Biology subjects

Shah, A.

Publications and source records attributed to Shah, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Cln3 can work independently of Whi5 on the cell size for Start in yeast

In yeast, cells commit to division at "Start" in G1 phase. The critical cell size for Start is regulated in part by the size-control genes CLN3 and WHI5. Cln3 is a G1 cyclin that activates Start by activating the Cdc28 cyclin dependent kinase. Null cln3 mutants have large cells, because they lack an activator, while hyperactive mutants have small cells. Whi5 inhibits Start. Null whi5 mutants have small cells, while hyperactive mutants have large cells. Previous studies suggested that CLN3 and WHI5 are in a linear, dependent pathway, in which Cln3 acts inhibits Whi5, possibly by phosphorylation. We compared isogenic WT, cln3, whi5, and cln3 whi5 mutants, and find that whi5 is not epistatic, or not fully epistatic, to CLN3--that is, CLN3 can work independently of WHI5. The cln3 and whi5 deletions have off-setting phenotypes, such that the double mutant is nearly wild-type in cell size, and has only the mildest phenotype, with well-controlled cell size, despite entirely lacking two major cell size regulators. Growth rates were also measured. Some mutants were larger and some mutants smaller than wild-type, but the wild-type had the fastest doubling time, consistent with the idea that wild-type size is optimal for growth rate.

genetics↗

bioRxiv2025

Glucose promotes neuron morphology abnormalities and egg-laying defects dependentofthe serotonin signaling pathway in Caenorhabditis elegans

A chronic hyperglycemic state can lead to neuropathological complications such as permanent nerve damage. Neuropathology is a debilitating ailment that affects nearly half of the individuals with diabetes, underscoring the relevance to investigate the impact of diet and glucose levels on the nervous system. Using the genetic model system Caenorhabditis elegans, we determined that a diet rich in glucose impacts biological processes dependent on neuronal function. The rate of intrauterine egg-hatching increased in animals fed a glucose diet and the inhibition of dopamine or serotonin is sufficient to counteract the impact of the glucose diet. The glucose-induced intrauterine egg-hatching phenotype is independent of the SER-1 and SER-7 receptors yet dependent on the DAF16/FOXO transcription factor. Furthermore, animals fed a glucose-supplemented diet displayed abnormal morphologies in the HSN and NSM serotonergic neurons and the HSN displayed axonal degeneration, which is a prominent pathological feature in neurological dysfunction and disease. Combined these data indicate that a glucose-diet affects nervous system and signaling pathways in C. elegans, which can be used to further model diet-induced neuropathy.

genetics↗

bioRxiv2025

MetaScope: A High-Resolution Framework for Species-Level 16S Metataxonomic Classification

Accurate species-level classification of microbial communities remains a major challenge in microbiome analysis, particularly when using traditional 16S rRNA amplicon sequencing pipelines such as QIIME2 and DADA2. These methods often fail to resolve taxonomy beyond the genus level due to limitations in clustering algorithms and ambiguous marker genes. To address this, we present MetaScope, a modular, R-based software package that reimplements and extends the PathoScope 2.0 framework for high-resolution microbial classification. MetaScope introduces two key innovations: (1) the integration of user-defined or empirical prior weights into the Bayesian read reassignment algorithm to improve abundance estimation, and (2) MetaBlast, a secondary BLAST-based validation module for refining species-level assignments. Benchmarking against mock and clinical datasets demonstrates that MetaScope significantly outperforms QIIME2 and DADA2, achieving up to 93.6% species-level classification accuracy. This translates to offering enhanced resolution for downstream analyses such as ecological diversity metrics. These results highlight MetaScope as a powerful tool for advancing microbial community profiling in both research and clinical settings.

bioinformatics↗

bioRxiv2025

Antitachycardia Pacing is More Effective When Delivered to the Left Bundle Branch Area Compared to the Right Ventricle in a Pre-clinical Model of Ischemic Ventricular Tachycardia

