Biology subjects

Pandey, P.

Publications and source records attributed to Pandey, P..

At least 55 records · Page 3Linked to original sources

bioRxiv2021

Self-ubiquitination of a pathogen type-III effector traps and blocks the autophagy machinery to promote disease

Beyond its role in cellular homeostasis, autophagy plays anti- and pro-microbial roles in host-microbe interactions, both in animals and plants. One prominent role of anti-microbial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in depletion of a bacterial virulence factor and unravels an unprecedented pathogen strategy to counteract defense-related autophagy.

plant biology↗

bioRxiv2021

An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees

MotivationIn the past few years, researchers have proposed numerous indexing schemes for searching large databases of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes--Mantis, VariMerge, and Bifrost--that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data. ResultsIn this paper, we show how to build a scalable and updatable exact sequence-search index. Specifically, we extend Mantis using the Bentley-Saxe transformation to support efficient updates. We demonstrate Mantiss scalability by constructing an index of{approx} 40K samples from SRA by adding samples one at a time to an initial index of 10K samples. Compared to VariMerge and Bifrost, Mantis is more efficient in terms of index-construction time and memory, query time and memory, and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Mantis scaled to more than 39K samples. Queries were over 24x faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Mantis indexes were about 2.5x smaller than Bifrosts indexes and about half as big as VariMerges indexes. AvailabilityThe updatable Mantis implementation is available at https://github.com/splatlab/mantis/tree/mergeMSTs. Contactrob@cs.umd.edu Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2021

Pupillary aperture is a potential biomarker ofmovement preparation

In response to variable light intensity, the pupils reflexively constrict or dilate to maintain a uniform retinal illumination. The pupillary light reflex (PLR) pathway receives projections from two important areas in primates brain that plan rapid saccadic eye-movement - frontal eye field (FEF) and superior colliculus (SC). The speed with which neurons in these areas increase firing rate to a threshold determines latency of a saccade. Micro-stimulation of FEF/SC neurons below this threshold modulates the magnitude of PLR. Nonetheless, how the saccade latency and pupil dynamics are related remains unknown. Our study shows that the appearance of a bright stimulus evokes pupil constriction at higher rate when the latency of impending saccade to the stimulus is shorter. This inverse relationship between the rate of pupil constriction and the saccade latency is robust irrespective of the reward outcome. In a homeomorphic biomechanical model of pupil, we have projected build-up signal similar to FEF and SC activity to the parasympathetic and sympathetic divisions of the PLR pathway, respectively. Model simulation mimics the observed data to indicate that the FEF and SC activity for eye movement modulates autonomic input to the pupillary muscle plant. A striking similarity between the dynamics of pupil constriction and stochastic rise in neural activity for saccade elicitation suggests that PLR is a potential proxy of movement preparation, and not mere an indicator of attentional orientation. Our study suggests a mechanism of how the retinal luminosity is timely regulated to aid perception by minimizing visual transients due to gaze orientation.

neuroscience↗

bioRxiv2020

Localized Proteotoxic Stress in Mitochondrial Intermembrane Space and Matrix Elicits Sub-compartment Specific Response Pathways Governed by Unique Modulators

The double-membrane-bound architecture of mitochondria, essential for ATP production, sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix possess contrasting oxido-reductive environments and distinct protein quality control (PQC) machineries resulting different protein folding environments. To understand the nature of stress response elicited by equivalent proteotoxic stress to sub-mitochondrial compartments, we fused well-described bipartite or matrix-targeting signal sequences to misfolding and aggregation-prone stressor proteins to target and impart stress to yeast mitochondrial IMS or matrix. We show, mitochondrial proteotoxicity leads to growth arrest of yeast cells of varying degrees depending on nature of stressor proteins and the intra-mitochondrial location of stress. Next, using transcriptomics and proteomics, we report a comprehensive stress response elicited by two types of targeting signal-fused stressor proteins. Among global responses by mitochondria-targeted stressors by both types of signal sequences, an adaptive response of abrogated mitochondrial respiration and concomitant upregulation of glycolysis is uncovered. Beyond shared stress responses, specific signatures due to stress within mitochondrial sub-compartments are also revealed. We report that bipartite signal sequence-fused stressor proteins eliciting stress to IMS, leads to specific upregulation of IMS-chaperones and TOM complex components. In contrast, matrix-targeted stressors lead to specific upregulation of matrix-chaperones and cytosolic PQC components. Finally, by systematic genetic interaction using deletion strains of differentially upregulated genes, we found prominent modulatory role of TOM complex components during IMS-stress response. In contrast, VMS1 markedly modulates the stress response originated from matrix.

