Biology subjects

Joshi, A.

Publications and source records attributed to Joshi, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

AtERF60 negatively regulates ABR1 to modulate salt, drought, and basal resistance in Arabidopsis

APETALA2 (AP2)/ERF family transcription factors (TFs) contribute an important function against various external cues. Our study reports AtERF60, an AP2/ERF TF, which plays a key role in regulating the ABR1 gene, leading to an altered basal resistance response in Arabidopsis. AtERF60 is induced in response to drought, salt, abscisic acid (ABA), salicylic acid (SA), and bacterial pathogen PstDC3000 infection. AtERF60 interacts with DEHYDRATION RESPONSE ELEMENTS and GCC box, indicating its ability to regulate multiple responses. The overexpressing lines of AtERF60 demonstrated increased resistance to PstDC3000 infection, whereas erf60 mutant lines showed increased susceptibility. Complementation of the erf60 mutant background exhibits no significant difference towards PstDC3000 infection compared with the WT Col-0. Microarray and qRT-PCR analysis of overexpression and mutant lines indicated that AtERF60 regulates stress-inducible genes. The induction of these differentially expressed transcripts was significantly increased in erf60 mutant lines, whereas it was reversed in wild-type lines when AtERF60 was complemented. ABR1 was one of the differentially expressed transcripts, and we discovered that AtERF60 interacts with the DRE cis-elements in the ABR1 promoter. Further, qRT-PCR expression analysis after infection with PstDC3000 in AtERF60-OX, erf60 and its complementation background suggest that the mutation in AtERF60 upregulates ABR1 activity, leading to the enhanced susceptibility towards PstDC3000. Conversely, AtERF60 overexpression suppresses ABR1 activity, strengthening the basal resistance responses of Arabidopsis.

plant biology↗

bioRxiv2021

mRNA-1273 and Ad26.COV2.S vaccines protect against the B.1.621 variant of SARS-CoV-2

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, viral variants with greater transmissibility or immune evasion properties have arisen, which could jeopardize recently deployed vaccine and antibody-based countermeasures. Here, we evaluated in mice and hamsters the efficacy of preclinical non-GMP Moderna mRNA vaccine (mRNA-1273) and the Johnson & Johnson recombinant adenoviral-vectored vaccine (Ad26.COV2.S) against the B.1.621 (Mu) South American variant of SARS-CoV-2, which contains spike mutations T95I, Y144S, Y145N, R346K, E484K, N501Y, D614G, P681H, and D950N. Immunization of 129S2 and K18-human ACE2 transgenic mice with mRNA-1273 vaccine protected against weight loss, lung infection, and lung pathology after challenge with B.1.621 or WA1/2020 N501Y/D614G SARS-CoV-2 strain. Similarly, immunization of 129S2 mice and Syrian hamsters with a high dose of Ad26.COV2.S reduced lung infection after B.1.621 virus challenge. Thus, immunity induced by mRNA-1273 or Ad26.COV2.S vaccines can protect against the B.1.621 variant of SARS-CoV-2 in multiple animal models.

microbiology↗

bioRxiv2021

SARS-CoV-2 spike conformation determines plasma neutralizing activity

Numerous safe and effective COVID-19 vaccines have been developed that utilize various delivery technologies and engineering strategies. The influence of the SARS-CoV-2 spike (S) glycoprotein conformation on antibody responses induced by vaccination or infection in humans remains unknown. To address this question, we compared plasma antibodies elicited by six globally-distributed vaccines or infection and observed markedly higher binding titers for vaccines encoding a prefusion-stabilized S relative to other groups. Prefusion S binding titers positively correlated with plasma neutralizing activity, indicating that physical stabilization of the prefusion conformation enhances protection against SARS-CoV-2. We show that almost all plasma neutralizing activity is directed to prefusion S, in particular the S1 subunit, and that variant cross-neutralization is mediated solely by RBD-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants and longer durability than current technologies.

immunology↗

bioRxiv2021

Temporal in vivo platelet labelling in mice reveals age-dependent receptor expression and conservation of specific mRNAs

