Biology subjects

Prakash, C.

Publications and source records attributed to Prakash, C..

7 recordsLinked to original sources

bioRxiv2026

Candida-Klebsiella interactions rewire fungal morphogenesis to create a host environment favoring pathogen survival with enhanced tissue pathology

Clinically relevant infections commonly develop within polymicrobial environments where interkingdom interactions shape host responses and disease trajectories. Candida albicans and Klebsiella pneumoniae are critical pathogens that can co-exist in the respiratory tract, yet the consequences of their interaction in terms of fungal physiology, pathogenicity and impact on disease outcomes remain poorly understood. Here, we show that K. pneumoniae enhances C. albicans virulence traits suggesting that co-infections could exacerbate lung disease. Mechanistically, bacterial presence induces fungal hyphal morphogenesis via MAPK-CEK signaling, coupled to metabolic rewiring and alterations in cell wall remodeling and septation, resulting in highly elongated hyphae that escape faster from macrophages. At the host level, co-infection reprograms macrophages into a non-canonical state characterized by overlapping pro- and anti-inflammatory modules, integrating type I interferon and IL-10 signaling. This response contributes to tissue damage and facilitates fungal persistence. Our findings reveal that the bacterial-fungal interactions coordinately reprogram pathogen behavior and host immunity, promoting pathogenic synergy and potentially conferring a negative impact on disease outcomes. HIGHLIGHTSCandida-Klebsiella interactions modulate hyphal morphogenesis. Ectopic morphogenesis encompasses septation, cell wall remodeling and carbon metabolism. Candida-Klebsiella co-infections trigger tissue hyperinflammation and compensatory regulation. Candida-Klebsiella co-infection establishes a host environment facilitating microbial dissemination and tissue pathology. Candida-Klebsiella interactions enhance fungal virulence potentially impacting the severity of co-infections

microbiology↗

bioRxiv2026

LINE-1 Retrotransposon Activation and 5-Gene Dysregulation as a Common Pathological Signature in Post-Traumatic and Status Epilepticus Models of Epilepsy.

The transition from an initial brain insult to chronic epilepsy remains a critical challenge in clinical neuroscience, often involving complex molecular shifts that are difficult to capture through single-gene analysis. This study investigated the existence of a convergent pathway of genomic instability across two distinct etiological models: iron-induced (FeCl3) post-traumatic epilepsy (PTE) and lithium-pilocarpine-induced (LiCl-Pilo) status epilepticus (SE). By integrating Electrophysiology (EEG), {gamma}-oscillation spectral analysis, multi-unit activity (MUA) recordings with behavioural assessments Morris Water Maze (MWM) and Open Field Test (OFT) we validated and established the chronic hyperexcitability and associated cognitive- emotional co-morbidities of these two models. Which further served as a functional backdrop for investigating a targeted 8-gene panel consisting of GABRA2, KCNN2, KCNAB1, GRIK1, BCL11A, BRD7, STX1B, and PNPO. RT-PCR analysis demonstrated a systemic dysregulation of 5 genes out of these 8 genes, mirroring the simultaneous collapse of inhibitory signalling, membrane stability, and neurotransmitter metabolism seen in human phenotypes. While the clinical roles of these genes are well documented, our study demonstrates that these rat models provide a high-fidelity platform for complex multigene studies and gene-level therapeutic exploration. Furthermore, in-silico docking identified Fisetin as a high-affinity ligand for the dysregulated proteins, offering a promising multi-target strategy for stabilizing the epileptic genome.

neuroscience↗

bioRxiv2025

BC-Predict Database: A Curated Resource of Experimentally Validated Markers in Multidrug Resistance in Breast Cancer

BackgroundIn this study, we aim to develop a yearly updatable database that could predict chemotherapeutic drug resistance and overall survival probability in breast cancer patients. Existing drug sensitivity databases depend on correlation-based predictions. In our study, candidates involved in drug resistance are chosen based on cell line validation (overexpression or downregulation or inhibition of candidates) studies, curated manually. Method28,773 mRNA expression signatures from 914 breast cancer patients were extracted from cProsite. 106 of these patients had clinical information and log2 fold change information required for this study. We categorized these patients into deceased and surviving groups from TCGA. To prepare a database that can predict drug resistance and overall survival, we included mRNAs that were over-expressed in at least 80% of the breast cancer patients and mRNAs over-expressed in deceased and surviving groups. In addition, we also reported breast cancer-associated drug resistance candidates which have been reported in cell-line based studies. The database matrix preparation involved an approximate of 15000 manual searches of cell validated studies. (750 candidates x 20 drugs). The database was validated using a publicly available breast cancer patient proteomics data. ResultsOur analysis identified a list of top priority candidates associated with multidrug resistance, categorized based on their resistance to >15 drugs, 5-15 drugs, and 2-4 drugs. Analysis of patient profiles in the database revealed that the number of proteins contributing to drug resistance was high in the poor prognosis category compared to the good prognosis category. ConclusionsOur study highlights the probable gaps in breast cancer drug resistance research, as only a small subset of overexpressed mRNA candidates found in patients are studied in vitro or in vivo experiments focusing on drug resistance. We also identified candidates involved in multidrug resistance, whose role in drug resistance has not been studied in more than 15 drugs. After further validations, this will benefit the clinicians and upcoming CRISPR gene therapeutics.

cancer biology↗

bioRxiv2025

The intracellular vacuolar pathogen Coxiella burnetii promotes exocytosis in a type IVB secretion system dependent manner

