Biology subjects

Wood, C.

Publications and source records attributed to Wood, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Human CD4 T cells coordinate antitumor immunity through indirect antigen presentation

Whether human tumor-specific CD4 T cells can drive antitumor immunity in cancers lacking tumor-cell MHC class II expression has not been established. In MHC class II-negative melanoma and breast cancer, CD4 T cells with a transcriptional signature of tumor specificity correlated with myeloid and CD8 T cell activation. Using a patient-derived NY-ESO-specific, HLA-DP04-restricted TCR, we tested whether human CD4 T cells could control tumors through indirect antigen presentation. In vitro, CD4 T cells inhibited HLA-DP-negative melanoma growth through recognition of tumor-derived antigen on antigen presenting cells (APC). In humanized mice, CD4 T cell transfer induced regression of HLA-DP-negative tumors, and control required HLA-matched human APCs. CD4 T cell transfer induced endogenous CD8 T cell proliferation and myeloid activation that mirrored immune programs correlated with the presence of these cells in patients. These findings establish that human tumor-specific CD4 T cells coordinate antitumor immunity through APC without direct tumor recognition, supporting their therapeutic relevance in MHC class II-negative cancers.

immunology↗

bioRxiv2026

A randomized trial of grant writing coaching groups: Qualitative interviews revealing key elements of intervention efficacy

Background Training in grant proposal writing is an essential component of professional development for academic scientists in the biomedical and behavioral sciences. Despite the expansion of inter- and intra-institutional grant writing coaching groups as an approach to honing these skills, specific features that enhance or limit coaching group effectiveness have not been rigorously studied. Methods Qualitative inerviews were conducted with a subset of early-career investigators (n=204 and coaches (n=36) engaged in a national, U.S. based, group-randomized trial of grant writing coaching groups to test the effects of two variables on submission and funding of national-level proposals: (1) coaching duration (regular/extended dose) and (2) mode of engaging a scientific advisor (someone with content-aligned expertise) in the coaching process. This report focuses on interviews conducted upon completion of the regular coaching dose - 5 months of biweekly, group-based coaching sessions to support active proposal writing. Interviews were designed to identify which coaching group elements were perceived to be the most critical. Transcribed interviews were analyzed using deductive (participants) or open (coaches) coding to identify themes. Results Triangulation of results from participant and coach interviews showed strong concordance that coaches, peers, and scientific advisors all played key roles in supporting intervention efficacy. Sufficient alignment of scientific fields and/or methodologies among group members was important, although breadth of perspectives was also valued. Other critical group features were skilled and well-organized coaches, detailed feedback, peer-to-peer support (technical and psychosocial), and clear expectations for group functioning. Factors attenuating impact included variation in participants' engagement and "readiness to write," within-group mismatches of expertise or grant mechanisms, and limited research support at some participants' home institutions. Conclusion This study identified key elements of successful grant writing coaching groups and potential barriers to their effectiveness, while yielding insights about tailoring this approach for individuals at different stages of proposal development.

scientific communication and education↗

bioRxiv2026

Strong effects of soil microbes on early-life defense alter phenotypic correlations in plant leaves

Microbes have wide-ranging effects on host phenotype. However, whether these effects extend to the relationships among host traits remains unknown. We tested whether microbes affect phenotypic correlations among early life traits in the weedy legume Medicago lupulina. In a field common garden, we inoculated plants with two types of microbes: nitrogen-fixing bacteria and rhizosphere microbial communities. We found that microbes modify phenotypic integration (phenotypic correlations) in leaves, primarily due to effects on independent effects on leaflet area and trichome density, a defense trait. While microbial effects on leaflet size were associated with overall plant growth, variation in trichome density was decoupled from growth and not predicted by investment in mutualism. Our results highlight the unique insights that can come from a multivariate approach to organismal plasticity, and raise the intriguing possibility that microbes may have an outsized impact on defense traits and their integration with organismal function.

