Biology subjects

Feng, B.

Publications and source records attributed to Feng, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

DNA Methylation in Sex Chromosomes and Genes under Selection Underpins the Emergence of Sexual Size Dimorphism

Sexual size dimorphism (SSD) refers to the differences in body size between males and females. Epigenetics such as methylation contribute to shaping phenotypes, nevertheless, their role in SSD is still unclear. Here, we used Cynoglossus semilaevis, a species with larger females known as female-biased SSD, as a model to investigate the role of methylation in the emergence and regulation of SSD. Methylomes and transcriptomes were constructed in four tissues (brain, liver, muscle, and gonad) from three key life stages: juveniles (3-months post fertilization), male mature stage (1-year post fertilization; ypf), and female mature stage (3 ypf). In 1 ypf and 3 ypf females showed lower methylation, while the number of differentially methylated regions between sexes increased during the lifetime. Genes at the top of the growth hormone/insulin-like growth factor (GH/IGF) axis and hypothalamus-pituitary-gonadal axis (gh1, igf1, gnrhr2r-like, err{gamma}, etc.) showed differential methylation between sexes, consistent with sex-related differences in growth. The female-specific W chromosome showed higher methylation than the autosomes or the Z chromosome. Genes of the IGF signaling network that negatively regulate growth and located on W chromosome were hyper-methylated than their Z homologs. Furthermore, genes with a faster evolutionary rate in C. semilaevis exhibited lower methylation levels than the background genes, suggesting an important evolutionary role for DNA methylation in shaping SSD. Our results provide a comprehensive depiction of methylation regulation of SSD in vertebrates, and improve our understanding of how methylation regulation can help organisms to respond to natural selection, and allocate resources between the sexes.

developmental biology↗

bioRxiv2025

Methods for Quantitative Analyses of Nerve Fiber Deformation in the Myenteric Plexus Under Loading of Mouse Distal Colon and Rectum

Visceral pain in the large bowel is a hallmark of irritable bowel syndrome (IBS) and the primary reason patients seek gastroenterological care. Notably, mechanical distension of the distal colon and rectum (colorectum) reliably evokes abdominal pain and thus understanding mechanotransduction of sensory nerve endings (nerve fibers) in the colorectum is crucial for understanding and treating IBS-related bowel pain. To facilitate such understanding we aimed to establish novel methods to mechanically test, image, and analyze large-strain deformations of networks of nerve fibers in the myenteric plexus of the colorectum, and thus enable quantitative analyses. We successfully delivered circumferential deformation (force or displacement driven) to intact segments of colorectum while maintaining the myenteric plexus in focus during fluorescent imaging to capture the deforming nerve fibers. We also established a semi-automated method to recapitulate the network morphology and a code to calculate the stretch ratios of individual nerve fibers deforming within the myenteric plexus of mouse colorectum. Our code allows plotting of stretch ratios for each fiber, stretch ratios vs. fiber angle, and stretch ratios vs. fiber length. Our methods not only facilitate analyses of deformations of networks of colorectal nerve fibers in the context of visceral nociception but are also applicable to analyzing the in-plane deformation of other two-dimensional fiber networks. We provide free, public access to our analysis code for MATLAB, including input files for a simple test case, at github.uconn.edu/imLab/Fiber-Network_Analyses.

bioengineering↗

bioRxiv2025

Colorectum and Embedded Networks of Nerve Fibers Present Auxetic Responses During Uniaxial Circumferential Extension

Understanding the multiscale mechanics of the colorectum is essential for uncovering the mechanotransductive pathways underlying visceral nociception. Intraluminal distension of the large intestine reliably evokes pain in disorders of gut-brain interaction (DGBIs), yet the tissue-level and nerve fiber-level responses to mechanical loading remain poorly defined. Here, we present results from a novel biomechanical testing framework that integrates uniaxial circumferential extension with high-resolution optical imaging to quantify deformation in both bulk colorectal tissue and embedded sensory nerve fibers. We tested intact, cylindrical colorectal segments from mice using a custom 3-D-printed chamber with intraluminal stainless-steel rods to apply circumferential stretch while maintaining a planar imaging field. We measured bulk-tissue deformation via Digital Image Correlation (DIC), while we assessed stretch in nerve fibers through fluorescence imaging of VGLUT2-labeled afferents analyzed using a custom fiber-network analyses. Across specimens, we observed a consistent auxetic response-characterized by positive axial strain during circumferential extension-at both the macroscale and microscale. Five out of six colorectal specimens exhibited positive axial Green-Lagrange strain (Exx), with an average median Exx of 0.0177, during circumferential extension generating an average median Eyy of 0.1273. Nerve fiber analysis across nine specimens revealed an average median stretch ratio of 1.0631, indicating 6.31% elongation, with substantial heterogeneity driven by fiber orientation. These findings demonstrate that the colorectum and its embedded network of nerve fibers exhibit auxetic behavior, a property that may amplify mechanical signaling and influence nociceptive signaling. Our methods and results provide foundational insight into structure-function relationships of colorectum and inform design of bioinspired auxetic materials.

