Biology subjects

Ma, Y.

Publications and source records attributed to Ma, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

New Evidence of Altered Gut Microbiota in Autism Spectrum Disorders through Metagenomic Analysis

Cumulative evidence suggests alterations of gut microbiota in children with Autism Spectrum Disorder (ASD). However, due to highly diverse research approaches, the distinctive microbial patterns and underlying mechanisms driving ASD etiology remain elusive. Here, we constructed the metagenomic dataset of gut microbiota derived from Chinese children with ASD, incorporating a longitudinal study to explore the pivotal role of gut microbiota in the pathogenesis of ASD. At the bacterial species level, we identified a notable increase in the relative abundance of Clostridium scindens, which exhibited a positive correlation with the cholate degradation pathway and showing a decline concurrent with improved behavior in ASD children. Within the fungal community, we observed significant dysbiosis in twenty-six species, underlining their robust discriminatory potential between ASD and neurotypical subjects. Metabolic pathways related to mitochondrial dysfunction were enriched in ASD, alongside peptidoglycan, glutamate, and nucleotide pathways, suggesting potential interactions between the gut and brain through the innate immune system and vagus nerve in ASD. Our findings underscore the significance of the fungal community and mitochondrial dysfunction in ASD etiology, while also shedding light on how perturbed metabolic functions of gut microbiota collectively contribute to the pathogenesis of ASD.

microbiology↗

bioRxiv2025

Lifestyle and transcriptional signatures associated with ethnicity/race-related variations in the functional connectome

Understanding the variation of functional architecture across individuals and populations is fundamental to advancing our knowledge of human health and behaviour. Yet, while functional organization differences related to ethnicity/race are consistently reported, their underlying mechanisms remain poorly understood. Here, we apply precision individualized functional mapping to systematically investigate ethnicity/race-related differences in the brains intrinsic organization and their associations with lifestyle and transcriptional signatures. We show that variations in network topography and functional connectivity across ethnic/racial groups follow a hierarchical sensorimotor- association axis and are constrained by brain morphology. Importantly, we identify lifestyle factors-- particularly education and substance use--that significantly mediate these associations between ethnicity/race and functional connectivity. Leveraging human brain gene expression data, we further demonstrate that cortical transcriptional patterns are spatially aligned with ethnicity/race-related variability in functional connectivity. Gene ontology analyses of associated genes reveal significant enrichment in biological processes such as synaptic signalling and neuronal system development. Together, these findings uncover a multi-layered framework linking ethnicity/race-related differences in brain function to structural constraints, lifestyle influences, and molecular signatures, and advance a more comprehensive and equitable understanding of human brain diversity.

neuroscience↗

bioRxiv2025

CRISPR-Cas13d-mediated targeting of a context-specific essential gene enables selective elimination of uveal melanoma

Uveal melanoma, the most common eye cancer in adults, remains limited to surgical intervention and chemotherapy, with a dismal survival rate that has not improved in over 50 years. To address this therapeutic impasse, we systematically analyzed public gene expression, RNAi, and CRISPR knockout datasets and identified RASGRP3 as an essential gene specifically for uveal melanoma. RasGRP3 is uniquely overexpressed and essential for survival in uveal melanoma cells, but dispensable in healthy cells. RasGRP3 remains "undruggable" due to its intracellular localization and lack of targetable binding pockets. To overcome this, we developed a CRISPR-Cas13d RNA-targeting therapeutic that specifically knocks down RasGRP3 mRNA. This Cas13d-based therapeutic mediates selective uveal melanoma killing through two synergistic mechanisms: (i) direct silencing of the essential RasGRP3 transcript, and (ii) collateral RNA degradation triggered by the cleavage of overexpressed RasGRP3. When delivered via optimized lipid nanoparticles encoding Cas13d mRNA and guide RNA, this strategy eliminated >97% of uveal melanoma cells while sparing healthy cells, including retinal pigment epithelial cells. This approach outperformed conventional Cas9 and siRNA methods in potency without inducing permanent genomic alterations. Our findings establish a RNA-targeting therapeutic for uveal melanoma and a framework for Cas13d-based interventions against broad "undruggable" cancers.

