Biology subjects

Smith, N.

Publications and source records attributed to Smith, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatial and functional mapping of the human pancreas reveals endocrine and exocrine cell states in health and metabolic disease

The human pancreas contains diverse endocrine and exocrine cell populations whose spatial organization is essential for tissue physiology. While single-cell and spatial transcriptomics revealed molecular heterogeneity across pancreatic cell types, linking these states to physiological activity in situ has remained challenging. Here, we combined single-nucleus RNA sequencing, spatial transcriptomics, and functional calcium imaging across pancreatic samples in health and metabolic disease. We identified heterogeneous endocrine and exocrine cell states associated with obesity and diabetes, including inflammatory remodeling of acinar and ductal populations. To directly couple tissue physiology with molecular state, we developed Slice-seq, which integrates calcium imaging with spatial transcriptomics in acute pancreatic slices. Slice-seq linked local endocrine composition and transcriptional programs with {beta} cell activity and identified extra-islet {beta} cells with reduced glucose responsiveness and mitochondrial oxidative metabolism. Together, our study provides a framework for linking pancreatic cell states to tissue organization and physiological activity in health and disease.

genomics↗

bioRxiv2026

Systematic functional annotation of thousands of BAHD acyltransferases in plant genomes using Protein Language Model and phylogenomic tools

The functional annotation of plant genes lags significantly behind their genomic annotation. Closing this gap requires thorough cataloging of reported protein activities alongside predictive methods that scale beyond sequence-similarity inference. Focusing on the BAHD acyltransferase enzyme family as a model, we assembled FuncZymeDB-BAHD, a large database of 2,705 LLM-retrieved and curated enzyme-acceptor-donor activities covering 336 BAHDs from 156 plant species, a 2-to-6-fold expansion over Swiss-Prot and prior compilations. We further developed FuncPred-OG, which maps queries to orthologous groups and previously characterized enzymes in FuncZymeDB-BAHD, returning hits with high evidence provenance. FuncPred-OG enabled functional prediction of over half of BAHDs across 85 plant proteomes, of which five novel predictions were validated via in vitro assays and recent studies. For the remaining BAHDs without FuncPred-OG annotation, we developed FuncPred-AI, where logistic-regression classifiers trained on protein language model embeddings achieved high Area-Under-the-Precision-Recall-curve (AUPR) scores and correct-hit rates up to 93%. FuncPred-AI yielded [≥]1 probable donor/acceptor annotation for 99.9% (8894/8897) of BAHDs in our pan-plant dataset. Finally, the FuncPred workflow and datasets were deployed on a web portal for broader utilization, potentially reducing experimentalists efforts for selecting candidates from days to minutes. Overall, this framework provides a generalizable template for functional annotation of entire enzyme families.

bioinformatics↗

bioRxiv2026

Multi-modal comparison of primary and stem cell-derived β-cells nominates targets for maturation

Stem-cell-derived {beta}-like-cells (SC{beta}-cells) provide a promising platform for diabetes modelling and cell replacement therapy, but their incomplete functional maturation remains a challenge. Here, we compared immature SC{beta}-cells to human primary {beta}-cells utilizing a multi-omic, single-cell framework integrating patch-clamp electrophysiology with scRNA sequencing (patch-seq), regulatory network inference, and functional phenotyping. Despite low insulin secretion and reduced insulin content, SC{beta}-cells displayed larger Na+ and Ca2+ currents and depolarization-induced exocytosis. Ultrastructural and metabolic profiling revealed immature insulin granules, altered mitochondrial morphology, elevated basal respiration and proton leak, and diminished spare respiratory capacity and glucose-responsive metabolism. Patch-seq linked exocytotic activity in SC{beta}-cells to oxidative phosphorylation and MYC target programs, consistent with incomplete terminal differentiation, whereas SC{beta}-cells expressing higher levels of mature identity markers showed reduced ion channel hyperactivity. Multi-omics profiling showed that electrophysiological features in SC{beta}-cells were embedded in transcriptional programs distinct from those of primary {beta}-cells and other endocrine cells. Network control theory nominated SREBP1, an endoplasmic reticulum tethered transcription factor regulating cholesterol and lipid homeostasis, as a promising candidate involved in this immature state. Inhibition of cholesterol trafficking increased SREBF1 expression and shifted metabolic and transcriptional features towards a more mature {beta}-like state. These data identify potential targets and pathways that can be leveraged to improve SC{beta}-cell maturation and validate cholesterol and lipid homeostasis through the SREBP1 axis as one such candidate.

