabolite profiles separated wakefulness from REM and NREM sleep, with changes in pathways such as glutathione, amino acid and purine metabolism, suggesting an antioxidative environment in the dentate gyrus during sleep. Fear conditioning produced weaker metabolic signatures than sleep-wake transitions, but purine metabolism changed in both settings. Oral supplementation with purine metabolites did not alter sleep architecture or average freezing, yet disrupted the within-animal correlations between conditioned responses before and after consolidation.", "research_question": "Which metabolites in the hippocampal dentate gyrus change across sleep-wake states and during contextual fear memory consolidation in sleep?", "approach": "Mice were sacrificed after a set time in REM sleep, NREM sleep or wakefulness (detected in real time by EEG/EMG), with or without prior fear conditioning, and dentate gyrus metabolites were quantified by GC-MS and LC-MS and analyzed by PCA, PLS-DA, permutation and enrichment analyses. Selected purine metabolites were then given in drinking water to test effects on sleep and fear memory.", "key_findings": [ { "finding": "More than 200 metabolites were consistently detected in the dentate gyrus, and PLS-DA separated REM and NREM sleep from wakefulness (Q2 value 0.52).", "evidence": "Fig. 1d", "species": "mouse", "n": "REM, n=10 mice; NREM, n=10 mice; Wake, n=11 mice", "stats": "permutation test, REM vs. Wake, p<0.05; NREM vs. Wake, p<0.05" }, { "finding": "Pairwise comparisons identified 86 metabolites (with some overlap) changed between sleep-wake states, including decreased GSSG and increased GSH, allantoin and cysteine during sleep, which the authors suggest reflects an antioxidative environment.", "evidence": "Fig. 1g-k", "species": "mouse", "n": null, "stats": "p<0.05, fold change>|1.5|" }, { "finding": "Fear conditioning produced less distinct metabolite phenotypes than sleep-wake transitions, but purine metabolism changed both across sleep-wake states and with fear memory consolidation.", "evidence": "Figs. 2, 3", "species": "mouse", "n": null, "stats": null }, { "finding": "One week of oral hypoxanthine, xanthine, allantoin or urea did not change sleep architecture except shorter REM sleep episodes with urea, and did not change mean freezing in context or tone tests.", "evidence": "Figs. 4, 5b-f", "species": "mouse", "n": "control, n=16; hypoxanthine, n=12; xanthine, n=13; allantoin, n=19; urea, n=16 (behavior)", "stats": "context test group effect F(4, 71)=0.90, p=0.47" }, { "finding": "Post-shock freezing correlated with freezing in the context test in control mice (r=0.58) but not in hypoxanthine (r=0.22, p=0.48) or urea (r=0.27, p=0.32) groups.", "evidence": "Fig. 5g-k", "species": "mouse", "n": "control n=16; hypoxanthine n=12; urea n=16", "stats": "two-tailed Pearson's correlation, control r=0.58, p<0.05" }, { "finding": "Freezing during the third conditioning tone correlated with tone-test freezing in controls (r=0.54) but not in purine-supplemented groups, suggesting purine supplementation alters relationships between conditioned responses across consolidation.", "evidence": "Fig. 5q-u", "species": "mouse", "n": "control n=14", "stats": "two-tailed Pearson's correlation, r=0.54, p<0.05" } ], "methods": [ "real-time EEG/EMG sleep-wake state detection", "contextual and tone fear conditioning (delayed shock, immediate shock, context only)", "GC-MS and LC-MS metabolomics of dentate gyrus tissue", "PCA, PLS-DA, permutation and pathway enrichment analyses", "oral purine metabolite supplementation in drinking water", "EEG power spectral analysis" ], "models": [ "male C57BL/6 mice" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/f6pbcvvbxb.1", "as_stated": "Data underlying the results described in this manuscript are available at Mendeley Data" } ], "limitations": [ "Mice were briefly awake during isoflurane inhalation before sampling, which may have hidden small metabolite differences between sleep-wake states.", "Metabolomic phenotypes could not determine whether fear memory had been established, indicating limited sensitivity to memory-related changes.", "The authors call for analyses with higher spatial and temporal resolution to clarify the role of purine metabolism." ], "keywords": [ "fear memory", "REM sleep", "NREM sleep", "dentate gyrus", "metabolomics", "purine metabolism" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md" }, { "id": "vergara-2020-front-cell-neurosci", "doi": "10.3389/fncel.2020.594401", "pmid": "33324167", "pmcid": "PMC7726349", "url": "https://doi.org/10.3389/fncel.2020.594401", "title": "Mechanisms Underlying Memory Consolidation by Adult-Born Neurons During Sleep", "authors": [ "Vergara P", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2020, "published_date": "2020-11-26", "journal": "Frontiers in Cellular Neuroscience", "volume": "14", "issue": null, "pages": "594401", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory" ], "tldr": "A mini review proposing how sparse, oscillation-decoupled activity and experience-driven synaptic remodeling of hippocampal adult-born neurons could support memory consolidation during REM sleep.", "summary": "Building on the authors' finding in mice that adult-born dentate gyrus neurons active during fear learning reactivate in later REM sleep and that their REM activity is required for consolidation, this mini review asks what mechanisms could underlie that role. It argues that weak inhibitory input and high excitability let young adult-born neurons fire ahead of mature granule neurons within a theta cycle, possibly priming CA3 ensembles or engaging CA3 inhibition for pattern separation. It further proposes that learning may speed the integration of a subset of these neurons into inhibitory circuits, so that REM theta could selectively maintain the synapses of oscillation-coupled cells. Finally, it questions whether adult-born neurons fit the classic definition of engram cells and lists experiments needed to test these hypotheses.", "research_question": "Through what cellular and circuit mechanisms might hippocampal adult-born neurons contribute to memory consolidation during REM sleep?", "approach": "A narrative mini review that integrates the authors' calcium imaging and optogenetic findings in mice with published work on adult-born neuron physiology, hippocampal oscillations, and engram research to formulate testable hypotheses.", "key_findings": [ { "finding": "The authors restate their prior evidence that adult-born neurons active during learning reactivate in subsequent REM sleep and that disrupting their activity in REM sleep, by either optogenetic activation or silencing, impairs memory consolidation.", "evidence": "Figure 1; Introduction", "species": "mouse", "n": null, "stats": null }, { "finding": "The review proposes that weaker inhibition and higher excitability let adult-born neurons fire before granule neurons within a theta cycle, which may prime a subset of CA3 neurons or drive CA3 inhibitory circuits that support pattern separation.", "evidence": "Figure 2C", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors hypothesize that learning accelerates integration of a subset of adult-born neurons into inhibitory circuits, so that REM sleep may maintain synapses of oscillation-coupled cells, consistent with their observation that silencing these neurons in REM sleep lengthens spine necks.", "evidence": "Figure 2D-E; section on REM sleep and synaptic plasticity", "species": "mouse", "n": null, "stats": null }, { "finding": "Because little overlap was found between adult-born neurons active during fear learning and during retrieval, the review suggests these neurons may not fit the conventional engram definition and may transiently encode information before an engram forms downstream during REM sleep.", "evidence": "Section 'Are ABNs engram cells?'", "species": "mouse", "n": null, "stats": null } ], "methods": [ "narrative literature review", "synthesis of in vivo calcium imaging and optogenetic findings" ], "models": [ "mice" ], "brain_regions": [ "dentate gyrus", "CA3", "CA1", "entorhinal cortex" ], "data_code_availability": [], "limitations": [ "The authors state that the exact mechanisms by which adult-born neurons consolidate memory during REM sleep remain unclear and that the proposed mechanisms are hypotheses requiring testing.", "They note that the sparse firing of adult-born neurons could be a major obstacle to recording their spike coupling to dentate gyrus oscillations." ], "keywords": [ "adult neurogenesis", "REM sleep", "memory consolidation", "theta oscillation", "synaptic plasticity", "hippocampus", "optogenetics", "calcium imaging" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2020-front-cell-neurosci.md" }, { "id": "kumar-2020-neuron", "doi": "10.1016/j.neuron.2020.05.008", "pmid": "32502462", "pmcid": null, "url": "https://doi.org/10.1016/j.neuron.2020.05.008", "title": "Sparse Activity of Hippocampal Adult-Born Neurons during REM Sleep Is Necessary for Memory Consolidation", "authors": [ "Kumar D", "Koyanagi I", "Carrier-Ruiz A", "Vergara P", "Srinivasan S", "Sugaya Y", "Kasuya M", "Yu TS", "Vogt KE", "Muratani M", "Ohnishi T", "Singh S", "Teixeira CM", "Chérasse Y", "Naoi T", "Wang SH", "Nondhalee P", "Osman BAH", "Kaneko N", "Sawamoto K", "Kernie SG", "Sakurai T", "McHugh TJ", "Kano M", "Yanagisawa M", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2020, "published_date": "2020-08", "journal": "Neuron", "volume": "107", "issue": "3", "pages": "552-565.e10", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": "Elsevier open archive user license (from 2021-08-05)", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory", "fear_memory_ptsd", "imaging_tools" ], "tldr": "In mice, young adult-born dentate gyrus neurons active during fear learning are reactivated in later REM sleep, and silencing their sparse REM-sleep activity impairs contextual fear memory consolidation.", "summary": "This study asked whether the small population of young adult-born neurons in the mouse dentate gyrus contributes to memory consolidation during sleep. Long-duration calcium imaging in freely moving mice showed that these neurons fire sparsely, even less in sleep, and that contextual fear learning further lowers their activity in REM sleep while the neurons active during learning tend to be reactivated in REM sleep. Optogenetically silencing young adult-born neurons only during REM sleep in the consolidation window left sleep architecture and dentate theta oscillations unchanged, but reduced activity-dependent gene expression, lengthened dendritic spine necks, and impaired contextual fear memory. Random optogenetic activation in REM sleep also impaired memory, which the authors interpret as a need for finely tuned activity.", "research_question": "Does the activity of young adult-born dentate gyrus neurons during sleep, and REM sleep in particular, contribute to hippocampus-dependent memory consolidation?", "approach": "Nestin-CreERT2 mice were used to express GCaMP3, halorhodopsin, or channelrhodopsin-2 in young adult-born neurons; activity was imaged across sleep-wake states with a head-mounted miniature microscope, and the neurons were silenced or activated in a sleep-stage-specific manner using real-time EEG/EMG staging after contextual fear conditioning, combined with RNA sequencing, spine morphology, and LFP analysis.", "key_findings": [ { "finding": "After contextual fear conditioning (delayed shock), the calcium event frequency of young adult-born neurons in REM sleep was further reduced, which did not occur in immediate-shock controls or in fully mature granule neurons.", "evidence": "Fig. 1G-H; Fig. S5A-C", "species": "mouse", "n": "n = 88, 47, 113, and 137 neurons in IS-BL, IS-AS, DS-BL, and DS-AS groups", "stats": "p < 0.05, bootstrap" }, { "finding": "About 37.9% of recorded young adult-born neurons were active at least once in post-learning REM sleep, and neurons active right after the shock were more likely to be active in subsequent REM sleep, whereas activity during the retrieval test did not predict REM activity.", "evidence": "Fig. 1I-K", "species": "mouse", "n": "n = 59 and 36 neurons in REM- and REM+ groups from 7 mice", "stats": "p < 0.05, p < 0.01, bootstrap" }, { "finding": "Silencing young adult-born neurons during REM sleep in the 6 h after conditioning did not change sleep architecture, EEG power spectra, or dentate gyrus theta autocorrelation (p = 0.72).", "evidence": "Fig. 3D-L", "species": "mouse", "n": "n = 11-13 mice/genotype; 434 and 468 LFP epochs", "stats": "p = 0.72, Mann-Whitney test" }, { "finding": "REM-sleep silencing of young adult-born neurons reduced dentate gyrus expression of immediate early genes such as Zif268, Npas4, and Fos, all decreased genes carried SRF binding motifs, and dendritic spine necks of these neurons became longer.", "evidence": "Fig. 4H-L; Fig. 5C-E", "species": "mouse", "n": "n = 4 mice each (RNA-seq); n = 30-40 dendrites/group (spines)", "stats": "SRF motif enrichment p < 0.0001" }, { "finding": "Silencing young adult-born neurons only during REM sleep within the consolidation window reduced contextual freezing the next day, while silencing outside the window (p = 0.98), during NREM sleep or wakefulness, or of 2-week-old or 10-week-old neurons did not significantly impair memory.", "evidence": "Fig. 6A-Q", "species": "mouse", "n": "n = 12-13/genotype (within window); n = 9/genotype (outside window)", "stats": "p < 0.05, two-tailed unpaired t test" }, { "finding": "Random 20-Hz optogenetic activation of young adult-born neurons during REM sleep also reduced contextual freezing, suggesting that finely tuned rather than simply more activity is needed for consolidation.", "evidence": "Fig. 6T-V", "species": "mouse", "n": "n = 10-12/genotype", "stats": "p < 0.05, two-tailed paired t test" } ], "methods": [ "in vivo calcium imaging with a head-mounted miniaturized microendoscope in freely moving mice", "tamoxifen-inducible genetic labeling of adult-born neurons (pNestin-CreERT2)", "closed-loop optogenetic silencing (halorhodopsin) and activation (channelrhodopsin-2) during EEG/EMG-defined sleep stages", "contextual and tone fear conditioning", "dentate gyrus local field potential recording", "slice patch clamp", "laser microdissection and RNA sequencing", "confocal 3D reconstruction of dendritic spines" ], "models": [ "male F1 transgenic mice on a C57BL/6J background (pNestin-CreERT2 crossed with Rosa26 Cre-dependent GCaMP3, halorhodopsin, channelrhodopsin-2, or tdTomato reporter lines)" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [ { "type": "data", "url": "https://doi.org/10.17632/gfbdv5kfrz.1", "as_stated": "Data underlying the results described in this manuscript, except raw data for RNA analysis, are available at Mendeley Data" }, { "type": "data", "url": "https://doi.org/10.17632/pfgkv43yn7.1", "as_stated": "RNaseq raw data are available at Mendeley Data" } ], "limitations": [ "Calcium indicators lack the temporal resolution needed to assess how adult-born neuron firing relates to theta phase.", "The sparseness of REM-active adult-born neuron activity prevented population-level ensemble analysis.", "Selectively controlling only the neurons active in REM sleep would require manipulation with temporal resolution matching single REM episodes of about a minute.", "The interval between conditioning and testing in the imaging experiments was shortened to 5.5 h to keep the same cells trackable, which lowered overall freezing." ], "keywords": [ "adult neurogenesis", "dentate gyrus", "REM sleep", "memory consolidation", "contextual fear conditioning", "calcium imaging", "optogenetics", "dendritic spines", "immediate early genes" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md" }, { "id": "maezono-2020-eneuro", "doi": "10.1523/eneuro.0093-20.2020", "pmid": "32321771", "pmcid": "PMC7196722", "url": "https://doi.org/10.1523/eneuro.0093-20.2020", "title": "Progressive Changes in Sleep and Its Relations to Amyloid-β Distribution and Learning in Single App Knock-In Mice", "authors": [ "Maezono SEB", "Kanuka M", "Tatsuzawa C", "Morita M", "Kawano T", "Kashiwagi M", "Nondhalee P", "Sakaguchi M", "Saito T", "Saido TC", "Hayashi Y" ], "pi_role": "co_author", "year": 2020, "published_date": "2020-04-22", "journal": "eNeuro", "volume": "7", "issue": "2", "pages": "ENEURO.0093-20.2020", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "rem_sleep_memory", "other" ], "tldr": "In App knock-in mice that model early Alzheimer's disease, REM sleep loss and REM-specific EEG slowing appear early, worsen with age, and track learning deficits and brainstem amyloid buildup.", "summary": "The study used AppNL-G-F knock-in mice, in which a mutated human App gene replaces the mouse gene so that expression follows the native pattern, to ask how sleep changes in an Alzheimer's disease model without overexpression artifacts. Male homozygous and heterozygous mice were recorded with EEG/EMG at six and 12 months, tested in trace fear conditioning, and examined histologically for amyloid-β plaques. Homozygous mice lost REM sleep from six months and lost more by 12 months, along with a shift toward slower EEG activity during REM sleep, while heterozygous mice slept largely normally. At the older age, learning performance correlated with REM sleep amount, and amyloid-β accumulation in REM-regulating brainstem areas followed a time course resembling the REM sleep loss. The authors propose that REM sleep changes may serve as an early marker of the disease.", "research_question": "How do sleep architecture and sleep-state EEG change with age in single App knock-in mice, and do these changes relate to learning deficits and regional amyloid-β deposition?", "approach": "Wild-type, heterozygous and homozygous AppNL-G-F male mice underwent 24-h EEG/EMG sleep recording at six or 12 months, followed by trace fear conditioning at seven or 13 months and immunohistochemical quantification of amyloid-β plaques in sleep-related brain regions.", "key_findings": [ { "finding": "Homozygous AppNL-G-F mice showed less total REM sleep and a lower REMS/total sleep ratio at six months, mainly during the light phase, with a further REM reduction plus reduced NREM sleep and more wake at 12 months.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": "Games-Howell multiple comparison test" }, { "finding": "Heterozygous mice had sleep architecture broadly similar to age-matched wild-type mice at both six and 12 months.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null }, { "finding": "During REM sleep, homozygous mice showed a lower gamma-to-delta power ratio from six months, resembling the EEG slowing reported in early-stage patients; by 12 months delta rose and theta and gamma fell in both sleep stages.", "evidence": "Fig. 3", "species": "mouse", "n": null, "stats": "Games-Howell multiple comparison test" }, { "finding": "In trace fear conditioning, homozygous mice froze less at retrieval at seven months, and at 13 months homozygous (and to a lesser extent heterozygous) mice showed impaired learning during training.", "evidence": "Fig. 5", "species": "mouse", "n": null, "stats": "mixed ANOVA; Games-Howell multiple comparison test" }, { "finding": "In 13-month-old homozygous mice, freezing during the third conditioned stimulus on day 1 correlated strongly and positively with total REM sleep, whereas no significant correlation with sleep parameters was found at seven months.", "evidence": "Fig. 6", "species": "mouse", "n": null, "stats": "Pearson's correlation" }, { "finding": "Amyloid-β in the pontine tegmental area and ventral medulla rose markedly from seven to 13 months in homozygous mice but was barely detectable in heterozygous mice, a pattern that somewhat resembled the progression of REM sleep loss.", "evidence": "Fig. 7", "species": "mouse", "n": null, "stats": "Welch's t test" } ], "methods": [ "EEG/EMG sleep recording with manual vigilance-state scoring", "EEG power spectral analysis", "novel object presentation during sleep recording", "open field test", "trace fear conditioning", "immunohistochemistry and image-based amyloid-β plaque quantification" ], "models": [ "AppNL-G-F knock-in mice (heterozygous and homozygous) on C57BL/6J background", "wild-type littermate controls" ], "brain_regions": [ "pontine tegmental area", "ventral medulla", "medial septum-diagonal band of Broca", "hippocampus", "cortex" ], "data_code_availability": [], "limitations": [ "Homozygous mice did not show the loss of deep NREM sleep seen in advanced disease, so the model may reflect only preclinical or early stages.", "Only male mice were studied.", "The correlation between REM sleep and learning does not establish which affected neurons cause the sleep deficits; further work is needed." ], "keywords": [ "Alzheimer's disease", "AppNL-G-F", "REM sleep", "EEG slowing", "amyloid-β", "brainstem", "trace fear conditioning" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md" }, { "id": "srinivasan-2019-bbrc", "doi": "10.1016/j.bbrc.2019.07.082", "pmid": "31376934", "pmcid": null, "url": "https://doi.org/10.1016/j.bbrc.2019.07.082", "title": "Miniaturized microscope with flexible light source input for neuronal imaging and manipulation in freely behaving animals", "authors": [ "Srinivasan S", "Hosokawa T", "Vergara P", "Chérasse Y", "Naoi T", "Sakurai T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2019, "published_date": "2019-09", "journal": "Biochemical and Biophysical Research Communications", "volume": "517", "issue": "3", "pages": "520-524", "type": "methods_protocol", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "imaging_tools" ], "tldr": "A modified open-source head-mounted microscope with a fiber-optic light port lets researchers image calcium activity and optogenetically silence the same hippocampal neurons in freely moving mice.", "summary": "The authors replaced the built-in LED of the open-source UCLA miniscope with a ferrule-based optical input port and an internal mirror, so that any combination of external lasers can be delivered through one device. The modification kept the device weight at about 1.9 g and left the imaging path unchanged. In freely moving mice expressing jGCaMP7c in hippocampal CA1, blue laser light revealed calcium events while orange light alone did not alter activity. When the inhibitory opsin Jaws was co-expressed, orange light reversibly suppressed calcium events in the imaged neurons, with activity returning after light offset. The design files were shared as supplemental material so other labs can build and adapt the device.", "research_question": "Can an open-source miniscope be simply modified to accept external light sources so that the same genetically defined neurons can be imaged and optogenetically manipulated in freely behaving animals?", "approach": "The LED board of the UCLA miniscope was replaced by an optic ferrule light input, mirror and drum lens, fed by combined blue (445 nm) and orange (590 nm) lasers; the device was tested in mice expressing jGCaMP7c alone or with Jaws in dorsal CA1, with CNMF-E extraction of single-neuron calcium signals during 30-s on/off light cycles.", "key_findings": [ { "finding": "Replacing the LED with a ferrule light input port and internal mirror did not increase miniscope weight (about 1.9 g) and preserved the original imaging capability.", "evidence": "Fig. 1; Results", "species": null, "n": null, "stats": null }, { "finding": "Blue laser light delivered through the miniscope revealed CA1 calcium events at a rate matching earlier reports (~0.02 events/s).", "evidence": "Fig. 2B-C", "species": "mouse", "n": null, "stats": null }, { "finding": "In neurons expressing only jGCaMP7c, orange laser light did not change calcium fluorescence signals.", "evidence": "Fig. 2E", "species": "mouse", "n": "7 neurons", "stats": "one-way repeated measures ANOVA with Geisser-Greenhouse correction, F(1.3, 9.1) = 0.41, p = 0.59" }, { "finding": "In neurons co-expressing Jaws and jGCaMP7c, orange light significantly decreased calcium fluorescence during light-on periods, and activity rose again after light offset.", "evidence": "Fig. 3B-E", "species": "mouse", "n": "7 neurons", "stats": "one-way repeated measures ANOVA with Geisser-Greenhouse correction, F(1.3, 78) = 40.0, p = 0.0002; Tukey's multiple comparisons, p < 0.002" }, { "finding": "Orange light did not excite jGCaMP7 even at light onset, indicating no biological crosstalk between Jaws and the calcium sensor.", "evidence": "Fig. 3C-D", "species": "mouse", "n": null, "stats": null } ], "methods": [ "head-mounted miniaturized microscope (modified UCLA miniscope) with optic ferrule light input", "in vivo calcium imaging with jGCaMP7c", "optogenetic silencing with Jaws", "AAV stereotaxic injection and GRIN lens implantation", "CNMF-E single-neuron signal extraction", "confocal histology" ], "models": [ "adult mice" ], "brain_regions": [ "hippocampal CA1" ], "data_code_availability": [ { "type": "design_files", "url": null, "as_stated": "The CAD files for the modified housing are available as supplemental files" } ], "limitations": [ "Laser delivery requires an optic cable in addition to the camera USB cable, which needs coaxial slip rings to avoid restricting movement.", "The demonstration used a small number of neurons with one sensor-opsin pair." ], "keywords": [ "miniaturized microscope", "GCaMP", "optogenetics", "UCLA miniscope", "hippocampus" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md" }, { "id": "koyanagi-2019-neural-regen-res", "doi": "10.4103/1673-5374.243695", "pmid": "30531064", "pmcid": "PMC6263001", "url": "https://doi.org/10.4103/1673-5374.243695", "title": "Memory consolidation during sleep and adult hippocampal neurogenesis", "authors": [ "Koyanagi I", "Akers KG", "Vergara P", "Srinivasan S", "Sakurai T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2019, "published_date": "2019", "journal": "Neural Regeneration Research", "volume": "14", "issue": "1", "pages": "20-23", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-SA 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory" ], "tldr": "A short review linking how new neurons born in the adult dentate gyrus join memory circuits with how sleep consolidates memory, and proposing sleep-stage-specific manipulation of these neurons.", "summary": "This mini-review updates the authors' earlier review on adult hippocampal neurogenesis, sleep and memory. It first outlines dentate gyrus circuitry and the evidence that dentate gyrus neurons, including adult-born ones, are needed to form and retrieve hippocampus-dependent memories, with a critical developmental window in which young neurons are especially plastic. It then summarizes how sleep oscillations, replay, cueing and synaptic rescaling may support memory consolidation. Finally, it reviews rodent work tying sleep deprivation to reduced adult neurogenesis, notes that stress confounds these studies, and argues for optogenetic manipulation of adult-born neurons during specific sleep stages.", "research_question": "How might adult-born dentate gyrus neurons contribute to the consolidation of memory during sleep?", "approach": "Narrative mini-review of rodent and human studies on dentate gyrus circuitry, adult neurogenesis, sleep oscillations and memory, based on a PubMed literature search.", "key_findings": [ { "finding": "Adult-born dentate gyrus neurons appear to be recruited into memory circuits during a narrow developmental window: silencing 4-week-old adult-born neurons impairs memory retrieval, whereas silencing 2- or 8-week-old neurons does not.", "evidence": "Section 'Mnemonic Function of the DG and Its Adult-Generated Neurons'; Fig. 1", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors propose that integration of adult-born neurons may act as a memory time-stamp that helps separate similar events according to when they occurred.", "evidence": "Section 'Mnemonic Function of the DG and Its Adult-Generated Neurons'", "species": null, "n": null, "stats": null }, { "finding": "Rodent studies report a dose-dependent reduction of adult dentate gyrus neurogenesis with sleep deprivation, but the stress induced by deprivation makes it hard to attribute these effects to sleep loss itself.", "evidence": "Section 'Sleep and Adult DG Neurogenesis'", "species": "rodent", "n": null, "stats": null }, { "finding": "The review argues that future studies should optogenetically manipulate adult-born neurons during specific sleep stages without altering overall sleep architecture to test their special role in sleep-dependent consolidation.", "evidence": "Section 'Sleep and Adult DG Neurogenesis'; Fig. 2", "species": null, "n": null, "stats": null } ], "methods": [ "narrative literature review based on a PubMed search" ], "models": [], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [], "limitations": [ "The authors note that sleep deprivation causes stress, inflammation and arousal, so its effects on hippocampal memory and neurogenesis are hard to separate from these confounds.", "The authors note it is not yet understood why cueing during sleep sometimes strengthens and sometimes weakens memory consolidation." ], "keywords": [ "rapid eye movement sleep", "sleep deprivation", "optogenetics", "real-time sleep analysis", "hippocampus", "fear memory", "synaptic plasticity", "memory processing", "adult neurogenesis", "dentate gyrus" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2019-neural-regen-res.md" }, { "id": "akers-2018-stemcells", "doi": "10.1002/stem.2815", "pmid": null, "pmcid": null, "url": "https://doi.org/10.1002/stem.2815", "title": "Concise Review: Regulatory Influence of Sleep and Epigenetics on Adult Hippocampal Neurogenesis and Cognitive and Emotional Function", "authors": [ "Akers KG", "Chérasse Y", "Fujita Y", "Srinivasan S", "Sakurai T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2018, "published_date": "2018-03-09", "journal": "Stem Cells", "volume": "36", "issue": "7", "pages": "969-976", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "rem_sleep_memory" ], "tldr": "A review proposing that sleep and epigenetic modifications interact to regulate adult hippocampal neurogenesis, and through it memory consolidation and emotional processing.", "summary": "This concise review brings together research on adult-born neurons in the dentate gyrus, the epigenetic control of their generation, and the influence of sleep on hippocampal function. It outlines what adult-born neurons are thought to contribute to cognition and mood, and how mechanisms such as histone acetylation and DNA methylation shape their production. The authors then link circadian clock genes, sleep loss, and memory replay or cueing during sleep to epigenetic changes that could affect neurogenesis. They propose that the interplay of sleep and epigenetics forms a regulatory pathway for adult neurogenesis, and discuss sleep-based and epigenetic-drug strategies as directions for future research on neurodegenerative and psychiatric disorders.", "research_question": "How might sleep and epigenetic modifications of gene expression jointly regulate adult dentate gyrus neurogenesis and thereby influence cognitive and emotional function?", "approach": "Narrative literature review synthesizing rodent and human studies on adult hippocampal neurogenesis, epigenetic regulation, circadian rhythms, sleep deprivation, and memory replay and targeted reactivation during sleep.", "key_findings": [ { "finding": "The authors propose that sleep regulates adult dentate gyrus neurogenesis by inducing, or being affected by, epigenetic modifications of gene expression.", "evidence": "Role of sleep in epigenetic regulation section; Fig. 3", "species": "rodents and humans (literature)", "n": null, "stats": null }, { "finding": "Cited work indicates sleep deprivation reduces adult hippocampal neurogenesis partly independently of stress hormones; in rats, 96 hours of sleep deprivation reduced dentate gyrus cell proliferation even after adrenalectomy with low-dose corticosterone.", "evidence": "Sleep Deprivation section", "species": "rat", "n": null, "stats": null }, { "finding": "The review suggests that sleep loss may act on neurogenesis through epigenetic routes, citing reduced hippocampal CBP expression and Bdnf-promoter histone acetylation after 3 days of sleep deprivation in mice.", "evidence": "Sleep Deprivation section", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors raise the possibility that targeted reactivation of memories during sleep induces epigenetic changes in adult-born dentate gyrus neurons that support further memory consolidation, and suggest combining sleep interventions with epigenetic drugs as a research direction.", "evidence": "Memory Replay During Sleep section; Conclusion", "species": null, "n": null, "stats": null } ], "methods": [ "narrative literature review" ], "models": [], "brain_regions": [ "dentate gyrus", "hippocampus", "suprachiasmatic nucleus" ], "data_code_availability": [], "limitations": [ "The authors note that the cellular and molecular mechanisms of targeted memory reactivation during sleep remain unclear and that cueing can either enhance or impair memory depending on conditions." ], "keywords": [ "neurogenesis", "dentate gyrus", "hippocampus", "memory", "sleep", "epigenomics" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2018-stemcells.md" }, { "id": "purple-2017-scirep", "doi": "10.1038/srep46247", "pmid": "28401950", "pmcid": "PMC5388892", "url": "https://doi.org/10.1038/srep46247", "title": "Auditory conditioned stimulus presentation during NREM sleep impairs fear memory in mice", "authors": [ "Purple RJ", "Sakurai T", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2017, "published_date": "2017-04-12", "journal": "Scientific Reports", "volume": "7", "issue": "1", "pages": "46247", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "rem_sleep_memory", "fear_memory_ptsd" ], "tldr": "In mice, replaying a fear-conditioned tone during NREM sleep, but not REM sleep, reduced later freezing to that tone, directly comparing cueing across the two sleep stages.", "summary": "This mouse study asked whether re-presenting an auditory conditioned stimulus during REM or NREM sleep strengthens or weakens a recently formed fear memory. After trace fear conditioning, mice heard the tone during NREM sleep, during REM sleep, or only white noise over a 4-hour post-training sleep period with EEG/EMG monitoring. Mice cued during NREM sleep froze less to the tone the next day than REM-cued mice, while contextual fear memory and initial learning did not differ between groups. Cueing caused only modest changes in sleep architecture but lowered slow-wave-range EEG power in both cued groups. The authors suggest that the conditioning protocol (e.g., a long trace interval engaging the hippocampus) and cue modality may determine whether sleep cueing enhances or impairs fear memory.", "research_question": "Does replaying an auditory fear-conditioned cue during NREM versus REM sleep enhance or weaken the consolidation of that fear memory in mice?", "approach": "Male C57BL/6 mice with EEG/EMG implants underwent auditory trace fear conditioning, then received the tone during NREM sleep, during REM sleep, or white noise only over a 4-hour sleep window; cued and contextual fear memory were tested the next day by scoring freezing.", "key_findings": [ { "finding": "Mice cued with the tone during NREM sleep froze significantly less to the tone in a novel context than REM-cued mice, on average 15.2% less than REM-cued and 20.6% less than control mice.", "evidence": "Fig. 5b; Table 2", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "ANOVA F= 4.32, p = 0.024; post-hoc t-tests with Bonferroni correction" }, { "finding": "Contextual fear memory was not affected: freezing on return to the training context without the tone did not differ between groups.", "evidence": "Fig. 5c; Table 2", "species": "mouse", "n": "29 mice in three groups", "stats": "ANOVA F= 1.25, p = 0.302" }, { "finding": "Initial learning was comparable across groups, as reactivity to the first foot shock during training did not differ.", "evidence": "Fig. 4a", "species": "mouse", "n": "29 mice in three groups", "stats": "ANOVA, F= 2.14, p = 0.14" }, { "finding": "Cueing changed sleep architecture only slightly: total NREM, REM and wake time did not differ significantly, but REM-cued mice showed more REM-to-NREM transitions than controls.", "evidence": "Table 1; Fig. 2", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "t-tests with post-hoc Bonferroni correction" }, { "finding": "Both cued groups showed reduced EEG power in the slow-wave range, at 3.5 Hz during NREM sleep and at 1.5, 2 and 3 Hz during REM sleep, which the authors suggest reflects some lightening of sleep.", "evidence": "Fig. 3", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "multivariate general linear models with post-hoc Bonferroni correction" } ], "methods": [ "auditory trace fear conditioning (20-s tone, 20-s trace interval, foot shock)", "sleep-stage-targeted presentation of the conditioned tone using real-time EEG/EMG monitoring", "EEG/EMG sleep scoring and FFT spectral analysis", "freezing-based cued and contextual fear memory tests" ], "models": [ "male C57BL/6 mice" ], "brain_regions": [], "data_code_availability": [], "limitations": [ "The authors note that whether NREM cueing impairs fear memory by extinction-like new inhibitory learning or by weakening the original association could not be resolved and would need further experiments such as reinstatement or spontaneous recovery tests.", "Cueing lowered slow-wave-range EEG power, suggesting some arousal-related lightening of sleep that could itself influence consolidation.", "No wake-cueing group was included in the design." ], "keywords": [ "targeted memory reactivation", "NREM sleep", "REM sleep", "fear conditioning", "trace conditioning", "auditory cue", "memory consolidation", "mice" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md" }, { "id": "fujinaka-2016-molbrain", "doi": "10.1186/s13041-015-0184-0", "pmid": "26745987", "pmcid": "PMC4706703", "url": "https://doi.org/10.1186/s13041-015-0184-0", "title": "Effect of context exposure after fear learning on memory generalization in mice", "authors": [ "Fujinaka A", "Li R", "Hayashi M", "Kumar D", "Changarathil G", "Naito K", "Miki K", "Nishiyama T", "Lazarus M", "Sakurai T", "Kee N", "Nakajima S", "Wang SH", "Sakaguchi M" ], "pi_role": "last_corresponding", "year": 2016, "published_date": "2016-01-08", "journal": "Molecular Brain", "volume": "9", "issue": "1", "pages": "2", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "fear_memory_ptsd" ], "tldr": "In mice, re-encountering a familiar safe context within hours of fear conditioning, but not a day later, made fear spread to that safe context.", "summary": "This study asked whether experiences shortly after fear learning shape whether fear later spreads to a safe context. Mice were habituated to two similar chambers, shocked in one, and then placed in the other at different delays. Exposure to the familiar unshocked chamber 3 or 6 h after training led to similar freezing in both chambers the next day, whereas exposure 24 h later left discrimination intact. Generalization did not appear when the second context was novel and dissimilar, when it was highly dissimilar from the shock context, or when mice had no prior habituation, suggesting that both the familiarity and the timing of post-learning context exposure govern fear generalization.", "research_question": "Does exposure to an unconditioned context soon after contextual fear learning cause the fear memory to generalize to that context?", "approach": "Thirteen groups of male C57BL/6 mice underwent single-shock contextual fear conditioning with varied pre-training habituation and varied timing, identity, and familiarity of post-training context exposure; freezing was scored automatically and compared between conditioned and unconditioned contexts.", "key_findings": [ { "finding": "Mice tested in contexts A and B 24 h after training froze more in the shock context A than in context B, indicating no generalization.", "evidence": "Fig. 1a-c", "species": "mouse", "n": "n = 15", "stats": "t(14) = 7.5, p < 0.001, paired t-test (day 1)" }, { "finding": "When contexts were first presented 6 h after training, mice froze similarly in A and B on day 1, and their freezing pattern differed from the 24 h group.", "evidence": "Fig. 1d-f", "species": "mouse", "n": "n = 30", "stats": "group x context interaction F(1,43) = 4.1, p < 0.05; day 1 A vs B t(29) = 2.0, p > 0.05" }, { "finding": "Exposure to the familiar unconditioned context B alone 3 h after training was enough to produce comparable freezing in A and B the next day.", "evidence": "Fig. 2a-c", "species": "mouse", "n": "n = 12", "stats": "t(11) = 0.70, p > 0.05, paired t-test" }, { "finding": "Without prior habituation to the contexts, mice still discriminated A from B on day 1, so familiarity was required for generalization.", "evidence": "Additional file 1: Figure S2", "species": "mouse", "n": "n = 10", "stats": "group x context interaction F(1,38) = 7.0, p < 0.05; day 1 A > B t(9) = 3.3, p < 0.01" }, { "finding": "Exposure to a novel, highly dissimilar context C 3 h after training did not produce generalization; these mice froze more in A than B on day 1, unlike the familiar-context group.", "evidence": "Fig. 2j-l", "species": "mouse", "n": "n = 10", "stats": "t(9) = 3.4, p < 0.005; group x context interaction F(1,20) = 5.6, p < 0.05" }, { "finding": "Discrimination indices were high only in the 24 h group and the novel dissimilar context group; all other groups showed lower indices than the 24 h group.", "evidence": "Additional file 1: Figure S8", "species": "mouse", "n": null, "stats": "main effect of group F(6,96) = 4.0, p < 0.01" } ], "methods": [ "contextual fear conditioning with a single foot shock", "pre-training context habituation", "automated video-based freezing scoring", "discrimination index analysis" ], "models": [ "male C57BL/6 mice" ], "brain_regions": [], "data_code_availability": [], "limitations": [ "The authors note that whether this form of generalization shares mechanisms with behavioral tagging remains to be tested.", "The authors raise, without testing, whether the generalization route requires NMDA receptor activation." ], "keywords": [ "fear memory", "generalization", "contextual fear conditioning", "memory consolidation", "familiarity" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md" }, { "id": "sakaguchi-2015-plos-one", "doi": "10.1371/journal.pone.0130163", "pmid": "26075894", "pmcid": "PMC4468217", "url": "https://doi.org/10.1371/journal.pone.0130163", "title": "Inhibiting the Activity of CA1 Hippocampal Neurons Prevents the Recall of Contextual Fear Memory in Inducible ArchT Transgenic Mice", "authors": [ "Sakaguchi M", "Kim K", "Yu LMY", "Hashikawa Y", "Sekine Y", "Okumura Y", "Kawano M", "Hayashi M", "Kumar D", "Boyden ES", "McHugh TJ", "Hayashi Y" ], "pi_role": "first", "year": 2015, "published_date": "2015-06-15", "journal": "PLOS ONE", "volume": "10", "issue": "6", "pages": "e0130163", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 4.0", "related_versions": [], "themes": [ "fear_memory_ptsd" ], "tldr": "A new doxycycline-regulated transgenic mouse expressing the light-driven silencer ArchT in forebrain excitatory neurons lets green light silence CA1 pyramidal cells and reversibly block contextual fear recall.", "summary": "The authors built a tetracycline-controlled transgenic mouse line carrying the inhibitory opsin ArchT fused to GFP, and crossed it with a CaMKII promoter-driven tTA line so that the opsin is