Biology subjects

Kashyap, P.

Publications and source records attributed to Kashyap, P..

12 recordsLinked to original sources

bioRxiv2026

An endolysin-expressing probiotic attenuates Clostridioides difficile infection in germ-free and dysbiotic microbiota-associated mice

Disruption of the intestinal microbiota increases susceptibility to Clostridioides difficile infection (CDI), creating an opportunity for prophylactic interventions before symptomatic disease develops. We investigated whether Escherichia coli Nissle 1917 (EcN) engineered to express the bacteriophage-derived endolysin CD27L could enhance pathogen inhibition and attenuate CDI. Using a plasmid-cured EcN chassis and pMUT2-derived vectors, we generated strains expressing CD27L under constitutive or anaerobically regulated promoter control. The constitutive strain, BioEcN1, reduced viable C. difficile recovery relative to parental EcN and was selected for animal studies. BioEcN1 remained recoverable from monoassociated mice without in vivo antibiotic selection, with similar recovery on selective and nonselective media supporting construct retention. Prophylactic administration reduced clinical disease, body-weight loss, and intestinal histopathological injury in germ-free mice. Observed survival was 100% in BioEcN1-treated challenged mice versus 50% in untreated challenged mice during the monitored period. Protection was accompanied by lower fecal and cecal pathogen burdens. In mice harboring a human-derived dysbiotic microbiota, prophylactic BioEcN1 also reduced clinical and stool-consistency scores, with lower early fecal pathogen recovery and less colon shortening. These findings establish preclinical proof of concept for prophylactic administration of an endolysin-expressing probiotic to attenuate CDI.

microbiology↗

bioRxiv2026

Protein-only centromeric chromatin assembly streamlines human artificial chromosome formation

Human artificial chromosomes (HACs) are inherited through cell divisions alongside natural chromosomes, serving as tools for interrogating chromosomal elements and as vectors for large genetic cargoes (1-5). Despite recent progress (6-8), large (i.e., multiple Mb) HACs have not been reported. Further, HAC formation via epigenetic seeding of centromeric chromatin currently requires prior engineering of recipient human cells (6-8), hampering their potential deployment in many useful cell types. Here, we designed, built, and delivered to human cells a 2 Mb HAC construct that is [~]3 times larger than the prior generation. We also report a robust epigenetic centromere seeding approach that initiates immediately upon delivery to the human cell cytoplasm and bypasses genetic engineering of target cells. The HACs are then faithfully inherited in the absence of selection. Thus, formation of functional centromeric chromatin in the same cell cycle of HAC delivery drives high efficiency HAC formation. TeaserA system for efficient protein-only centromere seeding permits visualizing the first step of HAC formation

synthetic biology↗

bioRxiv2025

Molecular Mechanisms Underlying the Regulation of VCAM-1 Expression by the Short-Chain Fatty Acid Butyrate

Over the past decade, cerebrovascular inflammation has been increasingly recognized as a contributor to the progression of neurodegenerative diseases, particularly Alzheimers disease (AD). One of the molecular hallmarks of cerebrovascular inflammation is the increased expression of vascular cell adhesion molecule (VCAM)-1 on blood-brain barrier (BBB) endothelial cells. Exposure to amyloid beta (A{beta}) peptides, one of the primary hallmarks of AD, and pro-inflammatory cytokines such as tumor necrosis factor-alpha (TNF-) induces VCAM-1 expression on the BBB endothelium, which facilitates extravasation of leukocytes into the brain thereby promoting an inflammatory response. Therefore, it is crucial to explore therapeutic agents that can inhibit VCAM-1 expression induced by A{beta} and TNF-. Short-chain fatty acids, such as butyrate, produced by the gut microbiota as byproducts of dietary fiber metabolism, are recognized for their anti-inflammatory properties. In this study, we successfully tested the hypothesis that butyrate mitigates A{beta} and TNF--induced VCAM-1 expression in polarized human cerebral microvascular endothelial cell monolayers, a widely used BBB in vitro model. Our findings indicated that pre-treatment with butyrate significantly reduced A{beta}42 and TNF- mediated upregulation of VCAM-1. Furthermore, we have shown STAT3/GATA6 axis as a key mediator of anti-inflammatory effects of butyrate. These findings provide mechanistic insight into butyrates protective role and highlight its potential to mitigate A{beta} and TNF--induced cerebrovascular inflammation in AD.

molecular biology↗

bioRxiv2025

Butyrate regulates the blood-brain barrier transport and intra-endothelial accumulation of Alzheimers disease Amyloid-beta peptides