Coxiella burnetii is an obligate intracellular bacterial pathogen that causes a zoonotic disease known as Q fever. Upon internalization into host cells, Coxiella extensively remodels host vesicle trafficking and replicates within acidic, lysosome-derived, spacious vacuoles by secreting a suite of effectors through the type IVB secretion system (T4BSS), and hijacking the host cell machinery. However, how fundamental lysosomal functions, such as exocytosis, are subverted during Coxiella infection has not been well understood. In this study, we aimed to investigate the regulation and role of exocytosis in the context of Coxiella infection. Biochemical and fluorescence-based imaging approaches indicated that C. burnetii infection promotes release of extracellular vesicles (EVs). Increase in extracellular levels of endolysosomal proteins (LAMP1 and cathepsin D) and surface LAMP1 expression were identified in both phagocytic and non-phagocytic cells, during later stages of infection. Interestingly, infection-induced exocytosis was dependent on the activity of the bacterial T4BSS. Modulating the activity of TRPML1, a host calcium channel that induces exocytosis by regulating the release of calcium from lysosomes into the cytosol, using synthetic agonist/antagonist, led to a decrease in intracellular C. burnetii replication, suggesting a complex, tightly regulated role of TRPML1 during infection. Together, this study demonstrates that infection by the lysosome-adapted pathogen Coxiella burnetii activates exocytosis in a temporal, host and bacterial factors-dependent manner.

cell biology↗

bioRxiv2022

Genetic analysis of a phenotypic loss in the mechanosensory entrainment of a circalunar clock

Genetic variants underlying traits that become either non-adaptive or selectively neutral are expected to have altered evolutionary trajectories. Uncovering genetic signatures associated with phenotypic loss presents the opportunity to discover the molecular basis for the phenotype in populations where it persists. Here we study circalunar clocks in populations of marine midge Clunio marinus. The circalunar clock synchronizes development to the lunar phase, and it is set by moonlight and tidal cycles of mechanical agitation. Two out of ten studied populations have lost their sensitivity to mechanical agitation while preserving sensitivity to moonlight. Intriguingly, the F1 offspring of the two insensitive populations regained the sensitivity to mechanical entrainment, implying a genetically independent loss of the phenotype. By combining quantitative trait locus mapping and genome-wide screens, we explored the genetics of this phenotypic loss. QTL analysis suggested an oligogenic origin with one prevalent additive locus in one of the strains. In addition, it confirmed a distinct genetic architecture in the two insensitive populations. Genomic screens further uncovered several candidate genes underlying QTL regions. The strongest signal under the most prominent QTL contains a duplicated STAT1 gene, which has a well-established role in development, and CG022363, an ortholog of the Drosophila melanogaster CG32100 gene, which plays a role in gravitaxis. Our results support the notion that adaptive phenotypes have a complex genetic basis with mutations occurring at several loci. By dissecting the most prevalent signals, we started to reveal the molecular machinery responsible for the entrainment of the circalunar clock.

genetics↗

bioRxiv2021

Polygenic adaptation from standing genetic variation allows rapid ecotype formation

Adaptive ecotype formation is the first step to speciation, but the genetic underpinnings of this process are poorly understood. Marine midges of the genus Clunio (Diptera) have recolonized Northern European shore areas after the last glaciation. In response to local tide conditions they have formed different ecotypes with respect to timing of adult emergence, oviposition behavior and larval habitat. Genomic analysis confirms the recent establishment of these ecotypes, reflected in massive haplotype sharing between ecotypes, irrespective of whether there is ongoing gene flow or geographic isolation. QTL mapping and genome screens reveal patterns of polygenic adaptation from standing genetic variation. Ecotype-associated loci prominently include circadian clock genes, as well as genes affecting sensory perception and nervous system development, hinting to a central role of these processes in ecotype formation. Our data show that adaptive ecotype formation can occur rapidly, with ongoing gene flow and largely based on a re-assortment of existing alleles.

evolutionary biology↗

bioRxiv2020

Acute radiofrequency electromagnetic radiation exposures cause neuronal DNA damage and impair neurogenesis in the young adolescent rat brain

Mobile phone is now a commonly used communication device in all age groups. Young adolescents use it for longer duration and effect of its radiofrequency electromagnetic radiation (RF-EMR) on their brain structure and function need detailed investigation. In the present study, we investigated the effect of RF-EMR emitted from mobile phones, on young adolescent rat brain. Wistar rats (5 weeks, male) were exposed to RF-EMR signal (2,115 MHz) from a mobile phone at a whole body averaged specific absorption rate (SAR) of 1.15 W/kg continuously for 8 h. Higher level of lipid peroxidation, carbon centered lipid radicals and DNA damage were observed in the brain of rat exposed to RF-EMR. Number of neural progenitor cells (NPCs) in dentate gyrus (DG) were found to be relatively low in RF-EMR exposed rats that may be due to reduced neurogenesis. Acute exposure to RF-EMR induced neuronal degeneration in DG region with insignificant variation in CA3, CA1 and cerebral cortex sub regions of hippocampus. Findings of this study, indicate that acute exposure of high frequency RF-EMR at relatively higher SAR may adversely impact the neurogenesis and function of adolescent rat brain. Generation of carbon centered lipid radicals, and nuclear DNA damage might be playing critical role in reduced neurogenesis and higher neuronal degeneration in the cortex and hippocampus of brain. Detailed understanding of RF-EMR induced alteration in brain function will be useful to develop appropriate interventions for reducing the impact caused by RF-EMR damage.

biochemistry↗