BackgroundAnti-tachycardia pacing (ATP) delivered from implantable cardioverter defibrillators (ICDs) provides critically timed pacing pulses to terminate ventricular tachycardia (VT). Physiological pacing through left bundle branch area (LBBA) pacing has emerged as a clinically relevant alternative to induce synchronous activation of the ventricles. The main objective of this study was to compare the efficacy and safety of ATP delivered to an LBBA lead and a conventional RV lead. MethodsUsing a preclinical animal model (n=7), pacing leads were implanted in the RV apex and LBBA and connected to ICDs. The left anterior descending artery was occluded for two hours to cause an ischemia-reperfusion injury (IRI). Four days following IRI, VT episodes were induced using programmed electrical stimulation (PES), and burst ATP therapy was delivered to the RV or LBBA leads for each VT episode. ResultsVT was induced 80 times, with a mean VT cycle length (VT CL) of 180.0{+/-}30.0 ms. ATP delivered to the LBBA terminated VT more often than RV ATP (70.2% vs 47.3%, P = 0.04), and there was no significant difference in negative outcomes of VT acceleration or VF induction. Activation sequences from the basket catheter were determined for the pre-therapy VT and captured ATP beats, and correlation coefficients were computed to the activation sequences during ATP delivery. The number of ATP pulses required for the activation sequences to correlate with the captured ATP pattern rather than the pre-therapy VT pattern was lower for LBBA ATP compared to RV ATP (4.1 vs. 5.1 beats, P = 0.04). Successful LBBA ATP demonstrated earlier and more frequent Purkinje activations preceding myocardial activation than successful RV ATP. ConclusionImproved performance of LBBA ATP compared to RV ATP provides further incentive for the wide use of LBBA leads in patients who need cardiac electrotherapy.

bioengineering↗

bioRxiv2025

Engineering Escherichia coli FAD synthetase for the biosynthesis of FAD nucleotide analogues results in aminoglycoside antibiotic tolerance

Cofactors such as flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide, coenzyme A, and S-adenosylmethionine cofactors share a common adenosine moiety that is generally not considered to contribute directly to catalysis. In FAD biosynthesis, the adenosine group is installed by the flavin mononucleotide adenylyltransferase (FMNAT) domain of the bifunctional FAD synthetase using FMN and ATP. This study explores the nucleotide selectivity of the Escherichia coli FMNAT domain and physiological effects of FAD nucleotide analogues synthesized with cellular nucleotides other than ATP. First, we engineer the FAD synthetase enzyme at an active site loop to produce FAD nucleotide analogues. Chromosomal substitution of the wild-type E. coli FAD synthetase with the mutated version results in the intracellular synthesis of these noncanonical FAD nucleotide analogues and confers tolerance to aminoglycoside antibiotics. Upon investigating their potential downstream metabolic roles, we find that their biosynthesis perturbs cellular metabolism and they could bind to a range of E. coli enzymes. These findings validate the FMNAT domain loop as a viable site for cofactor engineering, with potential for synthetic biology applications. Finally, the observed correlation between FAD analogue production and increased tolerance to aminoglycosides reveals novel metabolic mechanisms underlying antibiotic sensitivity.

microbiology↗

bioRxiv2025

Selective targeting of IL-1RAP-dependent eosinophilic inflammation in allergic fungal airway disease

