Biology subjects

Kumar, S.

Publications and source records attributed to Kumar, S..

At least 433 records · Page 24Linked to original sources

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

Biomechanical dependence of SARS-CoV-2 infections

Older people have been disproportionately vulnerable to the current SARS-CoV-2 pandemic, with an increased risk of severe complications and death compared to other age groups. A mix of underlying factors has been speculated to give rise to this differential infection outcome, including changes in lung physiology, weakened immunity, and severe immune response. Our study focuses on the impact of biomechanical changes in lungs that occur as individuals age, i.e., the stiffening of the lung parenchyma and increased matrix fiber density. We used hydrogels with an elastic modulus of 0.2 and 50 kPa and conventional tissue culture surfaces to investigate how infection rate changes with parenchymal tissue stiffness in lung epithelial cells challenged with SARS-CoV-2 Spike (S) protein pseudotyped lentiviruses. Further, we employed electrospun fiber matrices to isolate the effect of matrix density. Given the recent data highlighting the importance of alternative virulent strains, we included both the native strain identified in early 2020 and an early S protein variant (D614G) that was shown to increase the viral infectivity markedly. Our results show that cells on softer and sparser scaffolds, closer resembling younger lungs, exhibit higher infection rates by the WT and D614G variant. This suggests that natural changes in lung biomechanics do not increase the propensity for SARS-CoV-2 infection and that other factors, such as a weaker immune system, may contribute to increased disease burden in the elderly.

bioengineering↗

bioRxiv2022

Omicron (BA.1) and Sub-Variants (BA.1, BA.2 and BA.3) of SARS-CoV-2 Spike Infectivity and Pathogenicity: A Comparative Sequence and Structural-based Computational Assessment

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread throughout the world. We used computational tools to assess the spike infectivity, transmission, and pathogenicity of Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) in this study. BA.1 has 39 mutations, BA.1.1 has 40 mutations, BA.2 has 31 mutations, and BA.3 has 34 mutations, with 21 shared mutations between all. We observed 11 common mutations in Omicrons receptor-binding domain and sub-variants. In pathogenicity analysis, the Y505H, N786K, T95I, N211I, N856K, and V213R mutations in omicron and sub-variants are predicted to be deleterious. Due to the major effect of the mutations characterising, in the receptor-binding domain (RBD), we found that Omicron and sub-variants had a higher positive electrostatic surface potential. This could increase interaction between RBD and electronegative human angiotensin-converting enzyme 2 (hACE2). Omicron and sub-variants had a higher affinity for hACE2 and the potential for increased transmission when compared to the wild type. Among Omicron sub-lineages, BA.2 and BA.3 have a higher transmission potential than BA.1 and BA.1.1. We predicted that mutated residues in BA.1.1 (K478), BA.2 (R400, R490, R495), and BA.3 (R397 and H499) formation of new salt bridges and hydrogen bonds. Omicron and sub-variant mutations at Receptor-binding Motif (RBM) residues such as Q493R, N501Y, Q498, T478K, and Y505H all contribute significantly to binding affinity with human ACE2. Interactions with Omicron variant mutations at residues 493, 496, 498, and 501 seem to restore ACE2 binding effectiveness lost due to other mutations like K417N and Y505H.

bioinformatics↗

bioRxiv2022

Inducible Nitric Oxide Synthase deficiency leads to early demyelination by altering the balance between pro- and anti-inflammatory responses against Murine-β-Coronavirus

