Biology subjects

Mitra, S.

Publications and source records attributed to Mitra, S..

98 records · Page 6Linked to original sources

bioRxiv2019

De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

We report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. Comparative analysis with other felids and mammalian genomes unraveled the evolutionary history of Asiatic lion and its position among other felids. The genome is estimated to be 2.3 Gb (Gigabase) long with 62X sequence coverage and is found to have 20,543 protein-coding genes. About 2.66% of the genome is covered by simple sequence repeats (SSRs) and 0.4% is estimated to have segmental duplications. Comparison with seven well annotated genomes indicates the presence of 6,295 single copy orthologs, 4 co-orthologs, 21 paralogs uniquely present in Asiatic lion and 8,024 other orthologs. Assessment of male and female transcriptomes gave a list of genes specifically expressed in the male. Our genomic analyses provide candidates for phenotypes characteristic to felids and lion, inviting further confirmation of their contribution through population genetic studies. An Asiatic lion-specific expansion is detected in the Cysteine Dioxygenase-I (CDO-I) family that is responsible for taurine biosynthesis in cats. Wilms tumor-associated protein (WT1) family, a non-Y chromosome genetic factor underlying male-sex determination and differentiation is found to have undergone expansion, interestingly like that of the human genome. Another protein family, translation machinery-associated protein 7 (TMA7) that has undergone expansion in humans, also expanded in Asiatic lion and can be further investigated as a candidate responsible for mane in lions because of its role in hair follicle morphogenesis.

genomics↗

bioRxiv2018

Recruitment of human eIF4G1 or DAP5 to the 5’ untranslated regions of a subset of cellular mRNAs drives cap-independent translation

During unfavorable human cellular conditions (e.g., tumor hypoxia, viral infection, etc.), canonical, cap-dependent mRNA translation is suppressed. Nonetheless, a subset of physiologically important mRNAs (e.g., HIF-1, FGF-9, and p53) is still translated by an unknown, cap-independent mechanism. Additionally, expression levels of eIF4G and its homolog, death associated protein 5 (DAP5), are elevated. Using fluorescence anisotropy binding studies, luciferase reporter-based in vitro translation assays, and mutational analyses, here we demonstrate that eIF4GI and DAP5 specifically bind to the 5 UTRs of these cap-independently translated mRNAs. Surprisingly, we find that the eIF4E binding domain of eIF4GI increases not only the binding affinity, but also the selectivity among these mRNAs. We further demonstrate that the affinities of eIF4GI and DAP5 binding to these 5 UTRs correlate with the efficiency with which these factors drive cap-independent translation of these mRNAs. Integrating the results of our binding and translation assays, we show that eIF4GI and/or DAP5 are critical for recruitment of a specific subset of mRNAs to the ribosome and provide mechanistic insight into their cap-independent translation.

biophysics↗

bioRxiv2018

In Silico Analysis of Non Synonymous Single Nucleotide Polymorphisms (nsSNPs) of SMPX Gene in Hearing Impairment

BackgroundMutations in SMPX gene can disrupt the normal activity of the SMPX protein which is involved in hearing process.\n\nObjectiveIn this study, deleterious non-synonymous single nucleotide polymorphisms were isolated from the neutral variants by using several bioinformatics tools.\n\nMethodFirstly, dbSNP database hosted by NCBI was used to retrieve the SNPs of SMPX gene, secondly, SIFT was used primarily to screen the damaging SNPs. Further, for validation PROVEAN, PredictSNP and PolyPhen 2 were used. I-Mutant 3 was utilized to analyze the protein stability change and MutPred predicted the molecular mechanism of protein stability change. Finally evolutionary conservation was done to study their conservancy by using ConSurf server.\n\nResultsA total of 26 missense (0.6517%) and 3 nonsense variants (0.075%) were retrieved and among them 4 mutations were found deleterious by all the tools of this experiment and are also highly conserved according to ConSurf server. rs772775896, rs759552778, rs200892029 and rs1016314772 are the reference IDs of deleterious mutations where the substitutions are S71L, N19D, A29T and K54N. Loss of Ubiquitination, loss of methylation, loss of glycosylation, and loss of MoRF binding motifs are the root causes of protein stability change.\n\nConclusionThis is the first study regarding nsSNPs of SMPX gene where the most damaging SNPs were screened that are associated with the SMPX gene and can be used for further research to study their effect on protein structure and function, their dynamic behavior and how they actually affect proteins flexibility.