Plant Biology↗

bioRxiv2026

Lipopolysaccharide Precursor Mutants Disrupt Unipolar Polysaccharide Adhesin Synthesis and Cell Surface Functions in Agrobacterium tumefaciens

Agrobacterium tumefaciens is a facultative phytopathogen and causative agent of crown gall disease, capable of attaching to surfaces via a polarly localized unipolar polysaccharide (UPP) adhesin. The UPP is composed of two distinct forms, one characterized by N-acetylglucosamine residues (UPPGlcN) and the other by N-acetylgalactosamine residues (UPPGalN). Two genes with presumptive roles in dTDP-L-rhamnose biosynthesis, rfbA and rfbD, were identified in a transposon screen to be involved specifically in UPPGalN biosynthesis. Examination of independent rfbA and rfbD mutations validates the transposon mutant phenotypes, with UPPGalN specific defects observed as well as general attachment defects and UPP-mediated cellular aggregation across all rfb mutants. Additionally, despite retaining flagella, mutations in the rfb genes impart flagellar motility defects. Suppressor mutations that rescue the non-motile {Delta}rfbD phenotype disrupt the remaining rfb genes (rfbA, rfbB, and rfbC), the phosphoglucomutase exoC and a putative glycosyl transferase ATU-RS21610. Single deletion mutants in the dTDP-L-rhamnose pathway also have hallmarks of compromised outer membrane integrity, such as increased sensitivity to high-molecular weight antibiotics and increased expression of target genes for the widely conserved ChvG-ChvI two component system outer membrane stress response. Thus, defects in the dTDP-L-rhamnose pathway cause multiple cell surface deficiencies, resulting in outer membrane stress, impaired flagellar motility, defective UPP production, and irregular adhesion. ImportssssanceBiofilms are clinically and industrially relevant in many different contexts, with substantial health impacts and monetary costs. Surface attachment and motility are essential components necessary for bacterial biofilm formation. Many microbes utilize specific surface appendages or structures to facilitate attachment and motility. This study probes the process of surface attachment and subsequent biofilm formation in A. tumefaciens and has revealed connections between the creation of polysaccharide precursors required for biofilm formation and outer membrane functions such as motility and membrane integrity. These findings broaden our understanding of the complex interactions between outer membrane surface functions and how disruption of relevant precursor pools can have multifaceted impacts that may represent useful targets for new antimicrobial approaches.

microbiology↗

bioRxiv2026

Pericentromeric repeat copy number tunes heterochromatin dosage to control chromosome segregation and gene expression in fission yeast

Centromeres are essential for chromosome segregation, yet in many genomes they are composed entirely of rapidly evolving repetitive DNA, embedded in other repetitive DNA that forms pericentromeric heterochromatin. Due to the difficulties of manipulating these repeat-rich regions, how the relative size of pericentromeric repeat regions influences chromosome segregation remains an open question. Here, we take advantage of the tractable Schizosaccharomyces pombe system by combining population-level analysis, complete long-read assemblies, and engineered near-isogenic strains to test how pericentromeric repeat copy number affects chromosome biology in its native context. We find that pericentromeric dh/dg arrays on chromosome 3 vary almost tenfold in size among natural S. pombe isolates, ranging from 35 to 265 kb. We converted this natural diversity into an experimental system of nearly isogenic strains that primarily differ in pericentromere size (35 to >350 kb). We found that pericentromere size does not alter baseline growth under standard conditions. However, larger pericentromeres alter transcriptional output and sensitize cells to spindle stress. We show that this spindle-stress phenotype depends on heterochromatin: loss of the H3K9 methyltransferase Clr4 abolishes size-dependent differences, whereas artificial targeting of the Chromosomal Passenger Complex to heterochromatin partially rescues the defect. Thus, we find that larger pericentromeres act as sinks for limiting regulatory factors, weakening their effective concentration at centromeres and compromising faithful chromosome segregation under stress. These results establish that naturally occurring copy-number variation within repetitive pericentromeric DNA is not merely noise, but a functional source of variation in chromosome segregation and gene regulation. Our work provides an experimentally tractable framework for understanding how repeat expansion in centromere-proximal heterochromatin influences chromosome behavior across eukaryotes.

genetics↗

bioRxiv2026

PSF-Driven Spatio-Temporal Blending in Fluorescence Lifetime Imaging Microscopy and Its Mitigation via Mean-Shift Super-Resolution-Based Masking.

