Mano Ram Maurya

Bio: Mano Ram Maurya is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Systems biology & Fault detection and isolation. The author has an hindex of 28, co-authored 63 publications receiving 2427 citations. Previous affiliations of Mano Ram Maurya include San Diego Supercomputer Center & Purdue University.

Bioinformatics and systems biology of the lipidome.

Abstract: Lipids play an important role in physiology and pathophysiology of living systems. Until a few decades ago, the number of lipid molecules that were chemically characterized was a few hundred at most and were catalogued in monographs and compendia.1 Since the advent of the era of the genome and the proteome, there has been increasing recognition that other macromolecules like lipids and polysaccharides in living systems display considerable structural diversity and systematic efforts are underway to identify, characterize and catalog these molecules. With mass spectrometric techniques coming of age, several thousand distinct molecular species have been identified from living species and the roles of several of these are beginning to be characterized.2 Unlike genes and proteins, whose defined alphabets provide the framework for ontologies and classification at the sequence level, lipids and polysaccharides have been characterized for the large part by popular names, with no foundations for systematic classification. The past two decades have witnessed two major advances in lipid biology. In the first, mass spectrometry has enabled the identification of thousands of lipid molecular species from cells and tissues and this has pointed to the important need for developing a systematic ontology that can rationally name and catalog the molecules. Second, the ability to investigate the functional roles of lipid molecules through systematic phenotypic studies has led to the identification of lipids as extremely important players in physiology and pathophysiology of living species.3 In combination with proteins and nucleic acids, lipids are integrally involved in biochemical networks that lead to phenotypes such as homeostasis, differentiation, and death of cells and tissues. Any approach to systems characterization of living systems, of necessity, has to include lipids along with other macromolecules and all complex cellular pathways involving lipid molecular species. Systems biology now extends in its scope to identify biosynthetic and metabolic lipid networks, cellular signaling networks that explicitly include lipid molecules and transcriptional and epigenetic networks where lipids play an integral role.4 Several large scale projects to characterize lipids and their functional roles have been initiated as exemplified by the LIPID MAPS5 effort. The LIPID MAPS is an exemplar systems biology project that measures cell-wide lipid changes in an attempt to reconstruct biochemical pathways associated with lipid processing and signaling. The cell-wide measurements of components of these pathways include mass spectrometric measurements of lipid changes in response to stimulus in mammalian cells, changes in transcription profiles in response to stimulus and in select cases proteomic changes in response to stimulus. Figure 1 shows a schematic of the LIPID MAPS experiments related to different lipid categories/pathways and the subsequent processing of the experimental data generated. Network reconstruction efforts rely on organization, analysis and integration of these data and this requires a strong bioinformatics and systems biology effort. The former has to include development of a systematic and universal classification and nomenclature system, design and development of lipid and lipid-gene, lipid-protein databases with appropriate functional annotations, and efficient query and analysis systems that can be broadly useful to the biology research community. The latter has to include methods for analysis of large scale lipid measurements in cells, reconstruction of lipid metabolic and biosynthetic pathways, and quantitative models of lipid fluxes in cells under varied perturbations. In this review, we will provide a comprehensive summary of extant developments in lipid bioinformatics and systems biology and discuss the outlook for the future integration of lipidomics into cellular and organismic biology. The sections that follow are delineated into the informatics approaches specific to lipid biology followed by an overview and exemplar approach to analysis of large scale lipidomic data towards a systems description of mammalian cells. Figure 1 Overview of the process of performing a quantitative lipid analysis of macrophage cell sample (in this example, a time-course experiment using bone marrow derived macrophages). Extraction methods, LC/GC purification methods, MS acquisition strategies ... 2. Classification, Ontology, Nomenclature and Structure Representation of Lipid Molecules The first step towards classification of lipids is the establishment of an ontology that is extensible, flexible and scalable. One must be able to classify, name and represent these molecules in a logical manner which is amenable to data basing and computational manipulation. Lipids have been loosely defined as biological substances that are generally hydrophobic in nature and in many cases soluble in organic solvents.6 These chemical features are present in a broad range of molecules such as fatty acids, phospholipids, sterols, sphingolipids, terpenes and others. In view of the fact that lipids comprise an extremely heterogeneous collection of molecules from a structural and functional standpoint, it is not surprising that there are significant differences with regard to the scope and organization of current classification schemes. 2.1. Classification, Ontology and Nomenclature In order to address the lack of a consistent classification and nomenclature methodology for lipids, LIPID MAPS consortium members have developed a comprehensive classification system for lipids.7 The consortium has taken a more chemistry-based approach and defines lipids as hydrophobic or amphipathic small molecules that may originate entirely or in part by carbanion based condensations of thioesters (such as fatty acids and polyketides) and/or by carbocation based condensations of isoprene units (such as prenols and sterols). Figure 2 shows the mechanisms of lipid biosynthesis.8 Based on this classification system, lipids have been divided into eight categories: Fatty acyls, Glycerolipids, Glycerophospholipids, Sphingolipids, Sterol lipids, Prenol lipids, Saccharolipids, and Polyketides. Each category is further divided into classes and subclasses. Additionally, following the existing rules and recommendations proposed by the International Union of Biochemistry and Applied Chemists and the International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) commission on Biochemical Nomenclature, a consistent nomenclature scheme has also been developed to provide systematic names for various classes and subclasses of lipids.7 Figure 2 Mechanisms of lipid biosynthesis. Biosynthesis of ketoacyl- and isoprene-containing lipids proceeds by carbanion and carbocation-mediated chain extension, respectively.8 All lipids in the LIPID MAPS Structure Database (LMSD) are classified and annotated using this comprehensive classification and nomenclature system developed by the LIPID MAPS consortium.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

Global burden of NAFLD and NASH: trends, predictions, risk factors and prevention

Abstract: NAFLD is one of the most important causes of liver disease worldwide and will probably emerge as the leading cause of end-stage liver disease in the coming decades, with the disease affecting both adults and children. The epidemiology and demographic characteristics of NAFLD vary worldwide, usually parallel to the prevalence of obesity, but a substantial proportion of patients are lean. The large number of patients with NAFLD with potential for progressive liver disease creates challenges for screening, as the diagnosis of NASH necessitates invasive liver biopsy. Furthermore, individuals with NAFLD have a high frequency of metabolic comorbidities and could place a growing strain on health-care systems from their need for management. While awaiting the development effective therapies, this disease warrants the attention of primary care physicians, specialists and health policy makers.