cell biology↗

bioRxiv2020

Altering the solubility of the antibiotic candidate Nisin - a computational study

The growing bacterial resistance to available antibiotics makes it necessary to look for new drug candidates. An example is a lanthionine-containing nisin, which has a broad spectrum of antimicrobial activity. While nisin is widely utilized as a food preservative, its poor solubility and low stability at physiological pH hinder its use as an antibiotic. As the solubility of nisin is controlled by the residues of the hinge region, we have performed molecular dynamics simulations of various mutants and studied their effects on nisins solubility. These simulations are complicated by the presence of two uncommon residues (dehydroalanine and dehydrobutyrine) in the peptide. The primary goal of the present study is to derive rules for designing new mutants that will be more soluble at physiological pH and, therefore, may serve as a basis for the future antibiotic design. Another aim of our study is to evaluate whether existing force fields can model the solubility of these amino acids accurately, in order to motivate further developments of force fields to account for solubility information.

biophysics↗

bioRxiv2020

Does visitation dictate animal welfare in captivity? A case study of tigers and leopards from National Zoological Park, New Delhi

Zoological Parks serve a salient purpose of entertaining many visitors by housing various exclusive animal species. Big cats like tigers and leopard are among the most visited species in zoos globally. We investigated the behavioral response of the zoo-housed big cats to visitor densities and noise. We also aimed to understand the relationship between stereotypy, animal history, feeding schedules, and enclose design. The behavior of eight big cats housed in the National Zoological Park, New Delhi, was monitored using the focal sampling technique during the May and June 2019 to construct the ethograms. We also recorded the visitor density, ambient noise, for the same duration. Both species were found devoting a significant amount (>50%) of time in displaying inactive behaviors. Tigers and leopards performed stereotypic behaviors for 22% and 28% of their time, respectively. Pearson chi-square analysis revealed a significant variation of stereotypy in association with biological (age, sex, and rearing history) and captive (enclosure design) variables. Big cats stereotypic behaviors were found significantly influenced by the high visitor density. However, ambient noise did not impact the stereotypy of both the felid species. Visitors form an integral part of zoos, and their detrimental impact diminishes the well-being of captive animals. This study revealed that tigers and leopards in NZP display a high proportion of inactive and stereotypic behaviors. Thus, we suggest zoo authorities adopt more enclosure enrichment initiatives.

animal behavior and cognition↗

bioRxiv2020

Gone in 40 years, the curious case of the Himalayan Quail: an attempt at rediscovery and implications for conservation

Himalayan Quail (Ophrysia superciliosa) is a Galliforme species currently classified as Critically Endangered by the IUCN. Given the fact that the species has only been recorded over a period of 40 years in the 19th century, this classification needs more scrutiny. The aim of this study was to explore the possibility of detecting the species in their known historical distribution in the lower Himalayas, and understand if possible, the factors which led to their decline or extinction. The potential habitats in districts of Nainital and Dehradun of Uttrakhand (India), where the species which has been recorded between 1836 to 1876, have been scoured thoroughly insofar as logistics and other factors permitted using trail and point transects. We did not detect any sign of the species in any of the areas, thereby corroborating the results of past surveys/expeditions in search of this species. Domesticated/feral species (grazing pressure and hunting by dogs), natural predation by species such as Yellow-throated Marten (Martes flavigula), hunting by humans, population growth and resulting land-use change, biogeochemical events, and tourism may all have contributed in varying degrees to their decline or extinction. It was found that most, if not all, proposals of strategies to find the species have been thus far unemployed or futile. We suggest improving the chances of re-discovering this species using tools such as molecular/genetic analysis and Unmanned Aerial Vehicles. Management recommendations include stress on grazing laws, sterilization of dogs, awareness about unchecked human population growth and measures for limiting the effects of unsustainable tourism.

ecology↗

bioRxiv2020

The Irish potato famine pathogen subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface

Eukaryotic cells deploy autophagy to eliminate invading microbes. In turn, pathogens have evolved effector proteins to counteract antimicrobial autophagy. How and why adapted pathogens co-opt autophagy for their own benefit is poorly understood. The Irish famine pathogen Phythophthora infestans secretes the effector protein PexRD54 that selectively activates an unknown plant autophagy pathway, while antagonizing antimicrobial autophagy. Here we show that PexRD54 induces autophagosome formation by bridging small GTPase Rab8a-decorated vesicles with autophagic compartments labelled by the core autophagy protein ATG8CL. Rab8a is required for pathogen-triggered and starvation-induced but not antimicrobial autophagy, revealing that specific trafficking pathways underpin selective autophagy. We discovered that Rab8a contributes to basal immunity against P. infestans, but PexRD54 diverts a sub-population of Rab8a vesicles to lipid droplets that associate with autophagosomes. These are then diverted towards pathogen feeding structures that are accommodated within the host cells. We propose that PexRD54 mimics starvation-induced autophagy by channeling host endomembrane trafficking towards the pathogen interface possibly to acquire nutrients. This work reveals that effectors can interconnect independent host compartments to stimulate complex cellular processes that benefit the pathogen. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/000117v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@bfc9fforg.highwire.dtl.DTLVardef@166b5f8org.highwire.dtl.DTLVardef@34d581org.highwire.dtl.DTLVardef@ad397f_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2020

Poxvirus-encoded TNF receptor homolog dampens inflammation and protects the host from uncontrolled lung pathology and death during respiratory infection

Ectromelia virus (ECTV) causes mousepox, a surrogate mouse model for smallpox caused by variola virus in humans. Both viruses encode tumor necrosis factor receptor (TNFR) homologs termed cytokine response modifier (Crm) proteins, containing a TNF-binding domain and a chemokine-binding domain termed smallpox virus-encoded chemokine receptor (SECRET) domain. Infection of ECTV-resistant C57BL/6 mice with an ECTV CrmD deletion mutant resulted in uniform mortality due to excessive TNF secretion and dysregulated inflammatory cytokine production but viral load was not affected. CrmD dampened lung pathology, leukocyte recruitment and inflammatory cytokines including TNF, IL-6, IL-10 and IFN-{gamma}. Blockade of IL-6, IL-10R or TNF function with monoclonal antibodies reduced lung pathology and provided 60-100% protection from an otherwise lethal infection. IFN-{gamma} caused lung pathology only when both the TNF-binding and SECRET domains were deleted but it was neither necessary nor sufficient to cause pathology when only the CrmD SECRET domain was expressed by virus.

immunology↗

bioRxiv2019

VariantStore: A Large-Scale Genomic Variant Search Index

The ability to efficiently query genomic variants from thousands of samples is critical to achieving the full potential of many medical and scientific applications such as personalized medicine. Performing variant queries based on coordinates in the reference or sample sequences is at the core of these applications. Efficiently supporting variant queries across thousands of samples is computationally challenging. Most solutions only support queries based on the reference coordinates and the ones that support queries based on coordinates across multiple samples do not scale to data containing more than a few thousand samples. We present VariantStore, a system for efficiently indexing and querying genomic variants and their sequences in either the reference or sample-specific coordinate systems. We show the scalability of VariantStore by indexing genomic variants from the TCGA-BRCA project containing 8640 samples and 5M variants in 4 Hrs and the 1000 genomes project containing 2500 samples and 924M variants in 3 Hrs. Querying for variants in a gene takes between 0.002 - 3 seconds using memory only 10% of the size of the full representation.

bioinformatics↗

bioRxiv2019

TNF deficiency dysregulates inflammatory cytokine production leading to lung pathology and death during respiratory poxvirus infection

Excessive tumor necrosis factor (TNF) is known to cause significant pathology. Paradoxically, deficiency in TNF (TNF-/-) also caused significant pathology during respiratory ectromelia virus (ECTV) infection, a surrogate mouse model for smallpox. TNF-/- mice succumbed to fulminant disease whereas wild-type mice, and those expressing only transmembrane TNF, recovered. TNF deficiency did not affect viral load or leukocyte recruitment but caused severe lung pathology and excessive production of the cytokines IL-6, IL-10, TGF-{beta}, and IFN-{gamma}. Blockade of these cytokines reduced lung pathology concomitant with induction of protein inhibitor of activated STAT3 (PIAS3) and/or suppressor of cytokine signaling 3 (SOCS3), factors that inhibit STAT3 activation. Short-term inhibition of STAT3 activation in ECTV-infected TNF-/- mice with an inhibitor reduced lung pathology. TNF is essential for regulating inflammation and its deficiency exacerbates ECTV infection as a consequence of significant lung pathology caused by dysregulation of inflammatory cytokine production, in part via overactivation of STAT3.

