Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii

ACKNOWLEDGMENTS We acknowledge support from BBSRC grant no. BB/L009951/1, from the Scottish government Food, Land and People program, and from the Society for Applied Microbiology. E.A.B. is supported by a grant (no. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel, and by a grant from the United States-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of the Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry. Thanks are due to Fergus Nicol for proteomic analysis and to Auriane Bernard for enzyme assays on stationary-phase cultures. We also thank Julian Parkhill and Keith Turner (Wellcome Trust Sanger Institute, Cambridge, United Kingdom) for making the R. bromii L2-63 genome sequence available for analysis.Peer reviewedPublisher PD

Ruminococcal cellulosome systems from rumen to human

This article is protected by copyright. All rights reserved. The authors appreciate the kind assistance of Miriam Lerner (ImmunArray Ltd. Company, Rehovot, Israel) with experiments involving the MicroGrid II arrayer. This research was supported by a grant (No. 1349) to EAB also from the Israel Science Foundation (ISF) and a grant (No. 24/11) issued to RL by The Sidney E. Frank Foundation also through the ISF. Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation, from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, by the Weizmann Institute of Science Alternative Energy Research Initiative (AERI) and the Helmsley Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. HF and SHD acknowledge support from the Scottish Government Food Land and People programme and from BBSRC grant no. BB/L009951/1. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic ChemistryPeer reviewedPostprin

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine‐tuned system for cohesin‐dockerin recognition

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137458/1/emi13047.pd

When will Immersive Virtual Reality have its day? Challenges to IVR adoption in the home as exposed in studies with teenagers, parents and experts

In response to the pandemic, many countries have had multiple lockdowns punctuated by partial freedoms limiting physically being together. In 2020-21, during the COVID-19 pandemic parents were stressed and exhausted by the challenges of work, home schooling and barriers to typical childcare arrangements. Children were missing one another, their social lives and the variety of experiences that the world beyond the home brings. Immersive Virtual Reality (IVR) offers tried and tested ways to enable children to maintain beyond-household family activities and dynamics. However, it is not viewed as a solution. Instead, as demonstrated through a multiple method study involving a Rapid Evidence Assessment; workshops with 91 teenagers; interviews with 15 experts; a Delphi study with 21 experts; 402 parent questionnaires pre-pandemic; 232 parent questionnaires during the pandemic; and longitudinal interviews with 13 parents during the first UK lockdown in 2020, IVR is not viewed as having value in the home beyond gaming. Results highlight limited consideration of IVR as a way to enhance family life or the home, with a lack of evidence and direction from current research, innovation and policy. The paper empirically demonstrates that experts, teenagers and parents have limited expectations for VR. Further, with parental resistance to adoption and a lack of ideas or innovations in how Immersive Virtual Reality could be used, the likelihood of VR-headset adoption remains low as does its potential as a means of educating, entertaining and socially engaging children and teenagers

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition

Peer reviewedPublisher PD

2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition. Chapter 4: management options and their effectiveness

This chapter seeks to answer the following questions: 1. What are the values of the Great Barrier Reef? 2. How effective are better agricultural practices in improving water quality? 3. How can we improve the uptake of better agricultural practices? 4. What water quality improvement can non-agricultural land uses contribute? 5. How can Great Barrier Reef water quality improvement programs be improved? Each section summarises the currently available peer reviewed literature and comments on implications for management and research gaps. This chapter has a wider scope than previous Scientific Consensus Statements, including, for the first time, the social and governance dimensions of management and the management of non-agricultural land uses. These new sections are constrained by a lack of Great Barrier Reef–specific data and information. The relevance of information from other locations must be carefully considered. In comparison, the agricultural practice change and economics sections provide an update on material compiled as part of the 2013 Scientific Consensus Statement. This report has been confined to peer reviewed literature, which is generally published in books and journals or major reports. There is additional evidence in grey literature, such as project and program reports, that has not been included here. Each section of this chapter has been compiled by a writing team and then revised following a series of review processes

Interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles (IN2017-V01): Post-survey report

The authors wish to thank the CSIRO Marine National Facility (MNF) for its support in the form of sea time on RV Investigator, support personnel, scientific equipment and data management. All data and samples acquired on the voyage are made publicly available in accordance with MNF Policy. All raw and processed data acquired by MNF equipment on MNF voyages will be archived by MNF data support staff in the enduring CSIRO Data Access Portal, https://data.csiro.au. Metadata records will be made publicly available at http://www.marlin.csiro.au. Processed data and data products will be made publicly available through Data Trawler http://www.cmar.csiro.au/data/trawler/index.cfm, the MNF web data access tool http://www.cmar.csiro.au/data/underway/, and/or from national or world data centres most suitable for the dissemination of particular data types.Other Australian Program Support Smaller projects have attracted funding to support research activities post-cruise these include the following: 1. Australian and New Zealand IODP Committee (ANZIC) Special Analytical Support Grant. Project Title: Using ancient phytoplankton communities and genes to illuminate future ocean responses. Researchers involved: L. Armand, L. Armbrecht, M. Ostrowski, & S. George. 2. Australian Antarctic Division Australian Antarctic Science Grant (#4320). Project Title: Characterising East Antarctic seabed habitats. Researchers involved: Post, A.L., & Smith, J. 3. Australian Antarctic Division Australian Antarctic Science Grant (#4419). Project Title: Response of the Totten Glacier to past climate warming. Researchers involved: Noble, T., Armand, L., Chase, Z., & Halpin, J.The Sabrina Sea Floor Survey was a major marine geoscience expedition to the Antarctic margin which took place between 14 January and 7 March 2017. It sailed on the Australian Marine National Facility vessel RV Investigator. This document describes survey activities, data collected on the ship and important metadata. Some preliminary results are included and the location of samples and data sets reported for future use. The report also provides information on data ownership and acknowledgement for future use and publication. It is intended as an aid to future research and use of results and has not been rigorously edited and peer-reviewed.Australian Research Council (DP170100557), Australian Antarctic Science Grant Program (AAS #4333), Italian Antarctic program support PNRA TYTAN Project (PdR 14_00119), Spanish Ministry of Economy and Competitivity (MINECO) (CTM2015-60451-C2-1-P & CTM2015-60451-C2-2-P), United States National Science Foundation's Polar Program - Antarctic Integrated System Science. #1143834, 1143836, 1143837, 1143843, 1313826

Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production

The Rowett Institute and Biomathematics & Statistics Scotland receive financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services. Nicole Reichardt was funded by a Scottish Government Strategic Partnership on Food and Drink Science. We would like to thank Donna Henderson for carrying out GC analysis and Alan Walker for help and advice with bioinformatic sequence analysis. Supplementary information is available at ISME Journal’s website.Peer reviewedPostprin

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead