Biology subjects

James, M.

Publications and source records attributed to James, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparative genome analyses suggest a common blueprint for obligate endoparasitism in Strepsiptera

The twisted-wing parasites (order Strepsiptera) are well-known for their unusual life histories as obligate endoparasites of a wide variety of other insect orders. Here, we present the first high-quality genome assembly of a leafhopper-parasitizing strepsipteran species. We sequenced the genome of Elenchus koebelei using PacBio HiFi technology, yielding a primary assembly of 63.7Mb in 96 contigs, with an N50 of 1.60Mb and a BUSCO completeness score of 82.3%. In total, we recovered 8,167 protein-coding gene annotations, and 34.2% of the genome annotated as repeats. For the first time, we compare the genome content of three strepsipteran species and find that they are remarkably consistent in broad structure, with approximately 600 insect universal single-copy orthologs that appear to be completely missing from the order. These similarities imply a conserved genomic blueprint for strepsipteran parasitic strategy and/or differences that must be investigated at the post-translational level.

genomics↗

bioRxiv2026

A TmaT-AftD interaction is required for the CmpL4 mycomembrane biogenesis pathway in Corynebacterium glutamicum.

Bacteria in the Mycobacteriales order like mycobacteria and corynebacteria surround themselves with a multilayered cell envelope. Their cytoplasmic membrane is fortified by a peptidoglycan cell wall that is decorated with branched arabinogalactan (AG) polymers. The AG glycans are further modified with mycolic acids to form an outer membrane. Biogenesis of this mycomembrane requires the transport of mycolates from their site of synthesis in the cytoplasmic membrane to the cell surface. How mycolate transport is controlled and coordinated with AG synthesis has remained unclear. Mycolate transport is mediated by the essential RND-family transporter MmpL3 in mycobacteria and a pair of related, partially redundant transporters called CmpL1 and CmpL4 in corynebacteria. The acetyltransferase TmaT has also been implicated in mycolate transport in both types of bacteria. In corynebacteria, it is required for the production of acetylated mycolates, and this modification has been proposed to promote mycolate transport via both CmpL transporters in the model organism Corynebacterium glutamicum (Cglu). Here, we reinvestigated the function of TmaT in Cglu and found that it and several factors encoded in the tmaT locus are specifically required for mycolate transport via the CmpL4 transporter pathway. Notably, one of these additional genes encodes the arabinosyltransferase AftD involved in AG biogenesis. TmaT and AftD were found to interact, and our results indicate that this interaction is required for acetylated mycolate production, mycolate transport via the CmpL4 pathway, and normal arabinan synthesis. Thus, the TmaT-AftD interaction may serve as a regulatory link connecting mycolate transport with AG biogenesis. SIGNIFICANCEMycobacteriales bacteria, including pathogens like Mycobacterium tuberculosis (Mtb), have a complex cell surface comprising an inner membrane, a cell wall modified with arabinogalactan (AG), and an outer mycomembrane made of mycolic acids linked to AG polymers. Because these surface biogenesis pathways are targeted by frontline anti-Mtb drugs, there is great interest in elucidating their underlying mechanisms. Here, we identify an interaction between factors involved in mycomembrane (TmaT) and AG biosynthesis (AftD) in the model organism Corynebacterium glutamicum. We show that this interaction is important for proper surface biogenesis and may therefore function to coordinate mycomembrane assembly with AG synthesis. This and other potential regulatory connections controlling envelope biogenesis represent attractive targets for future antibiotic development.

microbiology↗

bioRxiv2026

Transvaginal ovum retrieval in scimitar horned oryx (Oryx dammah) and roan antelope (Hippotragus equinus)

Development and use of assisted reproductive technologies (ARTs) in non-domestic species provides novel tools for species conservation. As a first step towards in vitro embryo production, we developed an OPU technique for two antelope species, scimitar horned oryx (Oryx dammah) and roan antelope (Hippotragus equinus) utilizing a custom-made needle guide and existing OPU equipment utilized by livestock and human practitioners. Females were anesthetized and placed in sternal recumbency for transvaginal OPUs. Prior to OPUs (36 - 45 hours), SHO and roan were either hormonally stimulated with follicle stimulating hormone (FSH, 140 or 250IU) as a single injection or not. A total of 32 and 26 OPUs were completed in SHO (n=10) and roan (n=7), respectively, representing one to four OPUs per animal at monthly intervals. A total of 141 oocytes were recovered from 215 follicles in SHO and 31 oocytes from 58 follicles in roan. FSH dose (250IU) increased (P<0.05) the number of follicles aspirated and the number of oocytes recovered in SHO. No effects of FSH were observed in roan (P>0.05). Good quality oocytes were recovered from all females and procedures were conducted in four consecutive months with no evidence of scar tissue buildup or reduced capacity to recover quality oocytes. These ARTs can be used to develop in vitro embryo production tools for population management and the preservation of female genetics; bolstering genetic diversity and guarding against extinction.

physiology↗

bioRxiv2026

A major chromosome 4 region modulates early vigor under chilling through brassinosteroid signaling associated genes in maize

AbstractEarly sowing is a key strategy to improve maize productivity and resilience under climate change, but it exposes plants to prolonged chilling stress that can severely compromise seedling establishment. While previous genetic studies have focused on germination or very early stages, tolerance to long-term chilling during the autotrophic transition remains poorly characterized. Here, we combined genome-wide association studies (GWAS) and transcriptome analysis on QTL near-isogenic lines (NILs) to dissect the genetic architecture of early vigor under chilling in maize. We identified a major genomic region on chromosome 4 (LD_COL4), harboring two QTLs within a 2.7 Mb interval, that were consistently associated with early vigor under long-term chilling conditions. Transcriptomic analysis of contrasted NILs revealed a cluster of differentially expressed genes co-localizing with LD_COL4, pointing to two strong candidate genes, Zm00001d048582, an ortholog of the Arabidopsis OPS gene that regulates the brassinosteroid (BR) signaling pathway upstream of the key transcription factors BES1 and BZR1, and Zm00001d048612, a brassinosteroid-signaling kinase (BSK). Multiple orthologs of BES1/BZR1 modulators were differentially expressed between genotypes under chilling, supporting the involvment of brassinosteroid signaling in this response. These findings highlight both genes as promising targets for marker-assisted breeding and gene editing to improve maize adaptation to early sowing.

plant biology↗

bioRxiv2026

Multi-omic analysis of maize NILs for chilling tolerance QTLs uncover regulatory and metabolic signatures

Early sowing of maize (Zea mays L.) is increasingly required to mitigate summer drought under climate change, making the acquisition of chilling tolerance a major agronomic challenge. Here, we investigated the molecular and physiological bases of cold tolerance using two maize near-isogenic lines (NILs) differing at two major chilling tolerance quantitative trait loci (QTLs) located on chromosome 4. Plants were exposed to low temperature (14{degrees}C day/10{degrees}C night) for 20 days and analyzed using an integrated multi-omics approach combining transcriptomics, soluble and cell wall proteomics, and metabolomics (primary and specialized metabolites), together with physiological measurements. Univariate and multivariate analyses revealed significant chilling-induced variability across all molecular layers, affecting [~]0.2% of genes, [~]6% of proteins, and a subset of specialized metabolites, while primary metabolites were largely stable. Integrative statistical analyses demonstrated that the soluble and cell wall proteomes contributed most strongly to the genotype effect, highlighting protein-level regulation as a major determinant of chilling tolerance. A restricted 5.15 Mb divergence region on chromosome 4 was sufficient to drive contrasting physiological responses, including differences in photosynthetic charge separation efficiency and leaf development, favoring the chilling-tolerant NIL. Notably, several components of the benzoxazinoid pathway located within the divergence region, including BX1 and associated specialized metabolites (BZX-like glucoside, DIBOA-glucoside-2, HBOA-glucoside-2), were specifically associated with chilling tolerance, suggesting a role in stress signaling and hormonal crosstalk. Overall, this study demonstrates that integrative multi-omics analyses provide a powerful framework to resolve genotype-specific regulatory mechanisms underlying chilling tolerance in maize and to identify candidate molecular targets for breeding. HighlightsO_LIFirst organ-resolved multi-omics dissection of chilling responses in maize NILs. C_LIO_LIA 5.1Mb divergence on chromosome 4 drives major physiological and molecular differences. C_LIO_LIChilling tolerance is linked to more robust photochemical homeostasis and sustained leaf development. C_LIO_LISoluble and cell-wall proteomes dominate the genotype-discriminating -omics signal. C_LIO_LIBenzoxazinoids and defense-related transcriptional modules are differentially activated. C_LIO_LICell wall remodeling enzymes and apoplastic peroxidases emerge as key tolerance players. C_LI

plant biology↗

bioRxiv2026

Insights into strepsipteran flight

Because Strepsiptera can fly vertically from a standing start, at least [1/4] of their body mass must be dedicated to flight muscle. Adult male Strepsiptera also do not feed and die within a few hours of eclosing, so much normal adult insect anatomy has been discarded, leading to a flight muscle to total mass ratio (FMR) of at least 30%--this is medial for Hymenoptera, but as the lower bound for Strepsiptera, it indicates substantial aerial ability. On account of their high FMR and low wing loading, Strepsiptera are capable of widely varied flight. Moreover, the often incongruous descriptions thereof (that they fly slowly, fly quickly, are clumsy, are graceful, etc.) are paralleled in well-established phases of sex pheromone tracking in moths. For nearly all of their brief eclosed adult lives, male Strepsiptera are airborne, for which they are well-adapted. Correspondingly, strepsipteran propagation is utterly dependent on flight. Thus, flight is the lens through which much strepsipteran ecology is clarified. Accordingly, I photographed free-flying Triozocera texana (nocturnal) in the field and analyzed the images. Strepsipteran wings are remarkably flaccid and potentially teneral, leading to certain flight advantages. At night, spatial acuity is especially poor in tiny insects, but halteres apparently compensate so well that even later derived diurnal Strepsiptera identify calling females chemotactilely--not visually--and shun resolution for high sensitivity. Future directions are discussed, as well as experimental techniques that are problematic when applied to Strepsiptera.

ecology↗

bioRxiv2026

3D Light Sheet Microscopy Reveals Aging Osteoarthritis-associated Joint-innervated Nerve Remodeling in Mouse Knee Joints

ObjectivesOsteoarthritis (OA) is a prevalent age related joint disease-causing chronic pain. This study investigated how nociceptive and sympathetic nerve innervation in the mouse knee joint changes with age and OA progression, and how these changes relate to pain and disease severity. MethodsThirty-eight mice were assigned to four groups: young male (My), aged male (Ma), young female (Fy), and aged female (Fa). Pain sensitivity was evaluated via Pressure Application Measurement (PAM), and joint damage was graded using OARSI scoring. CGRP and PIEZO2 expressions in dorsal root ganglia (DRG) were also assessed. We employed iDISCO tissue clearing and 3D light sheet fluorescence microscopy to visualize total (PGP9.5), nociceptive (CGRP), and sympathetic (TH) nerve fibers in anterior regions of mouse knee joints. A MATLAB-based tool quantified nerve architecture. ResultsThe Ma group displayed the highest OA severity and markedly lower mechanical withdrawal thresholds compared with My (H = 11.59, {varepsilon}{superscript 2} = 0.64), suggesting an age effect on pain-related behavior. This phenotype was accompanied by a higher total PGP9.5 nerve fiber density in the knee joint (mean difference -0.3127, 95% CI -0.4551 to -0.1704) and increased CGRP nociceptive innervation. In contrast, female mice showed no age-dependent change in PAM withdrawal thresholds, consistent with preserved cartilage integrity and stable OARSI scores, and no detectable age-related differences in PGP9.5 or CGRP innervation. The TH sympathetic fiber distribution was comparable across sexes and ages. Consistent with joint-level findings, DRG analyses demonstrated increased CGRP and PIEZO2 expression in the Ma group, whereas females exhibited no significant change. ConclusionEnhanced nociceptive but not sympathetic nerve remodeling in knee cavities is associated with increased OA severity and knee pain in the Ma group. These findings emphasize the role of peripheral sensory plasticity in OA pain and demonstrate the value of 3D imaging for visualizing neuroanatomical changes in joint disorders.

neuroscience↗

bioRxiv2025

A proximity labeling approach to identify proteins that associate with synaptonemal complex components in Drosophila melanogaster females

