scholarly journals WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways

2021 ◽  
Vol 8 (8) ◽  
pp. 114
Author(s):  
Tatsuya Sekiguchi ◽  
Hiroyuki Hamada ◽  
Masahiro Okamoto
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Biological Systems ◽  
Layered Structures ◽  
Research Interest ◽  
Biochemical Reaction ◽  
Biochemical Reactions

We previously developed the biochemical reaction simulator WinBEST-KIT. In recent years, research interest has shifted from analysis of individual biochemical reactions to analysis of metabolic pathways as systems. These large-scale and complicated metabolic pathways can be considered as characteristic multi-layered structures, which, for convenience, are separated from whole biological systems according to their specific roles. These pathways include reactants having the same name but with unique stoichiometric coefficients arranged across many different places and connected between arbitrary layers. Accordingly, in this study, we have developed a new version of WinBEST-KIT that allows users (1) to utilize shortcut symbols that can be arranged with multiple reactants having the same name but with unique stoichiometric coefficients, thereby providing a layout that is similar to metabolic pathways depicted in biochemical textbooks; (2) to create layers that divide large-scale and complicated metabolic pathways according to their specific roles; (3) to connect the layers by using shortcut symbols; and (4) to analyze the interactions between these layers. These new and existing features allow users to create and analyze such multi-layered metabolic pathways efficiently. Furthermore, WinBEST-KIT supports SBML, making it possible for users to utilize these new and existing features to create and publish SBML models.

scholarly journals General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 336
Author(s):  
Boštjan Murovec ◽  
Leon Deutsch ◽  
Blaž Stres
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Enzymatic Reactions ◽  
Operational Taxonomic Units ◽  
Biochemical Pathways ◽  
Meaningful Information ◽  
Novel Biomarkers ◽  
Reproducible Analysis ◽  
Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

scholarly journals Proteomic responses of spores of Bacillus subtilis to thermosonication involve large-scale alterations in metabolic pathways

2020 ◽  
Vol 64 ◽  
pp. 104992
Author(s):  
Lihua Fan ◽  
Furong Hou ◽  
Aliyu Idris Muhammad ◽  
Balarabe Bilyaminu Ismail ◽  
Ruiling lv ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Proteomic Responses

Preparation of a fluorescent (anthracene labeled) cardiolipin on a large scale using the metabolic machinery of the bacterium Micrococcus luteus

1990 ◽  
Vol 68 (1) ◽  
pp. 373-376 ◽  
Author(s):  
E. Pérochon ◽  
J. de Bony ◽  
J. F. Tocanne
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Micrococcus Luteus ◽  
High Rate ◽  
Nonanoic Acid

Micrococcus luteus bacterium has been used as a tool for the preparation of a fluorescent (anthracene labeled) cardiolipin by a method involving two steps. First, 9-(2-anthryl)nonanoic acid is incorporated into the lipids of the bacterium by usual metabolic pathways; then phosphatidylglycerol, a major lipid in this bacterium, is converted into cardiolipin by endogeneous cardiolipin synthetase. It is shown that cardiolipin synthetase transforms anthracene–phosphatidylglycerol into anthracene–cardiolipin at a high rate. The method can be extended to the synthesis of cardiolipin molecules bearing other hydrophobic marker groups.Key words: cardiolipin, fluorescence, biosynthesis, Micrococcus luteus.

Transcriptomic and proteomic responses of Serratia marcescens to spaceflight conditions involve large-scale changes in metabolic pathways

2014 ◽  
Vol 53 (7) ◽  
pp. 1108-1117 ◽  
Author(s):  
Yajuan Wang ◽  
Yanting Yuan ◽  
Jinwen Liu ◽  
Longxiang Su ◽  
De Chang ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Proteomic Responses

Global metabolic profiling of clear cell renal cell carcinoma.

