Article
Microbiology
Manuela Carrasquilla, Angela M. Early, Aimee R. Taylor, Angelica Knudson Ospina, Diego F. Echeverry, Timothy J. C. Anderson, Elvira Mancilla, Samanda Aponte, Pablo Cardenas, Caroline O. Buckee, Julian C. Rayner, Fabian E. Saenz, Daniel E. Neafsey, Vladimir Corredor
Summary: This study examines the population structure and evolution of Plasmodium parasites in small populations with low genetic diversity. The researchers found that despite the low transmission and high proportion of monoclonal infections, the parasite population is evolutionarily labile and has successfully adapted to changes in drug regime. Identity by descent (IBD) analysis provides a detailed understanding of the inbred population structure and is more informative than other common population structure analyses. The study highlights the importance of IBD analyses for studying parasite population structure and drug resistance evolution in regions with low transmission.
Article
Microbiology
Eduard Rovira-Vallbona, Nguyen Van Hong, Johanna H. Kattenberg, Ro Mah Huan, Nguyen Thi Huong Binh, Nguyen Thi Hong Ngoc, Pieter Guetens, Nguyen Thi Thu Hien, Nguyen Luong Hieu, Vu Thi Sang, Nguyen Duc Long, Erin Sauve, Tran Thanh Duong, Nguyen Xuan Xa, Annette Erhart, Anna Rosanas-Urgell
Summary: The study evaluated the therapeutic efficacy of chloroquine against uncomplicated Plasmodium vivax malaria in Gia Lai Province, Vietnam. The results showed that chloroquine remained largely effective in treating P. vivax, with recurrences occurring late and in the presence of low blood concentrations, but potential emergence of low-grade resistance should be closely monitored using both whole-genome sequencing and gene expression analysis.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Immunology
Fernanda Maruri, Yan Guo, Amondrea Blackman, Yuri F. van der Heijden, Peter F. Rebeiro, Timothy R. Sterling
Summary: The study found that a predominant mutation allele frequency threshold of 2.5% was the most suitable for detecting DNA gyrase mutations that confer ofloxacin resistance in Mtb.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Emily LaVerriere, Philipp Schwabl, Manuela Carrasquilla, Aimee R. Taylor, Zachary M. Johnson, Meg Shieh, Ruchit Panchal, Timothy J. Straub, Rebecca Kuzma, Sean Watson, Caroline O. Buckee, Carolina M. Andrade, Silvia Portugal, Peter D. Crompton, Boubacar Traore, Julian C. Rayner, Vladimir Corredor, Kashana James, Horace Cox, Angela M. Early, Bronwyn L. MacInnis, Daniel E. Neafsey
Summary: Multiplexed PCR amplicon sequencing (AmpSeq) is a valuable tool for monitoring threatened species and managing wildlife populations, as well as for understanding the genomic epidemiology of infectious diseases. The study describes the design and evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites, and provides guidance on panel design and implementation for infectious disease research.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Lufeng Dan, Yuze Li, Shuhua Chen, Jingbo Liu, Yu Wang, Fangting Li, Xiangwei He, Lucas B. Carey
Summary: Most genetic changes have low reversion rates, but a study identified a rapid and reversible genetic variation mechanism that benefits adaptation to environmental fluctuations and evolutionary divergence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Naomi J. Wilcox, Martine Dumont, Anna Gonzalez-Neira, Sara Carvalho, Charles Joly Beauparlant, Marco Crotti, Craig Luccarini, Penny Soucy, Stephane Dubois, Rocio K. Nunez-Torres, Guillermo E. Pita, Eugene Gardner, Joe Dennis, M. Rosario Alonso, Nuria alvarez, Caroline Baynes, Annie Claude Collin-Deschesnes, Sylvie Desjardins, Heiko Becher, Sabine Behrens, Manjeet Bolla, Jose Castelao, Jenny Chang-Claude, Sten Cornelissen, Thilo Doerk, Christoph Engel, Manuela Gago-Dominguez, Pascal Guenel, Andreas Hadjisavvas, Eric Hahnen, Mikael Hartman, Belen Herraez, Marion Kiechle, Jingmei A. SGBCC Investigators, Audrey Jung, Renske Keeman, Jingmei I. Li, Maria Loizidou, Michael Lush, Kyriaki P. Michailidou, Mihalis E. Panayiotidis, Xueling Sim, Soo Hwang Teo, Jonathan Tyrer, Lizet van der Kolk, Cecilia K. Wahlstrom, Qin K. Wang, John R. B. Perry, Javier Benitez, Marjanka M. Schmidt, Rita Schmutzler, Paul D. P. Pharoah, Arnaud F. Droit, Alison Dunning, Anders Kvist, Peter Devilee, Douglas Easton, Jacques Simard
Summary: A meta-analysis of three large whole-exome sequencing datasets revealed associations between protein-truncating and rare missense variants in several genes, including ATM, BRCA1, BRCA2, and MAP3K1, with breast cancer susceptibility. Additionally, associations were found for LZTR1, ATR, BARD1, and CDKN2A.