The neurological disease Multiple sclerosis (MS) is characterized by neuroinflammation and demyelination orchestrated by the activated glial cells, the CNS infiltrating leukocytes, and their reciprocal interaction through inflammatory signals. Inducible nitric oxide synthase (iNOS), an enzyme that catalyzes sustained nitric oxide production in response to an inflammatory stimulus, is a pro-inflammatory marker expressed particularly by the microglia/macrophages (MG/M{varphi}) during neuroinflammation. In MS, iNOS has been reportedly associated with the disease pathology; however, studies dissecting its role in the underlying mechanisms, specifically demyelination, are limited. Therefore, we studied the role of iNOS in a recombinant beta-coronavirus-MHV-RSA59-induced neuroinflammation, which is a prototypic animal model used to investigate the pathological hallmarks of MS, neuroinflammatory demyelination, and axonal degeneration. During the acute phase of infection with RSA59, wildtype C57BL/6 (WT) mice had significantly upregulated iNOS expression in macrophages, natural killer cells, and natural killer T cells suggesting a role for iNOS in RSA59-induced neuroinflammation. Studies comparing RSA59-infected WT and iNOS-deficient mice revealed that iNOS deficiency aggravated the disease with increased CNS infiltration of macrophages and neutrophils and enhanced mortality. As early as 9-10 days after the infection, the CNS of iNOS-deficient mice had substantially higher demyelination marked with morphologically defined MG/M{varphi} in the demyelinating regions. Transcript analysis confirmed the significant upregulation of type2 macrophage (M2) markers-Arginase 1, CD206, and TREM2-in the CNS of iNOS-deficient mice. Corroborating to the phenotype, the iNOS-deficient mice showed a significantly higher expression of TGF{beta}-an anti-inflammatory cytokine- and increased T regulatory (Treg) cell infiltration, indicating an anti-inflammatory milieu established early after the infection. These observations highlight a protective role of iNOS in virus-induced neuroinflammation whereas its absence leads to MG/M{varphi} polarization towards a phenotype that may be involved in the exacerbated demyelination pathology. Author summaryContrary to the reported pathogenic role of inducible nitric oxide synthase (iNOS) in multiple sclerosis and related autoimmune animal models, we show that the mice deficient in iNOS show an exacerbated disease with accelerated demyelination accompanied by heightened production of an anti-inflammatory and phagocytic markers and more numbers of Tregs in a mouse model of a recombinant mouse hepatitis virus RSA59 infection. Therefore, iNOS may play protective and regulatory roles in this beta-coronavirus infection.

neuroscience↗

bioRxiv2022

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in- vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.

genomics↗

bioRxiv2022

Activity and state dependent modulation of salt taste behavior in Drosophila melanogaster

Sodium present in NaCl is a fundamental nutrient required for many physiological processes. In animals, including Drosophila, low-salt concentrations induce attraction and high-salt concentrations evoke aversive behavior. Although the cellular basis of low and high salt taste detection has been described, the mechanisms regulating high salt consumption and salt taste modulation in animals remain elusive. Thus, we investigated the neural mechanisms behind high NaCl consumption in adult Drosophila, focusing on how flies adjust their acceptance of high salt based on their diet. Our findings show that long-term exposure to high salt increases the taste sensitivity of pharyngeal LSO neurons, which, in turn, enhances high salt intake. Exposing flies to a high NaCl diet for three days shows a decline in high salt aversion under starvation. Our results suggest that this modulation requires active LSO neurons and a starvation state or dopamine as genetic suppression of LSO pharyngeal neuronal activity in high NaCl-fed flies inhibit excessive salt intake. We also found that several independent taste receptor neurons and pathways are involved in such a modulation. Silencing any one of multiple LSO neuronal types inhibits excessive salt intake. Our study suggests that flies can adapt to the amount of salt ingested over several days, indicating the presence of a critical mechanism that resets the salt appetite and related neural circuits.

