Biology subjects

Verma, V.

Publications and source records attributed to Verma, V..

30 records · Page 2Linked to original sources

bioRxiv2021

Developing selective FPR2 agonists can be a potential approach to treat moderate to severe asthma.

Formyl peptide receptor (FPR) family members have been reported to play important role in the resolution of inflammation. A few FPR2/FPR1 dual agonists are reported in the public domain for their anti-inflammatory properties. None of these molecules, however, have been successful as a therapy yet. Recent reports bring forward the ambiguous role of FPR1 in inflammation. These include both positive and negative outcomes. We, therefore, aimed to develop selective FPR2 agonists and evaluated their potential in mitigating the non-resolving inflammation in mouse models of moderate to severe asthma. Extensive structure-activity-relationship (SAR) studies were conducted on the imidazole and benzimidazole chemotype series to identify potent and selective FPR2 agonists. A few molecules were shortlisted based on their in vitro profile and absorption, distribution, metabolism and excretion (ADME) properties and were further evaluated in mouse models of asthma. We report herewith identification of 3 RCI compounds with low nanomolar potency for FPR2 agonism and >10,000 fold selectivity over FPR1 in Ca2+ release assay. These molecules also showed potency in other in vitro assays and potent efficacy in three distinct animal models of asthma. Our data suggest that FPR2 agonism can be a potential therapeutic approach to treat asthma. Our findings also propose that FPR1 can be spared to achieve the desired pharmacological activity.

pharmacology and toxicology↗

bioRxiv2020

Converting Microwave Ovens into Plasma-Generating Decontamination Units for N-95 Respirators

We show how a common microwave oven, a coat-hanger and a coffee cup can be used to decontaminate N-95 respirators in 30 seconds. Tulane virus in the artificial saliva was reduced by >3 log and Geobacillus stearothermophilus spores were reduced by >6 log. Respirators maintained filtration and fit even after 10 cycles. Filtration and fit tests performed by the CDC confirmed there was no damage to the respirators. Spectroscopy of the plasma reveals that OH and C-containing radicals as the most prevalent active species.

bioengineering↗

bioRxiv2020

HSPs, Ubiquitins and Antioxidants aid in Heat Tolerance in Tharparkar Indicine cattle

Transcriptome profiling of Vrindavani and Tharparkar cattle revealed that more numbers of genes dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.5 % of upregulated genes in Vrindavani were downregulated in Tharparkar and 17.5% upregulated genes in Tharparkar were downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naive unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.

physiology↗

bioRxiv2020

Chronic chemogenetic activation of forebrain excitatory neurons in postnatal life evokes long-lasting changes in mood-related behavior

Early adversity is a key risk factor for the development of adult psychopathology, including anxiety, depression and schizophrenia. Rodent models of early adversity program persistent behavioral, molecular, metabolic, and neurophysiological changes. Perturbed signaling via forebrain Gq-coupled neurotransmitter receptors is a common feature across multiple models of early adversity. We addressed whether enhanced Gq-mediated signaling in forebrain excitatory neurons during postnatal life can evoke long-lasting mood-related behavioral changes. Excitatory hM3Dq DREADD-mediated chemogenetic activation of CamKII-positive forebrain excitatory neurons during postnatal life (P2-14) increased anxiety- and despair-like behavior, and evoked sensorimotor gating deficits in adulthood. In contrast, chronic chemogenetic hM3Dq DREADD activation of forebrain excitatory neurons in the juvenile or adult window did not evoke any mood-related behavioral alterations, highlighting the criticality of the postnatal temporal window. The enhanced anxiety-, despair- and schizophrenia-like behavioral changes evoked by chronic chemogenetic activation of forebrain excitatory neurons in postnatal life, was accompanied by an increased cortical and hippocampal metabolic rate of glutamatergic and GABAergic neurons in adulthood. Furthermore, animals with a history of postnatal hM3Dq activation exhibited a decline in the expression of activity-dependent and plasticity-associated markers within the hippocampus, along with perturbed hippocampal excitatory and inhibitory currents in adulthood. These results indicate that Gq signaling mediated activation of forebrain excitatory neurons during the critical postnatal window is sufficient to program altered mood-related behavior, as well as metabolic and neurophysiological changes in forebrain glutamate and GABA systems, recapitulating specific aspects of the consequences of early adversity.