It is estimated that in excess of 10 million people around the globe are affected by severe asthma and fungal sensitisation (SAFS) or allergic bronchopulmonary aspergillosis (ABPA), severe asthma endotypes driven by hypersensitivity to environmentally ubiquitous fungal pathogens, primarily Aspergillus fumigatus. Here, we sought to define the immunological pathways underlying these allergic fungal airway diseases. To do so, we exploit the chronic exposure repeat challenge model using live A. fumigatus conidia to systematically define the key immunological pathways driving airway inflammation in allergic fungal airway disease. In response to daily intranasal challenge, we observed increased absolute numbers of neutrophils and eosinophils in bronchoalveolar lavage fluid (BALF), characteristic of human allergic fungal airway disease, with significant depletion of the alveolar macrophage population. Transcriptomic analysis of BALF cells identified increased expression of IL-1 family cytokines and receptors including IL-1{beta}, IL-1RL1, IL-1R2 and the IL-18 binding protein. Complementary proteomic analysis of BALF revealed increased levels of cell death related proteins calprotectin and IL-1 Receptor Accessory Protein (IL-1RAP). Targeting IL-1RAP, using knockout mice, led to selective reduction in eosinophilia, IL-5 and IL-13 in the airways without impairment of fungal killing. This study identifies a role for IL-1RAP in the generation of eosinophilia independent of neutrophil influx and highlights its potential as a novel immunotherapeutic target for the treatment of allergic fungal airway disease. Author SummaryAllergic bronchopulmonary aspergillosis (ABPA) is a form of lung disease primarily affecting those with asthma or cystic fibrosis induced by the ubiquitous pathogen Aspergillus fumigatus. Understanding the immunological mechanisms contributing to this airway disease is important for the development of novel treatments to improve quality of life and preserve lung function. In this study, we show that an Aspergillus fumigatus repeat challenge model phenocopies immunological features of allergic fungal airway disease and is hallmarked by increased IL-1 family signalling. We identify the IL-1RAP as a contributor to eosinophilia and the release of Type 2 cytokines during allergic fungal airway disease. This work represents major step in describing the molecular mechanisms of airway eosinophilia in response to fungal exposure and lays the groundwork for further dissection of inflammatory pathways to target with immunotherapeutic approaches.

immunology↗

bioRxiv2025

Prenatal Zika Virus Exposure Disrupts Social-Emotional Development and Cortical Visual Function in Infant Macaques

Prenatal exposure to Zika virus (ZIKV) results in a spectrum of outcomes, ranging from severe birth defects and early childhood developmental delays to no apparent deficits. However, the mechanisms underlying these outcomes, particularly in the context of different maternal infection conditions, remain poorly defined. In this study, we employed a translational rhesus macaque model of prenatal ZIKV infection to evaluate longitudinal visual and auditory development from 1 to 12 months of age and characterize neurodevelopmental outcomes at 12 months. Pregnant macaques, either flavivirus-naive or with prior dengue virus (DENV) exposure, were inoculated in the first trimester ([~]30 or 45 gestational days) with an Asian or African lineage of ZIKV or received a saline injection as controls. Maternal plasma viremia duration, viral RNA burden at the maternal-fetal interface, and neutralizing antibody titers did not differ between inoculation cohorts or controls. At 12 months, ZIKV-exposed infants demonstrated altered maternal attachment behaviors and reduced inhibition when approaching sensory stimuli compared to controls. Visual pathway function, assessed by electrophysiology, was significantly impaired at 3 months but normalized by 12 months. Hearing loss was more common among ZIKV-exposed infants, although not statistically significant. Developmental outcomes were associated with prenatal ZIKV exposure itself, independent of viremia duration, neutralizing antibody titer, viral lineage, or maternal DENV immunity, and were not mediated by visual impairment or hearing loss. These findings highlight that any prenatal ZIKV exposure can disrupt early neurobehavioral development and visual function, underscoring the need for prevention strategies focused on maternal infection and early intervention.

microbiology↗

bioRxiv2025

rDNAcaller: a fast and robust pipeline to call ribosomal DNA variants

Ribosomal DNA (rDNA) genes are essential components of the ribosome, organized as tandem repeats on the mammalian genomes. Extensive genetic and copy number variation in rDNA has been reported both within and between individuals, contributing to phenotypic diversity. However, previous rDNA variant calling strategies have relied on methods designed for diploid regions and have not been systematically benchmarked. With the recent availability of a telomere-to-telomere (T2T) genome assembly, rDNA regions have been fully assembled for the first time, enabling benchmarking and optimization of rDNA variant calling strategies. We developed a customized simulator that replicates real intra- and inter-individual rDNA variation based on the T2T assembly to benchmark the performance of commonly used variant callers, including GATK, Mutect2, and Lofreq. Additionally, we optimized the preprocessing and mapping steps to remove pseudogenes and significantly improve accuracy. Based on these optimizations, we introduce rDNAcaller, a novel pipeline for accurate rDNA variant detection using short-read whole-genome sequencing. rDNAcaller integrates optimized preprocessing with the top-performing variant caller and achieves 94% precision on experimental data from the T2T cell line. Applying our pipeline to data from the 1000 Genomes Project, we identify 5,607 novel rDNA variant positions across human populations, with African individuals showing the highest number of variants. Overall, rDNAcaller is a robust and versatile tool for analyzing rDNA variation, addressing the limitations of existing methods in handling high ploidies. By enabling accurate detection of rDNA variants, it facilitates deeper exploration of rDNAs role in phenotypic diversity, supporting future genomic studies and broadening our understanding of rDNA biology in health and disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/653643v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@148419borg.highwire.dtl.DTLVardef@cb3b42org.highwire.dtl.DTLVardef@9fa802org.highwire.dtl.DTLVardef@1cf4ff0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Small molecule bioactivity benchmarks are often well-predicted by counting cells

