ANNUAL REPORT Marine Science Institute UC SANTA BARBARA Table of Contents
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FIRE DEPARTMENT COUNTY Adair County Tri Community Volunteer Fire Dept
FIRE DEPARTMENT COUNTY Adair County Tri Community Volunteer Fire Dept. Adair Bell Rural Fire Department Inc Adair Chance Community Fire Department Inc. Adair Christie Proctor Fire Association Adair Greasy Volunteer Fire Department Inc. Adair Hwy 100 West Fire Protection Adair Hwy 51 West Rural Fire District, Inc. Adair Mid County Rural Fire Dept. Inc. Adair Town of Stilwell for Stilwell Fire Department Adair Town of Watts for Watts Fire Department Adair Town of Westville for Westville Fire Department Adair City of Cherokee for Cherokee Fire Department Alfalfa Nescatunga Rural Fire Association Alfalfa Town of Aline for Aline Fire Department Alfalfa Town of Burlington for Burlington Fire Department Alfalfa Town of Byron for A&B Fire Department Alfalfa Town of Carmen for Carmen Fire Department Alfalfa Town of Goltry for Goltry Fire Department Alfalfa Town of Helena for Helena Fire Department Alfalfa Town of Jet for Jet Fire Department Alfalfa Bentley Volunteer Fire District Atoka City of Atoka for Atoka Fire Department Atoka Crystal Volunteer Fire Department Association Atoka Daisy Volunteer Fire Department, Inc. Atoka Farris Fire District Atoka Harmony Fire Department Atoka Hopewell Community Firefighters Association Atoka Lane Volunteer Fire Department Association Atoka Town of Caney for Caney Fire Department Atoka Town of Stringtown for Stringtown Fire Department Atoka Town of Tushka for Tushka Fire Department Atoka Wards Chapel Fire Department, Inc. Atoka Wardville Rural Volunteer Fire Dept. Atoka Wilson Community Rural Fire Association -
Metaproteomics As a Tool for Studying the Protein Landscape of Human-Gut Bacterial Species
bioRxiv preprint doi: https://doi.org/10.1101/2021.09.02.458484; this version posted September 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species Moses Stamboulian1, Jamie Canderan1, and Yuzhen Ye1 1Luddy School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47408. Email address: Moses Stamboulian, [email protected] Jamie Canderan, [email protected] Yuzhen Ye, [email protected] Corresponding author: Yuzhen Ye, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.09.02.458484; this version posted September 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a pow- erful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associ- ated with a certain phenotype. -
A Decade of Metaproteomics: Where We Stand and What the Future Holds
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Open Repository and Bibliography - Luxembourg www.proteomics-journal.com Page 1 Proteomics Viewpoint A decade of metaproteomics: where we stand and what the future holds Paul Wilmes1, Anna Heintz-Buschart1 and Philip L. Bond2 1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg 2Advanced Water Management Centre, University of Queensland, Brisbane, Australia Correspondence: Paul Wilmes, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; Philip L. Bond, Advanced Water Management Centre, University of Queensland, Queensland 4072, Australia E-mail: [email protected]; [email protected] Fax: (352) 466644 6188; (61) 07 33654726 Received: 15-May-2015; Revised: 06-Jul-2015; Accepted: 05-Aug-2015. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/pmic.201500183. This article is protected by copyright. All rights reserved. www.proteomics-journal.com Page 2 Proteomics Abstract We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high-resolution “meta-omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype-phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities. -
And Metaproteomics-Based Rapid Assay of Individual 2 Microbiome Responses to Drugs
