TANAVDE Vivek

Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition

Published date : 08 Jan 2018

In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs.

type
Journal Paper
journal
Development, 8 Jan 2018, Vol 145, Issue 1, doi: 10.1242/dev.159566
Impact Factor
5.843

EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis

Published date : 21 Aug 2017

Epithelial carcinomas are well known to activate a prolonged wound-healing program that promotes malignant transformation. Wound closure requires the activation of keratinocyte migration via a dual-state molecular switch. This switch involves production of either the anti-migratory microRNA miR-198 or the pro-migratory follistatin-like 1 (FSTL1) protein from a single transcript; miR-198 expression in healthy skin is down-regulated in favor of FSTL1 upon wounding, which enhances keratinocyte migration and promotes re-epithelialization.

type
Journal Paper
journal
The Journal of Experimental Medicine, 2017,doi: 10.1084/jem.20170354
Impact Factor
11.991

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Published date : 19 Jul 2017

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type
Journal Paper
journal
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
Impact Factor
4.259

Mesenchymal Stromal Cells Derived from Human Embryonic Stem Cells, Fetal Limb and Bone Marrow Share a Common Phenotype but Are Transcriptionally and Biologically Different

Published date : 30 Jan 2017

Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to determine the optimal source of MSCs. We investigated if this biological heterogeneity in MSCs from different sources results in different mechanisms for their differentiation.

type
Journal Paper
journal
Stem Cell Discovery, 2017, 7, Pg 1-26, doi: 10.4236/scd.2017.71001

Comparative study of adipose-derived stem cells and bone marrow-derived stem cells in similar microenvironmental conditions

Published date : 19 Sep 2016

Mesenchymal stem cells (MSCs), which were first isolated from the bone marrow, are now being extracted from various other tissues in the body, including the adipose tissue. The current study presents systematic evidence of how the adipose tissue-derived stem cells (ASCs) and bone marrow-derived mesenchymal stem cells (Bm-MSCs) behave when cultured in specific pro-adipogenic microenvironments. The cells were first characterized and identified as MSCs in terms of their morphology, phenotypic expression, self-renewal capabilities and multi-lineage potential.

type
Journal Paper
journal
Experimental Cell Research, Vol. 348, Issue 2, 1 Nov 2016, Pg 155-164, doi: 10.1016/j.yexcr.2016.09.012
Impact Factor
3.378

Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

Published date : 13 Sep 2016

Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology.

type
Journal Paper
journal
PLoS One. 2016 Sep 13; 11(9):e0162541. doi: 10.1371/journal.pone.0162541
Impact Factor
3.1

Retinoic Acid Mediates Visceral-specific Adipogenic Defects of Human Adipose-derived Stem Cells

Published date : 07 Mar 2016

Increased visceral fat, rather than subcutaneous fat, during obesity onset is associated with higher risk of developing metabolic diseases. Human adipose-derived stem cells(ASCs) from visceral depots are compromised in their inherent adipogenic properties compared to ASCs from subcutaneous depots, but little is known about the underlying mechanisms. By ontology analysis of global gene expression studies, we demonstrate that many genes involved in retinoic acid (RA) synthesis or regulated by RA are differentially expressed in human tissues and ASCs from subcutaneous and visceral fat.

type
Journal Paper
journal
Diabetes, 2 Mar 2016, doi: 10.2337/db15-1315
Impact Factor
8.474

Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation

Published date : 22 Jan 2016

The presence of multiple variants for many mRNAs is a major contributor to protein diversity. The processing of these variants is tightly controlled in a cell-type specific manner and has a significant impact on gene expression control. Here we investigate the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC derived Neural Precursor Cells (NPCs) using polysome profiling coupled to RNA sequencing.

type
Journal Paper
journal
PLoS One. 2016 Jan 22;11 (1), doi: 10.1371/journal.pone.0143235
Impact Factor
3.23

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Published date : 16 Nov 2015

Background: The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation
also increases with increasing genome complexity. Though the number of genes appear to be equal between human
and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (miRBase Release 19).
It appears that most of the miRNAs in zebrafish are yet to be discovered.

Results: We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut

type
Journal Paper
journal
BMC Genomics (2015) 16:950, doi:10.1186/s12864-015-2135-7
Impact Factor
3.99

Research using Mesenchymal Stem/Stromal Cells: quality metric towards developing a reference material

Published date : 17 Aug 2015

Mesenchymal stem/stromal cells (MSCs) have been extensively investigated for their regenerative, immune-modulatory, and wound healing properties. While the laboratory studies have suggested that MSC's have a unique potential for modulating the etiopathology of multiple diseases, the results from clinical trials have not been encouraging or reproducible. One of the explanations for such variability is explained by the "art" of isolating and propagating MSCs.

type
Journal Paper
journal
Cytotherapy, 2015 Sep;17(9):1169-77. doi: 10.1016/j.jcyt.2015.07.008