Optimization based automated curation of metabolic reconstructions

<p>Abstract</p> <p>Background</p> <p>Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., <it>Escherichia coli, Saccharomyces cerevisiae</it>, <it>Bacillus subtilis</it>) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them.</p> <p>Results</p> <p>In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. This connectivity restoration is hypothesized to take place through four mechanisms: a) reversing the directionality of one or more reactions in the existing model, b) adding reaction from another organism to provide functionality absent in the existing model, c) adding external transport mechanisms to allow for importation of metabolites in the existing model and d) restore flow by adding intracellular transport reactions in multi-compartment models. We demonstrate this procedure for the genome- scale reconstruction of <it>Escherichia coli </it>and also <it>Saccharomyces cerevisiae </it>wherein compartmentalization of intra-cellular reactions results in a more complex topology of the metabolic network. We determine that about 10% of metabolites in <it>E. coli </it>and 30% of metabolites in <it>S. cerevisiae </it>cannot carry any flux. Interestingly, the dominant flow restoration mechanism is directionality reversals of existing reactions in the respective models.</p> <p>Conclusion</p> <p>We have proposed systematic methods to identify and fill gaps in genome-scale metabolic reconstructions. The identified gaps can be filled both by making modifications in the existing model and by adding missing reactions by reconciling multi-organism databases of reactions with existing genome-scale models. Computational results provide a list of hypotheses to be queried further and tested experimentally.</p

Citations analysis of LIS theses submitted to Kuvempu University and University of Mysore

A Citation analysis on 8289 citations cited in 59 LIS doctoral theses submitted to Kuvempu University (15 theses) and University of Mysore (44 theses) has been carried out to know the citation pattern. The data was collected using Shodhganga e-theses database. The study found that a total of 6883 journal citations were cited in 59 theses. The journal ‘Scientometrics’ has been cited 651 times and stands first in the rank list of journals. Annals of Library and Information Studies which is an Indian LIS journal stands in the third position in the rank list with 130 citations. The Bradford’s law of scattering is not applicable for this study. The rank list of country-wise journals showed that journals published from USA have highly cited followed by journals published from UK and India

Acquisition of Images using Neural Network

The application of computer vision to the image retrieval problem is Content-based image retrieval (CBIR). The interest in digital images is growing day by day. Users in professional fields are make use of the opportunities offered by the ability to access and manipulate remotely-stored images in different ways. The problems in image retrieval are becoming widely accepted, and the finding solution is an active area for research and development. This dissertation work aims at developing a hybrid scheme for intelligent image retrieval system using neural networks. Each image in the database is indexed by a visual feature vector, which is extracted using color moments and discrete cosine transform coefficients. The query is characterized by a set of predefined semantic labels. A novel method of similarity measure using dot product is used for ranking and retrieval for improved performance of the system DOI: 10.17762/ijritcc2321-8169.15050

Solvent extraction and separation of zinc and cobalt from ammoniacal solution

A process was developed to recover Zn and Co by solvent extraction from the raffinate generated during processing of sea nodules. From a model ammoniacal solution containing 0.2 g/L Zn or 0.2 g/L Co, extraction of Zn and Co by Versatic acid was studied. A maximum of 87% Zn was extracted with 1M Versatic acid in single stage, whereas extraction of Co was negligible due to its higher oxidation state. When Co(III) was reduced to Co(II) by the addition of cobalt powder, 1M Versatic acid extracted 76% Co in a single stage. From the McCabe Thiele diagram number of counter current extraction stages required for complete recovery of Zn and Co from ammoniacal solution was determined. Simulation of counter current extraction of Zn and Co was also carried out. Thus, this process can be used to recover Zn, leaving Co in the raffinate. Then Co can be recovered by solvent extraction with Versatic acid after reducing Co(III) to Co(II) state

Bio-hydrometallurgical approach in processing of low grade Indian uranium ore in Column Reactor

