Article
Multidisciplinary Sciences
Matthew L. Blank, Jing Xia, Mary M. Morcos, Mai Sun, Pamela S. Cantrell, Yang Liu, Xuemei Zeng, Cameron J. Powell, Nathan Yates, Martin J. Boulanger, Jon P. Boyle
Summary: Research identified interactions between a single parasite effector and multiple target host proteins at the interface between the Toxoplasma gondii vacuole and the host mitochondria, some of which are critical for the HMA phenotype itself.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Peter McHale, Aaron R. Quinlan
Summary: trfermikit is a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. It achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta, and complements it by recovering a significant number of deletions that Manta missed.
Review
Clinical Neurology
Daisuke Ito
Summary: Nucleic acid therapeutics, particularly antisense oligonucleotide treatments, show promising results in treating amyotrophic lateral sclerosis by targeting specific genetic mutations. The use of Tofersen has demonstrated significant reductions in superoxide dismutase 1 levels in patients with familial ALS. Clinical trials targeting other major ALS-causative genes and proteins are ongoing, expanding the therapeutic options for this debilitating disease.
ANNALS OF NEUROLOGY
(2022)
Article
Evolutionary Biology
Rick M. Maizels, Stuart J. Newfeld
Summary: This article introduces the discovery of the Transforming Growth Factor-β mimic (TGM) multigene family and its formation through unique evolutionary mechanisms. The article discusses the importance of TGM proteins for parasite survival and the timing of the origin of the TGM family, and suggests future research directions.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Xinhua Zeng, Hao Li, Keqi Li, Rong Yuan, Shengbo Zhao, Jun Li, Junling Luo, Xiaofei Li, Hong Ma, Gang Wu, Xiaohong Yan
Summary: The research identified that the MS5 gene in Brassica napus is inherited from a basic diploid ancestor and it has functional differences in the plant. This gene belongs to a Brassicaceae-specific new gene family and has gained a novel function crucial for male fertility in B. napus through neofunctionalization.
Article
Evolutionary Biology
Kathrin Helfenrath, Markus Sauer, Michelle Kamga, Michelle Wisniewsky, Thorsten Burmester, Andrej Fabrizius
Summary: Members of the globin superfamily, such as myoglobin, play important roles in oxygen transport and have shown multiple gene emergence in some fish species. The diverse expression patterns of myoglobin genes in gray bichir and reedfish suggest potential sub- and neofunctionalization during evolution, reflecting molecular adaptation to fluctuating oxygen concentrations in their habitats in tropical Africa.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Yanfeng Liu, Wei Wang
Summary: This study identified and analyzed the GRAS gene family in wheat, revealing 12 subfamilies and highlighting the potential role of TaGRAS in environmental adaptation and stress responses. Homoeolog retention during hexaploidization and epigenetic modifications were also investigated, providing insights into the evolutionary and functional characteristics of TaGRAS genes.
Article
Multidisciplinary Sciences
Warren A. Cheung, Adam F. Johnson, William J. Rowell, Emily Farrow, Richard Hall, Ana S. A. Cohen, John C. Means, Tricia N. Zion, Daniel M. Portik, Christopher T. Saunders, Boryana Koseva, Chengpeng Bi, Tina K. Truong, Carl Schwendinger-Schreck, Byunggil Yoo, Jeffrey J. Johnston, Margaret Gibson, Gilad Evrony, William B. Rizzo, Isabelle Thiffault, Scott T. Younger, Tom Curran, Aaron M. Wenger, Elin Grundberg, Tomi Pastinen
Summary: Long-read HiFi genome sequencing can accurately detect and directly phase single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis of regulatory element activity directly in HiFi reads. In this study, the authors applied HiFi genome sequencing in a rare disease cohort and identified rare hypermethylation events linked to genetic variants, providing indications for variation prioritization in unsolved rare disease cases.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Floortje van de Poll, Benjamin Sutter, Michelle Grace Acoba, Daniel P. Caballero, Samira S. Jahangiri, Yu-San K. Yang, Chien-Der S. Lee, Benjamin P. K. Tu
Summary: The study reveals that Pbp1 and its mammalian ortholog ataxin-2 are stress granule markers involved in regulating mRNA transcripts related to mitochondrial biogenesis. Pbp1 interacts with Puf3 to support the translation of target mRNAs involved in cytochrome c oxidase assembly and mitochondrial ribosome subunits. These findings highlight the role of Pbp1-containing assemblies in mitochondrial function and provide insights into the association between Pbp1/ataxin-2 and RNA, stress granule biology, mitochondrial function, and neuronal health.
