DOCSLIB.ORG

Abstracts Catalog

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Abstracts Catalog th 58 National Junior Sciences and Humanities Symposium: Abstracts Catalog The abstracts in this publication are from original scientific research conducted by participating students in the 58th National Junior Science and Humanities Symposium. JSHS is a collaborative effort between the research arm of the Department of Defense Tri-Services - U.S. Army, Navy, and Air Force and nationwide academic research institutes. Hosted via Zoom April 15-18, 2020 Administered by: National Science Teaching Association National Junior Science and Humanities Symposium Program Objectives Promote research and experimentation in sciences, technology, engineering, and mathematics (STEM) at the high school level. Recognize the significance of research in human affairs and the importance of humane and ethical principles in the application of research results. Identify talented youth and their teachers, recognize their accomplishments at symposia, and encourage their continued interest and participation in STEM. Expand the horizons of research-oriented students by exposing them to opportunities in STEM within the Department of Defense, academia, industry, and government. Increase the number of adults capable of conducting research and development. NJSHS 2020 Oral Presenters Environmental Science Vaughn Hughes Rincon Jagarlamudi Smrithi Balasubramanian Sarah Katz Krisangi Bhargava Alice Khomski Ella Dommert (3) James Lao Jadyn Henry John Lin Julia Kagiliery (1) Amara Orth Mithra Karamchedu Anya Razmi Emma Kitchin Caroline Reed (2) Lucas Ritzdorf Anushka Sanyal Hannah Rogers Emily Tianshi (3) Emma Romano Safiya Sankari Medicine & Health/Behavioral Sciences Elise Scheuring (2) Adyant Shankar Rachel Brooks Lea Wang Sarah Burkey (1) Kasyap Chakravadhanula Biomedical Sciences Daniel Choi Emmalyn Kartchner Sarah Barksdale Isabella Knott Evelyn Bodoni (1) Shan Lateef (2) Ishaan Brar (2) Rhea Malhotra Kevin Fan Irene Mamontov Victoria Hwang Michaela McCormack Kaeo Kekumano Viraj Mehta Aditi Kumari Saraswati Sridhar Anne Liang (3) Grace Sun (3) Ilhaam Mahoui Dasia Taylor Arundathi Nair Paulina Naydenkov Engineering & Technology Sahasra Pokkunuri Logan Ridenbaugh Yuvanshu Agarwal Eden Winga Reese Artero Keena Yin Joseph Clary Bryce Goodin Life Science Kelsey Krusen Catherine Kung Ahmad Abdel-Azim Luke Millam Audrey Anderson (1) Eliza Moore Sydney Assalita Axel S. Toro Vega (2) Vetri Vel (3) Physical Sciences Ryan Westcott (1) Jared Lenn Mathematics & Computer Science Josie Long Mina Mandic (1) Sam Florin Aniket Pant Melody Guo Alay Shah (2) Anu Iyer Owen Skriloff (3) Kabir Jolly Tarun Kumar Martheswaran (2) Chemistry Rachel Muppidi Ryan Park (1) Anna Grondolsky (3) Lillian Petersen Reagan Guerra (2) Jason Ping Emma Steude (1) Jacqueline Prawira Uyen Nhi Tran Michelle Tang (3) Ethan Weisberg NJSHS 2020 Oral Presenter Abstracts Using Single-Cell RNA Sequencing Data to Study Plastid Differentiation Dynamics with Nucleus-Encoded Plastid Gene Expression in Arabidopsis thaliana Ahmad Abdel-Azim Appleton North High School Appleton, Wisconsin Research Mentor: Tessa Green Department of Systems Biology Harvard Medical School Little is known on how cell differentiation dynamics are impacted by other biological systems, such as organelle development. The plant provides an interesting context to study this impact given its diverse array of cell and plastid types. Plastids are organelles that are unique to plant cells, synthesizing and storing critical chemical compounds and pigments. All plastids develop from undifferentiated proplastids in meristematic tissue; however, it is unknown how plastid development progresses relative to cell development, namely the extent to which plastid state is coupled with cell state. This coupling was explored via single cell RNA sequencing of the root of Arabidopsis thaliana. Cells and plastids were clustered based on distinct nucleus-encoded plastid genes and non- plastid-related genes, respectively, enabling independent assignment of plastid and cell types. A machine learning model was developed to classify cell types based solely on plastid gene expression profiles. The high accuracy of this model (>96%) suggests that each cell type houses a distinctive plastid type. A trajectory inference model was used to create a pseudotime axis between undifferentiated meristematic cells and mature endodermal cells, enabling the study of plastid development relative to cell development. Along this pseudotime axis, plastid state was found to be coupled with cell state. Our findings lead to advances in plastid engineering and may enable future biotechnological applications. Moreover, we offer a novel computational pipeline to actually study cell organelles at the single-cell level which opens the door for a wide variety of applications beyond plants. Virtual Assistant application to optimize the usage of