Phenotypic profiling methods, such as Cell Painting and gene expression, have been widely used to predict compound bioactivity, often showing improvement over predictive models based on chemical structures alone. We discovered that a large subset of assays in widely-used benchmark datasets either directly relate to cell health and cytotoxicity or are assays intending to capture a more specific phenotype but whose active compounds impact cell count, while inactives do not. As a result, counting cells can achieve similar predictive performance as Cell Painting or gene expression data. Filtering benchmarks to include only assays relating to protein targets reveals that Cell Painting can capture information that cannot be predicted by mere cell counting. We re-evaluated three benchmark datasets used with Cell Painting data and observed that, in many cases, cell count models produced an AUC comparable to models using the full Cell Painting profiles. However, in protein-target-specific benchmarks across 17 distinct protein targets, Cell Painting features demonstrated unique predictive power, outperforming mean balanced accuracy from cell count models with a relative improvement of 19.6%. We propose five practical recommendations for benchmarking machine learning models for predicting bioactivity, including using cell count as a baseline feature. Although multi-class classification applications (such as matching samples based on their morphological profile) are less likely to be predictable by cell count than bioactivity benchmarks, these recommendations are broadly applicable to machine learning for drug discovery.

bioinformatics↗

bioRxiv2025

Changes in nuclear and actin mechanics from G1 to G2 affect nuclear integrity

The structural integrity of the nucleus is dependent on nuclear mechanical elements of chromatin and lamins to resist antagonistic actin cytoskeleton forces. Imbalance results in nuclear blebbing, rupture, and cellular dysfunction found in many human diseases. We used Fluorescent Ubiquitin Cell Cycle Indicator (FUCCI) cells to determine how cell cycle changes affect the nucleus and actin force balance. While nuclear blebs are present equally throughout interphase, nuclear blebs form predominantly in G1 and then persist into G2 due to increased actin-based nuclear confinement and focal adhesion density in G1 vs. G2 cells. Upon artificial confinement, G2 nuclei ruptured more than G1 nuclei. Single nucleus micromanipulation force measurements confirmed that G1 nuclei are stronger than G2 nuclei in both the chromatin-based and lamin-based nuclear stiffness regimes. Decreased nuclear stiffness can be explained by loss of peripheral H3K9me3 from G1 to G2, recapitulated by H3K9me3 inhibition via Chaetocin. Cell cycle-based changes in nuclear and actin mechanics impact nuclear integrity and shape.

cell biology↗

bioRxiv2025

Coro1A and TRIM67 collaborate in netrin-dependent neuronal morphogenesis

Neuronal morphogenesis depends on extracellular guidance cues accurately instructing intracellular cytoskeletal remodeling. Here, we describe a novel role for the actin binding protein Coronin 1A (Coro1A) in neuronal morphogenesis, where it mediates responses to the axon guidance cue netrin-1. We found that Coro1A localizes to growth cones and filopodial structures and is required for netrindependent axon turning, branching, and corpus callosum development. We previously discovered that Coro1A interacts with TRIM67, a brain enriched E3 ubiquitin ligase that interacts with a netrin receptor and is also required for netrin-mediated neuronal morphogenesis. Loss of Coro1A and loss of TRIM67 shared similar phenotypes, suggesting that they may function together in the same netrin pathway. A Coro1A mutant deficient in binding TRIM67 was not able to rescue loss of Coro1A phenotypes, indicating that the interaction between Coro1A and TRIM67 is required for netrin responses. Together, our findings reveal that Coro1A is required for proper neuronal morphogenesis, where it collaborates with TRIM67 downstream of netrin.

