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Search Results: 1 - 10 of 139596 matches for " Dinesh K. Barupal "
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The volatile compound BinBase mass spectral database
Kirsten Skogerson, Gert Wohlgemuth, Dinesh K Barupal, Oliver Fiehn
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-321
Abstract: The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu webcite).The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://bi
Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry
Dinesh K Barupal, Tobias Kind, Shankar L Kothari, Do Lee, Oliver Fiehn
BMC Biotechnology , 2010, DOI: 10.1186/1472-6750-10-40
Abstract: In this study, we compared the hydrocarbon rich algae Botryococcus braunii against the photoautotrophic model algae Chlamydomonas reinhardtii using pyrolysis-gas chromatography quadrupole mass spectrometry (pyGC-MS). Sequences of up to 48 dried samples can be analyzed using pyGC-MS in an automated manner without any sample preparation. Chromatograms of 30-min run times are sufficient to profile pyrolysis products from C8 to C40 carbon chain length. The freely available software tools AMDIS and SpectConnect enables straightforward data processing. In Botryococcus samples, we identified fatty acids, vitamins, sterols and fatty acid esters and several long chain hydrocarbons. The algae species C. reinhardtii, B. braunii race A and B. braunii race B were readily discriminated using their hydrocarbon phenotypes. Substructure annotation and spectral clustering yielded network graphs of similar components for visual overviews of abundant and minor constituents.Pyrolysis-GC-MS facilitates large scale screening of hydrocarbon phenotypes for comparisons of strain differences in algae or impact of altered growth and nutrient conditions.The world requires a sustainable source of energy for the future. Autotrophic organisms have been proposed to reduce the energy dependence of world economy on the fossil oil [1]. Specifically, biofuel derived from microalgae [2] have been under active investigation. Hypothetical yield per hectare, land requirements, eco-friendly production, simple life structure and available scientific technologies are the major advantages to use the microalgae for large-scale biofuel production [3]. The hydrocarbon content of algae, specifically fatty acids, isoprenoids and triacylglycerides [4], have the potential to compensate for future decline of crude oil production [5] if algae growth and harvest can be sustained under economically and energetically feasible parameters. Genetic and environmental factors affect the lipid constituents of microalgae [2,4] a
Induced Pluripotent Stem Cells Show Metabolomic Differences to Embryonic Stem Cells in Polyunsaturated Phosphatidylcholines and Primary Metabolism
John K. Meissen, Benjamin T. K. Yuen, Tobias Kind, John W. Riggs, Dinesh K. Barupal, Paul S. Knoepfler, Oliver Fiehn
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046770
Abstract: Induced pluripotent stem cells are different from embryonic stem cells as shown by epigenetic and genomics analyses. Depending on cell types and culture conditions, such genetic alterations can lead to different metabolic phenotypes which may impact replication rates, membrane properties and cell differentiation. We here applied a comprehensive metabolomics strategy incorporating nanoelectrospray ion trap mass spectrometry (MS), gas chromatography-time of flight MS, and hydrophilic interaction- and reversed phase-liquid chromatography-quadrupole time-of-flight MS to examine the metabolome of induced pluripotent stem cells (iPSCs) compared to parental fibroblasts as well as to reference embryonic stem cells (ESCs). With over 250 identified metabolites and a range of structurally unknown compounds, quantitative and statistical metabolome data were mapped onto a metabolite networks describing the metabolic state of iPSCs relative to other cell types. Overall iPSCs exhibited a striking shift metabolically away from parental fibroblasts and toward ESCs, suggestive of near complete metabolic reprogramming. Differences between pluripotent cell types were not observed in carbohydrate or hydroxyl acid metabolism, pentose phosphate pathway metabolites, or free fatty acids. However, significant differences between iPSCs and ESCs were evident in phosphatidylcholine and phosphatidylethanolamine lipid structures, essential and non-essential amino acids, and metabolites involved in polyamine biosynthesis. Together our findings demonstrate that during cellular reprogramming, the metabolome of fibroblasts is also reprogrammed to take on an ESC-like profile, but there are select unique differences apparent in iPSCs. The identified metabolomics signatures of iPSCs and ESCs may have important implications for functional regulation of maintenance and induction of pluripotency.
