Biology subjects

Bhowmick, S.

Publications and source records attributed to Bhowmick, S..

18 recordsLinked to original sources

bioRxiv2026

A genome-wide genetic interaction platform for MRSA reveals connections between cell division and the cell envelope

The bacterial cell cycle is an ensemble of integrated pathways that coordinates cell growth and division. Although these pathways contain a suite of promising antimicrobial targets, their functional organization and interrelationships have only been sparsely mapped. Here, we established a dual-CRISPRi platform for systematic genetic interaction profiling in methicillin-resistant Staphylococcus aureus (MRSA), a major drug-resistant pathogen. Our platform achieved genome-wide coverage across a selected set of 51 cell cycle genes, surveying 115,497 gene-pairs and uncovering hundreds of genetic interactions, both positive (suppressors) and negative (synthetic sick/lethal). These interactions identified two major connections between cell division and the cell envelope. First, we identified a suppressive relationship between a defined set of cell division genes, including components of the major septal peptidoglycan biosynthesis complex PBP1-FtsWL-DivIBC, and fatty acid or phospholipid biosynthesis. Simultaneous inhibition of these lipid biosynthesis pathways suppressed the fitness and morphological defects caused by knocking down expression of cell division genes, revealing that toxic membrane accumulation contributes to the lethality of disrupting cell division. Second, we uncovered a synthetic lethal relationship between a distinct set of cell division genes and the conserved dltXABCD operon, linking cell division to the modification of teichoic acid surface polymers. Our results establish a versatile platform for interrogating selected gene sets in MRSA, providing a map of cell cycle interactions, and uncovering links between cell division and cell envelope pathways.

microbiology↗

bioRxiv2026

Functional Somatotopy of Lumbar Dorsal Rootlets and its Role in Selective Recruitment via Lateral Spinal Cord Stimulation

ObjectiveLateral spinal cord stimulation (LSCS) is a promising approach for restoring somatosensory feedback in lower-limb amputees, but its spatial selectivity remains limited. Percepts often spread to unintended regions of the residual limb, and reducing electrode contact size may not improve focality. This study investigated whether the anatomical organization of lumbar dorsal rootlets (DR) imposes fundamental constraints on LSCS selectivity. ApproachAcute neurophysiology experiments were performed in six adult cats. Both LSCS and individual DR stimulation were conducted in the same animals. For DR stimulation, bipolar hook electrodes were used to stimulate individual DR, while antidromic compound action potentials (CAPs) were recorded from femoral and sciatic nerve branches instrumented with nerve cuffs. For LSCS, custom 32-contact epidural paddle electrodes were placed over the lateral surface of the spinal cord at corresponding vertebral levels. Recruitment thresholds, dynamic ranges, and response patterns were analyzed across spinal levels, and DR recruitment patterns were directly compared to those evoked by LSCS within the same animals. Main resultsA clear rostrocaudal organization was observed across spinal levels during stimulation of individual DR, with femoral branches predominantly recruited at L4-L5 and sciatic branches at L6-L7. However, no somatotopic organization was found across DR within each spinal level; individual DR frequently co-activated multiple branches within the same group, and selective recruitment could only be maintained over a narrow dynamic range (median [~]10 {micro}A). LSCS exhibited even a narrower dynamic range ([~]5 {micro}A) but closely mirrored DR recruitment patterns, indicating that LSCS activates sensory afferents in a manner determined by the organizational structure of the DR. SignificanceThese findings demonstrate that the limited spatial selectivity of LSCS can largely be attributed to the coarse organization of DR within each root level rather than due to limitations of epidural electrode design. Moving electrodes intradurally or reducing contact size further is unlikely to substantially improve focality. Instead, improving paddle stability to ensure consistent placement over the appropriate spinal levels may be a more effective strategy for enhancing percept localization.

neuroscience↗

bioRxiv2026

Selectivity of Lateral Epidural Spinal Cord Stimulation with Varying Electrode Diameters and Stimulation Configurations