immunology↗

bioRxiv2019

Loss of dop-2 causes increased dopamine release and locomotory defects in the presence of ethanol

Ethanol is a widely used drug, excessive consumption of which could lead to medical conditions with diverse symptoms. Ethanol abuse causes disinhibition of memory, attention, speech and locomotion across species. Dopamine signaling plays an essential role in ethanol dependent behaviors in animals ranging from C. elegans to humans. We devised an ethanol dependent assay in which mutants in the dopamine autoreceptor, dop-2, displayed a unique sedative locomotory behavior causing the animals to move in circles while dragging the posterior half of their body. We identify the posterior dopaminergic sensory neuron as being essential to modulate this behavior. We further demonstrate that in dop-2 mutants, ethanol exposure increases dopamine secretion and results in enhanced function of the DVA interneuron. DVA releases the neuropeptide NLP-12 and leads to the excitation of cholinergic motor neurons that affect movement. Thus, DOP-2 modulates dopamine levels at the synapse and regulates alcohol induced movement through NLP-12.

neuroscience↗

bioRxiv2019

Wheat inositol pyrophosphate kinase (TaVIH2-3B) interacts with Fasciclin-like arabinogalactan (FLA6) protein and alters the plant cell-wall composition

BackgroundInositol pyrophosphates (PP-InsPs) are high-energy cellular molecules involved in different signalling and regulatory responses. Two distinct classes of inositol phosphate kinases responsible for the synthesis of PP-InsPs have been identified in Arabidopsis i.e. ITPKinase (inositol 1,3,4 trisphosphate 5/6 kinase) and PP-IP5Kinase (diphosphoinositol pentakisphosphate kinases). Plant PP-IP5Ks are capable of synthesizing InsP8 and were shown to control pathogenic defence and phosphate response signals. However, other roles offered by plant PP-IP5Ks, especially towards abiotic stress, remain poorly understood. ResultsHere, we characterized two Triticum aestivum L. (hexaploid wheat) PPIP5K homologs, TaVIH1 and TaVIH2, for their physiological functions. We demonstrated that wheat VIH proteins could utilize InsP7 as the substrate to produce InsP8, a process that requires the functional VIH-kinase domains. At the transcriptional level, both TaVIH1 and TaVIH2 are expressed in different wheat tissues, including developing grains, but show selective response to abiotic stresses during drought-mimic experiments. Overexpression of TaVIH2-3B homolog in Arabidopsis conferred tolerance to drought stress and rescued the sensitivity of Atvih2 mutants. RNAseq analysis of TaVIH2-3B transgenic lines of Arabidopsis showed a genome-wide reprogramming with remarkable effects on cell-wall biosynthesis genes with enhanced the accumulation of polysaccharides (arabinogalactan, cellulose and arabinoxylan). ConclusionsOverall, this work identifies a novel function of VIH proteins, implying their roles in modulating cell-wall homeostasis genes and providing water-deficit stress tolerance. This work suggests that the plant VIH enzymes could be linked to drought tolerance and also opens up investigations to address the roles of plant VIH derived products in generating drought resistant plants.

plant biology↗

bioRxiv2019

The mechanisms of dynamin-actin interaction

Cell-cell fusion is an indispensable process in the conception, development and physiology of multicellular organisms. Here we demonstrate a direct and noncanonical role for dynamin, best known as a fission GTPase in endocytosis, in cell-cell fusion. Our genetic and cell biological analyses show that dynamin colocalizes within the F-actin-enriched podosome-like structures at the fusogenic synapse, which is required for generating invasive membrane protrusions and myoblast fusion in vivo, in an endocytosis-independent manner. Biochemical, negative stain EM and cryo-electron tomography (cryo-ET) analyses revealed that dynamin forms helices that directly bundles actin filaments by capturing multiple actin filaments at their outer rim via interactions with dynamins proline-rich domain. GTP hydrolysis by dynamin triggers disassembly of the dynamin helix, exposes the sides of the actin filaments, promotes dynamic Arp2/3-mediated branched actin polymerization, and generates a mechanically stiff actin network. Thus, dynamin functions as a unique actin-bundling protein that enhances mechanical force generation by the F-actin network in a GTPase-dependent manner. Our findings have universal implications for understanding dynamin-actin interactions in various cellular processes beyond cell-cell fusion.