bioengineering↗

bioRxiv2025

Metabolic reinvigoration of NK cells by IL-21 enhances immunotherapy against MHC-I deficient solid tumors

Natural killer (NK) cells, a type of potent cytotoxic lymphocytes, are particularly promising for the treatment of cancers that lose or downregulate major histocompatibility complex class I (MHC-I) expression to evade T cell-mediated immunotherapy. However, the hostile and immune suppressive tumor microenvironment (TME) greatly hinders the function of tumor-infiltrating NK cells limiting the therapeutic efficacy against solid tumors. Here, we show that a fusion protein of interleukin-21 (IL-21-Fc), as a direct in vivo intervention, can safely and effectively reprogram NK cell metabolism and enhance their effector function in the TME. Our research demonstrates that combining IL-21-Fc with IL-15 superagonist (IL-15SA) or NK cell transfer leads to the eradication of MHC-I-deficient tumors and confers durable protection in syngeneic and xenograft tumor models. Mechanistically, we uncover that IL-21-Fc enhances NK cell effector function by upregulating glycolysis in a lactate dehydrogenase A (LDHA)-dependent manner. These findings not only underscore the considerable potential of IL-21-Fc as an in vivo therapeutic intervention to bolster NK cell-based immunotherapy, but also unveil an innovative strategy of metabolic reprogramming for NK cell rejuvenation within tumors. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/643961v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@daf24forg.highwire.dtl.DTLVardef@5a5029org.highwire.dtl.DTLVardef@144c978org.highwire.dtl.DTLVardef@106ed1c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINK cells display functional exhaustion in MHC-I deficient solid tumors C_LIO_LIIL-21-Fc as an in vivo-applicable and safe immunotherapy reinvigorates intratumoral NK cells for enhanced effector function C_LIO_LIIL-21-Fc enhances NK cell function by elevating glycolysis in a LDHA-dependent manner C_LIO_LICombining IL-21-Fc with low-dose IL-15SA or NK cell transfer eradicates syngeneic and xenografted solid tumors C_LI

cancer biology↗

bioRxiv2025

A foundation model for protein-ligand affinity prediction through jointly optimizing virtual screening and hit-to-lead optimization

The structure of the protein binding pocket governs the ligand binding affinity by providing crucial intermolecular interactions and spatial compatibility. While existing methods have leveraged these structural insights to advance affinity prediction, they often treat virtual screening and hit-to-lead optimization separately, mainly due to incompatible speed-accuracy requirements. However, these two tasks complement each other, and their integration enables broader chemical exploration while preserving focus on affinity-determining substructures. Here, we present LigUnity, a foundation model for affinity prediction that jointly embeds ligands and pockets into a shared space. In particular, LigUnity learns coarse-grained active/inactive distinction through scaffold discrimination and fine-grained pocket-specific ligand preference through pharmacophore ranking. We demonstrate the effectiveness and versatility of LigUnity on eight benchmarks across six settings. In virtual screening, LigUnity outperforms 24 methods with >50% improvement and demonstrates robust generalization to novel targets. In hit-to-lead optimization, it achieves state-of-the-art performance across split-by-time, split-by-scaffold, and split-by-unit settings, emerging as a cost-efficient alternative to free energy perturbation. We further showcase how LigUnity can be employed in an active learning framework for TYK2 to efficiently find optimal ligands. Collectively, these results establish LigUnity as a versatile foundation model for affinity prediction, offering broad applicability across the drug discovery pipeline.