The proportion of young platelets, also known as newly formed or reticulated, within the overall platelet population has been clinically correlated with adverse cardiovascular outcomes. Our understanding of this is incomplete, however, because of limitations in the technical approaches available to study platelets of different ages. In this study we have developed and validated an in vivo temporal labelling approach using injectable fluorescent anti-platelet antibodies to sub-divide platelets by age and assess differences in functional and molecular characteristics. With this approach we found that young platelets (<24h old) in comparison to older platelets respond to stimuli with greater calcium flux and degranulation, and contribute more to the formation of thrombi in vitro and in vivo. Sequential sampling confirmed this altered functionality to be independent of platelet size with no size differences or changes relative to the global population seen at any age. The age associated decrease in thrombotic function was accompanied by significant decreases in the surface expression of GPVI and CD31 (PECAM-1) and an increase in CD9. Platelet mRNA content also decreased with age but at different rates for individual mRNAs indicating apparent conservation of those encoding granule proteins. Our pulse-chase type approach to define circulating platelet age has allowed timely re-examination of commonly held beliefs regarding size and reactivity of young platelets whilst providing novel insights into the temporal regulation of receptor and protein expression. Overall, future application of this validated tool will inform on age-based platelet heterogeneity in physiology and disease.

physiology↗

bioRxiv2021

Delta breakthrough infections elicit potent, broad and durable neutralizing antibody responses

The SARS-CoV-2 Delta variant is currently responsible for most infections worldwide, including among fully vaccinated individuals. Although these latter infections are associated with milder COVID-19 disease relative to unvaccinated subjects, the specificity and durability of antibody responses elicited by Delta breakthrough cases remain unknown. Here, we demonstrate that breakthrough infections induce serum binding and neutralizing antibody responses that are markedly more potent, durable and resilient to spike mutations observed in variants of concern than those observed in subjects who were infected only or received only two doses of COVID-19 vaccine. However, wee show that Delta breakthrough cases, subjects who were vaccinated after SARS-CoV-2 infection and individuals vaccinated three times (without infection) have serum neutralizing activity of comparable magnitude and breadth indicate that multiple types of exposure or increased number of exposures to SARS-CoV-2 antigen(s) enhance spike-specific antibody responses. Neutralization of the genetically divergent SARS-CoV, however, was moderate with all four cohorts examined, except after four exposures to the SARS-CoV-2 spike, underscoring the importance of developing vaccines eliciting broad sarbecovirus immunity for pandemic preparedness.

immunology↗

bioRxiv2021

Characterizing Protein Conformational Spaces using Dimensionality Reduction and Algebraic Topology

Datasets representing the conformational landscapes of protein structures are high dimensional and hence present computational challenges. Efficient and effective dimensionality reduction of these datasets is therefore paramount to our ability to analyze the conformational landscapes of proteins and extract important information regarding protein folding, conformational changes and binding. Representing the structures with fewer attributes that capture the most variance of the data, makes for quicker and precise analysis of these structures. In this work we make use of dimensionality reduction methods for reducing the number of instances and for feature reduction. The reduced dataset that is obtained is then subjected to topological and quantitative analysis. In this step we perform hierarchical clustering to obtain different sets of conformation clusters that may correspond to intermediate structures. The structures represented by these conformations are then analyzed by studying their high dimension topological properties to identify truly distinct conformations and holes in the conformational space that may represent high energy barriers. Our results show that the clusters closely follow known experimental results about intermediate structures, as well as binding and folding events.

bioinformatics↗

bioRxiv2021

Structure, receptor recognition and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein

The recent isolation of CCoV-HuPn-2018 from a child respiratory swab indicates that more coronaviruses are spilling over to humans than previously appreciated. Here, we determined cryo-electron microscopy structures of the CCoV-HuPn-2018 spike glycoprotein trimer in two distinct conformational states and identified that it binds canine, feline and porcine aminopeptidase N (APN encoded by ANPEP) orthologs which serve as entry receptors. Introduction of an oligosaccharide at position N739 of human APN renders cells susceptible to CCoV-HuPn-2018 spike-mediated entry, suggesting that single nucleotide polymorphisms could account for the detection of this virus in some individuals. Human polyclonal plasma antibodies elicited by HCoV-229E infection and a porcine coronavirus monoclonal antibody inhibit CCoV-HuPn-2018 S-mediated entry, indicating elicitation of cross-neutralizing activity among -coronaviruses. These data provide a blueprint of the CCoV-HuPn-2018 infection machinery, unveil the viral entry receptor and pave the way for vaccine and therapeutic development targeting this zoonotic pathogen.

microbiology↗

bioRxiv2021

Density-dependent selection in Drosophila: evolution of egg size and hatching time

