Biology subjects

Tiwari, S.

Publications and source records attributed to Tiwari, S..

72 records · Page 4Linked to original sources

bioRxiv2022

UBA52 is crucial in HSP90 ubiquitylation and neurodegenerative signaling during early phase of Parkinson disease

Protein aggregation is one of the major pathological events in age-related Parkinsons disease (PD) pathology, predominantly regulated by the ubiquitin-proteasome system (UPS). UPS essentially requires core component ubiquitin however, its role in PD pathology is obscure. This study aimed to investigate the role of ubiquitin encoding genes in the early phase of PD pathology. Wild-type human Myc--synuclein transfected neurons, -synuclein-PFFs treated cells, rotenone-induced sporadic models of PD and SNCA C57BL/6J-Tg (Th-SNCA*A30P*A53T)39 Eric/J transgenic mice showed downregulated level of UBA52 in conjunction with significant downregulation of tyrosine hydroxylase (TH) and neuronal death. In silico predictions, mass spectrometric analysis and co-immunoprecipitation findings suggested strong interaction of UBA52 with -synuclein, HSP90 and E3-ubiquitin ligase CHIP, besides its co-localization with -synuclein in the mitochondrion. Next, in vitro ubiquitylation assay indicated an imperative requirement of the lysine-63 residue of UBA52 in CHIP-mediated HSP90 ubiquitylation. Myc-UBA52 expressed neurons exhibited the downregulated -synuclein protein abundance with increased TH and restored proteasome activity during the diseased condition. Furthermore, Myc-UBA52 expression inhibited the augmented HSP90 protein level along with its various client proteins, HSP75 (homologue of HSP90 in mitochondrion) and ER stress-related markers during early PD. Taken together, data highlights the critical role of UBA52 in HSP90 ubiquitylation in parallel to its potential contribution to the modulation of various disease-related neurodegenerative signaling targets during the early phase of PD pathology.

neuroscience↗

bioRxiv2022

Call count surveys as a tool to monitor habitats occupied by Cheer Pheasants (Catreus wallichii) in Shimla, Himachal Pradesh

The vulnerable Cheer Pheasant (Catreus wallichii) is found in the western Himalayas. It prefers successional grasslands which are maintained by residents near villages. Therefore, it is prone to anthropogenic pressures which have led to local extinctions and a decline in population. We conducted five call count surveys at dusk and dawn from 15 April - 15 May 2020 in grasslands of Dharbhog panchayat, Shimla, Himachal Pradesh to assess presence of Cheer Pheasants in different habitat types. We used frequency of occurrence (number of encounters / number of visits) to determine presence or absence of Cheer Pheasant in an area of 10.5 km2 with ten established call count stations. We encountered Cheer Pheasants at six call count stations and the frequency of occurrence of the species ranged from 0 - 0.60. This survey provides an index of occupancy of the species and can be used to assess the change in habitat occupied by the species with time. The local forest department can also use these results to regulate over grazing and burning of grasslands during the breeding season in areas where we recorded the species.

ecology↗

bioRxiv2022

A novel fluorescent multi-domain protein construct reveals the individual steps of the unfoldase action of Hsp70

A detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the detailed characterization of the aggregates, which are typically heterogeneous. To tackle this problem, we designed here a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase core, flanked by stress-resistant fluorescent mTFP and Venus domains, which upon denaturation formed a discrete stable population of small aggregates. Combining Forster Resonance Energy Transfer and enzymatic activity measurements provided unprecedent details on MLucV states, including native, aggregated, unfolded and chaperone-bound conformations. Using MLucV, we probed the various steps undertaken by bacterial Hsp70 to convert stable discrete aggregates into native proteins. The mechanism first involved an ATP-fuelled disaggregation and unfolding step of the stable pre-aggregated substrate, with a consequent stretching of MLucV beyond simply-unfolded conformations, followed, upon release, by native refolding. Furthermore, the ATP-fuelled unfolding action of Hsp70 on MLucV aggregates could accumulate native MLucV species under elevated denaturing temperatures, highly adverse to the native state. These results unambiguously excluded binding and preventing aggregation from the non-equilibirum mechanism by which Hsp70 converts stable aggregates into metastable native proteins.

