Biology subjects

Zhang, S.-Y.

Publications and source records attributed to Zhang, S.-Y..

14 recordsLinked to original sources

bioRxiv2026

From pose to behavior: SABER integrates identity-resolved multi-animal pose tracking with language-model-based behavioral factor discovery

Quantifying social behavior requires accurate assignment of posture and actions to individual animals, which is often hindered by close contact, occlusion, and identity switches. Meanwhile, current behavioral recognition pipelines still lack stable predictive accuracy. Here we developed SABER, a locally deployable framework that couples multianimal pose estimation with identity preserving tracking, interpretable behavioral factor mining, and multiscale temporal behavior prediction from a single overhead video stream. Across spontaneous two mice social interaction, mating, aggression, and four mice recordings, SABER improved pose estimation accuracy and tracking continuity relative to comparator pipelines. Its behavioral factor-mining procedure identified interpretable kinematic, postural, and social descriptors, and temporal integration improved classification of behavioral categories. SABER offers an intuitive, open-source interface to facilitate use. Applied to social defeat stress mice, SABER detected reduced approach behavior and a multivariate behavioral profile that distinguished depression susceptible from control animals. SABER outputs could also be synchronized with miniscope calcium recordings, enabling joint analysis of behavioral states and neuronal population activity. SABER therefore provides an accessible, identity resolved route from single view social interaction video to behavioral phenotyping and brain behavior analysis.

animal behavior and cognition↗

bioRxiv2026

A flow cytometry-based assay to quantify the binding of transmembrane ligands to their cognate receptors using fluorescent virus-like particles

The binding of transmembrane (TM) ligands to their cognate TM receptors on neighboring cells governs intercellular adhesion and direct cell-cell communication. However, these interactions are difficult to study in vitro because they depend on membrane presentation, ligand orientation, receptor clustering, and avidity, features often not captured by soluble recombinant ligands or cell-free assays. Here, we describe a flow cytometry-based assay using fluorescent, lentiviral-derived virus-like particles (VLPs) displaying TM ligands to quantify binding to their receptors on target cells. Fluorescent VLPs are generated in-house by plasmid transfection in HEK293T cells and enable direct fluorescent detection without fluorochrome-conjugated secondary antibodies. The system is modular and readily accommodates engineered ligand constructs, including patient-derived variants. We applied this platform to generate ICAM-1-displaying fluorescent VLPs and to study human LFA-1 function in patient-derived leukocytes. This protocol provides a detailed workflow for VLP production and in vitro binding assays, offering a simple, quantitative, and cost-effective approach for studying TM ligand-receptor interactions in a membrane context. The system is well suited for mechanistic studies, functional assessment of patient-derived variants, and direct binding assays using patient-derived cells. Integrating the assay into multicolor flow cytometry panels enables simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. Key featuresO_LIQuantifies TM ligand-receptor binding in a membrane context using fluorescent VLPs and flow cytometry. C_LIO_LIFully in-house, modular system based on plasmid transfection in HEK293T cells, without reliance on recombinant ligands or fluorochrome-conjugated secondary antibodies. C_LIO_LISupports testing of engineered ligand variants, including patient-derived alleles, and direct functional studies on patient-derived cells. C_LIO_LICompatible with multicolor flow cytometry panels, enabling simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. C_LI Graphical overview O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/725198v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@a43069org.highwire.dtl.DTLVardef@166491borg.highwire.dtl.DTLVardef@49c7d4org.highwire.dtl.DTLVardef@1de36a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Laboratory evolution can improve algal cell yield and lipid production under mildly cold conditions