Article
Biotechnology & Applied Microbiology
Xinguo Lu, Fang Liu, Qiumai Miao, Ping Liu, Yan Gao, Keren He
Summary: Our study aimed to reveal functional overlapping patterns in gene modules to elucidate regulatory relationships between overlapping genes and communities, as well as explore cancer formation and progression. We analyzed six cancer datasets and identified three types of gene functional modules for each cancer, with our method outperforming others in terms of identifying distinguishing communities and survival prognostics for patients. In conclusion, overlapping genes play a crucial role in constructing comprehensive carcinogenesis by establishing communication bridges between different specific functional groups.
Review
Biochemistry & Molecular Biology
Stephanie Calluori, Rebecca Stark, Brandon L. L. Pearson
Summary: Short tandem repeats (STRs) are repetitive sequences of 1-6 base pairs that can expand or contract, and have been linked to over 50 diseases affecting the central nervous system and muscles. Environmental factors play a role in the development of repeat expansion diseases by inducing DNA damage and repair pathways. Oxidative stress and epigenetic modifications are potential mediators of environmentally induced repeat instability. Further research is needed to identify environmental modulators and their mechanisms of action in order to inform prevention and treatment strategies.
Article
Clinical Neurology
Dandan Tan, Cuijie Wei, Zhao Chen, Yu Huang, Jianwen Deng, Jingjing Li, Yidan Liu, Xinhua Bao, Jin Xu, Zhengmao Hu, Suxia Wang, Yanbin Fan, Yizheng Jiang, Ye Wu, Yuan Wu, Shuang Wang, Panyan Liu, Yuehua Zhang, Zhixian Yang, Yuwu Jiang, Hong Zhang, Daojun Hong, Nanbert Zhong, Hong Jiang, Hui Xiong
Summary: This study confirms a novel subtype of spinocerebellar ataxia (SCA) caused by CAG repeat expansion in the THAP11 gene. The toxic polyQ protein formed intracellular aggregates and its toxicity was dependent on the length of pure CAG repeats. This finding expands the spectrum of polyQ diseases and provides new insights into polyQ-mediated toxic aggregation.
MOVEMENT DISORDERS
(2023)
Article
Plant Sciences
Jennifer A. Noble, Nicholas Bielski, Ming-Che James Liu, Thomas A. DeFalco, Martin Stegmann, Andrew D. L. Nelson, Kara McNamara, Brooke Sullivan, Khanhlinh K. Dinh, Nicholas Khuu, Sarah Hancock, Shin-Han Shiu, Cyril Zipfel, Alice Y. Cheung, Mark A. Beilstein, Ravishankar Palanivelu
Summary: This study investigates the evolution of the LLG gene family and the function and expression of angiosperm LLGs. The results show that LLG diversity is mainly due to lineage-specific duplication events, and expression divergence explains the retention of LLG paralogs. The expression of LLG duplicates in angiosperms is also found to be divergent.
Article
Plant Sciences
Kui Li, Bi Ma, Jinjuan Shen, Sa Zhao, Xiao Ma, Zhimin Wang, Yonghong Fan, Qinglin Tang, Dayong Wei
Summary: This study comprehensively analyzed the evolution and expansion of the EXP family in the Brassica genus, revealing clustering patterns, divergence rates, and the major driving force of segmental duplications during expansion. Purifying selection was identified as the main contributor to the expansion of Brassica EXPs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Genetics & Heredity
Ruihan Luo, Wenqiu Pan, Wenqiang Liu, Yuan Tian, Yan Zeng, Yihan Li, Zhimin Li, Licao Cui
Summary: Gene family expansion has significant impact on the evolutionary history and molecular function of barley. This study identified expanded and contracted gene families in barley and discovered key genes involved in expansion. The study also revealed the critical roles of these expanded genes in stress responses and provided candidate genes for improving barley production and resilience.
FRONTIERS IN GENETICS
(2022)
Article
Ecology
Alexis Simon, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John J. Welch, Nicolas Bierne
Summary: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones across temperate regions. The study showed local introgression is widespread and heterogeneous, with some loci near fixation for the heterospecific allele close to hybrid zones. Overall, there is high concordance among loci globally, along with some signals of asymmetric introgression.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sandra Nhim, Sylvie Gimenez, Rima Nait-Saidi, Dany Severac, Kiwoong Nam, Emmanuelle D'Alencon, Nicolas Negre
Summary: This study presents the first genome-wide ChIP-Seq analysis of H3K9me2 in S. frugiperda. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera.
