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OALib Journal期刊

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Network-based approaches for linking metabolism with environment
Sarath Janga, M Madan Babu
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-11-239
Abstract: The sequential nature of the reactions in metabolic pathways means that they can be modeled in the form of a graph (network) of enzymes and chemical transformations, and network theory can be used to represent and understand metabolism [1,2]. The connected collection of metabolic pathways, describing the set of all enzymatic interc-onversions of one small molecule into another, is defined as the metabolic network of an organism (Figure 1a).The most commonly used network representations are 'metabolite-centric'. They consider metabolites as the nodes of the graph and two metabolites are linked if one can be converted into the other by an enzymatic reaction (Figure 1b, left). An alternative network representation is 'enzyme-centric'. It considers the enzymes as nodes and links enzymes that catalyze successive reactions (Figure 1b, right). Although several studies have provided insights into the structure and evolution of a metabolic network, very few have addressed the influence of environment on metabolic network structure in species from diverse environmental conditions. The availability of many completely sequenced genomes means that metabolic-network analysis can now be extended from a few model organisms to species from different branches of the tree of life and living in very different environments. This should enable the elucidation of general principles underlying metabolic networks.Two recent studies, published in the Proceedings of the National Academy of Sciences by Eytan Ruppin and colleagues (Kreimer et al. [3] and Borenstein et al. [4]), provide important insights into links between the environment of an organism and the structure of its metabolic network. Using data from a large number of bacterial metabolic networks, Kreimer et al. address the question of how the topologies of the metabolic networks from different species reflect both genome size and the diversity of environmental conditions the species would encounter. Borenstein et al. set out to ide
Influence of electrolytes on the controlled release of verapamil hydrochloride from HPMC K15M matrix tablets
Vidyadhara Suryadevara,Babu Janga,krishna Talamanchi
Asian Journal of Pharmaceutics , 2011,
Abstract: Verapamil hydrochloride was formulated as oral-controlled release matrix tablets using hydrophilic polymer such as hydroxypropyl methylcellulose K 15 M (HPMC 15 M) along with electrolytes. In this work a new attempt was made for in situ interactions between drug and electrolytes were devised to control the release of highly water soluble drugs from oral hydrophilic monolithic systems. Electrolytes such as aluminum hydroxide and sodium carbonate were used at different concentrations in various formulations, while drug and polymer concentrations were maintained constantly at 1:2 ratios in all the formulations. These electrolytes were used to monitor matrix swelling and gel properties. Electrolytes at higher concentrations exhibited greater inhibition in drug release from the matrix and low concentrations were accounted for controlled release of the drug. The results indicated that the drug released at a controlled rate were due to differential swelling rate and matrix stiffening, and provides a uniform gel layer. These findings indicated that the swelling and gel formation in the presence of ionizable species within the hydrophilic matrices provide an attractive alternative for controlled drug delivery from a simple monolithic system. Accelerated stability studies were carried out as per ICH guidelines for some selected formulations, which indicated that these formulations were stable at accelerated storage conditions.
AN EFFICIENT AND ROBUST MODEL FOR DATA LEAKAGE DETECTION SYSTEM
Janga Ajay Kumar
Journal of Global Research in Computer Science , 2012,
Abstract: - In every enterprise, data leakage is very serious problem faced by it. An owner of enterprise has given sensitive data to itsemployee but in most of the situation employee leak the data. That leak data found in unauthorized place such as on the web of comparator enterprise or on laptop of employee of comparator enterprise or the owner of comparators laptop. It is either observed or sometimes not observed by owner. Leak data may be source code or design specifications, price lists, intellectual property and copy rights data, trade secrets, forecasts and budgets. In this case the data leaked out it leaves the company goes in unprotected the influence of the corporation. This uncontrolled data leakage puts business in a backward position. To find the solution on this problem we develop two models. First, when any employee of enterprise access sensitive data without the consent of owner in that case ,we developed data watcher model to identifying data leaker and suppose employee given data outside the enterprise for that we devolved second model for assessing the “guilt” of agents. Guilt model are used to improve the probability of identifying guilty third parties.For implementing this system, we used SSBT’S COET, Bambhori, and Jalgaon college database. In this system we consider, data owner is college management called as distributor and other employee is called as agents. For that we considered two condition sample or explicit condition because agents want data in sample or condition.
