bioRxiv : the preprint server for biology最新文献

{"title":"<i>Syngap1</i> Promotes Cognitive Function through Regulation of Cortical Sensorimotor Dynamics.","authors":"Thomas Vaissiere, Sheldon D Michaelson, Thomas Creson, Jessie Goins, Daniel Fürth, Diana Balazsfi, Camilo Rojas, Randall Golovin, Konstantinos Meletis, Courtney A Miller, Daniel O'Connor, Lorenzo Fontolan, Gavin Rumbaugh","doi":"10.1101/2023.09.27.559787","DOIUrl":"10.1101/2023.09.27.559787","url":null,"abstract":"<p><p>Perception, a cognitive construct, emerges through sensorimotor integration (SMI). The genetic mechanisms that shape SMI required for perception are unknown. Here, we demonstrate in mice that expression of the autism/intellectual disability gene, <i>Syngap1</i>, in cortical excitatory neurons is required for formation of somatomotor networks that promote SMI-mediated perception. Cortical <i>Syngap1</i> expression was necessary and sufficient for setting tactile sensitivity, sustaining tactile object exploration, and promoting tactile learning. Mice with deficient <i>Syngap1</i> expression exhibited impaired neural dynamics induced by exploratory touches within a cortical-thalamic network known to promote attention and perception. Disrupted neuronal dynamics were associated with circuit-specific long-range synaptic connectivity abnormalities. Our data support a model where autonomous <i>Syngap1</i> expression in cortical excitatory neurons promotes cognitive abilities through assembly of circuits that integrate temporally-overlapping sensory and motor signals, a process that promotes perception and attention. These data provide systems-level insights into the robust association between <i>Syngap1</i> expression and cognitive ability.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ba/80/nihpp-2023.09.27.559787v1.PMC10557642.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"\"Distinct inhibitory neurons differently shape neuronal codes for sound intensity in the auditory cortex\".","authors":"Melanie Tobin, Janaki Sheth, Katherine C Wood, Erin K Michel, Maria N Geffen","doi":"10.1101/2023.02.01.526470","DOIUrl":"10.1101/2023.02.01.526470","url":null,"abstract":"<p><p>Cortical circuits contain multiple types of inhibitory neurons which shape how information is processed within neuronal networks. Here, we asked whether somatostatin-expressing (SST) and vasoactive intestinal peptide-expressing (VIP) inhibitory neurons have distinct effects on population neuronal responses to noise bursts of varying intensities. We optogenetically stimulated SST or VIP neurons while simultaneously measuring the calcium responses of populations of hundreds of neurons in the auditory cortex of male and female awake, head-fixed mice to sounds. Upon SST neuronal activation, noise bursts representations became more discrete for different intensity levels, relying on cell identity rather than strength. By contrast, upon VIP neuronal activation, noise bursts of different intensity level activated overlapping neuronal populations, albeit at different response strengths. At the single-cell level, SST and VIP neuronal activation differentially modulated the response-level curves of monotonic and nonmonotonic neurons. SST neuronal activation effects were consistent with a shift of the neuronal population responses toward a more localist code with different cells responding to sounds of different intensity. By contrast, VIP neuronal activation shifted responses towards a more distributed code, in which sounds of different intensity level are encoded in the relative response of similar populations of cells. These results delineate how distinct inhibitory neurons in the auditory cortex dynamically control cortical population codes. Different inhibitory neuronal populations may be recruited under different behavioral demands, depending on whether categorical or invariant representations are advantageous for the task.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/55/40/nihpp-2023.02.01.526470v2.PMC9915672.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9744515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.","authors":"Simone Rancati, Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini","doi":"10.1101/2023.10.24.563721","DOIUrl":"10.1101/2023.10.24.563721","url":null,"abstract":"<p><p>The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, lineages, and sublineages, outcompeting previously circulating ones because of, among other factors, increased transmissibility and immune escape. We propose DeepAutoCoV, an unsupervised deep learning anomaly detection system to predict future dominant lineages (FDLs). We define FDLs as viral (sub)lineages that will constitute more than 10% of all the viral sequences added to the GISAID database on a given week. DeepAutoCoV is trained and validated by assembling global and country-specific data sets from over 16 million Spike protein sequences sampled over a period of about 4 years. DeepAutoCoV successfully flags FDLs at very low frequencies (0.01% - 3%), with median lead times of 4-17 weeks, and predicts FDLs ~5 and ~25 times better than a baseline approach For example, the B.1.617.2 vaccine reference strain was flagged as FDL when its frequency was only 0.01%, more than a year before it was considered for an updated COVID-19 vaccine. Furthermore, DeepAutoCoV outputs interpretable results by pinpointing specific mutations potentially linked to increased fitness, and may provide significant insights for the optimization of public health <i>pre-emptive</i> intervention strategies.