Life Sciences

<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

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RVB1/RVB2 (RuvBL1/RuvBL2 or pontin/reptin) are enigmatic AAA+ ATPase proteins that are present in multiple cellular complexes. Although they have been implicated in many cellular functions, the exact molecular function of RVB proteins in the various complexes is not clear. TIP60 complex (TIP60.com) is a tumor suppressor chromatin-remodeling complex containing RVB proteins. RVBs are required for the lysine acetyltransferase activity of TIP60.com but not for that of the pure recombinant TIP60 polypeptide. Here we describe two molecular functions of RVBs in TIP60.com. First, RVBs negate the repression of catalytic activity of TIP60 by another protein in TIP60.com, p400. RVBs competitively displace the SNF2 domain of p400 from the TIP60 polypeptide. In addition RVBs are also required for heat stability of TIP60.com by a p400-independent pathway. RVB1 and RVB2 are redundant with each other for these functions and do not require their ATPase activities. Thus, RVB proteins act as molecular adaptors that can substitute for one another to facilitate the optimal assembly, heat stability, and function of the TIP60 complex © 2013, American Society for Microbiology.

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Molecular and Cellular Biology

RVBs are required for assembling a functional TIP60 complex

Adenoviruses are linear double-stranded DNA viruses that infect human and rodent cell lines, occasionally transform them and cause tumors in animal models. The host cell challenges the virus in multifaceted ways to restrain viral gene expression and DNA replication, and sometimes even eliminates the infected cells by programmed cell death. To combat these challenges, adenoviruses abrogate the cellular DNA damage response pathway. Tip60 is a lysine acetyltransferase that acetylates histones and other proteins to regulate gene expression, DNA damage response, apoptosis and cell cycle regulation. Tip60 is a bona fide tumor suppressor as mice that are haploid for Tip60 are predisposed to tumors. We have discovered that Tip60 is degraded by adenovirus oncoproteins EIB55K and E4orf6 by a proteasome-mediated pathway. Tip60 binds to the immediate early adenovirus promoter and suppresses adenovirus EIA gene expression, which is a master regulator of adenovirus transcription, at least partly through retention of the virally encoded repressor pVII on this promoter. Thus, degradation of Tip60 by the adenoviral early proteins is important for efficient viral early gene transcription and for changes in expression of cellular genes. © 2013 Macmillan Publishers Limited.

Oncogene

Tip60 degradation by adenovirus relieves transcriptional repression of viral transcriptional activator EIA

Vascular endothelium is a dynamic cellular interface that displays a unique phenotypic plasticity. This plasticity is critical for vascular function and when dysregulated is pathogenic in several diseases. Human genotype-phenotype studies of endothelium are limited by the unavailability of patient-specific endothelial cells. To establish a cellular platform for studying endothelial biology, we have generated vascular endothelium from human induced pluripotent stem cells (iPSCs) exhibiting the rich functional phenotypic plasticity of mature primary vascular endothelium. These endothelial cells respond to diverse proinflammatory stimuli, adopting an activated phenotype including leukocyte adhesion molecule expression, cytokine production, and support for leukocyte transmigration. They maintain dynamic barrier properties responsive to multiple vascular permeability factors. Importantly, biomechanical or pharmacological stimuli can induce pathophysiologically relevant atheroprotective or atheroprone phenotypes. Our results demonstrate that iPSC-derived endothelium possesses a repertoire of functional phenotypic plasticity and is amenable to cell-based assays probing endothelial contributions to inflammatory and cardiovascular diseases. © 2013 The Authors.

Stem Cell Reports

Functional vascular endothelium derived from human induced pluripotent stem cells

Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq) has the potential to reveal unprecedented complexity of the transcriptomes. The transcriptome sequencing of an organism provides quick insights into the gene space, opportunity to isolate genes of interest, development of functional markers, quantitation of gene expression, and comparative genomic studies. Although becoming cheaper, transcriptome sequencing still remains an expensive endeavor. Further, the assembly of millions and billions of RNA-seq reads to construct the complete transcriptome poses great informatics challenges. Here, first we outline various important issues from experimental design to data analysis, including various strategies of transcriptome assembly, which need substantial consideration for a successful RNA-seq experiment. Further, we describe a method for using RNA-seq to characterize the transcriptome of a plant species, taking the example of a legume crop plant chickpea. Our aim is to provide a quick start guide to the nonexpert researchers for NGS-based transcriptome analysis. © 2013 Springer Science+Business Media, LLC.