Understanding Parijat through the Prism of Her Biography
Janga B Chauhan
Bodhi: An Interdisciplinary Journal , 2008, DOI: 10.3126/bodhi.v2i1.2863
Abstract: DOI: 10.3126/bodhi.v2i1.2863
Devkota in Russia
Janga B Chauhan
Bodhi: An Interdisciplinary Journal , 2009, DOI: 10.3126/bodhi.v3i1.2816
Abstract: DOI: 10.3126/bodhi.v3i1.2816 Bodhi Vol.3(1) 2009 p.99-105
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Pingzhao Hu,Sarath Chandra Janga,Mohan Babu,J. Javier Díaz-Mejía,Gareth Butland,Wenhong Yang,Oxana Pogoutse,Xinghua Guo,Sadhna Phanse,Peter Wong,Shamanta Chandran,Constantine Christopoulos,Anaies Nazarians-Armavil,Negin Karimi Nasseri,Gabriel Musso,Mehrab Ali,Nazila Nazemof,Veronika Eroukova,Ashkan Golshani,Alberto Paccanaro,Jack F. Greenblatt,Gabriel Moreno-Hagelsieb,Andrew Emili
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000096
Abstract: One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a “systems-wide” functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Pingzhao Hu equal contributor,Sarath Chandra Janga equal contributor,Mohan Babu equal contributor,J. Javier Díaz-Mejía equal contributor,Gareth Butland equal contributor,Wenhong Yang,Oxana Pogoutse,Xinghua Guo,Sadhna Phanse,Peter Wong,Shamanta Chandran,Constantine Christopoulos,Anaies Nazarians-Armavil,Negin Karimi Nasseri,Gabriel Musso,Mehrab Ali,Nazila Nazemof,Veronika Eroukova,Ashkan Golshani,Alberto Paccanaro,Jack F Greenblatt,Gabriel Moreno-Hagelsieb ,Andrew Emili
PLOS Biology , 2009, DOI: 10.1371/journal.pbio.1000096
Abstract: One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a “systems-wide” functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.
Ten Simple Rules for Organizing a Scientific Meeting
Manuel Corpas,Nils Gehlenborg,Sarath Chandra Janga,Philip E. Bourne
PLOS Computational Biology , 2008, DOI: 10.1371/journal.pcbi.1000080
Abstract:
A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes
Tanja Scherrer,Nitish Mittal,Sarath Chandra Janga,André P. Gerber
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015499
Abstract: Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known enzymes, many of them acting in metabolism, providing opportunities to directly connect intermediary metabolism with posttranscriptional gene regulation. We mapped the RNA targets for 13 proteins identified in this screen and found that they were associated with distinct groups of mRNAs, some of them coding for functionally related proteins. We also found that overexpression of the enzyme Map1 negatively affects the expression of experimentally defined mRNA targets. Our results suggest that many proteins may associate with mRNAs and possibly control their fates, providing dense connections between different layers of cellular regulation.
Tolvaptan in the Treatment of Acute Hyponatremia Associated with Acute Kidney Injury
Shilpa Gopinath,Kalyana C. Janga,Sheldon Greenberg,Shree K. Sharma
Case Reports in Nephrology , 2013, DOI: 10.1155/2013/801575
Abstract: Hyponatremia defined as a plasma sodium concentration of less than 135?mmol/L is a very common disorder, occurring in hospitalized patients. Hyponatremia often results from an increase in circulating arginine vasopressin (AVP) levels and/or increased renal sensitivity to AVP, combined with an increased intake of free water. Hyponatremia is subdivided into three groups, depending on clinical history and volume status: hypovolemic, euvolemic, and hypervolemic. Acute symptomatic hyponatremia is usually treated with hypertonic (3%) saline. Syndrome of inappropriate antidiuretic hormone hypersecretion (SIADH) and hypervolemic hyponatremia caused by heart failure or cirrhosis are treated with vasopressin antagonists (vaptans) since they increase plasma sodium (Na2+) concentration via their aquaretic effects (augmentation of free-water clearance). The role of tolvaptan in the treatment of acute hyponatremia and conversion of oliguric to nonoliguric phase of acute tubular necrosis has not been previously described. 1. Introduction Acute kidney injury is a frequent complication in critically ill patients and is difficult to manage as it is often accompanied by oliguria or anuria as well as total body fluid overload and edema. Optimal management of volume status as well as normalizing serum sodium levels is essential. Sodium concentration is the major determinant of plasma osmolality; therefore, hyponatremia usually indicates a low plasma osmolality. Low plasma osmolality rather than hyponatremia, per se, is the primary cause of the symptoms of hyponatremia. Hyponatremia not accompanied by hypoosmolality does not cause signs or symptoms and does not require specific treatment [1]. The limitation in the kidney’s ability to excrete water in hyponatremic states is, in most cases, due to the persistent action of antidiuretic hormone (ADH, vasopressin). ADH acts at the distal nephron to decrease the renal excretion of water. The action of ADH is, therefore, to concentrate the urine and, as a result, dilute the serum. Under normal circumstances, ADH release is stimulated primarily by hyperosmolality. However, under conditions of severe intravascular volume depletion or hypotension, ADH may be released even in the presence of serum hypoosmolality [1]. Hyponatremia and impaired urinary dilution can be caused by either a primary or a secondary defect in the regulation of AVP secretion or action. The primary forms are generally referred to as the syndrome of inappropriate antidiuresis (SIADH). When osmotic suppression of antidiuresis is impaired for any reason, retention
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