expressed in forebrain excitatory neurons, most strongly in hippocampal CA1 pyramidal cells. Recordings with an implanted optrode in awake mice showed that most putative CA1 pyramidal units fired far less while green light was on, with a smaller subset firing more. When light was delivered bilaterally to CA1 during a contextual fear memory test, mice froze little, yet they froze in the same context the next day without light. This indicates that silencing CA1 transiently interfered with recall rather than erasing the memory, and positions the line as a tool for testing causal links between defined neurons and memory.", "research_question": "Can an inducible transgenic mouse expressing ArchT in CA1 excitatory neurons be used to silence these cells in vivo and test their role in recalling a contextual fear memory?", "approach": "The authors generated TetO-ArchT-GFP mice, crossed them with alpha-CaMKII-tTA mice, and mapped transgene expression by in situ hybridization and GFP fluorescence. They then combined optical silencing with tetrode recording of CA1 units in freely moving mice and delivered light bilaterally to CA1 during a contextual fear memory test, followed by a light-off test the next day.", "key_findings": [ { "finding": "In the double-transgenic mice, transgene mRNA was found across the forebrain and was strong in CA1 pyramidal and subicular neurons but notably weaker in CA3 and the dentate gyrus, restricted to the pyramidal layer in CA1.", "evidence": "Fig 1A-1F; Fig 2", "species": "mouse", "n": null, "stats": null }, { "finding": "Of 41 putative CA1 pyramidal units recorded during 1 min of light delivery, 25 decreased their firing, 8 increased it and 8 showed no apparent change.", "evidence": "Fig 3B and 3C", "species": "mouse", "n": "41 units", "stats": null }, { "finding": "In the suppressed units, the drop in firing was time-locked to the light, with an average suppression of 89%.", "evidence": "Fig 3D", "species": "mouse", "n": "25 units", "stats": "F(2,48) = 11, p < 0.0001, repeated measures one-way ANOVA" }, { "finding": "Units whose firing rose during light showed an average increase of 120%, which the authors suggest may reflect homeostatic changes or loss of interneuron-mediated inhibition.", "evidence": "Fig 3E", "species": "mouse", "n": "8 units", "stats": "F(2,14) = 3.9, p < 0.05" }, { "finding": "Mice given bilateral green light to CA1 during the first contextual fear test froze little, but froze more in the second test without light, suggesting a transient recall deficit rather than memory loss.", "evidence": "Fig 4D", "species": "mouse", "n": "n = 10", "stats": "paired t-test, t(9) = 3.5, p < 0.005" } ], "methods": [ "generation of a tetracycline-controlled TetO-ArchT-GFP transgenic mouse line", "in situ hybridization and GFP fluorescence mapping of transgene expression", "optrode (optic fiber plus tetrodes) recording of CA1 single units with 532-nm light delivery in freely moving mice", "bilateral optic cannula implantation above CA1", "contextual fear conditioning with automated freezing scoring" ], "models": [ "alpha-CaMKII-tTA x TetO-ArchT-GFP double transgenic mice (C57BL/6J background)" ], "brain_regions": [ "hippocampal CA1", "hippocampus", "forebrain" ], "data_code_availability": [ { "type": "data", "url": null, "as_stated": "All relevant data are within the paper." } ], "limitations": [ "Some recorded units did not respond to light, which the authors attribute to being outside the effective light range or to low ArchT expression.", "A subset of units increased firing during light, an indirect effect the authors could only propose explanations for." ], "keywords": [ "optogenetics", "ArchT", "transgenic mouse", "tetracycline-controlled expression", "CA1", "contextual fear memory", "memory recall" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md" }, { "id": "arruda-carvalho-2014-jneurosci", "doi": "10.1523/JNEUROSCI.2336-13.2014", "pmid": "25411506", "pmcid": "PMC6608441", "url": "https://doi.org/10.1523/JNEUROSCI.2336-13.2014", "title": "Posttraining Ablation of Adult-Generated Olfactory Granule Cells Degrades Odor–Reward Memories", "authors": [ "Arruda-Carvalho M", "Akers KG", "Guskjolen A", "Sakaguchi M", "Josselyn SA", "Frankland PW" ], "pi_role": "co_author", "year": 2014, "published_date": "2014-11-19", "journal": "The Journal of Neuroscience", "volume": "34", "issue": "47", "pages": "15793-15803", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-SA 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory" ], "tldr": "Killing adult-born olfactory bulb granule cells soon after odor–reward learning in mice erased the memory, whereas killing them before learning or a month later did not.", "summary": "The authors asked whether olfactory granule cells born in adulthood become a necessary part of an odor–reward memory once it has been learned. Using nestin-CreERT2 mice crossed with Cre-inducible diphtheria toxin receptor mice, they tagged a cohort of newborn cells with tamoxifen and later killed them with diphtheria toxin either before or after mice learned to associate one carvone enantiomer with sugar. Ablation shortly after training abolished the learned odor preference in both adult and juvenile cohorts, but only when the tagged cells were older than 10 days at training. Ablation before training, or about one month after training, left the memory intact, suggesting that pre-existing granule cells can compensate during learning and that adult-born cells play a time-limited role in memory expression.", "research_question": "Do adult-generated olfactory granule cells that are present during learning become essential for later expression of an odor–reward memory?", "approach": "A tag-and-ablate strategy (nestin-CreERT2 x iDTR mice, tamoxifen tagging followed by diphtheria toxin) was used to delete tagged olfactory granule cells before, immediately after, or about a month after training in an odor–reward digging task, with memory measured as digging preference in probe tests.", "key_findings": [ { "finding": "Tamoxifen tagging labeled about 141,337 cells in the olfactory bulb of adult mice, roughly 10% of all olfactory granule cells.", "evidence": "Fig. 2h", "species": "mouse", "n": null, "stats": "141,337 ± 4106 LacZ+ cells" }, { "finding": "After posttraining ablation, adult-tagged 2×Tg mice no longer preferred the reinforced odor, whereas controls retained the preference.", "evidence": "Fig. 4b–d", "species": "mouse", "n": "CTR (n = 16) and 2×Tg (n = 26) mice", "stats": "genotype × test time interaction F(1,40) = 4.55, p < 0.05; 2×Tg post-DT t(25) = 0.97, p = 0.34" }, { "finding": "When training occurred only 10 d after tagging, posttraining ablation did not impair the memory, implicating cells older than 10 d at training.", "evidence": "Fig. 4e–h", "species": "mouse", "n": "CTR (n = 8) and 2×Tg (n = 10) mice", "stats": "genotype × test time ANOVA, no main effects or interactions, all F values <1" }, { "finding": "Ablating the same cell population before training did not prevent formation or 28 d persistence of the odor–reward memory in adult mice.", "evidence": "Fig. 5", "species": "mouse", "n": "CTR (n = 10) and 2×Tg (n = 11) mice", "stats": "2×Tg: t(10) = 3.66, p < 0.005 at 1 d; t(10) = 3.28, p < 0.01 at 28 d" }, { "finding": "Posttraining ablation of juvenile-generated granule cells similarly reduced odor preference, although the genotype × test time interaction only approached significance.", "evidence": "Fig. 6", "species": "mouse", "n": "CTR (n = 18) and 2×Tg (n = 19) mice", "stats": "2×Tg pre vs post t(18) = 4.19, p < 0.001; post-DT 2×Tg vs CTR t(35) = 2.70, p = 0.011; interaction F(1,35) = 3.02, p = 0.09" }, { "finding": "Ablation started about 4 weeks after training did not affect memory expression, suggesting a time-limited role for adult-born granule cells.", "evidence": "Fig. 8", "species": "mouse", "n": "CTR (n = 16) and 2×Tg (n = 8) mice", "stats": "2×Tg post-DT t(7) = 3.28, p < 0.05; genotype × test time ANOVA all F values < 1" } ], "methods": [ "tamoxifen-inducible genetic tagging of neural progenitor progeny (nestin-CreERT2)", "diphtheria toxin receptor-mediated cell ablation (iDTR mice)", "Rosa-LacZ fate mapping with stereological cell counting", "immunohistochemistry (nestin, DCX, NeuN, Ki67, cleaved caspase-3, zif268)", "odor–reward associative digging task with carvone enantiomers", "open-field testing" ], "models": [ "nestin-CreERT2 x iDTR double-transgenic mice (C57BL/6 background)", "nestin-CreERT2 x Rosa-LacZ reporter mice" ], "brain_regions": [ "olfactory bulb", "subventricular zone" ], "data_code_availability": [], "limitations": [ "The tagged population is heterogeneous in location and maturity, so the authors used a shorter tagging-to-training interval to narrow down which cells mattered.", "In juvenile mice the genotype by test-time interaction only approached significance, so the authors advise caution in interpreting that result.", "The lack of effect of remote ablation could in principle reflect degradation of the receptor in tagged cells over time, which the authors consider unlikely.", "The Cre driver also tags adult-born hippocampal dentate granule cells, although hippocampal lesions are known not to affect this odor–reward task." ], "keywords": [ "adult neurogenesis", "memory", "olfactory" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md" }, { "id": "sakaguchi-2012-molbrain", "doi": "10.1186/1756-6606-5-32", "pmid": "22999350", "pmcid": "PMC3462696", "url": "https://doi.org/10.1186/1756-6606-5-32", "title": "Catching the engram: strategies to examine the memory trace", "authors": [ "Sakaguchi M", "Hayashi Y" ], "pi_role": "first", "year": 2012, "published_date": "2012-09-21", "journal": "Molecular Brain", "volume": "5", "issue": "1", "pages": "32", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY 2.0", "related_versions": [], "themes": [ "fear_memory_ptsd", "other" ], "tldr": "A review of genetic strategies, from activity-dependent gene tagging to CREB-based allocation, optogenetics and synapse imaging, that let researchers see and control the neurons and synapses holding a memory.", "summary": "This review surveys how the physical trace of a memory, the engram, can be located and tested in the rodent brain. It moves from classic lesion and drug studies to methods that tag neurons by their activity-dependent expression of immediate early genes such as Arc and c-fos. It then covers approaches that bias which neurons store a memory by raising CREB levels, and optogenetic tools that switch tagged or targeted neurons on or off with precise timing. A final section discusses how potentiated synapses may be arranged on dendrites and how imaging can reveal them, and the authors close by outlining what would be needed before such targeted methods could inform therapies for human memory disorders.", "research_question": "Which genetic and imaging methods can identify and selectively manipulate the neuronal ensembles and synapses that encode a specific memory?", "approach": "Narrative review of rodent studies using immediate-early-gene mapping and tagging, CREB-driven memory allocation, chemogenetic and optogenetic control, and synapse-level imaging, organized from circuit to cellular to synaptic level.", "key_findings": [ { "finding": "The authors argue that tagging neurons via immediate-early-gene promoters such as c-fos lets researchers reactivate a learning-activated ensemble, and that light reactivation of such dentate gyrus neurons was reported sufficient to retrieve a fear memory.", "evidence": "Figures 3-4", "species": "mouse; rat", "n": null, "stats": null }, { "finding": "The review highlights that neurons with raised CREB levels are preferentially recruited into a fear memory trace, and that removing or silencing these neurons disrupted the memory, suggesting increased excitability as one underlying mechanism.", "evidence": "Figure 5", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors emphasize that optogenetic inhibition, with its finer timing, showed the hippocampus remains engaged in fear memory retrieval even at remote time points, contrasting with conventional lesion results.", "evidence": "Optogenetics section", "species": "mouse", "n": null, "stats": null }, { "finding": "At the synaptic level, the review discusses evidence that potentiated synapses may cluster on dendrites and share signaling molecules with neighbors, supporting a clustered rather than dispersed plasticity model.", "evidence": "Figure 6", "species": "rodent", "n": null, "stats": null } ], "methods": [ "immediate-early-gene mapping (Arc catFISH, c-fos immunostaining)", "activity-dependent genetic tagging with c-fos promoter tTA/TetO systems", "CREB overexpression with viral vectors", "diphtheria-toxin-receptor ablation and allatostatin-receptor silencing", "chemogenetics (hM3Dq/CNO)", "optogenetics (channelrhodopsin, halorhodopsin)", "two-photon and FRET imaging of dendritic spines" ], "models": [ "mice", "rats", "Aplysia" ], "brain_regions": [ "hippocampus", "CA1", "dentate gyrus", "amygdala", "nucleus accumbens", "medial prefrontal cortex", "motor cortex" ], "data_code_availability": [], "limitations": [ "The authors note that a correlation between c-fos induction and learning does not by itself prove that c-fos-expressing neurons store the memory.", "They state that safe and efficient gene delivery to the human brain still needs technical advances before such methods could be applied clinically." ], "keywords": [ "engram", "memory trace", "immediate early genes", "c-fos", "Arc", "CREB", "optogenetics", "systems consolidation", "synaptic plasticity", "fear conditioning" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-molbrain.md" }, { "id": "hirota-2012-stem-cells", "doi": "10.1002/stem.1137", "pmid": "22628050", "pmcid": null, "url": "https://doi.org/10.1002/stem.1137", "title": "Roles of Planar Cell Polarity Signaling in Maturation of Neuronal Precursor Cells in the Postnatal Mouse Olfactory Bulb", "authors": [ "Hirota Y", "Sawada M", "Kida YS", "Huang SH", "Yamada O", "Sakaguchi M", "Ogura T", "Okano H", "Sawamoto K" ], "pi_role": "co_author", "year": 2012, "published_date": "2012-07-24", "journal": "STEM CELLS", "volume": "30", "issue": "8", "pages": "1726-1733", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "adult_neurogenesis_memory" ], "tldr": "Disrupting the planar cell polarity components Dishevelled2 and Van Gogh like-2 in postnatal mouse neuronal precursors changed where new olfactory bulb neurons settled and how they grew dendrites.", "summary": "Neuronal precursors born in the postnatal subventricular zone travel to the olfactory bulb and become interneurons, but what controls their shape changes along the way is poorly understood. The authors tested whether Wnt/planar cell polarity signaling takes part, focusing on Dishevelled2 and Van Gogh like-2. They delivered knockdown or dominant-negative constructs of these genes into the subventricular zone by electroporation or lentivirus. The manipulated newborn neurons showed altered positioning and dendrite formation in the olfactory bulb, which the authors take to suggest a role for this pathway in new-neuron maturation.", "research_question": "Does Wnt/planar cell polarity signaling regulate the maturation of newborn neurons arriving in the postnatal mouse olfactory bulb?", "approach": "Knockdown or dominant-negative constructs of Dishevelled2 and Van Gogh like-2 were introduced into the postnatal subventricular zone by electroporation or lentiviral vectors, and the resulting newborn olfactory bulb neurons were examined for distribution and dendrite formation.", "key_findings": [ { "finding": "Interfering with Dishevelled2 or Van Gogh like-2 in subventricular zone precursors changed the distribution of newborn neurons in the olfactory bulb.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "The same manipulations also altered dendrite formation of the newborn olfactory bulb neurons.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors conclude that planar cell polarity signaling likely contributes to regulating the maturation of new olfactory bulb neurons.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null } ], "methods": [ "postnatal in vivo electroporation into the subventricular zone", "lentivirus-mediated gene delivery", "shRNA knockdown and dominant-negative constructs" ], "models": [ "postnatal mice" ], "brain_regions": [ "subventricular zone", "olfactory bulb" ], "data_code_availability": [], "limitations": [], "keywords": [ "planar cell polarity", "Wnt signaling", "Dishevelled2", "Van Gogh like-2", "postnatal neurogenesis", "olfactory bulb", "dendrite formation", "neuronal migration" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2012-stem-cells.md" }, { "id": "sakaguchi-2012-dev-neurobiol", "doi": "10.1002/dneu.22023", "pmid": "22488739", "pmcid": null, "url": "https://doi.org/10.1002/dneu.22023", "title": "Neural stem cells, adult neurogenesis, and galectin‐1: From bench to bedside", "authors": [ "Sakaguchi M", "Okano H" ], "pi_role": "first", "year": 2012, "published_date": "2012-06-09", "journal": "Developmental Neurobiology", "volume": "72", "issue": "7", "pages": "1059-1067", "type": "review", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "adult_neurogenesis_memory", "neural_regeneration_transplantation" ], "tldr": "A review arguing that the carbohydrate-binding protein Galectin-1 has opposite roles in the two adult neurogenic niches and can aid recovery in animal models of brain ischemia and spinal cord injury.", "summary": "This review summarizes what is known about Galectin-1, a multifunctional carbohydrate-binding protein, in adult neural stem cells of the hippocampal dentate gyrus and the subventricular zone. In the dentate gyrus, Galectin-1 is found mainly in early progenitor types and knockout data suggest it restrains their proliferation, whereas in the subventricular zone it appears to promote stem cell proliferation through its lectin activity, acting upstream of beta1 integrin signaling. The review also discusses why galectin-1 knockout phenotypes differ between mouse genetic backgrounds, and reports that galectin-1 deficient mice show deficits in hippocampus-dependent memory tasks. Finally, it reviews animal studies in which Galectin-1 infusion or transplantation of Galectin-1-expressing human neural stem cells improved tissue and functional recovery after brain ischemia and spinal cord injury, and argues that finding downstream regulators of Galectin-1 is needed before clinical use.", "research_question": "What is the expression, function and mechanism of Galectin-1 in adult neural stem cells, and how might it be used in stem-cell-based approaches to brain and spinal cord injury?", "approach": "Narrative review of published work, much of it from the authors' group, covering galectin-1 knockout mice, intraventricular infusion of recombinant Galectin-1 variants and neutralizing antibody, and transplantation of Galectin-1-expressing human neural stem cells in rodent and marmoset injury models.", "key_findings": [ { "finding": "In the adult mouse dentate gyrus, most Galectin-1-positive cells are type 2a progenitors and 7% match type 1 cells; knockout on a C57BL/6J background increased proliferation of these early progenitors, which the review takes to suggest Galectin-1 down-regulates them.", "evidence": "Section 'Function of Galectin-1 in Adult DG Neurogenesis' (Imaizumi et al., 2011)", "species": "mouse", "n": null, "stats": null }, { "finding": "In the adult subventricular zone, infusion of oxidation-resistant recombinant Galectin-1 (but not the oxidized form) promoted neural stem cell proliferation, while a neutralizing antibody or knockout reduced stem cell numbers; the review argues Galectin-1 acts through its lectin activity, upstream of beta1 integrin signaling.", "evidence": "Sections 'Function of Galectin-1 in Adult SVZ NSCs' and 'Mechanisms of Galectin-1 Function in Adult SVZ NSCs' (Sakaguchi et al., 2006, 2010)", "species": "mouse", "n": null, "stats": null }, { "finding": "Galectin-1 knockout mice on a C57BL/6J background, which have more adult-born dentate neurons, were impaired in contextual fear conditioning and the Morris water maze; the review notes it is unresolved whether this reflects increased neurogenesis or loss of Galectin-1 in other hippocampal cells.", "evidence": "Section 'Function of Galectin-1 in Hippocampal-Dependent Memory' (Sakaguchi et al., 2011)", "species": "mouse", "n": null, "stats": null }, { "finding": "In animal injury models, infusion of oxidation-resistant Galectin-1 after brain ischemia improved motor and sensory function, and transplanted human neural stem cells engineered to express Galectin-1 gave better recovery than unmodified cells after ischemia and in a marmoset spinal cord injury model.", "evidence": "Sections 'Galectin-1 in Brain Ischemia' and 'Galectin-1 in Spinal Cord Injury' (Ishibashi et al., 2007; Yamane et al., 2010, 2011)", "species": "rodent; common marmoset", "n": null, "stats": null } ], "methods": [ "literature review", "BrdU pulse-chase analysis (reviewed)", "galectin-1 knockout mice (reviewed)", "intraventricular infusion of recombinant Galectin-1 and neutralizing antibody (reviewed)", "lentiviral overexpression of Galectin-1 in human neural stem cells (reviewed)", "neural stem cell transplantation (reviewed)" ], "models": [ "galectin-1 knockout mice (C57BL/6J and 129 backgrounds)", "rodent brain ischemia models", "common marmoset spinal cord injury model" ], "brain_regions": [ "dentate gyrus", "subventricular zone", "olfactory bulb", "hippocampus", "spinal cord" ], "data_code_availability": [], "limitations": [ "The effect of galectin-1 loss on dentate neurogenesis differs between 129 and C57BL/6J backgrounds, and the reasons are not yet known.", "It is not yet clear whether the memory deficits of galectin-1 knockout mice come from increased dentate neurogenesis or from loss of Galectin-1 in hippocampal neurons and astrocytes.", "Downstream regulators of Galectin-1 in dentate progenitors are unknown, and binding partners in the subventricular zone other than beta1 integrin remain to be identified.", "The beneficial effects in the ischemia and spinal cord injury models rely on different mechanisms, so clinical application requires careful consideration of Galectin-1's opposite roles across niches." ], "keywords": [ "neural stem cells", "adult neurogenesis", "Galectin-1", "subventricular zone", "dentate gyrus", "beta1 integrin", "brain ischemia", "spinal cord injury", "regeneration" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-dev-neurobiol.md" }, { "id": "arruda-carvalho-2011-jneurosci", "doi": "10.1523/JNEUROSCI.3432-11.2011", "pmid": "22016545", "pmcid": "PMC6623574", "url": "https://doi.org/10.1523/JNEUROSCI.3432-11.2011", "title": "Posttraining Ablation of Adult-Generated Neurons Degrades Previously Acquired Memories", "authors": [ "Arruda-Carvalho M", "Sakaguchi M", "Akers KG", "Josselyn SA", "Frankland PW" ], "pi_role": "co_author", "year": 2011, "published_date": "2011-10-19", "journal": "The Journal of Neuroscience", "volume": "31", "issue": "42", "pages": "15113-15127", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-SA 4.