Article
Cell Biology
Qiang Zhang, Dimitrios-Ilias Balourdas, Bruno Baron, Alon Senitzki, Tali E. Haran, Klas G. Wiman, Thierry Soussi, Andreas C. Joerger
Summary: The extremophile Alvinella pompejana, an annelid worm living near hydrothermal vents in the Pacific Ocean, has a p53 family gene with a highly thermostable DNA-binding domain, which may play a crucial role in maintaining genome integrity.
CELL DEATH & DISEASE
(2022)
Editorial Material
Multidisciplinary Sciences
Michael Haslam
Summary: Investigating whether orangutans have the capacity to make stone tools, to gain insights into the origin of this behavior.
Article
Biochemistry & Molecular Biology
Alexander F. A. Keszei, Matthew C. J. Yip, Ta-Chien Hsieh, Sichen Shao
Summary: Cryo-EM structures of the cytosolic metazoan GET complex targeting nascent tail-anchored membrane proteins to the endoplasmic reticulum reveal interactions that coordinate client transfer between two protein chaperones.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Zhihengyu Chen, Zhijie Chen, Omar K. Farha, Karena W. Chapman
Summary: Understanding and controlling the structure, chemistry, and defects of nanomaterials is a challenge that has been explored using metal-organic frameworks (MOFs). The study found that the resulting nanoparticle structure, chemistry, and defect concentration depend on the node chemistry of the original MOF. This suggests that MOFs offer new potential control over nanomaterial synthesis under mild reaction conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Tianying Lan, Kalle Leppala, Crystal Tomlin, Sandra L. Talbot, George K. Sage, Sean D. Farley, Richard T. Shideler, Lutz Bachmann, Oystein Wiig, Victor A. Albert, Jarkko Salojarvi, Thomas Mailund, Daniela Drautz-Moses, Stephan C. Schuster, Luis Herrera-Estrella, Charlotte Lindqvist
Summary: Research finds that the effective population size of an ancient polar bear lineage experienced a dramatic decline, followed by a modest increase just before its extinction. The ancient polar bear had slightly higher genetic diversity, suggesting severe genetic erosion in modern polar bears during a prolonged bottleneck. The study also suggests the occurrence of a possible ancient introgression event from brown bears dating back over 150,000 years.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shao-Chen Cheng, Chun-Bing Liu, Xue-Qin Yao, Jing-Yang Hu, Ting-Ting Yin, Burton K. Lim, Wu Chen, Guo-Dong Wang, Cheng-Lin Zhang, David M. Irwin, Zhi-Gang Zhang, Ya-Ping Zhang, Li Yu
Summary: Highly specialized myrmecophagy has independently evolved multiple times in mammalian species of different orders, demonstrating a textbook example of phenotypic evolutionary convergence. Through multi-omic analyses and validating assays, we reveal the complex and diverse interactions between hosts and their gut microbiota, providing adaptive solutions for nutritional and detoxification challenges. This study contributes new insights into the dietary evolution of mammals and the coordination of physiological functions between animal hosts and their gut commensals.
NATIONAL SCIENCE REVIEW
(2023)
Article
Geochemistry & Geophysics
H. Hellevang, L. H. Line, C. H. Eide, J. Jahren, B. G. Haile
Summary: Recycled quartz grains with specific geochemical CL fingerprints can be used to track uplifted source terrains, providing important information about past tectonic activity. Regional mapping can reveal both intra-basinal recycling and recycled grains transported into the basin from external sources. This innovative method does not require specialized equipment and has wide applications in geoscientific disciplines.
GEOCHEMICAL PERSPECTIVES LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Yiqiong Zhang, Hanwen Liu, Siyuan Zhao, Chao Xie, Zhenguo Huang, Shuangyin Wang
Summary: This review focuses on the formation and preparation of defects, the dynamic evolution process of defects, and the influence of defect dynamic evolution on catalytic reactions. The summary of the current advances in the dynamic evolution process of defects in various catalytic reactions is expected to provide a comprehensive understanding of the role of defective electrocatalysts in the structural evolution process and reaction mechanisms.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Michael J. Owen
Summary: Schizophrenia is a complex psychiatric disorder with profound impacts on affected individuals and society. Genomics has provided new insight into the genetic basis of the condition, identified risk alleles, and shed light on its relationship with other mental disorders and childhood neurodevelopmental disorders. Furthermore, it has revealed the broad impacts of synaptic dysfunction on brain function and offered a plausible explanation for its persistence despite reduced fertility.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Nikita Orekhov, Nikolay Kondratyuk, Mikhail Logunov, Alexandra Timralieva, Vladimir Shilovskikh, Ekaterina Skorb
Summary: This study provides molecular insights into the self-assembly of melamine cyanurate in aqueous solution and identifies mechanisms of aggregation. The research suggests that the formation of small M-CA complexes is mainly stabilized through aromatic p-p stacking rather than hydrogen bond formation. It also demonstrates that changing the concentration ratio of M to CA leads to a variation in the structure of critical nuclei, indicating a potential for the programmable design of functional supramolecular materials.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Luo Chen, Wei-Tao Jin, Xin-Quan Liu, Xiao-Quan Wang
Summary: This study successfully resolved the intergeneric relationships of Podocarpaceae using a large number of nuclear and chloroplast orthologous groups, and revealed that morphological traits may have promoted its species diversification. Additionally, the results indicate that Podocarpaceae originated in Gondwana and both vicariance and dispersal have contributed to its current biogeographic patterns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
A. J. Shore, R. A. Wood, I. B. Butler, A. Yu Zhuravlev, S. McMahon, A. Curtis, F. T. Bowyer
Summary: Through exceptional preservation, a phylogenetic connection between Ediacaran and Cambrian metazoans is established. The discovery of three-dimensional, pyritized soft tissue in Namacalathus provides evidence of a lophotrochozoan affinity and suggests deep roots of modern lophotrochozoan phyla in the Ediacaran period. This supports molecular phylogenies and demonstrates the early development of biomineralization abilities in these ancient organisms.