Article
Biotechnology & Applied Microbiology
Yankai Jiang, Xinyue Cao, Haibin Wang
Summary: By identifying specific mutations that lead to limblessness in a pig, this research sheds light on the evolutionary trajectory of limb development in vertebrates. These findings have implications for further exploration in human genetics and evolutionary biology.
Article
Oncology
Chen-Hua Chuang, Madeleine Dorsch, Philip Dujardin, Sukrit Silas, Kristina Ueffing, Johanna M. Hoelken, Dian Yang, Monte M. Winslow, Barbara M. Gruener
Summary: Metastatic lung cancer cells exhibit altered mitochondrial functionality compared to non-metastatic cells, which can be targeted for therapeutic purposes.
Article
Infectious Diseases
Soon Young Park, Eun Hwa Lee, Dokyun Kim, Young Goo Song, Su Jin Jeong
Summary: Helicobacter pylori is a major causative agent of various gastrointestinal diseases and its eradication is often hindered by antibiotic resistance. This study aimed to identify clinical strains of H. pylori with amoxicillin resistance and analyze the genetic variations associated with it. Analysis of 368 clinical strains revealed amoxicillin resistance in 8.7% of the strains. Whole-genome sequencing analysis identified specific genetic variations in multiple genes related to amoxicillin resistance. Six specific genetic variations in PBP2 were found to be associated with high amoxicillin resistance. Consideration of amoxicillin resistance is important in the clinical setting for the failure of H. pylori eradication.
Article
Biochemical Research Methods
Giovanna Carpi, Lev Gorenstein, Timothy T. Harkins, Mehrzad Samadi, Pankaj Vats
Summary: The study introduces an accelerated, scalable, reproducible, and cost-effective framework for pathogen genomic variant identification. The evaluation on benchmark datasets of malaria genomes demonstrates superior performance and accuracy compared to standard pipelines.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Fredy E. Villena, Juan F. Sanchez, Oscar Nolasco, Greys Braga, Leonila Ricopa, Keare Barazorda, Carola J. Salas, Carmen Lucas, Stephen E. Lizewski, Christie A. Joya, Dionicia Gamboa, Christopher Delgado-Ratto, Hugo O. Valdivia
Summary: Malaria is a major health problem in Peru, and this study examined the population genetics of Plasmodium falciparum and P. vivax cases collected in the Peruvian Amazon Basin. The results showed low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of chloroquine-resistant mutations in P. falciparum may be influenced by the treatment scheme for P. vivax. These findings have implications for malaria elimination efforts in Peru.
SCIENTIFIC REPORTS
(2022)
Article
Engineering, Environmental
Elena Radu, Amandine Masseron, Fabian Amman, Anna Schedl, Benedikt Agerer, Lukas Endler, Thomas Penz, Christoph Bock, Andreas Bergthaler, Julia Vierheilig, Peter Hufnagl, Irina Korschineck, Jorg Krampe, Norbert Kreuzinger
Summary: This study utilized wastewater surveillance to detect the presence of the alpha variant of SARS-CoV-2 in samples from Vienna, Austria, prior to the official confirmation of clinical cases. The results support the use of wastewater monitoring as an effective tool for early detection of circulating SARS-CoV-2 lineages based on whole genome sequencing and signature mutations analysis.
