Biology subjects

Ghosh, A.

Publications and source records attributed to Ghosh, A..

10 recordsLinked to original sources

bioRxiv2018

Draft genome of the liver fluke Fasciola gigantica

Fascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Krebs cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.

bioinformatics↗

bioRxiv2018

A Sparse Unreliable Distributed Code Underlies the Limits of Behavioral Discrimination

The cortical code that underlies perception must enable subjects to perceive the world at timescales relevant for behavior. We find that mice can integrate visual stimuli very quickly (<100 ms) to reach plateau performance in an orientation discrimination task. To define features of cortical activity that underlie performance at these timescales, we measured single unit responses in the mouse visual cortex at timescales relevant to this task. In contrast to high contrast stimuli of longer duration, which elicit reliable activity in individual neurons, stimuli at the threshold of perception elicit extremely sparse and unreliable responses in V1 such that the activity of individual neurons do not reliably report orientation. Integrating information across neurons, however, quickly improves performance. Using a linear decoding model, we estimate that integrating information over 50-100 neurons is sufficient to account for behavioral performance. Thus, at the limits of perception the visual system is able to integrate information across a relatively small number of highly unreliable single units to generate reliable behavior.

neuroscience↗

bioRxiv2018

ROSeq: A rank based approach to modelling gene expression in single cells

1Systematic delineation of complex biological systems is an ever-challenging and resource-intensive process. Single cell transcriptomics allows us to study cell-to-cell variability in complex tissues at an unprecedented resolution. Accurate modeling of gene expression plays a critical role in the statistical determination of tissue-specific gene expression patterns. In the past few years, considerable efforts have been made to identify appropriate parametric models for single cell expression data. The zero-inflated version of Poisson/Negative Binomial and Log-Normal distributions have emerged as the most popular alternatives due to their ability to accommodate high dropout rates, as commonly observed in single cell data. While the majority of the parametric approaches directly model expression estimates, we explore the potential of modeling expression-ranks, as robust surrogates for transcript abundance. Here we examined the performance of the Discrete Generalized Beta Distribution (DGBD) on real data and devised a Wald-type test for comparing gene expression across two phenotypically divergent groups of single cells. We performed a comprehensive assessment of the proposed method, to understand its advantages as compared to some of the existing best practice approaches. Besides striking a reasonable balance between Type 1 and Type 2 errors, we concluded that ROSeq, the proposed differential expression test is exceptionally robust to expression noise and scales rapidly with increasing sample size. For wider dissemination and adoption of the method, we created an R package called ROSeq, and made it available on the Bioconductor platform.

genomics↗

bioRxiv2018

Proteostasis perturbation destabilizes respiratory complex assembly-intermediates via aggregation of subunits

Proteostasis is maintained by optimum expression, folding, transport, and clearance of proteins. Deregulation of any of these processes triggers widespread protein aggregation and loss of function. Here, we perturbed proteostasis by blocking proteasome-mediated protein degradation and investigated proteome partitioning from soluble to insoluble fraction. Aggregation of Respiratory Chain Complex (RCC) subunits highlights the early destabilization event as revealed by proteome redistribution. Sequence analyses followed by microscopy suggest that low complexity regions at the N-terminus are capable to facilitate aggregation of RCC subunits. As a result, respiratory complex assembly process is impaired due to destabilization of sub-complexes marking the onset of mitochondrial dysfunction and ROS accumulation. Redistribution of Histone proteins and their modifications indicated reprogramming of transcription as adaptive response. Together, we demonstrate susceptibility of RCC subunits to aggregation under multiple proteotoxic stresses providing an explanation for the simultaneous deregulation of proteostasis and bioenergetics in age-related degenerative conditions.

molecular biology↗

bioRxiv2018

Loss of CREST leads to neuroinflammatory responses and ALS-like motor defects in mice

Amyotrophic lateral sclerosis (ALS) is a late onset neurodegenerative disease with fast progression. Mutations of the CREST gene (also known as SS18L1) are identified in sporadic ALS patients. Whether CREST mutations may lead to ALS remained largely unclear. In this study, we showed that the ALS-related CREST-Q388X mutation exhibited loss-of-function effects. Importantly, we found that microglial activation were prevalent in CREST haploinsufficieny mice and the Q394X mice mimicking the human CREST Q388X mutation. Furthermore, we showed that both CREST haploinsufficieny and the Q394X mice displayed deficits in motor coordination. Finally, we identified the critical role of CREST-BRG1 complex in repressing the expression of immune-related cytokines including Ccl2 and Cxcl10 in neurons, via histone deacetylation, providing the molecular mechanisms underlying inflammatory responses lack of CREST. These findings indicate that elevated inflammatory responses in a subset of ALS may be caused by neuron-derived factors, suggesting potential therapeutic methods through inflammation pathways.\n\nIn BriefCheng et al. discovered that neuronal loss of CREST reduces the protein level of FUS, de-represses the transcriptional inhibition of chemokine genes which in turn causes microglial activation and proinflammation, and ultimately leads to axonal degeneration of motor neurons and impairment of locomotion.