cell biology↗

bioRxiv2026

Dietary fiber intake associates with improved survival and microbiomecomposition in allogeneic hematopoietic cell transplantation

Diet is linked to changes in gut microbiota and metabolite production with clinical relevance in several disease settings, although these effects remain poorly defined. We performed prospective, real-time diet monitoring (37,929 food items, 3,837 patient days) and longitudinal microbiome and metabolite profiling (1,230 fecal samples) in a clinical cohort of 173 patients undergoing allogeneic hematopoietic cell transplantation. Patients with pre-transplant fiber intake above the cohort average had significantly improved overall survival (p=0.014) and reduced incidence of grades 2-4 acute graft-versus-host disease (GVHD) (p=0.032) post-transplant. Those consuming insoluble fiber had increased microbial diversity, enriched butyrate-producing taxa, and depleted Enterococcus. Those who developed lower gastrointestinal GVHD had reduced fecal butyrate levels. In a GVHD preclinical model, we confirmed that a fiber-enriched diet increased survival, cecal butyrate, and regulatory-to-conventional T cell ratio. Thus, we demonstrated that dietary fiber has clinical significance as a modifiable factor with microbiome-mediated effects.

cancer biology↗

bioRxiv2026

Integrative prioritization of clinically and biologically relevant long noncoding RNAs across gastrointestinal cancers

Across gastrointestinal (GI) cancers, shared malignant programs are layered onto strong anatomical, lineage, and microenvironmental variation, making it difficult to distinguish disease-relevant long noncoding RNAs (lncRNAs) from context-dependent transcriptional signals. We developed a pan-GI integrative framework to classify lncRNAs across colorectal adenocarcinoma, gastric adenocarcinoma, and esophageal cancer using bulk and single-cell transcriptomic resources. This framework evaluates lncRNAs across four complementary dimensions: recurrent tumor-associated expression, clinical association with disease progression and overall survival, co-expression network context, and malignant epithelial expression at single-cell resolution. Paired tumor-normal RNA-seq analyses identified extensive tumor-associated lncRNA dysregulation and defined recurrent pan-GI lncRNAs consistently upregulated across cancer types. Clinical analyses further nominated transcripts linked to tumor extension, nodal involvement, metastatic dissemination, progression-linked expression, and adverse overall survival. Co-expression network analysis identified lncRNAs embedded within disease-associated transcriptional modules, providing functional context for otherwise poorly annotated transcripts. In parallel, single-cell-derived metacell analysis nominated malignant epithelial-associated and detection-supported lncRNAs, helping distinguish tumor-compartment-associated signals from stromal, immune, endothelial, and other microenvironmental contributions. Together, this study establishes an evidence-structured pan-GI lncRNA resource and a generalizable prioritization strategy for nominating disease-associated noncoding transcripts. More broadly, the framework provides a transferable strategy for systematic lncRNA prioritization across other cancers and heterogeneous disease contexts.

cancer biology↗

bioRxiv2026

A scalable approach to resolving variants of uncertain significance

Over 90% of missense variants across [~]4,000 disease-associated genes are variants of uncertain significance (VUS). Experimental variant effect measurements provide critical evidence about pathogenicity and inform disease biology, but most variants lack data and clinical translation has been limited. The Impact of Genomic Variation on Function Consortium generated experimental data for 62,215 variants across ten genes using multiplexed assays and 1,407 variants across 163 genes using arrayed assays, curated 193,139 additional community-generated variant effect measurements across 30 additional genes, and developed automated calibration methods for translating experimental data and variant effect predictions into clinical evidence. To reduce current VUS, we developed a scalable workflow using only experimental and predictive evidence, enabling reclassification of 75% of the 16,115 VUS in these genes as pathogenic or benign with <1% error. To minimize future VUS, we analyzed >90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine.

