Biology subjects

Shrivastava, V.

Publications and source records attributed to Shrivastava, V..

8 recordsLinked to original sources

bioRxiv2026

Rapid and Interpretable AMR Diagnostics via Genomics and Cell Painting using Differential Geometry-based Directed-Simplicial Neural Networks on Multimodal Data

Antimicrobial resistance (AMR) remains a critical global health challenge, particularly in high-prevalence regions such as India, where rapid and interpretable diagnostic tools are urgently needed. To address this challenge, we present a computational framework for AMR prediction that integrates genomic and cellular phenotypic data using an in-house developed differential geometry-based Directed Simplicial Neural Network (Dg-Dir-SNNs) applied to multimodal datasets. Using this framework, we analyzed 384 clinically relevant AMR isolates, including Escherichia coli and Klebsiella pneumoniae, integrating 256 genomic k-mer features with 503 cellular morphology descriptors derived from high-content Cell Painting assays. The Dg-Dir-SNNs model constructs an inferred-causal network of top-ranked biomarker-driving features, predicting potential directional dependencies among genomic motifs and phenotypic features. Network analysis identified kmer_TATG as the top-ranked driver associated with predicted resistance, with a local neighborhood including other genomic motifs (kmer_TTTT, kmer_CGTG, kmer_TCAC, kmer_CGTA, kmer_GAAA, kmer_TAAA, kmer_TACA, kmer_TGTG, kmer_TGAG, kmer_AAAA) and a key morphological feature (Cells_correlation_ER_Brightfield). These relationships suggest potential mechanistic associations in which specific genomic motifs may influence cellular phenotypes linked to antimicrobial resistance. Although not yet clinically deployed, this approach demonstrates the potential of multimodal AI-driven modeling for rapid in silico AMR prediction. By providing interpretable, biologically grounded insights, the framework may support future diagnostic development, targeted surveillance strategies, and experimental validation in high-resistance healthcare settings.

microbiology↗

bioRxiv2024

Wild yeast isolation by middle school students reveals features of North American oak populations of Saccharomyces cerevisiae and Kluyveromyces lactis

Features of the natural life cycle of the budding yeast Saccharomyces cerevisiae were crucial to its domestication as a laboratory experimental model, especially the ability to maintain stable haploid clones and cross them at will to combine alleles via meiosis. Stable haploidy results from mutations in HO, which encodes an endonuclease required for haploid-specific mating-type switching. Previous studies found an unexpected diversity of HO alleles among natural isolates within a small geographic area. We developed a hands-on field and laboratory activity for middle school students in Denver, Colorado, USA to isolate wild yeast from oak bark, identify species via DNA sequencing, and sequence HO from S. cerevisiae isolates. We find limited HO diversity in North American oak isolates, pointing to efficient, continuous dispersal across the continent. By contrast, we isolated the "dairy yeast", Kluyveromyces lactis, from a tree <10 m away and found that it represents a new population distinct from an oak population in an adjacent state, pointing to high genetic diversity. The outreach activity partnered middle school, high school, and university students in making scientific discoveries and can be adapted to other locations and natural yeast habitats. Indeed, a pilot sampling activity in southeast Texas yielded S. cerevisiae oak isolates with a new allele of HO and, from a nearby prickly pear cactus, a heat-tolerant isolate of Saccharomyces paradoxus.

evolutionary biology↗

bioRxiv2023

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a "Tier-2" database on BioCyc. ImportanceMetabolic reconstructions are vital for the systemic understanding of an organisms ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated "metabolic encyclopedia" for Alteromonas macleodii ATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.

microbiology↗

bioRxiv2021

Hypoxia induces early neurogenesis in human fetal neural stem cells by activating the WNT pathway.

Fetal neural stem cells (FNSCs) are present in the brain of human fetuses that differentiate into cells of neuronal and glial lineages. Difference in oxygen concentration between maternal and fetal circulation indicates that the developing fetus may be exposed to lower oxygen concentrations compared to adults. This physiological hypoxia may influence the growth and differentiation of the FNSCs. This study aimed to evaluate the effect of hypoxia on the differentiation potential of human FNSCs isolated from the sub-ventricular zone of aborted fetal brains (n=5). FNSCs were isolated, expanded, and characterized by Nestin and Sox2 expression, using immunocytochemistry and flowcytometry respectively. These FNSCs were exposed to 20% oxygen (normoxia) and 0.2% oxygen (hypoxia) concentrations for 48 hours, and hypoxia exposure (n=5) was evaluated by a panel of markers (CA9, PGK1 and VEGF). Whole human genome transcriptomic analyses (Genespring GX13) of FNSCs exposed to hypoxia (Agilent 4x44K human array slides), highlighted that genes associated with neurogenesis were getting enriched. The pathway analysis of these enriched genes (using Metacore) showed that WNT signaling played a role in determining the cell fate of FNSCs exposed to hypoxic environment. Microarray analyses was validated using neuronal and glial lineage commitment markers such as Ngn1, Ngn2, ASCL1, DCX, GFAP, Olig2 and Nkx2.2 using qPCR (n=9). This demonstrated upregulation of the neuronal commitment markers on hypoxia exposure, while no change was observed in astrocytic and oligodendrocyte lineage commitment markers. Increased expression of downstream targets of the WNT signaling pathway, TCF4 and ID2, by qPCR (n=9), indicated its involvement in mediating neuronal differentiation on exposure to hypoxia.