Methods in Molecular Biology

RNA-Seq for transcriptome analysis in non-model plants

Imidazoleglycerol-phosphate dehydratase (IGPD; HisB), which catalyses the conversion of imidazoleglycerol-phosphate (IGP) to imidazoleacetol-phosphate in the histidine biosynthesis pathway, is absent in mammals. This feature makes it an attractive target for herbicide discovery. Here, the crystal structure of Mycobacterium tuberculosis (Mtb) IGPD is reported together with the first crystal structures of substrate-bound and inhibited (by 3-amino-1,2,4-triazole; ATZ) forms of IGPD from any organism. The overall tertiary structure of Mtb IGPD, a four-helix-bundle sandwiched between two four-stranded mixed $\beta$-sheets, resembles the three-dimensional structures of IPGD from other organisms; however, Mtb IGPD possesses a unique structural feature: the insertion of a one-turn 310-helix followed by a loop ten residues in length. The functional form of IGPD is 24-meric, exhibiting 432 point-group symmetry. The structure of the IGPD-IGP complex revealed that the imidazole ring of the IGP is firmly anchored between the two Mn atoms, that the rest of the substrate interacts through hydrogen bonds mainly with residues Glu21, Arg99, Glu180, Arg121 and Lys184 which protrude from three separate protomers and that the 24-mer assembly contains 24 catalytic centres. Both the structural and the kinetic data demonstrate that the inhibitor 3-amino-1,2,4-triazole inhibits IGPD competitively. {\textcopyright} 2013 International Union of Crystallography.

Acta Crystallographica Section D: Biological Crystallography

Structures of native, substrate-bound and inhibited forms of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase

Legumes represent an important family of flowering plants in terms of providing human nutrition and capacity to fix atmospheric N for agricultural sustainability. The recent availability of genome sequence of several legume plants has helped boosting genomics research. Study of the transcriptome at a global level can provide insights into the gene space, gene function, transcriptional programs, and molecular basis of various cellular processes in legumes, even in the absence of genome sequence. Transcriptome analysis has been realized as an essential step for basic and applied research in any organism. Considering the importance of transcriptome analyses, a few studies have been performed in legumes, such as soybean [Glycine max (L.) Merr.], Medicago truncatula Gaertn., Lotus corniculatus L. var. japonicus Regel [syn. Lotus japonicus (Regel) K. Larsen], and chickpea (Cicer arietinum L.), to uncover the overall and specific transcriptional activity of genes across various tissues and/or organs and developmental stages. Several candidate genes putatively involved in important agronomic traits, such as nodule, flower, and seed development, have been identified. The availability of these transcriptome data and future investigations will enable a variety of functional genomic studies to characterize these genes and define their function in legumes. © Crop Science Society of America.

Plant Genome

Transcriptome analyses in legumes: A resource for functional genomics

The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates. © 2013 American Chemical Society.

Biochemistry

Unique structural modulation of a non-native substrate by cochaperone DnaJ

HU is a non-sequence-specific DNA-binding protein and one of the most abundant nucleoidassociated proteins in the bacterial cell. Like Escherichia coli, the genome of Porphyromonas gingivalis is predicted to encode both the HUα (PG1258) and the HUβ (PG0121) subunit. We have previously reported that PG0121 encodes a non-specific DNA-binding protein and that PG0121 is co-transcribed with the K-antigen capsule synthesis operon. We also reported that deletion of PG0121 resulted in downregulation of capsule operon expression and produced a P. gingivalis strain that is phenotypically deficient in surface polysaccharide production. Here, we show through complementation experiments in an E. coli MG1655 hupAB double mutant strain that PG0121 encodes a functio nal HU homologue. Microarray and quantitative RT-PCR analysis were used to further investigate global transcriptional regulation by HUβ using comparative expression profiling of the PG0121 (HUβ) mutant strain to the parent strain, W83. Our analysis determined that expression of genes encoding proteins involved in a variety of biological functions, including iron acquisition, cell division and translation, as well as a number of predicted nucleoid associated proteins were altered in the PG0121 mutant. Phenotypic and quantitative real-time-PCR (qRT-PCR) analyses determined that under iron-limiting growth conditions, cell division and viability were defective in the PG0121 mutant. Collectively, our studies show that PG0121 does indeed encode a functional HU homologue, and HUβ has global regulatory functions in P. gingivalis; it affects not only production of capsular polysaccharides but also expression of genes involved in basic functions, such as cell wall synthesis, cell division and iron uptake. © 2013 SGM.

Microbiology (United Kingdom)

The nucleoid-associated protein HUβ affects global gene expression in porphyromonas gingivalis

Cysticercosis is caused by larval stage of tape worms Taenia solium (T. solium). Human beings get infected by eating undercooked pork or vegetables and drinking contaminated water infected with eggs of T. solium. Human cysticercosis commonly manifests as subcutaneous and intramuscular nodules. This study highlights the role of fine needle aspiration cytology (FNAC) in the diagnosis of subcutaneous cysticercosis. FNAC was performed using 23/21 gauge needle and 20 ml disposable plastic syringe fitted to a specially designed holder. Total, 66 cases were diagnosed to have cysticercosis, some rare sites were also aspirated like midline neck swelling & breast. In 48 cases (72.72%) actual parasitic structures, like fragment of the wall or tegument of parasite were demonstrated. In rest of cases inflammatory cell and eosinophils were seen. if the FNAC is done by trained cytopathologist with thin needle and with precautions, then it is quite safe and cost effective method, thereby eliminating the need of histopathological examination.

International Journal of Pharma and Bio Sciences

"Role of fine needle aspiration cytology in diagnosis of subcutaneous cysticercosis - A report of 66 cases"

Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-à-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm. © 2013 Indian Academy of Sciences.