Many different laboratory studies of adaptation to larval crowding in Drosophila spp. have all yielded the evolution of pre-adult competitive ability, even though the ecological context in which crowding was experienced varied across studies. However, the evolution of competitive ability was achieved through different suites of traits in studies wherein crowding was imposed in slightly different ways. Earlier studies showed the evolution of increased competitive ability via increased larval feeding rate and tolerance to nitrogenous waste, at the cost of food to biomass conversion efficiency. However, more recent studies, with crowding imposed at relatively low food levels, showed the evolution of competitive ability via decreased larval development time and body size, and an increase in the time efficiency of conversion of food to biomass, with no change in larval feeding rate or waste tolerance. Taken together, these studies have led to a more nuanced understanding of how the specific details of larval numbers, food amounts etc. can affect which traits evolve to confer increased competitive ability. Here, we report results from a study in which egg size and hatching time were assayed on three sets of populations adapted to larval crowding experienced in slightly different ways, as well as their low density ancestral control populations. Egg size and hatching time are traits that may provide larvae with initial advantages under crowding through increased starting larval size and a temporal head-start, respectively. In each set of populations adapted to some form of larval crowding, the evolution of longer and wider eggs was seen, compared to controls, thus making egg size the first consistent correlate of the evolution of increased larval competitive ability across Drosophila populations experiencing crowding in slightly different ways. Among the crowding-adapted populations, those crowded at the lowest overall eggs/food density, but the highest density of larvae in the feeding band, showed the largest eggs, on an average. All three sets of crowding-adapted populations showed shorter average egg hatching time than controls, but the difference was significant only in the case of populations experiencing the highest feeding band density. Our results underscore the importance of considering factors other than just eggs/food density when studying the evolution of competitive ability, as also the advantages of having multiple selection regimes within one experimental set up, allowing for a more nuanced understanding of the subtlety with which adaptive evolutionary trajectories can vary across even fairly similar selection regimes.

evolutionary biology↗

bioRxiv2021

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry

Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures effective against SARS-CoV-2 variants and future spillovers of other sarbecoviruses. Here we describe the isolation and characterization of a human monoclonal antibody, designated S2K146, broadly neutralizing viruses belonging to all three sarbecovirus clades known to utilize ACE2 as entry receptor and protecting therapeutically against SARS-CoV-2 beta challenge in hamsters. Structural and functional studies show that most of the S2K146 epitope residues are shared with the ACE2 binding site and that the antibody inhibits receptor attachment competitively. Viral passaging experiments underscore an unusually high barrier for emergence of escape mutants making it an ideal candidate for clinical development. These findings unveil a key site of vulnerability for the development of a next generation of vaccines eliciting broad sarbecovirus immunity.

immunology↗

bioRxiv2021

Interleukin-33 coordinates a microglial phagocytic response and limits corticothalamic excitability and seizure susceptibility

Microglia are key remodelers of neuronal synapses during brain development, but the mechanisms that regulate this process and its ultimate impact on neural circuit function are not well defined. We previously identified the IL-1 family cytokine Interleukin-33 (IL-33) as a novel mediator of microglial synapse remodeling. Here we define the phagocytic program induced in microglia in response to IL-33. We find that IL-33 markedly alters the microglial enhancer landscape and exposes AP-1 transcription factor sites that promote target gene expression. We identify the scavenger receptor MARCO and the pattern recognition receptor TLR2 as downstream mediators of IL-33 dependent synapse engulfment. Conditional deletion of IL-33 in the CNS or its receptor on microglia results in increased numbers of excitatory synapses in the corticothalamic circuit and spontaneous epileptiform activity as well as increased seizure susceptibility by early adulthood. These findings define novel mechanisms through which IL-33 coordinates experience-dependent synaptic refinement to restrict hyperexcitability in the developing brain.

neuroscience↗

bioRxiv2021

Proteome and functional decline as platelets age in the circulation

Anucleate platelets circulate in the blood of healthy individuals for approximately 7-10 days during which time their protein composition may change. We hypothesized such changes would be linked to altered structure and function. Here, we separated platelets of different ages based on mRNA content and characterised them using proteomics, immunofluorescence and functional assays. Total protein content was 45{+/-}5% (n=4) lower in old platelets compared to young platelets. Predictive proteomic pathway analysis identified associations with 28 biological processes, notably increased haemostasis in young platelets and apoptosis in old platelets. Further studies confirmed platelet ageing was linked to a reduction decrease in cytoskeletal proteins, a reduction in mitochondria number, and lower calcium dynamics and granule secretion. This work delineates physical and functional changes in platelets as they age and serves as a base to examine differences associated with altered mean age of platelet populations in conditions such as immune thrombocytopenia and diabetes.

cell biology↗

bioRxiv2021

Extremely rapid development and early reproduction reduces sexual selection in D. melanogaster populations.