molecular biology↗

bioRxiv2022

SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine stimulation and an increasing antigenic and anti-inflammatory cytokine induction

Hyper-transmissibility with decreased disease severity are typical characteristics of Omicron variant. To understand this phenomenon, we used various bioinformatics approaches to analyze randomly selected genome sequences (one each) of the Gamma, Delta, and Omicron variants submitted to NCBI from 15 to 31 December 2021. We show that: (i) Pathogenicity of SARS-CoV-2 variants decreases in the order: Wuhan > Gamma > Delta > Omicron; however, the antigenic property follows the order: Omicron > Gamma > Wuhan > Delta. (ii) Omicron Spike RBD has lower pathogenicity but higher antigenicity than other variants. (iii) Decreased disease severity by Omicron variant may be due to its decreased pro-inflammatory and IL-6 stimulation and increased IFN-{gamma} and IL-4 induction efficacy. (iv) Mutations in N protein are associated with decreased IL-6 induction and human DDX21-mediated increased IL-4 production in Omicron. (v) Due to mutations, the stability of S, M, N, and E proteins decreases in the order: Omicron > Gamma > Delta > Wuhan. (vi) Stronger Spike RBD-hACE2 binding in Omicron is associated with increased transmissibility. However, the lowest stability of the Omicron Spike protein makes Spike RBD-hACE2 interaction weak for systemic infection and for causing severe disease. Finally (vii), the highest instability of Omicron E protein may also be associated with decreased viral maturation and low viral load leading to less severe disease and faster recovery. Our method may be used for other similar viruses, and these findings will contribute to the understanding of the dynamics of SARS-CoV-2 variants and the management of emerging variants.

bioinformatics↗

bioRxiv2021

SARS-CoV-2 genome sequences from Lucknow, Uttar Pradesh, India by Nanopore Sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a significant challenge worldwide. Rapid genome sequencing of SARS-CoV-2 is going on across the globe to detect mutations and genomic modifications in SARS-CoV-2. In this study, we have sequenced twenty-three SARS-CoV-2 positive samples collected during the first pandemic from the state of Uttar Pradesh, India. We observed a range of already reported mutations (2-22), including; D614G, L452R, Q613H, Q677H, T1027I in the S gene; S194L in the N gene; Q57H, L106F, T175I in the ORF3. Few unreported mutations such as P309S in the ORF1ab gene; T379I in the N gene; and L52F, V77I in the ORF3a gene were also detected. Phylogenetic genome analysis showed similarity with other SARS-CoV-2 viruses reported from Uttar Pradesh. The observed mutations may be associated with SARS-CoV-2 virus pathogenicity or disease severity.

genomics↗

bioRxiv2021

Protein kinase J regulates Rv0642c expression and sensitivity to rifampicin of mycobacteria

Mycobacterium tuberculosis (M.tb) persists for long-duration inside the human host in both active and latent form by modulating the immune response. The mechanisms employed by M.tb to survive inside the host and evade the host immune system need to be explored in greater depth for the rational design of novel treatment strategies. The phosphorylation and methylation of biomolecules need to be addressed in mycobacteria because it has an important role in infection establishment and persistence. In the present study, we elaxborate on the role of PknJ in the slow growth of BCG and its association with mmaA4 protein during extracellular and intracellular growth. The pknJ knock-out (KO) BCG has been used to decode the functional significance in mycobacteria. The mmaA4 expression and methyltransferase activity is decreased in knocked-out BCG strain (pknJ-/-) during extracellular growth, while mmaA4 expression and methyltransferase activity is increased during intracellular growth of mycobacteria. The knocked-out BCG strain is highly sensitive to the rifampicin antibiotics during extracellular growth in compared to control. A significant association of pknJ and mmaA4 was found in our studies during the growth and intracellular persistence of mycobacteria.

microbiology↗

bioRxiv2021

A Fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis.