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton, Oliver Fiehn
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-99
Abstract: We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development.MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu webcite.
Pharmacometabolomic Signature of Ataxia SCA1 Mouse Model and Lithium Effects
Bertrand Perroud, Paymaan Jafar-Nejad, William R. Wikoff, Jennifer R. Gatchel, Lu Wang, Dinesh K. Barupal, Juan Crespo-Barreto, Oliver Fiehn, Huda Y. Zoghbi, Rima Kaddurah-Daouk
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070610
Abstract: We have shown that lithium treatment improves motor coordination in a spinocerebellar ataxia type 1 (SCA1) disease mouse model (Sca1154Q/+). To learn more about disease pathogenesis and molecular contributions to the neuroprotective effects of lithium, we investigated metabolomic profiles of cerebellar tissue and plasma from SCA1-model treated and untreated mice. Metabolomic analyses of wild-type and Sca1154Q/+ mice, with and without lithium treatment, were performed using gas chromatography time-of-flight mass spectrometry and BinBase mass spectral annotations. We detected 416 metabolites, of which 130 were identified. We observed specific metabolic perturbations in Sca1154Q/+ mice and major effects of lithium on metabolism, centrally and peripherally. Compared to wild-type, Sca1154Q/+ cerebella metabolic profile revealed changes in glucose, lipids, and metabolites of the tricarboxylic acid cycle and purines. Fewer metabolic differences were noted in Sca1154Q/+ mouse plasma versus wild-type. In both genotypes, the major lithium responses in cerebellum involved energy metabolism, purines, unsaturated free fatty acids, and aromatic and sulphur-containing amino acids. The largest metabolic difference with lithium was a 10-fold increase in ascorbate levels in wild-type cerebella (p<0.002), with lower threonate levels, a major ascorbate catabolite. In contrast, Sca1154Q/+ mice that received lithium showed no elevated cerebellar ascorbate levels. Our data emphasize that lithium regulates a variety of metabolic pathways, including purine, oxidative stress and energy production pathways. The purine metabolite level, reduced in the Sca1154Q/+ mice and restored upon lithium treatment, might relate to lithium neuroprotective properties.
Inactivation of Metabolic Genes Causes Short- and Long-Range dys-Regulation in Escherichia coli Metabolic Network
Dinesh Kumar Barupal, Sang Jun Lee, Edward D. Karoly, Sankar Adhya
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0078360
Abstract: The metabolic network in E. coli can be severely affected by the inactivation of metabolic genes that are required to catabolize a nutrient (D-galactose). We hypothesized that the resulting accumulation of small molecules can yield local as well as systemic effects on the metabolic network. Analysis of metabolomics data in wild-type and D-galactose non-utilizing mutants, galT, galU and galE, reveal the large metabolic differences between the wild-type and the mutants when the strains were grown in D-galactose. Network mapping suggested that the enzymatic defects affected the metabolic modules located both at short- and long-ranges from the D-galactose metabolic module. These modules suggested alterations in glutathione, energy, nucleotide and lipid metabolism and disturbed carbon to nitrogen ratio in mutant strains. The altered modules are required for normal cell growth for the wild-type strain, explaining why the cell growth is inhibited in the mutants in the presence of D-galactose. Identification of these distance-based dys-regulations would enhance the systems level understanding of metabolic networks of microorganisms having importance in biomedical and biotechnological research.
Influence of Rigid Boundary and Initial Stress on the Propagation of Love Wave  [PDF]
Shishir Gupta, Amares Chattopadhyay, Sumit K. Vishwakarma, Dinesh K. Majhi
Applied Mathematics (AM) , 2011, DOI: 10.4236/am.2011.25078
Abstract: In the present paper we study the effect of rigid boundary on the propagation of Love waves in an inhomogeneous substratum over an initially stressed half space, where the heterogeneity is both in rigidity and density. The dispersion equation of the phase velocity has been derived. It has been found that the phase velocity of Love wave is considerably influenced by the rigid boundary, inhomogeneity and the initial stress present in the half space. The velocity of Love waves have been calculated numerically as a function of KH (where K is a wave number H is a thickness of the layer) and are presented in a number of graphs.