bioRxiv preprint doi: https://doi.org/10.1101/543256; this version posted June 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual 2 Microbiome responses to drugs 3 4 Authors: Leyuan Li1, Zhibin Ning1, Xu Zhang1, Janice Mayne1, Kai Cheng1, Alain Stintzi*1, 5 Daniel Figeys*1,2,3 6 Affiliations: 7 1 Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of 8 Medicine, University of Ottawa, Ottawa, Canada. 9 2 Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada. 10 3 Canadian Institute for Advanced Research, Toronto, Canada. 11 *To whom correspondence should be addressed: Emails: [email protected] (DF), and [email protected] (AS). 12 13 Abstract: 14 Background: Human-targeted drugs may exert off-target effects on the gut microbiota. 15 However, our understanding of such effects is limited due to a lack of rapid and scalable assay to 16 comprehensively assess microbiome responses to drugs. Drugs can drastically change the overall 17 microbiome abundance, microbial composition and functions of a gut microbiome. Although we 18 could comprehensively observe these microbiome responses using a series of tests, for the 19 purpose of a drug screening, it is important to decrease the number of analytical tools used. 20 Results: Here, we developed an approach to screen compounds against individual microbiomes 21 in vitro using metaproteomics adapted for both absolute bacterial abundances and functional 22 profiling of the microbiome. -
Fire Risk on the Centennial Specific Plan Project Site
December 6, 2018 Los Angeles County Board of Supervisors 856 Kenneth Hahn Hall of Administration 500 W. Temple Street Los Angeles CA, 90012 Submitted electronically to: [email protected], [email protected], [email protected], [email protected], [email protected], [email protected] CC: [email protected], [email protected] Clarification of Fire Risk on the Centennial Specific Plan Project Site Dear Los Angeles County Board of Supervisors, Thank you very much for the continued opportunity to provide input on the Centennial Specific Plan (“Centennial”). As an organization, the California Native Plant Society (“CNPS”) is very concerned with the potential impacts of Centennial. CNPS has detailed the reasons why we oppose Centennial in numerous comment letters that focus on the project’s unacceptable impacts to irreplaceable grassland habitats, lack of appropriate mitigation, inappropriate use of Cap-and-Trade, and other issues. One issue that continues to be a major concern to CNPS members and the general public is that the Centennial project site is a dangerous place to build a new city for nearly 60,000 people. Chief among our concerns are the facts that project site is designated by CalFire as a High or Very High Fire Severity Zone (see Attachment 1), and that Centennial would be built on/adjacent to California’s two largest earthquake faults, the Garlock and San Andreas (see Attachment 2). The issue of greenlighting large development projects in areas with high fire danger should be a primary concern to decision-makers. The Los Angeles County Board of Supervisors should regard wildfire as a major liability in their pending decision on Centennial. -
FIRE DEPARTMENT TOWN 106 Rural Fire District Association Newkirk Adair County Tri Community Volunteer Fire Dept
FIRE DEPARTMENT TOWN 106 Rural Fire District Association Newkirk Adair County Tri Community Volunteer Fire Dept. Stilwell Airport Road Fire Support Incorporated Bartlesville Albany Volunteer Fire Department Albany Albion Fire Department Association Albion Alden Fire Department Association Carnegie Alfalfa Rural Fire Company Carnegie Arlington Volunteer Fire Dept. Incorporated Prague Arrowhead Estates Voluntary Fire Department, Inc. Canadian Ash Creek Community Fire Department Inc. Wilburton Ashland Volunteer Fire Dept Association Stuart Baker Fire Protection Association Turpin Bar C Rural Fire Department, Inc Burbank Barnsdall Rural Fire Association Incorporated Barnsdall Basin Volunteer Fire Department, Inc. Mannford Bear Creek Rural Fire District Association Kaw City Bee Community Volunteer Fire Department Association Kenefic Bell Rural Fire Department Inc Stilwell Bengal Fire