Article
Plant Sciences
Julio Schneider, Juraj Paule, Tanja Jungcurt, Domingos Cardoso, Andre Marcio Amorim, Thomas Berberich, Georg Zizka
Summary: Plastid DNA sequence data are widely used in plant phylogenetics for their high copy number, uniparental inheritance, and divergent substitution rates. This study demonstrates the utility of using off-target sequence read fractions for assembling near-complete plastid genomes in the pantropical plant family Ochnaceae. The phylogenetic resolution was lower at the infrageneric level, with limited conflicts compared to nuclear loci analysis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Parasitology
Jin-Wei Gao, Xi-Ping Yuan, Hao Wu, Chuan-Yu Xiang, Min Xie, Rui Song, Zhong-Yuan Chen, Yuan-An Wu, Dong-Sheng Ou
Summary: This study provides the first molecular data for the genus Micracanthorhynchina by sequencing its mitochondrial genome. The results demonstrate the importance of attenuating compositional heterogeneity-driven long-branch attraction artifacts when using mitochondrial genomic data to resolve the phylogeny of Acanthocephala.
PARASITES & VECTORS
(2022)
Article
Ecology
Jeremy D. Wilson, Nicolas Mongiardino Koch, Martin J. Ramirez
Summary: Research suggests that selecting branch lengths most correlated with a character can enhance accuracy in ancestral state estimation. Phylogenetic signal statistics have limited utility in choosing the correct branch lengths, while model-fit statistics are more accurate.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Proceedings Paper
Biotechnology & Applied Microbiology
Berk A. Yakici, Huw A. Ogilvie, Luay Nakhleh
Summary: Dissimilarity measures for phylogenetic trees are widely used for analyzing inferred trees and evaluating the performance of phylogenetic methods. Existing measures only consider the topologies of phylogenetic networks and ignore branch lengths. This paper proposes two phylogenetic network dissimilarity measures that take both topology and branch lengths into account, and demonstrates their application in clustering analysis.
COMPARATIVE GENOMICS (RECOMB-CG 2022)
(2022)
Article
Genetics & Heredity
Zou Wu, Huang Chao-Bin, Wang Lu, Jiang Meng-na, Zhou Shan-yi, Zhang Jiang-tao, Zeng Ju-ping
Summary: The study revealed distinct genetic differences among different geographical populations of Teinopalpus aureus, supporting the classification of T. aureus wuyiensis and indicating a close genetic relationship between T. a. guangxiensis and T. a. aureus, suggesting they could be combined into one subspecies.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Rodrigo P. Baptista, Yiran Li, Adam Sateriale, Mandy J. Sanders, Karen L. Brooks, Alan Tracey, Brendan R. E. Ansell, Aaron R. Jex, Garrett W. Cooper, Ethan D. Smith, Rui Xiao, Jennifer E. Dumaine, Peter Georgeson, Bernard J. Pope, Matthew Berriman, Boris Striepen, James A. Cotton, Jessica C. Kissinger
Summary: We generated a new genome assembly and annotation for Cryptosporidium parvum IOWA and compared it with closely related species, revealing the potential genetic differences between them. The new assembly and annotation provide a more complete and accurate reference for future research.
Article
Biology
Aurelien Lowie, Barbara De Kegel, Mark Wilkinson, John Measey, James C. O'Reilly, Nathan J. Kley, Philippe Gaucher, Jonathan Brecko, Thomas Kleinteich, Dominique Adriaens, Anthony Herrel
Summary: This study explored the relationships between skull shape, head musculature, and in vivo bite forces in caecilians. The results showed that there is a correlation between bite force and external head shape, but no relationship between bite force and skull shape. Skull shape is constrained by factors other than demands for bite force generation, while muscles are the principal drivers of variation in bite force. There is a covariation between the shape of the cranium and mandible, as well as with jaw muscle architecture.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Jose Ramon Pardos-Blas, Manuel J. Tenorio, Juan Carlos G. Galindo, Rafael Zardoya
Summary: The venom duct transcriptomes and proteomes of cryptic cone snail species Virroconus ebraeus and Virroconus judaeus were compared, revealing differences in conotoxin precursor superfamilies and hormones expression, possibly reflecting adaptations to different diets. Additionally, machine learning algorithms were used to predict the 3D structures of selected venom proteins, providing insights into their potential functions.
Editorial Material
Parasitology
James A. Cotton, Stephen R. Doyle
Summary: The reduced efficacy of anthelmintic drug PZQ in controlling schistosomiasis is a major public health concern. Le Clec'h et al. identified a gene responsible for PZQ resistance in experimentally selected Schistosoma mansoni, but its importance in natural infections is yet to be determined.
TRENDS IN PARASITOLOGY
(2022)
Article
Microbiology
Adam J. Roberts, Han B. Ong, Simon Clare, Cordelia Brandt, Katherine Harcourt, Susanne U. Franssen, James A. Cotton, Nicole Mueller-Sienerth, Gavin J. Wright
Summary: This study aims to discover essential proteins for in vitro growth and host infection of Leishmania spp., with the goal of identifying subunit vaccine candidates. Through in silico analysis and genome editing, potential subunit vaccine candidates have been identified. Preclinical trials in a murine model showed significant levels of protection against splenic infection.