neuroscience↗

bioRxiv2022

NRP1 and furin as putative mediators of SARS-CoV-2 entry into human brain cells

COVID-19 has prominent neurological manifestations including psychiatric symptoms, indicating significant synaptic pathology. Surprisingly, existing evidence suggests negligible expression of the key SARS-CoV-2 host cell entry mediators ACE2 and TMPRSS2 in human brain, which complicates understanding of the pathomechanisms of the neuropsychiatric manifestations in COVID-19. Recent studies suggested that an alternative host-cell entry receptor, NRP1, can mediate entry of furin cleaved SARS-CoV-2 spike proteins into the host cells. However, the role of NRP1 and furin in mediating SARS-CoV-2 entry in human brain cells has been least explored and remains a lacuna in the literature. We performed an in silico analysis of the transcriptomic and proteomic expressions of SARS-CoV-2 host-cell entry receptors and associated tissue proteases in human brain tissue, using the publically available databases. Based on the expression analysis, SARS-CoV-2 entry in human brain cells is likely to be mediated through NRP1 and furin. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/476893v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1c818baorg.highwire.dtl.DTLVardef@1cf7c0corg.highwire.dtl.DTLVardef@d92e19org.highwire.dtl.DTLVardef@61866a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis)

The extant members of the Eurasian rhino species have experienced severe population and range declines through a combination of natural and anthropogenic factors since Pleistocene. The one-horned rhino is the only Asian species recovered from such strong population decline but most of their fragmented populations in India and Nepal are reaching carrying capacity. Implementation of any future reintroduction-based conservation efforts would greatly benefit from currently unavailable detailed genetic assessments and evolutionary history of these populations. We sequenced wild one-horned rhino mitogenome from all the extant populations (n=16 individuals) for the first time, identified the polymorphic sites and assessed genetic variation (2531bp mtDNA, n=111 individuals) across India. Results showed 30 unique rhino haplotypes distributed as three distinct genetic clades (Fst value 0.68-1) corresponding to the states of Assam (n=28 haplotypes), West Bengal and Uttar Pradesh (both monomorphic). Phylogenetic analyses suggest earlier coalescence of Assam ([~]0.5 Mya) followed by parallel divergence of West Bengal and Uttar Pradesh/Nepal ([~]0.06-0.05Mya), supported by the paleobiogeographic history of the Indian subcontinent. Combined together, we propose recognising three Evolutionary Significant Units (ESUs) of Indian rhino. As recent assessments suggest further genetic isolations of Indian rhinos at local scales, future management efforts should focus on identifying genetically variable founder animals and consider periodic supplementation events while planning future rhino reintroduction programs in India. Such well-informed, multidisciplinary approach is the only way to ensure evolutionary, ecological and demographic stability of the species across its range.

ecology↗

bioRxiv2022

Identification of Mfn2-S249 as a Phosphoregulatory Switch of Mitochondrial Fusion Dynamics

Mitochondrial remodeling is a fundamental process underlying cellular respiration and metabolism. Here we report TAK1 as a direct regulator of mitochondrial fusion. TAK1 is activated by a variety of mitogenic factors, cytokines and environmental stimuli, which we find induces rapid fragmentation through Mfn2 inactivation. TAK1 phosphorylates Mfn2 at Ser249, which inhibits the binding of GTP required for Mfn trans-dimerization and mitochondrial membrane fusion. Accordingly, expression of Mfn2-S249 phosphomimetics (Mfn2-E/D) constitutively promote fission whereas alanine mutant (Mfn2-A) yields hyperfused mitochondria and increased bioenergetics in cells. In mice, Mfn2-E knock-in yields embryonic lethality in homozygotes whereas heterozygotes are viable but exhibit increased visceral fat accumulation despite normal body weight and cognitive/motor functions compared to wildtype and Mfn2-A mice. Mature white adipocytes isolated from mutant mice reveal cell-autonomous TAK1-related effects on mitochondrial remodeling and lipid metabolism. These results identify Mfn2-S249 as a dynamic phosphoregulatory switch of mitochondrial fusion during development and energy homeostasis.