water and crop yield. Yuvansu Agarwal Morris Hills High School - Academy of Math, Science and Engineering Rockaway, New Jersey Currently, agriculture wastes 1,500 trillion liters of water annually and to sustain a growing population, we must grow 70% more food by 2050. My voice technology based virtual assistant application predicts crops’ water requirements and growth stage in languages like Hindi, French, Spanish, and English to optimize water and crop yield. The application extracts the required inputs using natural language processing. Based on the inputs it collects for different crops, the Python code mines for the PET (Potential Evapotranspiration) and the PPET (ratio of Precipitation to PET) from external APIs. The application utilizes an algorithm to compute the water requirements where if the weather forecast predicts no rain and PPET<1, then the water requirements (mm) i s computed as PET-Precipitation. Similarly, the application determines the crops’ growth stage by mining for each crops’ accumulated GDD (Growing Degree Days) and mapping it to particular thresholds of growth stages. The results of the application were within an average error margin of 5-7% as compared to crop research. By relaying accurate water requirements and growth stages to small farmers around the world in multiple languages, the application can help farmers grow healthy crops and drive insightful irrigation decisions. Resilin Distribution and Abundance in Apis mellifera Wing Joints across Biological Age Classes Audrey Anderson (1st Place Life Sciences) Omaha North High Magnet School Omaha, Nebraska Research Mentor: Dr. Fassbinder-Orth This study investigated the variance of resilin between Apis mellifera biological age classes. The presence of resilin, an elastomeric protein, in insect vein joints provides the flexible, passive deformations that are crucial to A. mellifera flight and the role of the forager, the oldest A. mellifera biological age class. Foragers collect the pollen necessary to feed the colony and their disappearance jeopardizes colony health, contributing to the onset of Colony Collapse Disorder (CCD). As CCD and other stressors continue to impact A. mellifera populations, it is increasingly important to understand and establish physiological markers of A. melliferahealth, allowing for early warning systems for apiarists to take preventative actions. Resilin is a potential novel and age-dependent indicator of health. Methodology included measuring the 1m-cu, 2m-cu, Cu-V, and Cu2-V joints on the forewing and the Cu- V joint of the hindwing using a fluorescence microscope equipped with an aniline blue filter. Quantitative fluorescence imaging analysis calculated Corrected Total Cell Fluorescence (CTCF). The 1m-cu and the Cu-V joints on the ventral forewing, and the Cu-V joint on the ventral hindwing varied significantly between age classes on the left and right sides of the wing. At the 1m-cu joint, CTCF continually decreased from the hatchling to forager age classes. At the Cu-V joints on the forewing and the hindwing, CTCF decreased from the hatchling to nurse age classes, and then increased between the nurse, guard, and forager age classes. The results of this study suggest that the CTCF of resilin is age-dependent. Disaster Proof Design for Pacific Housing Reese Artero Guam High School U.S. Naval Hospital Base Mentor: Paul Cuaresma Typhoon damage is a growing point of concern for the people of the Pacific; destroying homes, causing water shortages, power outages, flooding, and even death in the most extreme cases, prompting the idea to create a design that could successfully withstand all natural disasters within the Pacific Region. With the creation of a contoured dome model structure, typhoon damages would be significantly decreased, limiting the amount of damage control that would need to be done afterwards, and limiting the amount of people that could possibly be harmed during typhoons as well. Through extensive wind tests using sugar and wind, it was found that a contoured dome model is more effective in comparison to a smooth model dome, with an almost 50% higher wind diversion rate. Ultimately, the design for a disaster proof home for the pacific, maintains a higher windload than most other residential structures, and would be able to withstand some of the most damaging winds in the case of a super typhoon in the pacific. The Effect of Light Intensity on Planarian Regeneration: Using Planarian Regeneration Patterns as a Model for Human Regeneration Projects Sydney Assalita State College Area High School State College, Pennsylvania State College, Pennsylvania In a mere ten to twenty years, regeneration within human specimens may become
Load more

Recommended publications
  • Ecology and Evolution of Metabolic Cross-Feeding Interactions in Bacteria† Cite This: Nat