Article
Biology
Wee Tek Tay, Rahul Rane, Amanda Padovan, Tom K. Walsh, Samia Elfekih, Sharon Downes, Kiwong Nam, Emmanuelle D'Alencon, Jianpeng Zhang, Yidong Wu, Nicolas Negre, Daniele Kunz, Darren J. Kriticos, Cecilia Czepak, Michael H. Otim, Karl H. J. Gordon
Summary: This population genomics study uncovers the complex multiple introduction history of the fall armyworm from the Americas to Africa and Asia, providing insights into the directionality of gene flow and the extent of genomic exchange. The study highlights the potential of international partnership and population genomic approaches in addressing global emerging pest threats and biosecurity challenges. The study also challenges the previous hypothesis of west-to-east spread, instead finding evidence of directional gene flow from the East to eastern Africa.
COMMUNICATIONS BIOLOGY
(2022)
Article
Evolutionary Biology
Fanny Touchard, Alexis Simon, Nicolas Bierne, Frederique Viard
Summary: Portuarization, the repeated evolution of marine species in port ecosystems under human-altered selective pressures, drives various evolutionary processes including establishment of new connectivity hubs, adaptive responses to new chemicals or biotic communities, and hybridization between lineages. However, there are still important knowledge gaps and further research is needed to understand this phenomenon better.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Microbiology
Manon Fallet, Caroline Montagnani, Bruno Petton, Luc Dantan, Julien de Lorgeril, Sebastien Comarmond, Cristian Chaparro, Eve Toulza, Simon Boitard, Jean-Michel Escoubas, Agnes Vergnes, Jacqueline Le Grand, Ingo Bulla, Yannick Gueguen, Jeremie Vidal-Dupiol, Christoph Grunau, Guillaume Mitta, Celine Cosseau
Summary: This study found that early microbial exposure in Pacific oysters can significantly improve their survival rate against a pathogen causing mortality syndrome. The protection provided by microbial exposure is inheritable across generations and is associated with changes in epigenetic marks and immune gene expression. This discovery suggests that microbial exposure may be an important strategy for protecting oyster aquaculture from infectious diseases.
Article
Multidisciplinary Sciences
Terence Legrand, Anne Chenuil, Enrico Ser-Giacomi, Sophie Arnaud-Haond, Nicolas Bierne, Vincent Rossi
Summary: The study used gene flow to predict genetic differentiation among different populations in the Mediterranean basin, finding that the multi-generational coalescent connectivity model outperformed others significantly, which is of great significance for unraveling the eco-evolutionary forces shaping sedentary population structures.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Noemie De San Nicolas, Aromal Asokan, Rafael D. Rosa, Sebastien N. Voisin, Marie-Agnes Travers, Gustavo Rocha, Luc Dantan, Yann Dorant, Guillaume Mitta, Bruno Petton, Guillaume M. Charriere, Jean-Michel Escoubas, Viviane Boulo, Juliette Pouzadoux, Herve Meudal, Karine Loth, Vincent Aucagne, Agnes F. Delmas, Philippe Bulet, Caroline Montagnani, Delphine Destoumieux-Garzon
Summary: The study found that Cg-BigDefs peptides play an important role in controlling the oyster-associated microbial communities. They have a broad spectrum of antimicrobial activity and show specificity and synergy against bacteria associated with oyster pathologies.
Article
Multidisciplinary Sciences
Rahul Rane, Thomas K. Walsh, Pauline Lenancker, Andrew Gock, Thi Hang Dao, Van Liem Nguyen, Thein Nyunt Khin, Divina Amalin, Khonesavanh Chittarath, Muhammad Faheem, Sivapragasam Annamalai, Sathis Sri Thanarajoo, Y. Andi Trisyono, Sathya Khay, Juil Kim, Lastus Kuniata, Kevin Powell, Andrew Kalyebi, Michael H. Otim, Kiwoong Nam, Emmanuelle d'Alencon, Karl H. J. Gordon, Wee Tek Tay
Summary: The fall armyworm, a notorious agricultural pest, has rapidly spread from West Africa to East Asia since 2016. Genome analysis revealed that the majority of populations in this study were hybrids of C- and R-strains. The spread of the fall armyworm was facilitated by international trade of live/fresh plants and plant products, as well as the establishment of "bridgehead populations" in neighboring countries.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Sudeeptha Yainna, Wee Tek Tay, Karine Durand, Estelle Fiteni, Frederique Hilliou, Fabrice Legeai, Anne-Laure Clamens, Sylvie Gimenez, R. Asokan, C. M. Kalleshwaraswamy, Sharanabasappa S. Deshmukh, Robert L. Meagher, Carlos A. Blanco, Pierre Silvie, Thierry Brevault, Anicet Dassou, Gael J. Kergoat, Thomas Walsh, Karl Gordon, Nicolas Negre, Emmanuelle D'Alencon, Kiwoong Nam
Summary: The fall armyworm, a major agricultural pest insect, has spread globally and poses a threat to corn production. Genetic analysis reveals that invasive populations of the fall armyworm originated from the corn strain and exhibit adaptive evolution in detoxification, chemosensory, and digestion genes.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Aurelie Dotto-Maurel, Camille Pelletier, Benjamin Morga, Maude Jacquot, Nicole Faury, Lionel Degremont, Maelis Bereszczynki, Jean Delmotte, Jean-Michel Escoubas, Germain Chevignon
Summary: Whole-genome sequencing is widely used to study aquatic viruses, but their cultivation challenges necessitate the development of new sequencing methods. In this study, we successfully purified OsHV-1 infective particles using tangential flow filtration and sequenced the viral DNA using both Illumina short-read and Nanopore long-read sequencing. The combination of these methods provided a promising approach for in-field sequencing of unculturable aquatic DNA viruses.