Department Assn Wister Bennington Community Rural Volunteer Fire Department Assoc. Bennington Bennington Bentley Volunteer Fire District Atoka Berlin Volunteer Fire Association Sayre Berryhill Volunteer Fire Department, Inc. Tulsa Bethel Road Fire Department Association Lawton Big 4 Rural Fire District Association Kingfisher Big Beaver Fire Department Inc. Shidler Big Bend Volunteer Fire Department Inc. Ralston Big Cedar Volunteer Fire Dept., Inc. Muse Black Dog Fire Association Tulsa Blackburn Rural Fire Department Pawnee Blackgum Mountain Fire Department Vian Blackland Fire Corporation Pawhuska Blue Volunteer Fire Association McAlester Bluff Fire Department Inc Soper Boggy Fire Department Association Red Oak Boulanger Rural Fire Dept. Inc. Pawhuska Bowlin Springs Fire Protection Association Chelsea Brent Rural Fire District Inc. Sallisaw Bridge Creek Fire Fighters Association Blanchard Brooken Volunteer Fire Department Stigler Brooksville Volunteer Fire Dept Corporation Tecumseh Broxton Fire Dept. Company Assn. Fort Cobb Brushy Mt. Vol. Fire Dept. Muskogee Brushy Mt.-Sequoyah Co. -
Annual 2016-2017
ANNUAL 2016-2017 REPORT UCSB MARINE SCIENCE INSTITUTE | UC SANTA BARBARA Table of Contents Director’s Statement 3 Organizational Charts 5 Administrative Staff 6 Centers and Units 7 Other Projects & Activities 8 Seminars, Workshops, Conferences, and Meetings 9 Coastal Research Center 11 Marine Biotechnology Center 13 Ocean and Coastal Policy Center 20 UC Natural Reserve System 21 Analytical Laboratory 23 Education and Outreach 24 Awards Administered 25 Awards 26 Research Summaries 36 Space 129 Statistical Summary 135 Research Support Summary 136 Statistical Summary 2015-2016 138 Five-Year Research Support Summary 140 Funding Agencies 143 MSI Advisory Committee, 145 Administrative & Technical Staff Principal Investigators 148 2 DIRECTor’s STATEMENT 3 Director’s Statement As we move towards MSI’s 50th anniversary in 2019 the Marine Science Institute our scientists continue on a trajectory of engaging in cutting edge research and of solving pressing problems in ocean science. Our research portfolio continues to diversify with an ever growing set of funders representing a very large array of government agencies, private industry, non-profit foundations and individuals. Discoveries by MSI researchers are revealing wondrous new aspects of ocean systems from new insights into the ecology of coral reefs to the effects of ocean acidification. This new knowledge continues to improve our basic understanding of the seas and the wide range of services that they provide to society. I am proud of the contribution that our scientist make to society’s knowledge as these discoveries continually teach us how to be better stewards of the ocean realm. While ocean discovery is key to our mission, MSI researchers also act on this knowledge to solve pressing issues associated with the constructive use of ocean resources. -
Post-Wildfire Rebuilding and New Development in California Indicates Minimal Adaptation to Fire Risk
Land Use Policy 107 (2021) 105502 Contents lists available at ScienceDirect Land Use Policy journal homepage: www.elsevier.com/locate/landusepol Post-wildfire rebuilding and new development in California indicates minimal adaptation to fire risk H. Anu Kramer a,*, Van Butsic b, Miranda H. Mockrin c, Carlos Ramirez-Reyes a, Patricia M. Alexandre a,d, Volker C. Radeloff a a SILVIS Lab, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA b Department of Environmental Science, Policy and Management, University of California Berkeley, 231 Mulford Hall, Berkeley CA 94720, USA c Northern Research Station, USDA Forest Service, 5523 Research Park Dr. Suite 350, Baltimore, MD 21228, USA d Forest Research Centre, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal ARTICLE INFO ABSTRACT Keywords: Every year, wildfires destroy thousands of buildings in the United States, especially in the rapidly growing Wildfire wildland-urban interface, where homes and