Organisms use a specialized cell division called meiosis for the creation of haploid gametes. Multiple carefully orchestrated steps must occur at specific times and places for meiosis to be successful, including chromosome pairing, meiotic entry, recombination, synapsis, and two rounds of chromosome segregation. The regulation and molecular mechanisms for many of the steps of meiosis have not been fully elucidated. During synapsis, the synaptonemal complex (SC) builds along the entire lengths of the homologs to maintain the pairing of the homologs and promote the formation of the crossovers that help ensure proper segregation of homologs at the meiosis I division in many organisms. The SC is a large tripartite structure that is believed to function as a biomolecular condensate. To attempt to identify proteins that interact with SC components during female meiosis in Drosophila melanogaster, a protein of the lateral element, C(2)M, and a protein of the central element, Cona, were tagged with the APEX2 enzyme, which can biotinylate nearby proteins under the appropriate conditions. Under biotinylating promoting conditions, biotin labeled proteins were observed to be associated with the SC by immunofluorescence. Biotinylated proteins were isolated for mass spectrometry analysis, and multiple proteins were found to be enriched compared to control samples. RNAi knockdown lines targeting a subset of enriched proteins were examined for phenotypes in early Drosophila female meiosis. RNAi knockdown of Cpsf5, an mRNA cleavage factor, caused delayed or defective SC formation, as well as additional meiotic defects, indicating a role for maturation of mRNA in regulating processes of female meiosis. These results support proximity labeling as a strategy for identifying additional meiotic proteins.

genetics↗

bioRxiv2025

Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking

I.Establishing viable cell lines from endangered species is essential for conservation, yet traditional fibroblast derivation from skin biopsies faces challenges including variable success rates, contamination risk, and extended culture timelines. We demonstrate that endothelial progenitor cells (EPCs) and pericytes isolated from peripheral blood represent superior alternatives for biobanking across three mammalian genera (Canis, Bison, and Equus). Blood-derived cells exhibited 2-3 fold faster doubling rates (15-20 hours versus >35 hours for fibroblasts) and reduced time to generate banked lines from 3-4 weeks to 1.5-2 weeks. Proteomic profiling of 32 canonical markers confirmed EPCs and pericytes represent distinct populations with lineage-specific molecular signatures. Optical genome mapping demonstrated equivalent genomic stability across all cell types with no detectable structural variants or aneuploidies. Critically, interspecific somatic cell nuclear transfer (iSCNT) experiments confirmed both EPCs and pericytes generate viable embryos with efficiency meeting or exceeding fibroblasts. Gray wolf blood-derived cells produced six viable fetuses with 15% implantation rate, while bison EPCs showed higher blastocyst formation (7%) than fibroblasts (3%) from the same individual. Blood collection during routine veterinary procedures offers minimally invasive sampling with reduced contamination compared to skin biopsies. These findings support integrating blood-derived cell banking into conservation programs, enabling opportunistic genetic preservation during standard management activities and expanding options for genetic rescue through assisted reproductive technologies.

cell biology↗

bioRxiv2025

Chimeric Reference Panels for Genomic Imputation

Despite transformative advances in genomic technologies, missing data remains a fundamental constraint that limits the full potential of genomic research across biological systems. Genotype imputation offers a remedy by inferring unobserved genotypes from observed data. However, conventional methods typically rely on external reference panels constructed from complete genome sequences of hundreds of individuals, a costly approach largely inaccessible for non-model organisms. Moreover, these methods generally overlook novel genomic positions not captured in existing panels. To overcome these limitations, we developed Retriever, a framework that bypasses the need for external reference panels. Retriever constructs a chimeric reference panel directly from the target samples using a sliding-window approach to identify and retrieve genomic partitions with complete data. By exploiting the complementary distribution of missing data across samples, Retriever assembles a panel that preserves local patterns of linkage disequilibrium and captures novel variants. Integrated with Beagle, Retriever achieves genotype imputation with accuracy consistently exceeding 95% across diverse datasets, including plants, animals, and fungi. By eliminating the need for costly external panels, Retriever offers an accessible, cost-effective solution that broadens the application of sophisticated genomic analyses across species.

bioinformatics↗

bioRxiv2025

Age-associated inflammatory monocytes are increased in menopausal females and reversed by Hormone Replacement Therapy

