Article
Multidisciplinary Sciences
Taylorlyn Stephan, Shawn M. Burgess, Hans Cheng, Charles G. Danko, Clare A. Gill, Erich D. Jarvis, Klaus-Peter Koepfli, James E. Koltes, Eric Lyons, Pamela Ronald, Oliver A. Ryder, Lynn M. Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A. Ostrander, Elinor K. Karlsson
Summary: Genomics research has primarily focused on humans and a limited number of species, resulting in a lack of understanding about the genomes of the majority of species. However, a broad view that encompasses the vast diversity of life is necessary to comprehend how genomes function and how genetic variation shapes phenotypes. Integrating comparative genomics with other fields is crucial for scientific discovery and the protection of ourselves and our world.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Anurag Chaturvedi, Jiarui Zhou, Joost A. M. Raeymaekers, Till Czypionka, Luisa Orsini, Craig E. Jackson, Katina I. Spanier, Joseph R. Shaw, John K. Colbourne, Luc De Meester
Summary: Our study shows that genetic variation carried by only five founding individuals from the regional genotype pool is enough to fuel rapid evolution in response to strong selection pressures with no evidence of genetic erosion. Standing genetic variation allows natural populations to evolve rapidly.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Anubhab Khan, Kaushalkumar Patel, Harsh Shukla, Ashwin Viswanathan, Tom van der Valk, Udayan Borthakur, Parag Nigam, Arun Zachariah, Yadavendradev Jhala, Marty Kardos, Uma Ramakrishnan
Summary: Habitat fragmentation leads to small populations, increasing the risk of inbreeding depression. Small populations can reduce inbreeding depression by purging deleterious recessive alleles. The study on Indian tiger populations found differences in inbreeding levels and mutation load between small and large populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Adam J. Hockenberry, Claus O. Wilke
Summary: BACPHLIP is a tool that accurately predicts the lifestyle of bacteriophages by detecting conserved protein domains and using a trained classifier. It achieved an accuracy of 98% on a test set, greatly exceeding previous tools.
Article
Chemistry, Multidisciplinary
Soo Khim Chan, Zhongchao Zhao, Samuel Penziner, Ethan Khong, David Pride, Robert T. Schooley, Nicole F. Steinmetz
Summary: Antimicrobial resistance is a global health threat exacerbated by the misuse of antibiotics in medicine and agriculture. Phage therapy, as an alternative antimicrobial treatment, involves using bacteriophages to destroy bacterial pathogens. This study aimed to develop versatile tools for tracking and imaging phages by screening and isolating peptides that bind to specific phages.
Article
Microbiology
Nitasha D. Menon, Samuel Penziner, Elizabeth T. Montano, Raymond Zurich, David T. Pride, Bipin G. Nair, Geetha B. Kumar, Victor Nizet
Summary: Bacteriophage therapy is an alternative treatment to antibiotics for multidrug-resistant pathogens. This study found that phage therapy can lead to the emergence of phage-resistant mutants with pyomelanin pigmentation, but these mutants are less virulent due to large genomic deletions and retain susceptibility to the antibiotic colistin. This suggests that they do not pose a contraindication to using anti-pseudomonal phage therapy.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Jun Kwon, Sang Wha Kim, Sang Guen Kim, Jeong Woo Kang, Won Joon Jung, Sung Bin Lee, Young Min Lee, Sib Sankar Giri, Cheng Chi, Se Chang Park
Summary: This study isolated and characterized a novel bacteriophage, pPa_SNUABM_DT01, with strong lytic ability against Pseudomonas aeruginosa. Comparative genomic analysis revealed that this phage may belong to a novel genus. The phage showed potential as an alternative to antibiotics for treating antibiotic-resistant infections.
Review
Infectious Diseases
Guillermo Santamaria-Corral, Abrar Senhaji-Kacha, Antonio Broncano-Lavado, Jaime Esteban, Meritxell Garcia-Quintanilla
Summary: Phage therapy is an alternative therapy used as a last resort against multidrug-resistant bacteria infections. Pseudomonas aeruginosa, a pathogen that commonly infects immunocompromised individuals, can be effectively treated using bacteriophages alone or in combination with antibiotics. This review summarizes recent studies highlighting the synergistic effects of phage-antibiotic combinations and successful treatments.
Review
Plant Sciences
Ivan M. De-la-Cruz, Femke Batsleer, Dries Bonte, Carolina Diller, Timo Hytonen, Anne Muola, Sonia Osorio, David Pose, Martijn L. Vandegehuchte, Johan A. Stenberg
Summary: Aboveground plant-arthropod interactions play a crucial role in the evolution of plants and the sustainability of ecosystems. Advancements in technology have enabled us to study these interactions more comprehensively and address current environmental challenges.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Samuel Namonyo, Gilda Carvalho, Jianhua Guo, Karen D. Weynberg
Summary: This study isolated and characterized four novel phages against multi-drug resistant Pseudomonas aeruginosa clinical strains from Australia, and proposed their potential use as phage therapy candidates.
