Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
CHRISTINA “TINA” WARINNER (Last Updated October 18, 2018)
CHRISTINA “TINA” WARINNER (last updated October 18, 2018) Max Planck Institute University of Oklahoma for the Science of Human History (MPI-SHH) Department of Anthropology Department of Archaeogenetics Laboratories of Molecular Anthropology Kahlaische Strasse 10, 07743 Jena, Germany And Microbiome Research (LMAMR) +49 3641686620 101 David L. Boren Blvd, [email protected] Norman, OK 73019 USA www.christinawarinner.com [email protected] http://www.shh.mpg.de/employees/50506/25522 www.lmamr.org APPOINTMENTS W2 Group Leader, Max Planck Institute for the Science of Human History, Germany 2016-present University Professor, Friedrich Schiller University, Jena, Germany 2018-present Presidential Research Professor, Univ. of Oklahoma, USA 2014-present Assistant Professor, Dept. of Anthropology, Univ. of Oklahoma, USA 2014-present Adjunct Professor, Dept. of Periodontics, College of Dentistry, Univ. of Oklahoma, USA 2014-present Visiting Associate Professor, Dept. of Systems Biology, Technical University of Denmark 2015 Research Associate, Dept. of Anthropology, Univ. of Oklahoma, USA 2012-2014 Acting Head of Group, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2011-2012 Research Assistant, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2010-2011 EDUCATION Ph.D., Anthropology, Dept. of Anthropology, Harvard University 2010 Thesis Title: “Life and Death at Teposcolula Yucundaa: Mortuary, Archaeogenetic, and Isotopic Investigations of the Early Colonial Period in Mexico” A.M., Anthropology, Dept. of Anthropology, Harvard University 2008 B.A., with Honors, Anthropology, University of Kansas 2003 B.A., Germanic Literatures and Languages, University of Kansas 2003 SELECTED HONORS, AWARDS, AND FELLOWSHIPS Invited speaker, British Academy, Albert Reckitt Archaeological Lecture (forthcoming) 2019 Invited speaker, EMBL Science and Society (forthcoming, Nov. -
Ayshwarya Subramanian Updated June 10, 2021
Ayshwarya Subramanian Updated June 10, 2021 Contact Kuchroo Lab and Klarman Cell Observatory Information Broad Institute twitter: @ayshwaryas 5407G, 415 Main Street website: ayshwaryas.github.io Cambridge, MA 02412 USA email:[email protected] Areas of Computational Biology (Kidney disease, Cancer, Inflammatory Bowel Disease, RNA Biology), Ge- expertise nomic Data Analysis (Single-cell and Bulk-RNAseq, Metagenomics, Exome and single-nucleus DNA sequencing), Machine Learning, Probabilistic modeling, Phylogenetics, Applied Statistics Education 2013 Ph.D., Biological Sciences Carnegie Mellon University, Pittsburgh, PA USA Doctoral Advisor: Russell Schwartz, Ph.D. Dissertation: Inferring tumor evolution using computational phylogenetics 2007 M.Sc. (Hons), Biological Sciences (Undergraduate degree) Birla Institute of Technology and Science (BITS{Pilani), Rajasthan, India CGPA 9.21/10, Major GPA 10/10, with Distinction Undergraduate Honors Thesis: A mathematical model for phototactic responses in Halobac- terium salinarium, Max Planck Institute for Complex Technical Systems, Germany. Current Computational Scientist, Cambridge MA 2017{Present Appointment Mentors: Aviv Regev, Ph.D. & Vijay Kuchroo, Ph.D., D.V.M Research Summary: Single-cell portraits of disease and normal states using human data, mouse and organoid models Klarman Cell Observatory Broad Institute, Cambridge, MA 02142 Publications Pre-prints/Under review [1] Subramanian A†, Vernon KA†, Zhou Y† et al. Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution. bioRxiv 2021.05.30.446342; doi: https://doi.org/10.1101/2021.05.30.446342. [2] Subramanian A†,Vernon KA†, Slyper M, Waldman J, et al. RAAS blockade, kidney dis- ease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells. -
Microbiology of Endodontic Infections