Biological sex is a crucial, but poorly understood variable in age-related susceptibility to infections and chronic inflammation - inflammageing. Monocytes are important immune cells responsible for initiating and resolving inflammatory responses to infection. While changes in monocyte populations result in increased susceptibility to infection, there is limited research on the impact of age and sex on human monocyte phenotype and function. The aim of this work was to dissect the impact of increasing age and biological sex on human monocyte phenotype and function. Here we show that older females have increased inflammatory intermediate and non-classical monocytes compared to young. These monocyte subsets were the most inflammatory ex vivo and their frequency correlated with markers of systemic inflammation. Proteomic analysis of sorted monocyte populations demonstrated that the three human monocyte subsets have largely distinct phenotypes. Additionally, proteomic analysis identified key age-associated protein pathways, including complement cascade and phagocytosis, downregulated in monocytes from older compared to younger individuals. We confirmed the proteomics findings showing that circulating C3 concentrations were reduced with age in females but not males. This decrease in complement in older females resulted in reduced monocyte phagocytosis. Crucially, we demonstrate that in peri/menopausal females, Hormone Replacement Therapy (HRT) reversed this expansion in intermediate monocytes and decreased circulating CRP as compared to age matched controls. Importantly peri/menopausal females on HRT had increased C3 serum concentrations and significantly improved monocyte phagocytosis. The data presented here indicate the importance of menopause in ageing monocyte phenotype and function. This data highlights the potential use of HRT in restoring monocyte function in females during ageing.

immunology↗

bioRxiv2025

Multiplex-edited mice recapitulate woolly mammoth hair phenotypes

The woolly mammoth (Mammuthus primigenius) possessed a thick woolly coat and other cold-adaptive traits that enabled survival in harsh arctic environments. Current de-extinction efforts focus on genetically modifying the closely related Asian elephant to express woolly mammoth traits. In this study, we establish a multiplex-edited mouse model with modifications in genes associated with hair morphology and lipid metabolism, enabling insights into traits involved in developing woolly hair textures. Our optimized workflows achieved high editing efficiencies and produced genetically modified mice with simultaneous editing of up to seven different genes. Selected modifications include loss-of-function mutations in Fgf5, Tgm3, and Fam83g, among others. The resulting mice display exaggerated hair phenotypes including curly, textured coats, and golden-brown hair. This study advances methods of rapid establishment of complex genetic models. These approaches inform de-extinction efforts and research involving the genetic basis of mammalian hair development.

genetics↗

bioRxiv2025

Animal tracking with particle algorithms for conservation

The movements of aquatic animals affect their exposure to threats and the efficacy of conservation measures, such as Marine Protected Areas (MPAs). However, many species movements remain poorly understood and difficult to reconstruct from available datasets, hampering conservation efforts. This is especially the case for species that rarely surface, for which data are often limited to observations from acoustic telemetry (detections) and ancillary sensors, such as archival tags. Here, we pioneer the use of state-of-the-art particle algorithms to model animal movement, integrate datasets and assess MPA design, using a case study of the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. Our algorithms led to 5-fold improvements in maps of space use and 30-fold improvements in residency estimates (lower mean error) compared to prevailing heuristic methods. By formally integrating tracking datasets, we were uniquely able to examine movements beyond receivers into fished zones, MPA-scale residency and specific habitats beyond protected areas that may warrant protection. This work showcases a probabilistically sound modelling framework that is sufficiently fast, flexible and accessible to meet the demands of modern animal-tracking datasets in acoustic telemetry systems. This represents a marked advance for analyses of animal movements and MPA efficacy worldwide.

ecology↗

bioRxiv2024

Multi-scale phenotyping of senescence-related changes in roots of rapeseed in response to nitrogen deficiency

Senescence related markers have been widely studied in leaves in many plant species. Root senescence is more difficult to characterize. The existence of two different root organs in B. napus, with a taproot that appear to be specifically dedicated to the storage and remobilization of nutrients, offered the possibility of analysing the temporality of the changes linked to aging, based on the degradation of the taproot reserves. Microscopic and biochemical analyses showed that taproot plays an important role in carbon and nitrogen storage as reflected by the large quantities of starch and proteins present at early development stages. The proteomic study associated to the description of biochemical, morphological and anatomic changes provides a comprehensive picture of the main events occurring in the taproot and in the lateral roots with aging. Master modifications as protein and cell wall degradation, amino acid catabolism versus synthesis, nucleic acid degradation are presented and senescence related markers specific or not of the root types were identified. Comparison with Arabidopsis public data facilitated the identification of markers common to root and leaf senescence. The analysis of protease changes provides a list of candidates that may play a role in nitrogen and carbohydrate remobilization from taproot to the shoot and flowering organs and that would deserve attention for further functional analyses.