Article
Biochemistry & Molecular Biology
Peter Evseev, Anna Lukianova, Nina Sykilinda, Anna Gorshkova, Alexander Bondar, Mikhail Shneider, Marsel Kabilov, Valentin Drucker, Konstantin Miroshnikov
Summary: The genome of Pseudomonas phage MD8 exhibits extensive gene exchange and mosaic patterns with other lambda-like phages, challenging taxonomic classification principles. Multiple horizontal transfers and genomic mosaicism raise questions about the relatedness of MD8 and similar phages, leading to contradictory results in bioinformatics analysis. Suggestions for the origin of MD8 genome and taxonomic classification principles were made based on comparison of different bioinformatic approaches applied to lambda-like phage genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Maria Dolores Blanco Fernandez, Jochen Klumpp, Melina E. Barrios, Viviana A. Mbayed
Summary: Listeria bacteriophages, belonging to the genus Pecentumvirus, are promising tools for controlling Listeria monocytogenes in food and surfaces. The study of 21 phages in this genus has provided insight into Pecentumvirus evolution, showing distinct gene gain and loss propensity, recombination events, and two groups of distantly related species formed through diversification.
Article
Multidisciplinary Sciences
Derek S. Lundberg, Roger de Pedro Jove, Pratchaya Pramoj Na Ayutthaya, Talia L. Karasov, Or Shalev, Karin Poersch, Wei Ding, Anita Bollmann-Giolai, Ilja Bezrukov, Detlef Weigel
Summary: Sphingomonas is a highly abundant bacterial genus in the phyllosphere of wild Arabidopsis thaliana, but its interaction with plants is poorly understood. Genomic analysis reveals high intergenomic diversity and adaptability of Sphingomonas, indicating frequent biotic interactions. However, plant-protective phenotypes are rare among Sphingomonas isolates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Virology
Bahareh Lashtoo Aghaee, Mohammadali Khan Mirzaei, Mohammad Yousef Alikhani, Ali Mojtahedi, Corinne F. Maurice
Summary: Antibiotic resistance is a significant global threat, and using a combination of phages and antibiotics may be an effective strategy for treating multidrug-resistant Pseudomonas aeruginosa infections.
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)
Article
Multidisciplinary Sciences
Dana K. Howe, Anh D. Ha, Andrew Colton, Irma Tandingan De Ley, Robbie G. Rae, Jenna Ross, Michael Wilson, Jiri Nermut, Zhongying Zhao, Rory J. Mc Donnell, Dee R. Denver
Article
Microbiology
Anh D. Ha, Mohammad Moniruzzaman, Frank O. Aylward
Summary: Giant viruses from the Nucleocytoviricota phylum are diverse and active in coastal marine systems, expressing central metabolic enzymes and manipulating host cell physiology. They exhibit high expression of core genes commonly expressed during viral infection, along with complex functional gene expressions.
Article
Virology
Franziska Hufsky, Ana B. Abecasis, Artem Babaian, Sebastian Beck, Liam Brierley, Simon Dellicour, Christian Eggeling, Santiago F. Elena, Udo Gieraths, Anh D. Ha, Will Harvey, Terry C. Jones, Kevin Lamkiewicz, Gabriel L. Lovate, Dominik Luecking, Martin Machyna, Luca Nishimura, Maximilian K. Nocke, Bernard Y. Renard, Shoichi Sakaguchi, Lygeri Sakellaridi, Jannes Spangenberg, Maria Tarradas-Alemany, Sandra Triebel, Yulia Vakulenko, Rajitha Yasas Wijesekara, Fernando Gonzalez-Candelas, Sarah Krautwurst, Alba Perez-Cataluna, Walter Randazzo, Gloria Sanchez, Manja Marz
Summary: The 2023 International Virus Bioinformatics Meeting held in Valencia, Spain was a significant event for researchers and scientists worldwide interested in virus bioinformatics. With the primary objective of fostering discussions and collaborations, it provided a platform for sharing insights, research findings, and novel ideas related to virus bioinformatics research.
Article
Ecology
Anh D. D. Ha, Mohammad Moniruzzaman, Frank O. O. Aylward
Summary: Viruses of the phylum Nucleocytoviricota are widespread in ocean waters and have important impacts on marine ecosystems. This study used metagenomic data to investigate the biogeography of these viruses and found that they are most abundant in shallow waters. The study also identified latitudinal patterns in viral diversity, with the highest diversity observed at high latitudes in the northern hemisphere. These results contribute to our understanding of the distribution and diversity of viruses in marine systems.
ISME COMMUNICATIONS
(2023)
Article
Microbiology
Roxanna Farzad, Anh D. D. Ha, Frank O. O. Aylward
Summary: This study generated 11 metagenome-assembled genomes (MAGs) of giant viruses from samples collected from the North Pacific Subtropical Gyre and revealed their prevalence and diversity in oligotrophic ocean waters.
FRONTIERS IN MICROBIOLOGY
(2022)