bioinformatics↗

bioRxiv2018

Tissue-specific actions of Pax6 on proliferation-differentiation balance in the developing forebrain are Foxg1-dependent

Differences in the growth and maturation of diverse forebrain tissues depends on region-specific transcriptional regulation. Individual transcription factors act simultaneously in multiple regions that develop very differently, raising questions about the extent to which their actions vary regionally. We found that the transcription factor Pax6 affects the transcriptomes and the balance between proliferation and differentiation in opposite directions in murine diencephalon versus cortex. We tested several possible mechanisms to explain Pax6s tissue-specific actions and found that the presence of the transcription factor Foxg1 in cortex but not diencephalon was most influential. We found that Foxg1 is responsible for many of the differences in cell cycle gene expression between diencephalon and cortex. In cortex lacking Foxg1, Pax6s action on the balance of proliferation versus differentiation became diencephalon-like. Our findings reveal a mechanism for generating regional forebrain diversity in which the actions of one transcription factor completely reverse the actions of another.

developmental biology↗

bioRxiv2018

Deficiency of the E3 Ubiquitin Ligase RBCK1 Causes Diffuse Brain Polyglucosan Accumulation and Neurodegeneration

Glycogen synthesis is vital, malstructure resulting in precipitation and accumulation into neurotoxic polyglucosan bodies (PBs). One well-understood mechanism of PB generation is glycogen branching enzyme deficiency (GBED). Less understood is Lafora disease (LD), resulting from absence of the glycogen phosphatase laforin or the E3 ubiquitin ligase malin, and accumulation of hyperphosphorylated PBs. LD afforded first insight that glycogen sphericity depends on more than adequate branching activity. Unexpectedly, deficiencies of the Linear Ubiquitin Chain Assembly Complex (LUBAC) components RBCK1 and HOIP result in PBs in muscle tissues. Here we analyzed nervous system phenotypes of mice lacking RBCK1 and find profuse PB accumulations in brain and spinal cord with extensive neurodegeneration and neurobehavioral deficits. Brain glycogen in these mice is characterized by long chains and hyperphosphorylation, similar to LD. Like in LD, glycogen synthase and branching enzyme are unaltered. Regional PB distribution mirrors LD and not GBED. Perisynaptic PB localization is unlike LD or GBED. The results indicate that RBCK1 is part of a system supplementing laforin-malin in regulating glycogen architecture including in unique neuronal locales.

molecular biology↗

bioRxiv2018

Why not record from every channel with a CMOS scanning probe?