neuroscience↗

bioRxiv2019

Genetic Interaction between RLM1 and F-box Motif Encoding gene SAF1 Contributes to Stress Response in Saccharomyces cerevisiae

Stress response is mediated by transcription of stress responsive genes. F-box motif protein Saf1 involves in SCF-E3 ligase mediated degradation of the adenine deaminase, Aah1 upon nutrient stress. Four transcription regulators, BUR6, MED6, SPT10, SUA7, have been reported for SAF1 gene in genome database of Saccharomyces cerevisiae. Here in this study an in-silco analysis of gene expression and transcription factor databases was carried out to understand the regulation of SAF1 gene expression during stress for hypothesis generation and experimental analysis. The GEO profile database analysis showed increased expression of SAF1 gene when treated with clioquinol, pterostilbene, gentamicin, hypoxia, genotoxic, desiccation, and heat stress, in WT cells. SAF1 gene expression in stress conditions correlated positively whereas AAH1 expression negatively with RLM1 transcription factor, which was not reported earlier. Based on analysis of expression profile and regulatory association of SAF1 and RLM1, we hypothesized that inactivation of both the genes may contribute to stress tolerance. The experimental analysis with the double mutant, saf1{Delta}rlm1{Delta} for cellular growth response to stress causing agents, showed tolerance to calcofluor white, SDS, and hydrogen peroxide. On the contrary, saf1{Delta}rlm1{Delta} showed sensitivity to MMS, HU, DMSO, Nocodazole, Benomyl stress. Based on in-silico and experimental data we suggest that SAF1 and RLM1 both interact genetically in differential response to genotoxic and general stressors.

genetics↗

bioRxiv2019

Absence of Replication fork associated factor CTF4 and F-box motif Encoding Gene SAF1 leads to reduction in Cell Size and Stress Tolerance Phenotype in S. cerevisiae

Chromosome transmission fidelity factor, Ctf4 in S. cerevisiae associates with replication fork and helps in the sister chromatid cohesion. At the replication fork, Ctf4 links DNA helicase with the DNA polymerase. The absence of Ctf4 invokes replication checkpoint in the cells. The Saf1 of S.cerevisiae interacts with Skp1 of SCF-E3 ligase though F box-motif and ubiquitinates the adenine deaminase Aah1 during phase transition due to nutrient stress. The genetic interaction between the CTF4 and SAF1 has not been studied. Here we report genetic interaction between CTF4 and SAF1 which impacts the growth fitness and response to stress. The single and double gene deletions of SAF1 and CTF4 were constructed in the BY4741 genetic background. The strains were tested for growth on rich media and media containing stress causing agents. The saf1{Delta}ctf4{Delta} cells with reduced cell size showed the fastest growth phenotype on YPD medium when compared with the saf1{Delta}, ctf4{Delta}, and WT. The saf1{Delta}ctf4{Delta} cells also showed the tolerance to MMS, NaCl, Glycerol, SDS, Calcofluor white, H2O2, DMSO, Benomyl, and Nocodazole when compared with the saf1{Delta}, ctf4{Delta}, and WT cells. However, saf1{Delta}ctf4{Delta} cells showed the sensitivity to HU when compared with WT and saf1{Delta}. Based on these observations we suggest that SAF1 and CTF4 interact genetically to regulate the cell size, growth and stress response.

genetics↗

bioRxiv2019

The absence of F-box motif Encoding Gene SAF1 and Chromatin Associated factor CTF8 together contributes to MMS Resistant and HU Sensitive phenotype in S. cerevisiae