Objective. Our prior studies have demonstrated that lateral spinal cord stimulation can evoke somatosensory percepts in the missing foot in individuals with a lower-limb amputation. However, subjects reported concurrent sensations in their residual limb. In this study, we evaluate the hypothesis that using high-density paddle electrodes with smaller contact sizes, and multipolar stimulation configurations could evoke more focal sensations in the foot over a wide range of stimulation amplitudes. Approach. We used a combination of electrophysiology and computational modelling methods to investigate the selective activation of distal nerve branches in response to lateral spinal cord stimulation in cats. In six acute feline experiments, we performed an L3-S1 laminectomy and placed custom 32-electrode paddles laterally over the dura of the spinal cord. We recorded antidromic action potentials in the distal branches of the sciatic and femoral nerve trunks in response to stimulation using three contact diameters (150, 500 and 1000 {micro}m) and two stimulation configurations - monopolar and bipolar stimulation. We replicated the neural recruitment patterns from those experiments in a computational model of the feline lumbar spinal cord. We then used the model to examine neural recruitment with 1.8 mm and 2.5 mm contacts, as well as a tripolar guarded-cathode configuration. Main results. In the electrophysiology experiments, the 500 {micro}m-diameter electrodes achieved the most selective nerve activation (68%) compared to 62% for both 150 and 1000 {micro}m-diameter electrodes. The minimum amplitudes for recruiting nerve branches (i.e., threshold) as well as the dynamic ranges were largely similar for the different contact diameters (median: 35 {micro}A) and stimulation configurations (30 {micro}A for bipolar stimulation; 35 {micro}A for monopolar stimulation). The computational model reproduced the finding that selectivity did not differ significantly among the three contact sizes tested in cat experiments, though it revealed that increasing contact diameter above 1000 {micro}m raised the minimum amplitude required for selective activation and reduced spinal root selectivity. Across both approaches, we consistently recruited large-diameter afferents that are critical for somatosensory applications of spinal cord stimulation. Significance. Our results indicate that, relative to clinical electrodes, reducing the contact diameter of stimulation electrodes can evoke focal sensations, but further reductions below 1000 {micro}m may fail to improve selectivity. This study highlights potential constraints with achieving focal selectivity that are not dependent on the design of the electrodes.

bioengineering↗

bioRxiv2026

Nrf2 regulates ICAM-1-mediated neutrophil extracellular trap formation after traumatic brain injury.

Traumatic brain injury (TBI) triggers secondary neurovascular damage characterized by oxidative stress, blood-brain barrier (BBB) disruption, and neuroinflammation, leading to long-term cognitive deficits. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of cellular antioxidant defense, but its role in maintaining neurovascular integrity after TBI remains unclear. Here, using in vivo fluid percussion injury in wild-type, Nrf2-/-;, and ICAM-1-/-; mice, and in vitro stretch injury in human brain microvascular endothelial cells (hBMVECs), we demonstrate that TBI suppresses Nrf2 signaling, reducing antioxidant gene expression, and increasing oxidative and nitrosative stress. Nrf2 impairment enhances BBB permeability, ICAM-1-mediated leukocyte transmigration and promotes neutrophil extracellular trap (NET) formation. ICAM-1 deletion rescues these effects, confirming the mechanistic link between Nrf2, ICAM-1, and immune-mediated vascular damage. Preservation of Nrf2 signaling maintains antioxidant defenses, limits immune cell infiltration, and restricts NET-mediated injury. Importantly, Nrf2 deficiency impairs functional recovery, whereas its presence correlates with improved neurological outcomes. Targeting the Nrf2-ICAM-1 axis may reduce immune-mediated neurovascular injury, limit NET formation, and improve functional recovery after traumatic brain injury.

neuroscience↗

bioRxiv2026

Proviral dynamics and HIV-1C viral diversity in the context of HIV-TB co-infection

