Biology subjects

Shah, I.

Publications and source records attributed to Shah, I..

11 recordsLinked to original sources

bioRxiv2026

Flow-Dependent CFU Dynamics Reshape Polymicrobial Biofilm with a Pronounced Dominance Shift under Sub-Inhibitory Antibiotic Stress

Catheter-associated urinary tract infections (CAUTIs) are the most prevalent healthcare-associated infections globally, yet the ecological dynamics governing polymicrobial biofilm communities on indwelling catheters remain poorly understood under physiologically relevant conditions. Most prior work uses static in vitro models that fail to capture continuous urine flow and sub-inhibitory (sub-MIC) antibiotic gradients. We investigated how continuous flow and sub-MIC concentrations of ciprofloxacin and gentamicin reshape colony-forming unit (CFU) dynamics across attached biofilm and dispersed effluent fractions, and species dominance in mono- and polymicrobial biofilms of Pseudomonas aeruginosa (Pa), Klebsiella pneumoniae (Kp), and Enterococcus faecium (Ef) using silicone-coated latex catheter segments, volumetric infusion pumps, and ibidi {micro}-slide VI 0.4 microfluidic chambers. Under antibiotic-free conditions, Pa dominated both dual co-cultures (Pa+Kp, Pa+Ef) in static condition, but this dominance was not sustained under flow in the Pa+Ef pairing, where Ef rose to 62.5% relative abundance. Sub-MIC ciprofloxacin under flow promoted Kp dispersal (+15.87 log? fold change in dispersed-cell fraction(filter), cooperative Pa recovery via Ef co-occupancy, and pronounced Ef dominance in the triple-species community (64.71% relative abundance). Ef exhibited enhanced growth under sub-MIC gentamicin in static conditions that was abolished under flow. CLSM imaging revealed ciprofloxacin-induced Kp filamentation under flow, with Ef microcolonies localising at filament termini--a novel architectural interaction providing spatial scaffolding for the gram-positive partner. These findings establish that continuous flow and antibiotic class jointly determine polymicrobial dominance outcomes in ways invisible to static assays, underpinning Ef persistence in mature CAUTI biofilms and highlighting flow as a central ecological variable in infection pathogenesis.

microbiology↗

bioRxiv2026

Reversible chromatin remodeling enables Prosopis cineraria survival under recurrent heat extremes.

Recurrent seasonal heat and drought raise fundamental questions about how long-lived desert plants sustain physiological function across temperature extremes. We have used seasonal profiling at six time points with multilayered omics studies (Hi-C, transcriptomic, histone marks, and DNA methylation) to understand how Prosopis cineraria, a native Arabian desert legume tree, responds to different temperatures and the underlying mechanisms. A clear pattern emerges during peak heat. chromatin boundaries are selectively weakened, and candidate topological domains merge, activating clusters of heat-protective genes that gain active promoter and enhancer marks (H3K4me3 and H3K27ac). In the cool season, immune and developmental gene regulation is coupled with flowering, consistent with a temporal risk-strategy that shifts reproduction away from lethal heat. At the same time, promoter CHH methylation near transposable elements, together with reduced active promoter and enhancer marks (H3K4me3/H3K27ac), points to a proactive developmental phase rather than just surviving the stress. Integrating physiological data, we connect chromatin activation to an SA-ABA reciprocal seasonal profile, MIZ1-associated hydrotropism, and Stay-Green-mediated delayed senescence through chlorophyll retention. With Landscape genomics and phylogenetics, we further identified a housekeeping PEPC with a high predicted melting temperature that could sustain a malate-derived carbon supply, buffering metabolism under heat. Together, these findings reveal that reversible epigenetic gating enables desert trees to survive and recover from extreme seasonal stress.