wildland vegetation meet or intermingle. After a wildfire there is a Housing growth window of opportunity for residents and public agencies to re-shape patterns of development, and avoid Wildland urban interface development in locations that are inherently at higher risk of wildfire destruction. We examined 28 of the most Policy destructive wildfiresin California, the state where most buildings are destroyed by wildfires,to evaluate whether Planning locations of rebuilt and newly constructed buildings were adaptive (i.e., if building occurred in lower risk areas). In total, these fires burned 7,075 buildings from 1970 to 2009. We found minimal evidence for adaptation both in the number and placement of buildings post-fire. -
Annual Report Marinemarine Science Science Institute Institute |• UC UC Santa Santa Barbara Barbara 2013 2014
ANNUAL REPORT MarineMarine Science Science Institute Institute |• UC UC Santa Santa Barbara Barbara 2013 2014 ANNUAL REPORT | 2013-2014 1 ANNUAL REPORT | 2013-2014 Table of Contents Director’s Statement 3 Organizational Charts 5 Administrative Staff 6 Centers and Units 7 Other Projects and Activities 8 Seminars, Workshops, Conferences, and Meetings 9 Coastal Research Center 17 EcoInformatics Center 19 Marine Biotechnology Center 21 National Center for Ecological Analysis and Synthesis 23 Ocean and Coastal Policy Center 25 UC Natural Reserve System 26 Analytical Laboratory 28 REEF/Outreach 29 Awards Administered 30 Awards 31 Research Summaries 39 Space 142 Statistical Summary 148 Research Support Summary 149 Statistical Summary 2013-2014 151 Five-Year Research Support Summary 153 Funding Agencies 156 MSI Advisory Committee, 158 Administrative and Technical Staff Principal Investigators 161 2 ANNUAL REPORT | 2013-2014 Director’s Statement 3 ANNUAL REPORT | 2013-2014 Director’s Statement This year marks the 10th anniversary of the opening of the Marine Science Institute’s Marine Science Research Building, a state-of-the-art facility located on the bluff overlooking the Pacific Ocean on the eastern edge of the University of California, Santa Barbara’s campus. It is an inspiring facility and location, and it has taken the hard work of many individuals to make it a reality. At UCSB in the 1980’s and 1990’s, Marine Science facilities could be described as dispersed, inadequate, and not up to the standards of a world class research institution. Long-standing efforts to get a facility approved and built had met with no success. However, things began to change with the identification of a State of California program that provided a financing mechanism for research facilities dedicated to long-term scientific activities. -
A Community Proposal to Integrate Proteomics Activities In
F1000Research 2017, 6:875 Last updated: 05 OCT 2021 OPINION ARTICLE A community proposal to integrate proteomics activities in ELIXIR [version 1; peer review: 2 approved] Juan Antonio Vizcaíno 1, Mathias Walzer 1, Rafael C. Jiménez 2, Wout Bittremieux3, David Bouyssié4, Christine Carapito4, Fernando Corrales5, Myriam Ferro4, Albert J.R. Heck6,7, Peter Horvatovich 8, Martin Hubalek9, Lydie Lane10,11, Kris Laukens3, Fredrik Levander12, Frederique Lisacek13,14, Petr Novak15, Magnus Palmblad 16, Damiano Piovesan17, Alfred Pühler18, Veit Schwämmle 19, Dirk Valkenborg20-22, Merlijn van Rijswijk 23,24, Jiri Vondrasek9, Martin Eisenacher25, Lennart Martens26,27, Oliver Kohlbacher 28-31 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK 2ELIXIR Hub, Cambridge, CB10 1SD, UK 3Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium 4French Proteomics Infrastructure ProFI, Grenoble, (EDyP U1038, CEA/Inserm/ Grenoble Alpes University) Toulouse (IPBS, Université de Toulouse, CNRS, UPS), Strasbourg (LSMBO, IPHC UMR7178, CNRS-Université de Strasbourg), France 5ProteoRed, Proteomics Unit, Centro Nacional de Biotecnología (CSIC), Madrid, 28049, Spain 6Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3548 CH, The Netherlands 7Netherlands Proteomics Center, Utretcht, 3584 CH, The Netherlands 8Analytical Biochemistry, Department of Pharmacy, -