Fluorescence Lifetime Imaging Microscopy (FLIM) enables quantitative mapping of molecular environments in living systems with high biochemical specificity. However, spatial overlap dictated by the diffraction-limited point spread function (PSF) causes a mixing of temporal signals: photons from neighboring emitters collected within the same pixel yield composite decay profiles, generating apparent intermediate lifetimes that can be mistaken for variations in the local molecular environment. We introduce a workflow that applies Mean-Shift Super-Resolution (MSSR) to raw intensity data to generate intensity-derived spatial masks prior to phasor-based lifetime analysis. The method is computationally efficient and preserves decay kinetics because it operates on intensity-derived spatial information rather than modifying temporal data. In U2OS cells labeled with spectrally-overlapping fluorophores, phasor analysis reveals an intermediate lifetime population localized at PSF-overlap interfaces, consistent with optical mixing rather than intrinsic lifetime heterogeneity. MSSR-derived masking suppressed this mixed population while preserving stable phasor cluster centers -i.e. the distribution of similar phasor coordinates in the phasor plane- for each fluorophore. Simulations of strictly monoexponential fluorescence decay emitters further show that blended lifetime decay profiles are present at separations up to 4{sigma} and becomes maximal near [~]1.6{sigma}, indicating that conventional spatial resolution criteria can underestimate lifetime cross-talk. Application of this workflow to three-component FLIM showed also a reduced overlap of pixel distributions in phasor plots while maintaining distinct lifetime signatures. Overall, MSSR-based spatial refinement provides an accessible strategy to improve the spatial resolution while maintaining accuracy of FLIM measurements.

biophysics↗

bioRxiv2025

Horizontal Gene Transfer of E. coli by direct DNA uptake from extracellular liquid phase

The "fate of naked DNA" or "environmental DNA (eDNA)" from genetically engineered (GE) biomasses in relation to possible horizontal gene transfer (HGT) is an emerging area of biosafety research. Using a broad-host plasmid (pAM5409) as a mimic of eDNA containing a yellow fluorescent protein gene (yfp) and conferring spectinomycin/streptomycin (Sp/Sm) resistance, we incubated each of the E. coli strains DH5, DH10B and K12 with the plasmid eDNA to evaluate HGT through direct uptake of plasmid DNA from extracellular liquid phase. According to experimental observations, the HGT can occur within 1 day of donor (eDNA) and recipient cells liquid incubation in E. coli strains DH5 and DH10B, but not in K12 which has its intact genes encoding restriction enzymes and endonucleases. HGT occurrences were observed by analyzing colony forming units (CFU) expression of yellow fluorescent protein (YFP). The HGT frequency by direct uptake of plasmid DNA from the liquid phase was determined to be 1.2 x 10-8 per cell day for both DH5 and DH10B. The frequency of HGT was slightly higher than that of spontaneous mutation for natural antibiotic resistance development that was estimated to be 4.8 x 10-9 per cell day. Extension of the liquid eDNA and recipient cells incubation time from 1 day to 3 and 5 days did not increase the HGT frequency under the current experimental conditions. Despite K12 failing to form CFUs following exposure to eDNA, this does not imply K12 did not uptake eDNA; eDNA acquired could have been fragmented by K12 restriction enzymes into non-functional oligomers incapable of HGT.

molecular biology↗

bioRxiv2025

MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.

bioinformatics↗

bioRxiv2025

Single Cell Transcriptome Signatures of Sarcoidosis in Lung Immune Cell Populations