The Replication factor-C compex which related to cohesion, constitutes, three subunits called Ctf18, Ctf8 and Dcc1. These three subunit complex assist the loading of PCNA onto the chromosome. None of the replication factor C components are essential for cell viability. The null mutant of the CTF8 in S.cerevisiae shows the chromosome instability and high frequency of chromosome loss. The SAF1 gene product of S. cerevisiae involved in the degradation of adenine deaminase factor Aah1p by SCF-E3 ligase, which itself is the part of E3 ligase. The ubiquitin marked degradation of Aah1p occurs during nutrient stress which lead to cell enter into the quiescent state. The N-terminus of Saf1p interacts with the Skp1 of SCF-E3 ligase and at C-terminus recruits with Aah1p. Here we have investigated about the binary genetic interaction between the SAF1 and CTF8 genes. The strains containing single and double gene deletions of SAF1 and CTF8 were constructed in the BY4741 genetic background. Further the mutant strains were evaluated for growth fitness, genome stability and response to genotoxic stress caused by hydroxyurea (HU) and methyl methane sulfonate (MMS). The saf1{Delta}ctf8{Delta} strain showed the increased growth phenotype in comparison to saf1{Delta}, ctf8{Delta}, and WT strain on YPD medium. However saf1{Delta}ctf8{Delta} strain when grown in the presence MMS showed resistance and HU sensitive phenotype when compared with saf1{Delta}, ctf8{Delta}. The frequency of Ty1 retro-transposition was also elevated in saf1{Delta}ctf8{Delta} in comparison to either saf1{Delta} or ctf8{Delta}. The number of cells showing the two or multi-nuclei phenotype was also increased in saf1{Delta}ctf8{Delta} cells when compared with the either saf1{Delta} or ctf8{Delta}. Based on these observations, we report that the absence of both the gene SAF1 and CTF8 together leads to MMS resistance, HU sensitivity, and genome instability. This report warrants the investigation of mechanisms of differential growth phenotype due to loss of SAF1 and CTF8 together in presence of genotoxic stress in future.

genetics↗

bioRxiv2019

Loss of F-box Motif Encoding Gene SAF1 and RRM3 Together Leads to Synthetic Growth Defect and Sensitivity to HU, MMS in S.cerevisiae

Unearthing of novel genetic interaction which leads to synthetic growth defects due to inactivation of genes are needed for applications in precision medicine. The genetic interactions among the molecular players involving different biological pathways need to be investigated. The SAF1 gene of S.cerevisiae encodes for a protein product which contain N-terminal F-box motif and C-terminal RCC1 domain. The F-box motif interacts with Skp1subunit of the SCF-E3 ligase and C-terminus with Aah1 (adenine deaminase) for ubiquitination and subsequent degradation by 26S proteasome during phase transition from proliferation state to quiescence phase due to nutrient limitation stress. The replication fork associated protein Rrm3 of S.cerevisiae belongs to Pif1 family helicase and function in removal of the non-histone proteins during replication fork movement. Here we have investigated the genetic interaction among both the genes (SAF1 and RRM3) and their role in growth fitness and genome stability. The single and double gene knockout strains of SAF1and RRM3 genes was constructed in BY4741 genetic background and checked for the growth fitness in presence of genotoxic stress causing agents such as hydroxyurea and methyl methanesulfonate. The strains were also evaluated for nuclear migration defect by DAPI staining and for HIS3AI marked Ty1 retro-transposition. The saf1{Delta}rrm3{Delta} showed the extremely slow growth phenotype in rich medium and sensitivity to genotoxic agents such as HU and MMS in comparison to single gene mutant (saf1{Delta}, rrm3{Delta}) and WT cells. The saf1{Delta}rrm3{Delta} also showed the defects in nuclear migration as evident by multi-nuclei phenotype. The saf1{Delta}rrm3{Delta} also showed the elevated frequency of Ty1 retro-transposition in JC2326 background in comparison to either saf1{Delta} or rrm3{Delta}. Based on these observations we report that thatSAF1 and RRM3 functions in parallel pathway for growth fitness and stability of the genome.

genetics↗

bioRxiv2019

Prevalence and Determinants of Caesarean Section in South and South-east Asian Women