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "fear_memory_ptsd" ], "tldr": "Selectively killing mature adult-born dentate granule neurons after learning, but not before, degraded hippocampus-dependent memories in mice, even when done one month later.", "summary": "This study asked whether neurons born in the adult hippocampus become a necessary part of memories they help encode. The authors genetically tagged adult-generated neurons in mice with an inducible diphtheria toxin receptor, let them mature for several weeks, and then removed them with diphtheria toxin either before or after training. Removing these cells after training impaired contextual fear discrimination, spatial water maze memory and visual discrimination memory, whereas removing the same population before training left new learning intact. Amygdala-dependent tone fear and conditioned taste aversion memories were unaffected, and the spatial deficit also appeared when ablation was delayed by one month. The results suggest that adult-born neurons, when present at learning, become an enduring component of hippocampal memory traces. M.A.-C. and M.S. (Sakaguchi) contributed equally to this work.", "research_question": "Are adult-generated dentate granule neurons that were present during learning required for the later expression of hippocampus-dependent memories?", "approach": "A 'tag and ablate' strategy in nestin-CreERT2 x iDTR mice: tamoxifen permanently tags adult-born neurons with the diphtheria toxin receptor, and diphtheria toxin given before or after training ablates them; memory was then tested in contextual fear, water maze and visual discrimination tasks.", "key_findings": [ { "finding": "The tagged population was mostly mature neurons and made up about 6% of all dentate gyrus neurons, and diphtheria toxin virtually abolished the receptor-expressing cells.", "evidence": "Fig. 3, Fig. 4a, Table 2", "species": "mouse", "n": "DT n = 4, PBS n = 6 (ablation check)", "stats": "100% reduction; t(8) = 1.93, p < 0.05" }, { "finding": "Ablating adult-generated neurons after contextual fear training abolished discrimination between the trained context and a similar context, while tone fear memory was spared.", "evidence": "Fig. 7d-g", "species": "mouse", "n": "CTR n = 12, 2xTg n = 11", "stats": "Genotype x Context interaction F(1,21) = 17.66, p < 0.005; discrimination t(21) = 4.27, p < 0.001" }, { "finding": "Ablating the same population before training did not prevent formation of a new contextual fear memory, and both groups still discriminated the contexts.", "evidence": "Fig. 8", "species": "mouse", "n": "CTR n = 13, 2xTg n = 14", "stats": "effect of Context only, F(1,25) = 9.41, p < 0.005" }, { "finding": "Posttraining ablation made mice search less selectively for the hidden platform in the water maze probe test, whereas pretraining ablation did not impair new spatial learning.", "evidence": "Fig. 9a-c, 9g-i", "species": "mouse", "n": "CTR n = 12, 2xTg n = 12 (posttraining)", "stats": "Genotype x Zone interaction F(1,22) = 5.67, p < 0.05" }, { "finding": "Ablation delivered one month after water maze training also reduced time in the target zone, suggesting an enduring role of these neurons; the interaction term itself was only a trend.", "evidence": "Fig. 9j-l", "species": "mouse", "n": "CTR n = 14, 2xTg n = 12", "stats": "Genotype x Zone interaction F(1,24) = 3.53, p = 0.07; planned comparisons p < 0.05" }, { "finding": "Posttraining ablation abolished discrimination between reinforced and nonreinforced visual cues in the water maze, a milder deficit than hippocampal lesions, consistent with degradation rather than erasure of the memory.", "evidence": "Fig. 10e-h", "species": "mouse", "n": "CTR n = 12, 2xTg n = 11", "stats": "CTR paired t(11) = 3.02, p < 0.01; 2xTg p > 0.05" } ], "methods": [ "inducible genetic tagging of adult-born neurons with tamoxifen-dependent Cre recombinase", "diphtheria toxin receptor-mediated cell ablation", "stereological cell counting and immunohistochemistry", "contextual and tone fear conditioning", "hidden-platform and visual discrimination water maze", "conditioned taste aversion", "cytotoxic hippocampal lesions" ], "models": [ "nestin-CreERT2 x iDTR double transgenic mice", "nestin-CreERT2 x Rosa-LacZ reporter mice", "3T3 and 2-2 cell lines" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [], "limitations": [ "The ablated population included progenitor cells and immature neurons as well as mature neurons, so the deficit cannot be assigned to a single maturation stage.", "Ablating more than 30,000 cells might nonspecifically affect hippocampal function, although the authors argue the pre- versus posttraining dissociation argues against this.", "Tagging began at 4 weeks of age, so the tagged population includes cells born in the postjuvenile period as well as in adulthood." ], "keywords": [ "adult neurogenesis", "dentate gyrus", "memory trace", "diphtheria toxin", "retrograde amnesia", "contextual fear conditioning", "water maze" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md" }, { "id": "yamane-2011-molbrain", "doi": "10.1186/1756-6606-4-35", "pmid": "21951913", "pmcid": "PMC3215926", "url": "https://doi.org/10.1186/1756-6606-4-35", "title": "Transplantation of human neural stem/progenitor cells overexpressing galectin-1 improves functional recovery from focal brain ischemia in the mongolian gerbil", "authors": [ "Yamane J", "Ishibashi S", "Sakaguchi M", "Kuroiwa T", "Kanemura Y", "Nakamura M", "Miyoshi H", "Sawamoto K", "Toyama Y", "Mizusawa H", "Okano H" ], "pi_role": "co_author", "year": 2011, "published_date": "2011-09-27", "journal": "Molecular Brain", "volume": "4", "issue": "1", "pages": "35", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 2.0", "related_versions": [], "themes": [ "neural_regeneration_transplantation", "neural_stem_cells_galectin" ], "tldr": "In gerbils with unilateral focal brain ischemia, grafting human neural stem/progenitor cells engineered to overexpress galectin-1 shrank the lesion and aided motor recovery more than grafting unmodified cells.", "summary": "This short report first mapped where and when endogenous galectin-1 appears after transient focal ischemia in the Mongolian gerbil, finding it induced mainly in proliferating reactive astrocytes around the lesion and fading over time. The authors then grafted human fetal neural stem/progenitor cells carrying a lentiviral human galectin-1 transgene, or control cells, into the lesioned caudate nucleus four days after ischemia. Thirty days later, the galectin-1 group had a smaller ischemic volume than the control-graft group. In behavioral tests, the galectin-1 group showed better recovery on a motor asymmetry test, only a trend on a sensory test, and no group difference on a cognitive maze test. The mechanism was not determined; the authors suggest host tissue preservation via trophic or astrocyte-related effects as possibilities.", "research_question": "Does combining human neural stem/progenitor cell transplantation with sustained local galectin-1 delivery reduce ischemic damage and improve functional recovery beyond transplantation of the cells alone?", "approach": "Gal1 expression after unilateral carotid occlusion in gerbils was mapped by immunohistochemistry with BrdU labeling; lentivirally transduced hGal1-overexpressing or control human NSPCs were grafted 4 days post-ischemia and compared by Nissl-based lesion volume and three blinded behavioral tests over 30 days.", "key_findings": [ { "finding": "After ischemia, Gal1 was induced in and around the lesion, mostly in GFAP-positive astrocytes (many of them BrdU-positive and proliferating), with no more than 1% of Gal1-expressing cells being NeuN-positive neurons, and expression declined at later time points.", "evidence": "Fig. 1; Additional file 3, Fig. S3", "species": "Mongolian gerbil", "n": null, "stats": null }, { "finding": "Thirty days after transplantation, ischemic volume was significantly smaller in the hGal1-hNSPCs group than in the hNSPCs group (t(9) = 3, p = 0.01).", "evidence": "Fig. 2C, D; Additional file 5, Fig. S5", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "planned comparison t(9) = 3, p = 0.01" }, { "finding": "On the elevated body swing test of motor asymmetry, the hGal1-hNSPCs group recovered better than the hNSPCs group, with a day-30 planned comparison of t(11) = 4, p = 0.002.", "evidence": "Fig. 3C", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "time x group ANOVA interaction F(4, 44) = 6.4, p = 0.05; planned comparison on day 30 t(11) = 4, p = 0.002" }, { "finding": "On the bilateral asymmetry (sensory) test both groups recovered, with only a trend favoring the hGal1-hNSPCs group on day 30 (t(11) = 2, p = 0.06).", "evidence": "Fig. 3B", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "interaction F(4, 44) = 1.3, p = 0.3; planned comparison t(11) = 2, p = 0.06" }, { "finding": "On the T-maze spontaneous alternation test of cognition, both groups recovered over time with no group difference (interaction F(4, 44) = 0.52, p = 0.7).", "evidence": "Fig. 3A", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "interaction F(4, 44) = 0.52, p = 0.7" } ], "methods": [ "transient unilateral common carotid artery occlusion (focal brain ischemia model)", "lentiviral transduction of human neural stem/progenitor cells with hGal1-IRES-GFP or IRES-GFP", "stereotaxic intracerebral cell transplantation with cyclosporine A immunosuppression", "immunohistochemistry (Gal1, GFAP, NeuN, GFP) with BrdU labeling and confocal microscopy", "Nissl staining and infarct volume quantification", "elevated body swing test, bilateral asymmetry test, T-maze spontaneous alternation" ], "models": [ "male Mongolian gerbils", "human fetal forebrain-derived neural stem/progenitor cells (oh-NSC-3-fb)" ], "brain_regions": [ "caudate nucleus", "striatum", "cerebral cortex", "hippocampus", "subventricular zone" ], "data_code_availability": [], "limitations": [ "The exact number of surviving grafted cells could not be counted because the cells spread widely through the brain.", "The mechanisms by which galectin-1 overexpression reduced lesion volume and aided recovery were not identified and remain to be tested in future studies." ], "keywords": [ "galectin-1", "human neural stem/progenitor cells", "cell transplantation", "focal brain ischemia", "reactive astrocytes", "Mongolian gerbil", "motor recovery" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md" }, { "id": "sakaguchi-2011-mol-brain", "doi": "10.1186/1756-6606-4-33", "pmid": "21884595", "pmcid": "PMC3179925", "url": "https://doi.org/10.1186/1756-6606-4-33", "title": "Impaired spatial and contextual memory formation in galectin-1 deficient mice", "authors": [ "Sakaguchi M", "Arruda-Carvalho M", "Kang NH", "Imaizumi Y", "Poirier F", "Okano H", "Frankland PW" ], "pi_role": "first", "year": 2011, "published_date": "2011-09-01", "journal": "Molecular Brain", "volume": "4", "issue": "1", "pages": "33", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 2.0", "related_versions": [], "themes": [ "neural_stem_cells_galectin", "fear_memory_ptsd" ], "tldr": "Mice lacking the carbohydrate-binding protein galectin-1 learn contextual fear and the water maze less well, while tone fear and general behavior stay normal.", "summary": "Galectin-1 is a lectin expressed in putative neural stem cells and in mature hippocampal neurons, but its role in adult brain function was unknown. The authors mapped its expression in the adult mouse hippocampus and tested galectin-1 null mutant mice and wild-type littermates in a battery of behavioral tasks. Mutants froze less in the training context after single-pairing fear conditioning and searched less precisely in the water maze probe test, whereas tone fear memory was intact. Visible-platform swimming, startle, prepulse inhibition and the open-field distribution of activity were also normal, arguing against non-memory explanations. The results point to a role for galectin-carbohydrate signalling in hippocampus-dependent memory, with the underlying mechanism left open.", "research_question": "Does loss of galectin-1, which is expressed in hippocampal neural stem cells and neurons, affect hippocampus-dependent learning and memory?", "approach": "Immunohistochemistry located galectin-1 in the adult hippocampus, and galectin-1 null mutant mice backcrossed onto C57BL/6J were compared with wild-type littermates in contextual and tone fear conditioning, the hidden and visible water maze, open field, acoustic startle and prepulse inhibition.", "key_findings": [ { "finding": "In the adult hippocampus, galectin-1 in the dentate granule cell layer was confined to GFAP-positive cells (astrocytes or putative neural stem cells), whereas in CA3 it was found in NeuN-positive mature neurons.", "evidence": "Fig. 1", "species": "mouse", "n": null, "stats": null }, { "finding": "After a single tone-shock pairing, galectin-1 null mice froze less than wild-type littermates when returned to the training context 24 hours later.", "evidence": "Fig. 2C", "species": "mouse", "n": "WT n = 11, gal-1-/- n = 15", "stats": "t(24) = 1.75, P < 0.05, unpaired t-test" }, { "finding": "Tone-cued fear memory tested in an altered context did not differ between genotypes, suggesting the deficit is specific to hippocampus-dependent memory.", "evidence": "Fig. 2D", "species": "mouse", "n": "WT n = 11, gal-1-/- n = 15", "stats": "no main effect of genotype, F(1, 21) = 0.16, P = 0.69" }, { "finding": "With more intensive training (3 tone-shock pairings), galectin-1 null mice froze as much as wild-type mice in the context test, so the contextual deficit could be overcome.", "evidence": "Fig. 3", "species": "mouse", "n": "WT n = 10, gal-1-/- n = 12", "stats": "t(20) = 0.49, P = 0.32, unpaired t-test" }, { "finding": "In the hidden-platform water maze, mutants tended to have longer escape latencies and, although both genotypes searched the target zone selectively in the probe test, wild-type mice were more selective, indicating a less precise spatial memory in mutants.", "evidence": "Fig. 4", "species": "mouse", "n": "WT n = 14, gal-1-/- n = 15", "stats": "latency genotype effect F(1, 27) = 4.05, P = 0.054; probe target-zone time WT > mutant, t(27) = 2.06, P < 0.05" }, { "finding": "Control tests did not reveal non-memory deficits: visible-platform performance, startle and prepulse inhibition were normal, and although mutants were more active in the open field, their spatial distribution of activity was similar to wild-type mice.", "evidence": "Fig. 5", "species": "mouse", "n": "open field WT n = 12, gal-1-/- n = 17; startle/PPI WT n = 13, gal-1-/- n = 8; visible maze n = 3 per genotype", "stats": "open field activity genotype effect P < 0.01; PPI no main effect of genotype F(1, 19) = 0.02, P = 0.90" } ], "methods": [ "immunohistochemistry with galectin-1, GFAP and NeuN antibodies and confocal microscopy", "contextual and tone fear conditioning with automated freezing scoring", "hidden-platform and visible-platform water maze", "open field test", "acoustic startle and prepulse inhibition" ], "models": [ "galectin-1 null mutant mice backcrossed onto C57BL/6J", "wild-type littermate controls" ], "brain_regions": [ "hippocampus", "dentate gyrus", "CA3", "CA1" ], "data_code_availability": [], "limitations": [ "The mechanism behind the memory deficits is not established; altered adult neurogenesis, synaptic plasticity in mature neurons and developmental wiring are all proposed as possibilities.", "Because loss of galectin-1 increases rather than decreases hippocampal neurogenesis, the authors note that any causal link between neurogenesis and the deficits is unlikely to be straightforward.", "The contextual fear deficit disappeared with stronger training, possibly through compensation by other galectins or recruitment of other brain regions." ], "keywords": [ "galectin-1", "lectin", "carbohydrate signalling", "hippocampus", "contextual fear conditioning", "water maze", "spatial memory", "neural stem cells" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md" }, { "id": "leslie-2011-transl-psychiatry", "doi": "10.1038/tp.2011.38", "pmid": "22832609", "pmcid": "PMC3309502", "url": "https://doi.org/10.1038/tp.2011.38", "title": "Impact of early adverse experience on complexity of adult-generated neurons", "authors": [ "Leslie AT", "Akers KG", "Krakowski AD", "Stone SSD", "Sakaguchi M", "Arruda-Carvalho M", "Frankland PW" ], "pi_role": "co_author", "year": 2011, "published_date": "2011-08-30", "journal": "Translational Psychiatry", "volume": "1", "issue": "8", "pages": "e35", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": null, "related_versions": [], "themes": [ "adult_neurogenesis_memory" ], "tldr": "Mice repeatedly separated from their mothers in early life later produce fewer surviving adult-born hippocampal neurons, and those neurons have simpler dendrites and fewer spines.", "summary": "This study asked whether early-life adversity, an environmental risk factor for psychiatric disorders, changes adult hippocampal neurogenesis in a way resembling the effects of schizophrenia risk genes. Mouse pups underwent unpredictable maternal separation for 3 h a day over the first two postnatal weeks, and in adulthood new dentate gyrus cells were labelled with BrdU or a GFP-expressing retrovirus. Proliferation was unchanged, but fewer labelled cells survived and became neurons, and adult-born granule cells had reduced dendritic intersections, shorter dendrites and fewer total spines. The authors suggest that abnormal adult neurogenesis linked to psychiatric illness could arise from environmental influence alone or from its interaction with genetic predisposition.", "research_question": "Does early adverse experience in the form of repeated maternal separation alter the generation and morphological maturation of adult-born dentate gyrus neurons?", "approach": "Pups were exposed to unpredictable maternal separation from P1 to P14; at P60, BrdU injections quantified proliferation, 4-week survival and neuronal differentiation, and retroviral GFP labelling with Sholl analysis quantified dendritic complexity and spines of adult-generated granule neurons.", "key_findings": [ { "finding": "Maternal separation did not change the number of proliferating cells in the adult dentate gyrus 1 day after BrdU injection.", "evidence": "Fig. 1a", "species": "mouse", "n": "separated n = 15, control n = 15", "stats": "no significant group effect" }, { "finding": "Four weeks after BrdU labelling, maternally separated mice had fewer surviving new cells.", "evidence": "Fig. 1b", "species": "mouse", "n": "separated n = 16, control n = 18", "stats": "F1,32 = 7.88, P = 0.008" }, { "finding": "A smaller proportion of surviving cells expressed the mature neuronal marker NeuN in maternally separated mice.", "evidence": "Fig. 1c", "species": "mouse", "n": "separated n = 16, control n = 18", "stats": "F1,32 = 6.90, P = 0.013" }, { "finding": "Adult-born granule neurons in maternally separated mice had fewer dendritic intersections and shorter total dendritic length 4 weeks after retroviral labelling.", "evidence": "Fig. 2c-d", "species": "mouse", "n": "separated n = 5, control n = 5 mice", "stats": "intersections F1,8 = 9.09, P = 0.017; length F1,8 = 7.50, P = 0.026" }, { "finding": "Spine density was unchanged (5.54±0.60 vs 5.93±0.24 spines per 10 µm), but total spines per neuron were reduced, which the authors suggest means fewer synapses with incoming fibres.", "evidence": "Fig. 2e", "species": "mouse", "n": "separated n = 5, control n = 5 mice", "stats": "total spines F1,8 = 5.59, P = 0.046" } ], "methods": [ "unpredictable maternal separation (3 h/day, P1-P14)", "BrdU pulse labelling with stereological cell counts", "BrdU/NeuN double immunohistochemistry", "retroviral GFP labelling of adult-born neurons", "Sholl analysis and dendritic spine tracing (NeuroLeucida)" ], "models": [ "129Svev x C57Bl/6 hybrid mice" ], "brain_regions": [ "dentate gyrus", "hippocampus" ], "data_code_availability": [], "limitations": [ "The authors propose epigenetic and stress-hormone or neurotrophic mechanisms for the persistent effects but did not test them in this study." ], "keywords": [ "adult neurogenesis", "dentate gyrus", "maternal separation", "early adversity", "dendritic complexity", "schizophrenia", "depression" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md" }, { "id": "imaizumi-2011-mol-brain", "doi": "10.1186/1756-6606-4-7", "pmid": "21269521", "pmcid": "PMC3041742", "url": "https://doi.org/10.1186/1756-6606-4-7", "title": "Galectin-1 