Scient Open Journal of Dental and Oral Health Access Exploring the World of Science ISSN: 2369-4475 Short Communication Microbiology of Endodontic Infections This article was published in the following Scient Open Access Journal: Journal of Dental and Oral Health Received August 30, 2016; Accepted September 05, 2016; Published September 12, 2016 Harpreet Singh* Abstract Department of Conservative Dentistry & Endodontics, Gian Sagar Dental College, Patiala, Punjab, India Root canal system acts as a ‘privileged sanctuary’ for the growth and survival of endodontic microbiota. This is attributed to the special environment which the microbes get inside the root canals and several other associated factors. Although a variety of microbes have been isolated from the root canal system, bacteria are the most common ones found to be associated with Endodontic infections. This article gives an in-depth view of the microbiology involved in endodontic infections during its different stages. Keywords: Bacteria, Endodontic, Infection, Microbiology Introduction Microorganisms play an unequivocal role in infecting root canal system. Endodontic infections are different from the other oral infections in the fact that they occur in an environment which is closed to begin with since the root canal system is an enclosed one, surrounded by hard tissues all around [1,2]. Most of the diseases of dental pulp and periradicular tissues are associated with microorganisms [3]. Endodontic infections occur and progress when the root canal system gets exposed to the oral environment by one reason or the other and simultaneously when there is fall in the body’s immune when the ingress is from a carious lesion or a traumatic injury to the coronal tooth structure.response [4].However, To begin the with, issue the if notmicrobes taken arecare confined of, ultimately to the leadsintra-radicular to the egress region of pathogensIn total, and bacteria their by-productsdetected from from the the oral apical cavity foramen fall into to 13 the separate periradicular phyla, tissues. -
Case Studies in Bayesian Statistics Workshop 9 Poster Session
Case Studies in Bayesian Statistics Workshop 9 Poster Session Following is a tentative list of posters being presented during the workshop: 1. Edoardo Airoldi, Curtis Huttenhower, Olga Troyanskaya and David Botstein 2. Dipankar Bandyopadhyay, Elizabeth Slate, Debajyoti Sinha, Dikpak Dey and Jyotika Fernandes 3. Brenda Betancourt and Maria-Eglee Perez 4. Sham Bhat, Murali Haran, Julio Molineros and Erick Dewolf 5. Jen-hwa Chu, Merlise A. Clyde and Feng Liang 6. Jason Connor, Scott Berry and Don Berry 7. J. Mark Donovan, Michael R. Elliott and Daniel F. Heitjan 8. Elena A. Erosheva, Donatello Telesca, Ross L. Matsueda and Derek Kreager 9. Xiaodan Fan and Jun S. Liu 10. Jairo A. Fuquene and Luis Raul Pericchi 11. Marti Font, Josep Ginebra, Xavier Puig 12. Isobel Claire Gormley and Thomas Brendan Murphy 13. Cari G. Kaufman and Stephan R. Sain 14. Alex Lenkoski 15. Herbie Lee 16. Fei Liu 17. Jingchen Liu, Xiao-Li Meng, Chih-nan Chen, Margarita Alegria 18. Christian Macaro 19. Il-Chul Moon, Eunice J. Kim and Kathleen M. Carley 20. Christopher Paciorek 21. Susan M. Paddock and Patricia Ebener 22. Nicholas M. Pajewski, L. Thomas Johnson, Thomas Radmer, and Purushottam W. Laud 23. Mark W. Perlin, Joseph B. Kadane, Robin W. Cotton and Alexander Sinelnikov 24. Alicia Quiros, Raquel Montes Diez and Dani Gamerman 25. Eiki Satake and Philip Amato 26. James Scott 27. Russell Steele, Robert Platt and Michelle Ross 28. Alejandro Villagran, Gabriel Huerta, Charles S. Jackson and Mrinal K. Sen 29. Dawn Woodard 30. David C. Wheeler, Lance A. Waller and John O. -
The Oral Microbiome of Healthy Japanese People at the Age of 90
applied sciences Article The Oral Microbiome of Healthy Japanese People at the Age of 90 Yoshiaki Nomura 1,* , Erika Kakuta 2, Noboru Kaneko 3, Kaname Nohno 3, Akihiro Yoshihara 4 and Nobuhiro Hanada 1 1 Department of Translational Research, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 2 Department of Oral bacteriology, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 3 Division of Preventive Dentistry, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] (N.K.); [email protected] (K.N.) 4 Division of Oral Science for Health Promotion, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-45-580-8462 Received: 19 August 2020; Accepted: 15 September 2020; Published: 16 September 2020 Abstract: For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. -
UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial
UNIVERSITY OF CALIFORNIA SAN DIEGO Making sense of microbial populations from representative samples A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by James T. Morton Committee in charge: Professor Rob Knight, Chair Professor Pieter Dorrestein Professor Rachel Dutton Professor Yoav Freund Professor Siavash Mirarab 2018 Copyright James T. Morton, 2018 All rights reserved. The dissertation of James T. Morton is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii DEDICATION To my friends and family who paved the road and lit the journey. iv EPIGRAPH The ‘paradox’ is only a conflict between reality and your feeling of what reality ‘ought to be’ —Richard Feynman v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . .v Table of Contents . vi List of Abbreviations . ix List of Figures . .x List of Tables . xi Acknowledgements . xii Vita ............................................. xiv Abstract of the Dissertation . xvii Chapter 1 Methods for phylogenetic analysis of microbiome data . .1 1.1 Introduction . .2 1.2 Phylogenetic Inference . .4 1.3 Phylogenetic Comparative Methods . .6 1.4 Ancestral State Reconstruction . .9 1.5 Analysis of phylogenetic variables . 11 1.6 Using Phylogeny-Aware Distances . 15 1.7 Challenges of phylogenetic analysis . 18 1.8 Discussion . 19 1.9 Acknowledgements . 21 Chapter 2 Uncovering the horseshoe effect in microbial analyses . 23 2.1 Introduction . 24 2.2 Materials and Methods . 34 2.3 Acknowledgements . 35 Chapter 3 Balance trees reveal microbial niche differentiation . 36 3.1 Introduction . -
Bulleidia Extructa Gen. Nov., Sp. Nov., Isolated from the Oral Cavity
International Journal of Systematic and Evolutionary Microbiology (2000), 50, 979–983 Printed in Great Britain Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity Julia Downes,1 Bente Olsvik,†2 Sarah J. Hiom,1 David A. Spratt,1 Sarah L. Cheeseman,1 Ingar Olsen,2 Andrew J. Weightman3 and William G. Wade1 Author for correspondence: William G. Wade. Tel: j44 207 955 2849. Fax: j44 207 955 2847. e-mail: william.wade!kcl.ac.uk 1 Oral Microbiology Unit, Five strains of anaerobic non-sporing Gram-positive bacilli isolated from Division of Oral Medicine, advanced periodontitis (four strains) and a dentoalveolar abscess (one strain) Pathology, Microbiology and Immunology, Guy’s, that did not correspond to existing species were subjected to phenotypic and King’s and St Thomas’ genetic characterization. Following 16S rDNA sequence analysis, they were Dental Institute, found to constitute a novel branch of the low GMC Gram-positive division of King’s College London, Guy’s Hospital, London the phylogenetic tree related to Erysipelothrix rhusiopathiae and Holdemania SE1 9RT, UK filiformis. A new genus Bulleidia, and the species Bulleidia extructa, are 2 Institutt for oral biologi, proposed. Growth of B. extructa in broth media was poor but was enhanced by University of Oslo, the addition of fructose, glucose or maltose together with Tween 80. Glucose N-0316 Oslo, Norway and maltose were fermented and arginine was hydrolysed. Acetate, lactate 3 Cardiff School of and trace amounts of succinate were the end products of glucose Biosciences, Cardiff fermentation. The GMC content of the DNA of the type strain is 38 mol%. -
The Comparative Analysis of the Ruminal Bacterial Population in Reindeer (Rangifer Tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects
animals Article The Comparative Analysis of the Ruminal Bacterial Population in Reindeer (Rangifer tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects Larisa A. Ilina 1,*, Valentina A. Filippova 1 , Evgeni A. Brazhnik 1 , Andrey V. Dubrovin 1, Elena A. Yildirim 1 , Timur P. Dunyashev 1, Georgiy Y. Laptev 1, Natalia I. Novikova 1, Dmitriy V. Sobolev 1, Aleksandr A. Yuzhakov 2 and Kasim A. Laishev 2 1 BIOTROF + Ltd., 8 Malinovskaya St, Liter A, 7-N, Pushkin, 196602 St. Petersburg, Russia; fi[email protected] (V.A.F.); [email protected] (E.A.B.); [email protected] (A.V.D.); [email protected] (E.A.Y.); [email protected] (T.P.D.); [email protected] (G.Y.L.); [email protected] (N.I.N.); [email protected] (D.V.S.) 2 Department of Animal Husbandry and Environmental Management of the Arctic, Federal Research Center of Russian Academy Sciences, 7, Sh. Podbel’skogo, Pushkin, 196608 St. Petersburg, Russia; [email protected] (A.A.Y.); [email protected] (K.A.L.) * Correspondence: [email protected] Simple Summary: The reindeer (Rangifer tarandus) is a unique ruminant that lives in arctic areas characterized by severe living conditions. Low temperatures and a scarce diet containing a high Citation: Ilina, L.A.; Filippova, V.A.; proportion of hard-to-digest components have contributed to the development of several adaptations Brazhnik, E.A.; Dubrovin, A.V.; that allow reindeer to have a successful existence in the Far North region. These adaptations include Yildirim, E.A.; Dunyashev, T.P.; Laptev, G.Y.; Novikova, N.I.; Sobolev, the microbiome of the rumen—a digestive organ in ruminants that is responsible for crude fiber D.V.; Yuzhakov, A.A.; et al. -