MICROBIAL GENOMICS
(2022)
Article
Multidisciplinary Sciences
Daniel Oyanedel, Arnaud Lagorce, Maxime Bruto, Philippe Haffner, Amandine Morot, Yannick Labreuche, Yann Dorant, Sebastien de La Forest Divonne, Francois Delavat, Nicolas Inguimbert, Caroline Montagnani, Benjamin Morga, Eve Toulza, Cristian Chaparro, Jean-Michel Escoubas, Yannick Gueguen, Jeremie Vidal-Dupiol, Julien de Lorgeril, Bruno Petton, Lionel Degremont, Delphine Tourbiez, Lea-Lou Pimpare, Marc Leroy, Oceane Romatif, Juliette Pouzadoux, Guillaume Mitta, Frederique Le Roux, Guillaume M. Charriere, Marie-Agnes Travers, Delphine Destoumieux-Garzon
Summary: In Pacific Oyster Mortality Syndrome (POMS), Vibrio harveyi and ostreid herpesvirus 1 (OsHV-1) are the predominant bacteria causing the disease. V. harveyi synergizes with OsHV-1 by promoting mutual growth and inhibiting oyster's cellular defenses. Furthermore, V. harveyi produces metabolites that benefit the growth of coexisting V. rotiferianus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Murielle Alund, Meredith Cenzer, Nicolas Bierne, Janette W. Boughman, Jose Cerca, Mattheau S. Comerford, Alessandro Culicchi, Brian Langerhans, S. Eryn Mcfarlane, Markus H. Most, Henry North, Anna Qvarnstrom, Mark Ravinet, Richard Svanback, Scott A. Taylor
Summary: Anthropogenic impacts on the environment have both positive and negative effects on speciation processes. Human activities can generate spatial isolation and genetic divergence, but they can also cause sudden secondary contact and hybridization. Changes in the environment created by human actions can create new ecological niches and drive diversification, but they can also lead to niche loss and extinctions. It is important to monitor and understand these impacts in order to promote diversification and enhance biodiversity.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2023)
Article
Microbiology
Camille Clerissi, Xing Luo, Aude Lucasson, Shogofa Mortaza, Julien de Lorgeril, Eve Toulza, Bruno Petton, Jean-Michel Escoubas, Lionel Degremont, Yannick Gueguen, Delphine Destoumieux-Garzon, Annick Jacq, Guillaume Mitta
Summary: The study used metabarcoding and metatranscriptomic approaches to show that the pathogenesis of POMS is conserved across different infectious environments, and identified a core bacterial consortium that plays a role in POMS pathobiota. The core bacteria have complementary metabolic functions and a low competition for nutrients, which allows them to colonize host tissues and contribute to the conservation of POMS pathobiota.
Article
Ecology
Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher, Fabrice Legeai, Gael J. Kergoat, Nicolas Negre, Emmanuelle d'Alencon, Kiwoong Nam
Summary: The population structure of fall armyworm (FAW) is dominated by the genetic differentiation between corn and rice strains, which involves divergent selection at least three loci including a locus potentially causing reproductive isolation. These results suggest that host-plant speciation is a driver of incipient speciation in FAW.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Virology
Jean Delmotte, Camille Pelletier, Benjamin Morga, Richard Galinier, Bruno Petton, Jean-Baptiste Lamy, Oliver Kaltz, Jean-Christophe Avarre, Maude Jacquot, Caroline Montagnani, Jean-Michel Escoubas
Summary: This study investigated the genetic diversity of the causative agent of Pacific oyster mortality syndrome, OsHV-1, using deep sequencing and bioinformatics tools. The results revealed connectivity between OsHV-1 viral populations in different oyster-farming areas, with oyster transfers in France playing a major role in its dispersal.