bioinformatics↗

bioRxiv2024

Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injury

Wound healing after spinal cord injury involves highly coordinated interactions among multiple cell types, which is poorly understood. Astrocytes play a central role in creating a border against the non-neural lesion core. To do so, astrocytes undergo dramatic morphological changes by first thickening the processes and then elongating and overlap them. We show here show that the expression of a cell-surface receptor, Ryk, is induced in astrocytes after injury in both rodent and human spinal cord. Astrocyte-specific knockout of Ryk dramatically elongated the reactive astrocytes and accelerated the formation of the border and reduced the size of the scar. Astrocyte-specific knockout of Ryk also accelerated the injury responses of multiple cell types, including the resolution of neuroinflammation. Single cell transcriptomics analyses revealed a broad range of changes cell signaling among astrocytes, microglia, fibroblasts, endothelial cell, etc, after astrocyte-specific Ryk knockout, suggesting that Ryk not only regulates the injury response of astrocytes but may also regulate signals which coordinate the responses of multiple cell types. The elongation is mediated by NrCAM, a cell adhesion molecule induced by astrocyte-specific conditional knockout of Ryk after spinal cord injury. Our findings suggest a promising therapeutic target to accelerate wound healing and promote neuronal survival and enhance functional recovery.

neuroscience↗

bioRxiv2024

Suppression of Visceral Nociception by Selective C-Fiber Transmission Block Using Temporal Interference Sinusoidal Stimulation

Chronic visceral pain management remains challenging due to limitations in selective targeting of C-fiber nociceptors. This study investigates temporal interference stimulation (TIS) on dorsal root ganglia (DRG) as a novel approach for selective C-fiber transmission block. We employed (1) GCaMP6 recordings in mouse whole DRG using a flexible, transparent microelectrode array for visualizing L6 DRG neuron activation, (2) ex vivo single-fiber recordings to assess sinusoidal stimulation effects on peripheral nerve axons, (3) in vivo behavioral assessment measuring visceromotor responses (VMR) to colorectal distension in mice, including a TNBS-induced visceral hypersensitivity model, and (4) immunohistological analysis to evaluate immediate immune responses in DRG following TIS. We demonstrated that TIS (2000 Hz and 2020 Hz carrier frequencies) enabled tunable activation of L6 DRG neurons, with the focal region adjustable by altering stimulation amplitude ratios. Low-frequency (20-50 Hz) sinusoidal stimulation effectively blocked C-fiber and A{delta}-fiber transmission while sparing fast-conducting A-fibers, with 20 Hz showing highest efficacy. TIS of L6 DRG reversibly suppressed VMR to colorectal distension in both control and TNBS-induced visceral hypersensitive mice. The blocking effect was fine-tunable by adjusting interfering stimulus signal amplitude ratios. No apparent immediate immune responses were observed in DRG following hours-long TIS. In conclusion, TIS on lumbosacral DRG demonstrates promise as a selective, tunable approach for managing chronic visceral pain by effectively blocking C-fiber transmission. This technique addresses limitations of current neuromodulation methods and offers potential for more targeted relief in chronic visceral pain conditions.

neuroscience↗

bioRxiv2024

Discovery of novel 1,4-dicarbonylthiosemicarbazides as DNA gyrase inhibitors for the treatment of MRSA infection