neuroscience↗

bioRxiv2021

Human fetal neural stem cell-derived astrocytes maintain glutamate transport after hypoxic injury in vitro

Astrocytes are the most abundant glial cells that play many critical roles in the central nervous system physiology including the uptake of excess glutamate from the synapse by Excitatory Amino Acid Transporters (EAATs). Among the EAATs, EAAT2 are predominantly functional, astrocyte-specific glutamate transporters in the forebrain. Hypoxic brain injury is a pathological phenomenon seen in various clinical conditions including stroke and neonatal hypoxic ischemic encephalopathy. Glutamate excitotoxicity is an important cause of neuronal cell death in disorders involving hypoxic brain injury. As findings from rodent models cannot always be reliably extrapolated to humans, we aimed to develop a homogenous population of primary human astrocytes to study the effect of hypoxic injury on astrocyte function, especially glutamate uptake. We successfully isolated, established and characterized cultures of human fetal neural stem cells (FNSCs) from aborted fetal brains. FNSCs were differentiated into astrocytes, and characterized by increased expression of the astrocyte markers, glial fibrillary acidic protein (GFAP), EAAT1 and EAAT2. A concomitant decrease in neural stem cell marker, Nestin, was observed. Differentiated astrocytes were exposed to various oxygen concentrations mimicking normoxia (20% and 6%), moderate and severe hypoxia (2% and 0.2% respectively). Interestingly, no change was observed in the expression of glutamate transporter, EAAT2 and glutamate uptake by astrocytes, even after exposure to hypoxia. Our novel model of human FNSC derived astrocytes exposed to hypoxic injury, establishes that astrocytes are able to maintain glutamate uptake even after exposure to severe hypoxia for 48 hours, and thus provides evidence for the neuroprotective role of astrocytes in hypoxic injury.

neuroscience↗

bioRxiv2020

Heat Shock Protein 27 versus Estrogen Therapy for Post-Menopausal Atherosclerosis: Rethinking Mechanisms of Cholesterol Lowering

Aims The estrogen-inducible protein Heat Shock Protein 27 (HSP27) as well as anti-HSP27 antibodies are elevated in healthy subjects compared to cardiovascular disease patients. Vaccination of ApoE-/- mice with recombinant HSP25 (rHSP25, the murine ortholog), boosts anti-HSP25 levels and attenuates atherogenesis. As estrogens promote HSP27 synthesis, cellular release and blood levels, we hypothesize that menopause will result in loss of HSP27 atheroprotection. Hence, we now compare the efficacy of rHSP25 vaccination vs. estradiol (E2) therapy for the prevention of post-menopausal atherogenesis.Methods and Results ApoE-/- mice subjected to ovariectomy (OVX) showed a 65% increase atherosclerotic burden compared to sham mice after 5 weeks of a high fat diet. Relative to vaccination with rC1, a truncated HSP27 control peptide, atherogenesis was reduced by 5-weekly rHSP25 vaccinations (−43%), a subcutaneous E2 slow release pellet (−52%) or a combination thereof (−82%). Plasma cholesterol levels declined in parallel with the reductions in atherogenesis, but relative to rC1/OVX mice plasma PCSK9 levels were 52% higher in E2/OVX and 41% lower in rHSP25/OVX mice (p<0.0001 for both). Hepatic LDLR mRNA levels did not change with E2 treatment but increased markedly with rHSP25 vaccination. Conversely, hepatic PCSK9 mRNA increased 148% with E2 treatment vs. rC1/OVX but did not change with rHSP25 vaccination. In human HepG2 hepatocytes E2 increased PCSK9 promoter activity 303%, while the combination of [rHSP27 + PAb] decreased PCSK9 promoter activity by 64%.Conclusion The reduction in post-OVX atherogenesis and cholesterol levels with rHSP25 vaccination is associated with increased LDLR but not PCSK9 expression. Surprisingly, E2 therapy attenuates atherogenesis and cholesterol levels post-OVX without altering LDLR but increases PCSK9 expression and promoter activity. This is the first documentation of increased PCSK9 expression with E2 therapy and raises questions about balancing physiological estrogenic / PCSK9 homeostasis and targeting PCSK9 in women – are there effects beyond cholesterol?Competing Interest StatementEOB and YXC are inventors on US patents 8343915B2 and 8343916B2; EOB, CS and YXC are inventors on US patent application PCT/CA2016/051018; EOB is the inventor on US patent application 63/031,6402020; all intellectual property pertains to HSP27 diagnostics / therapeutics. EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.AbbreviationsAAbanti-HSP27 (or anti-HSP25) antibodiesApoE-/-apolipoprotein E nulla.u.absorbance unitsE217β estradiolHFDhigh fat dietHPRThypoxanthine-phosphoribosyltransferaseHSP27Heat Shock Protein 27HSP27o/eHSP27 over-expressingLDL-Clow density lipoprotein cholesterolLDLRlow density lipoprotein receptorMPmenopausemRNAmessenger RNANF-κBnuclear factor kappa light chain enhancer of activated B cellsONovernightOVXovariectomyPAbpolyclonal anti-HSP27 IgG antibodyPBSphosphate buffered salinePCSK9Proprotein Convertase Subtilisin/Kexin type 9rC1recombinant C-terminal truncation of HSP27 spanning amino acids 90-205rHSP27recombinant HSP27SDS-PAGEsodium dodecyl sulfate and polyacrylamide gelWBWestern BlotView Full Text