Alzheimers disease (AD) is characterized by the pathological deposition of amyloid beta (A) proteins as amyloid plaques, tau aggregates, and cerebrovascular dysfunction that drive disease progression. Butyrate, a gut microbial metabolite, has been found to be reduced in AD patients; butyrate supplementation improved cognition and decreased amyloid burden in animal models. However, the precise underlying mechanisms are unclear. Our previous studies have demonstrated that insulin signaling impacts A transport kinetics at the blood-brain barrier (BBB). In this study, we investigated the effect of butyrate treatment on intra-endothelial A accumulation and BBB integrity by modulating the insulin signaling pathway. The effect of butyrate on A accumulation was assessed by flow cytometry in BBB cell culture models. Insulin signaling activation and the expression of various receptors and transporters at the BBB were evaluated by Western blots and confocal microscopy. The roles of various molecular mediators were confirmed using specific inhibitors (MK2206, Trametinib, Rapamycin, VX-745). The effect of butyrate on the expression of BBB receptors and transporters that play a critical role in A trafficking was examined in mouse brains colonized with butyrate-producing bacteria via immunohistochemistry. Butyrate significantly decreased A{beta}42 accumulation in endothelial cells. This effect was associated with insulin signaling pathway activation, particularly AKT and ERK phosphorylation. Inhibitor studies established the critical role of these specific arms, as co-incubation with MK2206 (AKT inhibitor) or Trametinib (ERK inhibitor) reversed the protective effect of butyrate and increased A{beta}42 accumulation. However, mTOR and p38 inhibitors did not show a similar effect. In addition, butyrate restored P-glycoprotein efflux transporter expression and claudin-5 tight junction protein levels that were reduced with A{beta} treatment. These effects were supported by in vivo work, which demonstrated the upregulation of Tissue Inhibitor of Metalloproteinases-2 (TIMP-2). This protein is associated with AKT activation and extracellular matrix stabilization in mice colonized with butyrate-producing bacteria. In conclusion, we have demonstrated that butyrate decreases A{beta}42 uptake at the BBB endothelium by activating the AKT and ERK arms of the insulin signaling pathway. These changes may also improve the integrity of BBB tight junctions by increasing claudin-5 expression and extracellular matrix, and by upregulating TIMP-2 expression. This study highlights butyrates potential as a therapeutic modulator of AD-related BBB dysfunction.

neuroscience↗

bioRxiv2025

Rapid assembly of functional modules for generating human artificial chromosome constructs compatible with epigenetic centromere seeding

The ongoing development of human artificial chromosomes (HACs) will permit investigation into essential centromere processes and the means to deliver large genetic cargoes to target cells. Starting with large ([~]750 kb) yeast artificial chromosome (YAC)-based constructs limits the rampant multimerization that has complicated many prior types of HACs. Large YAC construction is accomplished using transformation-associated recombination (TAR) strategies that can become unwieldly when several functional modules are to be incorporated and tested. To address this issue, we developed an approach where modules are built using high-fidelity in vitro assembly strategies in a bacterial artificial chromosome (BAC) format. Then, the assembled modules are transferred in a simplified TAR step into a recipient YAC harboring the prokaryotic "stuffer" DNA that comprises a large portion of the final HAC construct. This approach is highly efficient with two-thirds of all screened yeast clones harboring the correct TAR product. Further, whole-genome Oxford Nanopore Technologies (ONT) sequencing/alignments, de novo assembly of the final YAC using a single ONT sequencing run, and close inspection of highly repetitive regions are all streamlined to rapidly validate clones that match the design. The fully sequenced, verified strain harboring a multi-module construct was then fused to human cells, where it efficiently formed functional HACs upon initial seeding with CENP-A-containing nucleosomes. We envision that the rapid assembly steps will be useful to quickly incorporate different functional modules, including diverse genetic cargoes, to engineer HACs with specific design features.

synthetic biology↗

bioRxiv2024

A Caenorhabditis elegans based system for high-throughput functional phenotyping of human gut microbiota

