A Database for TSSs of Human MicroRNAs

MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is still in progress. This information, even though limited, may be useful for further study on the regulation of miRNAs. In this paper, we provide a novel database of miRNA TSSs (miRT) that might be a valuable resource for advanced research on miRNA regulation

Mining the Largest Quasi-clique in Human Protein Interactome

A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem of finding quasicliques that are almost complete subgraphs of a graph. In sparse and very large scale-free networks, the problem of finding the largest quasi-clique becomes hard to manage with the existing approaches. Here, we propose a heuristic algorithm in this paper for locating the largest quasi-clique from the human protein-protein interaction networks. The results show promise in computational biology research by the exploration of significant protein modules

Integration of Co-expression Networks for Gene Clustering

Simultaneous overexpression or underexpression of multiple genes, used in various forms as probes in the high-throughput microarray experiments, facilitates the identification of their underlying functional proximity. This kind of functional associativity (or conversely the separability) between the genes can be represented proficiently using co-expression networks. The extensive repository of diversified microarray data encounters a recent problem of multi-experimental data integration for the aforesaid purpose. This paper highlights a novel integration method of gene co-expression networks, based on the search for their consensus network, derived from diverse microarray experimental data for the purpose of clustering. The proposed methodology avoids the bias arising from missing value estimation. The method has been applied on microarray datasets arising from different category of experiments to integrate them. The consensus network, thus produced, reflects robustness based on biological validation

Finding Bicliques in Digraphs: Application into Viral-host Protein Interactome

We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein interaction graphs. Strong and significant bicliques of HIV-1 and human proteins are derived using the proposed methodology, which provides insights into some novel regulatory functionalities in case of the acute immunodeficiency syndrome in human

Study of heterogeneity of sino-nasal lesions in urban population of north Kolkata and its fringes- a 5-year retrospective analysis: experience of a tertiary care centre

Background: Lesions of the nasal cavity and paranasal sinuses form a single functional unit as both of these are affected by common pathological processes. Accurate diagnosis and early treatment can significantly reduce the morbidities associated with these lesions. This study aims at portraying the morphological diversions of sinonasal lesions that is commonly encountered in populations of north Kolkata and its fringes. The multitude of histopathological variations of the sinonasal masses intrigues us histopathologists not only from academic point of view but also guides clinicians regarding treatment and prognosis.Methods: A retrospective study conducted in the Department of Pathology from May 2012 to April 2017.Results: Total 429 cases were assessed during this period out of which maximum cases were found in the age group of 31- 40years. Most cases were diagnosed with nasal polyps. The rare histopathological types were ameloblastoma, paraganglioma, Schwanoma, neurofibroma, inflammatory myofibroblastic tumor, sinonasal hemangiopericytoma, adenoid cystic carcinoma, low grade mucoepidermoid tumor, malignant peripheral nerve sheath tumor.Conclusions: Both neoplastic and non-neoplastic sino nasal lesions may present with indistinguishable features, leading to a delay in proper diagnosis and treatment. So, any tissue after surgical removal should be send for histopathological diagnosis without unnecessary delay to prevent further complications

Barreras naturales para las horquillas de replicación DNA en Schizosaccharomyces pombe