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92158355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data.","authors":"Rachael G Aubin, Javier Montelongo, Robert Hu, Elijah Gunther, Patrick Nicodemus, Pablo G Camara","doi":"10.1101/2023.02.06.527318","DOIUrl":"10.1101/2023.02.06.527318","url":null,"abstract":"<p><p>Single-cell RNA-sequencing has transformed the study of biological tissues by enabling transcriptomic characterizations of their constituent cell states. Computational methods for gene expression deconvolution use this information to infer the cell composition of related tissues profiled at the bulk level. However, current deconvolution methods are restricted to discrete cell types and have limited power to make inferences about continuous cellular processes like cell differentiation or immune cell activation. We present ConDecon, a clustering-independent method for inferring the likelihood for each cell in a single-cell dataset to be present in a bulk tissue. ConDecon represents an improvement in phenotypic resolution and functionality with respect to regression-based methods. Using ConDecon, we discover the implication of neurodegenerative microglia inflammatory pathways in the mesenchymal transformation of pediatric ependymoma and characterize their spatial trajectories of activation. The generality of this approach enables the deconvolution of other data modalities such as bulk ATAC-seq data.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10871695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Highly sensitive <i>in vivo</i> detection of dynamic changes in enkephalins following acute stress.","authors":"Marwa O Mikati, Petra Erdmann-Gilmore, Rose Connors, Sineadh M Conway, Jim Malone, Justin Woods, Robert W Sprung, R Reid Townsend, Ream Al-Hasani","doi":"10.1101/2023.02.15.528745","DOIUrl":"10.1101/2023.02.15.528745","url":null,"abstract":"<p><p>Enkephalins are opioid peptides that modulate analgesia, reward, and stress. <i>In vivo</i> detection of enkephalins remains difficult due to transient and low endogenous concentrations and inherent sequence similarity. To begin to address this we previously developed a system combining in vivo optogenetics with microdialysis and a highly sensitive mass spectrometry-based assay to measure opioid peptide release in freely moving rodents (Al-Hasani, 2018, eLife). Here we show improved detection resolution and stabilization of enkephalin detection, which allowed us to investigate enkephalin release during acute stress. We present an analytical method for real-time, simultaneous detection of Met- and Leu-Enkephalin (Met-Enk & Leu-Enk) in the mouse Nucleus Accumbens shell (NAcSh) after acute stress. We confirm that acute stress activates enkephalinergic neurons in the NAcSh using fiber photometry and that this leads to the release of Met- and Leu-Enk. We also demonstrate the dynamics of Met- and Leu-Enk release as well as how they correlate to one another in the ventral NAc shell, which was previously difficult due to the use of approaches that relied on mRNA transcript levels rather than post-translational products. This approach increases spatiotemporal resolution, optimizes the detection of Met-Enkephalin through methionine oxidation, and provides novel insight into the relationship between Met- and Leu-Enkephalin following stress.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9948958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9945891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrafast Power Doppler Ultrasound Enables Longitudinal Tracking of Vascular Changes that Correlate with Immune Response After Radiotherapy.","authors":"Shannon E Martello, Jixin Xia, Jiro Kusunose, Benjamin C Hacker, McKenzie A Mayeaux, Erica J Lin, Adrienne Hawkes, Aparna Singh, Charles F Caskey, Marjan Rafat","doi":"10.1101/2023.08.04.552076","DOIUrl":"10.1101/2023.08.04.552076","url":null,"abstract":"<p><strong>Background: </strong>While immunotherapy shows great promise in patients with triple negative breast cancer, many will not respond to treatment. Radiotherapy has the potential to prime the tumor-immune microenvironment for immunotherapy. However, predicting response is difficult due to tumor heterogeneity across patients, which necessitates personalized medicine strategies that incorporate tumor tracking into the therapeutic approach. Here, we investigated the use of ultrasound (US) imaging of the tumor vasculature to monitor the tumor response to treatment.</p><p><strong>Methods: </strong>We utilized ultrafast power doppler US to track the vascular response to radiotherapy over time. We used 4T1 (metastatic) and 67NR (non-metastatic) breast cancer models to determine if US measurements corroborate conventional immunostaining analysis of the tumor vasculature. To evaluate the effects of radiation, tumor volume and vascular index were calculated using US, and the correlation between vascular changes and immune cell infiltration was determined.</p><p><strong>Results: </strong>US tumor measurements and the quantified vascular response to radiation were confirmed with caliper measurements and immunostaining, respectively, demonstrating a proof-of-principle method for non-invasive vascular monitoring. Additionally, we found significant infiltration of CD8 ⁺ T cells into irradiated tumors 10 days after radiation, which followed a sustained decline in vascular index and an increase in splenic CD8 ⁺ T cells that was first observed 1 day post-radiation.</p><p><strong>Conclusions: </strong>Our findings reveal that ultrafast power doppler US can evaluate changes in tumor vasculature that are indicative of shifts in the tumor-immune microenvironment. This work may lead to improved patient outcomes through observing and predicting response to therapy.