is expressed in early-type neural progenitor cells and down-regulates neurogenesis in the adult hippocampus", "authors": [ "Imaizumi Y", "Sakaguchi M", "Morishita T", "Ito M", "Poirier F", "Sawamoto K", "Okano H" ], "pi_role": "co_author", "year": 2011, "published_date": "2011-01-27", "journal": "Molecular Brain", "volume": "4", "issue": "1", "pages": "7", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": "CC BY 2.0", "related_versions": [], "themes": [ "neural_stem_cells_galectin", "adult_neurogenesis_memory" ], "tldr": "In the adult mouse dentate gyrus, Galectin-1 marks early neural progenitors, and mice lacking it show more progenitor proliferation and more newborn neurons.", "summary": "This study asked which progenitor cells in the adult mouse hippocampus carry the carbohydrate-binding protein Galectin-1 and what the protein does there. Using multi-marker immunostaining and cell-shape criteria, the authors located Galectin-1 in a subset of type 1 and type 2a cells, the putative neural stem cells of the subgranular zone, but not in later-stage DCX+ or Calretinin+ cells. They generated galectin-1 knockout mice on a C57BL/6 background and used short- and longer-term BrdU labeling plus Ki67 and cleaved-Caspase-3 staining to follow each stage of neurogenesis. Knockout mice had more proliferating early progenitors and more new immature and mature neurons, while apoptosis was unchanged, suggesting that Galectin-1 normally restrains early progenitor proliferation in the adult hippocampus. This contrasts with its pro-proliferative role previously reported in the subventricular zone, which the authors suggest may reflect different redox forms of the protein.", "research_question": "Which neural progenitor cell types express Galectin-1 in the adult mouse dentate gyrus, and how does loss of Galectin-1 affect adult hippocampal neurogenesis?", "approach": "Multi-color immunohistochemistry with stage-specific markers and morphological classification in adult mice, combined with BrdU pulse-chase, Ki67 and cleaved-Caspase-3 quantification in galectin-1 knockout mice backcrossed onto C57BL/6 versus heterozygous littermate controls.", "key_findings": [ { "finding": "Galectin-1 was found in a subset of type 1 cells: 33.1% of DG cells with type-1 morphology expressed it, and 7.3% of Galectin-1+ cells had type-1 morphology, with most others resembling type 2 cells.", "evidence": "Fig. 2", "species": "mouse", "n": "n = 5 mice", "stats": null }, { "finding": "Galectin-1 did not co-label with DCX+, Calretinin+, SGZ NeuN+ or PE-CAM1+ endothelial cells, placing its expression in early-stage progenitors.", "evidence": "Fig. 2 G-J", "species": "mouse", "n": null, "stats": null }, { "finding": "After short-term BrdU labeling, knockout mice had more BrdU+ cells, more FABP7+/BrdU+ cells and more BrdU+ type 1 cells in the SGZ than controls.", "evidence": "Fig. 3 A-F", "species": "mouse", "n": "n = 5 mice each", "stats": "P < 0.05 (BrdU+, FABP7+/BrdU+); P < 0.01 (BrdU+ type 1 cells, main text)" }, { "finding": "After 7 days of BrdU in drinking water and a 10-day chase, knockout mice had more BrdU+, DCX+/BrdU+ and NeuN+/BrdU+ cells, indicating increased production of new neurons.", "evidence": "Fig. 3 G-J", "species": "mouse", "n": "n > 5 mice each", "stats": "P < 0.05" }, { "finding": "Total Ki67+ cells did not differ, but proliferating FABP7+/DCX- (type 1/2a) cells increased in knockouts while proliferating FABP7+/DCX+ (type 2b) cells did not differ.", "evidence": "Fig. 4 A-C", "species": "mouse", "n": "n > 5 mice each", "stats": "P = 0.25 (total Ki67+); P < 0.05 (type 1/2a); P = 0.08 (type 2b)" }, { "finding": "Apoptosis measured by cleaved-Caspase-3 was comparable between genotypes, both overall and in FABP7/DCX/cv-Casp3 triple-positive cells, so the increase is attributed to proliferation rather than reduced cell death.", "evidence": "Fig. 4 D-F", "species": "mouse", "n": "n > 22 mice each", "stats": "P = 0.18 (total); P = 0.44 (triple-positive)" } ], "methods": [ "multi-color immunohistochemistry with stage-specific progenitor markers", "morphological classification of type 1 radial glia-like cells", "BrdU pulse-chase labeling (short-term i.p. injections and drinking-water administration)", "Ki67 and cleaved-Caspase-3 quantification", "speed back-cross with microsatellite marker selection to generate congenic knockout mice", "confocal microscopy" ], "models": [ "galectin-1 knockout mice on C57BL/6 background", "heterozygous littermate controls", "8-week-old male mice" ], "brain_regions": [ "dentate gyrus", "subgranular zone" ], "data_code_availability": [], "limitations": [ "The authors note that the redox-state hypothesis explaining the opposite roles of Galectin-1 in the hippocampus and subventricular zone remains to be tested in future work.", "Results differ from a prior report using galectin-1 knockout mice on a 129 background, which the authors attribute to strain-dependent phenotypes." ], "keywords": [ "Galectin-1", "adult neurogenesis", "dentate gyrus", "neural stem cells", "type 1 cells", "knockout mice", "BrdU" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md" }, { "id": "ikeda-2010-stem-cells", "doi": "10.1002/stem.516", "pmid": "20827749", "pmcid": null, "url": "https://doi.org/10.1002/stem.516", "title": "Expression and Proliferation-Promoting Role of Diversin in the Neuronally Committed Precursor Cells Migrating in the Adult Mouse Brain", "authors": [ "Ikeda M", "Hirota Y", "Sakaguchi M", "Yamada O", "Kida YS", "Ogura T", "Otsuka T", "Okano H", "Sawamoto K" ], "pi_role": "co_author", "year": 2010, "published_date": "2010-11-01", "journal": "Stem Cells", "volume": "28", "issue": "11", "pages": "2017-2026", "type": "research_article", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "adult_neurogenesis_memory" ], "tldr": "Diversin, a Wnt pathway component, is present in migrating neuroblasts of the adult mouse subventricular zone and helps keep them dividing as they travel to the olfactory bulb.", "summary": "Unlike embryonic neuronal precursors, neuroblasts in the adult subventricular zone keep dividing while they migrate toward the olfactory bulb, and the reason was unclear. This study examined Diversin, a Wnt signaling component, in neonatal and adult mouse brain. Diversin was found in neuroblasts and mature neurons of the subventricular zone and hippocampus. Raising Diversin levels with a retrovirus increased neuroblast proliferation and the number of neuroblasts arriving in the olfactory bulb, whereas lowering it reduced proliferation. The authors conclude that Diversin has an important role in neuroblast proliferation in the adult subventricular zone.", "research_question": "What mechanism allows neuronally committed precursor cells in the adult subventricular zone to keep proliferating while they migrate?", "approach": "The authors mapped Diversin expression in neonatal and adult mouse brain and manipulated its levels in neuroblasts by retrovirus-mediated overexpression and by knockdown.", "key_findings": [ { "finding": "Diversin is expressed in neuroblasts and mature neurons in the subventricular zone and hippocampus of neonatal and adult mice.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Overexpressing Diversin increased neuroblast proliferation and the number of neuroblasts that reached the olfactory bulb.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Knocking down Diversin reduced neuroblast proliferation.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null } ], "methods": [ "retrovirus-mediated gene overexpression", "knockdown", "expression analysis in brain tissue" ], "models": [ "neonatal and adult mice" ], "brain_regions": [ "subventricular zone", "hippocampus", "olfactory bulb" ], "data_code_availability": [], "limitations": [], "keywords": [ "Diversin", "Wnt signaling", "neuroblast", "subventricular zone", "adult neurogenesis", "cell proliferation", "neuronal migration" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ikeda-2010-stem-cells.md" }, { "id": "hirota-2010-development", "doi": "10.1242/dev.050120", "pmid": "20685736", "pmcid": null, "url": "https://doi.org/10.1242/dev.050120", "title": "Planar polarity of multiciliated ependymal cells involves the anterior migration of basal bodies regulated by non-muscle myosin II", "authors": [ "Hirota Y", "Meunier A", "Huang S", "Shimozawa T", "Yamada O", "Kida YS", "Inoue M", "Ito T", "Kato H", "Sakaguchi M", "Sunabori T", "Nakaya MA", "Nonaka S", "Ogura T", "Higuchi H", "Okano H", "Spassky N", "Sawamoto K" ], "pi_role": "co_author", "year": 2010, "published_date": "2010-09-15", "journal": "Development", "volume": "137", "issue": "18", "pages": "3037-3046", "type": "research_article", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "other" ], "tldr": "In mouse lateral ventricle ependymal cells, basal bodies migrate as a group to the anterior apical membrane during postnatal differentiation, a process requiring non-muscle myosin II but not Dvl2-dependent planar cell polarity signaling.", "summary": "Multiciliated ependymal cells lining the brain ventricles show two planar polarities: the orientation of each cilium (rotational) and the anterior clustering of basal bodies within each cell (translational). Using whole-mount ventricular walls from postnatal mice, the authors found that translational polarity emerges between P5 and P9, and time-lapse imaging of GFP-labeled basal bodies showed all basal bodies in a cell moving together toward the anterior edge. Dominant-negative Dvl2 disrupted ciliary orientation and coordinated beating but left anterior basal body positioning intact. In contrast, inhibitors of myosin II or myosin light chain kinase and knockdown of the three non-muscle myosin heavy chains dispersed basal bodies without obviously changing ciliary beating, indicating that the two polarities are set by distinct mechanisms.", "research_question": "How is the anterior (translational) positioning of basal bodies established in differentiating multiciliated ependymal cells, and does it share mechanisms with ciliary orientation (rotational polarity)?", "approach": "Whole-mount immunostaining, live time-lapse and high-speed imaging of postnatal mouse lateral ventricular walls and cultured ependymal cells were combined with dominant-negative Dvl2 constructs, intraventricular injection of kinase/myosin inhibitors and in vivo electroporation of Myh9/Myh10/Myh14 knockdown vectors.", "key_findings": [ { "finding": "The share of ependymal cells whose ciliated-area centroid lay in the anterior quadrant rose during postnatal development, being significantly higher at P9 than at P7, indicating that translational polarity is acquired between P5 and P9.", "evidence": "Fig. 1E-H", "species": "mouse", "n": "P5, 105 cells; P7, 91 cells; P9, 109 cells; adult, 137 cells; from three mice in each case", "stats": "P=0.0486 (P9 vs P7)" }, { "finding": "Time-lapse imaging of Centrin 2-GFP basal bodies over 10 hours showed dispersed basal bodies in a single cell migrating simultaneously to accumulate at the anterior apical membrane.", "evidence": "Fig. 2; Movie 1", "species": "mouse", "n": null, "stats": null }, { "finding": "Cells with anteriorly localized basal bodies showed anteriorly directed coordinated ciliary beating, longer cilia and higher beat frequency than cells with dispersed basal bodies, so translational and rotational polarity arise at around the same stage.", "evidence": "Fig. 3G-I", "species": "mouse", "n": "dispersed, 43 cells; localized, 28 cells; both from four mice", "stats": "P<0.001 for beating direction, cilia length and beat frequency" }, { "finding": "Dominant-negative Dvl2 disturbed ciliary orientation in vivo (circular SD 55.1±9.3° vs 21.3±5.6° in controls) but did not change the number of cells with anteriorly located basal bodies, suggesting PCP signaling regulates rotational but not translational polarity.", "evidence": "Fig. 4K-R", "species": "mouse", "n": "CSD: four control cells from two mice, five Dvl2ΔPDZ cells from three mice; translational: control, 21 cells from three mice; Dvl2ΔPDZ, 29 cells from five mice", "stats": "anterior-quadrant comparison P=0.8782" }, { "finding": "Intraventricular blebbistatin or ML-9 reduced anterior basal body localization in a dose-dependent manner, whereas the ROCK inhibitor Y27632 did not; blebbistatin left ciliary beat frequency unchanged (19.1±0.87 Hz vs 19.0±1.05 Hz).", "evidence": "Fig. 6A-I; Movies 10, 11", "species": "mouse", "n": "control for blebbistatin and ML-9, 172 cells from five mice; 22 and 25 cilia from three mice each for beat frequency", "stats": "one-way ANOVA with Tukey's test; beat frequency P=0.9254" }, { "finding": "Electroporation-based knockdown of Myh9, Myh10 and Myh14 dispersed basal bodies and reduced the number of cells with anterior basal bodies without preventing basal body docking or cilia extension, suggesting cell-autonomous regulation by non-muscle myosin II.", "evidence": "Fig. 6J-P", "species": "mouse", "n": "control, 29 cells from five mice; NMII knockdown, 32 cells from three mice", "stats": "P=0.0316" } ], "methods": [ "whole-mount immunostaining of lateral ventricular walls with centroid-based quantification of basal body distribution", "time-lapse imaging of GFP-labeled basal bodies in cultured whole-mount ventricular walls", "high-speed confocal imaging of ciliary beating in brain slices and cultured ependymal cells", "scanning and immunotransmission electron microscopy of basal foot orientation", "primary ependymal cell culture with artificial fluid flow", "lentiviral and plasmid expression of dominant-negative Dvl2", "intraventricular injection of blebbistatin, ML-9, Y27632 and SP600125", "in vivo electroporation of miRNA-based knockdown vectors for Myh9, Myh10 and Myh14", "circular statistics (Rayleigh's test, circular standard deviation)" ], "models": [ "wild-type ICR mice", "Centrin 2::GFP transgenic mice", "primary cultured mouse ependymal cells" ], "brain_regions": [ "lateral ventricle wall (ependymal layer)" ], "data_code_availability": [], "limitations": [ "The authors state that the signal that activates non-muscle myosin II to drive basal body migration remains unclear.", "Fluid flow alone did not induce translational polarity in primary culture, so the trigger for anterior migration in vivo was not identified.", "The functional significance of translational polarity is not established; dispersed basal bodies still supported normal directional beating." ], "keywords": [ "ependymal cells", "basal bodies", "planar cell polarity", "translational polarity", "rotational polarity", "non-muscle myosin II", "Dvl2", "motile cilia", "lateral ventricle" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md" }, { "id": "stone-2011-hippocampus", "doi": "10.1002/hipo.20845", "pmid": "20824726", "pmcid": null, "url": "https://doi.org/10.1002/hipo.20845", "title": "Functional convergence of developmentally and adult‐generated granule cells in dentate gyrus circuits supporting hippocampus‐dependent memory", "authors": [ "Stone SSD", "Teixeira CM", "Zaslavsky K", "Wheeler AL", "Martinez‐Canabal A", "Wang AH", "Sakaguchi M", "Lozano AM", "Frankland PW" ], "pi_role": "co_author", "year": 2010, "published_date": "2010-09-07", "journal": "Hippocampus", "volume": "21", "issue": "12", "pages": "1348-1362", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "adult_neurogenesis_memory" ], "tldr": "Once mature, dentate granule cells born in embryonic, postnatal or adult life are recruited into hippocampal memory circuits at similar rates, suggesting they are functionally equivalent.", "summary": "This mouse study asked whether dentate granule cells born during development and those born in adulthood are recruited differently into circuits that support hippocampus-dependent memory. Cohorts of granule cells were birth-dated with thymidine analogs (BrdU, or CldU and IdU in the same animal), and recruitment was estimated from expression of the activity marker Fos after memory testing. Recruitment of adult-born cells into water maze memory depended on cell age and stabilized once cells were five weeks or older, with no transient peak. When cell age was matched, embryonically, postnatally and adult-born cells showed similar Fos rates in the water maze, in a within-animal comparison, and in contextual fear conditioning. The authors suggest developmentally and adult-generated granule cells are functionally equivalent once mature, so the contribution of adult neurogenesis to memory should scale with the number of adult-born cells.", "research_question": "Are dentate granule cells generated during development and in adulthood integrated into hippocampal memory circuits at different or equivalent rates?", "approach": "Separate cohorts of granule cells were labeled with BrdU, CldU or IdU at embryonic day 18, postnatal day 7 or adulthood (P60) in mice; after water maze or contextual fear training, the likelihood of Fos expression in labeled cells was quantified by immunohistochemistry, with PTZ seizure and home cage groups to control for cell-age differences in the ability to express Fos.", "key_findings": [ { "finding": "Fos was validated as an activity marker in dentate granule cells: spatial memory recall induced Fos in about 1% of granule cells, above home cage levels and well below PTZ seizure levels, and Fos and Arc were almost completely colocalized.", "evidence": "Fig. 1A-D", "species": "mouse", "n": "n = 3 per group (home cage, recall, PTZ)", "stats": "F2,6 = 43.3, P < 0.001" }, { "finding": "The probability that adult-born cells expressed Fos after water maze testing rose with the delay between BrdU labeling and training, with the largest change between 1 and 5 weeks and no difference across the 5-10 week groups.", "evidence": "Fig. 2F", "species": "mouse", "n": "n = 8 (1 week), n = 18 each (5, 7.5 and 10 weeks)", "stats": "F3,58 = 3.39, P < 0.05" }, { "finding": "Cells labeled one week before training and tested four weeks later (so the same age at testing as the five-week group) showed lower Fos overlap than the five-week group and no different from the one-week group, indicating week-old cells are too immature to be incorporated.", "evidence": "Fig. 2A, 2F", "species": "mouse", "n": "n = 10", "stats": "P < 0.05 vs five-week group; P = 0.39 vs one-week group" }, { "finding": "When cells born at E18, P7 or P60 were all 7.5 weeks old at training, the likelihood of Fos expression after the water maze probe test did not differ between groups, although labeled cell numbers did.", "evidence": "Fig. 3C-E", "species": "mouse", "n": "n = 6 (E18), n = 6 (P7), n = 18 (P60)", "stats": "Fos in labeled cells: F2,27 = 0.20, P = 0.82; labeled cell number: F2,27 = 181.0, P < 0.001" }, { "finding": "In a within-animal comparison using CldU and IdU, embryonically or postnatally generated cells and adult-generated cells in the same mice were equally likely to express Fos after water maze testing, arguing against preferential recruitment of adult-born neurons.", "evidence": "Fig. 5E, 5H", "species": "mouse", "n": "n = 12 (E18/P60 group), n = 14 (P7/P60 group)", "stats": "paired t-test E18/P60: t11 = 0.39, P = 0.70; P7/P60: t13 = 1.03, P = 0.32" }, { "finding": "In contextual fear conditioning, adult-born cells trained six weeks after labeling were more likely to express Fos than those trained after one week, while postnatally (P7) and adult (P60) generated cells were recruited at similar rates.", "evidence": "Fig. 6E, Fig. 7F", "species": "mouse", "n": "n = 10 (one week), n = 18 (six weeks); n = 6 (P7), n = 27 (P60)", "stats": "six vs one week: t26 = 2.12, P < 0.05; P7 vs P60: t31 = 0.55, P = 0.58" } ], "methods": [ "thymidine analog birth-dating (BrdU, CldU, IdU)", "immunohistochemistry for Fos, Arc and NeuN", "confocal and epifluorescence microscopy cell counting", "Morris water maze", "contextual fear conditioning", "pentylenetetrazole (PTZ)-induced seizures as a Fos induction control", "high-frequency entorhinal cortex electrical stimulation" ], "models": [ "male C57Bl/6NTacfBr x 129Svev hybrid mice" ], "brain_regions": [ "dentate gyrus", "hippocampus", "entorhinal cortex", "olfactory bulb" ], "data_code_availability": [], "limitations": [ "Integration was inferred indirectly from immediate early gene (Fos) expression in labeled cells, not from direct measures of circuit function.", "Week-old adult-born cells cannot express Fos well, so cell-age confounds had to be controlled with additional groups.", "Labeling sensitivity of CldU and IdU may be below that of BrdU." ], "keywords": [ "adult neurogenesis", "dentate granule cells", "developmental neurogenesis", "Fos", "immediate early genes", "thymidine analogs", "water maze", "contextual fear conditioning", "hippocampus" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md" }, { "id": "sakaguchi-2010-j-neurochem", "doi": "10.1111/j.1471-4159.2010.06712.x", "pmid": "20367753", "pmcid": null, "url": "https://doi.org/10.1111/j.1471-4159.2010.06712.x", "title": "Regulation of adult neural progenitor cells by Galectin‐1/β1 Integrin interaction", "authors": [ "Sakaguchi M", "Imaizumi Y", "Shingo T", "Tada H", "Hayama K", "Yamada O", "Morishita T", "Kadoya T", "Uchiyama N", "Shimazaki T", "Kuno A", "Poirier F", "Hirabayashi J", "Sawamoto K", "Okano H" ], "pi_role": "first", "year": 2010, "published_date": "2010-06", "journal": "Journal of Neurochemistry", "volume": "113", "issue": "6", "pages": "1516-1524", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "adult_neurogenesis_memory" ], "tldr": "In the adult mouse subependymal zone, the lectin Galectin-1 binds beta1 Integrin, and this interaction is needed for Galectin-1 to raise neural progenitor numbers and promote progenitor adhesion.", "summary": "Galectin-1, a carbohydrate-binding protein made by adult neural stem cells, was known to increase neural progenitor numbers in the adult mouse subependymal zone (SEZ), but its partner molecule was unknown. Using a Galectin-1 affinity column on adult SEZ tissue, the authors isolated beta1 Integrin as a carbohydrate-dependent binding partner. Galectin-1 binding was found on astrocytes, neuroblasts and ependymal cells of the SEZ, largely overlapping with beta1 Integrin-expressing cells. Blocking beta1 Integrin with a neutralizing antibody in vivo abolished the Galectin-1-induced increase in long-term BrdU-retaining cells, and in culture Galectin-1-enhanced progenitor adhesion required intact beta1 Integrin. The authors suggest that Galectin-1 regulates adult progenitor numbers through beta1 Integrin, possibly by modifying cell adhesion.", "research_question": "Which molecule does Galectin-1 interact with in the adult mouse subependymal zone, and does this interaction mediate Galectin-1's effect on adult neural progenitor cells?", "approach": "Galectin-1 affinity chromatography of adult SEZ lysate with western blotting, histochemistry with biotinylated Galectin-1, 7-day intraventricular infusion of Galectin-1 and/or a beta1 Integrin-neutralizing antibody with BrdU long-labeling, and in vitro adhesion assays of cultured neural progenitor cells.", "key_findings": [ { "finding": "Beta1 Integrin was isolated from adult SEZ tissue as a Galectin-1-binding molecule, appearing at around 130 kDa in the lactose-eluted fraction but not in the mannose wash fraction.", "evidence": "Fig. 1", "species": "mouse", "n": null, "stats": null }, { "finding": "Galectin-1 bound SEZ cells including astrocytes, neuroblasts and ependymal cells, and this binding was reduced by excess lactose, indicating dependence on its carbohydrate-binding activity.