genomics↗

bioRxiv2026

Outpacing E. coli: Development of Vibrio natriegens as a Next-Generation Cloning Host

Despite transformative advances in DNA synthesis, sequencing, and automation that have accelerated recombinant DNA workflows, molecular cloning hosts have scarcely evolved past the Escherichia coli strains adopted out of convenience in the 1970s. We present NBx CyClone - an engineered strain of Vibrio natriegens - as a next-generation host for molecular cloning. This non-pathogenic marine bacterium combines broad plasmid and genetic tool compatibility, a versatile metabolism, and the fastest known doubling time of any free-living organism. By shortening growth-dependent steps, this host offers a practical route to faster, more efficient recombinant DNA workflows across research and industry.

synthetic biology↗

bioRxiv2026

Computational modeling and preclinical validation support targeting somatic instability for Huntington's disease treatment

Huntingtons disease (HD) is caused by an expanded CAG trinucleotide repeat within the huntingtin (HTT) gene. Genetic modifiers of disease onset and progression in HD implicate somatic instability (SI) of the expanded CAG repeat as a key pathogenic driver, with MSH3 emerging as a leading therapeutic target. Reducing SI, particularly in the most affected neuronal cell type, medium spiny neurons (MSNs) of the striatum, is thus a rational therapeutic strategy for HD. To inform the development of an SI-targeted therapy, we generated a computational model simulating SI in MSNs to infer therapeutic effects on MSN survival resulting from an intervention that reduces SI. The model takes advantage of HD patient data to predict therapeutic benefit across a range of inherited CAG lengths and ages of intervention, considering the degree of target engagement regionally and per cell. To target SI experimentally, we designed an artificial microRNA to lower MSH3 mRNA (miMSH3) after delivery with AAV-DB-3, a previously described MSN-targeting AAV capsid variant. AAV-DB-3.miMSH3 achieved from 48 to 94% MSH3 mRNA reduction in MSNs of nonhuman primates (NHPs), which, when modeled, would reduce the composite Unified Huntington Disease Rating Scale change over baseline from 50 to over 120% as well as delay motor symptom onset by many years. AAV-DB-3.miMSH3 also showed robust target engagement in vivo with up to 46% reduction in SI in HdhQ111 mice. The integration of preclinical experimental data and the computational model support the translational potential of AAV-DB-3.miMSH3 as a disease-modifying therapy applicable for HD patients with a broad range of inherited repeat lengths. One Sentence SummaryPredictive modeling to guide therapeutic targeting of disease modifiers in Huntingtons disease.

neuroscience↗

bioRxiv2025

Trichome formation in Nicotiana benthamiana is induced by Agrobacterium

Plant trichomes are specialised epidermal appendages found on various organs of many plant species. They play important roles in plant protection against pests, pathogens, herbivores, resistance to abiotic stress, light perception, mechanosensitivity etc. They are of direct agricultural importance, providing fibre (e.g. cotton) and producing secondary metabolites essential for agriculture, medicine, and industry. Trichomes can be relatively sparsely distributed, making their biological investigation and commercial exploitation more challenging. Here we show that infiltration of Nicotiana benthamiana leaf tissue with certain nopaline-type Agrobacterium tumefacians strains induces extremely dense, localised formation of glandular trichomes 15 days post infiltration (dpi). This Agrobacterium-strain specific effect was shown to be due to the presence of a trans-zeatin synthase (tzs) gene located on some Ti plasmids, which results in the bacterial production of the cytokinin trans-zeatin. This simple procedure enables dramatically increased trichome density to be compared biologically with adjacent isogenic plant tissues on the same leaf.

plant biology↗

bioRxiv2025

Lymphotoxin-driven cancer cell eradication by tumoricidal CD8+ tumor-infiltrating lymphocytes

