Biology subjects

Rana, N.

Publications and source records attributed to Rana, N..

11 recordsLinked to original sources

bioRxiv2026

Gram-negative-dominated polymicrobial microbiome of necrotizing soft tissue infections from North India: an integrated culture and 16S rRNA metagenomics prospective cohort study

Necrotizing soft tissue infections (NSTIs) carry 10 to 30% mortality. Current empirical antimicrobial guidance derives almost entirely from Western cohorts dominated by Streptococcus pyogenes and aerobic-anaerobic consortia, yet whether this microbial paradigm applies to tropical, high-antimicrobial-pressure settings has not been tested with culture-independent methods. We did a prospective cohort study of 169 patients with intraoperatively confirmed NSTI at a North Indian tertiary center (2021 to 2024). Wound tissue underwent aerobic and anaerobic culture, QIIME2-based 16S rRNA gene amplicon sequencing (V3-V4), and targeted SYBR Green quantitative PCR (qPCR) for Acinetobacter baumannii and S. pyogenes. The wound microbiota was overwhelmingly Gram-negative and polymicrobial, anchored by A. baumannii (culture, 33.7%; metagenomics, 49.1%; qPCR, 37.9%), Escherichia coli (32.0%), and Klebsiella pneumoniae (20.7%); S. pyogenes contributed only 4.7% of culture-positive cases. Polymicrobial wounds had higher Shannon diversity (2.59 versus 2.33; P = 0.048) and discrete community composition (PERMANOVA R2 = 0.511; P = 0.010). Culture-metagenomics agreement ranged from almost perfect for Escherichia ({kappa} = 0.849) to slight for Streptococcus ({kappa} = 0.131). North Indian NSTIs present a microbial picture distinct from the Western paradigm, with implications for empirical therapy. IMPORTANCENecrotizing soft tissue infections kill rapidly, and physicians must choose antibiotics before laboratory results are available. Globally, treatment guidelines assume the dominant pathogen is Streptococcus pyogenes, a Gram-positive organism, because nearly all molecular evidence comes from Western countries. We show that in a large Indian cohort, the infection is instead dominated by Gram-negative bacteria, especially Acinetobacter baumannii, with S. pyogenes rarely present. Polymicrobial status, not wound location or injury mechanism, most strongly determines community composition. These findings challenge the one-size-fits-all antibiotic approach and argue for region-specific empirical regimens prioritizing Gram-negative coverage in tropical, high-antimicrobial-pressure settings.

microbiology↗

bioRxiv2024

Imaging Intra- and Extracellular Conductivity using MR based Conductivity Tensor Imaging

Imaging electrical conductivity may reveal relationships between biological tissues, cellular structures, and physiological processes. Biological tissues are primarily composed of major ions such as Na+ and K+, with varying concentrations and mobility within the cellular structures. These tissues consist of intracellular and extracellular fluids separated by cell membranes, and their electrical conductivity can be expressed as a function of ion concentration and mobility. This study introduces Conductivity Tensor Imaging (CTI) to independently reconstruct the electrical conductivity of intra- and extracellular compartments in biological tissues using MRI. We validated this method using a conductivity phantom with three compartments filled with electrolytes and/or giant vesicle suspensions. These vesicles mimic cell-like materials with thin insulating membranes, providing a realistic model for cellular structures. Measurements showed that high-frequency conductivity closely matched low-frequency conductivity in normal electrolytes. However, in the giant vesicle compartment, the conductivity of extracellular (EC) and intracellular (IC) regions correlated with cell volume fraction. In vivo human brain imaging using CTI revealed significant EC and IC conductivity variations across different brain regions, corresponding to underlying cellular compositions and structures. CTI introduces a novel MR contrast mechanism to distinctly measure IC and EC conductivities. Our findings highlight the potential of CTI to enhance our understanding of brain microstructure and its physiological processes through detailed conductivity mapping. This method signifies a notable advancement in non-invasive imaging, providing novel insights into the electrical properties of biological tissues and their implications for biophysical properties.

bioengineering↗

bioRxiv2023

Claudin-2 limits pancreatitis development through regulating tight junction-controlled pancreatic ductal transport