RationaleTo identify cell specific molecular changes associated with sarcoidosis risk and progression, we aimed to characterize the cellular composition, gene expression patterns, and cell-cell interactions in BAL cells from patients with sarcoidosis (both progressive and non-progressive) and healthy controls. MethodsSingle cell RNA-seq data were collected on 12 sarcoidosis and 4 control participants. We combined scRNA-seq data from these participants with our previously collected data on 4 sarcoidosis and 10 control participants for a final sample size of 16 sarcoidosis cases (8 progressive and 8 non-progressive) and 14 controls. Following initial preprocessing in CellRanger, data were quality controlled, combined, and clustered in Seurat. We tested differences in cell proportions by disease group using F-tests on cell proportions and differences in gene expression using pseudobulk analysis. Cell to cell communication and pathway analysis were performed using CellChat. ResultsWe identified five macrophage populations: resident, high metallothionein (MT) resident, recruited, profibrotic recruited, and proliferating macrophages. Each subpopulation displayed unique gene expression profiles, with notable differential expression of genes and pathways linked to sarcoidosis in resident macrophages, recruited macrophages, and proliferating macrophages. We also observed changes in gene expression associated with disease progression in resident and recruited macrophages. In non-macrophages cells, we observed a significant reduction in the number of B cells in sarcoidosis patients compared to controls. Among T cell populations, we identified specific transcriptional alterations at gene and pathway level. Additionally, we observed distinct differences in cell-to-cell interactions of macrophages and T cells between sarcoidosis patients and healthy controls. ConclusionsThese findings underscore the complexity of immune cell involvement in sarcoidosis and highlight potential cellular and molecular targets for further investigation.

genomics↗

bioRxiv2025

Testing for divergence in a plant symbiont across two natural environmental gradients

Many plant endosymbionts are facultative, switching between host-associated and free-living stages. Extensive genomic and experimental studies suggest that adaptation during the saprophytic, off-host phase, rather than adaptation to hosts, primarily constrains the biogeographic distribution of these microbes. To test this hypothesis, we analyzed the growth capacities and genomic features of 38 Sinorhizobium strains nodulating Medicago lupulina (black medic), collected from two regions with distinct thermal environments. The warmer region is predominantly inhabited by S. meliloti, while S. medicae and non-symbiotic strains (lacking symbiosis genes, such as S. canadensis and S. adherens) are more common in the cooler region. Laboratory assays demonstrated that at 40{degrees}C, the upper temperature limit of their region of origin, S. meliloti remained viable, albeit with reduced growth, whereas S. medicae and non-symbiotic strains failed to grow under heat stress. Comparative genomics revealed isolation-by-distance in both the core and accessory genomes, particularly in S. meliloti in the warmer region, which exhibits less within-region thermal variation. This is consistent with an isolation-by-distance model where population divergence is governed by restricted gene flow. These findings suggest that metabolic constraints shape the regional distribution of this facultative microbial symbiont, while limited gene flow influences local population structure.

evolutionary biology↗

bioRxiv2024

Cave Adaptation Favors Aging Resilience in the Mexican Tetra

All animals age, but the rate at which some species age varies widely. What environmental pressures and what molecular factors underlie the remarkable diversity in aging and lifespan across species remains largely enigmatic. The Mexican tetra, Astyanax mexicanus, serves as an intriguing new model to study how adaptations to different environments can change aging. This species exists as two morphotypes: the river-dwelling surface fish, which inhabits environments rich in food and light, and the blind cave-adapted cavefish, that thrive in dark, nutrient-limited but predator free environments. Nutrient limitation and lack of predation are known to impact lifespan, however, how adaption to such environments changes the aging trajectory in this species remains unknown. Here, we compared aging markers between surface and cavefish populations, focusing on morphological and behavioral changes, as well as molecular signatures, and found that aging markers are pronounced and evident in surface fish, whereas these signatures are less distinct in aged cavefish. Using zebrafish, we explored the contribution of the cavefish insulin receptor mutation to longevity. Although the insulin receptor mutation is sufficient to increase lifespan in fish, our findings suggest its impact is limited. Instead, our data indicate that metabolic shifts, particularly those related to mitochondrial function, may be key contributors to the extended longevity observed in cavefish.

evolutionary biology↗

bioRxiv2024

Genome-Wide Association Study and transcriptome analysis reveals a complex gene network that regulates opsin gene expression and cell fate determination in Drosophila R7 photoreceptor cells.