synthetic biology↗

bioRxiv2025

StCEL-based platform enables detection and sequencing of native sialoglycoRNA

Glycosylated RNAs (glycoRNAs) are an emerging class of biomolecules characterized by glycans attached to RNA molecules. Currently, glycoRNA detection remains largely confined to cellular models, substantially impeding its functional characterization and clinical translation. Here, we developed sialyltransferase-mediated chemical enzymatic labeling (StCEL), in which azido-modified sialic acid was transferred to the natural sialic acid on sialoglycoRNA, enabling the detection of native sialoglycoRNA across diverse biological samples with high specificity and sensitivity. Using StCEL, we found that sialoglycoRNA was significantly upregulated in multiple cancer types. StCEL combined with a microplate reader was applied to detect sialoglycoRNA in large-scale samples, revealing that elevated sialoglycoRNA levels correlate positively with tumor malignancy and poor patient prognosis. Furthermore, StCEL-based sialoglycoRNA enrichment and sequencing identified dysregulated sialoglycoRNAs in tumor tissues. Collectively, StCEL establishes a multifunctional platform that enables sensitive and specific detection of sialoglycoRNA, alongside sequencing analysis, demonstrating significant potential for clinical translation.

molecular biology↗

bioRxiv2025

Mitochondrial Response to Psychological Stress and Its Medial Prefrontal Biomarker Correlates

BackgroundStress response obligates increased mitochondrial activities to meet stress-induced high energy requirement. This stress-mitochondrial response process involves glucocorticoid but also multiple alternative pathways that are top-down regulated by the medial prefrontal cortex (mPFC). These pathways are important for many neuropsychiatric conditions that are sensitive to stress. However, the field lacks a reliable, clinically accessible stress-mitochondrial response paradigm to study the process in humans. MethodWe used an established psychological stress challenge combined with assaying salivary cell-free mitochondrial DNA (cf-mtDNA), thought to reflect heightened mitochondrial changes or disruptions, in 35 healthy individuals (21 males). We also explored if these stress-induced cf-mtDNA marker elevations were associated brain metabolites as measured by magnetic resonance spectroscopy (MRS), as well as high-resolution brain imaging based cortical thickness focusing on the mPFC. ResultsWe found that salivary cf-mtDNA was significant elevated immediately after the stress challenge (p=2.0x10-7) and gradually declined after. Exploratory causal analysis showed that this cf-mtDNA response was not primarily driven by cortisol response. Instead, individuals with higher baseline dACC lactate+ levels, thought to in part reflect mitochondrial dysfunctions, was significantly associated with the cf-mtDNA response (r=0.80, p<0.001). Higher mtDNA response was also significantly associated with thinner dorsomedial prefrontal cortex (r=-0.52, p=0.01). Age had a U-shape effect such that cf-mtDNA response trended lower in earlier adulthood but higher in older people, explaining 33.8% of the ct-mtDNA response variance (p=0.003). ConclusionThis stress challenge-salivary cf-mtDNA assay paradigm may offer a new, non-invasive approach to evaluate the stress-mitochondrial pathway functioning in aging, psychopharmacology, and neuropsychiatric conditions where psychological stress plays a role.

neuroscience↗

bioRxiv2025

Liquid-Liquid Phase Separation of Sp100-HMG: Driving Biogenesis and Functional Diversity of PML Nuclear Bodies