Pancreatitis is an inflammatory disease of the pancreas that can arise due to various factors, including environmental risks such as diet, alcohol, and smoking, as well as genetic predispositions. In some cases, pancreatitis may progress and become chronic, leading to irreversible damage and impaired pancreatic function. Genome-wide association studies (GWAS) have identified polymorphisms at the X-linked CLDN2 locus as risk factors for both sporadic and alcohol-related chronic pancreatitis. CLDN2 encodes claudin-2 (CLDN2), a paracellular cation-selective channel localized at tight junctions and expressed in the pancreas and other secretory organs. However, whether and how CLDN2 may modify pancreatitis susceptibility remains poorly understood. We aimed to clarify the potential role of CLDN2 in the onset and progression of pancreatitis. We employed multiple methodologies to examine the role of CLDN2 in human pancreatic tissue, caerulein-induced experimental pancreatitis mouse model, and pancreatic ductal epithelial organoids. In both human chronic pancreatitis tissues and caerulein-induced experimental pancreatitis, CLDN2 protein was significantly upregulated in pancreatic ductal epithelial cells. Our studies using pancreatic ductal epithelial organoids and mice demonstrated the inflammatory cytokine IFN{gamma} upregulates claudin-2 expression at both RNA and protein levels. Following caerulein treatment, Ifng KO mice had diminished upregulation of CLDN2 relative to WT mice, indicating that caerulein-induced claudin-2 expression is partially driven by IFN{gamma}. Functionally, Cldn2 knockout mice developed more severe caerulein-induced experimental pancreatitis, indicating CLDN2 plays a protective role in pancreatitis development. Pancreatic ductal epithelial organoid-based studies demonstrated that CLDN2 is critical for sodium-dependent water transport and necessary for cAMP-driven, CFTR-dependent fluid secretion. These findings suggest that functional crosstalk between CLDN2 and CFTR is essential for fluid transport in pancreatic ductal epithelium, which may protect against pancreatitis by adjusting pancreatic ductal secretion to prevent worsening autodigestion and inflammation. In conclusion, our studies suggest CLDN2 upregulation during pancreatitis may play a protective role in limiting disease development, and decreased CLDN2 function may increase pancreatitis severity. These results point to the possibility of modulating pancreatic ductal CLDN2 function as an approach for therapeutic intervention of pancreatitis.

pathology↗

bioRxiv2023

Protein unfolding thermodynamics predict multicomponent phase behavior

An increasing number of proteins are known to undergo liquid-liquid phase separation (LLPS), with or without nucleic acids or partner proteins, forming dense liquid-like phases termed biomolecular condensates. This physical phenomenon has been implicated in the existence of cellular membraneless organelles as well as in the formation of pathological protein aggregates in several human diseases. While common structural features of proteins with a propensity to undergo LLPS have been well documented, currently there is no thermodynamic framework capable of predicting the phase behavior of native proteins. Here, we show that two fundamental thermodynamic properties associated with the unfolding of a native protein, change in heat capacity ({Delta}Cunfold) and change in Gibbs free energy ({Delta}Gunfold), are sufficient to predict the formation of multicomponent biomolecular condensates. We find that proteins with small{Delta} Cunfold and{Delta} Gunfold values, which indicate a native state that is thermodynamically similar to the fully unfolded state, promote LLPS. In contrast, proteins with large{Delta} Cunfold and{Delta} Gunfold values promote aggregation. We also demonstrate that the stability of the liquid-like condensate can be predicted from the proximity of a proteins thermodynamic variable values to the phase boundary. This work elucidates a deep connection between single-protein thermodynamics and multicomponent phase behavior, and provides an avenue for predicting pathological droplet-aggregate transition. Significance StatementBiomolecular phase transitions, such as LLPS of proteins and nucleic acids, is emerging as an important concept in understanding the link between dysregulation of membraneless compartmentalization in cells and several human diseases. Currently, analysis of structural features such as intrinsic disorder and charged residue content is the "rule-of-thumb" to predict a proteins propensity to undergo LLPS. There are several instances where this qualitative approach fails, potentially due to not accounting for a proteins native structure. We demonstrate an empirical correlation between the unfolding thermodynamics of native proteins and their phase behavior, which enables a quantitative prediction of multicomponent LLPS. This novel approach, based on single-protein thermodynamics, has the potential to quantitatively predict pathological phase transitions of proteins in degenerative human diseases.

biophysics↗

bioRxiv2023

Prostaglandin E2 controls the metabolic adaptation of T cells to the intestinal microenvironment

Immune cells must adapt to different environments during the course of an immune response. We studied the adaptation of CD8+ T cells to the intestinal microenvironment and how this process shapes their residency in the gut. CD8+ T cells progressively remodel their transcriptome and surface phenotype as they acquire gut residency, and downregulate expression of mitochondrial genes. Human and mouse gut-resident CD8+ T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We found that the intestinal microenvironment is rich in prostaglandin E2 (PGE2), which drives mitochondrial depolarization in CD8+ T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE2 sensing promotes CD8+ T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell population. Thus, a PGE2-autophagy-glutathione axis defines the metabolic adaptation of CD8+ T cells to the intestinal microenvironment, to ultimately influence the T cell pool.

immunology↗

bioRxiv2022

HIGHLY PHAGOCYTIC LIPID-ASSOCIATED MACROPHAGES (LAMs) ARE INCREASED IN COLONIC LAMINA PROPRIA IN OBESITY

Little is known about the effects of high fat diet (HFD)-induced obesity on resident colonic lamina propria (LP) macrophages (LPMs) function and metabolism. Here, we report that obesity and diabetes resulted in increased macrophage infiltration in the colon. These macrophages exhibited the residency phenotype CX3CR1hiMHCIIhi, and were CD4-TIM4-. During HFD, resident colonic LPM exhibited a lipid metabolism gene expression signature that overlapped that used to define lipid associated macrophages (LAMs). Via single cell RNA sequencing, we identified a sub-cluster of macrophages, increased in HDF, that were responsible for the LAM signature. Compared to other macrophages in the colon, these cells were characterized by elevated glycolysis, phagocytosis and efferocytosis signatures. CX3CR1hiMHCIIhi colonic resident LPMs had fewer lipid droplets (LD) and decreased triacylglycerol (TAG) content compared to equivalent cells in lean mice, and exhibited increased phagocytic capacity, suggesting that HFD induces adaptive responses in LPMs to limit bacterial translocation.

immunology↗

bioRxiv2022

Human mutations in SLITRK3 implicated in GABAergic synapse development in mice

We report on biallelic homozygous and monoallelic de-novo variants in SLITRK3 in 3 unrelated families presenting with epileptic encephalopathy associated with a broad neurological involvement characterized by microcephaly, intellectual disability, seizures, and global developmental delay. SLITRK3 encodes for a transmembrane protein that is involved in controlling neurite outgrowth and inhibitory synapse development and that has an important role in brain function and neurological diseases. Using primary cultures of hippocampal neurons carrying patients SLITRK3 variants and in combination with electrophysiology, we demonstrate that recessive variants are loss-of-function alleles. By analyzing the development and phenotype of SLITRK3 KO (SLITRK3-/-) mice, we bring additional evidence of enhanced susceptibility to pentylenetetrazole-induced seizure with the appearance of spontaneous epileptiform EEG, as well as developmental deficits such as higher motor activities and reduced parvalbumin interneurons. Taken together, our results exhibit impaired development of peripheral and central nervous system and support a conserved role of this transmembrane protein in neurological function. Our study delineates an emerging spectrum of human core synaptopathies caused by variants in genes that encode SLITRK proteins and essential regulatory components of the synaptic machinery. The hallmark of these disorders is impaired postsynaptic neurotransmission at nerve terminals; an impaired neurotransmission resulting in a wide array of (often overlapping) clinical features, including neurodevelopmental impairment, weakness, seizures, and abnormal movements. The genetic synaptopathy caused by SLITRK3 mutations highlights the key roles of this gene in human brain development and function.

genetics↗

bioRxiv2022

Carrier based formulation of plant growth promoting Rhizobium species and their effect on albizia procera seedling

The carrier-based formulation of rhizobial cultures in general, excels to register their effects on various plant growth parameters of Albizia procera seedlings. Carrier based bio-inoculant prepared with rhizobial isolate FA6 of Uttrakhand performed better for all plant growth characteristics. Charcoal based application of rhizobial isolates also increased the N, P, K content of soil. In case of seedlings treated with charcoal-based formulation of rhizobial isolate from Himachal Pradesh maximum available N (323.30 kg/ha), P (38.97 kg/ha) and K (395.9 kg/ha) content was recorded in T2 (Charcoal based formulation of BA2 strain+20kg/ha N) which was significantly superior to T3 and uninoculated control. Among the charcoal-based formulation of rhizobial isolate from Uttrakhand seedlings under treatment T2 (Charcoal based formulation of FA6 strain+20kg/ha N) registered maximum available N (327.7kg/ha), P (39.01 kg/ha) and K (397.4 kg/ha) content in soil. Charcoal based application of rhizobial isolates significantly influenced the activity of soil enzymes (Dehydrogenase and Phosphatase). Application of Carrier based formulation of rhizobial isolate BA2 from Himachal Pradesh showed maximum dehydrogenase (11.20 g TPF g-1h-1) and phosphatase (536.2 molL-1g-1h-1) activity as compare to uninoculated control. Whereas, among the rhizobial isolates from Uttrakhand maximum dehydrogenase (11.39 g TPFg-1h-1) and phosphatase (545.4 mol L-1g-1h-1) activity was also recorded with T2 (charcoal-based formulation of strain FA6+20kg/ha N) which was significantly superior to T3 and uninoculated control.

microbiology↗

bioRxiv2022

Resident T cells orchestrate adipose tissue remodeling in a site peripheral to infection

Infection with helminth parasites can affect adiposity, but underlying mechanisms that regulate this process are unclear. We found that fat content of mesenteric adipose tissue (mAT) declined in mice during infection with gut-restricted parasitic worms. This was associated with the accumulation of metabolically activated, immunostimulatory cytokine- and extracellular matrix-secreting multipotent stromal cells, which had potential to differentiate into preadipocytes. Concomitantly, mAT became infiltrated with Th2 lymphocytes that took up long-term residence and responded to signals from stromal cells by producing stromal cell-stimulating cytokines, including Amphiregulin. Signals delivered by Amphiregulin to stromal cells were required for immunity to infection. Our findings reveal intricate intercellular communication between Th2 cells and adipocyte progenitors and link immunity to intestinal infection to T cell-dependent effects on the adipocyte lineage.

immunology↗

bioRxiv2020

Triacylglycerol synthesis enhances macrophage inflammatory function

Macrophages are integral to most tissues. Foam cells, macrophages with lipid droplets (LDs) which are stores of triacylglycerols (TGs) and cholesterol esters (CEs), are found in various disease states1. LDs can act as energy stores since TG lipolysis releases fatty acids (FAs) for mitochondrial oxidation (FAO), a process that relies on long-chain FA conversion into acylcarnitines by the enzyme Cpt1a2. However, in macrophages, proinflammatory signals result in diminished FAO and increased TG synthesis with LD development3,4. We explored the significance of LDs in cells that do not utilize FAO. We show that macrophages stimulated with lipopolysaccharide (LPS) plus interferon-{gamma} (IFN{gamma}) accumulate TGs in LDs, and long-chain acylcarnitines. In these cells, inhibition of TG synthesis results in diminished LD development, and increased long chain acylcarnitine levels, suggesting that FA fate is balanced between TG and acylcarnitine synthesis. Nevertheless, TG-synthesis is required for inflammatory macrophage function, since its inhibition negatively affects production of proinflammatory IL-1{beta}, IL-6 and PGE2, and phagocytic capacity, and protects against LPS-induced shock in vivo. Failure to make PGE2 is critical for this phenotype, since exogenous PGE2 reverses the anti-inflammatory effects of TG-synthesis inhibition. These findings place LDs in a position of central functional importance in inflammatory macrophages.

immunology↗

bioRxiv2019

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform specific start-loss mutations of essential genes can cause genetic diseases

Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early onset, therapy resistant seizures and developmental delay. Here we report on 12 individuals from 10 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly and visual disturbance. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A>G) in the essential UDP-glucose pyrophosphorylase (UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in brain cell types, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modelled during pluripotent stem cell differentiation in vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2b in vivo in zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE. Importantly, it also shows that isoform specific start-loss mutations causing expression loss of a tissue relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies.

genetics↗