The L-arginine biosynthesis pathway consists of eight enzymes that catalyse the conversion of L-glutamate to L-arginine, appears to be attractive target for anti-Tuberculosis (TB) drug discovery. Starvation of M. tuberculosis deleted for either argB or argF genes led to rapid sterilization of these strains in mice while Chemical inhibition of ArgJ with Pranlukast was also found to clear chronic M. tuberculosis infection in animal models. In this work, the ligandability of four enzymes of the pathway ArgB, ArgC, ArgD and ArgF is explored using a fragment-based approach. We reveal several hits for these enzymes validated with biochemical and biophysical assays, and X-ray crystallographic data, which in the case of ArgB were further confirmed to have on-target activity against M. tuberculosis. These results demonstrate the potential of more enzymes in this pathway to be targeted with dedicated drug discovery programmes.

biochemistry↗

bioRxiv2021

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

bioinformatics↗

bioRxiv2020

Habitat patch size and tree species richness shape the bird community in urban green spaces of rapidly urbanizing region of India.

Rapid urbanization and associated biodiversity loss is rampant globally but especially a cause of concern for developing countries. However, numerous studies investigating the role of urban green spaces have established their key role in conserving larger suites of species in urban area. Yet our knowledge is lopsided due to lag in research in developing countries. We examined how landscape and local scale features of urban green spaces influence bird species richness, density, fine-foraging guild richness and composition during breeding and non-breeding season. This is the first study of this nature in one the Himalayan states of India. We quantified landscape level variables in the 250m buffer around 18 urban green spaces. We sampled vegetation and bird community during breeding and non-breeding season through 52 intensive sampling point spread across 18 urban green spaces. Size of the urban green space at landscape level and tree richness at the local scale emerged as important predictor variables influencing bird species richness, density and richness of imperiled insectivorous guild across seasons. Urban green spaces within education institutions and offices experiencing much less management supported higher bird richness and density whereas city parks were the most species poor. Community composition was affected more strongly by built-up cover and barren area in the matrix and also by tree species richness within urban green spaces. City planners should focus on establishing larger city parks during design stage whereas biodiversity potential of the existing urban green spaces could be enhanced by selecting native tree and shrub species to increase overall habitat complexity.

ecology↗

bioRxiv2020

Heterozygous deletion of SYNGAP enzymatic domains in rats causes selective learning, social and seizure phenotypes

Pathogenic variants in SYNGAP1 are one of the most common genetic causes of nonsyndromic intellectual disability (ID) and are considered a risk for autism spectrum disorder (ASD). SYNGAP1 encodes a synaptic GTPase activating protein that modulates the intrinsic GTPase activity of several small G-proteins and is implicated in regulating the composition of the postsynaptic density. By targeting the deletion of exons encoding the calcium/lipid binding (C2) and GTPase activating protein (GAP) domains, we generated a novel rat model to study SYNGAP related pathophysiology. We find that rats heterozygous for the C2/GAP domain deletion (Syngap+/{Delta}-GAP) exhibit reduced exploration and fear extinction, altered social behaviour, and spontaneous seizures, while homozygous mutants die within days after birth. This new rat model reveals that the enzymatic domains of SYNGAP are essential for normal brain function and provide an important new model system in the study of both ID/ASD and epilepsy.

neuroscience↗

bioRxiv2020

Imbalance of flight-freeze responses and their cellular correlates in the Nlgn3-/y rat model of autism