Promyelocytic leukemia nuclear bodies (PML NBs) are membraneless organelles (0.1-1 m) integral to fundamental cellular processes, yet the molecular logic governing their hierarchical organization is unclear. Contrary to the classical "PML-sole-scaffold" model, we identify Sp100-HMG as the unique isoform that autonomously nucleates into liquid-like condensates. Our findings establish an "inside-out" assembly paradigm, where Sp100-HMG initiates a liquid core that recruits PML and other client proteins (DAXX, ATRX) through three distinct cooperative processes: I. Multimerization domain- and intrinsically disordered region (IDR)-mediated LLPS of Sp100-HMG, nucleating the core; II. C-terminal-dependent protein-protein interactions enriching client components; and III. SUMOylation-directed PML recruitment, facilitating the formation of a stabilizing peripheral shell. This assembly paradigm extends beyond Sp100-HMG, as evidenced by ZBTB16--a PML NB-associated oncoprotein implicated in acute promyelocytic leukemia -- adopting an analogous mechanism to organize PML-positive condensates. Using HEp-2 cells as a main model, we show this hierarchical assembly is critical for orchestrating transcriptional programs and cell-cycle dynamics. Together, our study defines a new biogenesis mode for PML-NBs, where a master liquid nucleator coordinates shell integrity and plasticity for nuclear homeostasis. Significance StatementPML nuclear bodies (PML NBs) serve as essential organizers of the cell nucleus, yet the assembly principles underlying their biogenesis and linking it to functional heterogeneity, spatial positioning, and compositional diversity remain elusive. This study overturns the long-standing "PML-centric" view by establishing an LLPS-driven, hierarchical "inside-out" assembly paradigm. We identify Sp100-HMG as a master liquid nucleator that initiates a core to organize the outer PML shell. This inner-core LLPS-driven assembly logic is shared by other PML NB-associated factors, such as the oncoprotein ZBTB16, providing a unified biophysical framework to explain the structural integrity and plasticity of nuclear condensates. Functionally, this organizational process is critical for shaping the compositional diversity and spatial specificity of PML bodies, thereby modulating transcriptional programs and cell-cycle dynamics in a context-dependent manner. These findings offer broad insights into how organized protein condensation sustains nuclear homeostasis and its dysfunction in diseases such as leukemia.

cell biology↗

bioRxiv2025

Blood and Neuronal Extracellular Vesicle Mitochondrial Disruptions in Schizophrenia

The high energy demand of the human brain obligates robust mitochondrial energy metabolism, while mitochondrial dysfunctions have been linked to neuropsychiatric disorders including schizophrenia spectrum disorders (SSD). However, in vivo assessments that can directly inform brain mitochondrial functioning and its etiopathophysiological path to SSD remain difficult to obtain. We hypothesized that system and brain mitochondrial dysfunctions in SSD may be indexed by elevated cell-free mitochondrial DNA (cf-mtDNA) levels in the blood and in neuronal extracellular vesicles (nEVs). We also explored if these mtDNA marker elevations were associated brain metabolites as measured by magnetic resonance spectroscopy (MRS). We examined blood cf-mtDNA in 58 SSD patients and 33 healthy controls, followed by assessing nEV mtDNA and metabolite levels using MRS in a subgroup of patients and controls. We found that people with SSD had significantly elevated cf-mtDNA levels in both the blood (p=0.0002) and neuronal EVs (p=0.003) compared to controls. These mtDNA abnormalities can be linked back to brain lactate+ levels such that higher blood and nEV mtDNA levels were significantly associated with higher lactate+ levels measured at the anterior cingulate cortex (r=0.53, 0.53; p=0.008, 0.03, respectively) in SSD patients. Furthermore, higher developmental stress and trauma were significantly associated with higher cf-mtDNA levels in both the blood and neuronal EVs in SSD patients (r=0.29, 0.49; p=0.01, 0.03, respectively). In conclusion, if replicated and fully developed, blood and neuronal EV-based cell free mtDNA may provide a clinically accessible biomarker to more directly evaluate the mitochondrial hypothesis and the abnormal bioenergetics pathways in schizophrenia.

neuroscience↗

bioRxiv2025

Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally imaged calcium dynamics of grid cells over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting slow plasticity. The backward shifts partially reset daily, reflecting a slower consolidation timescale. While individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics on the same two-dimensional torus. Spatial learning leads to systematic changes and stabilization of their population phase trajectory, including lateral shift, rotation, and phase resets at landmarks, forming a landmark-fragmented representation for the environment. Next, we build an entorhinal-hippocampal model that provides a mechanistic explanation of the diverse phenomena - grid field shifts, increasing fidelity, and fragmentation of the spatial map - and predicts slow Hebbian plasticity in the hippocampus-to-entorhinal pathway. Supporting this, electrophysiology demonstrates that learning-performance-correlated weakening of local inhibition facilitates potentiation of indirect hippocampal inputs to superficial MEC. Together, our study provides multifaceted evidence of slow hippocampus-to-MEC plasticity, elucidating the formation of stable and fragmented cognitive maps that combine internal and cue-driven positional estimates in rich environments during learning. This mechanism may extend to broader memory processes involving this circuit.