Tumor-infiltrating lymphocyte (TIL) therapy is FDA-approved for patients with treatment-resistant advanced melanoma, but the TIL subpopulations critical for tumor eradication remains incompletely understood. Using patient-derived TIL-melanoma co-cultures, we identified and characterized a novel subset of CD8+ TIL, capable of class I HLA-independent cancer cell lysis. The lymphotoxin {beta} receptor (LT{beta}R) and interferon (IFN) sensing pathways were nominated as key determinants of TIL-mediated cancer cell killing from a whole-genome, loss-of-function CRISPR screen. Validation studies confirmed that dual LT{beta}R and IFN sensing is necessary and sufficient for cancer cell lysis, and that expanded CD8+ TIL express high lymphotoxin {beta} (LTB) and upregulate lymphotoxin (LTA) upon coculture with cancer cells. Leveraging paired scRNA-seq and scTCR-seq data, we confirmed that enrichment of LTB+CD8+ T cells is associated with clinical response to TIL, and that LTB+CD8+ TIL are expanded from putative neoantigen-reactive, LTBlo CD8+ T cells in resected tumors. SignificanceWe have uncovered a previously unrecognized mechanism of TIL-mediated tumor eradication, providing mechanistic insights into the role of LTBR/IFN signaling in TIL-mediated cancer cell killing, and potentially offering insights into novel strategies to isolate, enrich, and expand tumoricidal TIL or augment specific TIL functions to enhance tumor control.

cancer biology↗

bioRxiv2025

Disruption of GABA-Regulated Network Resilience in Human Cerebral Organoids Leads to Fragmented Small-World States and Reduced Connectivity

Neuronal network resilience, the ability of brain circuits to maintain and recover functional connectivity following perturbation, is fundamental to cognitive stability and adaptability. Using human cerebral organoids and multi-electrode arrays (MEAs), we investigated how mechanical stress disrupts network stability and identified key mechanisms regulating recovery. Blast overpressure exposure destabilized small-world network (SWN) organization, increasing network fragmentation and reducing overall integration. Merged SWNs, which exhibit high connectivity, were particularly vulnerable, while fragmented and single SWNs persisted for extended periods, indicating a shift toward less resilient network states. Optogenetic stimulation promoted network recovery, reducing the persistence of fragile states and facilitating transitions toward more cohesive network structures. GABAergic signaling emerged as a critical regulator of network resilience, with pharmacological inhibition exacerbating fragmentation and impairing network reorganization. These findings reveal fundamental principles of how inhibitory networks regulate circuit stability, with implications extending beyond mechanical injury to broader conditions characterized by network dysfunction, including anxiety, depression, PTSD, and neurodegenerative disorders. Understanding the mechanisms governing network adaptation and resilience could inform new therapeutic strategies aimed at stabilizing disrupted neural circuits across a range of neurological conditions. Significance statementNeuronal networks must dynamically adapt to maintain function in the face of disruption, yet the mechanisms that govern network resilience remain poorly understood. Using human cerebral organoids, we demonstrate that primary blast overpressure destabilizes small-world networks, increasing fragmentation and reducing overall connectivity. Critically, GABAergic signaling emerges as a key stabilizer, with inhibition of GABA receptors amplifying network fragmentation and impairing recovery. These findings provide fundamental insight into how neural circuits resist and recover from mechanical stress, bridging gaps between basic neuroscience, injury pathology, and potential therapeutic interventions. By identifying inhibitory signaling as a regulator of network resilience, our work informs not only traumatic brain injury treatment strategies but also broader efforts to restore functional connectivity in neurological disorders, from epilepsy to neurodegeneration.

neuroscience↗

bioRxiv2025

eDNA metabarcoding and whole genome sequencing detect European-American Eel hybrids in northeastern Canada

American and European Eels (Anguilla rostrata and Anguilla anguilla, respectively) are sister species of conservation concern, as they have declined in abundance in recent decades. Although there is evidence of gene flow between the two species, most previous hybrid detections have been found in Iceland. Here we expand upon existing reports of interspecific hybrids using a combination of an environmental DNA (eDNA) survey and whole genome sequencing of 347 eels from Newfoundland and Labrador. Metabarcoding of eDNA samples at multiple loci detected the presence of European Eel mitochondrial DNA (mtDNA) at eight locations primarily along the south coast of Newfoundland. Genome sequencing of eels collected in the region revealed three hybrid individuals with levels of European admixture consistent with one first generation hybrid and two North American backcrosses, all with European mtDNA. This work supports the presence of a previously unknown, seemingly localized region of hybrid occurrence in southern Newfoundland and expands our understanding of the relationship between these species across the North Atlantic.