neuroscience↗

bioRxiv2018

Non-productive Binding Modes as a Prominent Feature of Aβ1-40 Fiber Elongation: Insights from Molecular Dynamics Simulation

AbstractAmyloid formation has been implicated in a number of neurodegenerative diseases. The elongation of amyloid fibers is thermodynamically strongly favorable but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and thus so far has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 310 helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and monomer. A Markov state model shows the unfolded monomer is trapped at the end of the fiber in a set of interconverting anti-parallel {beta}-hairpin conformations. The simulation here may serve as a model for the binding of other non-{beta}-sheet conformations to amyloid fibers.

biophysics↗

bioRxiv2017

Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology

Amyloid beta (A{beta}) peptides impair multiple cellular pathways in the brain and play a causative role in Alzheimers disease (AD) pathology, but how the brain proteome is remodeled during this process is unknown. To identify new protein networks associated with AD-like pathology, we performed global quantitative proteomic analysis in three mouse models at pre- and post-symptomatic ages. Our analysis revealed a robust and consistent increase in Apolipoprotein E (ApoE) levels in nearly all transgenic brain regions with increased A{beta} levels. Taken together with prior findings on ApoE driving A{beta} accumulation, this analysis points to a pathological dysregulation of the ApoE-A{beta} axis. We also found dysregulation of protein networks involved in excitatory synaptic transmission consistent with AD pathophysiology. Targeted analysis of the AMPA receptor complex revealed a specific loss of TARP{gamma}-2, a key AMPA receptor trafficking protein. Expression of TARP{gamma}-2 in vivo in hAPP transgenic mice led to a restoration of AMPA currents. This database of proteome alterations represents a unique resource for the identification of protein alterations responsible for AD.\n\nHighlightsO_LIProteomic analysis of mouse brains with AD-like pathology reveals stark remodeling\nC_LIO_LIProteomic evidence points to a dysregulation of ApoE levels associated with A{beta} clearance rather than production\nC_LIO_LICo-expression analysis found distinctly impaired synapse and mitochondria modules\nC_LIO_LIIn-depth analyses of AMPAR complex points to loss of TARP{gamma}-2, which may compromise synapses in AD\nC_LI\n\neTOC BlurbProteome-wide profiling of brain tissue from three mouse models of AD-like pathology reveals A{beta}, brain region, and age dependent alterations of protein levels. This resource provides a new global protein expression atlas for the Alzheimers disease research community.

neuroscience↗

bioRxiv2017

Chaperone Network Based On Cellular Response Reveals The Non-Optimal Response To Perturbed Proteostasis

The proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding; some with over-lapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. To this effect, we have used S. cerevisiae to understand the route a cell takes as a response when challenged with different proteostasis impairments. Using 14 single deletion strains of genes of Protein Quality Control (PQC) system, we quantify their proteostasis impairment and the transcriptional response. In most cases cellular response was incapable of restoring proteostasis. The response did not activate proteostasis components or pathways that could complement the function of the missing PQC gene. Over-expression of alternate machineries, could restore part of the proteostasis defect in deletion strains. We posit that epistasis guided synthetic biology approaches may be helpful in realizing the true potential of the cellular chaperone machinery.

genetics↗

bioRxiv2017

Investigation Of Protein Synthesis In Drosophila Larvae Using Puromycin Labelling

Translational control of gene expression is an important regulator of growth, homeostasis and aging in Drosophila. The ability to measure changes in protein synthesis in response to genetic and environmental cues is therefore important in studying these processes. Here we describe a simple and cost effective approach to assay protein synthesis in Drosophila larval cells and tissues. The method is based on the incorporation of puromycin into nascent peptide chains. Using an ex vivo approach, we label newly synthesized peptides in larvae with puromycin and then measure levels of new protein synthesis using an anti-puromycin antibody. We show that this method can detect changes in protein synthesis in specific cells and tissues in the larvae, either by immunostaining or western blotting. We find that the assay reliably detects changes in protein synthesis induced by two known stimulators of mRNA translation - the nutrient/TORC1 kinase pathway and the transcription factor dMyc. We also use the assay to describe how protein synthesis changes through larval development and in response to two environmental stressors - hypoxia and heat-shock. We propose that this puromycin-labelling assay is a simple but robust method to detect protein synthesis changes at the levels of cells, tissues or whole body in Drosophila.

developmental biology↗

bioRxiv2016

EuMicrobedbLite: A lightweight genomic resource and analytic platform for draft oomycete genomes

We have developed EuMicrobedbLite - A light weight comprehensive genome resource and sequence analysis platform for oomycete organisms. EuMicrobedbLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, the GUS schema has been greatly simplified with removal of many obsolete modules and redesign of others to incorporate contemporary data. Several dependencies such as perl object layers used for data loading in VMD have been replaced with independent light weight scripts. EumicrobedbLite now runs on a powerful annotation engine developed at our lab called \"Genome Annotator Lite\". Currently this database has 26 publicly available genomes and 10 EST datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44,777 core conserved proteins from twelve oomycete organisms that form 2974 clusters. Synteny viewing is enabled by incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every six months to ensure quality. The database resource is available at www.eumicrobedb.org.

bioinformatics↗