neuroscience↗

bioRxiv2025

Genomic Regions and Variant Analysis Reveal Candidate Genes Associated with Age at First Service in Chinese Holstein Heifers

Understanding the genetic basis and identifying quantitative trait loci (QTL) for age at first service (AFS) is essential for improving reproductive efficiency and reducing economic costs in heifers rearing. We conducted a genome-wide association study (GWAS) for AFS using the genomic estimated breeding values (GEBVs) of 3,686 Chinese Holstein heifers, genotyped with 7,964,217 single nucleotide polymorphisms (SNPs) after quality control. Significant SNPs and candidate genes were identified and investigated through colocalization analysis of GWAS, expression QTL (eQTL), and splicing QTL (sQTL), and expression analysis in blood RNA sequencing (RNA-seq). The heritability estimate for AFS was moderate at 0.276 {+/-}0.025. Three QTL regions associated with AFS were identified: Region 1 on BTA6 (43688837-45007127 bp, 1.3 Mb with three 200kb windows), explaining 0.47% of genetic variance; Region 2 on BTA6 (62770788-62967316 bp) explaining 0.27% of the genetic variance; and Region 3 on BTA18 (6299721-6498934 bp) explaining 0.17% of the genetic variance. Combining GWAS and colocalization analysis, we identified ANAPC4, RBPJ, SEPSECS, SLC34A2, ZCCHC4, CCDC149, GNPDA2, GUF1, DHX15, SOD3, GUF1 and GNPDA2 as candidate genes. These genes are enriched in signaling pathways such as progesterone-mediated oocyte maturation, parathyroid hormone synthesis, secretion and action, and selenocompound metabolism. ANAPC4, DHX15, GUF1, SEPSECS, and SOD3 were also differently expressed genes (DEGs) in blood RNA-seq. Integrating the GWAS, colocalization, differential expression analysis, and existing literature, ANAPC4 and rs136363104 were highlighted as the putative causal gene and variant for puberty, respectively. In conclusion, our study identified three candidate regions and 12 candidate genes, confirming ANAPC4 as a putative causal gene influencing AFS. This research enhances the understanding of the genetic basis of AFS in Chinese Holstein heifers. The identified key genomic regions, candidate genes, and variants have the potential to improve reproductive efficiency and reduce economic costs in heifer rearing. Interpretative summaryThe economic burden of heifer-raising and reproductive inefficiency in dairy cattle is evident. The most important strategy for optimizing heifer-raising is selecting heifers with earlier puberty (sexual maturity) to shorten age at first service (AFS). In this study, we have identified key genomic regions and candidate genes on AFS in Chinese Holstein heifers by genome-wide association study, and validated them by colocalization and RNA-seq analysis. The findings have the potential to enhance the understanding of the genetic basis of reproductive traits, leading to more targeted breeding strategies for improved reproductive efficiency.

genetics↗

bioRxiv2025

Keystone Bacterial Taxa Drive Denitrification and N2O Emission via Adaptive Genomic and Metabolic Strategies in Contrasting Agricultural Soils

