Biology subjects

Mondal, R.

Publications and source records attributed to Mondal, R..

6 recordsLinked to original sources

bioRxiv2023

The GIAB genomic stratifications resource for human reference genomes

Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in difficult regions in the human genome. Here we describe a set of genomic stratifications for the human reference genomes GRCh37, GRCh38, and T2T-CHM13v2.0. Generating stratifications for the new complete CHM13 reference genome is critical to understanding improvements in variant caller performance when using this new complete reference. The GIAB stratifications can be used when benchmarking variant calls to analyze difficult regions of the human genome in a standardized way. Here we present stratifications in the CHM13 genome in comparison to GRCh37 and GRCh38, highlighting expansions in hard-to-map and GC-rich stratifications which provide useful insight for accuracy of variants in these newly-added regions. To evaluate the reliability and utility of the new stratifications, we used the stratifications of the three references to assess accuracy of variant calls in diverse, challenging genomic regions. The means to generate these stratifications are available as a snakemake pipeline at https://github.com/ndwarshuis/giab-stratifications.

genomics↗

bioRxiv2023

Efficient Prohibitin 2 exposure during mitophagy depends on Voltage-dependent anion-selective channel protein 1.

Autophagic elimination of depolarized mitochondria (mitophagy) depends on Ubiquitin proteasome complex to expose the inner mitochondrial membrane-resident protein-Prohibitin 2 (PHB2). This uncovering facilitates its interaction with autophagosomal membrane-associated protein LC3. It remains unclear whether PHB2 is uncovered randomly through mitochondrial rupture sites. Prior knowledge and initial screening indicated that Voltage-dependent anion-selective channel protein 1 (VDAC1) might play a role in this process. Through in vitro biochemical assays and imaging, we have found that VDAC1-PHB2 interaction increases during mitochondrial depolarization. Subsequently, this interaction enhances the efficiency of PHB2 exposure and mitophagy. To investigate the relevance in vivo, we utilized a Porin (equivalent to VDAC1) knockout Drosophila line. Our findings demonstrate that during rotenone-induced mitochondrial stress, Porin is essential for PHB2 exposure, PHB2-LC3 interaction, and mitophagy. This study highlights that VDAC1 predominantly synchronizes efficient PHB2 exposure through mitochondrial rupture sites during mitophagy. These findings may provide insights to understand progressive neurodegeneration.

cell biology↗

bioRxiv2023

Protective intravenous BCG vaccination induces enhanced immune signaling in the airways

Intradermal (ID) Bacillus Calmette-Guerin (BCG) is the most widely administered vaccine in the world. However, ID-BCG fails to achieve the level of protection needed in adults to alter the course of the tuberculosis epidemic. Recent studies in non-human primates have demonstrated high levels of protection against Mycobacterium tuberculosis (Mtb) following intravenous (IV) administration of BCG. However, the protective immune features that emerge following IV BCG vaccination remain incompletely defined. Here we used single-cell RNA-sequencing (scRNAseq) to transcriptionally profile 157,114 unstimulated and purified protein derivative (PPD)-stimulated bronchoalveolar lavage (BAL) cells from 29 rhesus macaques immunized with BCG across routes of administration and doses to uncover cell composition-, gene expression-, and biological network-level signatures associated with IV BCG-mediated protection. Our analyses revealed that high-dose IV BCG drove an influx of polyfunctional T cells and macrophages into the airways. These macrophages exhibited a basal activation phenotype even in the absence of PPD-stimulation, defined in part by IFN and TNF- signaling up to 6 months following BCG immunization. Furthermore, intercellular immune signaling pathways between key myeloid and T cell subsets were enhanced following PPD-stimulation in high-dose IV BCG-vaccinated macaques. High-dose IV BCG also engendered quantitatively and qualitatively stronger transcriptional responses to PPD-stimulation, with a robust Th1-Th17 transcriptional phenotype in T cells, and augmented transcriptional signatures of reactive oxygen species production, hypoxia, and IFN-{gamma} response within alveolar macrophages. Collectively, this work supports that IV BCG immunization creates a unique cellular ecosystem in the airways, which primes and enables local myeloid cells to effectively clear Mtb upon challenge.