Antibiotic resistance has become a serious threat to public health, thus novel antibiotics are urgently needed to combat drug-resistant bacteria including MRSA (methicillin-resistant S. aureus). The 1,4-dicarbonylthiosemicarbazide is an interesting chemotype that could exhibit antibacterial activity. However, the currently available compounds are not as potent as clinical antibiotics. Herein, we adopted the computer-aided drug design strategy, substructure search, to retrieve antibacterial 1,4-dicarbonylthiosemicarbazide derivatives, and identified compound B5 (Specs ID: AG-690/15432331) from the Specs chemical library that exhibited moderate activity (minimum inhibitory concentration (MIC): 6.25 {micro}g/mL) against S. aureus (ATCC 29213). Based on that compound, we further designed and synthesized 45 derivatives, and evaluated their antibacterial activity. Eight derivatives were more potent than or equivalent to vancomycin (MIC: 1.56 {micro}g/mL). We compared the three most potent ones for their cytotoxicity to HepG2 and HUVEC cells and selected compound 1b as our lead compound for comprehensive biological evaluation. As a result, compound 1b exhibited a bacteriostatic mode, and was active against a panel of gram-positive bacteria strains, metabolically stable, and effective to protect the mice from MRSA infection. More importantly, we applied 2D similarity calculation and reverse docking to predict potential targets of compound 1b. Through experimental validation and molecular dynamics simulation, we were able to confirm that compound 1b inhibited S. aureus DNA gyrase (IC50: 1.81 {micro}M) and DNA supercoiling, potentially by binding to the ATPase domain, where ASP81, GLU58 and GLN91 formed key hydrogen bonds. Taken together, we have discovered a new class of DNA gyrase inhibitors represented by compound 1b for the treatment of MRSA infection, through the design, synthesis, and biological evaluation of novel 1,4-dicarbonylthiosemicarbazides. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/611349v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@549dadorg.highwire.dtl.DTLVardef@13bff64org.highwire.dtl.DTLVardef@1fc2c00org.highwire.dtl.DTLVardef@acee76_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAn interesting 1,4-dicarbonylthiosemicarbazide derivative B5 with moderate antibacterial activity for S. aureus was discovered by substructure search. C_LIO_LIBased on B5, 45 new 1,4-dicarbonylthiosemicarbazides were designed, synthesized and biologically evaluated, which led to the discovery of a promising lead compound 1b. C_LIO_LICompound 1b exhibited good antibacterial activity for a panel of gram-positive bacteria strains, and was effective to protect mice from MRSA infection. C_LIO_LIThe 1,4-dicarbonylthiosemicarbazides represented by compound 1b were discovered as a new class of DNA gyrase inhibitors, by target prediction and experimental validation. C_LI

pharmacology and toxicology↗

bioRxiv2024

A bone-derived protein primes rapid visual escape via GPR37 receptor in a subpopulation of VTA GABAergic neurons

Rapid escape against visual threats is critical for survival. Whether it requires a permissive mechanism is unknown. Here, we show that osteocalcin (OCN), a protein produced by bone and persisted in the brain, primes rapid visual escape response by increasing excitability of VTA GABAergic neuron subpopulation via OCN-GPR37-cAMP-THIK-1 (K2P13.1) pathway. Knock-out of OCN or its receptor GPR37, and conditional knock-out of GPR37 in VTA GABAergic or glutamatergic neurons caused delayed escape. Reconstituting OCN-GPR37 signaling specifically in VTA was sufficient to restore normal response. Single-cell transcriptomics combined with electrophysiology showed that OCN decreases potassium currents in a subpopulation of VTA GABAergic neurons via GPR37-induced cAMP reduction and subsequent THIK-1 suppression. This elevation of excitability in VTA neuron subpopulation can be recapitulated by HM4Di, an inhibitory chemogenetic GPCR commonly used to suppress neuronal activity. Our study demonstrated that visual behavior requires a bone-derived protein that tunes electrophysiology of central nervous system neurons. Graph AbstractO_ST_ABSIn briefC_ST_ABSThe bone-brain axis regulates visual escape behavior. Osteocalcin (OCN), a small protein secreted by bone, plays a permissive role in rapid visual escape. This is achieved through GPR37 receptor expressed in a subpopulation of VTA GABAergic neurons. OCN-GPR37 signaling increases neuronal excitability by decreasing K+ current via THIK-1 channel suppression. HighlightsO_LIThe bone-derived protein osteocalcin and its receptor GPR37 in VTA are required for rapid visual escape response. C_LIO_LIGPR37 is expressed in a subpopulation of VTA GABAergic neurons and primes rapid visual escape. C_LIO_LIOsteocalcin-GPR37 signaling increases neuronal excitability by suppressing THIK-1 (K2P13.1) channel via cAMP reduction. C_LIO_LIActivation of HM4Di increases excitability of subpopulation of VTA GABAergic neurons and enhances rapid visual escape. C_LI O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/607510v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1b7ef5dorg.highwire.dtl.DTLVardef@c3eea2org.highwire.dtl.DTLVardef@167dd75org.highwire.dtl.DTLVardef@1fc5613_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses--commensurate with a narrowing of metabolic niche breadth--but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

evolutionary biology↗

bioRxiv2024

CircRNA_012164/MicroRNA-9-5p axis mediates cardiac fibrosis in diabetic cardiomyopathy