Soil denitrification mediated by microbial communities is a major driver of nitrous oxide (N2O) emissions, yet the regulatory roles of keystone taxa remain largely unexplored, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, providing a unique model system for disentangling microbial mechanisms underlying soil-specific denitrification dynamics. Here, we integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the above mentioned two contrasting agricultural soils, BS and FS. Structural equation modeling (SEM) and correlation analyses revealed that keystone taxa are significantly associated with soil denitrification rates and N2O emission patterns. Among these, Ramlibacter ASV104 was identified as a conserved keystone in both soils, exhibiting genomic potential for key denitrification genes (nirK/nirS/norB/nosZ) to mediate N2O turnover. In contrast, Ensifer ASV205 was a FS-specific keystone taxon, exhibiting strain-level niche specialization. Comparative genomics revealed that variations in denitrification gene composition and carbon-nitrogen metabolism enable different Ensifer strains to function either as N2O sources or sinks. This functional divergence was linked to their genomic plasticity and growth strategies under nutrient-rich conditions. Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study improves our understanding of the microbial mechanisms driving N2O emissions and provides a foundation for future strategies targeting microbial taxa to mitigate N2O emissions in agricultural soils. IMPORTANCEThis study provides new insights into the ecological complexity underlying soil N2O emissions by integrating strain-level diversity, genomic attributes, and microbial interaction networks. Key microbial taxa involved in denitrification and N2O emissions were identified in black soil and fluvo-aquic soil. By combining network-based ecological modeling and functional assays, it is revealed that taxa such as Ramlibacter ASV104 and Ensifer ASV205 play significant roles in regulating N2O emissions. Strain-level functional diversity within the keystone taxa of Ensifer ASV205 highlights their varying contributions to nitrogen cycling. Our findings provide a deeper understanding of the microbial mechanisms governing N2O emissions, offering valuable insights for developing microbial-based strategies to mitigate N2O emissions in agricultural soils in the future.

ecology↗

bioRxiv2025

Characterization and Genome Insights of Two Novel Plastic-Degrading Acinetobacter Species

The ubiquitous presence of Acinetobacter species in the environment holds significant biotechnology potential, particularly in the degradation of various pollutants. In this study, we present two plastic-degrading bacteria, strains CAAS 2-6T and CAAS 2-13T, isolated from landfill leachate and a strawberry farmland, respectively. Strain CAAS 2-6T showed the highest 16S rRNA sequence similarity (97.7%) with Acinetobacter gerneri DSM 14967T, while strain CAAS 2-13T was most closely related (99.6%) to Acinetobacter gerneri PS-1T. Phylogenetic analysis of 16S rRNA and gyrB-rpoB genes placed both strains on distinct branches. Genomic comparisons revealed the highest digital DNA-DNA hybridization (dDDH) / average nucleotide identity (ANI) values for CAAS 2-6T with Acinetobacter indicus CIP 110367T (22.7%/77.0%) and for CAAS 2-13T with Acinetobacter gerneri PS-1T (66.5%/96.0%). Based on phenotypic and chemotaxonomic data, we propose strain CAAS 2-6T as the novel species Acinetobacter lentus sp. nov. (type strain CAAS 2-6T = GDMCC 1.3951T = JCM 36321T = KCTC 8156T), and strain CAAS 2-13T as the novel subspecies Acinetobacter kanungonis subsp. fragariae subsp. nov. (type strain CAAS 2-13T = GDMCC 1.3956T = JCM 36322T = KCTC 8157T). Both strains utilized PLA, PBSA, PBS, PBAT, and PBT as sole carbon sources, with CAAS 2-6T exhibiting superior growth on PBSA, PBS, and PBAT. Genomic annotation identified genes encoding plastic-degrading enzymes multicopper oxidase AbMCO and alkane hydroxylase AlkB. Enzymatic depolymerization assays confirmed in vitro production of plastic monomers. These findings expand the known metabolic capabilities of Acinetobacter and provide promising new candidates for plastic bioremediation. IMPORTANCEAcinetobacter spp. demonstrate significant potential for plastic bioremediation. We characterize two novel strains: CAAS 2-6T (A. lentus sp. nov.) and CAAS 2-13T (A. kanungonis subsp. fragariae subsp. nov.), capable of degrading five major polyesters (PLA, PBAT, PBT, PBS, PBSA) as sole carbon sources. Genomic and enzymatic analyses identified multicopper oxidase (AbMCO) and alkane hydroxylase (AlkB) as key depolymerase. This work: (i) Expands plastic-degrading Acinetobacter diversity; (ii) Provides novel biocatalysts and genomic resources; (iii) Delivers engineerable microbial chassis.