cell biology↗

bioRxiv2022

A visual atlas of genes tissue-specific pathological roles

Dysregulation of a genes function, either due to mutations or impairments in regulatory networks, often triggers pathological states in the affected tissue. Comprehensive mapping of these apparent gene-pathology relationships is an ever daunting task, primarily due to genetic pleiotropy and lack of suitable computational approaches. With the advent of high throughput genomics platforms and community scale initiatives such as the Human Cell Landscape (HCL) project [1], researchers have been able to create gene expression portraits of healthy tissues resolved at the level of single cells. However, a similar wealth of knowledge is currently not at our finger-tip when it comes to diseases. This is because the genetic manifestation of a disease is often quite heterogeneous and is confounded by several clinical and demographic covariates. To circumvent this, we mined ~18 million PubMed abstracts published till May 2019 and selected ~6.1 million of them that describe the pathological role of genes in different diseases. Further, we employed a word embedding technique from the domain of Natural Language Processing (NLP) to learn vector representation of entities such as genes, diseases, tissues, etc., in a way such that their relationship is preserved in a vector space. Notably, Pathomap, by the virtue of its underpinning theory, also learns transitive relationships. Pathomap provided a vector representation of words indicating a possible association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS). The first manuscript reporting this finding was not part of our training data. Key pointsO_LIWe mined ~18 million PubMed abstracts to extract latent knowledge pertaining to tissue specific pathological roles of genes. C_LIO_LIWe found well-defined gene modules implicated in disease pathogenesis in anatomically proximal tissues. C_LIO_LIWe demonstrated an ahead of time discovery of the association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS), as a knowledge synthesis use-case. C_LI

bioinformatics↗

bioRxiv2021

Synaptosome microRNAs regulate synapse functions in Alzheimer's disease

MicroRNAs (miRNAs) are found in nerve terminals, synaptic vesicles, and synaptosomes, but it is unclear whether synaptic and cytosolic miRNA populations differ in Alzheimers disease (AD) or if synaptosomal miRNAs affect AD synapse activity. To address these questions, we generated synaptosomes and cytosolic fractions from postmortem brains of AD and unaffected control (UC) samples and analyzed them using a global Affymetrix miRNAs microarray platform. A group of miRNAs significantly differed (p<0.0001) with high fold changes variance (+/- >200-fold) in their expressions in different comparisons- 1) UC synaptosome vs UC cytosol, 2) AD synaptosomes vs AD cytosol, 3) AD cytosol vs UC cytosol, and 4) AD synaptosomes vs UC synaptosomes. MiRNAs data analysis revealed that some potential miRNAs were consistently different across sample groups. These differentially expressed miRNAs were further validated using AD postmortem brains, brains of APP transgenic (Tg2576), Tau transgenic (P301L), and wild type mice. The miR-501-3p, miR-502-3p and miR-877-5p were identified as potential synaptosomal miRNAs upregulated with disease progression based on AD Braak stages. Gene Ontology Enrichment and Ingenuity Pathway Analysis of synaptosomal miRNAs showed the involvement of miRNAs in nervous system development, cell junction organization, synapse assembly formation, and function of GABAergic synapse. This is the first description of synaptic versus cytosolic miRNAs in AD and their significance in synapse function.

neuroscience↗

bioRxiv2021

TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity

MotivationBuilding reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of SARS-CoV-2 strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites and millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate phylogenetic inference of resolvable phylogenetic features. ResultsWe present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. To assess topological robustness, we develop a bootstrap resampling strategy that resamples genomes spatiotemporally. The application of TopHap to build a phylogeny of 68,057 genomes (68KG) produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major variants of concern. AvailabilityTopHap is available on the web at https://github.com/SayakaMiura/TopHap. Contacts.kumar@temple.edu

bioinformatics↗

bioRxiv2021

Minor intron splicing efficiency increases with the development of lethal prostate cancer