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null }, { "finding": "Most beta1 Integrin-expressing cells in the adult SEZ showed affinity for Galectin-1.", "evidence": "Fig. 3c", "species": "mouse", "n": null, "stats": null }, { "finding": "Infusing a beta1 Integrin-neutralizing antibody into the lateral ventricle reduced BrdU long-labeled cells and blocked the increase in these cells produced by Galectin-1 infusion.", "evidence": "Fig. 3d-f", "species": "mouse", "n": null, "stats": "ANOVA, p < 0.05" }, { "finding": "In culture, Galectin-1 increased progenitor adhesion, a Galectin-1-neutralizing antibody inhibited adhesion to Laminin-coated dishes, and a beta1 Integrin-neutralizing antibody dose-dependently inhibited adhesion in a way that added Galectin-1 could not overcome.", "evidence": "Fig. 4", "species": "mouse", "n": null, "stats": "ANOVA, p < 0.05" } ], "methods": [ "Galectin-1 affinity column chromatography", "western blotting", "histochemistry with biotinylated recombinant Galectin-1", "confocal immunohistochemistry", "intraventricular infusion with osmotic pumps", "BrdU long-labeling", "neural progenitor cell adhesion assay" ], "models": [ "adult mice (8 weeks old at start)", "Galectin-1 knockout mice", "cultured adult neural progenitor cells" ], "brain_regions": [ "subependymal zone", "lateral ventricle" ], "data_code_availability": [], "limitations": [ "The authors state that whether Galectin-1 binding to beta1 Integrin regulates adult progenitors by modifying cell adhesion is a hypothesis that remains to be tested.", "The role of this interaction during early brain development was not studied." ], "keywords": [ "beta1 Integrin", "adult neural progenitor cells", "Galectin-1", "lectin", "subependymal zone", "adult neurogenesis" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md" }, { "id": "akers-2010-jneurosci", "doi": "10.1523/JNEUROSCI.0443-10.2010", "pmid": "20357101", "pmcid": "PMC6632296", "url": "https://doi.org/10.1523/JNEUROSCI.0443-10.2010", "title": "Functional Contribution of Adult-Generated Olfactory Bulb Interneurons: Odor Discrimination versus Odor Memory: Table 1.", "authors": [ "Akers KG", "Sakaguchi M", "Arruda-Carvalho M" ], "pi_role": "co_author", "year": 2010, "published_date": "2010-03-31", "journal": "The Journal of Neuroscience", "volume": "30", "issue": "13", "pages": "4523-4525", "type": "review", "peer_reviewed": true, "open_access": true, "license": "CC BY-NC-SA 4.0", "related_versions": [ { "doi": null, "pmid": "19955377", "relation": "commentary_on: Breton-Provencher et al. 2009, J Neurosci 29(48):15245-15257" } ], "themes": [ "adult_neurogenesis_memory" ], "tldr": "A Journal Club commentary arguing that adult-born olfactory bulb interneurons appear to support odor memory rather than odor discrimination, and examining why mouse studies disagree.", "summary": "This Journal Club article reviews a 2009 study in which blocking adult neurogenesis in mice weakened inhibition of olfactory bulb mitral cells, shifted gamma oscillations, and impaired short-term odor memory while leaving odor discrimination intact. The authors compare this result with earlier mouse studies that reported conflicting effects of reduced bulb neurogenesis on discrimination and memory, summarized in a table. They propose three factors that may explain the discrepancies: how similar the test odors are, whether neurogenesis is disrupted during development or only in adulthood, and the maturational age of the affected neurons. They also point out an unresolved tension between failed odor habituation after an hour and intact odor-reward memory over days.", "research_question": "Do neurons generated in the adult olfactory bulb contribute to perceptual discrimination between odors, to memory for odors, or to both?", "approach": "Critical commentary on Breton-Provencher et al. (2009), placing its cellular, network and behavioral findings alongside prior studies of reduced adult olfactory bulb neurogenesis in mice.", "key_findings": [ { "finding": "In the reviewed study, antimitotic AraC infusion cut doublecortin-expressing olfactory bulb cells by 75% and lowered the peak gamma oscillation frequency from about 45 Hz to about 39 Hz.", "evidence": "Main text (discussion of Breton-Provencher et al., 2009)", "species": "mouse", "n": null, "stats": null }, { "finding": "Mice with reduced adult neurogenesis discriminated odors normally but failed to habituate when the interval between odor presentations was lengthened from 30 to 60 min, while still retaining an odor-food association for at least 7 d.", "evidence": "Main text", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors argue that conflicting reports may reflect odor similarity, developmental versus adult-only disruption of neurogenesis, and the maturational stage of the affected neurons, with discrimination deficits appearing mainly after genetic manipulations acting throughout development.", "evidence": "Main text; Table 1", "species": "mouse", "n": null, "stats": null } ], "methods": [ "literature commentary (Journal Club)", "comparative table of studies reducing adult olfactory bulb neurogenesis" ], "models": [ "mice (reviewed studies)" ], "brain_regions": [ "olfactory bulb", "subventricular zone", "rostral migratory stream" ], "data_code_availability": [], "limitations": [ "The authors note that short- and long-term odor memory in the reviewed study were measured with different behavioral tasks, which may depend differently on adult-born neurons.", "The authors note that odors used in some studies may have been too distinct to reveal subtle discrimination deficits." ], "keywords": [ "adult neurogenesis", "olfactory bulb", "granule cells", "odor discrimination", "odor memory", "gamma oscillations", "AraC" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2010-jneurosci.md" }, { "id": "yamane-2010-j-neurosci-res", "doi": "10.1002/jnr.22322", "pmid": "20091712", "pmcid": null, "url": "https://doi.org/10.1002/jnr.22322", "title": "Transplantation of galectin‐1‐expressing human neural stem cells into the injured spinal cord of adult common marmosets", "authors": [ "Yamane J", "Nakamura M", "Iwanami A", "Sakaguchi M", "Katoh H", "Yamada M", "Momoshima S", "Miyao S", "Ishii K", "Tamaoki N", "Nomura T", "Okano HJ", "Kanemura Y", "Toyama Y", "Okano H" ], "pi_role": "co_author", "year": 2010, "published_date": "2010-01-20", "journal": "Journal of Neuroscience Research", "volume": "88", "issue": "7", "pages": "1394-1405", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "neural_regeneration_transplantation" ], "tldr": "Human neural stem/progenitor cells engineered to express galectin-1 survived and differentiated after grafting into contused marmoset cervical spinal cord, and grafted animals showed larger motor recovery and more preserved fibers than comparison groups.", "summary": "Building on earlier work that grafted human neural stem/progenitor cells (NS/PCs) into injured spinal cord, this study asked whether making the grafted cells express galectin-1, a carbohydrate-binding protein, adds to recovery in a nonhuman primate. Human fetal NS/PCs were lentivirally transduced with galectin-1 plus a fluorescent reporter or the reporter alone; transduction did not change proliferation or in vitro differentiation, while galectin-1 cells grew longer neurites. Cells were grafted into adult common marmosets 9 days after a C5 contusion and animals were followed for 13 weeks with motor tests, MRI and histology. Grafted cells survived and gave rise to neurons, astrocytes and oligodendrocytes without tumor formation, and in these animals the galectin-1 group showed the largest lesion-site myelin, corticospinal and serotonergic fiber areas and the best recovery on activity, grip and treadmill measures; the authors suggest this approach merits further study.", "research_question": "Does galectin-1 expression in grafted human neural stem/progenitor cells increase motor and histological recovery after contusive cervical spinal cord injury in adult common marmosets?", "approach": "Human NS/PCs transduced with galectin-1-IRES-Venus or Venus alone were characterized in vitro and transplanted, versus vehicle, into the lesion epicenter 9 days after C5 contusion in marmosets; outcomes were spontaneous motor activity, bar grip power, treadmill speed, MRI, and histology at 13 weeks.", "key_findings": [ { "finding": "Lentiviral transduction did not change NS/PC proliferation (doubling time approximately 150 hr) or the proportions of neurons and astrocytes in vitro, while neurons from galectin-1-expressing NS/PCs had neurites about 1.5 times as long as those from reporter-only NS/PCs.", "evidence": "Fig. 1C-G", "species": "human (cultured fetal NS/PCs)", "n": null, "stats": "P < 0.05 for neurite length" }, { "finding": "Grafted human NS/PCs survived mainly around the lesion cavity, with some found up to 10 mm rostral and caudal, differentiated into oligodendrocytes, neurons and astrocytes, and showed no tumor formation 13 weeks after transplantation.", "evidence": "Fig. 4", "species": "common marmoset", "n": "Gal-NS/PCs or GFP-NS/PCs, n = 7", "stats": null }, { "finding": "Contusion reduced myelin and corticospinal fiber areas at the epicenter to approximately 20% of laminectomy values; both graft groups had more myelin, corticospinal and serotonergic fiber area than vehicle controls, with the galectin-1 group highest.", "evidence": "Fig. 3", "species": "common marmoset", "n": null, "stats": "one-way ANOVA with Tukey-Kramer test; *P < 0.05, **P < 0.01" }, { "finding": "Spontaneous motor activity at 13 weeks after injury had returned to approximately 80%, 50% and 40% of preinjury levels in the galectin-1 graft, reporter-only graft and vehicle groups, with significant group differences 4–7 weeks after injury.", "evidence": "Fig. 5A", "species": "common marmoset", "n": null, "stats": "one-way ANOVA with multiple comparisons" }, { "finding": "Grip strength fell to approximately 5% of preinjury values and plateaued at approximately 70%, 60% and 40% in the three groups, differing significantly from 9 weeks after injury onward.", "evidence": "Fig. 5B", "species": "common marmoset", "n": null, "stats": "significant group differences 9 weeks after injury and thereafter" }, { "finding": "On the treadmill, maximum walking speed reached approximately 90% of preinjury velocity in the galectin-1 graft group versus a plateau of approximately 50% in the reporter-only group, differing significantly at 10 weeks and later; vehicle animals were excluded because some could not walk on the treadmill.", "evidence": "Fig. 5C", "species": "common marmoset", "n": null, "stats": "significant differences between graft groups at 10 weeks after SCI and thereafter" } ], "methods": [ "neurosphere culture of human fetal forebrain neural stem/progenitor cells", "lentiviral transduction with galectin-1-IRES-Venus or Venus alone", "in vitro ATP proliferation, differentiation and neurite length assays", "C5 contusive spinal cord injury with a modified weight-drop device", "intralesional cell transplantation 9 days after injury under cyclosporine immunosuppression", "7.0-Tesla MRI of the injured spinal cord", "motor testing: spontaneous activity by infrared sensors, bar grip power, treadmill velocity", "histology: Luxol fast blue myelin, CaMKIIa corticospinal and 5HT serotonergic fiber areas, graft cell fate immunostaining" ], "models": [ "adult female common marmosets (Callithrix jacchus) with contusive cervical spinal cord injury", "human fetal neural stem/progenitor cells" ], "brain_regions": [ "cervical spinal cord (C5)" ], "data_code_availability": [], "limitations": [ "The authors note that spontaneous activity and grip tests did not distinguish the two graft groups in post hoc tests, which led them to add a treadmill test.", "Vehicle-control animals were excluded from treadmill analysis because some could not walk on the treadmill.", "The mechanism by which galectin-1 adds to graft effects was not determined; the authors favor trophic support but cannot exclude axonal guidance or new synapse formation.", "Lentiviral integration sites and copy numbers are uncertain and could in principle affect cell phenotype." ], "keywords": [ "galectin-1", "neural stem/progenitor cells", "spinal cord injury", "common marmoset", "cell transplantation", "lentiviral vector", "nonhuman primate", "corticospinal tract" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md" }, { "id": "frankland-2008-molbrain", "doi": "10.1186/1756-6606-1-5", "pmid": "18803858", "pmcid": "PMC2546401", "url": "https://doi.org/10.1186/1756-6606-1-5", "title": "Starting at the endophenotype: A role for alpha-CaMKII in schizophrenia?", "authors": [ "Frankland PW", "Sakaguchi M", "Arruda-Carvalho M" ], "pi_role": "co_author", "year": 2008, "published_date": "2008-09-10", "journal": "Molecular Brain", "volume": "1", "issue": "1", "pages": "5", "type": "review", "peer_reviewed": null, "open_access": true, "license": "CC BY 2.0", "related_versions": [], "themes": [ "adult_neurogenesis_memory", "other" ], "tldr": "Editorial arguing that a mutant-mouse endophenotype screen linking alpha-CaMKII loss to schizophrenia-like behavior and an immature dentate gyrus points to disrupted adult neurogenesis in psychiatric disease.", "summary": "This editorial comments on a companion study in the same issue by Miyakawa and colleagues, who screened genetically engineered mouse lines for behaviors relevant to schizophrenia. Mice heterozygous for alpha-CaMKII showed working memory deficits, high aggression, low anxiety and disrupted daily activity rhythms, together with an immature dentate gyrus in which newborn neurons were overproduced but failed to mature. The authors highlight the idea that abnormal adult hippocampal neurogenesis could lie at the core of schizophrenia and other psychiatric disorders. They also argue that screening previously engineered mutants combines the strengths of forward- and reverse-genetic approaches for linking endophenotypes to genes.", "research_question": "What does an endophenotype-driven behavioral screen of mutant mice reveal about molecular and cellular mechanisms that may underlie schizophrenia?", "approach": "Editorial commentary on a comprehensive behavioral and histological screen of calcineurin-related mutant mouse lines reported by Miyakawa and colleagues, placed in the context of the literature on alpha-CaMKII and adult neurogenesis.", "key_findings": [ { "finding": "Of 7 mouse lines carrying mutations related to calcineurin signaling that were screened, alpha-CaMKII heterozygous mice showed the most striking behavioral phenotype.", "evidence": "Editorial text (discussing Miyakawa et al., Molecular Brain 2008, 1:6)", "species": "mouse", "n": null, "stats": null }, { "finding": "The alpha-CaMKII heterozygous mice showed severe working memory deficits, unusual aggression, reduced anxiety and strongly disrupted daily activity patterns, a cluster of schizophrenia-related endophenotypes.", "evidence": "Editorial text", "species": "mouse", "n": null, "stats": null }, { "finding": "In the dentate gyrus of these mice, proliferation was increased by about 50% but new neurons did not appear to mature normally, leading to the proposal of an immature dentate gyrus.", "evidence": "Editorial text", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors suggest that abnormal adult hippocampal neurogenesis may contribute to psychiatric disorders such as schizophrenia, so genes regulating neuronal development or adult neurogenesis deserve special attention as susceptibility candidates.", "evidence": "Editorial text", "species": null, "n": null, "stats": null } ], "methods": [ "comprehensive behavioral test battery in mutant mice (as discussed)", "analysis of adult hippocampal neurogenesis in the dentate gyrus (as discussed)" ], "models": [ "alpha-CaMKII heterozygous mutant mice", "forebrain-specific calcineurin knockout mice" ], "brain_regions": [ "hippocampus", "dentate gyrus" ], "data_code_availability": [], "limitations": [ "The authors note that many schizophrenia symptoms are uniquely human and cannot be modeled in mice, so only heritable endophenotypes can be studied.", "The authors note that forward-genetic screens make finding causal mutations slow and costly, while reverse-genetic studies require prior knowledge of which gene to target." ], "keywords": [ "schizophrenia", "endophenotype", "alpha-CaMKII", "adult neurogenesis", "dentate gyrus", "working memory", "mutant mouse screen" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/frankland-2008-molbrain.md" }, { "id": "ishibashi-2007-expneurol", "doi": "10.1016/j.expneurol.2007.06.024", "pmid": "17706645", "pmcid": null, "url": "https://doi.org/10.1016/j.expneurol.2007.06.024", "title": "Galectin-1 regulates neurogenesis in the subventricular zone and promotes functional recovery after stroke", "authors": [ "Ishibashi S", "Kuroiwa T", "Sakaguchi M", "Sun L", "Kadoya T", "Okano H", "Mizusawa H" ], "pi_role": "co_author", "year": 2007, "published_date": "2007-10", "journal": "Experimental Neurology", "volume": "207", "issue": "2", "pages": "302-313", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "neural_regeneration_transplantation" ], "tldr": "In gerbils with focal brain ischemia, galectin-1 rose in subventricular-zone and reactive astrocytes, and infusing its carbohydrate-binding form increased new neurons and sensorimotor recovery, while blocking it did the opposite.", "summary": "This study asked whether the carbohydrate-binding protein galectin-1, previously shown to drive adult neural stem cell proliferation, takes part in neurogenesis after focal brain ischemia. Using a gerbil model of unilateral carotid occlusion, the authors mapped galectin-1 expression over 16 weeks and found it rose in subventricular-zone astrocytes and in reactive astrocytes around the striatal infarct, with a time course resembling that of subventricular-zone cell proliferation. They then infused, for 7 days into the lateral ventricle, a cysteine-to-serine galectin-1 variant that keeps its carbohydrate-binding activity, an oxidized form that lacks it, a neutralizing antibody, or control IgG. The carbohydrate-binding form increased BrdU-labeled neuroblasts and neurons in the subventricular zone, striatum and olfactory bulb and was associated with better sensorimotor scores, the antibody had the opposite effects, and the oxidized form did not change proliferation; infarct volume did not differ among groups. The authors suggest galectin-1 acts as a regulator of post-ischemic subventricular-zone neurogenesis through carbohydrate binding, while cautioning that the link between the new neurons and functional recovery is not established.", "research_question": "Does galectin-1 regulate subventricular-zone neurogenesis after focal ischemia, does this depend on its carbohydrate-binding activity, and is it associated with functional recovery?", "approach": "Time-course immunohistochemistry and confocal double labeling of endogenous galectin-1 and BrdU after unilateral carotid occlusion in gerbils, followed by 7-day intraventricular infusion of carbohydrate-binding or oxidized galectin-1, a neutralizing antibody or control IgG, with histological counts of new neurons and repeated sensorimotor and cognitive testing over 28 days.", "key_findings": [ { "finding": "Galectin-1-positive cells were confined to the subventricular zone in sham animals; after ischemia they increased in the ipsilateral striatum, peaking at 2 weeks and still elevated at 16 weeks, and in the ipsilateral subventricular zone, peaking at 2 weeks before returning to control levels, a pattern similar to BrdU-labeled proliferating cells there.", "evidence": "Figs. 2F–N, 3A–C", "species": "gerbil", "n": "group 1: n = 25 ischemic and n = 5 sham-operated gerbils across time points (per-time-point n not stated)", "stats": "P < 0.01 and P < 0.001 versus sham-operated controls, one-way ANOVA with Bonferroni post hoc test" }, { "finding": "Most galectin-1-positive cells co-expressed GFAP, both in the subventricular zone and in the zone of selective neuronal death around the striatal infarct, where they had the enlarged morphology of reactive