cell biology↗

bioRxiv2025

Predicting Personalised Therapeutic Combinations in Non-Small Cell Lung Cancer Using In Silico Modelling

The disease burden from non-small cell lung cancer (NSCLC) adenocarcinoma is substantial, with around a million new cases diagnosed globally each year, and a 5-year survival rate of less than 20%. A lack of therapeutic options personalized to individual patient genetics, and the targeted therapies that exist quickly succumbing to resistance, leads to high variation in survival. Patient stratification combined with greater personalisation of therapies have the potential to improve outcomes, however, the wide variation in mutations found in NSCLC adenocarcinoma patients mean that experimentally determining suitable treatment combinations is time-consuming and expensive. Here we present an in silico model encompassing tumour intrinsic key oncogenic signalling pathways, including EGFR, AKT, JAK/STAT and WNT for efficiently predicting rational drug-drug and drug-radiotherapy combination therapies in NSCLC. Using this model, we simulate diverse genetic profiles and test over 10,000 therapeutic combinations to identify optimal strategies to overcome resistance mechanisms specific to genetic profiles and p53 status. Our in silico model reproduces drug additivity experiments, predicts radio-sensitising genes validated in a CRISPR screen and identifies 53BP1 as a potential drug target that improves the therapeutic window during radiotherapy, as well as potential to use ATM inhibitors to overcome p53 loss-of-function driven radiotherapy resistance. We further use the in silico model to identify a 19-gene signature to stratify patients most likely to benefit from radiotherapy and validated this using TCGA data. These results further demonstrate the utility of in silico mechanistic modelling and present a bespoke computational resource for large-scale screening of personalised therapies applied to NSCLC.

cancer biology↗

bioRxiv2025

Optimal sparsity in autoencoder memory models of the hippocampus

Storing complex correlated memories is significantly more efficient when memories are recoded to obtain compressed representations. Previous work has shown that compression can be implemented in a simple neural circuit, which can be described as a sparse autoencoder. The activity of the encoding units in these models recapitulates the activity of hippocampal neurons recorded in multiple experiments. However, these investigations have assumed that the level of sparsity is fixed and that inputs have the same statistics and, hence, that they are uniformly compressible. In contrast, biological agents encounter environments with vastly different memory demands and compressibility. Here, we investigate whether the compressibility of inputs determines optimal sparsity in sparse autoencoders. We find 1) that as the compressibility of inputs increases, the optimal coding level decreases, 2) that the desired coding level diverges from the observed coding level as a function of both memory demand and input compressibility, and 3) that optimal memory capacity is achieved when sparsity is weakly enforced. In addition, we characterize how sparsity and the strength of sparsity enforcement jointly control optimal performance. These results provide predictions for how sparsity in the hippocampus should change in response to environmental statistics and theoretical grounds for why sparsity is dynamically tuned in the brain.

neuroscience↗

bioRxiv2024

Deregulation of epigenetic factor, KDM6A, is involved during Candida albicans mediated delayed wound healing

Deregulation of wound healing process leads to chronic non-healing wounds. Opportunistic fungal pathogens like Candida albicans is known to colonize open wounds leading to delayed, insufficient, or disorganized healing. In our study, we investigate the regulatory mechanisms orchestrating this C. albicans mediated delay of wound healing and underscore a critical role for the transcription factor c-AMP Response Element Binding Protein (CREB) in regulating pro-inflammatory cytokines and genes implicated in wound healing. Parallelly, we found the epigenetic factor, KDM6A (Ubiquitously Transcribed tetratricopeptide repeat on chromosome X, also known as UTX) to be downregulated upon infection and modulating expression of metalloproteinases during C. albicans governed wound healing impairment. Mechanistically, we observed enhanced recruitment of EZH2, a methyl transferase, over the promoters of KDM6A during infection, hence, governing its expression. Our findings, therefore, underscore a role of KDM6A and CREB in C. albicans mediated delayed wound healing.