Propagation of Torsional Surface Waves under the Effect of Irregularity and Initial Stress  [PDF]
Shishir Gupta, Dinesh K. Majhi, Sumit K. Vishwakarma, Santimoy Kundu
Applied Mathematics (AM) , 2011, DOI: 10.4236/am.2011.212207
Abstract: The present paper has been framed to study the influence of irregularity, initial stress and porosity on the propagation of torsional surface waves in an initially stressed anisotropic poro-elastic layer over a semi-infinite heterogeneous half space with linearly varying rigidity and density due to irregularity at the interface. The irregularity has been taken in the half-space in the form of a parabola. It is observed that torsional sur- face waves propagate in this assumed medium. In the absence of irregularity the velocity of torsional surface wave has been obtained. Further, it has been seen that for a layer over a homogeneous half space, the velo- city of torsional surface waves coincides with that of Love waves.
Molecular Profiling of Drug Resistant Isolates of Mycobacterium tuberculosis in North India  [PDF]
Dinesh K. Tripath, Kanchan Srivastava, Surya Kant, Kishore K. Srivastava
Advances in Microbiology (AiM) , 2012, DOI: 10.4236/aim.2012.23038
Abstract: Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem because treatment is complicated, cure rates are well below those for drug susceptible tuberculosis (TB), and patients may remain infectious for months or years despite receiving the best available therapy. To gain a better understanding of MDR-TB, we characterized isolates recovered from 69 patients with MDR-TB, by use of IS6110 restriction fragment-length polymorphism (RFLP) analysis; spacer oligonucleotide genotyping (i.e. spoligotyping). Clinical isolates from patients with tuberculosis have been considered to contain clonally expanded Mycobacterium tuberculosis (MTB) strain. Over the years, the identification method based on IS6110 insertion sequences has been established as the standard for typing strains of MTB. IS6110 RFLP fingerprinting is very convincing when it is applied to classify MTB isolates harboring a large number of IS6110 in their chromosomes. Therefore, in the present study we have characterized the isolates from the patients suffering from MDR TB, on the basis of conserved Variable Number Tandem Repeats (VNTR), Direct Repeats (DR) and Insertion Sequences (IS) IS6110 elements. The polymorphic data showed significant level of dissimilarities among all the MDR isolates of MTB. Comparative studies with the DR and VNTR data substantiate that polymorphism occur among MDR-TB cases as shown by the number of repeats present in different clinical isolates.
Relation between Solar Wind Parameter and Geomagnetic Storm Condition during Cycle-23  [PDF]
Balveer S. Rathore, Dinesh C. Gupta, K. K. Parashar
International Journal of Geosciences (IJG) , 2014, DOI: 10.4236/ijg.2014.513131
Abstract: In the present paper dependence of geomagnetic activity on the solar-wind plasma and interplanetary magnetic field (IMF) parameters has been studied. We have taken interplanetary solar wind data at the instant of Dst minimum. Our study consists of 200 geomagnetic storms weighed by disturbance storm time (Dst) < -50 nT, observed during solar cycle 23. The study suggests that the strength of the geomagnetic storm is strongly dependent on the total magnetic field Btotal. The correlation (-0.72) has been found reasonable. In perspective of previous studies, the strength of the geomagnetic storm is strongly dependent on the southward component (Bz) whereas in present study exposes that the correlation (0.22) is weak. This result indicates that solar wind southward magnetic field component Bz has significant growth particularly before the main phase of geomagnetic storm (not during the main phase). The present result implies that neither density nor temperature is significantly related to the variation of geomagnetic disturbance; rather the effects of the pressure and speed. However, a low plasma beta during highly geoeffective event seems to be an important criterion.
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