Environmental Molecular Sciences Laboratory

About: Environmental Molecular Sciences Laboratory is a facility organization based out in Richland, Washington, United States. It is known for research contribution in the topics: Mass spectrometry & Ion. The organization has 1471 authors who have published 3010 publications receiving 169961 citations.

Proteomics-based Compositional Analysis of Complex Cellulase–Hemicellulase Mixtures

Abstract: Efficient deconstruction of cellulosic biomass to fermentable sugars for fuel and chemical production is accomplished by a complex mixture of cellulases, hemicellulases, and accessory enzymes (e.g., >50 extracellular proteins). Cellulolytic enzyme mixtures, produced industrially mostly using fungi like Trichoderma reesei, are poorly characterized in terms of their protein composition and its correlation to hydrolytic activity on cellulosic biomass. The secretomes of commercial glycosyl hydrolase-producing microbes was explored using a proteomics approach with high-throughput quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we show that proteomics-based spectral counting approach is a reasonably accurate and rapid analytical technique that can be used to determine protein composition of complex glycosyl hydrolase mixtures that also correlates with the specific activity of individual enzymes present within the mixture. For example, a strong linear correlation was seen between Avicelase activity and total cellobiohydrolase content. Reliable, quantitative and cheaper analytical methods that provide insight into the cellulosic biomass degrading fungal and bacterial secretomes would lead to further improvements toward commercialization of plant biomass-derived fuels and chemicals.

Atomic origins of water-vapour-promoted alloy oxidation.

Abstract: The presence of water vapour, intentional or unavoidable, is crucial to many materials applications, such as in steam generators, turbine engines, fuel cells, catalysts and corrosion1–4. Phenomenologically, water vapour has been noted to accelerate oxidation of metals and alloys5,6. However, the atomistic mechanisms behind such oxidation remain elusive. Through direct in situ atomic-scale transmission electron microscopy observations and density functional theory calculations, we reveal that water-vapour-enhanced oxidation of a nickel–chromium alloy is associated with proton-dissolution-promoted formation, migration, and clustering of both cation and anion vacancies. Protons derived from water dissociation can occupy interstitial positions in the oxide lattice, consequently lowering vacancy formation energy and decreasing the diffusion barrier of both cations and anions, which leads to enhanced oxidation in moist environments at elevated temperatures. This work provides insights into water-vapour-enhanced alloy oxidation and has significant implications in other material and chemical processes involving water vapour, such as corrosion, heterogeneous catalysis and ionic conduction. In situ transmission electron microscopy observations reveal atomistic mechanism of water-vapour-enhanced oxidation of Ni–Cr alloys. Protons derived from water promote vacancy formation, migration and clustering.

Strategies to improve reference databases for soil microbiomes

Abstract: A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.

Significant Interactions between Uranium and Noble‐Gas Atoms: Coordination of the UO2+ Cation by Ne, Ar, Kr, and Xe Atoms

Abstract: Laser-ablated uranium cation reacts with O2 to give UO2+, which is found to form UO2+(Ng)n (Ng = Ne, Ar, Kr, Xe) complexes on condensation with excess noble gas. Experiments with mixtures of noble gases lead to five new absorptions for the mixed UO2+(Ng)x(Ng')y complexes and show that the coordination number is five for Ng = Ar, Kr, and Xe. These results are consistent with predictions by relativistic density functional calculations and indicate significant bonding between U and noble-gas atoms.

Proteome analysis of mitochondrial outer membrane from Neurospora crassa.

Abstract: The mitochondrial outer membrane mediates numerous interactions between the metabolic and genetic systems of mitochondria and the rest of the eukaryotic cell. We performed a proteomic study to discover novel functions of components of the mitochondrial outer membrane. Proteins of highly pure outer membrane vesicles (OMV) from Neurospora crassa were identified by a combination of LC-MS/MS of tryptic peptide digests and gel electrophoresis of solubilized OMV proteins, followed by their identification using MALDI-MS PMF. Among the 30 proteins found in at least three of four separate analyses were 23 proteins with known functions in the outer membrane. These included components of the import machinery (the TOM and TOB complexes), a pore-forming component (porin), and proteins that control fusion and fission of the organelle. In addition, proteins playing a role in various biosynthetic pathways, whose intracellular location had not been established previously, could be localized to the mitochondrial outer membrane. Thus, the proteome of the outer membrane can help in identifying new mitochondria-related functions.