106 p.-35 fig.En la naturaleza, el crecimiento vegetativo de S. pombe es normalmente haploide. Sólo bajo condiciones ambientales adversas, como en condiciones de ayuno de fuentes nitrógeno, dos células de tipos de apareamiento contrarios, P (plus) y M (minus), conjugan y forman un cigoto diploide (Egel, 1989; Dalgaard y Klar, 2001). Para cada tipo de apareamiento, existen células denominadas switchable (s) y células unswitchable (u). Cada célula de S. pombe que acaba de adquirir un tipo de apareamiento concreto, da lugar a otra del tipo de apareamiento contrario tras dos divisiones mitóticas. Cuando una célula u se divide da lugar a dos células del mismo tipo de apareamiento que la célula parental, una de ellas s y la otra u. Cuando se divida, la célula s dará lugar a una célula u de tipo de apareamiento contrario a la parental y a otra célula s del mismo tipo de apareamiento que la parental (Miyata y Miyata, 1981; Egel y Eie, 1987; Klar, 1987, 1990). Aunque el mecanismo molecular responsable del cambio del tipo de apareamiento en S. pombe no se conoce aún en detalle, algunas de las claves han sido ya descifradas (ver Dalgaard y Klar, 2001 y apartado 1.4.2.). Una vez que producida la conjugación, los núcleos se fusionan y el cigoto diploide resultante sufre meiosis inmediatamente. El cigoto se convierte en una estructura de resistencia denominada asca, que contiene cuatro esporas haploides. Este proceso representa un ejemplo de diferenciación celular. Cuando las condiciones ambientales vuelven a ser favorables, las esporas son liberadas y pueden germinar, cerrándose de este modo el ciclo. Las poblaciones naturales de S. pombe, son homotálicas, es decir, están compuestas por células de los dos tipos de apareamiento y entran en diferenciación sexual bajo condiciones de estrés ambiental. En el laboratorio, a menudo se emplean estirpes heterotálicas, las cuales necesitan otra estirpe del tipo de apareamiento contrario para aparear. En el laboratorio se puede promover la entrada de los cigotos a la división mitótica y seleccionarlos usando mutaciones auxotróficas complementarias en el proceso de conjugación, obteniendo así estirpes diploides que, eventualmente, pueden inducirse a entrar en ciclo mitótico colocándolas en unas condiciones de cultivo adecuadas.Financiación del Proyecto SAF2001-1740; de la Beca del CSIC de Postgrado para la Formación y Especialización en Líneas de Investigación para el Sector Industrial con REF.: I3P-BPG2004 y del Proyecto BFU2004-00125/BMC.Peer reviewe

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

<p>Abstract</p> <p>Background</p> <p>Some of the recent investigations in systems biology have revealed the existence of a complex regulatory network between genes, microRNAs (miRNAs) and transcription factors (TFs). In this paper, we focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. A putative TF of an miRNA is considered here as those binding within the close genomic locality of that miRNA with respect to its starting or ending base pair on the chromosome. Recent studies suggest that these putative TFs are possible regulators of those miRNAs.</p> <p>Description</p> <p>The interface is built around two datasets that consist of the exhaustive lists of putative TFs binding respectively in the 10 kb upstream region (USR) and downstream region (DSR) of human miRNAs. A web server, named as PuTmiR, is designed. It provides an option for extracting the putative TFs for human miRNAs, as per the requirement of a user, based on genomic locality, i.e., any upstream or downstream region of interest less than 10 kb. The degree distributions of the number of putative TFs and miRNAs against each other for the 10 kb USR and DSR are analyzed from the data and they explore some interesting results. We also report about the finding of a significant regulatory activity of the YY1 protein over a set of oncomiRNAs related to the colon cancer.</p> <p>Conclusion</p> <p>The interface provided by the PuTmiR web server provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether an miRNA can also be regulated by the TFs binding to their DSR.</p

Mapping child growth failure across low- and middle-income countries

Child growth failure (CGF), manifested as stunting, wasting, and underweight, is associated with high 5 mortality and increased risks of cognitive, physical, and metabolic impairments. Children in low- and middle-income countries (LMICs) face the highest levels of CGF globally. Here we illustrate national and subnational variation of under-5 CGF indicators across LMICs, providing 2000–2017 annual estimates mapped at a high spatial resolution and aggregated to policy-relevant administrative units and national levels. Despite remarkable declines over the study period, many LMICs remain far from the World Health 10 Organization’s ambitious Global Nutrition Targets to reduce stunting by 40% and wasting to less than 5% by 2025. Large disparities in prevalence and rates of progress exist across regions, countries, and within countries; our maps identify areas where high prevalence persists even within nations otherwise succeeding in reducing overall CGF prevalence. By highlighting where subnational disparities exist and the highest-need populations reside, these geospatial estimates can support policy-makers in planning locally 15 tailored interventions and efficient directing of resources to accelerate progress in reducing CGF and its health implications