plant biology↗

bioRxiv2024

GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control (QC), and genome-wide association studies (GWAS) capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools "Ancestry" module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization, specified to the users genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIHs Center for Alzheimers and Related Dementias (CARD) and the Global Parkinsons Genetics Program (GP2). GenoTools was used to process and analyze the UK Biobank and major Alzheimers Disease (AD) and Parkinsons Disease (PD) datasets with over 400,000 genotypes from arrays and 5000 sequences and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous QC, and conducted genetic ancestry-specific GWAS to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotype data with reproducible and scalable ancestry, QC, and GWAS pipelines.

genomics↗

bioRxiv2024

A longevity-specific bank of induced pluripotent stem cells from centenarians and their offspring

Centenarians provide a unique lens through which to study longevity, healthy aging, and resiliency. Moreover, models of human aging and resilience to disease that allow for the testing of potential interventions are virtually non-existent. We obtained and characterized over 50 centenarian and offspring peripheral blood samples including those connected to functional independence data highlighting resistance to disability and cognitive impairment. Targeted methylation arrays were used in molecular aging clocks to compare and contrast differences between biological and chronological age in these specialized subjects. Isolated peripheral blood mononuclear cells (PBMCs) were then successfully reprogrammed into high-quality induced pluripotent stem cell (iPSC) lines which were functionally characterized for pluripotency, genomic stability, and the ability to undergo directed differentiation. The result of this work is a one-of-a-kind resource for studies of human longevity and resilience that can fuel the discovery and validation of novel therapeutics for aging-related disease.

molecular biology↗

bioRxiv2024

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

The crisis of biodiversity loss in the anthropogenic era requires new tools for studying non-model organisms. Elephants, for example, are both an endangered species and excellent models studying complex phenotypes like size, social behavior, and longevity, but they remain severely understudied. Here we report the first derivation of elephant (Elephas maximus) induced pluripotent stem cells (emiPSCs) achieved via a two-step process of chemical-media induction and colony selection, followed by overexpression of elephant transcription factors OCT4, SOX2, KLF4, MYC {+/-} NANOG and LIN28A, and modulation of the TP53 pathway. Since the seminal discovery of reprogramming by Shinya Yamanaka, iPSCs from many species including the functionally extinct northern white rhinocerous have been reported, but emiPSCs have remained elusive. While for multiple species the reprogramming protocol was adopted with little changes compared to model organisms like mouse and human, our emiPSC protocol requires a longer timeline and inhibition of TP53 expansion genes that are hypothesized to confer unique cancer resistance in elephants. iPSCs unlock tremendous potential to explore cell fate determination, cell and tissue development, cell therapies, drug screening, disease modeling, cancer development, gametogenesis and beyond to further our understanding of this iconic megafauna. This study opens new frontiers in advanced non-model organism cellular models for genetic rescue and conservation.

cell biology↗

bioRxiv2024

Quantifying forms and functions of intestinal bile acid pools in mice

Bile acids (BAs) are gastrointestinal metabolites that serve dual functions in lipid absorption and cell signaling. BAs circulate actively between the liver and distal small intestine (i.e., ileum), yet the dynamics through which complex BA pools are absorbed in the ileum and interact with intestinal cells in vivo remain ill-defined. Through multi-site sampling of nearly 100 BA species in individual wild type mice, as well as mice lacking the ileal BA transporter, Asbt/Slc10a2, we calculate the ileal BA pool in fasting C57BL/6J mice to be [~]0.3 moles/g. Asbt-mediated transport accounts for [~]80% of this pool and amplifies size, whereas passive absorption explains the remaining [~]20%, and generates diversity. Accordingly, ileal BA pools in mice lacking Asbt are [~]5-fold smaller than in wild type controls, enriched in secondary BA species normally found in the colon, and elicit unique transcriptional responses in cultured ileal explants. This work quantitatively defines ileal BA pools in mice and reveals how BA dysmetabolism can impinge on intestinal physiology.

physiology↗