The role of sexual selection in mediating levels of sexual conflict has been demonstrated in many experimental evolution studies on Drosophila spp. where competition among males for mating was the target of selection. Sexual selection has also been shown to affect the evolution of life-histories. However, the influence of divergent life-histories on reproductive strategies and, therefore, sexual selection and possibly sexual conflict, has been less well studied. We examined D. melanogaster populations selected for a short development time and early age at reproduction for changes in reproductive behaviour and traits that are proxies of sexual selection. We report a large reduction in reproductive competition experienced by the males of these populations, compared to ancestral populations that are not consciously selected for rapid development or early reproduction, potentially leading to reduced sexual selection. We show that rapidly developing and early reproducing populations have very low levels of mating in their lifetime (females are more or less monandrous), low courtship levels, shorter copulation duration, and longer time from eclosion to first mating, compared to the controls. These results are discussed in the context of the previously demonstrated reduction of inter-locus sexual conflict in these populations. We show that life-history strategies might have a large and significant impact on sexual selection, with each influencing the other and contributing to the complexities of adaptation. Significance statementSexual conflict, often manifested as an arms-race between males and females trying to enhance their own reproductive success at some cost to the other, is of great evolutionary interest because it can maintain genetic variation in populations, prevent the independent optimization of male and female traits, and also promote speciation. Sexual selection, or variation in mating success, is well known to affect levels of sexual conflict. However, it is not so clear whether, and how, the regular evolution of life-histories also affects sexual selection. Here, we show that life-history evolution in fruit fly populations selected for traits not directly related to sexual conflict might, nevertheless, mediate the possible evolution of altered sexual conflict levels through effects on sexual selection. Populations that evolved to develop to adulthood fast, and reproduce relatively early in life, are shown to potentially experience less sexual selection, which can explain the low sexual conflict levels earlier observed in them.

evolutionary biology↗

bioRxiv2021

A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

The emergence of antigenically distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility is a public health threat. Some of these variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies, which principally target the receptor binding domain (RBD) on the virus spike glycoprotein. Here, we describe 2C08, a SARS-CoV-2 mRNA vaccine-induced germinal center B cell-derived human monoclonal antibody that binds to the receptor binding motif within the RBD. 2C08 broadly neutralizes SARS-CoV-2 variants with remarkable potency and reduces lung inflammation, viral load, and morbidity in hamsters challenged with either an ancestral SARS-CoV-2 strain or a recent variant of concern. Clonal analysis identified 2C08-like public clonotypes among B cell clones responding to SARS-CoV-2 infection or vaccination in at least 20 out of 78 individuals. Thus, 2C08-like antibodies can be readily induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern. One Sentence SummaryProtection against SARS-CoV-2 variants by a potently neutralizing vaccine-induced human monoclonal antibody.

immunology↗

bioRxiv2021

Evolution of lower levels of inter-locus sexual conflict in D. melanogaster populations under strong selection for rapid development.

D. melanogaster laboratory populations subjected to selection for rapid development and early reproduction have been found to have evolved reduced adult body size and lower levels of inter-locus sexual conflict compared to their ancestral controls. We tested the contribution of a smaller body to the evolution of reduced sexual conflict in these populations, since body size differences are known to affect sexual conflict levels in this species. We cultured larvae from the control populations at high density to obtain flies as small as those from the selected populations. The effect of body size reduction on sexual conflict was asymmetric, with smaller body size resulting in reduced male manipulative ability but not female resistance to mating-induced harm. These results were not due to differences in behavioural patterns of smaller flies, such as differences in overall mating exposure of females to different types of males. We hypothesize that evolution for rapid development and the correlated reduction in body size has resulted in lower male manipulative ability, and sexually antagonistic co-evolution has lowered female resistance to such manipulations. These populations have also evolved incipient reproductive isolation from their controls, likely through sexual conflict (reported earlier), and our results support the view that this is an outcome of strong, directional selection for rapid development.

evolutionary biology↗

bioRxiv2021

Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients

We present an updated version of our automated computational pipeline, Infection Pathogen Detector IPD 2.0 with a SARS-CoV-2 module, to perform genomic analysis to understand the pathogenesis and virulence of the virus. Analysing the currently available 208911 SARS-CoV2 genome sequences (as accessed on 28 Dec 2020), we generate an extensive database of sample- wise variants and clade annotation, which forms the core of the SARS-CoV-2 analysis module of the analysis pipeline. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil along with data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Thus, the persistence of pandemic may lead to the emergence of newer regional strains with improved fitness. IPD 2.0 also adopts the recent dynamic clade nomenclature and shows improvement in accuracy of clade assignment, processing time and portability, to its predecessor and thus could be a vital tool to help facilitate genomic surveillance in a population to identify variants involved in breakthrough infections.

bioinformatics↗

bioRxiv2021

Multiple Shoot Regeneration from Excised Embryonic Axis Explants of Jute, Corchorus capsularis cv. JRC321