Article
Microbiology
Luke Diorio-Toth, Meghan A. A. Wallace, Christopher W. W. Farnsworth, Bin Wang, Danish Gul, Jennie H. H. Kwon, Saadia Andleeb, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study tracks the long-term colonization patterns of intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan using whole-genome sequencing. The analysis of 822 bacterial genomes reveals long-term contamination by opportunistic pathogens and transient appearance of other common pathogens. Bacteria recovered from the ICU have more antibiotic resistance genes in their genomes compared to matched community spaces.
Review
Biology
Olusegun Philip Akoniyon, Taiye Samson Adewumi, Leah Maharaj, Olukunle Olugbenle Oyegoke, Alexandra Roux, Matthew A. Adeleke, Rajendra Maharaj, Moses Okpeku
Summary: WGS plays an important role in malaria elimination, but its availability and affordability in sub-Saharan Africa need improvement. This review highlights the applications and challenges of WGS in controlling malaria parasites, and emphasizes the importance of WGS in disease management and pursuit of malaria reduction and elimination.
Article
Microbiology
Nguyen Thi Le Hang, Minako Hijikata, Shinji Maeda, Pham Huu Thuong, Hoang Van Huan, Nguyen Phuong Hoang, Do Bang Tam, Pham Thu Anh, Nguyen Thu Huyen, Vu Cao Cuong, Nobuyuki Kobayashi, Keiko Wakabayashi, Akiko Miyabayashi, Shintaro Seto, Naoto Keicho
Summary: This study analyzed the clinico-epidemiological factors and blood transcriptomic signatures associated with rifampicin (RIF) resistance-conferring mutations of Mycobacterium tuberculosis (Mtb). The results showed that rpoB mutations have a significant impact on host response, and identified a mutation in the Rv1830 gene that is related to antibiotic resilience in the H445Y strain.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xiao Zhang, Jack G. Rayner, Mark Blaxter, Nathan W. Bailey
Summary: This study on Hawaiian crickets shows evidence of parallel adaptation to the same lethal parasitoid in different island populations, despite strong ongoing gene flow that was traditionally thought to impede local adaptation via parallel evolution.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Carlos Caurcel, Dominik R. Laetsch, Richard Challis, Sujai Kumar, Karim Gharbi, Mark Blaxter
Summary: The article introduces MolluscDB, a genome and transcriptome database for molluscs, and demonstrates its utility and data quality in molluscan research. MolluscDB provides an easy-to-use and openly accessible data resource for the research community.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Tejaswi Yarra, Kirti Ramesh, Mark Blaxter, Anne Huening, Frank Melzner, Melody S. Clark
Summary: Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is crucial for aquaculture and animal resilience under future climate change. In this study, gene expression dynamics during shell repair in adult blue mussels were explored using RNA-Seq, identifying a large number of differentially expressed transcripts related to shell biology and repair. The results provide insights into the genes and pathways involved in biomineralization processes, offering potential for future functional analyses.
Article
Biochemistry & Molecular Biology
Timothe Cezard, Fiona Cunningham, Sarah E. Hunt, Baron Koylass, Nitin Kumar, Gary Saunders, April Shen, Andres F. Silva, Kirill Tsukanov, Sundararaman Venkataraman, Paul Flicek, Helen Parkinson, Thomas M. Keane
Summary: The European Variation Archive (EVA) is a resource for sharing genetic variation data for all species, hosting over 3 billion records. EVA and dbSNP have established a global system to assign unique identifiers to all submitted genetic variants. EVA is active within GA4GH, maintaining and implementing standards such as VCF, Refget, and VRS.