    Natural Product Reports View Article Online REVIEW View Journal | View Issue Ecology and evolution of metabolic cross-feeding interactions in bacteria† Cite this: Nat. Prod. Rep.,2018,35,455 Glen D'Souza, ab Shraddha Shitut, ce Daniel Preussger,c Ghada Yousif,cde Silvio Waschina f and Christian Kost *ce Literature covered: early 2000s to late 2017 Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has fi fi Creative Commons Attribution 3.0 Unported Licence. shown that bacterial genotypes can signi cantly bene t from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution Received 25th January 2018 and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight DOI: 10.1039/c8np00009c general principles that underlie the adaptive evolution of interconnected microbial metabolic networks rsc.li/npr as well as the evolutionary consequences that result for cells living in such communities. 1 Introduction 2.5 Mechanisms of metabolite transfer This article is licensed under a 2 Metabolic cross-feeding interactions 2.5.1 Contact-independent mechanisms 2.1 Historical account 2.5.1.1 Passive diffusion 2.2 Classication of cross-feeding interactions 2.5.1.2 Active transport 2.2.1 Unidirectional by-product cross-feeding 2.5.1.3 Vesicle-mediated transport Open Access Article.
    [Show full text]
  • Quorum Sensing Modulates the Epibiotic-Parasitic Relationship
    fmicb-09-02049 September 24, 2018 Time: 16:12 # 1 ORIGINAL RESEARCH published: 24 September 2018 doi: 10.3389/fmicb.2018.02049 Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x Joseph K. Bedree1,2, Batbileg Bor2, Lujia Cen2, Anna Edlund3, Renate Lux4, Jeffrey S. McLean5, Wenyuan Shi2* and Xuesong He2* 1 Section of Oral Biology, Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States, 2 Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States, 3 Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States, 4 Section of Periodontics, Division of Constitutive and Regenerative Sciences, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States, 5 Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, United States Edited by: The ultra-small, obligate parasitic epibiont, TM7x, the first and only current member of Sebastian Fraune, Christian-Albrechts-Universität zu Kiel, the long-elusive Saccharibacteria (formerly the TM7 phylum) phylum to be cultivated, Germany was isolated in co-culture with its bacterial host, Actinomyces odontolyticus subspecies Reviewed by: actinosynbacter, XH001. Initial phenotypic characterization of the TM7x-associated Jürgen Tomasch, XH001 co-culture revealed enhanced biofilm formation in the presence of TM7x Helmholtz-Gemeinschaft Deutscher Forschungszentren (HZ), Germany compared to XH001 as monoculture. Genomic analysis and previously published Tim Miyashiro, transcriptomic profiling of XH001 also revealed the presence of a putative AI-2 quorum Pennsylvania State University, United States sensing (QS) operon, which was highly upregulated upon association of TM7x with *Correspondence: XH001.
    [Show full text]
  • Phenotypic and Physiological Characterization of the Epibiotic Interaction Between Tm7x and Its Basibiont Actinomyces
    HHS Public Access Author manuscript Author Manuscript Author ManuscriptMicrob Author ManuscriptEcol. Author manuscript; Author Manuscript available in PMC 2017 January 01. Published in final edited form as: Microb Ecol. 2016 January ; 71(1): 243–255. doi:10.1007/s00248-015-0711-7. Phenotypic and physiological characterization of the epibiotic interaction between TM7x and its basibiont Actinomyces Batbileg Bor1, Nicole Poweleit2, Justin S. Bois3, Lujia Cen1, Joseph K. Bedree1, Z. Hong Zhou2,4, Robert P. Gunsalus2, Renate Lux1, Jeffrey S. McLean5, Xuesong He1,*, and Wenyuan Shi1,* 1Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA 90095 2Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 3Division of Biology and Biological Engineering, California Institute of Technology, MC 114-96, Pasadena, CA 91125 4California Nanosystems Institute, University of California, Los Angeles, California 90095 5Department of Periodontics, University of Washington, Seattle, WA 98195 Abstract Despite many examples of obligate epibiotic symbiosis (one organism living on the surface of another) in nature, such an interaction has rarely been observed between two bacteria. Here, we further characterize a newly reported interaction between a human oral obligate parasitic bacterium TM7x (cultivated member of Candidatus Saccharimonas formerly Candidate Phylum TM7), and its basibiont Actinomyces odontolyticus species (XH001), providing a model system to study epiparasitic symbiosis in the domain Bacteria. Detailed microscopic studies indicate that both partners display extensive morphological changes during symbiotic growth. XH001 cells manifested as short rods in monoculture, but displayed elongated and hyphal morphology when physically associated with TM7x. Interestingly, these dramatic morphological changes in XH001 were also induced in oxygen-depleted conditions, even in the absence of TM7x.