The conventional bottom-up approach to probing the human gut microbiomes link with hosts in germ-free models is hampered by considerable costs and time. To address this, our study introduces the nematode Caenorhabditis elegans as an innovative high-throughput model for exploring the gut microbiomes impact on functional phenotypes. Traditionally, C. elegans studies have used continuous feeding for bacterial administration, a method that is unsuitable for anaerobes. For the first time, we have standardized a protocol for colonizing C. elegans with human gut anaerobes. By screening a microbial culturomics library representing 70% of the gut microbiomes functional capacity, we showed successful colonization for 46% of the library. Functional phenotyping revealed that 5 of 10 strains, previously identified in vitro as inhibiting C. difficile, also inhibited in vivo. Validation of a selected strain in a germ-free mouse model confirmed colonization resistance and an immune response consistent with findings in C. elegans, underscoring the models translational potential.

microbiology↗

bioRxiv2023

Machine learning analysis of lung adenocarcinoma and squamous cell carcinoma microbiome datasets reveals biomarkers for early diagnosis

IntroductionLung cancer (LC) is the second most frequent cancer worldwide with high incidences and mortality rates and non-small-cell-lung cancer (NSCLC) accounts for 80-85% cases of LC. It is further majorly sub-classified into adenocarcinoma (AC), and squamous-cell carcinoma (SCC). A late diagnosis at an advanced stage, a high rate of metastasis, and the development of therapy resistance are responsible for approximately 95% of mortality. Owing to high heterogeneity and variances in subtypes, it is important to precisely classify them for treatment. However, it poses a challenge in clinical practices, as it requires accurate quantification of each proportion subtype which is time-consuming and sometimes erroneous. The lower airways are home to a dynamic bacterial population sustained by the immigration, elimination, and migration of microbes from the gastrointestinal tract and upper airway tracts. The disruption in the homeostasis of microbiome compositions was found to be correlated with the increased risk of LC. Artificial intelligence (AI) techniques are used extensively in the early screening, and treatment of NSCLC have made significant strides in recent years. Recently, the use of CT/MRI scan image data in prediction models also results in false-positive rates and requires subsequent tests for further exploration which delays the prognostication. Therefore, early diagnosis, prevention, and treatment are critical to enhance survival and reduce death. Here, we aim for the classification of AC and SCC using the lung microbiome of lung tissue samples, implementing AI-based algorithms. MethodsWe have obtained raw sequencing data from the NCBI online database, and 149 AC samples and 145 SCC samples in patients were analyzed for their lung microbiome present in the lung tissue samples. The metadata such as patient age, sex, smoking history, and environmental material (malignant or not) were also analyzed. Using these data, machine learning algorithms were applied to select the best microbiome features for the classification of subtypes. ResultsA supervised ML and DL based model was developed that can discriminate NSCLC subtypes based on their microbial information, exploring the microbiome as predictive information for early screening. Consequently, 17 features were identified as a biomarker, and they showed good performance in distinguishing AC from SCC with an accuracy of 81% in KNN and 71% in DNN when demonstrated on the validation dataset. ConclusionThis study proposed a supervised machine learning framework where we can rely on taxonomic features and AI techniques to classify overlapped AC and SCC metagenomic data providing lung microbiome as a predictive and diagnostic biomarker in LC. Moreover, our framework will also be very helpful to other researchers to obtain further biomarkers and perform analysis in overlapped subtypes in different diseases.

bioinformatics↗

bioRxiv2023

An optogenetic method for the controlled release of single molecules

We developed a system for optogenetic release of single molecules in live cells. We confined soluble and transmembrane proteins to the Golgi apparatus via a photocleavable protein and released them by short pulses of light. Our method allows for the controlled delivery of functional proteins to cytosol and plasma membrane in amounts compatible with single molecule imaging, greatly simplifying access to single molecule microscopy of any protein in live cells. Furthermore, we could reconstitute cellular functions such as ion conductance by delivering BK and VRAC ion channels to the plasma membrane. Finally, we could induce NF-kB signaling in T-Lymphoblasts stimulated by IL-1 by controlled release of a signaling protein that had been knocked-out in the same cells. We observed light induced formation of functional inflammatory signaling complexes that could trigger IKK phosphorylation in single cells. We thus developed an optogenetic method for the reconstitution and investigation of cellular function at the single molecule level.