Here we explored the role of minor spliceosome (MiS) function and minor intron-containing gene (MIG) expression in prostate cancer (PCa). We show MIGs are enriched as direct interactors of cancer-causing genes and their expression discriminates PCa progression. Increased expression of MiS U6atac snRNA, including others, and 6x more efficient minor intron splicing was observed in castration-resistant PCa (CRPC) versus primary PCa. Notably, androgen receptor signalling influenced MiS activity. Inhibition of MiS through siU6atac in PCa caused minor intron mis-splicing and aberrant expression of MIG transcripts and encoded proteins, which enriched for MAPK activity, DNA repair and cell cycle. Single cell-RNAseq confirmed cell cycle defects and lineage dependency on the MiS from primary to CRPC and neuroendocrine PCa. siU6atac was [~]50% more efficient in lowering tumor burden of CRPC cells and organoids versus current state-of-the-art combination therapy. In all, MiS is a strong therapeutic target for lethal PCa and potentially other cancers. Graphical AbstractU6atac expression, MiS activity, and minor intron splicing correlate with PCa therapy resistance and PCa progression to CRPC-adeno and transdifferentiation to CRPC-NE. One major MiS regulator during that process is the AR-axis, which is re-activated during CRPC-adeno and blocked in CRPC-NE. Molecularly, an increase in MiS dependent splicing promotes changes of transcriptome and proteome. This results in cell cycle activation, increased MAPK signalling and increased DNA repair. U6atac mediated MiS inhibition renders MiS splicing error-prone through increased intron retention and alternative splicing events, which results in cell cycle block and decreased MAPK signalling and DNA repair. MiS inhibition blocks all stages of PCa. Figure created with BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/471104v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1c1c296org.highwire.dtl.DTLVardef@1ce1416org.highwire.dtl.DTLVardef@88d842org.highwire.dtl.DTLVardef@2ddf96_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant

BackgroundEmergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. MethodsWe have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. ResultsWhole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). ConclusionDelta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.

genomics↗

bioRxiv2021

Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein

Emerging SARS-CoV-2 variants, especially those of concern, may have an impact on the viruss transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS-CoV-2 Delta variant (B.1.617.2) emerged during Indias second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, WHO identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behaviour. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this work and found that the Omicron variant had a higher affinity for human ACE2 than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor binding domain, indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the proteins core and are required for structural stability. Omicron has a higher percentage of alpha-helix structure than the Delta variant in both whole spike protein and RBD, indicating that it has a more stable structure. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.

bioinformatics↗

bioRxiv2021

SARS-CoV-2 Delta derivatives impact on neutralization of Covishield recipient sera

The emergence of SARS-CoV-2 Delta variant and its derivatives has created grave public health problem worldwide. The high transmissibility associated with this variant has led to daily increase in the number of SARS-CoV-2 infections. Delta variant has slowly dominated the other variants of concern. Subsequently, Delta has further mutated to Delta AY.1 to Delta AY.126. Of these, Delta AY.1 has been reported from several countries including India and considered to be highly infectious and probable escape mutant. Considering the possible immune escape, we had already evaluated the efficacy of the BBV152 against Delta and Delta AY.1 variants. Here, we have evaluated the neutralizing potential of sera of COVID-19 naive vaccinees (CNV) immunized with two doses of vaccine, COVID-19 recovered cases immunized with two doses of vaccine (CRV) and breakthrough infections (BTI) post immunization with two doses of vaccine against Delta, Delta AY.1 and B.1.617.3 using 50% plaque reduction neutralization test (PRNT50). Our study observed low NAb titer in CNV group against all the variants compared to CRV and BTI groups. Delta variant has shown highest reduction of 27.3-fold in NAb titer among CNV group compared to other groups and variants. Anti-S1-RBD IgG immune response among all the groups was also substantiated with NAb response. Compromised neutralization was observed against Delta and Delta AY.1 compared B.1 in all three groups. However, it provided protection against severity of the disease and fatality.

molecular biology↗

bioRxiv2021

How synchrony and metastable network dynamics are affected in fast and slow timescales with aging: Implication for Cognition

