Our understanding of the human gut microbiome continues to evolve at a rapid pace, but practical application of thisknowledge is still in its infancy. This review discusses the type of studies that ...will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host.
Our understanding of the human gut microbiome continues to evolve at a rapid pace, but practical application of thisknowledge is still in its infancy. This review discusses the type of studies that will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host.
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference ...genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).
Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately ...detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered "high-quality" metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.
Encyclopedia of Microbiology, Fourth Edition gathers both basic and applied dimensions in this dynamic field that includes virtually all environments on Earth. This range attracts a growing number of ...cross-disciplinary studies, which the encyclopedia makes available to readers from diverse educational backgrounds. The new edition builds on the solid foundation established in earlier versions, adding new material that reflects recent advances in the field. New focus areas include `Animal and Plant Microbiomes' and 'Global Impact of Microbes`. The thematic organization of the work allows users to focus on specific areas, e.g., for didactical purposes, while also browsing for topics in different areas.
open set \Omega \mathbb{R}^nfrom within. In this note we show that, nevertheless, the latter type of approximation is possible under the mild hypothesis that the (n{-}1) \partial \Omega . We also ...discuss an optimality property of this hypothesis, and we establish a corresponding result on strict approximation of -functions from a prescribed Dirichlet class.>
Tuning the surface structure at the atomic level is of primary importance to simultaneously meet the electrocatalytic performance and stability criteria required for the development of ...low-temperature proton-exchange membrane fuel cells (PEMFCs). However, transposing the knowledge acquired on extended, model surfaces to practical nanomaterials remains highly challenging. Here, we propose 'surface distortion' as a novel structural descriptor, which is able to reconciliate and unify seemingly opposing notions and contradictory experimental observations in regards to the electrocatalytic oxygen reduction reaction (ORR) reactivity. Beyond its unifying character, we show that surface distortion is pivotal to rationalize the electrocatalytic properties of state-of-the-art of PtNi/C nanocatalysts with distinct atomic composition, size, shape and degree of surface defectiveness under a simulated PEMFC cathode environment. Our study brings fundamental and practical insights into the role of surface defects in electrocatalysis and highlights strategies to design more durable ORR nanocatalysts.
The Strep-tag II is an eight-residue minimal peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) that exhibits intrinsic affinity toward streptavidin and can be fused to recombinant proteins in ...various fashions. We describe a protocol that enables quick and mild purification of corresponding Strep-tag II fusion proteins--including their complexes with interacting partners--both from bacterial and eukaryotic cell lysates using affinity chromatography on a matrix carrying an engineered streptavidin (Strep-Tactin), which can be accomplished within 1 h. A high-affinity monoclonal antibody (StrepMAB-Immo) permits stable immobilization of Strep-tag II fusion proteins to solid surfaces, for example, for surface plasmon resonance analysis. Selective and sensitive detection on western blots is achieved with Strep-Tactin/enzyme conjugates or another monoclonal antibody (StrepMAB-Classic). Thus, the Strep-tag II, which is short, biologically inert, proteolytically stable and does not interfere with membrane translocation or protein folding, offers a versatile tool both for the rapid isolation of a functional gene product and for its detection or molecular interaction analysis.
One hindrance to the development of fuel cells and electrolyzers are the oxygen electrodes, which suffer from high overpotentials and slow kinetics. Perovskite oxides have been shown to be promising ...oxygen electrode catalysts because of their low cost, flexibility, and tailorable properties. In order to improve perovskite catalysts for the oxygen reduction (ORR) and oxygen evolution (OER) reactions, a better understanding of their reaction mechanisms is needed. This Perspective aims to inform researchers of the current proposed reaction mechanisms for ORR and OER on perovskites and perovskite/carbon composites in order to guide future catalyst development. Additionally, important experimental practices will be recommended. A recent development for OER is the lattice oxygen evolution reaction, which is a possible addition to the conventional four consecutive proton-coupled electron transfer mechanism. Carbon additives are consistently added to perovskites to enhance conductivity and ORR/OER activity. However, carbon plays an active role in ORR, and there is evidence of a synergistic relationship between perovskite and carbon in perovskite/carbon composites.
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