BackgroundART effectively suppresses HIV replication and restores CD4+ T cells; however, long-lived HIV latent reservoirs enable viral persistence. Tuberculosis (TB) co-infection further impacts HIV latency and enhances viral replication. Given the high prevalence of latent TB infection (LTBI) in TB-endemic settings, understanding its impact on HIV biology is critical. Our study aims to investigate the influence of TB co-infection on HIV reservoir dynamics, viral diversity, and drug resistance mutations in ART-naive individuals. MethodologySamples from 90 ART-naive HIV-1C individuals, stratified based on IGRA and TB diagnosis, were used in this study. Plasma and PBMCs were isolated for viral RNA and DNA extraction respectively. Total proviral DNA was quantified using gag PCR. Full-length env and pol genes were amplified, purified and sequenced using ONT and Illumina platforms. Pol sequences were subjected to Drug Resistance Mutation (DRM) analysis via Stanford HIVdb with a minimum threshold mutation frequency of [≥]10%. Full length env sequences were used for phylogenetic analysis by aligning with Indian Subtype C reference sequence and phylogenetic tree was generated using ggplot2. ResultProviral load analysis showed no significant differences across HIV+LTBI-, HIV+LTBI+, and HIV+TB+ groups, although a trend toward higher levels was observed in HIV+TB+ individuals. Correlation analysis revealed distinct immune associations, with HIV+LTBI+ individuals showing positive correlations with activation and PD-1 expression. Longitudinal analysis of proviral loads demonstrated a modest decline in proviral load post-ART but remained persistent for up to 18-20 months following initiation of ART accompanied by low level ongoing viral replication. DRM analysis revealed a 33% prevalence in ART-naive individuals, with higher occurrence in HIV+LTBI+ group. Of the identified DRMs, 38% (5/13) and 71% (5/7) in sequences obtained from PBMC and plasma respectively were attributed to polymorphic mutations associated with Integrase strand transfer inhibitors (INSTIs). DRMs within plasma and PBMC derived viruses showed high concordance. Phylogenetic analysis of env sequences indicated overlapping viral populations between the 3 groups, with greater diversity in PBMCs compared to plasma. ConclusionThe study highlights that HIV reservoir dynamics, drug resistance, and viral diversity are significantly influenced by TB co-infection. While proviral loads were comparable, LTBI-associated immune activation and granuloma niches may have driven viral diversification and DRM emergence. High concordance between compartments and presence of transmitted resistance underscore the need for baseline screening, multi-compartment analysis, and sustained surveillance.

microbiology↗

bioRxiv2025

Evaluation of Leishmania Homologue of Activated C Kinase (LACK) of Leishmania donovani in comparison to glycoprotein 63 as vaccine candidate against visceral leishmaniasis

Leishmaniasis, caused by Leishmania protozoa transmitted via sand fly bites, affects over 12 million people annually, manifesting as self-limiting cutaneous lesions or fatal visceral leishmaniasis (VL). The diseases immune response involves a Th1/Th2 paradigm, with Th1 promoting resistance and Th2 linked to susceptibility. Despite no available human vaccine, the Leishmania homologue of activated C kinase (LACK) protein has shown promise as a candidate due to its conservation across species. In this study, we purified native 34-kDa LACK protein from Leishmania donovani promastigotes and compared its efficacy with gp63 in cationic DSPC liposomes. While gp63 exhibited protective efficacy, LACK failed to protect BALB/c mice. Recombinant LACK, which was cloned, expressed, and purified, also did not confer protection. Immunological assays revealed a Th2-biased immune response characterized by a high IgG1/IgG2a ratio, elevated Th2 cytokines, and an unaltered delayed-type hypersensitivity (DTH) response, highlighting its limited potential. ImportanceThis study underscores the limitations of LACK as a standalone vaccine candidate against VL. Both native and recombinant LACK forms, despite liposomal encapsulation, elicited a Th2- dominated immune response, inadequate for protection. These findings suggest that LACKs intrinsic immunogenic properties may not support the robust Th1 response crucial for combating Leishmania donovani infections. Future research should prioritize alternative antigens or combination formulations to promote Th1-driven immunity. This work contributes to the growing body of knowledge guiding vaccine development for VL, emphasizing the need for immunogens that effectively target protective immune pathways.