BackgroundAn animals ability to discriminate between differing wavelengths of light (i.e., color vision) is mediated, in part, by a subset of photoreceptor cells that express opsins with distinct absorption spectra. In Drosophila R7 photoreceptors, expression of the rhodopsin molecules, Rh3 or Rh4, is determined by a stochastic process mediated by the transcription factor spineless. The goal of this study was to identify additional factors that regulate R7 cell fate and opsin choice using a Genome Wide Association Study (GWAS) paired with transcriptome analysis via RNA-Seq. ResultsWe examined Rh3 and Rh4 expression in a subset of fully-sequenced inbred strains from the Drosophila Genetic Reference Panel and performed a GWAS to identify 42 naturally-occurring polymorphisms--in proximity to 28 candidate genes--that significantly influence R7 opsin expression. Network analysis revealed multiple potential interactions between the associated candidate genes, spineless and its partners. GWAS candidates were further validated in a secondary RNAi screen which identified 12 lines that significantly reduce the proportion of Rh3 expressing R7 photoreceptors. Finally, using RNA-Seq, we demonstrated that all but four of the GWAS candidates are expressed in the pupal retina at a critical developmental time point and that five are among the 917 differentially expressed genes in sevenless mutants, which lack R7 cells. ConclusionsCollectively, these results suggest that the relatively simple, binary cell fate decision underlying R7 opsin expression is modulated by a larger, more complex network of regulatory factors. Of particular interest are a subset of candidate genes with previously characterized neuronal functions including neurogenesis, neurodegeneration, photoreceptor development, axon growth and guidance, synaptogenesis, and synaptic function.

genomics↗

bioRxiv2024

Population sequencing for diversity and transmission analyses

Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of colonies to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences of Burkholderia pseudomallei from the sputum of a single patient. We also analyzed population sequences of Staphylococcus aureus derived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses of B. pseudomallei populations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses of S. aureus samples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity. Author SummaryThe ability to characterize diversity in a single bacterial population (i.e., a single host or even a single body site) is critical for understanding adaptation and evolution, with far-reaching implications on disease treatment and prevention that include revealing patterns of spread and persistence. While the scientific community has made great strides in sequencing methods to characterize single colonies and entire communities, there is a dearth of studies at the population level. This is because 1) the need to culture and sequence a sufficiently representative number of isogenic colonies is prohibitive, and 2) the theoretical foundation for characterizing a population by sequencing a single sample (as is done for microbiome and metagenomic analyses) has not been developed. Here, we introduce this theoretical foundation and validate its applicability by characterizing a lung infection caused by Burkholderia pseudomallei. We also demonstrate the utility of this method in determining the directionality of spread of Staphylococcus aureus between people and across body sites within the same host (a level of spatial resolution that has not been previously performed). We anticipate that this work will open the door to a host of new studies and discoveries across a diverse set of microbiological fields.

evolutionary biology↗

bioRxiv2024

Environmental and molecular control of tissue-specific ionocyte differentiation in zebrafish

Organisms adjust their physiology to cope with environmental fluctuations and maintain fitness. These adaptations occur via genetic changes over multiple generations or through acclimation, a set of reversible phenotypic changes that confer resilience to the individual. Aquatic organisms are subject to dramatic seasonal fluctuations in water salinity, which can affect the function of lateral line mechanosensory hair cells. To maintain hair cell function when salinity decreases, ion-regulating cells, Neuromast-associated ionocytes (Nm ionocytes), increase in number and invade lateral line neuromasts. How environmental changes trigger this adaptive differentiation of Nm ionocytes and how these cells are specified is still unknown. Here, we identify Nm ionocyte progenitors as foxi3a/foxi3b-expressing skin cells and show that their differentiation is associated with sequential activation of different Notch pathway components, which control ionocyte survival. We demonstrate that new Nm ionocytes are rapidly specified by absolute salinity levels, independently of stress response pathways. We further show that Nm ionocyte differentiation is selectively triggered by depletion of specific ions, such as Ca2+ and Na+/Cl-, but not by low K+ levels, and is independent of media osmolarity. Finally, we demonstrate that hair cell activity plays a role in Nm ionocyte recruitment and that systemic factors are not necessary for Nm ionocyte induction. In summary, we have identified how environmental changes activate a signaling cascade that triggers basal skin cell progenitors to differentiate into Nm ionocytes and invade lateral line organs. This adaptive behavior is an example of physiological plasticity that may prove essential for survival in changing climates.

developmental biology↗

bioRxiv2023

The Neonatal Gyrencephalic Cortex Maintains Regionally Distinct Streams of Neuroblasts