Mutations in the postsynaptic transmembrane protein neuroligin-3 are highly correlative with autism spectrum disorders (ASDs) and intellectual disabilities (IDs). Fear learning is well studied in models of these disorders, however differences in fear response behaviours are often overlooked. Whilst examining fear in a rat model of ASD/ID lacking Nlgn3, we observed that they display a greater propensity to exhibit flight responses in contrast to classic freezing seen in wildtypes during fearful situations. Consequently, we examined the physiological underpinnings of this in neurons of the periaqueductal grey (PAG), a midbrain area involved in flight-or-freeze responses. In ex vivo slices from Nlgn3-/y, rats, dorsal PAG (dPAG) neurons showed intrinsic hyperexcitability. Further analysis of this revealed lower magnitude in vivo dPAG stimulation evoked flight behaviour in Nlgn3-/y, rats, indicating the functional impact of the increased cellular excitability. This study provides new insight into potential pathophysiologies leading to emotional disorders in individuals with ASD.

neuroscience↗

bioRxiv2020

Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples

The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.

microbiology↗

bioRxiv2020

BioViz Connect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser

Genomics researchers do better work when they can interactively explore and visualize data. However, due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and storage resources, but typically lack interactive visualization capability. In this paper, we present BioViz Connect, a middleware Web application that links the CyVerse science gateway to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the users personal computer. Using BioViz Connect, users can (i) stream data from the CyVerse data store into IGB for visualization, (ii) improve the IGB user experience for themselves and others by adding IGB specific metadata to CyVerse data files, including genome version and track appearance, and (iii) run compute-intensive visual analytics functions on CyVerse infrastructure to create new datasets for visualization in IGB or other applications. To demonstrate how BioViz Connect facilitates interactive data visualization, we describe an example RNA-Seq data analysis investigating how heat and desiccation stresses affect gene expression in the model plant Arabidopsis thaliana. Lastly, we discuss limitations of the technologies used and suggest opportunities for future work. BioViz Connect is available from https://bioviz.org.

bioinformatics↗

bioRxiv2020

GroEL/ES Buffers Entropic Traps In Folding Pathway During Evolution Of A Model Substrate

The folding landscape of proteins can change during evolution with the accumulation of mutations that may introduce entropic or enthalpic barriers in the protein folding pathway, making it a possible substrate of molecular chaperones in vivo. Can the nature of such physical barriers of folding dictate the feasibility of chaperone-assistance? To address this, we have simulated the evolutionary step to chaperone-dependence keeping GroEL/ES as the target chaperone and GFP as a model protein in an unbiased screen. We find that the mutation conferring GroEL/ES dependence in vivo and in vitro encode an entropic trap in the folding pathway rescued by the chaperonin. Additionally, GroEL/ES can edit the formation of non-native contacts similar to DnaK/J/E machinery. However, this capability is not utilized by the substrates in vivo. As a consequence, GroEL/ES caters to buffer mutations that predominantly cause entropic traps, despite possessing the capacity to edit both enthalpic and entropic traps in the folding pathway of the substrate protein.

molecular biology↗

bioRxiv2020

The 5 regulatory region of the β actin gene in Clarias species is complex and variable in relation to ecological needs

The {beta} actin gene is involved in various cellular housekeeping processes including transcription, mRNA processing, cell signaling and chromosome remodeling. For regulating the expression of this gene under different environmental conditions, the promoter region of the {beta} actin gene is structurally dynamic with multiple regulatory features in the upstream region. Most previous information about the 5 regulatory region of the {beta} actin gene has been limited to in vitro laboratory experiments. Considering the need for functional versatility of expression of this gene in the Catfish Clarias batrachus in different environments, here we have analyzed the 5 regulatory region of {beta} actin and identified numerous elements that are variable. We have made comparisons of individuals from three populations found in three different diverse ecological systems, as well as in three sister species, to elucidate its structural diversity. Our results show that the 5 regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5 regulatory region of a housekeeping gene like {beta} actin, modify its architecture as per the environmental conditions. These modifications specifically includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5 regulatory region is conserved which was yet not highlighted. Author summaryPromoter is a regulatory region where the basal transcription machinery assembles to initiate the process of transcription. It plays crucial role in controlling the gene expression. The 5 regulatory region includes TATA box, CAAT box, GC box and Cis -acting regulatory elements. Most previous information about the 5 regulatory region of the {beta} actin gene has been limited to in vitro laboratory experiments. Our study results show that the 5 regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5 regulatory region of a housekeeping gene like {beta} actin, modify its architecture as per the environmental requirements. These modifications precisely includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5 regulatory region is conserved. These findings clearly define a novel role of promotor of {beta} actin gene which was yet not highlighted. These findings can broaden our understanding in linking TF in 5 regulatory regions to a specific environmental variable/disease conditions. This may become a simple strategy in understanding complex gene-environment interactions.