immunology↗

bioRxiv2023

A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Therapeutic importance in inhibiting Bromodomain and WD Repeat Domain containing BRWD1 against numerous human pathophysiological processes including cancers prompts prediction of a workable structure of this large protein. Here, a novel divide and conquer strategy was adopted to utilize smaller overlapping sequence-fragments of BRWD1 to further utilize their predicted structures as derived templates for prediction of complete BRWD1 structure in absence of its desired homologues in the template database. The novelty of this methodology stemmed from the requirement of templates of high sequence similarity in any comparative model based predictors whereas, the own fragments of the same target protein, BRWD1 could successfully fulfill this criteria. Additionally, the outputs of different high performing predictors including AlphaFold and RoseTTAFold were systematically integrated under the premise of Inductive Reasoning. The resultant structures were validated using existing validation parameters. Finally, a new validation paradigm was adopted to screen the best structure from the result presenting in-silico studies of known interactions of BRWD1 with various small molecules like, BD inhibitors, modified histone tails, DNA motifs and interacting proteins. The algorithm proposed in this work also paved the way for prediction of authentic structures of large size proteins.

bioinformatics↗

bioRxiv2023

Genome size, genetic diversity, and phenotypic variability imply the effect of genetic variation instead of ploidy on trait plasticity in the cross-pollinated tree species ofmulberry

Genome size, genetic diversity, and phenotypic vitiation were estimated to develop a model-based population structure and identify ploidy-associated traits of a wide collection of cross-pollinated, highly heterozygous tree species of Morus.Elucidation of genome size (GS), genetic and phenotypic variation is the fundamental aspect of crop improvement programs. Mulberry is a cross-pollinated, highly heterozygous tree eudicot, and comprised of huge ploidy variation with great adaptability across the world. However, because of inadequate information on GS, ploidy-associated traits, as well as the correlation between genetic and phenotypic variation hinder the further improvement of mulberry. In this present research, a core set of 157 germplasm accessions belonging to eight accepted species of Morus including promising functional varieties were chosen to represent the genetic spectrum from the whole germplasm collection. To estimate the GS, accessions were subjected to flow cytometry (FCM) analysis and the result suggested that four different ploidies (2n=2x, 3x, 4x, and 6x) with GS ranging from 0.72{+/-}0.005 (S-30) to 2.89{+/-}0.015 (M. serrata), accounting [~]4.01 fold difference. The predicted polyploidy was further confirmed with metaphase chromosome count. In addition, the genetic variation was estimated by selecting a representative morphologically, diverse population of 82 accessions comprised of all ploidy variations using simple sequence repeats (SSR). The estimated average Polymorphism Information Content (PIC) and expected heterozygosity showed high levels of genetic diversity. Additionally, three populations were identified by the model-based population structure (k=3) with a moderate level of correlation between the populations and different species of mulberry, which imply the effect of genetic variation instead of ploidy on trait plasticity that could be a consequence of the high level of heterozygosity imposed by natural cross-pollination. Further, the correlation between ploidies, especially diploid and triploid with selected phenotypic traits was identified, however, consistency could not be defined with higher ploidy levels (>3x). Moreover, incite gained here can serve as a platform for future omics approaches to the improvement of mulberry traits.

genetics↗

bioRxiv2022

The extracellular RNA pool within Zea mays apoplast: composition and differential expression during Ustilago maydis infection

The existence of an extracellular pool of RNA (exRNA) has been documented in both animal and plant cells in a number of instances. These exRNA species play important role in host response against different environmental stimuli. The mechanism of their function however remains largely unknown. In this study we report the composition of the exRNA pool within the leaf apoplast of Z. mays under normal growth condition. We could detect RNA transcripts originating from both the genic as well as the intergenic regions of the nuclear, mitochondrial and chloroplast genomes of maize in our exRNA sequencing data. Our data showed increased abundance of about 75% of the exRNA transcripts during infection with a basidiomycete smut fungi, Ustilago maydis. Functional classification of the differentially abundant exRNA transcripts within U. maydis SG200 WT infected maize apoplast with respect to uninfected apoplast revealed significant enrichment of the exRNA transcripts corresponding to the ribosome biogenesis pathway. Data related to the effect of two extracellular T2 type ribonucleases, Nuc1 and Nuc2 from U. maydis on the composition of exRNA pool of maize is also presented.

plant biology↗