plant biology↗

bioRxiv2026

Desert Cucurbit Microbiomes: Spatiotemporal Dynamics and Functional Adaptations

BackgroundPlant microbiomes can contribute to host adaptation in extreme environments, particularly deserts where high temperatures, intense radiation, water limitation, and nutrient-poor soils constrain plant survival. Citrullus colocynthis is a desert-adapted cucurbit with medicinal and agricultural relevance, yet integrated understanding of its microbiome across seasons, tissues, habitats, and functional traits remains limited. Here, we asked whether spatiotemporal microbiome dynamics in C. colocynthis are linked to microbial functional potential and cultivable traits relevant to persistence under arid conditions. ResultsTo address this, we profiled the microbiome of C. colocynthis across two sites, two seasons, and multiple compartments using 16S rRNA amplicon screening, shotgun metagenomics, culture-based phenotyping, and genome analysis. Amplicon profiling provided an exploratory framework and showed that plant-associated bacterial communities were shaped primarily by season and tissue type, with roots emerging as the most season-responsive compartment. Shotgun metagenomics confirmed stronger seasonal restructuring in root bacterial communities than in leaves and extended taxonomic profiling to fungal and archaeal fractions, which were interpreted descriptively because of low read representation. Summer root communities were enriched in actinobacterial genera, including Saccharopolyspora, Amycolatopsis, Pseudonocardia, and Nonomuraea, while functional profiling indicated coordinated shifts in central metabolism, cofactor salvage, exopolysaccharide-related pathways, and redox-associated functions. Twenty-four cultured bacterial isolates exhibited diverse stress-tolerance and plant growth-promoting traits, and whole-genome analyses identified biosynthetic, osmoprotective, oxidative-stress, and phytohormone-related gene content. Pangenome analysis of Pseudomonas orientalis revealed an open pangenome and lifestyle-associated accessory genes linked to host-associated functions. ConclusionsTogether, these findings connect seasonal bacterial community turnover, metagenomic functional potential, and cultivable microbial traits in a desert plant holobiont, highlighting desert-native bacteria and pathways relevant to microbiome-guided strategies for arid agriculture.

microbiology↗

bioRxiv2026

Lithium drives coordinated changes in the mouse synaptic phosphoproteome

Lithium is the gold standard mood stabiliser used to treat cycling mania and depression in bipolar disorder. Despite seven decades of clinical use, the mechanisms of its mood stabilisation are incompletely understood, fundamentally limiting development of improved alternatives. Two established lithium targets, glycogen synthase kinase 3{beta} (GSK3{beta}) and inositol monophosphatase, both modulate phosphorylation, suggesting lithium may exert broad effects on neuronal phosphorylation networks. We performed a discovery-phase in vitro screen of 140 kinases at 10mM LiCl and demonstrated that lithium inhibits 17 kinases beyond GSK3{beta}. We therefore used untargeted quantitative phosphoproteomics to create a comprehensive map of lithiums neural phosphorylation signature in lithium-treated mouse synaptoneurosomes. Samples were collected at dawn and dusk to match the peaks in phosphorylation that are induced by the sleep/wake cycle. Pathway analysis revealed convergence on synaptic plasticity, neurotransmitter release, and chemical transmission. Critically, lithium-sensitive phosphoproteins are significantly enriched in bipolar disorder genome-wide association study (GWAS) loci, providing independent genomic evidence that the phosphorylation networks we identified are relevant to bipolar pathophysiology. We identified novel kinase targets and phosphorylation sites not previously associated with lithiums mechanism of action and tied them to bipolar pathology. We further refined existing models of lithiums action by showing that GSK3{beta} inhibition is temporally restricted to dawn, indicating cross talk with sleep/wake cycles of phosphorylation. Overall, our data demonstrate that lithiums pleiotropic effects result from coordinated multi-kinase network reorganisation rather than single-target inhibition -- a principle with direct implications for rational polypharmacology in mood stabiliser development.

