Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “network analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed2003

Metabolic network analysis during fed-batch cultivation of Corynebacterium glutamicum for pantothenic acid production: first quantitative data and analysis of by-product formation.

A first generation genetically modified strain of Corynebacterium glutamicum has been assessed for its potential to synthesise and accumulate the vitamin pantothenic acid in the medium using fed-batch cultivation technology, with biomass concentration controlled by isoleucine limitation. Kinetic analysis of specific rates throughout the process has been used to model carbon flux through both central metabolism and the specific pathways involved in product formation. Flux towards pantothenic acid is potentially high but much of this flux is dissipated as by-products within associated pathways, notably linked to amino acid synthesis. The major limitation of vitamin production in this strain is linked to the tenfold higher flux of keto-isovalerate towards valine rather than pantothenic acid. Attempts to modify this ratio by imposing nitrogen limitation provoked carbon overflow as unidentified non-nitrogenous compounds. The observed accumulation of glycine suggests that the flux towards pantothenate production may by limited by the rate of the pathway intermediate (5,10-methylene-tetrahydrofolate) regeneration.

Bioreactors↗
PubMed1984

Shunt haemodynamics and extracorporeal dialysis: an electrical resistance network analysis.

A time-dependent resistance model is used to study haemodynamic aspects of haemodialysis treatment. In the first part of the paper one model circuit, consisting of a pressure source, upstream and downstream resistances and a branching resistance, is shown to represent the haemodynamics of any type of arteriovenous fistula (AVF). Simple algebraic relations are derived for the haemodynamic determinants of AVFS, including finger ischaemia and AVF-maturation. The second part of the paper analyses the influences of a two-needle extracorporeal dialysis (ECD) circuit on the systemic vascular haemodynamics. The main result of the analysis is that the ECD-circuit can be considered as virtually independent of the systemic circulation. Consequently the dialysis flow does not depend on systemic vascular determinants and there are no instantaneous changes in the systemic circulation after switching on the ECD circuit. The ECD flow at onset of AVF collapse is shown to be (slightly) larger than the undisturbed AVF flow. Hence, onset of collapse strongly depends on the systemic blood pressure and vascular resistances. It can be used diagnostically to assess AVF capacities. Optimisation of haemodialysis through the ECD circuit is predicted to be inefficient.

Arm↗
PubMed2003

Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways.

The intrinsic recombination rate of human immunodeficiency virus (HIV) exceeds the point mutation rate by a factor of 10. As the majority of infected cells in vivo harbour multiple proviruses, the stage is set for rampant recombination. Therefore, it may be presumed that phylogenic relationships and mutation frequencies will probably be affected by recombination. However, the proportion of homoplasies arising from recombination and mutation is not known. By studying the evolution of the hypervariable regions of the simian immunodeficiency virus envelope gene among four macaques, it is shown that homoplasies arise more from recombination than from point mutation. When recombination is accounted for, the minimum number of substitutions in a sequence set may be reduced by as much as 45 %. In fact, the true number of point mutations in a set of HIV sequences tends to the number of discrete substitutions. Hence, lineages are younger than anticipated previously, although not in proportion to the ratio of the intrinsic recombination/point mutation rate. Recombination also inflates codon polymorphisms.

Animals↗
PubMed2005

Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces species with an active entner-doudoroff pathway.

Streptomyces tenebrarius is an industrially important microorganism, producing an antibiotic complex that mainly consists of the aminoglycosides apramycin, tobramycin carbamate, and kanamycin B carbamate. When S. tenebrarius is used for industrial tobramycin production, kanamycin B carbamate is an unwanted by-product. The two compounds differ only by one hydroxyl group, which is present in kanamycin carbamate but is reduced during biosynthesis of tobramycin. (13)C metabolic flux analysis was used for elucidating connections between the primary carbon metabolism and the composition of the antibiotic complex. Metabolic flux maps were constructed for the cells grown on minimal medium with glucose or with a glucose-glycerol mixture as the carbon source. The addition of glycerol, which is more reduced than glucose, led to a three-times-greater reduction of the kanamycin portion of the antibiotic complex. The labeling indicated an active Entner-Doudoroff (ED) pathway, which was previously considered to be nonfunctional in Streptomyces. The activity of the pentose phosphate (PP) pathway was low (10 to 20% of the glucose uptake rate). The fluxes through Embden-Meyerhof-Parnas (EMP) and ED pathways were almost evenly distributed during the exponential growth on glucose. During the transition from growth phase to production phase, a metabolic shift was observed, characterized by a decreased flux through the ED pathway and increased fluxes through the EMP and PP pathways. Higher specific NADH and NADPH production rates were calculated in the cultivation on glucose-glycerol, which was associated with a lower percentage of nonreduced antibiotic kanamycin B carbamate.

Aminoglycosides↗
PubMed2005

Understanding platelets. Lessons from proteomics, genomics and promises from network analysis.

New large-scale analysis techniques such as bioinformatics, mass spectrometry and SAGE data analysis will allow a new framework for understanding platelets. This review analyses some important options and tasks for these tools and examines an outline of the new, refined picture of the platelet outlined by these new techniques. Looking at the platelet-specific building blocks of genome, (active) transcriptome and proteome (notably secretome and phospho-proteome), we summarize current bioinformatical and biochemical approaches, tasks as well as their limitations. Understanding the surprisingly complex platelet regarding compartmentalization, key cascades, and pathways including clinical implications will remain an exciting and hopefully fruitful challenge for the future.

Animals↗
PubMed2006

Illuminating cancer health disparities using ethnogenetic layering (EL) and phenotype segregation network analysis (PSNA).

BACKGROUND: Resolving cancer health disparities continues to befuddle simplistic racial models. The racial groups alluded to in biomedicine, public health, and epidemiology are often profoundly substructured. METHODS: EL and PSNA are computational assisted techniques that focus on microethnic group (MEG) substructure. RESULTS: Geographical variations in cancer may be due to differences in MEG ancestry or similar environmental exposures to a recognized carcinogen. Examples include breast and prostate cancers in the Chesapeake Bay region and Bight of Biafra biological ancestry, hypertension and stroke in the Carolina Coast region and Central African biological ancestry, and pancreatic cancer in the Mississippi Delta region and dietary/medicinal exposure to safrol from Sassafras albidum.

Cultural Diversity↗