Article
Infectious Diseases
Yegnasew Takele, Emebet Adem, Tadele Mulaw, Ingrid Muller, James Anthony Cotton, Pascale Kropf
Summary: Neutrophil activation status and effector functions are not fully restored in Visceral leishmaniasis (VL) patients co-infected with HIV (VL/HIV patients), suggesting impaired host defence against pathogens in these patients.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Yegnasew Takele, Emebet Adem, Susanne Ursula Franssen, Rebecca L. Womersley, Myrsini C. Kaforou, Michael L. Levin, Ingrid C. Mueller, James Anthony L. Cotton, Pascale C. Kropf
Summary: The study found that lymphocytes from visceral leishmaniasis patients expressed a marker called PD1, and the ligand of this marker, PDL1, was also expressed on different blood cells. Blocking the interaction between PD1 and PDL1 increased the production of IFN gamma, suggesting that therapy using immune checkpoint inhibitors may improve disease control.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Sarah M. Coker, Erin K. Box, Natalie Stilwell, Elizabeth A. Thiele, James A. Cotton, Ellen Haynes, Michael J. Yabsley, Christopher A. Cleveland
Summary: Dracunculus medinensis, or Guinea worm, is a parasitic nematode that causes the debilitating disease dracunculiasis in humans. The global Guinea Worm Eradication Program has made significant progress in reducing human infections. However, the detection of animal infections poses challenges. To improve species confirmation time, a quantitative PCR assay targeting the mitochondrial cytochrome b gene of Guinea worm was developed. The assay demonstrated high sensitivity and specificity and can potentially eliminate the need for DNA sequencing.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Tushabe John Vianney, Duncan J. Berger, Stephen R. Doyle, Geetha Sankaranarayanan, Joel Serubanja, Prossy Kabuubi Nakawungu, Fred Besigye, Richard E. Sanya, Nancy Holroyd, Fiona Allan, Emily L. Webb, Alison M. Elliott, Matthew Berriman, James A. Cotton
Summary: This study aims to understand the impact of praziquantel (PZQ) treatment on the genetics of schistosomes. The authors obtained whole-genome sequence data from 174 individual miracidia collected from fishing communities in Uganda and investigated the genetic variation and genomic signatures of natural selection in pre- and post-treatment parasite populations. The study found higher genetic diversity in pre-treatment parasite populations and identified genes with evidence of recent positive selection in post-treatment and intensively treated parasites that could be related to reduced susceptibility to PZQ treatment.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Biology
Hector Lorente-Martinez, Ainhoa Agorreta, Iker Irisarri, Rafael Zardoya, Scott V. Edwards, Diego San Mauro
Summary: This study investigated the role of aquaporins (AQPs) in the adaptation of amphibious fishes to terrestrial environments. Evidence of adaptive evolution was found in 21 AQPs belonging to 5 different classes, with the AQP11 class being predominant. These sequence changes suggest modifications in molecular function and/or structure related to the process of adapting to an amphibious lifestyle.
Article
Microbiology
Aya Hefnawy, Gabriel Negreira, Marlene Jara, James A. Cotton, Ilse Maes, Erika D'Haenens, Hideo Imamura, Bart Cuypers, Pieter Monsieurs, Christina Mouchtoglou, Hans De Winter, Isabel Pintelon, Jean-Pierre Timmermans, Matt Berriman, Mandy Sanders, Julio Martin, Geraldine de Muylder, Jean-Claude Dujardin, Yann G-J Sterckx, Malgorzata Anna Domagalska
Summary: The study demonstrates the importance of prospective drug resistance (DR) studies for neglected tropical diseases (NTDs) using Leishmania donovani as a paradigm. By experimentally selecting resistance to a promising compound for visceral leishmaniasis and characterizing resistant parasites, a new DR mechanism involving LdoDLP1 was discovered. This highlights the practical relevance of prospective DR studies.
Article
Parasitology
Janneke Wit, Matthew L. Workentine, Elizabeth Redman, Roz Laing, Lewis Stevens, James A. Cotton, Umer Chaudhry, Qasim Ali, Erik C. Andersen, Samuel Yeaman, James D. Wasmuth, John S. Gilleard
Summary: This study fills the knowledge gaps in the detection of selection signatures in parasitic nematodes and provides a framework for maximizing the power of genome-wide approaches in detecting drug resistance loci. The study detected clear signatures of drug selection in Haemonchus contortus populations and identified the isotype-1 6-tubulin gene as the most important resistance locus.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2022)
Article
Immunology
Susanne U. Franssen, Mandy J. Sanders, Matt Berriman, Christine A. Petersen, James A. Cotton
Summary: This study presents genomic data from Leishmania-infected dogs in the United States, demonstrating vertical transmission of the parasites without vector transmission. The parasites were introduced to the US separately from the Old World and more recently than L. infantum from South America. The unusual genetics of the parasite population suggest limited or no sexual reproduction. The findings have important implications for the population genetics of Leishmania parasites and highlight the need to consider vertical transmission in addition to vector transmission when studying transmission in complex natural settings.
EMERGING INFECTIOUS DISEASES
(2022)
Article
Biochemical Research Methods
Hector Lorente-Martinez, Ainhoa Agorreta, Diego San Mauro
Summary: This study introduces a comprehensive and versatile workflow that provides convenience for molecular evolution research based on genomic data. The workflow involves steps such as searching and capturing gene sequences of interest, processing and purifying the sequences, generating multiple sequence alignments, selecting the best-fit model of evolution, and reconstructing a reliable phylogenetic tree.
METHODS AND PROTOCOLS
(2022)
Article
Cell Biology
Yegnasew Takele, Tadele Mulaw, Emebet Adem, Caroline Jayne Shaw, Susanne Ursula Franssen, Rebecca Womersley, Myrsini Kaforou, Graham Philip Taylor, Michael Levin, Ingrid Muller, James Anthony Cotton, Pascale Kropf
Summary: (Summary in English)
Visceral leishmaniasis (VL) has a high relapse rate in HIV patients, and these patients still exhibit pathological abnormalities after treatment. Three immunological markers associated with VL relapse in HIV patients have been identified, and these markers can be measured in primary hospital settings in Ethiopia, helping to predict relapse risk and improve disease management and patient care.
CELL REPORTS MEDICINE
(2022)