genomics↗

bioRxiv2025

Linking molecular pathways and islet cell dysfunction in human type 1 diabetes

Type 1 diabetes (T1D) is characterized by the autoimmune destruction of most insulin-producing {beta}-cells, along with dysregulated glucagon secretion from pancreatic -cells. We conducted an integrated analysis that combines electrophysiological and transcriptomic profiling, along with machine learning, of islet cells from T1D donors to investigate the mechanisms underlying their dysfunction. Surviving {beta}-cells exhibit altered electrophysiological properties and transcriptomic signatures indicative of increased antigen presentation, metabolic reprogramming, and impaired protein translation. In -cells, we observed hyper-responsiveness and increased exocytosis, which are associated with upregulated immune signaling, disrupted transcription factor localization and lysosome homeostasis, as well as dysregulation of mTORC1 complex signaling. Notably, key genetic risk signals for T1D were enriched in transcripts related to -cell dysfunction, including MHC class I which were closely linked with -cell dysfunction. Our data provide novel insights into the molecular underpinnings of islet cell dysfunction in T1D, highlighting pathways that may be leveraged to preserve residual {beta}-cell function and modulate -cell activity. These findings underscore the complex interplay between immune signaling, metabolic stress, and cellular identity in shaping islet cell phenotypes in T1D. HighlightsO_LISurviving {beta}-cells in T1D show disrupted electrical function linked to metabolic reprogramming and immune stress. C_LIO_LITranscripts associated with -cell dysfunction are enriched in genetic risk alleles for T1D. C_LIO_LIUpregulated MHC class I and impaired nuclear localization of key transcription factors associate with -cell dysfunction in T1D. C_LIO_LIT1D -cells exhibit increased hyper-activity, lysosomal imbalance and impaired mTORC1 signaling, which promotes dysregulated glucagon secretion. C_LI

cell biology↗

bioRxiv2025

Whole-body Bacteriophage Distribution Characterized by a Physiologically based Pharmacokinetic Model

In 2019 there were over 2.8 million cases of antibiotic-resistant bacterial infection in the US with gram negative organisms having up to a 6% rate of mortality. Bacteriophage (phage) therapy holds great promise to treat such infections. However, the biologic features which influence the pharmacokinetics (PK) of phage have been difficult to characterize due to a lack of standardized protocols of phage purification, tissue assay, and labeling. Here we present robust methods for ultrapure phage preparation as well as non-destructive highly stable attachment of radio-iodide to phage using the well described Sulfo-SHPP linker. We purified and radiolabeled the phage strains, PAML-31-1, OMKO1, and Luz24 lytic to drug-resistant Pseudomonas aeruginosa for biodistribution assay in normal young adult CD-1 mice injected via penile vein. Groups of 5 mice were euthanized and tissues/organs removed for weighing and scintillation well counting of I-125 activity at 30 min, 1h, 2h, 4h, 8h, and 24h. A physiologically based PK (PBPK) model was then constructed focusing on compartments describing blood, lung, muscle, bone, liver, stomach, spleen, small intestines, large intestines, and kidney. Model permeability coefficient (PS) was estimated across all organs as being 0.0227. Tissue partition coefficients (KP) were estimated for high perfusion organs (lung and kidney) as 0.000138, GI organs (liver, spleen, and stomach) as 0.627, and all other organs as 0.220. Elimination was governed by MPS-mediated elimination (TMPS,deg) and active secretion at epithelial barriers (CLActive), which were estimated as 0.00301 h and 0.0145 L/h/kg, respectively. Monte Caro simulations showed that the rapid elimination phage in humans is expected, resulting in phage blood concentrations being lower than 102 PFU/mL (limit of quantification by plaque assay) by 12 hours. As such, multi-dose regimens and continuous infusion regimens were the only strategies that allowed continuously detectible phage concentrations. Evaluation of different dose levels showed that at a maximum dose of 1012 PFU, phage concentrations are expected to be approximately 107 PFU/g. Our physiologically based PK model of phage represents the first rigorous pre-clinical assessment of phage PK utilizing contemporary pharmacometric approaches amenable to both pre-clinical and clinical study design.

