109 research outputs found
Warm calibration unit of the mid-infrared ELT instrument METIS: overview and current status towards FDR
Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes
Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β2-adrenergic receptor (β2AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β2AR. We show that the select ligands bind preferentially to different predicted conformers of β2AR, and identify a role of β2AR extracellular region as an allosteric binding site for larger drugs such as salmeterol. Thus, drugs and ligands can be used as "computational probes" to systematically identify protein conformers with likely biological significance. © 2012 Isin et al
Biochemical mutagens affect the preservation of fungi and biodiversity estimations
Many fungi have significant industrial applications
or biosafety concerns and maintaining the original
characteristics is essential. The preserved fungi have to
represent the situation in nature for posterity, biodiversity
estimations, and taxonomic research. However, spontaneous
fungal mutations and secondary metabolites affecting
producing fungi are well known. There is increasing
interest in the preservation of microbes in Biological
Resource Centers (BRC) to ensure that the organisms
remain viable and stable genetically. It would be anathema
if they contacted mutagens routinely. However, for
the purpose of this discussion, there are three potential
sources of biochemical mutagens when obtaining individual
fungi from the environment: (a) mixtures of microorganisms
are plated routinely onto growth media
containing mutagenic antibiotics to control overgrowth
by contaminants, (b) the microbial mixtures may contain
microorganisms capable of producing mutagenic secondary
metabolites, and (c) target fungi for isolation may
produce “self” mutagens in pure culture. The probability
that these compounds could interact with fungi undermines
confidence in the preservation process and the
potential effects of these biochemical mutagens are considered
for the first time on strains held in BRC in this
review
Plasma redox status is impaired in the portacaval shunted rat – the risk of the reduced antioxidant ability
Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment
Although statins are widely prescribed medications, there remains considerable variability in therapeutic response. Genetics can explain only part of this variability. Metabolomics is a global biochemical approach that provides powerful tools for mapping pathways implicated in disease and in response to treatment. Metabolomics captures net interactions between genome, microbiome and the environment. In this study, we used a targeted GC-MS metabolomics platform to measure a panel of metabolites within cholesterol synthesis, dietary sterol absorption, and bile acid formation to determine metabolite signatures that may predict variation in statin LDL-C lowering efficacy. Measurements were performed in two subsets of the total study population in the Cholesterol and Pharmacogenetics (CAP) study: Full Range of Response (FR), and Good and Poor Responders (GPR) were 100 individuals randomly selected from across the entire range of LDL-C responses in CAP. GPR were 48 individuals, 24 each from the top and bottom 10% of the LDL-C response distribution matched for body mass index, race, and gender. We identified three secondary, bacterial-derived bile acids that contribute to predicting the magnitude of statin-induced LDL-C lowering in good responders. Bile acids and statins share transporters in the liver and intestine; we observed that increased plasma concentration of simvastatin positively correlates with higher levels of several secondary bile acids. Genetic analysis of these subjects identified associations between levels of seven bile acids and a single nucleotide polymorphism (SNP), rs4149056, in the gene encoding the organic anion transporter SLCO1B1. These findings, along with recently published results that the gut microbiome plays an important role in cardiovascular disease, indicate that interactions between genome, gut microbiome and environmental influences should be considered in the study and management of cardiovascular disease. Metabolic profiles could provide valuable information about treatment outcomes and could contribute to a more personalized approach to therapy
A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism
Small molecule drugs target many core metabolic enzymes in humans and pathogens,
often mimicking endogenous ligands. The effects may be therapeutic or toxic, but
are frequently unexpected. A large-scale mapping of the intersection between
drugs and metabolism is needed to better guide drug discovery. To map the
intersection between drugs and metabolism, we have grouped drugs and metabolites
by their associated targets and enzymes using ligand-based set signatures
created to quantify their degree of similarity in chemical space. The results
reveal the chemical space that has been explored for metabolic targets, where
successful drugs have been found, and what novel territory remains. To aid other
researchers in their drug discovery efforts, we have created an online resource
of interactive maps linking drugs to metabolism. These maps predict the
“effect space” comprising likely target enzymes for each of
the 246 MDDR drug classes in humans. The online resource also provides
species-specific interactive drug-metabolism maps for each of the 385 model
organisms and pathogens in the BioCyc database collection. Chemical similarity
links between drugs and metabolites predict potential toxicity, suggest routes
of metabolism, and reveal drug polypharmacology. The metabolic maps enable
interactive navigation of the vast biological data on potential metabolic drug
targets and the drug chemistry currently available to prosecute those targets.
Thus, this work provides a large-scale approach to ligand-based prediction of
drug action in small molecule metabolism
Fungal volatile organic compounds: emphasis on their plant growth-promoting
Fungal volatile organic compounds (VOCs) commonly formed bioactive interface between plants and countless of microorganisms on the above- and below-ground plant-fungus interactions. Fungal-plant interactions symbolize intriguingly biochemical complex and challenging scenarios that are discovered by metabolomic approaches. Remarkably secondary metabolites (SMs) played a significant role in the virulence and existence with plant-fungal pathogen interaction; only 25% of the fungal gene clusters have been functionally identified, even though these numbers are too low as compared with plant secondary metabolites. The current insights on fungal VOCs are conducted under lab environments and to apply small numbers of microbes; its molecules have significant effects on growth, development, and defense system of plants. Many fungal VOCs supported dynamic processes, leading to countless interactions between plants, antagonists, and mutualistic symbionts. The fundamental role of fungal VOCs at field level is required for better understanding, so more studies will offer further constructive scientific evidences that can show the cost-effectiveness of ecofriendly and ecologically produced fungal VOCs for crop welfare
The Epidemiology, Genetics and Future Management of Syndactyly
Syndactyly is a condition well documented in current literature due to it being the most common congenital hand defect, with a large aesthetic and functional significance
Improving the performance of finite element simulations on the wheel–rail interaction by using a coupling strategy
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