    [Show full text]
  • Metabolic Network Percolation Quantifies Biosynthetic Capabilities
    RESEARCH ARTICLE Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome David B Bernstein1,2, Floyd E Dewhirst3,4, Daniel Segre` 1,2,5,6,7* 1Department of Biomedical Engineering, Boston University, Boston, United States; 2Biological Design Center, Boston University, Boston, United States; 3The Forsyth Institute, Cambridge, United States; 4Harvard School of Dental Medicine, Boston, United States; 5Bioinformatics Program, Boston University, Boston, United States; 6Department of Biology, Boston University, Boston, United States; 7Department of Physics, Boston University, Boston, United States Abstract The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems. *For correspondence: DOI: https://doi.org/10.7554/eLife.39733.001 [email protected] Competing interests: The authors declare that no Introduction competing interests exist.
    [Show full text]
  • Deep Metagenomics Examines the Oral Microbiome During Dental Caries, Revealing Novel Taxa and Co-Occurrences with Host Molecules
    Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Research Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules Jonathon L. Baker,1 James T. Morton,2 Márcia Dinis,3 Ruth Alvarez,3 Nini C. Tran,3 Rob Knight,4,5,6,7 and Anna Edlund1,5 1Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California 92037, USA; 2Systems Biology Group, Flatiron Institute, New York, New York 10010, USA; 3Section of Pediatric Dentistry, UCLA School of Dentistry, Los Angeles, California 90095-1668, USA; 4Center for Microbiome Innovation, University of California at San Diego, La Jolla, California 92161, USA; 5Department of Pediatrics, University of California at San Diego, La Jolla, California 92161, USA; 6Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA; 7Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, USA Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria.
    [Show full text]
  • Evidence of Independent Acquisition and Adaption of Ultra-Small Bacteria to Human Hosts Across the Highly Diverse Yet Reduced Genomes of the Phylum Saccharibacteria
    bioRxiv preprint doi: https://doi.org/10.1101/258137; this version posted February 2, 2018. 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-NC-ND 4.0 International license. Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria Jeffrey S. McLeana,b,1 , Batbileg Borc#, Thao T. Toa#, Quanhui Liua, Kristopher A. Kernsa, Lindsey Soldend, Kelly Wrightond, Xuesong Hec, Wenyuan Shic a Department of Periodontics, University of Washington, Seattle, WA, 98195, USA b Department of Microbiology, University of Washington, Seattle, WA, 98195, USA c Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142 dDepartment of Microbiology, The Ohio State University, Columbus, OH, USA Short title: Host Adaptation of the Saccharibacteria Phylum Keywords: TM7, Saccharibacteria, Candidate Phyla Radiation, epibiont, oral microbiome, # These authors contributed equally to this work. 1To whom correspondence should be addressed. Email: [email protected] Author contribution: JSM, XH, BB and WS conceived the study and designed experiments. XH, JSM, BB, TT, KK, LS, KW, QL conducted experiments. All authors listed analyzed the data. JSM, XH, BB wrote the paper with input from all other authors. All authors have read and approved the manuscript. This research was funded by NIH NIGMS R01GM095373 (J.S.M.), NIH NIDCR Awards 1R01DE023810 (W.S., X.H., and J.M.), 1R01DE020102 (W.S., X.H., and J.S.M.), F32DE025548-01 (B.B.), T90DE021984 (T.T.) 1R01DE026186 (W.S., X.H., and J.S.M.).