immunology↗

bioRxiv2025

A Dual-Action Liposome-Peptide Formulation Synergistically Counteracts A Gain-of-Function p53 Mutant

ObjectiveInactivation of p53 tumor suppressor functions, often through missense mutations, is essential for carcinogenesis. A sub-class of such p53 missense mutations gains new functions, including drug resistance and enhanced proliferation, in addition to its loss of function. Among the most frequent gain-of-function p53 mutants, R273H occurs in tumors of many tissue origins and imparts aggressive character and resistance to drugs to the tumor. Tumors bearing p53R273H are generally resistant to all available therapies, and need for novel interventions are urgently needed. Interaction of p53R273H with Positive Coactivator 4 (PC4), an abundant chromatin-associated protein, is essential for acquiring the gain-of-function properties. Previously, we developed a chemically modified peptide, NLS-p53(380-386), targeting PC4 that abrogated the interaction of p53R273H with PC4 and reversed many of its gain-of-function properties. We earlier demonstrated that cationic phosphatidylcholine-stearylamine (PC-SA) liposomes possess inherent anti-tumor properties. To improve efficacy, pharmacokinetics, and delivery, we entrapped the PC4-targeted peptide into PC-SA liposome. MethodsWe synthesized the NLS-p53(380-386) peptide and entrapped in PC-SA liposome. We used MTT assay, confocal microscopy, flow cytometry, qRT-PCR, and western blotting to investigate the biological effects of the p53-entrapped PC-SA. ResultsPre-treatment with the PC-SA liposome entrapped peptide enhanced the chemosensitivity of widely used anticancer drug doxorubicin in cell lines bearing p53R273H mutation. The doxorubicin-induced cell-killing effect was much more enhanced when pre- treated with the liposome-entrapped peptide than when pre-treated with either the free peptide or the liposome alone. ConclusionThe liposome-encapsulated peptide is a promising formulation for developing therapies targeting tumors bearing the p53R273H.

cancer biology↗

bioRxiv2025

Distinct region-specific neutralization profiles of contemporary HIV-1 clade C against best-in-class broadly neutralizing antibodies

Broadly neutralizing antibodies (bnAb) have been clinically proven to be an excellent choice for HIV-1 prevention. However, the relative effectiveness of best-in-class bnAbs against regionally relevant circulating HIV-1 forms is not clear. In the present study, we compared the degree of neutralization sensitivity of contemporary HIV-1 Indian clade C with that of South African origin. Phylogenetic analysis revealed that these clade C viruses continue to evolve distinctly from one another. Env-pseudotyped viruses prepared using contemporary HIV-1 clade C env genes (N=115) obtained from nine geographically distinct sites in India (between 2020-2023) were found to be most sensitive to V3-directed bnAbs 10-1074 and BG18, and second generation CD4 binding site (CD4bs) directed bnAbs (VRC07, N6 and 1-18), however they were found to be significantly resistant to V1/V2 apex directed bnAbs. Moreover, we observed that the degree of sensitivity varied between contemporary Indian and South African clade C viruses. Differences in degree of neutralization susceptibility were associated with differences observed in key residues that form bnAb contact sites, gp120 loop lengths and the number of N-linked glycans in the V4 hypervariable region. Interestingly, the second generation CD4bs bnAbs (VRC07, N6, 1-18) showed neutralization of VRC01 and 3BNC117 resistant viruses but with 2-7-fold reduced potency compared to the VRC01 sensitive counterparts, likely due to the enrichment of resistance associated residues observed in loop D. Predictive analysis indicated that combination of BG18, N6 and PGDM1400 can provide over 95% neutralization coverage at 1g/mL of contemporary India clade C, an observation found to be distinct to that reported for the Africa clade C viruses. Taken together, we found distinct neutralization patterns and env signatures associated with resistance to key bnAbs. Our study highlights that towards achieving clinical effectiveness, both the complementarity of bnAb classes and the regionally relevant HIV forms need to be considered. Author summaryWhile the development of vaccines to prevent HIV infection remains a global priority, their potential effectiveness is limited by the extraordinarily diversified circulating forms of HIV-1. The prospect of best-in-class bnAbs as potential prevention option has been demonstrated in several studies including the Phase II Antibody Mediated Prevention (AMP) trial; however, to be broadly applicable, bnAbs will need to overcome the substantial variability of HIV env. The present study highlights that the contemporary HIV-1 clade C viruses are evolving to be less sensitive to the best-in-class bnAbs and HIV-1 clade C that predominates in India and South Africa vary in their degree of susceptibility to best-in-class clinically relevant bnAbs. This indicates differences in the antigenic properties between globally circulating HIV-1 clade C at a population level. Overall, the outcome of this study highlights the need for periodic assessment of sequence and neutralization profiles of the circulating regionally relevant HIV-1 forms towards prioritizing the bnAb combination suitable for effective intervention.

