Biology subjects

Kapoor, N.

Publications and source records attributed to Kapoor, N..

9 recordsLinked to original sources

bioRxiv2025

Petri Net-Based Framework for Oxygen-Sensitive Regulation of Pyruvate Metabolism in M. tuberculosis

Pyruvate serves as a central hub of cellular metabolism, linking glycolysis with downstream pathways such as the tricarboxylic acid (TCA) cycle, gluconeogenesis, and fermentation. Its metabolic flexibility enables organisms to switch between oxidative and fermentative fates depending on oxygen availability and environmental stress. In this study, a Petri net (PN) model of pyruvate metabolism in Mycobacterium tuberculosis H37Rv was developed to capture and simulate these dynamic transitions. Using Snoopy 2.0 for model construction and COPASI for simulation, the framework incorporated key metabolites, cofactors, and enzymatic processes regulating aerobic and anaerobic states. The model demonstrated that oxygen availability acts as a regulatory switch, channeling pyruvate either toward acetyl-CoA for ATP generation under aerobic conditions or toward lactate production under hypoxia to regenerate NAD+. Structural validation confirmed boundedness, conservativeness, and deadlock-free behavior, underscoring the robustness of the framework. Sensitivity analyses highlighted enzymatic kinetics as critical determinants of flux distribution and system stability. Collectively, the PN model provides a scalable and biologically relevant computational framework for exploring oxygen-dependent metabolic reprogramming, offering insights into energy adaptation and potential therapeutic targets in pathogenic systems.

bioinformatics↗

bioRxiv2025

Exploration of the Anticancer Activity of Selaginella bryopteris-derived Silver Nanoparticles

AbstractOvarian cancer is characterized by chronic hormonal imbalances and associated symptoms like irregular menstruation, fertility problems and abdominal discomfort. Poly ADP-ribose polymerases (PARPs) are proteins that play a crucial role in DNA repair pathways like base excision repair (BER). PARP family proteins exhibit catalytic activities which facilitate the transport of ADP-ribose to targeted proteins. Inhibition of PARP proteins in cancer cells with BRAC1/2 gene mutations impairs the process of Single Strand Break (SSBs) repairs followed by Double Strand Breaks (DSBs), stalling replication, leading to apoptosis. PARP1 protein inhibition is an innovative therapeutic approach in cancer treatment. Commercially available drugs like Olaparib and Rucaparib are used as PARP1 inhibitors to treat ovarian cancer, however the development of effective new therapeutic drugs is urgently needed to overcome drug toxicity and resistance. In this study, we synthesized silver nanoparticles (AgNPs) from the leaf extract of Selaginella bryopteris demonstrating their cytotoxic nature against the ovarian cancer SKOV-3 cell line, with an IC50 value of 7.81{micro}g/ml. We also observed cell death in cancer cells with an ROS upsurge induced by S. bryopteris AgNPs. Our findings also elaborate on the role of Rhamnetin, a S. bryopteris phytochemical that exhibits active site targeting of PARP-1 residues.

biochemistry↗

bioRxiv2024

Evaluating the Effects of Aircraft Noise on Hearing and Physiological Indicators: A Study of Military Personnel Using iTRAQ Proteomics and Cognitive Assessments