neuroscience↗

bioRxiv2025

Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics

We applied the TempO-LINC(R) platform to generate single-cell transcriptomic (SCTr) profiles of [~]40,000 HepaRG cells exposed to etoposide, brefeldin A, cycloheximide, rotenone, tBHQ, troglitazone, and tunicamycin at three concentrations for 24 hours. SCTr enabled a detailed analysis of adaptive stress response pathways (SRPs), including the unfolded protein response (UPR), oxidative stress response (OSR), heat shock response (HSR), and DNA damage response (DDR). Troglitazone upregulated lipid metabolism genes (PLIN2, ACOX1) along with HSR and UPR activation, with co-expression of DNAJA1, HSP90AA1, and DDIT3 in subsets of cells. Brefeldin A and tunicamycin strongly induced UPR markers (HSPA5, SYVN1, LMF2, PDIA4) in subsets of cells, with some also expressing apoptotic (DDIT3, CASP8) and autophagic (SQSTM1) genes, indicating diverse stress responses. Rotenone activated GDF15, TRIB3, and DDIT3 in a fraction of cells, accompanied by PLIN2 and mild UPR induction, reflecting heterogeneous mitochondrial stress responses. We scored individual cells using literature-derived SRP gene signatures to characterize overall stress phenotypes and clustered them using a generalized Jaccard metric. The clustering revealed five phenotypic groups spanning cell states associated with homeostasis, adaptive responses, terminal outcomes, autophagy, and apoptosis. By systematically analyzing the distributions of cells in different states across treatments, we visualized dynamic shifts in cellular subpopulations responding to chemicals, revealing early stress responses and potential transitions to cell death. Our findings suggest the utility of SCTr in decoding stress states that could provide possible insights into transitions between cellular adaptive and terminal transitions involved in toxicity.

pharmacology and toxicology↗

bioRxiv2024

A Ketogenic Diet Sensitizes Pancreatic Cancer to Inhibition of Glutamine Metabolism

Pancreatic cancer is the third leading cause of cancer death in the United States, and while conventional chemotherapy remains the standard treatment, responses are poor. Safe and alternative therapeutic strategies are urgently needed1. A ketogenic diet has been shown to have anti-tumor effects across diverse cancer types but will unlikely have a significant effect alone. However, the diet shifts metabolism in tumors to create new vulnerabilities that can be targeted (1). Modulators of glutamine metabolism have shown promise in pre-clinical models but have failed to have a marked impact against cancer in the clinic. We show that a ketogenic diet increases TCA and glutamine-associated metabolites in murine pancreatic cancer models and under metabolic conditions that simulate a ketogenic diet in vitro. The metabolic shift leads to increased reliance on glutamine-mediated anaplerosis to compensate for low glucose abundance associated with a ketogenic diet. As a result, glutamine metabolism inhibitors, such as DON and CB839 in combination with a ketogenic diet had robust anti-cancer effects. These findings provide rationale to study the use of a ketogenic diet with glutamine targeted therapies in a clinical context. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/604377v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1ebeefforg.highwire.dtl.DTLVardef@97e2ceorg.highwire.dtl.DTLVardef@1ab45c3org.highwire.dtl.DTLVardef@1713540_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Description: Mechanistic rationale for combining a ketogenic diet and glutamine metabolism inhibitors. The combination of low glucose from a ketogenic diet and pharmacologic glutamine inhibition impairs nutrient input to mitochondria, reducing cancer growth.

cancer biology↗

bioRxiv2024

Highly conserved brain vascular receptor ALPL mediates transport of engineered viral vectors across the blood-brain barrier

Delivery of systemically administered therapeutics to the central nervous system (CNS) is restricted by the blood-brain barrier (BBB). Bioengineered Adeno-Associated Virus (AAV) capsids have been shown to penetrate the BBB with great efficacy in mouse and non-human primate models, but their translational potential is often limited by species selectivity and undefined mechanisms of action. Here, we apply our RNA-guided TRACER AAV capsid evolution platform to generate VCAP-102, an AAV9 variant with markedly increased brain tropism following intravenous delivery in both rodents and primates. VCAP-102 demonstrates a similar CNS tropism in cynomolgus macaque, african green monkey, marmoset and mouse, showing 20- to 400-fold increased transgene expression across multiple brain regions relative to AAV9. We demonstrate that the enhanced CNS tropism of VCAP-102 results from direct interaction with alkaline phosphatase (ALPL), a highly conserved membrane-associated protein expressed on the brain vasculature. VCAP-102 interacts with human, primate and murine ALPL isoforms, and ectopic expression of ALPL is sufficient to initiate receptor-mediated transcytosis of VCAP-102 in an in vitro transwell model. Our work identifies VCAP-102 as a cross-species CNS gene delivery vector with a strong potential for clinical translation and establishes ALPL as a brain delivery shuttle capable of efficient BBB transport to maximize CNS delivery of biotherapeutics.