Gut Microbiome’ on 7Th & 8Th June 2018 in Brussels
THE ESSENTIAL ROLES OF CARBOHYDRATES IN PROMOTING GUT MICROBIOTA FUNCTION THROUGH ALL STAGES OF LIFE This paper was co-authored by Nathalie Juge†, Sabine Flitsch‡, Rodney Townsend§ and Claire Doherty‡ using input from group discussions that took place at the CarboMet workshop ‘The Role of Carbohydrates in the Gut Microbiome’ on 7th & 8th June 2018 in Brussels. CarboMet (Metrology of Carbohydrates for European Bioindustries) is a four-year Coordination and Support Action (CSA) funded by Horizon 2020 FET-OPEN (Grant agreement no. 737395). https://carbomet.eu/) The primary aim of the CSA is to mobilise the European academic and industrial community to identify generic measurement, data management and metrological challenges that must be met in order to advance and exploit carbohydrate knowledge and applications. The potential for exploitation of carbohydrates lies in their diversity and structural complexity – subtle changes in the three-dimensional structure of a carbohydrate profoundly affects (for example) its ability to protect against or fight infectious disease. However, these subtle structural differences present a challenge for their analysis. Sophisticated measurement and metrological capabilities for analysing carbohydrates are available but are nowhere near as advanced or as routinely used in other areas such as gene sequencing. Therefore as a first stage CarboMet has organised some open, Europe-wide workshops to identify key topics where our understanding needs to be advanced urgently, and where current limitations in our measurement, data management and metrological capabilities are hindering progress. The Workshops were also asked to recommend appropriate Work Programmes that should be supported by Horizon 2020 and its successor, Horizon Europe. -
Evaluating Tradeoffs Among Ecosystem Services to Inform Marine Spatial Planning
Evaluating tradeoffs among ecosystem services to inform marine spatial planning Lester, S. E., Costello, C., Halpern, B. S., Gaines, S. D., White, C., & Barth, J. A. (2013). Evaluating tradeoffs among ecosystem services to inform marine spatial planning. Marine Policy, 38, 80-89. doi:10.1016/j.marpol.2012.05.022 10.1016/j.marpol.2012.05.022 Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse 1 Title: Evaluating tradeoffs among ecosystem services to inform marine spatial planning 2 3 Sarah E. Lestera, Christopher Costellob, Benjamin S. Halpernc, Steven D. Gainesd, Crow Whitee, 4 John A. Barthf 5 6 a Marine Science Institute and Bren School of Environmental Science & Management, 7 University of California, Santa Barbara, CA 93106-6150, USA. [email protected] 8 b Bren School of Environmental Science & Management, 4410 Bren Hall, University of 9 California, Santa Barbara, CA 93106, USA. [email protected] 10 c National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa 11 Barbara, CA 93101, USA. [email protected] 12 d Bren School of Environmental Science & Management, 4410 Bren Hall, University of 13 California, Santa Barbara, CA 93106, USA. [email protected] 14 e Bren School of Environmental Science & Management, 4410 Bren Hall, University of 15 California, Santa Barbara, CA 93106, USA. [email protected] 16 f College of Oceanic & Atmospheric Sciences, Oregon State University, 104 COAS Admin Bldg, 17 Corvallis, OR 97331, USA. [email protected] 18 19 Corresponding author: 20 Sarah E. Lester 21 Marine Science Institute / Bren School of Environmental Science & Management 22 University of California 23 Santa Barbara, CA 93106-6150, USA 24 Ph: 805.893.5175 25 Fax: 805.893.8062 26 Email: [email protected] 27 28 Running Title: Ecosystem service tradeoffs 1 Ecosystem service tradeoffs 1 Abstract 2 A central challenge for natural resource management is developing rigorous yet practical 3 approaches for balancing the costs and benefits of diverse human uses of ecosystems.