NUCLEIC ACIDS RESEARCH
(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)
Article
Multidisciplinary Sciences
Mark L. Blaxter
Summary: The Earth Biogenome Project aims to sequence the genomes of all eukaryotic life on earth, and the Darwin Tree of Life Project focuses on delivering high-quality genome sequences for the British and Irish islands. The collaboration between biodiversity organizations and genomics institutes has established a workflow that collects specimens, performs sequencing, generates curated assemblies, and openly releases the data for global use in future scientific and conservation efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Multidisciplinary Sciences
ThankGod Echezona Ebenezer, Anne W. T. Muigai, Simplice Nouala, Bouabid Badaoui, Mark Blaxter, Alan G. Buddie, Erich D. Jarvis, Jonas Korlach, Josiah O. Kuja, Harris A. Lewin, Roksana Majewska, Ntanganedzeni Mapholi, Suresh Maslamoney, Michele Mbo'o-Tchouawou, Julian O. Osuji, Ole Seehausen, Oluwaseyi Shorinola, Christian Keambou Tiambo, Nicola Mulder, Cathrine Ziyomo, Appolinaire Djikeng
Article
Plant Sciences
Suo Qiu, James M. Bradley, Peijun Zhang, Roy Chaudhuri, Mark Blaxter, Roger K. Butlin, Julie D. Scholes
Summary: This study reveals diverse strategies used by Striga hermonthica to overcome different layers of host resistance. Understanding the maintenance of variation at virulence loci by balancing selection is crucial for controlling the evolution of parasite virulence.
Article
Ecology
Solomon A. Sloat, Luke M. Noble, Annalise B. Paaby, Max Bernstein, Audrey Chang, Taniya Kaur, John Yuen, Sophia C. Tintori, Jacqueline L. Jackson, Arielle Martel, Jose A. Salome Correa, Lewis Stevens, Karin Kiontke, Mark Blaxter, Matthew V. Rockman
Summary: The distribution and abundance of species are influenced by various factors, including life-history traits, population structure, and colonization-extinction dynamics. Caenorhabditis nematodes species were observed in two well-studied tropical field sites, with the majority of them being globally distributed androdiecious species. These species were able to colonize baits through phoresy and showed preference for baits in direct contact with the ground.
ECOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Medicinal
Anyse P. Essoh, Angela Liberal, Angela Fernandes, Maria Ines Dias, Carla Pereira, Filipa Mandim, Margarida Moldao-Martins, Pedro Cravo, Maria Paula Duarte, Monica Moura, Maria M. Romeiras, Lillian Barros
Summary: The present study investigated the bioactive properties of three native plants from Cabo Verde Islands, showing that they have good antioxidant and anti-tumor properties, as well as some anti-inflammatory effects. These findings contribute to the understanding of these plants and open up new possibilities for their use in a wider range of health conditions.
Article
Parasitology
Pedro Cravo
Summary: Malaria is a devastating disease, and the evolution and propagation of drug-resistant parasites are major barriers to its control. By experimentally evolving drug resistance and comparing genomes, the genes and mutations responsible for resistance can be identified. P. chabaudi serves as a fast-track predictive model to identify candidate genetic markers of resistance and enhance our understanding of resistance biology.
PARASITOLOGY INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Emmelien Vancaester, Mark Blaxter
Summary: The Darwin Tree of Life (DToL) project aims to sequence all described terrestrial and aquatic eukaryotic species found in Britain and Ireland. From data generated by the DToL project, 110 complete Wolbachia genomes from 93 host species spanning 92 families were identified and assembled. Different insect orders had distinct patterns of Wolbachia infection, with Lepidopteran hosts mostly infected with supergroup B, while infections in Diptera and Hymenoptera were dominated by A-type Wolbachia. Host and Wolbachia phylogenies revealed no (or very limited) cophylogeny, indicating frequent host switching events in the evolutionary history of Wolbachia. Mining raw genome data generated for reference genome assemblies is an effective way to analyze cobiont genomes and provide ecological context for their hosts.
Article
Plant Sciences
Anyse P. Essoh, Gustavo Capatti Cassiano, Filipa Mandim, Lillian Barros, Isildo Gomes, Marcia Melo Medeiros, Monica Moura, Pedro Vitor Lemos Cravo, Maria M. Romeiras
Summary: This study investigated the in vitro antiplasmodial activities of four native plants from Cabo Verde. The results showed that the ethanolic extract of Artemisia gorgonum and infusions of Tamarix senegalensis exhibited high antiplasmodial activities without cytotoxicity. Lavandula rotundifolia and Sideroxylon marginatum extracts showed moderate activities. The findings support the traditional use of these plants against malaria and suggest their potential as future antimalarials.