It is an uninformative truism to state that the brain operates at multiple spatial and temporal scales, each with each own set of emergent phenomena. More worthy of attention is the point that our current understanding of it cannot clearly indicate which of these phenomenological scales are the significant contributors to the brains function and primary output (i.e. behaviour). Apart from the sheer complexity of the problem, a major contributing factor to this state of affairs is the lack of instrumentation that can simultaneously address these multiple scales without causing function altering damages to the underlying tissue. One important facet of this problem is that standard neural recording devices normally require one output connection per electrode. This limits the number of electrodes that can fit along the thin shafts of implantable probes generating a limiting balance between density and spread. Sharing a single output connection between multiple electrodes relaxes this constraint and permits designs of ultra-high density probes. Here we report the design and in-vivo validation of such a device, a complementary metal-oxide-semiconductor (CMOS) scanning probe with 1344 electrodes; the outcome of the European research project NeuroSeeker. We show that this design targets both local and global spatial scales by allowing the simultaneous recording of more than 1000 neurons spanning 7 functional regions with a single shaft. The neurons show similar recording longevity and signal to noise ratio to passive probes of comparable size and no adverse effects in awake or anesthetized animals. Addressing the data management of this device we also present novel visualization and monitoring methods. Using the probe with freely moving animals we show how accessing a number of cortical and subcortical brain regions offers a novel perspective on how the brain operates around salient behavioural events. Finally, we compare this probe with lower density, non CMOS designs (which have to adhere to the one electrode per output line rule). We show that an increase in density results in capturing neural firing patterns, undetectable by lower density devices, which correlate to self-similar structures inherent in complex naturalistic behaviour. To help design electrode configurations for future, even higher density, CMOS probes, recordings from many different brain regions were obtained with an ultra-dense passive probe.

neuroscience↗

bioRxiv2018

Is IκBζ constitutively expressed in mammalian airway epithelium?

I{kappa}B{zeta} is a transcriptional factor induced primarily in immune cells upon Toll-like receptor (TLR) activation that drives important cytokine responses. Recent studies have demonstrated constitutive I{kappa}B{zeta} expression in the epithelial cells of mouse skin and eyes, possibly reflecting the activation of TLRs by pathogen-associated molecular patterns (PAMPs). In this context, another mucosal surface, the lung epithelium, may not be as actively exposed to the external environment as the skin and the conjunctiva, especially since the lower lung airways are typically conceived to be sterile. Whether I{kappa}B{zeta} expression in the lungs is constitutive or induced remains largely unexplored. This is especially important since I{kappa}B{zeta} has been shown to promote the expression of protective cytokine and antimicrobial peptide responses, supporting a role for I{kappa}B{zeta} in lung host defense. We hence evaluated I{kappa}B{zeta} expression in airway epithelia of both humans and mice using immunostaining with antiserum raised against recombinant I{kappa}B{zeta} in our laboratory. We observed positive signal in the nuclei of ciliated epithelial cells lining the central airways. Airway cells of gnotobiotic mice also stained positive, suggesting that I{kappa}B{zeta} expression does not require induction by bacterial PAMPs. Unexpectedly, we also observed staining in the lung epithelia of I{kappa}B{zeta} knockout mice, indicating possible false positive signals from our immunohistochemistry experiments. In this context, 2D gel analysis followed by mass spectrometry revealed that our I{kappa}B{zeta} antiserum also detected a nuclear protein lamin B1. Nevertheless, immunoblotting tissue homogenates from gnotobiotic mouse lungs and primary human airway epithelial cells showed the appropriate 86 kDa band for I{kappa}B{zeta}. Together, these results demonstrate constitutive I{kappa}B{zeta} expression in airway epithelium, suggesting that lung epithelial cells may depend upon I{kappa}B{zeta} expression for airway protection.

immunology↗

bioRxiv2017

DIVERSITY In Binding, Regulation, And Evolution Revealed From High-Throughput ChIP

A high-throughput chromatin immunoprecipitation (ChIP) experiment is like a black-box: it reports all regions that are associated with the profiled protein based on the initial cross-linking step. These regions can be a highly diverse set of DNA sequences, with some making direct contact with the protein, some binding through intermediaries, and some being a result of long-range interactions involving the protein. We present O_SCPLOWDIVERSITYC_SCPLOW, a method that identifies the distinct components of such a mixture, leaving no data behind, while at the same time, using no prior motif knowledge. Using the example of the REST protein, we show that these different components give insights into the various complexes that may be forming along the chromatin and their regulatory functions.\n\nhttp://diversity.ncl.res.in/ (webserver)\n\nhttps://github.com/NarlikarLab/DIVERSITY (standalone for Mac OSX/Linux)

bioinformatics↗