NCBI Reference Sequences: current status, policy and new initiatives

NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system

A standard numbering scheme for class C β-lactamases

Unlike classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315), is adaptable to new variants or enzymes yet to be discovered, and includes a variation for genetic and epidemiological applications

TraR, a Homolog of a RNAP Secondary Channel Interactor, Modulates Transcription

Recent structural and biochemical studies have identified a novel control mechanism of gene expression mediated through the secondary channel of RNA Polymerase (RNAP) during transcription initiation. Specifically, the small nucleotide ppGpp, along with DksA, a RNAP secondary channel interacting factor, modifies the kinetics of transcription initiation, resulting in, among other events, down-regulation of ribosomal RNA synthesis and up-regulation of several amino acid biosynthetic and transport genes during nutritional stress. Until now, this mode of regulation of RNAP was primarily associated with ppGpp. Here, we identify TraR, a DksA homolog that mimics ppGpp/DksA effects on RNAP. First, expression of TraR compensates for dksA transcriptional repression and activation activities in vivo. Second, mutagenesis of a conserved amino acid of TraR known to be critical for DksA function abolishes its activity, implying both structural and functional similarity to DksA. Third, unlike DksA, TraR does not require ppGpp for repression of the rrnB P1 promoter in vivo and in vitro or activation of amino acid biosynthesis/transport genes in vivo. Implications for DksA/ppGpp mechanism and roles of TraR in horizontal gene transfer and virulence are discussed

Contextualizing climate justice activism: knowledge, emotions, motivations, and actions among climate strikers in six cities

In August 2018, Swedish teenager Greta Thunberg started to strike from school on Fridays to protest against a lack of action on the climate crisis. Her actions sparked a historically large youth movement, leading to a series of school strikes across the world. Over the course of one week in September 2019, striking school children, students and other grassroots movements, such as Extinction Rebellion, called for everyone to participate in a global Climate Strike. This paper is based on comparative research with climate protesters in six cities: Brighton and London (United Kingdom), Montreal (Canada), New Haven and New York (USA), and Stavanger (Norway). Based on original interviews with 64 protesters, the study examines their knowledge, emotions, motivations, and actions in relation to climate change, including any lifestyle changes they have undertaken before or after their protests. Our findings show that protesters have varying degrees of knowledge about climate change, and have taken a range of actions in their own lives to address climate change. They also manifest a wide spectrum of emotions about climate change, and different motivations for taking part in climate strikes. These features are under-studied and dynamically evolving at the present conjuncture. On this basis, we call for expanded academic attention to human, emotional, epistemic, and seemingly mundane aspects of climate protests, their structural tendencies and relational expressions, and the implications for our ability to address underlying drivers

Unprecedented High-Modulus High-Strength Tapes and Films of Ultrahigh Molecular Weight Polyethylene via Solvent-Free Route

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Macromolocules, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see: http://dx.doi.org/10.1021/ma200667