Review
Respiratory System
Kuppan Gokulan, Manish Joshi, Sangeeta Khare, Thaddeus Bartter
Summary: Recent research shows that lung inflammation in COPD changes the lung microbiome, playing a role in the ongoing inflammation and injury processes. The gut and lungs communicate and may participate in the inflammatory process.
CURRENT OPINION IN PULMONARY MEDICINE
(2022)
Article
Multidisciplinary Sciences
Jacob S. Sherkow, Katharine B. Barker, Irus Braverman, Robert Cook-Deegan, Richard Durbin, Carla L. Easter, Melissa M. Goldstein, Maui Hudson, W. John Kress, Harris A. Lewin, Debra J. H. Mathews, Catherine McCarthy, Ann M. McCartney, Manuela da Silva, Andrew W. Torrance, Henry T. Greely
Summary: The Earth BioGenome Project (EBP) aims to obtain whole-genome sequences of all eukaryotic species on Earth. This paper, from the EBP's Ethical, Legal, and Social Issues (ELSI) Committee, highlights the legal, ethical, and social concerns faced by the project, including issues related to sample collection, international treaties, intellectual property, and biosecurity. The paper also discusses the ethical implications of sampling from indigenous territories, protecting endangered species, and cross-border collections. The authors conclude by providing a starting point for addressing these issues and considering ethical frameworks for future projects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Multidisciplinary Sciences
Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklos Balint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O'Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mara K. N. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards
Summary: The Earth BioGenome Project (EBP) is a global international initiative that requires agreement and coordination on standards. To ensure rapid progress towards its goals, EBP has established five technical standards committees and made the current versions of the standards documents available on its website.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Agriculture, Dairy & Animal Science
R. Michael Roberts, Harris A. Lewin
ANNUAL REVIEW OF ANIMAL BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Pravin Parajuli, Kuppan Gokulan, Sangeeta Khare
Summary: This study established an in vitro model to mimic gastrointestinal tract exposure to xenobiotics via oral or intravenous routes and evaluated the effects of arsenic on intestinal permeability and cytotoxicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Meeting Abstract
Toxicology
S. Khare, A. Bright, K. J. Harris, B. Zolnik, S. Chakder, K. Gokulan
TOXICOLOGY LETTERS
(2022)
Review
Microbiology
Erik Munson, Sara D. D. Lawhon, Claire R. R. Burbick, Amanda Zapp, Maia Villaflor, Elizabeth Thelen
Summary: Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations, especially in zoonotic diseases. The expansion of research on the microbiota of humans, animals, and insects has potential implications for the taxonomy of clinically relevant organisms. This study addresses novel revisions in veterinary taxonomy and nomenclature, focusing on descriptions of new pathogens and revisions in various bacterial families.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Review
Microbiology
Sara D. Lawhon, Claire R. Burbick, Erik Munson, Amanda Zapp, Elizabeth Thelen, Maia Villaflor
Summary: Revisions and new additions to bacterial taxonomy have a significant impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. Genome sequencing technologies have revolutionized our understanding of the microbiota of humans, animals, and insects.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kuppan Gokulan, Aakriti Mathur, Amit Kumar, Michelle M. Vanlandingham, Sangeeta Khare
Summary: This study compared the immune response and the mRNA expression levels of genes related to intestinal permeability in CD-1 mice exposed to sodium arsenite via intravenous injection and oral gavage. The results showed that intravenous injection induced transient changes in immune-related gene expression and cytokine levels, as well as downregulation of genes related to cell permeability. Oral exposure caused fewer changes in cell permeability-related genes. These findings suggest that the route of exposure can differentially affect intestinal responses due to first-pass metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Genetics & Heredity
Sophie Visvikis-Siest, Maria G. Stathopoulou, Raute Sunder-Plassmann, Behrooz Z. Alizadeh, Robert Barouki, Ekaterina Chatzaki, Georges Dagher, George Dedoussis, Panagiotis Deloukas, Alexander Haliassos, Brigitte Boisson Hiegel, Vangelis Manolopoulos, Christine Masson, Guillaume Pare, Markus Paulmichl, Alexandros M. Petrelis, Csilla Sipeky, Belgin Susleyici, Georges Weryha, Alex Chenchik, Paul Diehl, Robin E. Everts, Alexander Haushofer, John Lamont, Ruth Mercado, Heiko Meyer, Herna Munoz-Galeano, Helena Murray, Ferrier Nhat, Charity Nofziger, Wolfgang Schnitzel, Stavroula Kanoni
FRONTIERS IN GENETICS
(2023)
Article
Veterinary Sciences
Aiden McFadden, Katie Martin, Gabriel Foster, Micaela Vierra, Erica W. Lundquist, Robin E. Everts, Erik Martin, Erin Volz, Kaitlyn McLoone, Samantha A. Brooks, Christa Lafayette
Summary: Mutations causing depigmentation are common in horses, with over 40 alleles in multiple genes associated with increased white spotting. The splashed white phenotype, resembling a horse splashed with white paint, is linked to variants in the PAX3 and MITF genes. Two novel mutations, one in PAX3 and one in MITF, show a strong association with increased depigmentation in Pura Raza Espanola horses. The functional impact of these mutations is predicted to be moderate to extreme, and they are proposed to be designated as Splashed White 9 and Splashed White 10.
JOURNAL OF EQUINE VETERINARY SCIENCE
(2023)
Article
Veterinary Sciences
Aiden McFadden, Katie Martin, Gabriel Foster, Micaela Vierra, Erica W. Lundquist, Robin E. Everts, Erik Martin, Erin Volz, Kaitlyn McLoone, Samantha A. Brooks, Christa Lafayette
Summary: Mutations in the KIT gene result in white spotting in mammals. We identified an association between increased white spotting and a variant in the 5'UTR of the KIT gene (rs1149701677). Horses with this variant show similar phenotypic characteristics to other KIT mutations, with increased depigmentation on the skin and coat.
JOURNAL OF EQUINE VETERINARY SCIENCE
(2023)
Article
Computer Science, Artificial Intelligence
Kuppan Gokulan, Sangeeta Khare, Steven L. Foley
Summary: Bacterial species have different types of secretory systems for communication and transfer of genetic materials and toxins. The bacterial type IV secretory system (T4SS) is more versatile compared to other systems as it can transfer genetic materials, proteins, and toxins. This study models the structure of VirD4 in Salmonella enterica and predicts its functional importance in the secretion process.
FRONTIERS IN ARTIFICIAL INTELLIGENCE
(2022)