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9991213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cohesin organizes 3D DNA contacts surrounding active enhancers in <i>C. elegans</i>.","authors":"Jun Kim, Haoyu Wang, Sevinç Ercan","doi":"10.1101/2023.09.18.558239","DOIUrl":"10.1101/2023.09.18.558239","url":null,"abstract":"<p><p>In mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication between <i>cis</i>-regulatory elements. Many organisms, including <i>S. cerevisiae</i>, <i>C. elegans</i>, and <i>A. thaliana</i> contain cohesin but lack CTCF. Here, we used <i>C. elegans</i> to investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called \"fountains\", which are also reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ~20-40 kb in <i>C. elegans</i>. Hi-C analysis upon cohesin and WAPL depletion support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly due to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers and fountain strength is associated with transcription. Compared to mammals, average processivity of <i>C. elegans</i> cohesin is ~10-fold shorter and NIPBL binding does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/aa/e7/nihpp-2023.09.18.558239v1.PMC10541618.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fast and accurate local ancestry inference with Recomb-Mix.","authors":"Yuan Wei, Degui Zhi, Shaojie Zhang","doi":"10.1101/2023.11.17.567650","DOIUrl":"10.1101/2023.11.17.567650","url":null,"abstract":"<p><p>The availability of large genotyped cohorts brings new opportunities for revealing the high-resolution genetic structure of admixed populations via local ancestry inference (LAI), the process of identifying the ancestry of each segment of an individual haplotype. Though current methods achieve high accuracy in standard cases, LAI is still challenging when reference populations are more similar (e.g., intra-continental), when the number of reference populations is too numerous, or when the admixture events are deep in time, all of which are increasingly unavoidable in large biobanks. Here, we present a new LAI method, Recomb-Mix. Recomb-Mix integrates the elements of existing methods of the site-based Li and Stephens model and introduces a new graph collapsing trick to simplify counting paths with the same ancestry label readout. Through comprehensive benchmarking on various simulated datasets, we show that Recomb-Mix is more accurate than existing methods in diverse sets of scenarios while being competitive in terms of resource efficiency. We expect that Recomb-Mix will be a useful method for advancing genetics studies of admixed populations.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10680832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coordinated stimulation of axon regenerative and neurodegenerative transcriptional programs by ATF4 following optic nerve injury.","authors":"Preethi Somasundaram, Madeline M Farley, Melissa A Rudy, Katya Sigal, Andoni I Asencor, David G Stefanoff, Malay Shah, Puneetha Goli, Jenny Heo, Shufang Wang, Nicholas M Tran, Trent A Watkins","doi":"10.1101/2023.03.29.534798","DOIUrl":"10.1101/2023.03.29.534798","url":null,"abstract":"<p><p>Stress signaling is important for determining the fates of neurons following axonal insults. Previously we showed that the stress-responsive kinase PERK contributes to injury-induced neurodegeneration (Larhammar et al., 2017). Here we show that PERK acts primarily through Activating Transcription Factor-4 (ATF4) to stimulate not only pro-apoptotic but also pro-regenerative responses following optic nerve damage. Using conditional knockout mice, we find an extensive PERK/ATF4-dependent transcriptional response that includes canonical ATF4 target genes and modest contributions by C/EBP Homologous Protein (CHOP). Overlap with c-Jun-dependent transcription suggests interplay with a parallel stress pathway that orchestrates regenerative and apoptotic responses. Accordingly, neuronal knockout of ATF4 recapitulates the neuroprotection afforded by PERK deficiency, and PERK or ATF4 knockout impairs optic axon regeneration enabled by disrupting the tumor suppressor PTEN. These findings reveal an integral role for PERK/ATF4 in coordinating neurodegenerative and regenerative responses to CNS axon injury.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10081193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9265433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autism candidate gene <i>rbm-26</i> (<i>RBM26/27</i>) regulates MALS-1 to protect against mitochondrial dysfunction and axon degeneration during neurodevelopment.","authors":"Tamjid A Chowdhury, David A Luy, Garrett Scapellato, Dorian Farache, Amy Sy Lee, Christopher C Quinn","doi":"10.1101/2023.10.12.562060","DOIUrl":"10.1101/2023.10.12.562060","url":null,"abstract":"<p><p>Mitochondrial dysfunction is thought to be a key component of neurodevelopmental disorders such as autism, intellectual disability, and ADHD. However, little is known about the molecular mechanisms that protect against mitochondrial dysfunction during neurodevelopment. Here, we address this question through the investigation of <i>rbm-26</i>, the <i>C. elegans</i> ortholog of the <i>RBM27</i> autism candidate gene, which encodes an RNA-binding protein whose role in neurons is unknown. We report that RBM-26 (RBM26/27) protects against axonal defects by negatively regulating expression of the MALS-1 (MALSU1) mitoribosomal assembly factor. Autism-associated missense variants in RBM-26 cause a sharp decrease in RBM-26 protein expression along with defects in in axon overlap and axon degeneration that occurs during larval development. Using a biochemical screen, we identified the mRNA for the MALS-1 mitoribosomal assembly factor as a binding partner for RBM-26. Loss of RBM-26 function causes a dramatic overexpression of <i>mals-1</i> mRNA and MALS-1 protein. Moreover, genetic analysis indicates that this overexpression of MALS-1 is responsible for the mitochondrial and axon degeneration defects in <i>rbm-26</i> mutants. These observations reveal a mechanism that regulates expression of a mitoribosomal assembly factor to protect against axon degeneration during neurodevelopment.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}