immunology↗

bioRxiv2024

Increased NFAT and NFκB signalling contribute to the hyperinflammatory phenotype in response to Aspergillus fumigatus in cystic fibrosis

Aspergillus fumigatus (Af) is a major mould pathogen found ubiquitously in the air. It commonly infects the airways of people with cystic fibrosis (CF) leading to Aspergillus bronchitis or allergic bronchopulmonary aspergillosis. Resident alveolar macrophages and recruited neutrophils are important first lines of defence for clearance of Af in the lung. However, their contribution to the inflammatory phenotype in CF during Af infection is not well understood. Here, utilising CFTR deficient mice we describe a hyperinflammatory phenotype in both acute and allergic murine models of pulmonary aspergillosis. We show that during aspergillosis, CFTR deficiency leads to increased alveolar macrophage death and persistent inflammation of the airways in CF, accompanied by impaired fungal control. Utilising CFTR deficient murine cells and primary human CF cells we show that at a cellular level there is increased activation of NF{kappa}B and NFAT in response to Af which, as in in vivo models, is associated with increased cell death and reduced fungal control. Taken together, these studies indicate that CFTR deficiency promotes increased activation of inflammatory pathways, the induction of macrophage cell death and reduced fungal control contributing to the hyper-inflammatory of pulmonary aspergillosis phenotypes in CF. Author SummaryThe airways of people with cystic fibrosis (pwCF) are commonly colonised with Aspergillus fumigatus (Af) resulting in a persistent hyperinflammatory state and the development of allergy. Understanding how first line defence innate cells, such as alveolar macrophages and neutrophils, contribute to this hyperinflammatory phenotype is important in developing novel treatments to preserve lung function in pwCF. In this study, we report that CFTR deficiency leads to increased alveolar macrophage death and persistent inflammation of the airways in pwCF, which is associated with impaired control of infection. We identify the increased activation of the transcription factors NF{kappa}B and NFAT as the mechanism of increased inflammatory cytokine production in CFTR deficient cells. This work is the first step in describing molecular mechanisms of hyperinflammation in CF in response to fungal infection and lays the groundwork for further dissection of inflammatory pathways to target with immunotherapeutic approaches.

immunology↗

bioRxiv2024

RNA methylation controls stress granule formation and function during erythropoiesis

Stress granules (SGs) are crucial in RNA regulation, affecting cell fate and function. SGs contain RNAs, some of which can be methylated. We studied m6A RNA modifications during the human CD34+ HSPCs (hCD34+) differentiating into erythroid cells and found that mRNAs encoding many erythroid-specific proteins had decreased methylation during differentiation. Increased levels ALKBH5 demethylase during erythropoiesis controls the levels of the 3UTR methylation of these mRNAs. hCD34+ carrying ALKBH5 mutations demonstrated a block in erythropoiesis, and mass-spectrometry studies of the mutant cells showed decreased levels of SG proteins, including the core granule protein ATXN2. ALKBH5 directly regulates the methylation of the mRNA of ATXN2. ATXN2 overexpression accelerated the erythroid differentiation of HSPCs and rescued the erythroid differentiation of ALKBH5 mutant cells. Very few SGs are found in normal human erythroid progenitors. SGs accumulated substantially in ALKBH5 mutant cells, and surprisingly overexpression of ATNX2 reduced SG numbers to normal. Polysome analysis demonstrated m6A-modified RNAs to be enriched in the pre-polysome fractions that were less translated. This work establishes a mechanism by which during stress, ATXN2 facilitates the release of SG-stored m6A-modified RNAs including erythroid-specific and SG-enriched RNAs that are loaded onto functional ribosomes, allowing better translation and accelerated erythroid differentiation during stress.

cell biology↗

bioRxiv2024

Exploring Organ-Specific Extracellular Vesicles in Metabolic Improvements Following Bariatric Surgery in Adolescents with Obesity