Interspecific hybrids development by traditional breeding is challenging because of the incompatibility between two cultivated species of genus Corchorus. Under this condition, plant genetic transformation is an alternative tool for the improvement of jute cultivar. In the present study, in vitro multiple shoot regeneration protocol has been developed in jute (Corchorus capsularis cv. JRC 321) from excised embryonic axis as an explant by removing cotyledons, radicle, and tip of epicotyl. The explant is cultured in medium SMM1 supplemented with BAP (1.0 mg/L) for one week and sub-cultured in SMM6 containing IBA (0.5 mg/L) and BAP (0.2 mg/L). Direct adventitious shoot bud formation was observed from cotyledonary nodes and the adjacent region of excised embryonic axis. Interestingly, shoot bud formation was reduced when excised explants with intact epicotyl were cultured in the media combination (SMM1+SMM6) indicating the presence of apical dominance might be the cause of fewer shoot bud formation. While, hypocotyl explants did not produce any shoot in this media combination because nodal meristem was removed. However, the shoot buds developed from the excised embryonic axis were differentiated successfully into multiple shoots and showed further elongation in SMM6 which ultimately rooted in MS-B5 medium (+0.5 mg/L IBA). The plants were transferred successfully in the glasshouse conditions and appeared phenotypically normal.

plant biology↗

bioRxiv2020

Midbrain and lateral nucleus accumbens dopamine depletion affects free-choice high-fat high-sugar diet preference in male rats

Dopamine influences food intake behavior. Reciprocally, food intake, especially of palatable dietary items, can modulate dopamine-related brain circuitries. Among these reciprocal impacts, it has been observed that an increased intake of dietary fat results in blunted dopamine signaling and, to compensate this lowered dopamine function, caloric intake may subsequently increase. To determine how dopamine regulates food preference we did 6-hydroxydopamine (6-OHDA) lesions, depleting dopamine in specific brain regions in male Sprague Dawley rats. The food preference was assessed by providing the rats with free choice access to control diet, fat, 20% sucrose and tap water. Rats with midbrain lesions targeting the substantia nigra (which is also a model of Parkinsons disease) consumed fewer calories, as reflected by a decrease in control diet intake, but they surprisingly displayed an increase in fat intake, without change in the sucrose solution intake compared to sham animals. To determine which of the midbrain dopamine projections may contribute to this effect, we next compared the impact of 6-OHDA lesions of terminal fields, targeting the dorsal striatum, the lateral nucleus accumbens and the medial nucleus accumbens. We found that 6-OHDA lesion of the lateral nucleus accumbens, but not of the dorsal striatum or the medial nucleus accumbens, led to increased fat intake. These findings indicate a role for lateral nucleus accumbens dopamine in regulating food preference, in particularly the intake of fat. HIGHLIGHTSO_LIDopamine influences fat intake C_LIO_LIAnimal model of Parkinsons disease display lower kcal intake but increased fat choice C_LIO_LIDopamine depletion in the lateral nucleus accumbens favors fat intake C_LI

neuroscience↗

bioRxiv2020

Degeneracy and stability in neural circuits of neuromodulators

Degenerate neural circuits perform the same function despite being structurally different. However, it is unclear whether neural circuits with interacting neuromodulator sources can themselves be degenerate while maintaining the same neuromodulatory function. Here, we address this by computationally modelling the neural circuits of neuromodulators serotonin and dopamine, local glutamatergic and GABAergic interneurons, and their possible interactions, under reward/punishment-based conditioning tasks. The neural modelling is constrained by relevant experimental studies of the VTA or DRN system using e.g. electrophysiology, optogenetics, and voltammetry. We first show that a single parsimonious, sparsely connected neural circuit model can recapitulate several separate experimental findings that indicated diverse, heterogeneous, distributed and mixed DRN-VTA neuronal signalling in reward and punishment tasks. The inability for this model to recapitulate all observed neuronal signalling suggests potentially multiple circuits acting in parallel. Then using computational simulations and dynamical systems analysis, we demonstrate that several different stable circuit architectures can produce the same observed network activity profile, hence demonstrating degeneracy. Due to the extensive D2-mediated connections in the investigated circuits, we simulate D2 receptor agonist by increasing the connection strengths emanating from the VTA DA neurons. We found that the simulated D2 agonist can distinguish among sub-groups of the degenerate neural circuits based on substantial deviations in specific neural populations activities in reward and punishment conditions. This forms a testable model prediction using pharmacological means. Overall, this theoretical work suggests the plausibility of degeneracy within neuromodulator circuitry and has important implication for the stable and robust maintenance of neuromodulatory functions.

neuroscience↗