2013 ◽  
Vol 31 (6_suppl) ◽  
pp. 379-379
Author(s):  
A. Ari Hakimi ◽  
Chung-Han Lee ◽  
Justin R. Cross ◽  
Zhen Li ◽  
Yang Chen ◽  
...  
Keyword(s):  
Disease Progression ◽  
Metabolic Profiling ◽  
Metabolic Pathways ◽  
Renal Cell ◽  
Normal Tissue ◽  
Large Scale ◽  
Clear Cell ◽  
Locally Advanced ◽  
P Value ◽  
Cell Renal Cell Carcinoma

379 Background: Recent data has suggested that metabolomic profiling in various cancer states may lead to novel biomarkers and innovative therapeutic strategies. We profiled the metabolome of 140 clear cell renal cell carcinomas (ccRCC) and matched normal tissue of various clinical stages. Methods: In collaboration with Metabolon, Inc., 140 clinically annotated tumors were subject to three global metabolic profiling mass spectroscopy platforms. Demographic, clinical, and pathologic data were recorded and patients were grouped into local, locally advanced and metastatic categories using clinical and pathologic criteria. Welch’s paired two sample t tests were used to identify biochemicals that differed significantly between the tumor and normal tissue groups (p value ≤0.001). Supervised clustering using random forest analysis was performed to identify metabolites that differentiated tumors and normals, as well as those associated with tumor progression. Results: A total of 877 biochemicals (including 300 unnamed metabolites) were identified. Several known cancer metabolic pathways were found to be altered consistent with the Warburg effect including accelerated glycolysis and pentose phosphate pathway (PPP), increased lipogenesis, elevated polyamine production, altered nitrogen handling, cell membrane metabolism, inflammation, and oxidative stress. Interestingly, several novel unexpected pathways were found to be altered and associated with disease progression including alterations in the 2-hydroxyglutarate pathway (2HG). 2HG levels were increased over 6 fold in tumors compared to normal and increased further with respect to disease progression (p = 0.019, q = 0.055). Several promising biomarker candidates were identified as well. Conclusions: We provide the first report of large scale metabolomic analysis of ccRCC, revealing several known and novel alterations to cancer-specific metabolic pathways. Investigation of novel pathway biology and biomarker validation in blood and urine samples is currently underway.

Large-scale quantum effects in biological systems

2005 ◽  
Vol 102 (6) ◽  
pp. 1116-1130 ◽  
Author(s):  
Marcus V. Mesquita ◽  
�urea R. Vasconcellos ◽  
Roberto Luzzi ◽  
Sergio Mascarenhas
Keyword(s):  
Large Scale ◽  
Biological Systems ◽  
Quantum Effects

Cardiovascular disease: primary prevention, disease modulation and regenerative therapy

Vascular ◽  
2012 ◽  
Vol 20 (5) ◽  
pp. 243-250 ◽  
Author(s):  
Sherif Sultan ◽  
Niamh Hynes
Keyword(s):  
Primary Prevention ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Cochrane Review ◽  
Insulin Level ◽  
Gene Interaction ◽  
Regenerative Therapy ◽  
Vascular Medicine ◽  
Randomized Controlled

Cardiovascular primary prevention and regeneration programs are the contemporary frontiers in functional metabolic vascular medicine. This novel science perspective harnesses our inherent ability to modulate the interface between specialized gene receptors and bioavailable nutrients in what is labeled as the nutrient–gene interaction. By mimicking a natural process through the conveyance of highly absorbable receptor specific nutrients, it is feasible to accelerate cell repair and optimize mitochondrial function, thereby achieving cardiovascular cure. We performed a comprehensive review of PubMed, EMBASE and Cochrane Review databases for articles relating to cardiovascular regenerative medicine, nutrigenomics and primary prevention, with the aim of harmonizing their roles within contemporary clinical practice. We searched in particular for large-scale randomized controlled trials on contemporary cardiovascular pharmacotherapies and their specific adverse effects on metabolic pathways which feature prominently in cardiovascular regenerative programs, such as nitric oxide and glucose metabolism. Scientific research on ‘cardiovascular-free’ centenarians delineated that low sugar and low insulin are consistent findings. As we age, our insulin level increases. Those who can decelerate the rapidity of this process are prompting their cardiovascular rejuvenation. It is beginning to dawn on some clinicians that contemporary treatments are not only failing to impact on our most prevalent diseases, but they may be causing more damage than good. Primary prevention programs are crucial elements for a better outcome. Cardiovascular primary prevention and regeneration programs have enhanced clinical efficacy and quality of life and complement our conventional endovascular practice.

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