Aims/hypothesisVertical sleeve gastrectomy (VSG) leads to significant metabolic improvements, though the underlying molecular mechanisms are not yet fully understood. Emerging evidence suggests that small extracellular vesicles (sEVs) contribute to metabolic improvements post-VSG; however, it is still unclear which organ-specific sEV correlate with various metabolic parameters and how they exert these effects. The study aimed to establish the role of organ-specific sEVs in the metabolic improvements associated with VSG. MethodsDemographic, anthropometric, and blood samples were collected pre-VSG and 3- and 6-month post-VSG in adolescents with obesity. Blood samples were utilized to measure metabolic parameters and to isolate sEVs. sEV RNAs were analyzed via small RNA sequencing then bioinformatics analyses. ResultsA significant reduction in mRNA cargo from liver-specific genes was observed post- VSG, whereas adipose tissue- or skeletal muscle-specific genes showed no such reduction. Liver-derived RNA correlated with BMI, leptin, and resistin, while adipose-derived RNA correlated with leptin. Analysis of delta values (post-minus pre-surgery) revealed that adipose-derived RNA cargo correlated with markers of liver damage and HOMA-IR, whereas liver-derived RNA cargo correlated with BCAAs. ConclusionsVSG modulates the EV system in the liver and adipose tissue. Liver-derived sEVs appear to regulate adipose metabolism, while adipose-derived sEVs are associated with liver function, suggesting a dynamic crosstalk between these tissues through sEVs that shapes systemic metabolic outcomes. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABS- Vertical sleeve gastrectomy (VSG) is the most performed bariatric surgery, leading to significant metabolic improvements. - Small extracellular vesicles (sEVs) and their RNA cargo play a crucial role in metabolic regulation. - Levels of branched-chain amino acids (BCAAs), which are known metabolic regulators, decrease following bariatric surgery. What is the key question?- How do sEVs, BCAA and other metabolic molecules interact to drive the significant metabolic improvements observed after VSG? What are the new findings?- The levels of liver-specific RNA cargo in sEVs decrease after VSG and are correlated with BMI and leptin levels at 6 months post-surgery, suggesting a potential role for liver-specific RNA cargo in the metabolic benefits associated with VSG. - Changes in BCAA levels from baseline to 6 months post-surgery correlate with changes in liver-specific RNA cargo in sEVs, indicating liver-specific RNA cargo in sEVs may influence metabolic parameters through BCAA modulation. - Changes in the level of adipose-specific RNA cargo in sEVs from baseline to 6 month post-surgery correlate with changes HOMA-IR and ALT levels. How might this impact on clinical practice in the foreseeable future?The study identifies liver- and adipose-derived sEV RNA cargo as potential targets for non-invasive therapies that could replicate the metabolic benefits of VSG. While further investigation is needed, these findings suggest a tentative alternative for adolescents facing obesity who may be ineligible or reluctant to undergo bariatric surgery.

cell biology↗

bioRxiv2024

Odd prey in mixed species groups suffer fewer attacks than lone individuals

Mixed-species groups are common in nature. Such groups are characterised by the presence of one or more majority species, and smaller numbers of minority species. Minority individuals are expected to be subject to oddity effects; by looking or behaving differently to majority members they should be disproportionately targeted by predators. Given this, why might minority species remain in mixed-species groups? To address this question, we used threespine sticklebacks (Gasterosteus aculeatus) as predators and two species of virtual prey presented via videos. We compared predator attacks on solitary prey, and odd and majority grouped prey individuals in groups of different sizes. We found that solitary prey were attacked significantly more than odd and majority grouped prey, while, in fact, odd and majority grouped prey did not differ from each other in terms of attacks received. We also found that prey in smaller groups suffered significantly more attacks than prey in larger groups. These findings provide no evidence for oddity effects but suggest evidence of a confusion effect. Natural mixed-species groups persist for various reasons, for example as foraging guilds, or because some members take advantage of more effective vigilance or alarm calls of others. We suggest, based on these findings, an additional non-mutually exclusive reason; under some circumstances, odd individuals might join larger heterospecific groups because any costs of being odd are greatly outweighed by the predation risk costs of remaining alone.

animal behavior and cognition↗