microbiology↗

bioRxiv2025

Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids

A bioengineered kidney using a decellularized kidney scaffold (DKS) offers a promising solution to the kidney shortage. However, the transplantation of bioengineered kidneys using DKS recellularized with human endothelial, renal cells or others has not yet successfully achieved the vascular and renal reconstruction in vivo. In this study, we identified another type of stem cells, designated as human placenta-derived angiogenic stem cells (hPASCs), which serve as seeding cells for the vascularization of DKS. These hPASCs encompass angiogenic subpopulations, exhibit both stem cell properties and the capacity for vascular differentiation. Human fetal kidney organoids (KIO) were established as a source of renal parenchymal cells, comprising renal, immune, and vascular cell populations. We developed a vascularized bioengineered kidney by recellularizing DKS with hPASCs and KIO using a circulation perfusion culture system. The hPASCs bioengineered kidney demonstrated enhanced angiogenesis and reconstructed renal architecture in vivo, by transplantation into rat models of renal subcapsular and partial nephrectomy. Furthermore, immunofluorescence and single-cell analyses revealed that the hPASCs revascularized bioengineered kidney regenerated both vascular and renal parenchymal cells within the host. This study offers another strategy for kidney bioengineering and regeneration.

bioengineering↗

bioRxiv2025

Thioredoxin-1 inhibits granulosa cell ferroptosis to rescue ovarian aging through mitophagy-dependent activation of BNIP3L

Ovarian aging is closely associated with a decline in fertility and an increase in reproductive dysfunction. Ovarian granulosa cells (GCs) support oocyte homeostasis and development, yet insight into GC dysfunction during aging is limited. Here, we show that aged GCs of humans and mice have indications of elevated ferroptosis, including increased ferroptosis-related metabolites, lipid peroxidation, and iron accumulation. The ferroptosis inhibitor Ferrostatin-1 reversed ovarian impairment and fertility of aged mice in vivo. We show that the age-related reduction in the expression of TXN (thioredoxin) leads to ferroptosis in human and mouse GCs by blocking BNIP3L-dependent mitophagy. Exogenous activation of TXN could promote mitophagy, thereby clearing excessive ROS and inhibiting ferroptosis. These results suggest that anti-ferroptosis-related treatments may assist in treating aging-related reproductive disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/664497v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1b97e8forg.highwire.dtl.DTLVardef@123f8d0org.highwire.dtl.DTLVardef@a44c61org.highwire.dtl.DTLVardef@92b32e_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsO_LIFerroptosis signatures are upregulated in aged GCs from human and mouse ovaries C_LIO_LITXN is deregulated in aged GCs, leading to mitochondrial and ROS metabolic dysfunction C_LIO_LITXN binds to DNA to regulate autophagy and mitophagy genes, including BNIP3L C_LIO_LIInhibition of ferroptosis can ameliorate GC dysfunction C_LI

cell biology↗

bioRxiv2025

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of analysis designed to meet diverse research needs. PromptGenie is a multi-agent system that enables stepwise, human-in-the-loop workflows using prevalidated domain-standard tools. Within PromptGenie, specialized agents--including DataAgent, OmicsAgent, AnalysisAgent, and QAgent--collaborate to manage tasks such as data ingestion, pipeline execution, statistical analysis, and interactive summarization. DiscoverFlow provides integrated, automated workflows for large-scale multi-omics analysis, offering end-to-end execution and streamlined orchestration. ToolsGenie complements these modes by dynamically generating executable bioinformatics code for custom, user-defined analyses, enabling flexibility beyond standardized workflows. PromptGenie and DiscoverFlow leverage a suite of domain-specific tools, including Omics Tools for standardized omics pipelines, Analysis Tools for downstream statistical interpretation, and MLGenie for machine learning and multi-omics modeling. We present the design, capabilities, and validation of these components, highlight their integration into automated and customizable workflows, and discuss extensibility, monitoring, and compliance. PromptBio aims to democratize high-throughput bioinformatics through a large language model-powered, natural language understanding, workflow generation and agent orchestration.

bioinformatics↗

bioRxiv2025

Global analysis of membrane protein S-acylation in the model plant Arabidopsis thaliana