astrocytes.", "evidence": "Fig. 4A–B", "species": "gerbil", "n": null, "stats": null }, { "finding": "Infusion of the carbohydrate-binding galectin-1 variant increased BrdU-labeled cells in the ipsilateral subventricular zone and the numbers of new neuroblasts and neurons in the subventricular zone, striatum and olfactory bulb, whereas the neutralizing antibody decreased them and the oxidized form, which cannot bind carbohydrate, did not change BrdU-labeled cell numbers relative to IgG controls.", "evidence": "Figs. 5A–L, 6A–D", "species": "gerbil", "n": "group 2: n = 40 ischemic gerbils split across four infusion conditions and two survival times (per-group n for histology not stated)", "stats": "P < 0.05 and P < 0.01 versus rabbit IgG controls, one-way ANOVA with Bonferroni post hoc test" }, { "finding": "Total infarct volume at 14 and 28 days did not differ significantly among the four infusion groups (for example 24.5% ± 4.3% and 22.5% ± 2.5% with the carbohydrate-binding variant versus 25.1% ± 5.3% and 22.2% ± 8.7% with control IgG), so the authors saw no neuroprotective action.", "evidence": "Results, infarct volume section", "species": "gerbil", "n": null, "stats": "not significant" }, { "finding": "Over 28 days of behavioral testing, animals given the carbohydrate-binding variant showed less biased body swing from 3 weeks and faster removal of an adhesive stimulus from the affected forelimb at 4 weeks than IgG controls, the antibody group was slower, and T-maze spontaneous alternation did not differ among groups.", "evidence": "Fig. 7A–D", "species": "gerbil", "n": "n = 5 per group", "stats": "repeated-measures ANOVA: significant group factor for body swing (P < 0.01), removal time (P < 0.01) and body weight (P < 0.001), not for spontaneous alternation; Bonferroni post hoc versus rabbit IgG" } ], "methods": [ "unilateral common carotid artery occlusion (two 10-min occlusions 5 h apart) as a focal ischemia model", "BrdU labeling of proliferating cells", "7-day intraventricular infusion through an implanted guide cannula", "cysteine-to-serine galectin-1 variant retaining carbohydrate binding versus oxidized galectin-1", "anti-galectin-1 neutralizing antibody with rabbit IgG control", "immunohistochemistry and confocal double immunofluorescence (GFAP, PSA-NCAM, NeuN, Iba1)", "infarct volume measurement on Klüver-Barrera-stained sections", "elevated body swing test, bilateral asymmetry (adhesive removal) test, T-maze spontaneous alternation", "one-way and repeated-measures ANOVA with Bonferroni post hoc tests" ], "models": [ "male gerbils (Meriones unguiculatus), 16–18 weeks old" ], "brain_regions": [ "subventricular zone", "lateral ventricle", "striatum", "olfactory bulb", "cerebral cortex", "hippocampus" ], "data_code_availability": [], "limitations": [ "The authors state they cannot conclude that the functional recovery was a direct result of the increased neurogenesis.", "They did not show that the newly generated cells integrate into the injured circuit or are electrically active, so the neurogenesis–recovery link should be read with caution.", "How galectin-1-expressing reactive astrocytes in the ischemic striatum act remains unclear.", "Whether the carbohydrate-binding variant promotes neurite outgrowth in the injured brain, which could contribute to recovery, was not tested.", "Densities of new neurons are hard to compare with earlier studies because of differences in ischemia model, species and BrdU protocol." ], "keywords": [ "galectin-1", "adult neurogenesis", "subventricular zone", "focal ischemia", "stroke", "carbohydrate binding", "astrocytes", "neuroblasts", "gerbil", "sensorimotor function" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md" }, { "id": "adachi-2007-stem-cells", "doi": "10.1634/stemcells.2007-0177", "pmid": "17673525", "pmcid": null, "url": "https://doi.org/10.1634/stemcells.2007-0177", "title": "β-Catenin Signaling Promotes Proliferation of Progenitor Cells in the Adult Mouse Subventricular Zone", "authors": [ "Adachi K", "Mirzadeh Z", "Sakaguchi M", "Yamashita T", "Nikolcheva T", "Gotoh Y", "Peltz G", "Gong L", "Kawase T", "Alvarez-Buylla A", "Okano H", "Sawamoto K" ], "pi_role": "co_author", "year": 2007, "published_date": "2007-08-02", "journal": "Stem Cells", "volume": "25", "issue": "11", "pages": "2827-2836", "type": "research_article", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin" ], "tldr": "In the adult mouse subventricular zone, beta-catenin signaling drives proliferation of Mash1-positive progenitors, and boosting it increases new olfactory bulb neurons.", "summary": "The adult subventricular zone (SVZ) continuously produces neuroblasts that migrate to the olfactory bulb via fast-dividing transit-amplifying progenitors. This study asked whether Wnt/beta-catenin signaling, known to control progenitor proliferation in the embryonic brain, also acts in the adult SVZ. Using a beta-catenin reporter mouse and retroviral gain- and loss-of-function manipulations, the authors found that beta-catenin activity is present in SVZ progenitors and promotes proliferation of Mash1-positive cells. Pharmacological GSK3 beta inhibition likewise expanded these progenitors and raised the number of new olfactory bulb neurons two weeks later, suggesting a role for beta-catenin signaling in adult SVZ progenitor proliferation.", "research_question": "Does beta-catenin signaling regulate proliferation and differentiation of progenitor cells in the adult mouse subventricular zone?", "approach": "Axin2-d2EGFP reporter mice were used to map beta-catenin-dependent activity, and retroviruses expressing stabilized beta-catenin or the Wnt inhibitor Dkk1, plus a GSK3 beta inhibitor, were used to manipulate the pathway in the adult SVZ.", "key_findings": [ { "finding": "A beta-catenin-dependent destabilized GFP reporter was active in progenitor cells of the adult SVZ.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Retroviral expression of stabilized beta-catenin increased proliferation of Mash1-positive cells and blocked their differentiation into neuroblasts, whereas Dkk1 expression reduced their proliferation.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "A GSK3 beta inhibitor promoted Mash1-positive cell proliferation and increased new neurons in the olfactory bulb 14 days later.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null } ], "methods": [ "Wnt/beta-catenin reporter mouse imaging", "retrovirus-mediated gene expression in the adult SVZ", "pharmacological GSK3 beta inhibition" ], "models": [ "Axin2-d2EGFP reporter mice", "adult mice" ], "brain_regions": [ "subventricular zone", "olfactory bulb" ], "data_code_availability": [], "limitations": [], "keywords": [ "beta-catenin", "Wnt signaling", "subventricular zone", "adult neurogenesis", "transit-amplifying cells", "Mash1", "Dkk1", "GSK3 beta", "olfactory bulb" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/adachi-2007-stem-cells.md" }, { "id": "okano-2007-j-neurochem", "doi": "10.1111/j.1471-4159.2007.04674.x", "pmid": "17697047", "pmcid": null, "url": "https://doi.org/10.1111/j.1471-4159.2007.04674.x", "title": "Regeneration of the central nervous system using endogenous repair mechanisms", "authors": [ "Okano H", "Sakaguchi M", "Ohki K", "Suzuki N", "Sawamoto K" ], "pi_role": "co_author", "year": 2007, "published_date": "2007-04-27", "journal": "Journal of Neurochemistry", "volume": "102", "issue": "5", "pages": "1459-1465", "type": "review", "peer_reviewed": true, "open_access": null, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "neural_regeneration_transplantation", "adult_neurogenesis_memory" ], "tldr": "A short review of how the injured brain and spinal cord can repair themselves through their own neural stem cells, glia and blood vessels, and which molecules regulate each step.", "summary": "This mini-review surveys repair of the damaged central nervous system that relies on the tissue's own resources rather than transplanted cells. It follows insult-induced neurogenesis step by step: activation of resident neural stem cells (for example by Galectin-1 and Musashi-1), expansion of transit-amplifying cells and migration of neuroblasts toward injured striatum, and the survival and maturation of the new neurons. It then argues that glia, including oligodendrocyte progenitors and reactive astrocytes, and the vascular system are also active players in repair. The authors close by cautioning that more neurogenesis is not always better and that the function of new neurons in vivo is still poorly understood.", "research_question": "Which endogenous cellular and molecular mechanisms could be harnessed to regenerate central nervous system tissue after injuries such as stroke or spinal cord injury?", "approach": "Narrative review of published animal and human tissue studies, including the authors' own collaborative work on adult neural stem cells, neuroblast migration, and glial responses after injury.", "key_findings": [ { "finding": "The review presents Galectin-1, expressed in slowly dividing GFAP-positive astrocytes of the adult subventricular zone, as an endogenous factor that promotes neural stem cell proliferation through its carbohydrate-binding activity.", "evidence": "Fig. 2; Sakaguchi et al. 2006", "species": "mouse", "n": null, "stats": null }, { "finding": "After stroke, subventricular zone astrocytes are argued to be the main source of neuroblasts that migrate in chains along blood vessels into the injured striatum, yet only a tiny fraction of lost neurons is replaced, so survival and maturation of new neurons need to be improved.", "evidence": "Yamashita et al. 2006; Arvidsson et al. 2002", "species": "rodents", "n": null, "stats": null }, { "finding": "Endogenous repair is described as extending beyond neurogenesis: reactive astrocytes, through Stat3-dependent migration, help contract the lesion during the subacute phase of spinal cord injury, and oligodendrocyte progenitors and blood vessels also take part.", "evidence": "Okada et al. 2006; Menn et al. 2006; Palmer et al. 2000", "species": "rodents", "n": null, "stats": null }, { "finding": "The authors caution that boosting adult neurogenesis is not uniformly beneficial, as excess neurogenesis can be harmful, for example in epilepsy models, and the in vivo function of new neurons remains incompletely understood.", "evidence": "Conclusion and perspectives", "species": null, "n": null, "stats": null } ], "methods": [ "narrative literature review" ], "models": [ "rodent middle cerebral artery occlusion stroke models", "rodent spinal cord injury models", "gerbil transient global ischemia model" ], "brain_regions": [ "subventricular zone", "dentate gyrus", "striatum", "olfactory bulb", "spinal cord" ], "data_code_availability": [], "limitations": [ "The authors note that the in vivo functions of newly generated neurons are still poorly understood and that enhancing neurogenesis may be harmful in some conditions." ], "keywords": [ "adult neurogenesis", "Musashi-1", "neural stem cells", "reactive astrocytes", "Galectin-1", "stroke", "spinal cord injury" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2007-j-neurochem.md" }, { "id": "sakaguchi-2007-cell-mol-life-sci", "doi": "10.1007/s00018-007-6476-5", "pmid": "17364145", "pmcid": "PMC11136428", "url": "https://doi.org/10.1007/s00018-007-6476-5", "title": "Expression and function of galectin-1 in adult neural stem cells", "authors": [ "Sakaguchi M", "Imaizumi Y", "Okano H" ], "pi_role": "first", "year": 2007, "published_date": "2007-03-15", "journal": "Cellular and Molecular Life Sciences", "volume": "64", "issue": "10", "pages": "1254-1258", "type": "review", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin" ], "tldr": "A short review arguing that the lectin galectin-1 is expressed on adult subventricular zone neural stem cells and drives their proliferation through its carbohydrate-binding activity.", "summary": "This review summarizes the authors' earlier work on whether lectins act on neural stem cells in the adult mammalian brain. It describes how galectin-1 was found in GFAP-expressing cells of the mouse subventricular zone and in slowly dividing, label-retaining cells enriched for stem cells. It then outlines infusion and knockout experiments indicating that galectin-1 promotes stem cell proliferation, and mutant-protein experiments indicating that this depends on its sugar-binding ability. The authors close by proposing that fucosylation of the LeX glycan on stem cells might tune galectin-1 binding, a question left for future work.", "research_question": "Is the lectin galectin-1 expressed on adult neural stem cells, and does it regulate their proliferation through glycan binding?", "approach": "A review of the authors' prior mouse studies using immunostaining, long-term BrdU label retention, neurosphere assays, intraventricular infusion of recombinant or mutant galectin-1, and galectin-1 knockout mice, set against published data on galectin-1 in the nervous system.", "key_findings": [ { "finding": "In the adult mouse subventricular zone, galectin-1 was found in GFAP-expressing cells and in a subset of long-term BrdU-retaining cells, which the authors take as evidence that adult neural stem cells express galectin-1.", "evidence": "Fig. 1F-H", "species": "mouse", "n": null, "stats": null }, { "finding": "Intraventricular infusion of recombinant galectin-1 increased neurosphere formation and long-term BrdU-retaining cells in the subventricular zone without changing apoptotic cell numbers, whereas galectin-1 knockout mice had fewer neural stem cells, supporting a role in promoting stem cell proliferation.", "evidence": "Fig. 2B-D", "species": "mouse", "n": null, "stats": "p<0.05" }, { "finding": "A cysteine-to-serine mutant that keeps its carbohydrate-binding activity under oxidative conditions increased label-retaining cells, whereas oxidized galectin-1 did not, suggesting that carbohydrate binding is required for the proliferative effect.", "evidence": "text, citing ref. 18", "species": "mouse", "n": null, "stats": null }, { "finding": "The authors propose that fucosylation of lactosamine to form the LeX antigen on neural stem cells, which lowers galectin-1 affinity, may regulate galectin-1 binding and thus stem cell proliferation, a hypothesis they leave for future studies.", "evidence": "section 'Expression and function of glycan in NSCs'", "species": "mouse", "n": null, "stats": null } ], "methods": [ "immunohistochemistry for galectin-1 and GFAP", "long-term BrdU label retention", "neurosphere assay", "intraventricular infusion of recombinant galectin-1 by osmotic pump", "infusion of oxidation-resistant mutant and oxidized galectin-1" ], "models": [ "adult mice", "galectin-1 knockout mice" ], "brain_regions": [ "subventricular zone", "lateral ventricle", "olfactory bulb" ], "data_code_availability": [], "limitations": [ "Whether fucosylation of stem cell glycans actually controls galectin-1 binding and proliferation was not tested and is posed as an open question." ], "keywords": [ "galectin-1", "lectin", "glycan", "neural stem cells", "adult neurogenesis", "subventricular zone", "LeX antigen" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2007-cell-mol-life-sci.md" }, { "id": "yamashita-2006-jneurosci", "doi": "10.1523/JNEUROSCI.0149-06.2006", "pmid": "16775151", "pmcid": "PMC6674034", "url": "https://doi.org/10.1523/JNEUROSCI.0149-06.2006", "title": "Subventricular Zone-Derived Neuroblasts Migrate and Differentiate into Mature Neurons in the Post-Stroke Adult Striatum", "authors": [ "Yamashita T", "Ninomiya M", "Hernandez Acosta P", "Garcia-Verdugo JM", "Sunabori T", "Sakaguchi M", "Adachi K", "Kojima T", "Hirota Y", "Kawase T", "Araki N", "Abe K", "Okano H", "Sawamoto K" ], "pi_role": "co_author", "year": 2006, "published_date": "2006-06-14", "journal": "Journal of Neuroscience", "volume": "26", "issue": "24", "pages": "6627-6636", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_regeneration_transplantation" ], "tldr": "Genetic lineage tracing in mice shows that after stroke, the subventricular zone, not the striatum itself, supplies neuroblasts that migrate along blood vessels into the injured striatum and mature into synapse-forming neurons.", "summary": "After focal cerebral ischemia, new neuroblasts appear in the adult mouse striatum, but their origin was unclear. The authors labeled either striatal cells or subventricular zone (SVZ) cells with Cre-loxP and cell-type-specific retroviral methods and followed their progeny after middle cerebral artery occlusion. Striatum-labeled cells never became neuroblasts, whereas SVZ-labeled cells, including GFAP-expressing cells, produced neuroblasts that reached the peri-infarct striatum. These migrating cells formed chain-like aggregates wrapped around blood vessels and oriented mainly mediolaterally, and some matured into NeuN-positive neurons with synapses by 90 days. The authors note that the number of new neurons is small and the neuron subtypes remain unknown.", "research_question": "Do neuroblasts that appear in the adult striatum after stroke come from the subventricular zone or from latent progenitors within the striatum itself?", "approach": "Region- and cell-type-specific labeling (adenoviral or plasmid-PEI Cre delivery into CAG-CAT-EGFP mice, RCAS-EGFP infection of GFAP-tva mice) combined with transient middle cerebral artery occlusion, followed by confocal immunohistochemistry and electron microscopy up to 90 days after ischemia.", "key_findings": [ { "finding": "Stroke transiently increased Dcx-positive neuroblasts in the striatum, peaking above preoperative levels at 18 and 21 days, and 98% of them co-expressed the neuronal marker betaIII-tubulin.", "evidence": "Fig. 1C, 1E", "species": "mouse", "n": "n = 3 at each time point; n = 1108 cells", "stats": "p < 0.01 versus preoperative value (ANOVA, Bonferroni's correction)" }, { "finding": "Striatal cells labeled with a Cre adenovirus before stroke did not give rise to neuroblasts: none of the 695 GFP-labeled striatal cells expressed Dcx 18 days after occlusion.", "evidence": "Fig. 2J-K", "species": "mouse", "n": "n = 695 cells in three MCAO mice", "stats": null }, { "finding": "After stroke, SVZ cells labeled by intraventricular Cre plasmid appeared in the ipsilateral striatum (82.0 ± 12.1 cells per hemisphere), and 37% of them were Dcx-positive migrating neuroblasts, whereas none reached the striatum in non-ischemic controls.", "evidence": "Fig. 3D-G", "species": "mouse", "n": "control n = 4, MCAO n = 6; n = 45 cells", "stats": null }, { "finding": "GFAP-expressing SVZ cells infected via the RCAS-TVA system produced Dcx-positive neuroblasts in the peri-infarct striatum in all 3 brains (5 of 13 GFP cells), while striatal infection yielded none (0 of 498).", "evidence": "Fig. 4F-J", "species": "mouse", "n": "n = 3 brains (SVZ); n = 498 cells (striatum)", "stats": null }, { "finding": "Neuroblast chains in the injured striatum wrapped around blood vessels (all 12 chains) and were mostly oriented mediolaterally toward the lesion (83%), suggesting vessel-associated directed migration.", "evidence": "Fig. 5A-F", "species": "mouse", "n": "n = 12 chains; n = 6 spherical clusters", "stats": "p < 0.05 (χ2 test)" }, { "finding": "By 90 days after stroke, 29% of SVZ-derived GFP cells in the striatum expressed NeuN, and labeled axons contained presynaptic vesicles and formed synapses with neighboring cells.", "evidence": "Fig. 6C-F", "species": "mouse", "n": "n = 13 cells (figure legend)", "stats": null } ], "methods": [ "transient middle cerebral artery occlusion (intraluminal filament, 30 min)", "Cre-loxP lineage tracing with adenoviral or plasmid-polyethylenimine Cre delivery", "RCAS-TVA avian retrovirus labeling of GFAP-expressing cells", "confocal immunohistochemistry", "immunoelectron microscopy" ], "models": [ "ICR mice", "CAG-CAT-EGFP transgenic mice", "GFAP-tva transgenic mice" ], "brain_regions": [ "subventricular zone", "striatum", "rostral migratory stream", "olfactory bulb" ], "data_code_availability": [], "limitations": [ "The authors could not directly confirm that the SVZ cells first infected by the retrovirus were expressing GFAP, so other SVZ cell types may contribute.", "A rare neurogenic population in the striatum that was undetectable under these conditions cannot be excluded.", "The types of neurons generated remain unclear, and the number of new neurons is considered too small for functional recovery." ], "keywords": [ "subventricular zone", "cerebral ischemia", "migration", "neurogenesis", "regeneration", "striatum" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md" }, { "id": "sakaguchi-2006-pnas", "doi": "10.1073/pnas.0508793103", "pmid": "16636291", "pmcid": "PMC1447526", "url": "https://doi.org/10.1073/pnas.0508793103", "title": "A carbohydrate-binding protein, Galectin-1, promotes proliferation of adult neural stem cells", "authors": [ "Sakaguchi M", "Shingo T", "Shimazaki T", "Okano HJ", "Shiwa M", "Ishibashi S", "Oguro H", "Ninomiya M", "Kadoya T", "Horie H", "Shibuya A", "Mizusawa H", "Poirier F", "Nakauchi H", "Sawamoto K", "Okano H" ], "pi_role": "first", "year": 2006, "published_date": "2006-05-02", "journal": "Proceedings of the National Academy of Sciences", "volume": "103", "issue": "18", "pages": "7112-7117", "type": "research_article", "peer_reviewed": true, "open_access": true, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "adult_neurogenesis_memory" ], "tldr": "Galectin-1, a sugar-binding protein found in slowly dividing astrocytes of the adult subventricular zone, acts as an endogenous factor that supports neural stem and progenitor cell proliferation in mice.", "summary": "Using a mass-spectrometry protein screen of stromal-cell conditioned medium that boosted neurosphere formation, the authors identified Galectin-1 as a candidate factor for neural stem cell growth. Recombinant