Noncoding RNAs play a part in many chronic diseases and interact with each other to regulate gene expression. MicroRNA-9-5p (miR9) has been thought to be a potential inhibitor of diabetic cardiomyopathy. Here we examined the role of miR9 in regulating cardiac fibrosis in the context of diabetic cardiomyopathy. We further expanded our studies through investigation of a regulatory circularRNA, circRNA_012164, on the action of miR9. We showed at both the in vivo and in vitro level that glucose induced downregulation of miR9 and upregulation of circRNA_012164 resulted in the subsequent upregulation of downstream fibrotic genes. Further, knockdown of circRNA_012164 shows protective effects in cardiac endothelial cells and reverses increased transcription of genes associated with fibrosis and fibroblast proliferation through a regulatory axis with miR9. This study presents a novel regulatory axis involving noncoding RNA that is evidently important in the development of cardiac fibrosis in diabetic cardiomyopathy.

pathology↗

bioRxiv2023

Identification of arginine-vasopressin receptor 1a (Avpr1a/AVPR1A) as a novel candidate gene for chronic visceral pain.

Chronic abdominal pain in the absence of ongoing disease is the hallmark of disorders of gut-brain interaction (DGBIs), including irritable bowel syndrome (IBS). While the etiology of DGBIs remains poorly understood, there is evidence that both genetic and environmental factors play a role. In this study, we report the identification and validation of Avpr1a as a novel candidate gene for visceral hypersensitivity (VH), a primary peripheral mechanism underlying abdominal pain in DGBI/IBS. Comparing two C57BL/6 (BL/6) substrains (C57BL/6NTac and C57BL/6J) revealed differential susceptibility to the development of chronic VH following intrarectal zymosan (ZYM) instillation, a validated preclinical model for post-inflammatory IBS. Using whole genome sequencing, we identified a SNP differentiating the two strains in the 5 intergenic region upstream of Avpr1a, encoding the protein arginine-vasopressin receptor 1A (AVPR1A). We used behavioral, histological, and molecular approaches to identify distal colon- specific gene expression differences and neuronal hyperresponsiveness covarying with Avpr1a genotype and VH susceptibility. While the two BL/6 substrains did not differ across other gastrointestinal (GI) phenotypes (e.g., GI motility), VH-susceptible BL/6NTac mice had higher colonic Avpr1a mRNA and protein expression. Moreover, neurons of the enteric nervous system were hyperresponsive to the AVPR1A agonist AVP, suggesting a role for enteric neurons in the pathology underlying VH. These results parallel our findings that patients colonic Avpr1a mRNA expression was higher in patients with higher pain ratings. Taken together, these findings implicate differential regulation of Avpr1a as a novel mechanism of VH-susceptibility as well as a potential therapeutic target specific to VH. SummaryA combination of approaches, from genomic analysis to functional analyses, confirm Avpr1a as a high priority candidate gene for visceral pain.

genetics↗

bioRxiv2023

A foundation model for bioactivity prediction using pairwise meta-learning

Compound bioactivity plays an important role in different stages of drug development and discovery. Existing machine learning approaches have poor generalization ability in compound bioactivity prediction due to the small number of compounds in each assay and incompatible measurements among assays. Here, we propose ActFound, a foundation model for bioactivity prediction trained on 2.3 million experimentally-measured bioactivity compounds and 50, 869 assays from ChEMBL and BindingDB. The key idea of ActFound is to employ pairwise learning to learn the relative value differences between two compounds within the same assay to circumvent the incompatibility among assays. ActFound further exploits meta-learning to jointly optimize the model from all assays. On six real-world bioactivity datasets, ActFound demonstrates accurate in-domain prediction and strong generalization across datasets, assay types, and molecular scaffolds. We also demonstrated that ActFound can be used as an accurate alternative to the leading computational chemistry software FEP+(OPLS4) by achieving comparable performance when only using a few data points for fine-tuning. The promising results of ActFound indicate that ActFound can be an effective foundation model for a wide range of tasks in compound bioactivity prediction, paving the path for machine learning-based drug development and discovery.

bioinformatics↗

bioRxiv2023

The rapid diversification of Boletales is linked to Early Eocene and Mid-Miocene Climatic Optima