immunology↗

bioRxiv2024

Identifying potential dopamine receptor D2 antagonist from Rauwolfia serpentina An in-silico virtual screening approach

BackgroundTo combat the alarming rise of neuropsychiatric diseases like Schizophrenia, new drugs with fewer side effects have to be identified and characterized for the symptomatic treatment of Scz. Positive symptoms associated with Scz are hallucinations and delusions mainly due to the overactivation of the D2 dopaminergic receptors in the cortical pathways. D2 receptor antagonists identified from Rauwolfia serpentina are employed for controlling positive symptoms. Materials and methodsThe IMPPAT database was used to identify phytoconstituents from the root of Rauwolfia serpentina that can be used for antagonizing D2 dopaminergic receptor. 39 compounds were identified and SDF files were obtained from the PubChem database molecular docking with the modelled dopamine D2 receptor was used as a virtual screening tool followed by ADMET screening of the potential lead compound. ResultsAfter docking analysis, 11 compounds having binding affinity [≥] -9 kcal/mol were shortlisted for ADMET analysis. After analysis, 4 compounds (1,2-dihydrovomilenine, Corynanthine, Rauwolscine, and Yohimbine) were identified as potential leads. Among these 4 compounds, 1,2-dihydrovomelenine has been identified as the lead compound. ConclusionThe present study identified a potential new therapeutic compound that can be used for controlling the positive symptoms of Scz patients in vitro as well as in vivo.

pharmacology and toxicology↗

bioRxiv2023

Computational modeling of dorsal root ganglion stimulation using an Injectrode

ObjectiveMinimally invasive neuromodulation therapies like the Injectrode, which is composed of a tightly wound polymer-coated platinum/iridium microcoil, offer a low-risk approach for administering electrical stimulation to the dorsal root ganglion (DRG). This flexible electrode is aimed to conform to the DRG. The stimulation occurs through a transcutaneous electrical stimulation (TES) patch, which subsequently transmits the stimulation to the Injectrode via a subcutaneous metal collector. However, effectiveness of stimulation relies on the specific geometrical configurations of the Injectrode-collector-patch system. Hence, there is a need to investigate which design parameters influence the activation of targeted neural structures. ApproachWe employed a hybrid computational modeling approach to analyze the impact of the Injectrode system design parameters on charge delivery and the neural response to stimulation. We constructed multiple finite element method models of DRG stimulation and multi-compartment models of DRG neurons. We simulated the neural responses using parameters based on prior acute preclinical experiments. Additionally, we developed multiple human-scale computational models of DRG stimulation to investigate how design parameters like Injectrode size and orientation influenced neural activation thresholds. Main resultsOur findings were in accordance with acute experimental measurements and indicated that the Injectrode system predominantly engages large-diameter afferents (A{beta}-fibers). These activation thresholds were contingent upon the surface area of the Injectrode. As the charge density decreased due to increasing surface area, there was a corresponding expansion in the stimulation amplitude range before triggering any pain-related mechanoreceptor (A{delta}-fibers) activity. SignificanceThe Injectrode demonstrates potential as a viable technology for minimally invasive stimulation of the DRG. Our findings indicate that utilizing a larger surface area Injectrode enhances the therapeutic margin, effectively distinguishing the desired A{beta} activation from the undesired A{delta}-fiber activation.

bioengineering↗

bioRxiv2022

LHX2 in germ cells control tubular organization in the developing mouse testis

In the gonads of mammalian XY embryos, the organization of cords is the hallmark of testis development. This organization is thought to be controlled by interactions of the Sertoli cells, endothelial and interstitial cells with little or no role of germ cells. Challenging this notion, herein we show that the germ cells play an active role in the organization of the testicular tubules. We observed that the LIM-homeobox gene, Lhx2 is expressed in the germ cells of the developing testis between E12.5-E15.5. In Lhx2 knockout-fetal testis there was altered expression of several genes not just in germ cells but also in the supporting (Sertoli) cells, endothelial cells, and interstitial cells. Further, loss of Lhx2 led to disrupted endothelial cell migration and expansion of interstitial cells in the XY gonads. The cords in the developing testis of Lhx2 knockout embryos are disorganized with a disrupted basement membrane. Together, our results show an important role of Lhx2 in testicular development and imply the involvement of germ cells in the tubular organization of the differentiating testis. HighlightO_LILhx2 is expressed in germ cells of developing mouse testis but is dispensable for germ cell and Sertoli cell specification C_LIO_LILoss of Lhx2 disrupts testicular vascularization, leads to the expansion of interstitial cells, and alters the tubular organization C_LIO_LIGerm cells govern the tubular organization in the developing testis C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/522214v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1a1761dorg.highwire.dtl.DTLVardef@1519f12org.highwire.dtl.DTLVardef@1a263baorg.highwire.dtl.DTLVardef@4167f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

Identifying common genes, proteins, and pathways from human miRNA and gene blood profiles in multiple sclerosis patients.

The molecular pathway associated with Multiple sclerosis (MS) is complex and symptomatic treatments are only available right now. Early diagnosis of MS creates a window for healthcare providers to manage the disease more efficiently. Blood-based biomarker study has been done in the past to identify the upregulated and downregulated genes but in this present study, a novel approach has been taken for identifying genes associated with the disease. In this present study, hub genes are identified and the top ten hub genes were used to identify drugs associated with them. Upregulated genes were identified using the dataset GSE21942 (which contains information related to genes identified in the blood of multiple sclerosis patients) and datasets GSE17846 and GSE61741(which contains information related to microRNAs taken from multiple sclerosis patients). Genes associated with microRNAs were identified using miRWalk. Common genes from both miRWalk and the dataset GSE21942 were identified and were subjected to STRINGdb for the creation of a protein-protein interaction network and this network was then imported to Cytoscape for identifying the top ten hub genes. The top ten hub genes were subjected to EnrichR for enrichment analysis of genes. In our study, it was found that CTNNB1 is the gene with the highest degree (116).

neuroscience↗

bioRxiv2022

Identification and characterisation of potent anti-MRSA phloroglucinol derivatives of Dryopteris crassirhizoma Nakai