One challenge to large-scale microalgae cultivation, e.g., for biodiesel production, is the seasonal low-temperature conditions. We argue that seasonally varying selection in natural environments has prevented algae from better adapting to cold temperatures, and that laboratory evolution offers a promising approach for obtaining cold-adapted algal materials. We conducted a population-level artificial selection experiment with the unicellular green microalgae Chlorella sorokiniana at both a benign temperature (25) and a mildly cold temperature (15). Four artificial selection regimes were established: random selection, selection for high biomass (i.e., cell yield), selection for high lipid production, and rotation between high-biomass and high-lipid selection. We did not observe significant differences among the four selection regimes in evolutionary changes of algal cell yield or lipid yield, suggesting that natural selection at the individual level had dominated the evolutionary changes in our experiment. Compared with the ancestral strain, selection lines that had evolved at 15 typically exhibited increased cell yield and reduced lipid content per cell, indicating a trade-off relationship. However, substantial increases in cell yield may compensate for the reduction in lipid content per cell. Notably, three out of 16 selection lines showed > 1-fold increase in cell yield, and one exhibited > 1-fold increase in population-level lipid yield. Selection lines that had evolved at 25 displayed even greater increases in both cell and lipid yields, with a positive relationship between cell yield and lipid content per cell. Our results demonstrated the potential for laboratory evolution to obtain algal materials suitable for biofuel production under seasonal low-temperature conditions. HighlightsO_LIAlgae from natural environments not well-adapted to seasonal cold conditions. C_LIO_LILaboratory evolution under constant conditions with Chlorella sorokiniana. C_LIO_LIBoth cell yield and lipid production at a low temperature increased. C_LI

ecology↗

bioRxiv2024

Elevated levels of intracellular RNA lariats suppress the antiviral response

Recent studies report the genetic loss of the lariat debranching enzyme (DBR1) activity increases susceptibility to viral infection. Here, we show that more than 25% of human introns contain large hairpin structures created by the folding of two Alu elements inserted in opposite orientation. In wildtype cells, this large reservoir of endogenous dsRNA is efficiently degraded. In DBR1-null cells, lariats accumulate in the cytosol and dsRNA becomes enriched. We demonstrate how the chronic exposure to these lariats attenuates the dsRNA sensors, reducing the response of the MDA5, RIG-I, RNase L and PKR sensing pathways. We observe evidence for both attenuation and endogenous dsRNA in anti-viral response and viral evasion. Lariats are transiently elevated during infection (e.g. HSV-1, influenza, KSHV). The HSV-1 genome expresses multiple, stable lariats that may attenuate dsRNA sensors during latency. HIGHLIGHTSO_LIIntronic inverted repeat Alu elements constitute largest source of endogenous dsRNA. C_LIO_LIIn the absence of DBR1, lariats accumulate in the cytoplasm and form dsRNA. C_LIO_LIChronic exposure to endogenous dsRNA in a DBR1-depleted environment desensitizes the dsRNA sensing pathway. C_LIO_LIICP0 intron 1 of HSV-1 has a highly-structured stable lariat. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/627371v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@3698bborg.highwire.dtl.DTLVardef@654727org.highwire.dtl.DTLVardef@1229245org.highwire.dtl.DTLVardef@b10622_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

N-acetyltransferase 10-mediated mRNA N4-acetylation is Essential for the Translational Regulation During Oocyte Meiotic Maturation in Mice

Mammalian oocyte maturation is driven by the strict translational regulation of maternal mRNAs stored in the cytoplasm. However, the function and mechanism of post-transcriptional chemical modifications, especially the newly identified N4-acetylcytidine (ac4C) modification catalyzed by N-acetyltransferase 10 (NAT10), are unknown. In this study, we developed a low-input ac4C sequencing technology, ac4C LACE-seq, and mapped 8241 ac4C peaks at the whole-transcriptome level using 50 mouse oocytes at the germinal vesicle stage. We profiled the mRNA landscapes of NAT10-interactions and ac4C modifications. The NAT10-interacted and ac4C-modified transcripts are associated with high translation efficiency in oocytes. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. ac4C LACE-seq results indicated that Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors, such as MSY2, ZAR1, BTG4, and cyclin B1, which regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes showed decreased mRNA translation efficiency during meiotic maturation, partially due to the direct inhibition of ac4C sites on specific transcripts. In summary, we developed a low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in the precise regulation of oocyte meiotic maturation by enhancing translation efficiency.

developmental biology↗

bioRxiv2023

Localization and connectivity of rodent equivalent of the primate posterior cingulate cortex (area 23)