O_LIInvestigating the mechanisms that underpin the diversity and distribution patterns of species is fundamental in ecology and evolution. However, the study of fungi, particularly the ectomycorrhizal group, has been relatively constrained in this field. C_LIO_LIWe conducted a high-resolution phylogenomic analysis of Boletales, an ecologically and economically significant group of fungi, covering 83 genera across 15 families. We subsequently investigated its evolutionary history using sequences at four genes obtained from 984 species across 121 genera within 15 families. C_LIO_LIThe findings unveiled that Boletales likely originated in Early Jurassic and underwent two remarkable episodes of rapid diversification, commencing in early Eocene ([~]54 Mya) and early Miocene ([~]17 Mya) epochs. The notable surges were predominantly driven by ectomycorrhizal clades, with a specific emphasis on East Asia and North America. These expansions were strongly correlated with the warm-humid paleoclimates during the Early Eocene Climatic Optimum and Mid-Miocene Climatic Optimum, as well as the rapid expansion of Fagales and Pinaceae hosts. C_LIO_LIThis study provides novel insights into the spatiotemporal evolution of fungi, highlighting the synergistic impact of abiotic factors, such as warm and humid paleoclimates, and the biotic factor of rapid diversification of host plants on the fungal diversification. C_LI

evolutionary biology↗

bioRxiv2023

Morphological, molecular, and functional characterization of mouse glutamatergic myenteric neurons

The enteric nervous system (ENS) functions largely independently of the central nervous system (CNS). Correspondingly, glutamate, the dominant neurotransmitter in the CNS and sensory afferents, is not a primary neurotransmitter in the ENS. Only a fraction (approximately 2%) of myenteric neurons in the mouse distal colon and rectum (colorectum) are positive for vesicular glutamate transporter type 2 (VGLUT2), the structure and function of which remain undetermined. Here, we systematically characterized VGLUT2-positive enteric neurons (VGLUT2-ENs) through sparse labeling with adeno-associated virus, single-cell mRNA sequencing (scRNA-seq), and GCaMP6f calcium imaging. Our results reveal that the majority of VGLUT2-ENs (29 out of 31, 93.5%) exhibited Dogiel type I morphology with a single aborally projecting axon; most axons (26 out of 29, 89.7%) are between 4 and 10 mm long, each traversing 19 to 34 myenteric ganglia. These anatomical features exclude the VGLUT2-ENs from being intrinsic primary afferent or motor neurons. The scRNA-seq conducted on 52 VGLUT2-ENs suggests different expression profiles from conventional descending interneurons. Ex vivo GCaMP6f recordings from flattened colorectum indicate that almost all VGLUT2-EN (181 out of 215, 84.2%) are indirectly activated by colorectal stretch via nicotinic cholinergic neural transmission. In conclusion, VGLUT2-ENs are a functionally unique group of enteric neurons with single aborally projecting long axons that traverse multiple myenteric ganglia and are activated indirectly by colorectal mechanical stretch. This knowledge will provide a solid foundation for subsequent studies on the potential interactions of VGLUT2-EN with extrinsic colorectal afferents via glutamatergic neurotransmission. New & NoteworthyWe reveal that VGLUT2-positive enteric neurons (EN), although constituting a small fraction of total EN, are homogeneously expressed in the myenteric ganglia, with a slight concentration at the intermediate region between the colon and rectum. This concentration coincides with the entry zone of extrinsic afferents into the colorectum. Given that VGLUT2-ENs are indirectly activated by colorectal mechanical stretch, they are likely to participate in visceral nociception through glutamatergic neural transmission with extrinsic afferents.

neuroscience↗

bioRxiv2022

A schema for digitized surface swab site metadata in open-source DNA sequence databases

Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens from swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata associated with swab site locations. However, the swab site location information is currently collected in a single, free-text "isolation source" field promoting generation of poorly detailed descriptions with varying word order, granularity, and linguistic errors, making automation difficult and reducing machine-actionability. We assessed 1,498 free-text swab site descriptions generated during routine foodborne pathogen surveillance. The lexicon of free-text metadata was evaluated to determine the informational facets and quantity of unique terms used by data collectors. Open Biological Ontologies (OBO) foundry libraries were used to develop hierarchical vocabularies connected with logical relationships to describe swab site locations. Five informational facets described by 338 unique terms were identified via content analysis. Term hierarchy facets were developed as were statements (called axioms) about how entities within these five domains were related. The schema developed through this study has been integrated into a publicly available pathogen metadata standard, facilitating ongoing surveillance and investigations. The One Health Enteric Package is available at NCBI BioSample beginning in 2022. Collective use of metadata standards increases the interoperability of DNA sequence databases, enabling large-scale approaches to data sharing, artificial intelligence, and big-data solutions to food safety. IMPORTANCERegular analysis of whole genome sequence data in collections such as NCBIs Pathogen Detection Database is used by many public health organizations to detect outbreaks of infectious disease. However, isolate metadata in these databases are often incomplete and poor quality. These complex raw metadata must often be re-organized and manually formatted for use in aggregate analysis. These processes are inefficient and time-consuming, increasing the interpretative labor needed by public health groups to extract actionable information. Future use of open genomic epidemiology networks will be supported through the development of an internationally applicable vocabulary system to describe swab site locations.

genomics↗

bioRxiv2022

Beyond BRCA: Discovery of novel causes and consequences of homologous recombination deficiencies

Since the discovery of BRCA1 and BRCA2 mutations as cancer risk factors, we have gained substantial insight into their role in maintaining genomic stability through homologous recombination (HR) DNA repair. However, upon pan-cancer analysis of tumors from The Cancer Genome Atlas (TCGA), we found that mutations in BRCA1/2 and other classical HR genes only identified 10-20% of tumors that display genomic evidence of HR deficiency (HRD), suggesting that the cause of the vast majority of HR defects in tumors is unknown. As HRD both predisposes individuals to cancer development and leads to therapeutic vulnerabilities, it is critical to define the spectrum of genetic events that drive HRD. Here, we employed a network-based approach leveraging the abundance of molecular characterization data from TCGA to identify novel drivers of HRD. We discovered that over half of putative genes driving HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA binding protein (RBP)-encoding genes. These novel drivers of HRD were cross-validated using an independent ICGC cohort, and were enriched in GWAS loci associated with cancer risk. Experimental approaches validated over 90% of our predictions in a panel of 50 genes tested by siRNA and 31 additional engineered mutations identified from TCGA patient tumors. Moreover, genetic suppression of identified RBPs or pharmacological inhibition of RBPs induced PARP inhibition. Further mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD and their contributions to DNA damage repair, which has implications for not only future mechanistic studies, but also for genetic screening and therapy stratification. HIGHLIGHTSO_LIThe majority of HR deficiencies detected cannot be directly attributed to aberrations in canonical HR genes. C_LIO_LIIntegrated network analysis identifies RNA binding proteins (RBPs) as a novel driver of HR deficiency in patient tumors. C_LIO_LIRBP dysfunction can produce HR deficiencies through both dysregulation of canonical HR genes and action at sites of DNA damage. C_LI

systems biology↗

bioRxiv2022

RGA1 alleviates low-light-repressed pollen tube growth by improving the metabolism and allocation of sugars and energy

Low-light stress compromises photosynthetic and energy efficiency and leads to spikelet sterility; however, the effect of low-light stress on pollen tube elongation in the pistil remains poorly understood. The gene RGA1, which encodes a G subunit of the heterotrimeric G protein, enhanced low-light tolerance in rice plants at anthesis by preventing the cessation of pollen tube elongation in the pistil. The levels of reactive oxygen species were higher and the content of ATP and ATPase was lower in RGA1 mutant (d1) plants compared with wild-type and RGA1-overexpressing (OE-1) plants under low-light conditions. Energy deficits, rather than interference with signaling transduction pathways, were the main contributors to the inhibition of pollen tube elongation in the pistil by low-light stress. In this process, marked increases in the activities of acid invertase (INV), sucrose synthase (SUS), and mitochondrial respiratory electron transport chain complexes, as well as the relative expression levels of SUTs, SWEETs, SUSs, INVs, CINs, SnRK1A, and SnRk1B, were observed in OE-1 plants. INV and ATPase activators (sucrose and Na2SO3, respectively) increased spikelet fertility by improving the energy status in the pistil under low-light conditions, and the ATPase inhibitor Na2VO4 induced spikelet sterility and decreased ATPase activity. Therefore, RGA1 could alleviate the low-light stress-induced impairment of pollen tube elongation to increase spikelet fertility by promoting sucrose unloading in the pistil and improving the metabolism and allocation of energy.

plant biology↗