molecular biology↗

bioRxiv2019

Land Use Change Increases Wildlife Parasite Diversity in Anamalai Hills, Western Ghats, India

Anthropogenic landscape change such as land use change and habitat fragmentation are known to alter wildlife diversity. Since host and parasite diversities are strongly connected, landscape changes are also likely to change wildlife parasite diversity with implication for wildlife health. However, research linking anthropogenic landscape change and wildlife parasite diversity is limited, especially comparing effects of land use change and habitat fragmentation, which often cooccur but may affect parasite diversity substantially differently. Here, we assessed how anthropogenic land use change (presence of plantation, livestock foraging and human settlement) and habitat fragmentation may change the gastrointestinal parasite diversity of wild mammalian host species (n=23) in Anamalai hills, India. We found that presence of plantations, and potentially livestock, significantly increased parasite diversity due possibly to spillover of parasites from livestock to wildlife. However, effect of habitat fragmentation on parasite diversity was not significant. Together, our results showed how human activities may increase wildlife parasite diversity within human-dominated landscape and highlighted the complex pattern of parasite diversity distribution as a result of cooccurrence of multiple anthropogenic landscape changes.

ecology↗

bioRxiv2018

Y chromosomal noncoding RNA regulates autosomal gene expression via piRNAs in mouse testis

Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which shows unprecedented number of splice variants in testis. Further, Pirmy transcript variants act as templates for several piRNAs. We identified ten differentially expressed autosome-encoded sperm proteins in mutant mice. Pirmy transcript variants have homology to 5/3UTRs of these deregulated autosomal genes. Thus, subfertility in Y-deleted mice appears to be a polygenic phenomenon that is partially regulated epistatically by the Y-chromosome. Our study provides novel insights into possible role of MSY-derived ncRNAs in male fertility and reproduction. Finally, sperm phenotypes from the Y-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of Y-derived ncRNAs in male sterility and speciation.

genomics↗

bioRxiv2017

A potential link between tuberculosis and lung cancer through non-coding RNAs

Pulmonary tuberculosis caused by Mycobacterium and lung cancer are two major causes of deaths worldwide and the former increases the risk of developing lung cancer. However, the precise molecular mechanism of Mycobacterium associated increased risk of lung cancer is not entirely understood. Here, using in silico approaches, we show that hsa-mir-21 and M. tuberculosis sRNA_1096 and sRNA_1414 could play important roles in the pathogenesis of both these diseases. Further, we postulated a \"Genetic remittance\" hypothesis where these sRNAs may play important roles. The sRNA_1096 could be involved in tuberculosis through multiple infectious processes, and if transferred to the host, it may activate the TLR8 mediated pro-metastatic inflammatory pathway by acting as a ligand to TLR8 similar to the mir-21 leading to lung tumorigenesis and chemo-resistance. Analogous to SH3GL1, it may also regulate cell cycle. On the other hand, sRNA_1414 is probably involved in survivability and drug response of the pathogen. However, it may be a metastatic factor for lung cancer providing EPS8L1 and SORBS1 like functions upon remittance. Further, all these three non-coding RNAs are predicted to act in rifampicin resistance in Mycobacterium. Currently, we are applying robust bioinformatics strategies and conducting experimental validations to confirm our in-silico findings and hypothesis.

cancer biology↗