The posterior cingulate cortex (mainly area 23) in human and non-human primates is a critical component of the default mode network and is involved in many neurological and neuropsychiatric diseases such as Alzheimers disease, autism, depression, attention deficit hyperactivity disorder and schizophrenia. However, cingulate area 23 has not yet identified in rodents and other lower mammals and this makes modeling related circuits and diseases in rodents very difficult. Using a comparative approach and unique connectional patterns the present study has uncovered the location and extent of rodent equivalent of the primate cingulate area 23. Like in monkeys, area 23 but not adjoining retrosplenial and visual areas in the rats and mice displays strong reciprocal connections with the anteromedial thalamic nucleus. Rodent area 23 also reciprocally connects with the medial pulvinar and claustrum as well as with the anterior cingulate, granular retrosplenial, medial orbitofrontal, postrhinal, and visual and auditory association cortices. The rodent A23 also projects to the subcortical effectors such as the dorsal striatum, ventral lateral geniculate nucleus, zona incerta, pretectal nucleus, superior colliculus, periaqueductal gray, and brainstem reticular formation. All these connectional findings support the versatility of area 23 in the integration and modulation of multimodal information underlying spatial processing, episodic memory, self-reflection, attention, value assessment and many adaptive behaviors. Additionally, this study also suggests that the rodents can be used to model primate and human area 23 in future structural, functional, pathological and neuromodulation studies.

neuroscience↗

bioRxiv2022

Genome-wide detection of human variants that disrupt intronic branchpoints

Pre-mRNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Fifty-six rare variants in 44 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach has been available to efficiently detect such variants in next-generation sequencing (NGS) data. We established a comprehensive human genome-wide BP database by integrating existing BP data, and by generating new BP data from RNA-seq of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We in-depth characterize multiple features of BP in major and minor introns, and find that BP and BP-2 (two-nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, whilst being comparable to the exonic background. We develop BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition in NGS data. BPHunter retrospectively identifies 48 of the 56 known pathogenic BP mutations in which we summarize a strategy for prioritizing BP mutation candidates, and the remaining 8 all create AG dinucleotides between BP and acceptor site which is probably the reason for mis-splicing. We demonstrate the utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of STAT2 in a patient with critical COVID-19 pneumonia, and a novel somatic intronic 59-nucleotide deletion of ITPKB in a lymphoma patient, both of which we validate experimentally. BPHunter is publicly available from https://hgidsoft.rockefeller.edu/BPHunter and https://github.com/casanova-lab/BPHunter.

genetics↗

bioRxiv2022

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq

Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.

immunology↗

bioRxiv2022

Chemo-architecture of area prostriata in adult and developing mice: comparison with presubiculum and parasubiculum

Retrosplenial area 29e, which was a cortical region described mostly in earlier rodent literature, is often included in the dorsal presubiculum (PrSd) or postsubiculum (PoS) in modern literature and commonly used brain atlases. Recent anatomical and molecular studies have revealed that retrosplenial area 29e belongs to the superficial layers of area prostriata, which in primates is found to be important in fast analysis of quickly moving objects in far peripheral visual field. As in primates, the prostriata in rodents adjoins area 29 (granular retrosplenial area), area 30 (agranular retrosplenial area), medial visual cortex, PrSd-PoS, parasubiculum (PaS) and postrhinal cortex (PoR). The present study aims to reveal the chemo-architecture of the prostriata versus PrSd-PoS or PaS by means of a systematic survey of gene expression patterns in adult and developing mouse brains. First, we find many genes that display differential expression across the prostriata, PrSd-PoS and PaS and that show obvious laminar expression patterns. Second, we reveal subsets of genes that selectively express in the dorsal or ventral parts of the prostriata, suggesting the existence of at least two subdivisions. Third, we detect some genes that shows differential expression in the prostriata of postnatal mouse brains from adjoining regions, thus enabling identification of the developing area prostriata. Fourth, gene expression difference of the prostriata from the medial visual cortex and PoR is also observed. Finally, molecular and connectional features of the prostriata in rodents and non-human primates are discussed and compared.

neuroscience↗

bioRxiv2021

High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high ([~]10 vs [~]100 mg kg-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCEArsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels, and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

microbiology↗

bioRxiv2021

A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem inflammatory syndrome in children (MIS-C) with severe myocarditis

SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often including myocarditis. To better understand these cases, we applied a multi-parametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. The most severe forms of MIS-C (multisystem inflammatory syndrome in children related to SARS-CoV-2), that resulted in myocarditis, were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomic analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of severe myocarditis, characterized by sustained NF-{kappa}B activity, TNF- signaling, associated with decreased gene expression of NF-{kappa}B inhibitors. We also found a weak response to type-I and type-II interferons, hyperinflammation and response to oxidative stress related to increased HIF-1 and VEGF signaling. These results provide potential for a better understanding of disease pathophysiology.