biophysics↗

bioRxiv2023

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria

The human gut microbiota is a complex community comprising hundreds of species, with a few present in high abundance and the vast majority in low abundance. The biological functions and effects of these low-abundant species on their hosts are not yet fully understood. In this study, we assembled a bacterial consortium (SC-4) consisting of B. paravirosa, C. comes, M. indica, and A. butyriciproducens, which are low-abundant, short-chain fatty acid (SCFA)-producing bacteria isolated from healthy human gut, and tested its effect on host health using germfree and human microbiota-associated colitis mouse models. The selection also favored these four bacteria being reduced in abundance in either Ulcerative Colitis (UC) or Crohns disease (CD) metagenome samples. Our findings demonstrate that SC-4 can colonize germ-free (GF) mice, increasing mucin thickness by activating MUC-1 and MUC-2 genes, thereby protecting GF mice from Dextran Sodium Sulfate (DSS)-induced colitis. Moreover, SC-4 aided in the recovery of human microbiota-associated mice from DSS-induced colitis, and intriguingly, its administration enhanced the alpha diversity of the gut microbiome, shifting the community composition closer to control levels. The results showed enhanced phenotypes across all measures when the mice were supplemented with Inulin as a dietary fiber source alongside SC-4 administration. We also showed a functional redundancy existing in the gut microbiome, resulting in the low abundant SCFA producers acting as a form of insurance, which in turn accelerates recovery from the dysbiotic state upon the administration of SC-4. SC-4 colonization also upregulated iNOS gene expression, further supporting its ability to produce an increasing number of goblet cells. Collectively, our results provide evidence that low-abundant SCFA-producing species in the gut may offer a novel therapeutic approach to IBD.

microbiology↗

bioRxiv2020

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations

Microbiota-accessible carbohydrates (MACs) are powerful modulators of microbiota composition and function. These substrates are often derived from diet, such as complex polysaccharides from plants or human milk oligosaccharides (HMOs) during breastfeeding. Host-derived mucus glycans on gut-secreted mucin proteins may serve as a continuous endogenous source of MACs for resident microbes; here we investigate the potential role of purified, orally-administered mucus glycans in maintaining a healthy microbial community. In this study, we liberated and purified O-linked glycans from porcine gastric mucin and assessed their efficacy in shaping the recovery of a perturbed microbiota in a mouse model. We found that porcine mucin glycans (PMGs) and HMOs enrich for taxonomically similar resident microbes. We demonstrate that PMGs aid recovery of the microbiota after antibiotic treatment, suppress C. difficile abundance, delay the onset of diet-induced obesity, and increase relative abundance of resident Akkermansia muciniphila. In silico analysis revealed that genes associated with mucus utilization are abundant and diverse in prevalent gut commensals and rare in enteric pathogens, consistent with these glycan-degrading capabilities being selected for during host development and throughout evolution of the host-microbe relationship. Importantly, we identify mucus glycans as a novel class of prebiotic compounds that can be used to mitigate perturbations to the microbiota and provide benefits to host physiology.

microbiology↗

bioRxiv2020

Levo in fimo test : A simple test for fecal microbial reconstituted mice

Here we report the first method for rapid on-site monitoring of germfree C57BL/6 mice colonized with feces from conventionally raised mice. The method, named levo in fimo test, readily distinguishes feces from germfree mice and conventionalized germfree mice based on its properties to float or sink in Trumps fixative solution. We validated the test using feces from conventionally raised mice, germfree mice and conventionalized germfree mice, and cross-validated using multiple indicators of microbial presence in feces. Levo in fimo test is a simple, cost-effective, instant yet robust method for on-site monitoring of gut microbial reconstitution in germfree mice.

microbiology↗

bioRxiv2018

Cholesterol depletion by MβCD enhances membrane tension, its heterogeneity and affects cellular integrity.

Cholesterol depletion in cells by M{beta}CD remodels the plasma membranes mechanics and its interactions with the underlying cytoskeleton. Decoupling the two effects and studying various alterations to the membranes mechanical parameters is important for understanding cholesterols role in cellular response to stress. By mapping membrane height fluctuations in single cells, we report that M{beta}CD treatment reduces temporal fluctuations and flattens out the membrane - but does not supress activity-driven fluctuations. We find that membrane tension increase contributes most to the altered fluctuations, among the multiple mechanical parameters computed. Maps also reveal an enhanced long-range heterogeneity within single cells, both in amplitude of fluctuations and membrane tension on cholesterol depletion. To check if this alters the tenacity of membrane to mechanical stress we use hypo-osmotic shock. We find that on M{beta}CD treatment, cells are more prone to rupture than control cells, and this is not hindered by actomyosin perturbations. We report increased rupture sizes on cholesterol depletion and argue that, together, this indicates decreased lysis and line tension. Therefore, we show that cholesterol depletion directly affects cell membranes not only by enhancing membrane-cytoskeleton interactions, but also by increasing membrane tension while reducing lysis tension - hence making cells prone to rupture.

biophysics↗