cell biology↗

bioRxiv2019

HiLDA: a statistical approach to investigate differences in mutational signatures

We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to somatic mutations in colon cancer with mutations classified by the time of occurrence, before or after tumor initiation. Applying the methods to 16 colon cancers, we found significant associations between the relative frequencies of mutational patterns and the time of occurrence of mutations. Our novel method provides higher statistical power for detecting differences in mutational signatures.

genomics↗

bioRxiv2019

Locality sensitive hashing for the edit distance

MotivationSequence alignment is a central operation in bioinformatics pipeline and, despite many improvements, remains a computationally challenging problem. Locality Sensitive Hashing (LSH) is one method used to estimate the likelihood of two sequences to have a proper alignment. Using an LSH, it is possible to separate, with high probability and relatively low computation, the pairs of sequences that do not have an alignment from those that may have an alignment. Therefore, an LSH reduces in the overall computational requirement while not introducing many false negatives (i.e., omitting to report a valid alignment). However, current LSH methods treat sequences as a bag of k-mers and do not take into account the relative ordering of k-mers in sequences. And due to the lack of a practical LSH method for edit distance, in practice, LSH methods for Jaccard similarity or Hamming distance are used as a proxy. ResultsWe present an LSH method, called Order Min Hash (OMH), for the edit distance. This method is a refinement of the minHash LSH used to approximate the Jaccard similarity, in that OMH is not only sensitive to the k-mer contents of the sequences but also to the relative order of the k-mers in the sequences. We present theoretical guarantees of the OMH as a gapped LSH. Contactgmarcais@cs.cmu.edu, carlk@cs.cmu.edu

bioinformatics↗

bioRxiv2019

Chloroplasts navigate towards the pathogen interface to counteract infection by the Irish potato famine pathogen

Upon immune activation, chloroplasts switch off photosynthesis, produce anti-microbial compounds, and associate with the nucleus through tubular extensions called stromules. Although it is well-established that chloroplasts alter their position in response to light, little is known about the dynamics of chloroplasts movement in response to pathogen attack. Here, we report that chloroplasts accumulate at the pathogen interface during infection by the Irish potato famine pathogen Phytophthora infestans, associating with the specialized membrane that engulfs the pathogen haustorium. Chemical inhibition of actin polymerization reduces the accumulation of chloroplasts at the pathogen haustoria, suggesting this process is partially dependent on the actin cytoskeleton. However, chloroplast accumulation at haustoria does not necessarily rely on movement of the nucleus to this interface and is not affected by light conditions. Stromules are typically induced during infection, embracing haustoria and interconnecting chloroplasts, to form dynamic organelle clusters. We found that infection-triggered stromule formation relies on BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) mediated surface immune signaling, whereas chloroplast repositioning towards haustoria does not. Consistent with the defense-related induction of stromules, effector mediated suppression of BAK1 mediated immune signaling reduced stromule formation during infection. On the other hand, immune recognition of the same effector stimulated stromules, presumably via a different pathway. These findings implicate chloroplasts in a polarized response upon pathogen attack and point to more complex functions of these organelles in plant-pathogen interactions.

plant biology↗

bioRxiv2018

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

The colored de Bruijn graph (cdbg) and its variants have become an important combinatorial structure used in numerous areas in genomics, such as population-level variation detection in metagenomic samples, large scale sequence search, and cdbg-based reference sequence indices. As samples or genomes are added to the cdbg, the color information comes to dominate the space required to represent this data structure.\n\nIn this paper, we show how to represent the color information efficiently by adopting a hierarchical encoding that exploits correlations among color classes -- patterns of color occurrence -- present in the de Bruijn graph (dbg). A major challenge in deriving an efficient encoding of the color information that takes advantage of such correlations is determining which color classes are close to each other in the high-dimensional space of possible color patterns. We demonstrate that the dbg itself can be used as an efficient mechanism to search for approximate nearest neighbors in this space. While our approach reduces the encoding size of the color information even for relatively small cdbgs (hundreds of experiments), the gains are particularly consequential as the number of potential colors (i.e. samples or references) grows to thousands of experiments.\n\nWe apply this encoding in the context of two different applications; the implicit cdbg used for a large-scale sequence search index, Mantis, as well as the encoding of color information used in population-level variation detection by tools such as Vari and Rainbowfish. Our results show significant improvements in the overall size and scalability of representation of the color information. In our experiment on 10,000 samples, we achieved more than 11x better compression compared to RRR.

bioinformatics↗