Traditional Chinese Medicine (TCM) has been used to treat infectious diseases and could offer potential drug leads. This study evaluates the in vitro antimicrobial activities commercially sourced Dryopteris crassirhizoma Nakai whose authenticity was confirmed by DNA barcoding based on the ribulose bisphosphate carboxylase (rbcL) gene. Powdered rhizomes were sequentially extracted using n-hexane, dichloromethane, ethyl acetate and methanol at ambient temperature. The dried extracts at different concentrations were tested for antimicrobial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus (MRSA), and Mycobacterium smegmatis. D. crassirhizoma extracts exhibited significant antimicrobial activities only against MRSA. Activity-led fractionations of D. crassirhizoma and characterisation by Ultra performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS) identified two potent anti-MRSA phloroglucinol derivatives: Norflavaspidic acid AB and flavaspidic acid AB. The impact of norflavaspidic acid AB on MRSA cells was examined using untargeted metabolomic analysis and compared to that of other established antibiotics (all treatments normalized to MIC50 at 6 h). This suggested that norflavaspidic acid AB had a distinctive effect which involved targeting bioenergetic transformation, metabolism, and particularly acetyl CoA, in MRSA cells. No cytotoxicity was observed for norflavaspidic acid AB against murine HepG2 cells. This study requires further experimental validation but can have indicated a naturally available compound that could help counter the threat of clinically relevant strains with antibiotic resistance.

microbiology↗

bioRxiv2021

Identifying potential key genes and existing drugs for Multiple sclerosis, Schizophrenia, and Autism- an in silico approach

Nowadays, neurological conditions are a major concern as it not only preys on a patients health but also is a huge economic burden that is placed on the patients family. The diagnosis and treatment of disease sometimes cause methodological limitations. This is mainly common for individuals who have the signs of MS and schizophrenia (SZ). Patients suffering from multiple sclerosis are more likely to develop schizophrenia. Besides, a significant portion of patients who have been diagnosed with Autism Spectrum Disorder (ASD) later acquire the symptoms of Schizophrenia. In this study, we used bioinformatics tools to determine differentially expressed genes (DEGs) in all these diseases, and then we created a protein-protein interaction network using the online software STRING and identified 15 significant genes with the help of Cytohubba a plug-in tool in Cytoscape, the offline software (version3.8.2). We then used a drug-gene interaction database to conduct a drug-gene interaction study of the 15 hub genes and from there we identified 37 FDA-approved drugs. These findings may provide a new and common therapeutic approach for MS, SZ, and ASD therapy.

neuroscience↗

bioRxiv2021

Isolation and characterisation of quercitrin as a potent anti-sickle cell anaemia agent from Alchornea cordifolia.

Alchornea cordifolia Mull. Arg. (commonly known as Christmas Bush) has been used traditionally in Africa to treat sickle cell anaemia (a recessive disease, arising from the S haemoglobin [Hb] allele) but the active compounds are yet to be characterised. Herein we describe the use of sequential fractionation coupled with in vitro anti-sickling assays to purify the active component. Sickling was induced in HbSS genotype blood samples using sodium metabisulphite (Na2S2O5) or incubation in 100 % N2. Methanol extracts of A. cordifolia leaves and its sub-fractions showed >70 % suppression of HbSS erythrocyte sickling. Purified compound demonstrated 87.2 {+/-} 2.39 % significant anti-sickling activity and 93.1 {+/-} 2.69 % erythrocyte sickling-inhibition at 0.4 mg/mL. Nuclear magnetic resonance (NMR) spectra and high-resolution mass spectroscopy identified it as quercitrin (quercetin 3-rhamnoside). Purified quercitrin also inhibited the polymerisation of isolated HbS and stabilized sickle erythrocytes membranes. Metabolomic comparisons of blood samples using flow-infusion electrospray-high resolution mass spectrometry indicated that quercitrin could convert HbSS erythrocyte metabolomes to be similar to HbAA. Sickling was associated with changes in anti-oxidants, anaerobic bioenergy and arachidonic acid metabolism, all of which were reversed by quercitrin. The findings described could inform efforts directed to the development of an anti-sickling drug or quality control assessments of A. cordifolia preparations.