    [Show full text]
  • Downloaded from the Integrated Microbial Genomes and Microbiomes Database (IMG/M) (Chen Et Al., 2019C) and Refined (See Methods) and a MAG from Marcy Et Al
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.29.069278; this version posted April 30, 2020. 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. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome Alon Shaiber1,2, Amy D. Willis3, Tom O. Delmont4, Simon Roux5, Lin-Xing Chen6, Abigail 5 C. Schmid7, Mahmoud Yousef8, Andrea R. Watson1,9, Karen Lolans1, Özcan C. Esen1, Sonny T. M. Lee10, Nora Downey11, Hilary G. Morrison11, Floyd E. Dewhirst12,13, Jessica L. Mark Welch11,*, A. Murat Eren1,2,9,11,* 1Department of Medicine, University of Chicago, Chicago, IL 60637, USA; 2Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA; 3Department of Biostatistics, 10 University of Washington, Seattle WA 98195, USA; 4Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; 5Department of Energy Joint Genome Institute, Berkeley CA 94720, USA; 6Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA; 7Undergraduate Student, Computational and Applied Mathematics, University of Chicago, Chicago, IL 60637, USA; 15 8Undergraduate Student, Computer Science, University of Chicago, Chicago, IL 60637, USA; 9Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; 10
    [Show full text]
  • Of the Human Oral Microbiome Using Cultivation-Dependent and –Independent Approaches
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2019 Investigating the microbial “dark matter” of the human oral microbiome using cultivation-dependent and –independent approaches Karissa Cross University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Cross, Karissa, "Investigating the microbial “dark matter” of the human oral microbiome using cultivation- dependent and –independent approaches. " PhD diss., University of Tennessee, 2019. https://trace.tennessee.edu/utk_graddiss/5637 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Karissa Cross entitled "Investigating the microbial “dark matter” of the human oral microbiome using cultivation-dependent and –independent approaches." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Mircea Podar, Major Professor We have read this dissertation and recommend its acceptance: Heidi Goodrich-Blair, Erik Zinser, Frank Loeffler, Stephen Kania Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Investigating the microbial “dark matter” of the human oral microbiome using cultivation-dependent and –independent approaches A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Karissa Lynn Cross August 2019 Copyright © 2019 by Karissa Lynn Cross All rights reserved.
    [Show full text]
  • Deep Metagenomics Examines the Oral Microbiome During Dental Caries, Revealing Novel Taxa and Co-Occurrences with Host Molecules
    Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules Authors: Baker, J.L.1,*, Morton, J.T.2., Dinis, M.3, Alverez, R.3, Tran, N.C.3, Knight, R.4,5,6,7, Edlund, A.1,5,* 1 Genomic Medicine Group J. Craig Venter Institute 4120 Capricorn Lane La Jolla, CA 92037 2Systems Biology Group Flatiron Institute 162 5th Avenue New York, NY 10010 3Section of Pediatric Dentistry UCLA School of Dentistry 10833 Le Conte Ave. Los Angeles, CA 90095-1668 4Center for Microbiome Innovation University of California at San Diego La Jolla, CA 92023 5Department of Pediatrics University of California at San Diego La Jolla, CA 92023 6Department of Computer Science and Engineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 7Department of Bioengineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 *Corresponding Authors: JLB: [email protected], AE: [email protected] ORCIDs: JLB: 0000-0001-5378-322X, AE: 0000-0002-3394-4804 Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome, and 38 host cytokines and chemokines, were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species.
    [Show full text]
  • The Vaginal Microbiome and Preterm Birth Jennifer M
    The vaginal microbiome and preterm birth Jennifer M. Fettweis, Virginia Commonwealth University Myrna G. Serrano, Virginia Commonwealth University J. Paul Brooks, Virginia Commonwealth University David J. Edwards, Virginia Commonwealth University Philippe H. Girerd, Virginia Commonwealth University Hardik I. Parikh, Virginia Commonwealth University Bernice Huang, Virginia Commonwealth University Tom J. Arodz, Virginia Commonwealth University Laahirie Edupuganti, Virginia Commonwealth University Abigail L. Glascock, Virginia Commonwealth University Only first 10 authors above; see publication for full author list. Journal Title: Nature Medicine Volume: Volume 25, Number 6 Publisher: Nature Research (part of Springer Nature) | 2019-06-01, Pages 1012-+ Type of Work: Article | Final Publisher PDF Publisher DOI: 10.1038/s41591-019-0450-2 Permanent URL: https://pid.emory.edu/ark:/25593/v30zx Final published version: http://dx.doi.org/10.1038/s41591-019-0450-2 Copyright information: © 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). Accessed October 5, 2021 11:23 AM EDT ARTICLES https://doi.org/10.1038/s41591-019-0450-2 The vaginal microbiome and preterm birth Jennifer M. Fettweis 1,2,3, Myrna G. Serrano1,3, J. Paul Brooks3,4, David J. Edwards3,5, Philippe H. Girerd2,3, Hardik I. Parikh1, Bernice Huang1, Tom J. Arodz3,6, Laahirie Edupuganti1,3, Abigail L. Glascock7, Jie Xu3,8,9, Nicole R. Jimenez1,3, Stephany C. Vivadelli1,3, Stephen S. Fong3,10, Nihar U. Sheth11, Sophonie Jean1, Vladimir Lee1,3, Yahya A.