neuroscience↗

bioRxiv2023

Polymer Model Unveils Quantitative Association of Chromatin Conformation and Gene Regulation

The spatial organization of chromatin in the nucleus is of essence for regulating gene transcription. However, the mechanisms governing the intricate interplay of chromatin structure and gene transcription remain poorly understood. Hi-C experiments have unveiled a multiscale chromatin organization, significantly enriching our understanding of the structural control of gene expression. We introduce a computational framework to link chromatin structural modifications to gene regulation. This framework generates an ensemble of three-dimensional conformations of a given genomic locus using a bead-spring polymer model where the cHiC contact map is used as an input. We then correlate such chromatin conformations to the transcription level of the encoded genes using a Markov chain-based model, where binding/unbinding rates extracted from the molecular dynamics trajectories are used. By considering a specific example, we have demonstrated that the deletion of the CTCF binding domain between two consecutive TADs leads to a significant change in the enhancer-promoter interaction and gene transcription of the encoded genes, namely sox9 and kcnj2, responsible for limb development. Such a change in gene expression level is quantitatively consistent with experiments. Further insight from the polymer-based 3D conformation reveals that the higher gene expression level of the kcnj2 gene is caused by the specific enhancers of kcnj2, present in the sox9 TAD, which become accessible after boundary deletion. By quantifying the impact of these enhancers, our model can also be used to identify the functional enhancers. Together, the present computational framework not only advances our understanding of the relationship between the spatial architecture of the chromosome and the function of the cell but also provides invaluable insights into potential therapeutic interventions targeting aberrant gene regulation in pathological contexts.

biophysics↗

bioRxiv2023

Sex specific regulation of the cortical transcriptome in response to sleep deprivation

Multiple studies have documented sex differences in sleep behaviour, however the molecular determinants of such differences remain unknown. Furthermore, most studies addressing molecular mechanisms have been performed only in males, leaving the current state of knowledge biased towards the male sex. To address this, we studied the differences in the transcriptome of the cerebral cortex of male and female C57Bl/6J mice after six hours of sleep deprivation. We found that several genes, including the neurotrophin growth factor Bdnf, immediate early genes Fosb and Fosl2, and the adenylate cyclase Adcy7 are differentially upregulated in males compared to females. We identified the androgen-receptor activating transcription factor EZH2 as the upstream regulatory element specifying sex differences in the sleep deprivation transcriptome. We propose that the pathways downstream of these transcripts, which impact on cellular re-organisation, synaptic signalling and learning may underpin the differential response to sleep deprivation in the two sexes.

molecular biology↗

bioRxiv2023

Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis using LuxR-type Regulators

A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that gram-negative and gram-positive bacteria generally communicate via homoserine lactones (HSL) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors ([≥] 20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.

synthetic biology↗

bioRxiv2020

Computational vaccinology based development of multi-epitope subunit vaccine for protection against the Norovirus infections

Human Norovirus belong to family Calciviridae, it was identified in the outbreak of gastroenteritis in Norwalk, due to its seasonal prevalence known as "winter vomiting disease". Treatment of Norovirus infection is still mysterious because there is no effective antiviral drugs or vaccine developed to protect against the infection, to eradicate the infection an effective vaccine should be developed. In this study capsid protein (A7YK10), small protein (A7YK11) and polyprotein (A7YK09) were utilized. These proteins were subjected to B and T cell epitopes prediction by using reliable immunoinformatics tools. The antigenic and non-allergenic epitopes were selected for subunit vaccine, which can activate cellular and humoral immune responses. Linkers joined these epitopes together. The vaccine structure was modelled and validated by using Errat, ProSA and rampage servers. The modelled vaccine was docked with TLR-7. Stability of the docked complex was evaluated by MD simulation. In order to apply the concept in a wet lab, the reverse translated vaccine sequence was cloned in pET28a (+). The vaccine developed in this study requires experimental validation to ensure its effectiveness against the disease.

immunology↗