Bioinformatics Opening Workshop September 8 - 12, 2014
Bioinformatics Opening Workshop September 8 - 12, 2014 Mihye Ahn James (Paul) Brooks University of North Carolina Virginia Commonwealth Alexander Alekseyenko Greg Buck New York University Virginia Commonwealth Baiguo An Mark Burch University of North Carolina Ohio State University Jeremy Ash Christopher Burke North Carolina State University University of Cincinnati Deepak Nag Ayyala Hongyuan Cao University of Maryland University of Missouri Keith Baggerly Vincent Carey MD Anderson Center Harvard University Veera Baladandayuthapani Luis Carvalho MD Anderson Center Boston University Pallavi Basu Alberto Cassese University of Southern California Rice University Munni Begum Changgee Chang Ball State University Emory University Emanuel Ben-David Hegang Chen Columbia University University of Maryland Anindya Bhadra Chen Chen Purdue University Purdue University Yuanyuan Bian Mengjie Chen University of Missouri University of North Carolina Huybrechts Frazier Achard Bindele Hyoyoung Choo-Wosoba University of South Alabama University of Louisville Kristen Borchert Pankaj Choudhary BD Technologies University of Texas Russell Bowler Hyonho Chun National Jewish Health Purdue University Bioinformatics Opening Workshop September 8 - 12, 2014 Robert Corty Yang Feng University of North Carolina Columbia University Xinping Cui Hua Feng University of California, Riverside University of Idaho Hongying Dai Jennifer Fettweis Children's Mercy Hospital Virginia Commonwealth Susmita Datta Dayne Filer University of Louisville EPA Sujay Datta Christopher Fowler -
Quantitative and Qualitative Analysis of Microorganisms in Root‑Filled Teeth with Persistent Infection: Monitoring of the Endodontic Retreatment
Published online: 2019-09-26 Original Article Quantitative and qualitative analysis of microorganisms in root‑filled teeth with persistent infection: Monitoring of the endodontic retreatment Marcos S. Endo1, Caio C. R. Ferraz1, Alexandre A. Zaia1, Jose F. A. Almeida1, Brenda P. F. A. Gomes1 1Department of Restorative Dentistry, Endodontics Correspondence: Dr. Brenda PFA Gomes Division, Piracicaba Dental School – State University Email: [email protected] of Campinas – UNICAMP, Piracicaba, SP, Brazil ABSTRACT Objective: The aim of this study was to investigate in vivo microorganisms detected in root‑filled teeth with post‑treatment apical periodontitis and quantify colony‑forming units (CFU) during endodontic retreatment. Materials and Methods: Fifteen root‑filled teeth had their previous gutta‑percha removed and were randomly instrumented before being divided into three groups and medicated with either [Ca (OH) 2 + 2% CHX gel], [Ca (OH) 2 + 0.9% NaCl] or 2% CHX gel. Samples were taken after removal of gutta‑percha (S1), after chemomechanical preparation using 2% CHX gel (S2), and after inter‑appointment dressing (S3) for 7 or 14 days later. Cultivable bacteria recovered from infected root canals at the three stages were counted and identified by means of culture and PCR assay (16S rDNA). Quantitative data were statistically analyzed by using Mann‑Whitney test in which pairs of groups were compared (P < 0.05). Results: CFU counts decreased significantly from S1 to S2 (P < 0.05). No significant difference was found between S2 and S3 (P = 0.3093) for all three experimental groups. Chemomechanical preparation and intra‑canal dressing promoted significant median reductions of 99.61% and 99.57%, respectively, in the number of bacteria compared to S1 samples. -
Microbes from Sequencing 16S Ribosomal DNA and Internal Transcribed Spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui*
Cheng et al. Annals of Clinical Microbiology and Antimicrobials 2014, 13:1 http://www.ann-clinmicrob.com/content/13/1/1 RESEARCH Open Access Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui* Abstract Background: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study. Methods: Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank. Results: The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature).