Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

Author correction : roadmap for naming uncultivated archaea and bacteria

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity

West Valley Demonstration Project Annual Site Environmental Report Calendar Year 2012

The West Valley Demonstration Project (WVDP) Annual Site Environmental Report (ASER) for Calendar Year 2012. The report, prepared for the U.S. Department of Energy West Valley Demonstration Project office (DOE-WVDP), summarizes the environmental protection program at the WVDP for calendar year (CY) 2012. Monitoring and surveillance of the facilities used by the DOE are conducted to verify protection of public health and safety and the environment. The report is a key component of DOE’s effort to keep the public informed of environmental conditions at the WVDP. The quality assurance protocols applied to the environmental monitoring program ensure the validity and accuracy of the monitoring data. In addition to demonstrating compliance with environmental laws, regulations, and directives, evaluation of data collected in 2012 continued to indicate that WVDP activities pose no threat to public health or safety, or to the environment

Primary Apocrine Adenocarcinoma of the Axilla

Primary apocrine adenocarcinoma (AA) is a rare malignant cutaneous neoplasm that typically arises in areas of high apocrine gland density such as the axillae and the anogenital region. Due to the nonspecific clinical manifestation of AA, the differential diagnosis may be broad. The rarity of this neoplasm has led to a relative lack of well-established histologic and immunohistochemical diagnostic criteria, further complicating the diagnosis of AA. We report the case of a 49-year-old man with primary AA of the left axilla and provide a review of the clinical and histologic findings, epidemiology, and treatment modalities of this rare cutaneous neoplasm

Activation of Elk-1, an Ets transcription factor, by glucose and EGF treatment of insulinoma cells

Elk-1, a member of the ternary complex factor family of Ets domain proteins that bind serum response elements, is activated by phosphorylation in a cell-specific manner in response to growth factors and other agents. The purpose of the current study was to determine whether Elk-1 activation contributes to glucose-/depolarization-induced Ca2+-dependent induction of immediate early response genes in pancreatic islet β-cells. The results of experiments in insulinoma (MIN6) cells demonstrated that Elk-1-binding sites (Ets elements) in the Egr-1 gene promoter contribute to transcriptional activation of the gene. Treatment with either epidermal growth factor (EGF), a known inducer of β-cell hyperplasia, glucose, or KCl-induced depolarization resulted in Ser383 phosphorylation and transcriptional activation of Elk-1 (4 ± 0.3-, P = 0.003, 2.3 ± 0.19-, P = 0.002, and 2.2 ± 0.1- fold, P= 0.001 respectively). The depolarization response was inhibited by the Ca2+ channel blocker verapamil and by the MEK inhibitor PD98059 (53 ± 6 and 55 ± 0.5%, respectively). EGF-induced activation of Elk-1 was also inhibited by PD98059 (60 ± 5%). A dominant negative Ras produced partial inhibition (42%) of the depolarization-induced Elk-1 transcriptional activation. Transfection with a constitutively active Ca2+/calmodulin kinase IV plasmid also resulted in Elk-1 transcriptional activation. Experiments with p38, phosphatidylinositol 3-kinase, and protein kinase A inhibitors indicated that these pathways are not involved. We conclude that Elk-1 activation contributes to glucose-/depolarization-induced Ca2+-dependent induction of immediate early growth response genes in pancreatic islet β-cells. Furthermore, the results demonstrated a convergence of nutrient- and growth factor-mediated signaling pathways on Elk-1 activation through induction of Ras/mitogen-activated protein kinase ERK-1 and -2. The role of these pathways in the glucose-induced proliferation of islet β-cells can now be assessed

Actionable knowledge and the art of engagement

What makes knowledge relevant to environmental sustainability actionable, and how can its societal impacts be evaluated? Scholars and practitioners have increasingly advocated that the traditional linear model of knowledge production, with its unidirectional flow of information from researchers to policy-makers, be replaced by a new approach in which researchers and knowledge-users meaningfully interact to co-create knowledge that is actionable in decision-making. This popular model — co-production — has advanced thinking on how to create usable knowledge. In practice, however, co-production has not been a single approach, but instead a diversity of forms of engaged research. Further, the jargon may both obfuscate governance dimensions and limit understanding of what works. Improved distinction among the different ways researchers and societal partners interact can enable attentive and effective engagement across contexts. Recognition of this diversity is necessary in advancing the processes and impacts of actionable knowledge for sustainability

A research agenda for the science of actionable knowledge: Drawing from a review of the most misguided to the most enlightened claims in the science-policy interface literature

Linking science with action affords a prime opportunity to leverage greater societal impact from research and increase the use of evidence in decision-making. Success in these areas depends critically upon processes of producing and mobilizing knowledge, as well as supporting and making decisions. For decades, scholars have idealized and described these social processes in different ways, resulting in numerous assumptions that now variously guide engagements at the interface of science and society. We systematically catalog these assumptions based on prior research on the science-policy interface, and further distill them into a set of 26 claims. We then elicit expert perspectives (n = 16) about these claims to assess the extent to which they are accurate or merit further examination. Out of this process, we construct a research agenda to motivate future scientific research on actionable knowledge, prioritizing areas that experts identified as critical gaps in understanding of the science-society interface. The resulting agenda focuses on how to define success, support intermediaries, build trust, and evaluate the importance of consensus and its alternatives – all in the diverse contexts of science-society-decision-making interactions. We further raise questions about the centrality of knowledge in these interactions, discussing how a governance lens might be generative of efforts to support more equitable processes and outcomes. We offer these suggestions with hopes of furthering the science of actionable knowledge as a transdisciplinary area of inquiry

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

A research agenda for the science of actionable knowledge: Drawing from a review of the most misguided to the most enlightened claims in the science-policy interface literature

Linking science with action affords a prime opportunity to leverage greater societal impact from research and increase the use of evidence in decision-making. Success in these areas depends critically upon processes of producing and mobilizing knowledge, as well as supporting and making decisions. For decades, scholars have idealized and described these social processes in different ways, resulting in numerous assumptions that now variously guide engagements at the interface of science and society. We systematically catalog these assumptions based on prior research on the science-policy interface, and further distill them into a set of 26 claims. We then elicit expert perspectives (n = 16) about these claims to assess the extent to which they are accurate or merit further examination. Out of this process, we construct a research agenda to motivate future scientific research on actionable knowledge, prioritizing areas that experts identified as critical gaps in understanding of the science-society interface. The resulting agenda focuses on how to define success, support intermediaries, build trust, and evaluate the importance of consensus and its alternatives – all in the diverse contexts of science-society-decision-making interactions. We further raise questions about the centrality of knowledge in these interactions, discussing how a governance lens might be generative of efforts to support more equitable processes and outcomes. We offer these suggestions with hopes of furthering the science of actionable knowledge as a transdisciplinary area of inquiry