pathology↗

bioRxiv2020

Heat Shock Protein 27 Immune Complex Upregulates LDLR Expression Thereby Reducing Plasma Cholesterol and Atherogenesis

Elevated Heat Shock Protein 27 levels predict relative freedom from cardiovascular events. In ApoE-/- mice HSP27 over-expression or twice daily subcutaneous injections reduce blood and plaque cholesterol levels, inflammation and atherogenesis. While natural antibodies to HSP27 are present in human blood their role is unknown. Here, we show that blood levels of both HSP27 and anti-HSP27 IgG antibodies are elevated in healthy controls compared to patients with cardiovascular disease. ApoE-/- mice vaccinated with recombinant HSP25 (murine ortholog) develop elevated anti-HSP25 IgG antibodies and reduced levels of cholesterol, inflammation and atherosclerosis. The effects on cholesterol metabolism were divergent: increased hepatic LDLR expression and reduced plasma PCSK9 levels. In vitro, a polyclonal anti-HSP27 IgG antibody combined with rHSP27 to upregulate hepatocyte LDLR expression via an NF-kB-dependent pathway that is independent of SREBP2 expression and intracellular cholesterol levels. HSP27 immunotherapy represents a novel means of lowering not only cholesterol but also PCSK9.Competing Interest StatementEOB and YXC are inventors on US patents 8343915B2 and 8343916B2 and EOB, CS and YXC are inventors on US patent application PCT/CA2016/051018, all pertaining to HSP27 diagnostics / therapeutics. EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.View Full Text

pathology↗

bioRxiv2019

Regulation of islet function and gene expression by prolactin during pregnancy

Pancreatic islets adapt to insulin resistance of pregnancy by up regulating {beta}-cell proliferation and increase insulin secretion. Previously, we found that prolactin receptor (Prlr) signaling is important for this process, as heterozygous prolactin receptor-null (Prlr+/-) mice are glucose intolerant, had a lower number of {beta} cells and lower serum insulin levels than wild type mice during pregnancy. However, since Prlr expression is ubiquitous, to determine its {beta}-cell specific effects, we generated a transgenic mouse with a floxed Prlr allele under the control of an inducible promoter, allowing conditional deletion of Prlr from {beta} cells in adult mice. In this study, we found that {beta}-cell-specific Prlr reduction resulted in elevated blood glucose during pregnancy. Similar to our previous finding in mouse with global Prlr reduction, {beta}-cell-specific Prlr loss led to a lower {beta}-cell mass and a lower in vivo insulin level during pregnancy. However, these islets do not have an intrinsic insulin secretion defect when tested in vitro. Interestingly, when we compared the islet gene expression profile, using islets isolated from mice with global versus {beta}-cell-specific Prlr reduction, we found some important differences in genes that regulate apoptosis and insulin secretion. This suggests that Prlr has both cell-autonomous and non-cell-autonomous effect on {beta} cells, beyond its regulation of pro-proliferative genes.

physiology↗