A5057750162- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Enzyme Catalysis and Immobilization
- Protein Structure and Dynamics
- Renal and related cancers
- Biomedical Text Mining and Ontologies
- Bacteriophages and microbial interactions
- Cardiovascular and exercise physiology
- Epigenetics and DNA Methylation
- Microbial Community Ecology and Physiology
- Pharmacological Effects of Natural Compounds
- bioluminescence and chemiluminescence research
- Genetics, Bioinformatics, and Biomedical Research
- Bacterial biofilms and quorum sensing
- Evolution and Genetic Dynamics
- Cancer Genomics and Diagnostics
- Renal cell carcinoma treatment
- Parkinson's Disease and Spinal Disorders
- Metabolomics and Mass Spectrometry Studies
Amyris (United States)
2023
University of California, San Diego
2010-2016
La Jolla Bioengineering Institute
2013
Acuity Technologies (United States)
2012
Abstract Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes eukaryotes. Due to the successes with metabolism, there is an increasing effort apply COBRA reconstruct analyze integrated models cellular processes. The Toolbox MATLAB a leading software package analysis metabolism; however, it was not designed elegantly capture complexity inherent biological lacks integration framework...
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict pathway usage and growth phenotypes. Furthermore, they generate test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories high-quality must established, adhere established standards model components linked relevant databases. Tools for visualization further enhance their utility. meet needs, we present BiGG Models...
After hundreds of generations adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models (GEMs). However, it is not known whether the pathway usage in FBA solutions consistent with gene and protein expression wild‐type evolved strains. Here, we report that >98% active reactions from optimal growth are supported by transcriptomic proteomic data. Moreover, when E. adapts to rate selective pressure, strains...
Transcription and translation use raw materials energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology metabolism will facilitate comprehensive quantitative computations an organism's constitution as a function genetic environmental parameters. Here we formulate expression. Prototyping it using simple microorganism Thermotoga maritima, show our accurately simulates...
Significance Multiple Escherichia coli genome sequences have recently been made available by advances in DNA sequencing. Analysis of these genomes has demonstrated that the fraction genes common to all E. strains species represents a small entire gene pool. This observation raises question: what is strain and species? In this study, genome-scale metabolic reconstructions multiple are used reconstruct network for an its strain-specific variants. The models determine functional differences...
Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% its enzymes act on variety substrates and catalyze 65% the known metabolic reactions. However, it is not apparent why these generalist remain. Here, show there marked differences between specialist enzymes, single chemical reaction one particular substrate in vivo. Specialist (i) frequently essential,...
Abstract Rapid growth in size and complexity of biological data sets has led to the ‘Big Data Knowledge’ challenge. We develop advanced integration methods for multi-level analysis genomic, transcriptomic, ribosomal profiling, proteomic fluxomic data. First, we show that pairwise primary omics reveals regularities tie cellular processes together Escherichia coli : number protein molecules made per mRNA transcript ribosomes required translated molecule. Second, genome-scale models, based on...
There has been growing interest in disrupting bacterial virulence mechanisms as a form of infectious disease control through the use 'anti-infective' drugs. Pseudomonas aeruginosa is an opportunistic pathogen noted for its intrinsic antibiotic resistance that causes serious infections requiring new therapeutic options. In this study, analysis P. PAO1 deduced proteome was performed to identify pathogen-associated proteins. A computational screening approach then used discover drug repurposing...
Membranes play a crucial role in cellular functions. provide physical barrier, control the trafficking of substances entering and leaving cell, are major determinant ultra-structure. In addition, components embedded within membrane participate cell signaling, energy transduction, other critical All these processes must share limited space membrane; thus it represents notable constraint on Membrane- location-based have not yet been reconstructed explicitly integrated into genome-scale...
Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain small fraction hundreds genes that are regulated during shifts. Here we propose qualitative accounts for full breadth by detailing two global transcription factors (TFs), ArcA Fnr E. key metabolic redox ratios act on genome-wide basis regulate...
The generation of genome-scale data is becoming more routine, yet the subsequent analysis omics remains a significant challenge. Here, an approach that integrates multiple datasets with bioinformatics tools was developed produces detailed annotation several microbial genomic features. This methodology used to characterize genome Thermotoga maritima--a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental were generated for whole-genome resequencing, transcription start...
Yersinia pestis is a gram-negative bacterium that causes plague, disease linked historically to the Black Death in Europe during Middle Ages and several outbreaks modern era. Metabolism Y. displays remarkable flexibility robustness, allowing proliferate both warm-blooded mammalian hosts cold-blooded insect vectors such as fleas. Here we report genome-scale reconstruction mathematical model of metabolism for CO92 supporting experimental growth metabolite measurements. The contains 815 genes,...
Abstract Engineering microbes to synthesize molecules of societal value has historically been a time consuming and artisanal process, with the synthesis each new non-native molecule typically warranting its own separate publication. Because most microbial strain engineering efforts leverage finite number common metabolic design tactics, we reasoned that automating these steps would help create pipeline can quickly, cheaply, reliably generate so-called factories. In this work describe...
Article1 July 1934FURTHER OBSERVATIONS ON THE HEART IN MYXEDEMAJ. LERMAN, M.D., R. J. CLARK, H. MEANS, F.A.C.P.J. F.A.C.P.Author, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-8-1-82 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptIn a previous paper1 we presented data dealing with changes in the size of heart, blood pressure electrocardiograms resulting from thyroid medication myxedema...
You have accessJournal of UrologyKidney Cancer: Basic Research & Pathophysiology II (PD51)1 May 2024PD51-05 ALLELE-SPECIFIC DNA METHYLATION AFFECTING THE STEAP3 GENE IN RENAL CELL CARCINOMAS Mauricio Menagati Rigo, Angelica Castano, Martha C. Salas, Mariam Tariq, Joshua Lerman, Sophia Hartley, Fidi Nagy, Peter L. Michael Raver, Kar Chow, Nitin Yerram, D. Stifelman, and Benjamin Tycko RigoMauricio Rigo , CastanoAngelica Castano SalasMartha Salas TariqMariam Tariq LermanJoshua Lerman...