Both healthy and pathological aging exhibits gradual deterioration of structure but in-terestingly in healthy aging adults often maintains a high level of cognitive performance in a variety of cognitively demanding task till late age. What are the relevant network measures that could possibly track these dynamic changes which may be critically relevant for maintenance of cognitive functions through lifespan and how does these measures affected by the specific alterations in underlying anatomical connectivity till day remains an open question. In this work, we propose that whole-brain computational models are required to test the hypothesis that aging affects the brain network dynamics through two highly relevant network measures synchrony and metastability. Since aging entails complex processes involving multiple timescales we test the additional hypothesis that whether these two network measures remain invariant or exhibit different behavior in the fast and slow timescales respectively. The altered global synchrony and metastability with aging can be related to shifts in the dynamic working point of the system based on biophysical parameters e.g., time delay, and inter-areal coupling constrained by the underlying structural connectivity matrix.Using diffusion tensor imaging (DTI) data, we estimate structural connectivity (SC) of individual group of participants and obtain network level synchrony, metastability indexing network dynamics from resting state functional MRI data for both young and elderly participants in the age range of 18-89 years. Subsequently, we simulate a whole-brain Kuramoto model of coupled oscillators with appropriate conduction delay and interareal coupling strength to test the hypothesis of shifting of dynamic working point with age-associated alteration in network dynamics in both neural and ultraslow BOLD signal time scales. Specifically, we investigate the age-associated difference in metastable brain dynamics across large-scale neurocognitive brain networks e.g., salience network (SN), default mode network (DMN), and central executive network (CEN) to test spatio-temporal changes in default to executive coupling hypothesis with age. Interestingly, we find that the metastability of the SN increases substantially with age, whereas the metastability of the CEN and DMN networks do not substantially vary with age suggesting a clear role of conduction delay and global coupling in mediating altered dynamics in these networks. Moreover, our finding suggests that the metastability changes from slow to fast timescales confirming previous findings that variability of brain signals relates differently in slower and faster time scales with aging. However, synchrony remains invariant network measure across timescales and agnostic to the filtering of fast signals. Finally, we demonstrate both numerically and analytically longrange anatomical connections as oppose to shot-range or mid-range connection alterations is responsible for the overall neural difference in large-scale brain network dynamics captured by the network measure metastability. In summary, we propose a theoretical framework providing a systematic account of tracking age-associated variability and synchrony at multiple time scales across lifespan which may pave the way for developing dynamical theories of cognitive aging.

neuroscience↗

bioRxiv2021

Homologous recombination repair creates mutations in the non-coding genome that alter Topoisomerase-1 cleavage sites & orchestrates irinotecan resistance

Resistance to chemotherapy is a leading cause of treatment failure. Drug-resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to treatment and are selected during the treatment. However, selection of drug-resistant mutants in culture could be achieved by multiple drug exposures of cloned genetically identical cells, and thus cannot result from selection of pre-existent mutations. Accordingly, adaptation must involve generation of mutations de-novo upon drug treatment. Here we explored the origin of resistance mutations to a widely used Top1 inhibitor irinotecan, which triggers DNA breaks, causing cytotoxicity. Resistance mechanism involved gradual accumulation of recurrent mutations in non-coding regions of DNA at Top1-cleavage sites. Surprisingly, cancer cells had higher number of such sites than reference genome, which may define their increased sensitivity to irinotecan. Homologous recombination repair of DNA double strand breaks at these sites following initial drug exposures gradually reverted cleavage-sensitive "cancer" sequences back to cleavage-resistant "normal" sequences. These mutations reduced generation of DNA breaks upon subsequent exposures, thus gradually increasing the drug resistance. Together, large target size for mutations and their Top1-guided generation lead to their gradual and rapid accumulation, synergistically accelerating development of resistance. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/470089v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@d9d93forg.highwire.dtl.DTLVardef@45b88forg.highwire.dtl.DTLVardef@157cafeorg.highwire.dtl.DTLVardef@cff4a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