BackgroundNoise pollution poses a significant public health risk, with prolonged exposure to high levels of noise linked to various adverse outcomes such as annoyance, sleep disturbances, cognitive impairment, hypertension, and cardiovascular diseases. Noise-induced hearing loss (NIHL) is a prominent concern in noisy occupational settings. MethodThis study investigated NIHL among 621 male Air Force soldiers aged 18-45, exposed to intense aircraft noise. Auditory assessments included pure-tone audiometry (125 Hz to 8 kHz) to categorize hearing into normal, mild, moderate, and severe impairment. Distortion product otoacoustic emissions (DPOAE) and auditory brainstem response (ABR) were used to evaluate cochlear and auditory nerve function. Heart rate variability (HRV) provided insights into autonomic responses. Cognitive functions were assessed through computerized tests, and blood plasma was analyzed for cardiac biomarkers, oxidative stress indicators, inflammatory markers, and neurotransmitters. Proteomic analysis used iTRAQ labeling, MudPIT, and MALDI-TOF/TOF mass spectrometry for protein quantification and identification, with validation through ELISA. ResultsThe audiometric tests revealed varying degrees of hearing impairment, with significant threshold differences at 2000, 3000, 4000, and 6000 Hz, especially pronounced at 6000 Hz. The right ear showed greater impairment, and a characteristic high-frequency notch was observed, consistent with noise exposure. Proteomic analysis indicated that NIHL is associated with oxidative stress and systemic inflammation, with differential protein expression related to hearing, coagulation, and inflammation. ConclusionThis study highlights the severe impact of aircraft noise on hearing and systemic health, demonstrating correlations between hearing impairment and biochemical markers. It emphasizes the role of oxidative stress and inflammation in NIHL development and underscores the need for effective noise management and protective measures in noisy work environments.

molecular biology↗

bioRxiv2024

The novel ECM protein SNED1 mediates cell adhesion via α5β1 integrin

The extracellular matrix (ECM) is a complex meshwork comprising over 100 proteins. It serves as an adhesive substrate for cells and, hence, plays critical roles in health and disease. We have recently identified a novel ECM protein, SNED1, and have found that it is required for neural crest cell migration and craniofacial morphogenesis during development and in breast cancer, where it is necessary for the metastatic dissemination of tumor cells. Interestingly, both processes involve the dynamic remodeling of cell-ECM adhesions via cell surface receptors. Sequence analysis revealed that SNED1 contains two amino acid motifs, RGD and LDV, known to bind integrins, the largest class of ECM receptors. We thus sought to investigate the role of SNED1 in cell adhesion. Here, we report that SNED1 mediates breast cancer and neural crest cell adhesion via its RGD motif. We further demonstrate that cell adhesion to SNED1 is mediated by the RGD integrins 5{beta}1 and v{beta}3. These findings are a first step toward identifying the signaling pathways activated downstream of the SNED1-integrin interactions guiding craniofacial morphogenesis and breast cancer metastasis. SUMMARY STATEMENTWe report that the novel extracellular matrix protein SNED1 promotes the adhesion of breast cancer cells and neural crest cells via interaction with 5{beta}1 and v{beta}3 integrins, the first SNED1 receptors identified to date.

cell biology↗

bioRxiv2023

Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity

Aims/HypothesisInsulin resistance and blunted mitochondrial capacity in skeletal muscle are often synonymous; however, this association remains controversial. The aim of this study was to perform an in-depth multi-factorial comparison of skeletal muscle mitochondrial capacity between individuals who were lean and active (Active), individuals with obesity (Obese) and individuals with Obesity, insulin resistance and type 2 diabetes (T2D). MethodsSkeletal muscle biopsies were obtained from the Vastus Lateralis of individuals who were lean and active (Active- n = 9), individuals with obesity (Obese- n = 9) and individuals with obesity insulin resistance and T2D (T2D- n =22) in this cross-sectional design. Mitochondrial capacity was assessed by ex vivo mitochondrial respiration with fatty-acid and glycolytic supported protocols adjusted for mitochondrial content (mtDNA and citrate synthase activity). Supercomplex assembly was measured by BN-PAGE and immunoblot. TCA cycle intermediates were assessed with targeted metabolomics. Exploratory transcriptomics and DNA methylation analyses were performed to uncover molecular differences affecting mitochondrial function among the three groups. ResultsActive had greater mitochondrial capacity compared to both Obese and T2D for ex vivo mitochondrial respiration with fatty-acid and glycolytic supported protocols adjusted for mitochondrial content (P < 0.05). Complex IV supercomplex assembley was greater in Active compared to Obese and T2D (P < 0.05) whereas Complex I and III supercomplex assembly was greater in Active compared to T2D only (P < 0.05). TCA cycle intermediates; citrate, succinate, fumarate and malate were all significantly greater in Active compared to Obese and T2D (P < 0.05). Strikingly, Obese and T2D do not differ in any of the skeletal muscle mitochondrial measurements. Active had an upregulation of genes related to respiration/mitochondrial capacity compared to both Obese and T2D. Transcriptional differences between Obese and T2D were not driven by mitochondrial related process. Active had reduced methylation correlated with increased gene expression for important mitochondrial-related genes, including ATP5PD and MFN2. Conclusions/InterpretationsWe reveal no discernable differences in skeletal muscle mitochondrial content, mitochondrial capacity and mitochondrial molecular profiles between obese individuals with and without T2D that had comparable levels of confounding factors (BMI, age, aerobic capacity) that affect mitochondrial capacity. We highlight that lean, active individuals have enhanced skeletal muscle mitochondrial capacity that is also reflected at the level of DNA methylation and gene transcription. The collective observation of comparable muscle mitochondrial capacity in individuals with obesity and T2D (vs. individuals without T2D) underscores a dissociation from skeletal muscle insulin resistance. Clinical trial numberNCT0191110

molecular biology↗

bioRxiv2022

Molecular tools for early detection of invasion of malaria vector Anopheles stephensi

There are increasing reports of the expansion of the Asian malaria vector Anopheles stephensi in new geographical areas posing a threat to the elimination of urban malaria. Efficient surveillance of this vector in affected areas and early detection in new geographical areas is key for the containment and control of this species. To overcome the practical difficulties associated with the morphological identification of immature stages and adults of An. stephensi, a species-specific PCR and a Real-Time PCR assay were developed for their identification targeting a unique segment of ITS2 lacking homology to any other organism. Both PCRs can be used to identify An. stephensi individually or in pooled samples of mixed species, including when present in extremely low proportion. This study also reports a method for selective amplification and sequencing of An. stephensi for their confirmation in pooled samples of mixed species.

molecular biology↗

bioRxiv2021

B.1.1.7 and B.1.351 variants are highly virulent in K18-ACE2 transgenic mice and show different pathogenic patterns from early SARS-CoV-2 strains

SARS-CoV-2 continues to circulate globally resulting in emergence of several variants of concern (VOC), including B.1.1.7 and B.1.351 that show increased transmissibility and enhanced resistance to antibody neutralization. In a K18-hACE2 transgenic mouse model, we demonstrate that Both B.1.1.7 and B.1.351 are 100 times more lethal than the original SARS-CoV-2 bearing 614D. Mice infected with B.1.1.7 and B.1.351 exhibited more severe lesions in internal organs than those infected with early SARS-CoV-2 strains bearing 614D or 614G. Infection of B.1.1.7 and B.1.351 also results in distinct tissue-specific cytokine signatures, significant D-dimer depositions in vital organs and less pulmonary hypoxia signaling before death as compared to the mice infected with early SARS-CoV-2 strains. However, K18-hACE2 mice with the pre-existing immunity from prior infection or immunization were resistant to the lethal reinfection of B.1.1.7 or B.1.351, despite having reduced neutralization titers against these VOC. Our study reveals distinguishing pathogenic patterns of B.1.1.7 and B.1.351 variants from those early SARS-CoV-2 strains in K18-hACE2 mice, which will help to inform potential medical interventions for combatting COVID-19.

immunology↗

bioRxiv2019

A new knockdown resistance (kdr) mutation F1534L in Aedes aegypti associated with insecticide resistance