pharmacology and toxicology↗

bioRxiv2021

In-silico analysis: common biomarkers of NDs

Neurodegenerative disorders (NDs) are a class of rapidly rising devastating diseases and the reason behind are might be an improper function of related genes or a mutation in a particular gene or even could be autoimmune also. Parkinsons disease (PD), Multiple sclerosis (MS), Huntingtons disease (HD) are some of the NDs, and still, incurable fully. Apart from the similarities in symptoms, there are common genes that express somehow a differential manner in patients of PDs, MSs, and HDs. A total of 1197 differentially expressed genes (DEGs) are obtained by analyzing the chosen datasets. The protein interactions by STRING online tool and degree sorted hubs obtained through a plug-in in Cytoscape; Cyto-Hubba. Among the sorted hubs KRAS, CREB1, PIK3CA, JAK2 are the ones that are not only common to all the studied datasets of NDs but also in other neurological disorders like Alzheimers. The enriched pathways with biological process, molecular function, cellular component, and KEGG pathway details are obtained and analyzed using Enricher. This paper frames that the obtained hub genes could be potential biomarkers also and a need for further drug design for finding a possible cure.

neuroscience↗

bioRxiv2021

Improved HIV-1 drug resistance mutation prediction using quasispecies reconstruction supported analysis

Accurate and sensitive approaches to detect HIV-1 drug resistance mutations (DRMs) are indispensable for the paradigm of treatment as prevention. While HIV-1 proviral DNA allows sensitive high throughput sequencing (HTS)-based DRM detection, its applicability is limited by presence of defective genomes. This study demonstrates application of quasispecies reconstruction algorithms (QRAs) to improve DRM detection sensitivity from proviral DNA. A robust benchmarking of 5 QRAs was performed with 2 distinct experimental control-datasets including a stringent, novel control: DCPM, simulating in-vivo variant distribution (0.08%-86.5%). Selected QRA was further evaluated for its ability to differentiate DRMs from hypermutated sequences using an in-silico control. PredictHaplo outperformed all others in terms of precision and was selected for further analysis. Near full-genome HTS was performed on proviral DNA from 20 HIV-1C infected individuals, at different stages of ART, from Mumbai, India. DRM detection was performed through residue-wise variation analysis and implementation of QRAs. Both analyses were highly concordant for DRM frequencies >10% (spearman r=0.91, p<0.0001). Phylogenetic association in HTS datasets with shared transmission history could also be demonstrated by PredictHaplo. This study highlights utility of QRAs as an adjunct to traditional residue-wise variation-based DRM detection leading to optimal personalized ART as well as better disease management.

bioinformatics↗

bioRxiv2020

The anti-mycobacterial activity of Artemisia annua L is based on deoxyartemisinin and artemisinic acid

The discovery of antimalarial artemisinin from Artemisia annua L. is an example of how Traditional Chinese Medicine (TCM) may be exploited to meet a recognized need. In this study, we systemically investigated A. annua L. for its antimicrobial activity and assessed it as a source of bioactive natural products for anti-mycobacterial activity. We used a silica gel column to perform antimicrobial activity-guided purification of the A. annua leaf, whose identity was confirmed by rbcL DNA barcoding, and used UHPLC-HRMS and NMR to elucidate the structure of purified active compounds. The antimicrobial activity of crude extracts, isolated compounds and the control artemisinin (Apollo Scientific Ltd) was assessed against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium smegmatis strains by serial micro dilution method (31.25-1000 g/mL). The isolated compounds were tested for synergistic effects against mycobacterium. Bioactive compounds were purified and identified as deoxyartemisinin and artemisinic acid. Artemisinic acid (MIC 250 g/mL) was more effective in comparison to deoxyartemisinin (MIC 500 g/mL) and artemisinin (MIC 1000 g/mL) against M. smegmatis. We used a molecular docking approach to investigate the interactions between selected anti-mycobacterial compounds and proteins involved in vital physiological functions in M. tuberculosis, namely MtPks13, MtPknB, MtPanK, MtKasA, MtInhA and MtDprE1 and found artemisinic acid showed docking scores superior to the control inhibiters for MtKasA, suggesting it to be a potential nick for further in vitro biological evaluation and anti-TB drug design.

pharmacology and toxicology↗