microbiology↗

bioRxiv2025

Positive allosteric modulation of emodepside sensitive Brugia malayi SLO-1F and Onchocerca volvulus SLO-1A potassium channels by GoSlo-SR-5-69

Human lymphatic filariasis and onchocerciasis are Neglected Tropical Diseases (NTDs), of major public health concern. Prophylaxis and treatment rely on anthelmintics that effectively eliminate migrating microfilariae but lack efficacy against adult filarial worms. To expedite the elimination of both diseases, the introduction of drugs with adulticidal activity is paramount. The broad-spectrum anthelmintic emodepside, a nematode selective SLO-1 K channel activator, has been considered a promising candidate for the treatment of onchocerciasis due to its macrofilaricidal activity against Onchocerca volvulus. Nevertheless, it is less effective against adult Brugia malayi, one of the causative agents of human lymphatic filariasis. Characterizing molecular and pharmacological disparities between highly conserved splice variant isoforms of B. malayi and O. volvulus SLO-1 K channels and identifying allosteric modulators that can increase emodepside potency on B. malayi SLO-1 K channels is necessary for therapeutic advance. In this study, we tested the effects of emodepside and the mammalian BK channel activator, GoSlo-SR-5-69 alone and in combination on Xenopus expressed B. malayi SLO-1F and O. volvulus SLO-1A channels. Additionally, binding poses of emodepside, and GoSlo-SR-5-69 were predicted on both channels using molecular docking. Ovo-SLO-1A was more sensitive to emodepside than Bma-SLO-1F. GoSlo-SR- 5-69 was a positive allosteric modulator, potentiating the effects of emodepside. Emodepside was docked at the S6 pocket below the selectivity filter for Bma-SLO-1F and Ovo-SLO-1A. The binding of emodepside in the S6 pocket indicated a stabilizing{pi} -{pi} interaction between F342 and the phenyl rings of emodepside which may contribute to the potency of emodepside on these filaria channels. Molecular docking suggested that GoSlo-SR-5-69 binds at the RCK1 pocket. This study reveals for the first time, allosteric modulation of filarial nematode SLO-1 K channels by a mammalian BK channel activator and highlights its ability to increase emodepside potency on the B. malayi SLO-1 K channel. Author SummaryB. malayi is one of the causative agents of lymphatic filariasis, while O. volvulus causes onchocerciasis. Elimination of adult B. malayi and O. volvulus is impeded by anthelmintics lacking adequate macrofilaricidal activity. The anthelmintic emodepside has microfilaricidal and macrofilaricidal activity. However, it exhibits poor efficacy against adult B. malayi in vivo. Here, we conducted a comparative pharmacological characterization of two closely related splice variants SLO-1 K channels of B. malayi and O. volvulus. Using voltage clamp, we tested the effects of emodepside and GoSlo-SR-5-69 independently and in combination on Xenopus expressed B. malayi SLO-1F and O. volvulus SLO-1A channels. Binding poses of emodepside, and GoSlo-SR-5-69 were predicted on both channels using molecular docking. We demonstrate that the O. volvulus SLO-1A receptor is more sensitive to emodepside than the B. malayi SLO-1F receptor. GoSlo-SR-5-69 is also a potentiator of emodepside responses. Homology modelling revealed that emodepside probably binds in the pore region of the B. malayi SLO-1F and O. volvulus SLO-1A channels, while GoSlo-SR-5-69 probably binds to the RCK1 domain of the channels. Our study provides new insights into similarities and differences shared between SLO-1 K channels of each species and reveals positive allosteric modulation by a mammalian SLO-1 K activator.