Protein S-acylation is the addition of fatty acids to the cysteine residues in a protein, catalyzed by protein S-acyltransferases (PATs). Despite extensive research on protein S-acylation in animals, our understanding of this process in plants remains limited. In this study, we sought to characterize the S-acylproteome of membrane proteins in Arabidopsis and identify potential substrates for two important plant immunity-related PATs (PAT5 and PAT9). To achieve this, S-acylated membrane proteins were first enriched via our optimized acyl-biotinyl exchange strategies at both the protein-level and peptide-level. The enriched samples were then analyzed by label-free quantitative liquid chromatography-mass spectrometry. The results from the two enrichment methods demonstrated that they were complementary in identifying S-acylated proteins and S-acylation sites. Using these methods, over 2500 S-acylation sites in more than 2000 putative S-acylated proteins were identified. Proteins involved in vesicle trafficking, plant phosphorylation, immune responses, and signal transduction pathways were significantly enriched. Additionally, certain amino acid patterns surrounding the S-acylation sites were identified. Comparisons of the S-acylproteomes between the wild type and the PAT5 and PAT9 mutants revealed over 100 potential substrates for both S-acyltransferases. The high quality of our data was supported by the significant overlap with the previously reported data and successful experimental verification of selected candidate proteins. Overall, our study revealed a well-represented S-acylproteome for Arabidopsis (especially its membrane proteins) and identified potential substrates for PAT5 and PAT9. These findings will facilitate the functional characterization of S-acylated proteins in plants.

plant biology↗

bioRxiv2025

Structure and function of a cross-neutralizing influenza neuraminidase antibody that accommodates recent N2 NA Asn245 glycosylation

Monoclonal antibodies (mAbs) that recognize and inhibit a diverse range of influenza viruses, although relatively rare, have been isolated following infection or vaccination. Study of their ontology and mechanisms of action informs universal vaccine and therapeutic development. We have previously described a potent and broad neuraminidase (NA)-neutralizing human mAb, 1122A11, that neutralizes a wide range of H3N2 viruses. Here, further characterization of 1122A11 reveals reactivity to cross-group influenza A virus NAs, including group-1 N1 and N8, and group-2 N2 and N3 NAs. Recent H3N2 viruses have acquired Asn245 glycosylation on the active site rim. Crystal structures of an N2 NA from A/Singapore/INFIMH-16-0019/2016 (H3N2) at 2.3 [A] (apo) and 2.2 [A] (Fab bound) resolution showed that 1122A11 binding causes local changes to the periphery of NA active site to accommodate the glycan. The CDRH3 of 1122A11 inserts into the active site and mimics the substrate sialic acid. We then determined that the ability of 1122A11 to protect from lethal challenge in mice is not dependent on Fc-effector function. These results highlight the therapeutic potential of 1122A11 as a broad protective anti-viral and reinforce pursuit of immunogen development of NA antibodies toward achieving more universal influenza protection.

immunology↗

bioRxiv2025

An atlas of cell type specific regulatory effects in cattle

Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding.

genetics↗

bioRxiv2025

Single cell analysis of HIV expression and integration sites reveals robust viral expression across diverse chromatin environments

Entry of HIV into latency is determined by a combination of factors, including fluctuations in the viral Tat protein, as well as the transcriptomic phenotype of the host cell. Determining the impact of the proviral integration site on viral expression has been challenging due to difficulty in measuring integration site and viral expression from the same cell. To investigate the influence of the HIV integration site on HIV expression, we analyzed a combined scRNAseq/scATACseq dataset from 117,610 HIV infected primary CD4 T cells. We used the scATACseq data to recover HIV integration site information from 1530 cells, and correlated this information with viral RNA reads in the scRNAseq data. We observed that, overall, HIV expression did not differ depending on the genomic features of viral integration, such as genic vs non genic, intron vs exon and forward versus reverse orientation. Furthermore, we found that there was no significant difference in HIV expression across 15 distinct chromatin compartments. Additionally, analysis of expression for host genes that were the target of proviral integration revealed strong upregulation of expression of the targeted host gene in [~]5% of the infected cells. This insertional activation occurred almost exclusively when HIV was integrated in the same orientation as the host cell gene and occurred as a result of integration within diverse positions across a gene. These findings suggest that HIV expression is relatively robust to the genomic context of the HIV integration site, and that HIV can strongly upregulate expression of integration site genes during infection.

microbiology↗