To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a ...case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymes having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. High-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.
A novel cytochrome P450 enzyme, TxtE, was recently shown to catalyze the direct aromatic nitration of L‐tryptophan. This unique chemistry inspired us to ask whether TxtE could serve as a platform for ...engineering new nitration biocatalysts to replace current harsh synthetic methods. As a first step toward this goal, and to better understand the wild‐type enzyme, we obtained high‐resolution structures of TxtE in its substrate‐free and substrate‐bound forms. We also screened a library of substrate analogues for spectroscopic indicators of binding and for production of nitrated products. From these results, we found that the wild‐type enzyme accepts moderate decoration of the indole ring, but the amino acid moiety is crucial for binding and correct positioning of the substrate and therefore less amenable to modification. A nitrogen atom is essential for catalysis, and a carbonyl must be present to recruit the αB′1 helix of the protein to seal the binding pocket.
Active site revealed: The first high‐resolution structures of the nitrating cytochrome P450 TxtE, with and without substrate, are reported. In combination with a substrate survey, we outline a set of substrate criteria that must be met for nitration. Our results provide key insights for future engineering of TxtE for nitration of diverse substrates.
The COVID-19 pandemic has profoundly changed outdoor recreation. As a result of the pandemic, parks and protected areas around the world have witnessed dramatic increases in recreation visitation. ...While various studies have examined this premise, this is one of the first to examine the influence of the COVID-19 pandemic upon recreation visitation across an entire parks and protected areas system in New England, utilizing both spatial and temporal scales. Study findings provide empirical evidence to inform future research and theory related to the social-ecological systems and recreation opportunity spectrum frameworks. A unique combination of primary, secondary, and geospatial data was used to explore recreation visitors' decision-making, behaviors, and visitation trends during the pandemic. Inferential and regression analyses suggest overall recreation visitation increased by ∼61% (2+ million additional site visits) during the summer of 2020 at the height of the pandemic. Moreover, significant changes in visitation, site, and geo-spatial characteristics were observed for both in-state and out-of-state visitors during the pandemic. This research validates the influence of the pandemic upon parks and protected areas in the United States.
The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is ...designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms.
To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms.
Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for ...the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.
The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological ...knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.
Gene Ontology annotations and resources Blake, J A; Dolan, M; Drabkin, H ...
Nucleic acids research,
01/2013, Letnik:
41, Številka:
Database issue
Journal Article
Recenzirano
Odprti dostop
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled ...vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
High school is an important time in the educational career of students. It is also a time when adolescents face many behavioral, academic, and social-emotional challenges. Current statistics about ...the behavioral, academic, and social-emotional challenges faced by adolescents, and the impact on society through incarceration and dropout, have prompted high schools to direct their attention toward keeping students engaged and reducing high-risk behavioral challenges. The purpose of the study was to examine the effects of School-Wide Positive Behavioral Interventions and Supports (SW-PBIS) on the levels of individual student problem behaviors during a 3-year effectiveness trial without random assignment to condition. Participants were 36,653 students in 12 high schools. Eight schools implemented SW-PBIS, and four schools served as comparison schools. Results of a multilevel latent growth model showed statistically significant decreases in student office discipline referrals in SW-PBIS schools, with increases in comparison schools, when controlling for enrollment and percent of students receiving free or reduced price meals. In addition, as fidelity of implementation increased, office discipline referrals significantly decreased. Results are discussed in terms of effectiveness of a SW-PBIS approach in high schools and considerations to enhance fidelity of implementation.
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of ...GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.
As a ribonucleoprotein complex, the plant ribosome consists of four ribosomal RNAs (rRNAs) and 75–92 ribosomal proteins (r-proteins), depending on the species.
Arabidopsis thaliana r-protein genes ...exist in multi-gene families ranging in size from two to seven transcriptionally active members. The cytosolic
RPS15a gene family consists of four members that, at the amino acid level, share 87–100% identity. The 5′ regulatory regions of the four genes contain many of the same putative regulatory elements but share only 46–49% nucleotide sequence identity. Semi-quantitative RT-PCR (sqRT-PCR) was used to determine
RPS15a transcript abundance patterns and identify possible regulatory differences among the four genes.
RPS15aC expression was not detected in any tissue under any treatment while transcript abundance for
RPS15aA, -
D and -
F was highest in mitotically active tissues e.g. bud and flower. Seedlings showed increased transcript abundance following treatment with the cytokinin 6-benzylaminopurine (BAP) while the auxin indole acetic acid (IAA) induced an increase in
RPS15aF abundance only. Abscisic acid (ABA) treatment resulted in decreased transcript abundance while gibberellic acid (GA
3) had little effect on all four genes. Similar trends were established for
RPS15aA,
-D and -
F transcript abundance as a result of temperature mechanical stress. This study reports the differences in transcript abundance of the four cytosolic
RPS15a genes in Arabidopsis and we suggest that
RPS15a genes should no longer be considered ‘housekeeping’ genes.
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