Galectin-1 increased neurosphere formation in culture, and the protein was found in a subset of GFAP-positive subventricular zone astrocytes that includes slowly dividing, label-retaining cells. Infusing Galectin-1 into the lateral ventricle of adult mice increased proliferating type B and type C cells and long-term label-retaining cells, and this effect required the carbohydrate-binding (reduced) form. Conversely, galectin-1-null mice and mice given a neutralizing antibody had fewer proliferating and slowly dividing progenitors, without changes in apoptosis, indicating that endogenous Galectin-1 supports adult neural progenitor proliferation.", "research_question": "Which soluble factors promote proliferation of adult neural stem cells in the subventricular zone, and does Galectin-1 play this role in vivo?", "approach": "A ProteinChip mass-spectrometry screen of OP9 conditioned medium identified Galectin-1, which was then tested with neurosphere assays, immunohistochemistry and BrdU label-retention, intraventricular protein or antibody infusion, and analysis of galectin-1 knockout mice.", "key_findings": [ { "finding": "OP9 conditioned medium enabled clonal neurosphere formation from 12.4% of single cells, and recombinant Galectin-1 enhanced neurosphere formation in culture.", "evidence": "Fig. 1A-B", "species": "mouse", "n": "n 400 cells (OP9CM)", "stats": "P 0.01, ANOVA (Galectin-1)" }, { "finding": "In the adult subventricular zone, 32.7% of cells were Galectin-1-positive and 71.4% of GFAP-positive cells also expressed Galectin-1, including slowly dividing label-retaining cells.", "evidence": "Fig. 2", "species": "mouse", "n": "n 336 cells from three mice", "stats": null }, { "finding": "Intraventricular Galectin-1 infusion increased short-term BrdU-labeled proliferating cells in the subventricular zone without changing apoptosis, and raised proliferating type B and C cell counts by 1.7- and 1.4-fold relative to saline.", "evidence": "Fig. 3D-E; Table 1", "species": "mouse", "n": "n 3 mice each", "stats": "P 0.01; P 0.05, Mann-Whitney U test" }, { "finding": "Galectin-1 infusion increased slowly dividing BrdU-retaining cells at day 17 and day 37, and the reduced carbohydrate-binding form (CS-Galectin-1) did so while the oxidized form did not.", "evidence": "Fig. 3F-H; Fig. 11", "species": "mouse", "n": "n 3 each; n 5 mice each (CS-Galectin-1)", "stats": "day 17, P 0.01; day 37, P 0.001" }, { "finding": "galectin-1-null mice had fewer PCNA-positive cycling cells, fewer Mash1-positive type C cells, and fewer slowly dividing cells in the subventricular zone than wild-type littermates, and a neutralizing antibody reproduced the loss of slowly dividing cells.", "evidence": "Fig. 4; Fig. 12", "species": "mouse", "n": "n 3 each", "stats": "P 0.01 (PCNA); P 0.05 (Mash1); P 0.01 (slowly dividing)" } ], "methods": [ "ProteinChip (SELDI) mass-spectrometry screen and tandem mass spectrometry sequencing", "clonal neurosphere formation assay", "immunohistochemistry with confocal microscopy", "BrdU short-term and long-term label-retention labeling", "intraventricular infusion with osmotic pumps", "knockout mouse phenotyping" ], "models": [ "adult male mice (8 weeks old)", "galectin-1 knockout mice (129/SJ background)", "OP9 stromal cell line conditioned medium" ], "brain_regions": [ "subventricular zone", "lateral ventricle", "dentate gyrus" ], "data_code_availability": [], "limitations": [ "Galectin-1 alone did not reproduce the full activity of OP9 conditioned medium, so other factors likely contribute.", "Binding of CS-Galectin-1 to subventricular zone cells was reported as unpublished data." ], "keywords": [ "Galectin-1", "adult neural stem cells", "subventricular zone", "neurosphere", "lectin", "stem cell niche", "carbohydrate binding" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md" }, { "id": "okano-2006-tissue-stem-cells", "doi": null, "pmid": null, "pmcid": null, "url": null, "title": "Neural stem cells: Isolation and self-renewal", "authors": [ "Okano H", "Kohyama J", "Ohba H", "Sakaguchi M", "Tokunaga A", "Shimazaki T", "Okano HJ" ], "pi_role": "co_author", "year": 2006, "published_date": null, "journal": "Tissue Stem Cells", "volume": null, "issue": null, "pages": null, "type": "book_chapter", "peer_reviewed": null, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin" ], "tldr": null, "summary": null, "research_question": null, "approach": null, "key_findings": [], "methods": [], "models": [], "brain_regions": [], "data_code_availability": [], "limitations": [], "keywords": [], "source_basis": "metadata_only", "summary_status": "bibliographic_only", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2006-tissue-stem-cells.md" }, { "id": "sakaguchi-2005-inflamm-regen", "doi": "10.2492/jsir.25.50", "pmid": null, "pmcid": null, "url": "https://doi.org/10.2492/jsir.25.50", "title": "A method for gene transfer, single isolation and in vitro assay for neural stem cells", "authors": [ "Sakaguchi M", "Sawamoto K", "Shimazaki T", "Kitamura T", "Shibuya A", "Okano H" ], "pi_role": "first", "year": 2005, "published_date": "2005", "journal": "Inflammation and Regeneration", "volume": "25", "issue": "1", "pages": "50-54", "type": "methods_protocol", "peer_reviewed": true, "open_access": true, "license": null, "related_versions": [], "themes": [ "neural_stem_cells_galectin", "imaging_tools" ], "tldr": "A method paper combining retroviral gene transfer with FACS to introduce a GFP-marked transgene into neural stem cells and isolate a transduced subpopulation for in vitro functional assays.", "summary": "This methods paper describes a strategy for studying gene function in neural stem cells (NSCs) grown as neurospheres. The authors infect neurosphere cultures with a serum-free pMX-IG retrovirus that co-expresses a transgene and GFP, then use fluorescence-activated cell sorting (FACS) with a CD15 antibody to isolate the GFP-positive, CD15-positive cells that are enriched for NSCs. The sorted cells retain self-renewal and multipotency and can be used in subsequent self-renewal and differentiation assays. Working without serum lets the authors omit the ultracentrifugation step and use a MuLV-derived envelope that is not infectious to humans.", "research_question": "How can a transgene be introduced into neural stem cells and the transduced cells reliably isolated so that gene function can be assayed in vitro?", "approach": "Neurospheres from E14 mouse forebrain were infected with the GFP-co-expressing pMX-IG retrovirus produced in serum-free medium, then dissociated, stained for CD15, and sorted by FACS; sorted cells were tested in secondary neurosphere-formation (self-renewal) and differentiation assays.", "key_findings": [ { "finding": "The retrovirus transduced neurosphere cells at a low multiplicity of infection, so most GFP-expressing cells were expected to carry only a single copy of the transgene.", "evidence": "Fig. 1; Results", "species": "mouse", "n": null, "stats": null }, { "finding": "FACS staining for CD15 and GFP resolved the dissociated neurosphere cells into double-positive and other fractions, identifying a small CD15+/GFP+ population.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null }, { "finding": "Cells sorted on both GFP and CD15 formed significantly more secondary neurospheres than cells sorted on GFP alone, indicating enrichment for NSCs.", "evidence": "Fig. 3", "species": "mouse", "n": "n > 200, 10 cells/well", "stats": "p < 0.01, one-tail unpaired-T test" }, { "finding": "Neurospheres derived from single sorted CD15+ cells remained multipotent, differentiating into neurons, astrocytes and oligodendrocytes.", "evidence": "Fig. 4", "species": "mouse", "n": null, "stats": null }, { "finding": "Transgene expression from the vector persisted long-term without silencing, remaining detectable months after infection.", "evidence": "Results", "species": "mouse", "n": null, "stats": null } ], "methods": [ "neurosphere formation assay from E14 mouse forebrain cells", "retrovirus-mediated gene transfer with the serum-free pMX-IG vector produced in Plat-E cells", "fluorescence-activated cell sorting (FACS) with CD15 antibody and GFP", "secondary neurosphere-formation (self-renewal) assay", "differentiation assay with immunostaining for βIII-tubulin, GFAP and O4" ], "models": [ "E14 CD-1 mouse embryo forebrain neurosphere cultures" ], "brain_regions": [ "telencephalon", "forebrain" ], "data_code_availability": [], "limitations": [ "The CD15 (LeX) epitope was validated on mouse embryonic neurospheres; applicability to human NSCs is only suggested from unpublished observations." ], "keywords": [ "FACS", "functional assay", "neural stem cell", "retrovirus", "self-renew" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md" }, { "id": "ishibashi-2004-j-neurosci-res", "doi": "10.1002/jnr.20246", "pmid": "15378509", "pmcid": null, "url": "https://doi.org/10.1002/jnr.20246", "title": "Human neural stem/progenitor cells, expanded in long‐term neurosphere culture, promote functional recovery after focal ischemia in Mongolian gerbils", "authors": [ "Ishibashi S", "Sakaguchi M", "Kuroiwa T", "Yamasaki M", "Kanemura Y", "Shizuko I", "Shimazaki T", "Onodera M", "Okano H", "Mizusawa H" ], "pi_role": "co_author", "year": 2004, "published_date": "2004-08-02", "journal": "Journal of Neuroscience Research", "volume": "78", "issue": "2", "pages": "215-223", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_regeneration_transplantation" ], "tldr": "Human fetal neural stem/progenitor cells kept in neurosphere culture for over 24 weeks still survived, matured and formed synapses after grafting into ischemic gerbil brains, with smaller infarcts and better behavior.", "summary": "Clinical use of human neural stem cells for stroke would require large numbers of cells grown over many passages, so this study asked whether cells expanded for a long time keep their capacity to repair the ischemic brain. Neurosphere-forming cells from one human fetal forebrain, passaged for more than 24 weeks, were injected into the caudate nucleus of Mongolian gerbils 4 days after repeated unilateral carotid occlusion. Over the following 4 weeks, grafted animals had a smaller infarct volume than medium-injected controls and recovered faster in motor, sensory and spatial memory tasks. A fraction of the grafted cells survived around the lesion, became neurons, astrocytes or oligodendrocytes, and some donor-derived neurons formed synapse-like contacts with host neurons. The authors suggest that both circuit reconstruction and trophic support from the grafted cells may contribute to the recovery.", "research_question": "Can human neural stem/progenitor cells expanded in long-term neurosphere culture survive, differentiate, integrate and support functional recovery after focal ischemia in gerbils?", "approach": "Human fetal neurospheres passaged for over 24 weeks were xenografted into the lesioned caudate nucleus of immunosuppressed gerbils 4 days after focal ischemia, then compared with medium-injected, ischemia-only and sham groups by histology, double immunostaining, retroviral GFP labeling with electron microscopy, and blinded behavioral tests over 32 days.", "key_findings": [ { "finding": "Four weeks after grafting, total infarct volume was 22.5% in NSPC-grafted gerbils versus 31.3% in medium-grafted and 29.9% in ischemia-only animals, a significant reduction relative to medium grafts.", "evidence": "Fig. 1A", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group", "stats": "P < 0.05 vs medium-grafted; one-way ANOVA with Bonferroni post-hoc test" }, { "finding": "About 8% of the grafted human cells survived, mostly in the injected hemisphere (27,900 cells) with fewer contralaterally (9,300 cells), and they migrated into areas of selective neuronal death rather than the ischemic cavity.", "evidence": "Fig. 1B-C", "species": "Mongolian gerbil", "n": "n = 7 NSPC-grafted animals", "stats": null }, { "finding": "Surviving donor cells expressed neuronal (NeuN, 36.2%), astrocytic (GFAP, 46.3%) or oligodendrocytic (CNPase, 3.8%) markers, while 10.3% carried none of these and none co-labeled with endothelial or microglial markers.", "evidence": "Fig. 2A-E", "species": "Mongolian gerbil", "n": "n = 7 NSPC-grafted animals", "stats": null }, { "finding": "Retroviral GFP labeling (transduction efficiency 97.9%) followed by electron microscopy showed donor-derived structures forming synapse-like contacts with host neurons in areas of selective neuronal death.", "evidence": "Fig. 3A-F", "species": "Mongolian gerbil", "n": "n = 4 animals grafted with GFP-labeled cells", "stats": null }, { "finding": "Grafted gerbils showed less contralateral body-swing bias than medium-grafted animals, approaching the 50% baseline by 4 weeks, and removed adhesive stimuli from the affected forelimb faster from 2 weeks after grafting.", "evidence": "Fig. 4A-B", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group; n = 8 sham", "stats": "P < 0.001 (body swing) and P < 0.01 (removal time) vs medium-grafted; repeated-measures ANOVA with Bonferroni test" }, { "finding": "Focal ischemia lowered T-maze spontaneous alternation to 23.5% from 75.2% in sham animals, and NSPC-grafted animals recovered this spatial cognitive measure relative to medium-grafted animals.", "evidence": "Fig. 4C-F", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group; n = 8 sham", "stats": "P < 0.01 vs medium-grafted" } ], "methods": [ "neurosphere culture of human fetal forebrain neural stem/progenitor cells", "repeated unilateral common carotid artery occlusion model of focal ischemia", "stereotaxic intracerebral xenotransplantation with cyclosporine A immunosuppression", "infarct volume measurement on hematoxylin/eosin sections", "double immunofluorescence with human nuclear antigen and cell-type markers", "retroviral EGFP labeling with immuno-electron microscopy", "elevated body swing test, bilateral asymmetry test and T-maze spontaneous alternation" ], "models": [ "male Mongolian gerbils", "human fetal neural stem/progenitor cells (neurospheres)" ], "brain_regions": [ "caudate nucleus", "cerebral cortex", "hippocampus", "thalamus", "corpus callosum" ], "data_code_availability": [], "limitations": [ "Functional recovery appeared within 7-14 days, earlier than expected for new synapse formation, so the authors note that circuit reconstruction alone is unlikely to explain it.", "The contribution of trophic factors and of endogenous neurogenesis to recovery was not tested directly.", "The optimal timing of transplantation after ischemia for cell survival and neuronal differentiation remains to be determined." ], "keywords": [ "experimental stroke", "stem cell transplantation", "human neural stem cells", "neurosphere", "focal ischemia", "Mongolian gerbil", "cell differentiation" ], "source_basis": "full_text", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md" }, { "id": "mikami-2004-j-neurosci-res", "doi": "10.1002/jnr.20086", "pmid": "15114617", "pmcid": null, "url": "https://doi.org/10.1002/jnr.20086", "title": "Implantation of dendritic cells in injured adult spinal cord results in activation of endogenous neural stem/progenitor cells leading to de novo neurogenesis and functional recovery", "authors": [ "Mikami Y", "Okano H", "Sakaguchi M", "Nakamura M", "Shimazaki T", "Okano HJ", "Kawakami Y", "Toyama Y", "Toda M" ], "pi_role": "co_author", "year": 2004, "published_date": "2004-04-12", "journal": "Journal of Neuroscience Research", "volume": "76", "issue": "4", "pages": "453-465", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": null, "related_versions": [], "themes": [ "neural_regeneration_transplantation" ], "tldr": "In adult mice with spinal cord injury, implanted dendritic cells activated resident neural stem/progenitor cells, supporting new neuron generation and locomotor recovery.", "summary": "This mouse study asked whether immune cells, specifically dendritic cells, could stimulate the spinal cord's own neural stem/progenitor cells after injury. In culture, dendritic cells were the most potent of the immune cell types tested at promoting proliferation and survival of these progenitors. After implantation into the injured adult spinal cord, endogenous progenitors divided and gave rise to new neurons, and the implanted cells produced neurotrophin-3 and activated local microglia. Implanted mice showed better locomotor scores than controls, and the authors suggest the cells act through trophic support of endogenous progenitors.", "research_question": "Can implanted dendritic cells activate endogenous neural stem/progenitor cells and support repair after adult spinal cord injury?", "approach": "Immune cell types were compared in vitro for effects on neural stem/progenitor cells, then dendritic cells were implanted into injured adult mouse spinal cord and neurogenesis, neurotrophin production, microglial activation and locomotion were assessed.", "key_findings": [ { "finding": "Of the immune cell types tested in vitro, dendritic cells most strongly promoted proliferation and survival of neural stem/progenitor cells.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "In injured adult mice receiving dendritic cells, endogenous progenitors in the spinal cord were activated and produced new neurons through cell division.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "The implanted dendritic cells produced neurotrophin-3 and activated resident microglia in the injured cord.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Locomotor function recovered significantly more in dendritic cell-implanted mice than in control mice; the authors suggest a trophic mechanism.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null } ], "methods": [ "in vitro co-culture of immune cells with neural stem/progenitor cells", "dendritic cell implantation into injured spinal cord", "behavioral locomotor assessment" ], "models": [ "adult mice with spinal cord injury" ], "brain_regions": [ "spinal cord" ], "data_code_availability": [], "limitations": [], "keywords": [ "dendritic cells", "spinal cord injury", "neural stem/progenitor cells", "neurogenesis", "neurotrophin-3", "microglia" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/mikami-2004-j-neurosci-res.md" }, { "id": "ohba-2004-neurosci-lett", "doi": "10.1016/j.neulet.2004.01.026", "pmid": "15039105", "pmcid": null, "url": "https://doi.org/10.1016/j.neulet.2004.01.026", "title": "Sox21 is a repressor of neuronal differentiation and is antagonized by YB-1", "authors": [ "Ohba H", "Chiyoda T", "Endo E", "Yano M", "Hayakawa Y", "Sakaguchi M", "Darnell RB", "Okano HJ", "Okano H" ], "pi_role": "co_author", "year": 2004, "published_date": "2004-04", "journal": "Neuroscience Letters", "volume": "358", "issue": "3", "pages": "157-160", "type": "research_article", "peer_reviewed": true, "open_access": false, "license": "Elsevier TDM user license (https://www.elsevier.com/tdm/userlicense/1.0/)", "related_versions": [], "themes": [ "neural_stem_cells_galectin" ], "tldr": "The HMG-box transcription factor Sox21, present in neural stem/progenitor cells, holds back neuronal differentiation in PC12 cells, and its binding partner YB-1 partly counteracts this.", "summary": "This study examined where the transcription factor Sox21 is expressed in the mouse brain and what it does during neuronal differentiation. Sox21 was found in immature neural stem/progenitor cells of the embryonic ventricular zone and, in adults, only in the subventricular zone. In PC12 cells, Sox21 expression disappeared as nerve growth factor drove the cells toward a neuronal fate, and forcing Sox21 expression blocked much of the neurite outgrowth. A biochemical search identified Y-box binding protein 1 (YB-1) as a Sox21 partner that partly relieves this block, which the authors suggest marks Sox21 as a brake on neuronal differentiation in the developing nervous system.", "research_question": "Does Sox21, expressed in neural stem/progenitor cells, regulate neuronal differentiation, and which proteins modulate its activity?", "approach": "Expression of Sox21 was mapped in embryonic and adult mouse brain and followed in PC12 cells during NGF-induced differentiation; Sox21 was overexpressed in PC12 cells and a Sox21-binding protein was identified biochemically and tested for its effect on neurite outgrowth.", "key_findings": [ { "finding": "Sox21 is expressed in immature neural stem/progenitor cells of the embryonic ventricular zone but not the cortical plate, and is confined to the subventricular zone in the adult mouse brain.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null }, { "finding": "Endogenous Sox21 is present in undifferentiated PC12 cells but disappears during NGF-induced neuronal differentiation, and overexpressing Sox21 substantially represses NGF-induced neurite outgrowth.", "evidence": "Abstract", "species": "rat (PC12 cell line)", "n": null, "stats": null }, { "finding": "Y-box binding protein 1 (YB-1) binds Sox21 and partially restores the NGF-induced neurite outgrowth that Sox21 inhibits, suggesting Sox21 acts as a repressor of neuronal differentiation.", "evidence": "Abstract", "species": "rat (PC12 cell line)", "n": null, "stats": null } ], "methods": [ "expression analysis in embryonic and adult mouse brain", "overexpression in PC12 cells with NGF-induced neurite outgrowth assay", "biochemical identification of a Sox21-associating protein" ], "models": [ "mouse brain (embryonic and adult)", "PC12 cells" ], "brain_regions": [ "ventricular zone", "cortical plate", "subventricular zone" ], "data_code_availability": [], "limitations": [], "keywords": [ "Sox21", "HMG box", "YB-1", "neuronal differentiation", "neural stem/progenitor cells", "PC12", "NGF", "neurite outgrowth" ], "source_basis": "abstract_only", "summary_status": "summarized", "page_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2004-neurosci-lett.md" } ] }