    [Show full text]
  • Evidence of Independent Acquisition and Adaption of Ultra-Small Bacteria to Human Hosts Across the Highly Diverse Yet Reduced Genomes of the Phylum Saccharibacteria
    bioRxiv preprint doi: https://doi.org/10.1101/258137; this version posted February 2, 2018. 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-NC-ND 4.0 International license. Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria Jeffrey S. McLeana,b,1 , Batbileg Borc#, Thao T. Toa#, Quanhui Liua, Kristopher A. Kernsa, Lindsey Soldend, Kelly Wrightond, Xuesong Hec, Wenyuan Shic a Department of Periodontics, University of Washington, Seattle, WA, 98195, USA b Department of Microbiology, University of Washington, Seattle, WA, 98195, USA c Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142 dDepartment of Microbiology, The Ohio State University, Columbus, OH, USA Short title: Host Adaptation of the Saccharibacteria Phylum Keywords: TM7, Saccharibacteria, Candidate Phyla Radiation, epibiont, oral microbiome, # These authors contributed equally to this work. 1To whom correspondence should be addressed. Email: [email protected] Author contribution: JSM, XH, BB and WS conceived the study and designed experiments. XH, JSM, BB, TT, KK, LS, KW, QL conducted experiments. All authors listed analyzed the data. JSM, XH, BB wrote the paper with input from all other authors. All authors have read and approved the manuscript. This research was funded by NIH NIGMS R01GM095373 (J.S.M.), NIH NIDCR Awards 1R01DE023810 (W.S., X.H., and J.M.), 1R01DE020102 (W.S., X.H., and J.S.M.), F32DE025548-01 (B.B.), T90DE021984 (T.T.) 1R01DE026186 (W.S., X.H., and J.S.M.).
    [Show full text]
  • Supplemental Material
    Supplemental Material: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules Authors: Baker, J.L.1,*, Morton, J.T.2., Dinis, M.3, Alverez, R.3, Tran, N.C.3, Knight, R.4,5,6,7, Edlund, A.1,5,* 1 Genomic Medicine Group J. Craig Venter Institute 4120 Capricorn Lane La Jolla, CA 92037 2Systems Biology Group Flatiron Institute 162 5th Avenue New York, NY 10010 3Section of Pediatric Dentistry UCLA School of Dentistry 10833 Le Conte Ave. Los Angeles, CA 90095-1668 4Center for Microbiome Innovation University of California at San Diego La Jolla, CA 92023 5Department of Pediatrics University of California at San Diego La Jolla, CA 92023 6Department of Computer Science and Engineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 7Department of Bioengineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 *Corresponding AutHors: JLB: [email protected], AE: [email protected] ORCIDs: JLB: 0000-0001-5378-322X, AE: 0000-0002-3394-4804 SUPPLEMENTAL METHODS Study Design. Subjects were included in tHe study if tHe subject was 3 years old or older, in good general HealtH according to a medical History and clinical judgment of tHe clinical investigator, and Had at least 12 teetH. Subjects were excluded from tHe study if tHey Had generalized rampant dental caries, cHronic systemic disease, or medical conditions tHat would influence tHe ability to participate in tHe proposed study (i.e., cancer treatment, HIV, rHeumatic conditions, History of oral candidiasis). Subjects were also excluded it tHey Had open sores or ulceration in tHe moutH, radiation tHerapy to tHe Head and neck region of tHe body, significantly reduced saliva production or Had been treated by anti-inflammatory or antibiotic tHerapy in tHe past 6 montHs.
    [Show full text]