BackgroundAedes aegypti is a primary vector of dengue, chikungunya and zika infections in India. In the absence of specific drugs or safe and effective vaccines for these infections, their control relies mainly on vector control measures. The emergence of insecticide resistance in vectors, especially against pyrethroids, is a serious threat to the insecticide-based vector control programme. This study reports the presence of multiple knockdown resistance (kdr) mutations present in an Ae. aegypti population from Bengaluru (India), including a new mutation F1534L. MethodsAedes aegypti collected from Bengaluru were subjected to insecticide susceptibility tests with DDT, deltamethrin and permethrin. The DNA sequencing of partial domain II, III and IV of the voltage-gated sodium channel (VGSC) was performed to screen kdr mutations present in the population and PCR-based assays were developed for their detection. Genotyping of kdr mutations was done using PCR-based assays, allelic frequencies were determined, and tests of genetic association of kdr mutations with the insecticide resistance phenotype were performed. ResultsThe Ae. aegypti population were resistant to DDT, deltamethrin and permethrin. The DNA sequencing of the VGSC revealed the presence of four kdr mutations, i.e., S989P and V1016G in domain II and two alternative kdr mutations F1534C and F1534L in domain III. Allele-specific PCR assays (ASPCR) were developed for the detection of kdr mutations S989P and V1016G and an existing PCR-RFLP based strategy was modified for the genotyping of all three known kdr mutations in domain III (F1534L, F1534C and T1520I). Genotyping of Ae. aegypti samples collected between October 2014 and April 2015 revealed a moderate frequency of S989P/V1016G (18.27%) and F1534L (17.48%), a relatively high frequency of F1534C (50.61%) and absence of T1520I in the population. Mutations S989P and V1016G were in complete linkage disequilibrium in this population while they were in linkage equilibrium with kdr mutations F1534C and F1534L. The alleles F1534C and F1534L are genetically associated with permethrin resistance. ConclusionsA new kdr mutation, F1534L, was found in an Ae. aegypti population from Bengaluru (India), co-occurring with the other three mutations S989P, V1016G and F1534C. The findings of a new mutation and development of PCR-based diagnostics have implications for insecticide resistance management. Monitoring of F1534L-kdr in other populations and studies on their functional role in altering neuro-sensitivity is warranted.

molecular biology↗

bioRxiv2017

Endothelial Cell-Specific MCPIP Deletion Causes Endothelial Dysfunction and Impairs Post-ischemic Angiogenesis in Vivo

Vascular endothelial cells (ECs) play an important role in angiogenesis and inflammatory responses. MCPIP (also known as Zc3h12a or Regnase-1), a newly identified suppressor of cytokine signaling, is expressed in endothelial cells. To directly test the role of endothelium-derived MCPIP in cardiovascular pathophysiology, we specifically targeted deletion of the murine MCPIP gene in the endothelium by using the loxP/Cre system. A floxed MCPIP knock in mouse line was crossbred with VEcadherin5-Cre mice to generate offspring with deletion of the MCPIP gene in ECs (ECKO). Ablation of MCPIP in ECs resulted in systemic inflammation, anemia, splenomegaly, increased vessel permeability, muscle wasting, endothelial dysfunction, thrombus formation, impaired blood perfusion, and reduced lifespan in these mice. Serum levels of cytokines, chemokines, and biomarkers of EC dysfunction were significantly elevated in the ECKO mice, suggesting a hypercytokinemia. These mice also were more susceptible to lipopolysaccharide-induced death. When subjected to ischemia, these mice showed defective post-ischemic angiogenesis and impaired blood flow recovery in hind limb ischemia and stroke models, as well as in wound healing. This effect was associated with an increased cellular infiltration, cytokine expression, and decreased angiogenic factors. Moreover, MCPIP-deficient ECs displayed decreased vascular sprouting and tube elongation in ex vivo aortic ring assay. MCPIP-knockdown in cultured ECs enhanced NF-{kappa}B activity and dysregulated synthesis of microRNAs linked with elevated cytokines and biomarkers of EC dysfunction. These data show, for the first time, that constitutive expression of MCPIP in ECs is essential to maintain ECs in a quiescent state by serving as an important negative feedback regulator that keeps the inflammatory signaling suppressed.

pathology↗