immunology↗

bioRxiv2020

Basal Expression of Interferon-Stimulated Genes Drives Population Differences in Monocyte Susceptibility to Influenza Infection

There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use an ex vivo model to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. Using single-cell RNA-sequencing, we show widespread inter-individual variability in the percentage of IAV-infected monocytes. We show that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. While this host defense strategy is shared between CD16+/CD16- monocytes, we also uncover CD16+-specific mRNA expression of IL6 and TNF in response to IAV, and a stronger resistance of CD16+ monocytes to IAV infection. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3, MX1, and OAS3. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16+ monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Collectively, our results reveal the effects of IAV infection on the transcriptional landscape of human monocytes and highlight previously unappreciated differences in cellular susceptibility to IAV infection between individuals of African and European ancestry, which may account for the greater susceptibility of Africans to severe influenza. Significance StatementMonocytes may play a critical role during severe viral infections. Our study tackles how heterogeneity in monocyte subsets and activation contributes to shape individual differences in the transcriptional response to viral infections. Using single-cell RNA-sequencing, we reveal heterogeneity in monocyte susceptibility to IAV infection, both between CD16+/CD16- monocytes and across individuals, driven by differences in basal activation of an IRF/STAT-induced antiviral program. Furthermore, we show a decreased ability of IAV to infect and replicate in monocytes from African-ancestry individuals, with possible implications for antigen presentation and lymphocyte activation. These results highlight the importance of early cellular activation in determining an individuals innate immune response to viral infection.

genomics↗

bioRxiv2020

Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance

BackgroundGenetic variants underlying severe diseases are less likely to be transmitted to the next generation, and are thus gradually and selectively eliminated from the population through negative selection. Here, we study the determinants of this evolutionary process in genes underlying severe diseases in humans. ResultsWe propose a novel approach, CoNeS, integrating known negative selection scores through principal component projection. We compare evidence for negative selection at 319 genes underlying inborn errors of immunity (IEI), which are life-threatening monogenic disorders. We find that genes underlying autosomal dominant (AD) or X-linked IEI are under stronger negative selection than those underlying autosomal recessive (AR) IEI, which are under no stronger selection than genes not known to be disease-causing. However, we find that genes with mutations causing AR IEI that are lethal before reproductive maturity and that display complete penetrance are under stronger negative selection than other genes underlying AR IEI. We also find that genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. Finally, we replicate these results in a study of 1,140 genes causing inborn errors of neurodevelopment. ConclusionsThese findings collectively show that the clinical outcomes of inborn errors, together with the mode and mechanism of inheritance of these errors, determine the strength of negative selection acting on severe disease-causing genes. These findings suggest that estimating the intensity of negative selection with CoNeS may facilitate the selection of candidate genes in patients suspected to carry an inborn error.

genetics↗

bioRxiv2018

Varicella-zoster virus CNS vasculitis and RNA polymerase III gene mutation in identical twins

Deficiency in the cytosolic DNA sensor RNA Polymerase III was recently described in children with severe varicella zoster infection in the CNS or lungs. Here we describe a pair of monozygotic female twins, who both experienced severe recurrent CNS vasculitis caused by VZV reactivation. The clinical presentation and findings included recurrent episodes of headache, dizziness, and neurological deficits, cerebrospinal fluid with pleocytosis and intrathecal VZV antibody production, and magnetic resonance scan of the brain showing ischaemic lesions. We performed whole exome sequencing and identified a rare mutation in the Pol III subunit POLR3F. The identified R50W POLR3F mutation is predicted to be damaging by bioinformatics and when tested in functional assays, patient PBMCs exhibited impaired antiviral and inflammatory responses to the PoL III agonist Poly(dA:dT) as well as increased viral replication in patient cells compared to controls. Altogether, these cases add genetic and immunological evidence to the novel association between defects in sensing of AT-rich DNA present in the VZV genome and increased susceptibility to severe manifestations of VZV infection in the CNS in humans.\n\nAbbreviations

immunology↗