BackgroundCaesarean section is considered a preferable and safe method of delivery. In the last decade, its prevalence has increased in both developed and developing countries. In the context of developing countries viz., South Asia (the highest populated region) and South-east Asia (the third highest populated region), the preference for, and variation in, caesarean section delivery and its associated maternal socioeconomic characteristics are still to be determined.\n\nObjectiveTo study the magnitude of caesarean delivery in the South and South-east Asian countries, by correlating the maternal socioeconomic characteristics with the preference for caesarean sections.\n\nMethodologyData on ever-married women of nine developing countries of South and South-east Asia viz., Vietnam, India, Maldives, Timor-Leste, Nepal, Indonesia, Pakistan, Bangladesh and Cambodia, from Demographic and Health Survey has considered. Both bivariate and multivariate binary logistic regression models were used to estimate the probability that a woman undergoes caesarean section and to assess the influence of maternal socioeconomic characteristics towards the preference for caesarean section.\n\nConclusionIn seven urban and four rural regions of nine South and South-East Asian countries, a significant inclination towards the caesarean delivery above the more recent outdate WHO recommended optimal range of 10-15% or the more recent study by top researchers of 19% has been found. The analysis confirmed that the prevalence of caesarean section and its associated maternal socioeconomic characteristics varied widely among these nine South and South-East Asian countries.

scientific communication and education↗

bioRxiv2019

Direct observation of branching MT nucleation in living animal cells.

Centrosome-mediated microtubule (MT) nucleation has been well-characterized; however, numerous non-centrosomal MT nucleation mechanisms exist. The branching MT nucleation pathway envisages that the {gamma}-tubulin ring complex ({gamma}-TuRC) is recruited to MTs by the augmin complex to initiate nucleation of new MTs. While the pathway is well-conserved at a molecular and functional level, branching MT nucleation by core constituents has never been directly observed in animal cells. Here, multi-color TIRF microscopy was applied to visualize and quantitatively define the entire process of branching MT nucleation in dividing Drosophila cells. The stereotypical branching nucleation event entailed augmin first binding to a \"mother\" MT, recruitment of {gamma}-TuRC after 16s, followed by nucleation 15s later of a \"daughter\" MT at a 36{degrees} branch angle. Daughters typically remained attached throughout their ~40s lifetime unless the mother depolymerized past the branch point. Assembly of branched MT arrays, which did not require D-TPX2 (Drosophila TPX2) or evident regulation by a RanGTP gradient, enhanced localized RhoA activation during cytokinesis.

cell biology↗

bioRxiv2018

Minimization of cross-talk between Spindle Assembly Checkpoint silencing and error correction

Accurate chromosome segregation during cell division requires that the pair of sister kinetochores on each chromosome attach to microtubules originating from opposite spindle poles. This is ensured by the combined action of the Spindle Assembly Checkpoint (SAC), which detects unattached kinetochores, and an error correction mechanism that destabilizes incorrect attachment of both sister kinetochores to the same spindle pole. These processes are downregulated by Protein Phosphatase 1 (PP1), which both silences the SAC and stabilizes kinetochore-microtubule attachments. We find that this dual PP1 role can be problematic: if PP1 is recruited to the kinetochore for SAC silencing prior to chromosome biorientation, it interferes with error correction. We show that to mitigate this cross-talk, the yeast kinetochore uses independent PP1 sources to stabilize correct attachments and to silence the SAC, and also delays the recruitment of PP1 for SAC silencing. Consequently, chromosome biorientation precedes SAC silencing ensuring accurate chromosome segregation.

cell biology↗

bioRxiv2018

Microtubule plus-tips act as signaling hubs for positioning the cleavage furrow during cytokinesis.

Cell division in animal cells culminates with the formation of a contractile ring that divides the cytosol through formation of a cleavage furrow. Microtubules (MTs) are essential for furrow positioning, but the molecular nature of MT-derived spatial signals is unresolved. In this study essential cytokinesis regulators (the centralspindlin complex, aurora B kinase (ABK), and polo kinase) were visualized in Drosophila melanogaster (Dm) cells and found localize to and track MT plus-ends during cytokinesis. The RhoA GEF Pebble (Dm ECT2) did not robustly tip-track but became enriched at MT plus-tips rapidly following cortical contact resulting in RhoA activation and enrichment of myosin-regulatory light chain. Abrogation of cytokinesis regulator tip-tracking by EB1 depletion or deletion of a novel EB1-interaction motif (hxxPTxh) in the centralspindlin component RacGAP50C resulted in higher incidences of cytokinesis failure. We propose that EB1-dependent, MT plus-tip-based signaling hubs recruit cortical Dm ECT2 upon contact to locally activate RhoA.

cell biology↗