In order to augment the supply of uranium for electricity generation, bioleaching is being considered for exploiting a low-grade uranium ore (with 0.024% U3O8 of Turamdih Mines, Jharkhand, India). This ore contains silicate and magnetite as the main minerals and uraninite and hematite as minor minerals. At NML, efforts have been made to use Acidithiobacillus ferrooxidans (Ac.Tf) initially on bench scale in shake flask and then in column to recover uranium. In shake flasks, ~98% uranium dissolution was achieved in 30days at 1.7pH, 35oC temperature and 20% (w/v) pulp density. In a laboratory scale column containing 2.5kg ore, uranium bio-recovery of 55.48% was obtained in 30 days at 1.7pH. To scale up the process, the bio-leaching experiments carried out on 80kg ore showed uranium recovery of 69.8% as against a recovery of 55.12% in control set at 1.7 pH in 50 days. Bio-recovery of uranium has been correlated with the change in redox potential (Eh) and ferric ion concentration

Biosorption of trivalent chromium from a model tanning solution by adapted aspergillus niger

Industrial effluents containing metallic species are responsible for environmental degradation which have been prioritised as major inorganic contaminants. Conventional methods are quite expensive resulting in need for cost-effective process for removing heavy metals from discharging effluents. The use of microbial biomass for removal of heavy metals from aqueous solutions (biosorption) is one such approach gaining increasing attention. Trivalent chromium ion present in tannery effluents has been the targeted ionic species for removal due to its exceeding limits in industrial discharges (<--0.3 ppm as per WHO). At NML, efforts were made for biosorption of trivalent chromium from tannery effluents with Cr (III) concentration in the range 1500-5000ppm. Aspergillus niger, obtained from a culture bank has been used in biosorption of trivalent chromium of tannery effluents. The fungal species grown in Czapek Dox Medium and adapted on Cr(III) ions ranging from 10-2000ppm at 2.5 pH and 35°C, was used for biosorption of chromium from a model tanning solution. A.niger was used in forms such as live, adapted and pre-treated (autoclaved, alkali-treated) for biosorption at pH 2.5 and 35°C. At Cr(IlI) conc. of 2000ppm in the aqueous solution, the adsorption efficiency followed the order: alkali treated (52%)>live(38%)>autoclaved dead mass(27%). The varying biosorption capacities may be attributed to exposed metal binding sites in alkali treated fungus causing high biosorption efficiency which also obeyed the sorption isotherm

CD4+ T-lymphocytes exhibit biphasic kinetics post-myocardial infarction

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Solvent extraction in copper metallurgy recovery of acid and metals from copper bleed stream

Solvent extraction in copper metallurgy has been the first major application for producing nonferrous metals beyond the production of rare earths/nuclear metals. With the advent of solvent extrac-tion (SX), several lean grade, complex, rnultimetal and pocket deposits including byproducts could be processed to produce copper economically. Though, the SX technology is proven internationally, it has yet to find an industrial application in the Indian context. This paper outlines the possibility of using solvent extraction in copper metallurgy particularly in the Indian scenario. Specific example of the processing of copper bleed stream has also been mentioned. Some of the details and the flowsheet coven here shows how the sulphuric acid can be recov-ered from the copper bleed stream for recycling in the system. Besides, the recovery of copper and nickel in convenient form like metal sulphates and electrolytic grade metal cathodes can be taken u

Recovery of Cu and Ni from a Secondary Resource by Hydrometallurgical Route

A high iron containing copper and nickel based secondary resource analysing 22.43% Cu, 7.94% Ni and 36.28% iron has been treated to recover valuable metals by leaching with sulphuric acid. It was found that recovery of copper and nickel increased with increase in temperature and sulphuric acid concentration and in a two-stage leaching with 20% (v/v) sulphuric acid at 368 K above 99.9% copper and 82.35% nickel were recovered. The leaching data best fitted into chemical controlled kinetic model showing chemical reaction at the surface of the solid matrix. Activation energy of 20 kJ/mol and 44 kJ/mol were acquired for dissolution of copper and nickel, respectively. Attempts were also made to separate iron from the leach liquor by using Versatic 10 and recovery of copper and nickel in the form of their sulphate by solvent extraction; the copper and nickel could then be recovered as salts, metal cathodes or metal powder