pathology↗

bioRxiv2024

TMEM55A-mediated PI5P signaling regulates α-cell actin depolymerization and glucagon secretion

Diabetes is associated with the dysfunction of glucagon-producing pancreatic islet -cells, although the underlying mechanisms regulating glucagon secretion and -cell dysfunction remain unclear. While insulin secretion from pancreatic {beta}-cells has long been known to be partly controlled by intracellular phospholipid signaling, very little is known about the role of phospholipids in glucagon secretion. Here we show that TMEM55A, a lipid phosphatase that dephosphorylates phosphatidylinositol-4,5-bisphosphate (PIP2) to phosphatidylinositol-5-phosphate (PI5P), regulates -cell exocytosis and glucagon secretion. TMEM55A knockdown in both human and mouse -cells reduces exocytosis at low glucose, and this is rescued by the direct reintroduction of PI5P. This does not occur through an effect on Ca2+ channel activity, but through a re-modelling of cortical F-actin dependent upon TMEM55A lipid phosphatase activity which occurs in response to oxidative stress. In summary, we reveal a novel pathway by which TMEM55A regulates -cell exocytosis by manipulating intracellular PI5P level and the F-actin network.

cell biology↗

bioRxiv2024

Sugar-rich foods exacerbate antibiotic-induced microbiome injury

Intestinal microbiota composition is implicated in several diseases; understanding the factors that influence it are key to elucidating host-commensal interactions and to designing microbiome-targeted therapies. We quantified how diet influences microbiome dynamics in hospitalized patients. We recorded 9,419 meals consumed by 173 patients undergoing hematopoietic cell transplantation and profiled the microbiome in 1,009 longitudinally collected stool samples from 158 of them. Caloric intake was correlated with fecal microbiota diversity. Bayesian inference revealed associations between intake of sweets or sugars during antibiotic exposure with microbiome disruption, as assessed by low diversity or expansion of the pathobiont Enterococcus. We validated this observation experimentally, finding that sucrose exacerbated antibiotic-induced Enterococcus expansion in mice. Taken together, our results suggest that avoiding sugar-rich foods during antibiotic treatment may reduce microbiome injury. One Sentence SummaryAnalyses of hematopoietic cell transplant patients and of mice uncover links between foods and microbiome disruption.

microbiology↗

bioRxiv2024

FuncFetch: An LLM-assisted workflow enables mining thousands of enzyme-substrate interactions from published manuscripts

MotivationThousands of genomes are publicly available, however, most genes in those genomes have poorly defined functions. This is partly due to a gap between previously published, experimentally-characterized protein activities and activities deposited in databases. This activity deposition is bottlenecked by the time-consuming biocuration process. The emergence of large language models (LLMs) presents an opportunity to speed up text-mining of protein activities for biocuration. ResultsWe developed FuncFetch -- a workflow that integrates NCBI E-Utilities, OpenAIs GPT-4 and Zotero -- to screen thousands of manuscripts and extract enzyme activities. Extensive validation revealed high precision and recall of GPT-4 in determining whether the abstract of a given paper indicates presence of a characterized enzyme activity in that paper. Provided the manuscript, FuncFetch extracted data such as species information, enzyme names, sequence identifiers, substrates and products, which were subjected to extensive quality analyses. Comparison of this workflow against a manually curated dataset of BAHD acyltransferase activities demonstrated a precision/recall of 0.86/0.64 in extracting substrates. We further deployed FuncFetch on nine large plant enzyme families. Screening 27,120 papers, FuncFetch retrieved 32,605 entries from 5547 selected papers. We also identified multiple extraction errors including incorrect associations, non-target enzymes, and hallucinations, which highlight the need for further manual curation. The BAHD activities were verified, resulting in a comprehensive functional fingerprint of this family and revealing that [~]70% of the experimentally characterized enzymes are uncurated in the public domain. FuncFetch represents an advance in biocuration and lays the groundwork for predicting functions of uncharacterized enzymes. Availability and ImplementationCode and minimally-curated activities available at: https://github.com/moghelab/funcfetch and https://tools.moghelab.org/funczymedb

bioinformatics↗