Neurodevelopmental mechanisms have evolved to support the formation of diverse brain structures, such as in humans, during the perinatal period. Here, we demonstrate that neonatal gyrencephalic brains harbor an expanded subventricular zone, termed the Arc, defined by tiered arrangement of doublecortin (DCX)-expressing neuroblasts and vascular enrichment at the ventricular wall. The Arc is the origin of dorsal and ventral populations of migratory neuroblasts that target multiple regions involved in higher cognitive functions. Arc-derived migratory streams, primarily from the caudal ganglionic eminence, are composed of diverse neuronal subtypes with distinct spatial and migratory-receptor profiles. Our findings indicate the Arc is a structure present in phylogenetically divergent species that supports the expansion of postnatal neuronal migration, contributing to a protracted formation of cortical circuits in gyrencephalic brains. One-Sentence SummaryThe ventricular cytoarchitecture of gyrencephalic brains supports an ongoing supply of migratory neurons to the neonatal cortex.

neuroscience↗

bioRxiv2022

The python-derived 16α-hydroxylated bile acid, pythocholic acid decreases food intake and increases jejunal fatty acid ethanolamides in mice.

ObjectiveModulation of bile acid (BA) structure is a potential strategy for obesity and metabolic disease treatment. BAs act not only as signaling molecules involved in energy expenditure and glucose homeostasis, but also as regulators of food intake. The structure of BAs, particularly the position of the hydroxyl groups of BAs impacts food intake partly by intestinal effects: (1) modulating the activity of N-acyl phosphatidylethanolamine phospholipase D (NAPE-PLD), which produces the anorexigenic bioactive lipid oleoylethanolamide (OEA), or (2) regulating lipid absorption and the gastric emptying-satiation pathway. We hypothesized that 16-hydroxylated BAs uniquely regulate food intake, because of the long intermeal intervals in snake species in which these BAs are abundant. However, the effects of 16-hydroxylated BAs in mammals are completely unknown, because 16-hydroxylated BAs are not naturally found in mammals. To test the effect of 16-hydroxylated BAs on food intake, we isolated the 16-hydroxylated BA pythocholic acid from ball pythons (Python regius). MethodsPythocholic acid or deoxycholic acid (DCA) were given by oral gavage in mice. DCA is known to increase NAPE-PLD activity better than other mammalian BAs. We evaluated food intake, OEA levels and gastric emptying in mice. ResultsWe successfully isolated pythocholic acid from ball pythons for experimental use. Pythocholic treatment significantly decreased food intake compared with DCA treatment, and this was associated with increased jejunal OEA, but no change in gastric emptying or lipid absorption. ConclusionThe exogenous bile acid pythocholic acid is a novel regulator of food intake and the satiety signal OEA in the mouse intestine. HighlightsO_LIPythocholic acid decreases food intake. C_LIO_LIPythocholic acid increases intestinal OEA and other fatty acid ethanolamides. C_LIO_LIThe effects of pythocholic acid on OEA and hypophagia are greater than the effects of DCA. C_LIO_LIPythocholic acid does not affect lipid absorption or gastric emptying. C_LI

pathology↗

bioRxiv2022

Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube

Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here we optimized single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the RA response.

developmental biology↗

bioRxiv2022

ADOLESCENT EXPOSURE TO LOW-DOSE THC DISRUPTS ENERGY BALANCE AND ADIPOSE ORGAN HOMEOSTASIS IN ADULTHOOD

One of cannabis most iconic effects is the stimulation of hedonic high-calorie eating - the munchies - yet habitual cannabis users are on average leaner than non-users. We asked whether this unexpected phenotype might result from lasting changes in energy balance established during adolescence, when habitual use of the drug often begins. We found that daily low-dose administration of cannabis intoxicating constituent, {Delta}9-tetrahydrocannabinol (THC), to adolescent mice causes an adult metabolic phenotype characterized by reduced fat mass, increased lean mass and utilization of fat as fuel, partial resistance to diet-induced obesity and dyslipidemia, and enhanced thermogenesis. Multi-omics analyses revealed that this phenotype is associated with multiple molecular anomalies in the adipose organ, which include ectopic overexpression of muscle-associated proteins and heightened anabolic processing. Thus, adolescent exposure to THC may promote an enduring pseudo-lean state that superficially resembles healthy leanness but might in fact be rooted in adipose organ dysfunction.

pharmacology and toxicology↗