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We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https//metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https//oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https//metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing less then 1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.Herein an unprecedented iron(II)-catalyzed redox-neutral radical cascade reaction of [60]fullerene with γ,δ-unsaturated oxime esters is reported for the preparation of novel free (N-H) pyrrolidino[2',3'1,2]fullerenes. The transformation undergoes an intramolecular cyclization/intermolecular cyclization/oxidation/hydrolysis cascade, and features simple operation, broad substrate scope/high functional group compatibility as well as suitable for scale-up synthesis, providing a facile and practical access to a range of free pyrrolidino[2',3'1,2]fullerenes.Control over the surface roughness of colloidal particles offers exciting opportunities to tailor the properties and the processing of a broad range of soft matter systems. Moreover, identifying surface roughness as a design parameter reveals the possibility to connect seemingly distinct phenomena and materials via the role played by roughness effects. In this feature article, we concisely review some approaches to synthesize and characterize rough colloidal particles, with a focus on model spherical colloids. We then discuss the impact that surface roughness has on both the high-shear rheology of dense suspensions and the stabilization of Pickering emulsions. Commenting on developments of our own research, we aim to offer an original perspective for a property-oriented development of colloidal particles that transcends classical divisions between materials and processes toward innovative solutions.Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions "Where is my protein of interest?", "Who makes it?", and "How much is there?" and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.Redox flow batteries (RFBs) operate by storing electrons on soluble molecular anolytes and catholytes, and large increases in the energy density of RFBs could be achieved if multiple electrons could be stored in each molecular analyte. Here, we report an organoaluminum analyte, [(I2P-)2Al]+, in which four electrons can be stored on organic ligands, and for which charging and discharging cycles performed in a symmetric nonaqueous RFB configuration remain stable for over 100 cycles at 70% state of charge and 97% Coulombic efficiency (I2P is a bis(imino)pyridine ligand). The stability of the analyte is promoted by the kinetic inertness of the anolyte to trace water in solvents and by the redox inertness of the Al(III) ion to the applied current. The solubility of the analyte was optimized by exchanging the counteranion for trifluoromethanesulfonate (triflate), and the cell was further optimized using graphite rods as electrodes which, in comparison with glassy carbon and reticulated vitreous carbon, eliminated deposition of analyte on the electrode. Proof-of-principle experiments performed with an asymmetric NRFB configuration further demonstrate that up to four electrons can be stored in the cell with no degradation of the analyte over multiple cycles that show 96% Coulombic efficiency.We present an extension of the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) theory for computing X-ray L-edge spectra, both in the absorption (XAS) and in the photoelectron (XPS) regimes. The approach is based on the perturbative evaluation of spin-orbit couplings using the Breit-Pauli Hamiltonian and nonrelativistic wave functions described by the fc-CVS-EOM-CCSD ansatz (EOM-CCSD within the frozen-core core-valence separated (fc-CVS) scheme). learn more The formalism is based on spinless one-particle density matrices. The approach is illustrated by modeling XAS and XPS of several model systems ranging from Ar to small molecules containing sulfur and silicon.
Website: https://www.selleckchem.com/products/odm208.html
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