Review
Oncology
Sonya Hessey, Petros Fessas, Simone Zaccaria, Mariam Jamal-Hanjani, Charles Swanton
Summary: Metastasis is the main cause of cancer-related death worldwide and recent studies have used genomic sequencing data to understand the origins and mechanisms of metastasis. The reliability of these studies depends on the representative nature of the samples. The role of research autopsies in achieving comprehensive sampling is discussed.
Article
Biochemistry & Molecular Biology
Zhidan Li, Yiming Zhang, Stephen J. Bush, Chao Tang, Li Chen, Dan Zhang, Araxi O. Urrutia, Jing-wen Lin, Lu Chen
Summary: Alternative splicing is a widespread phenomenon in eukaryotic genomes that increases transcriptomic diversity. MeDAS is a database resource that allows users to study alternative splicing in a developmental context and provides detailed time course data for various species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Meggie Hudspith, Laura Rix, Michelle Achlatis, Jeremy Bougoure, Paul Guagliardo, Peta L. Clode, Nicole S. Webster, Gerard Muyzer, Mathieu Pernice, Jasper M. de Goeij
Summary: Sponges are recognized as key ecosystem engineers in aquatic habitats, with the ability to process organic matter efficiently. Through experiments, it is found that microbial communities in high and low microbial abundance sponges interact with hosts in nutrient exchange and symbiotic relationships.
Article
Environmental Sciences
Isabelle Boutet, Camille Lacroix, Simon Devin, Arnaud Tanguy, Dario Moraga, Michel Auffret
Summary: The study found that the response capacity of mussels in coastal ecosystems is influenced by both water temperature increase and environmental history, with a possible genetic basis in physiological response. Immune parameters of blue mussels were notably affected by extreme warming. There was no significant difference in response between hybrids and M galloprovincialis.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Genetics & Heredity
Alexis Bioy, Anne-Sophie Le Port, Emeline Sabourin, Marie Verheye, Patrice Piccino, Baptiste Faure, Stephane Hourdez, Jean Mary, Didier Jollivet
Summary: The polychaete Alvinella pompejana, which lives on deep-sea hydrothermal chimneys, has specific adaptations to withstand high temperatures and hypoxia. A balanced polymorphism on the enzyme phosphoglucomutase has been discovered, with different optimal activities and thermostabilities exhibited by different allozymes. The maintenance of highly divergent allelic lineages encoding different electromorphs is governed by two linked amino acid replacements. These functional phenotypes have likely been maintained through a thermodynamic trade-off between protein thermostability and catalysis.
Article
Biotechnology & Applied Microbiology
Sarah Farhat, Eric Bonnivard, Emmanuelle Pales Espinosa, Arnaud Tanguy, Isabelle Boutet, Nadege Guiglielmoni, Jean-Francois Flot, Bassem Allam
Summary: The study generated a 1.86 Gb chromosome-level assembly of the hard clam genome, revealing a high proportion of repeated elements and major chromosome rearrangements compared to other assemblies. Comparative analysis showed a diversification in immune-related proteins, particularly tumor necrosis factors and C1q domain-containing proteins. Additionally, a range of LTR-retrotransposons elements, especially Steamer elements, were identified, indicating a potential target for investigating cancer cell development and transmission in bivalve mollusks.
Article
Biochemistry & Molecular Biology
Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S. Roos, Toni Gabaldon, David Thybert, Paul D. Thomas, Yanhui Hu, David M. Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J. Martin, Christophe Dessimoz, Adrian Altenhoff
Summary: The Orthology Benchmark Service is a valuable resource for evaluating orthology inference methods in comparative genomics and phylogenetic analysis. It is supported and maintained by the Quest for Orthologs consortium and provides a standard dataset and common procedures for comparing different methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Jade Castel, Stephane Hourdez, Florence Pradillon, Claire Daguin-Thiebaut, Marion Ballenghien, Stephanie Ruault, Erwan Corre, Adrien Tran Y. Lu, Jean Mary, Pierre-Alexandre Gagnaire, Francois Bonhomme, Corinna Breusing, Thomas Broquet, Didier Jollivet
Summary: This study assessed the species range and divergence of Alviniconcha snails in the Western Pacific vent fields. Using genetic and morphological data, the study confirmed high levels of genetic divergence among the three species. Surprisingly, despite long periods of isolation, gene flow was still observed between the species in certain locations.
Article
Biotechnology & Applied Microbiology
Ljudevit Luka Bostjancic, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklos Balint, Klaus Schwenk, Odile Lecompte, Kathrin Theissinger
Summary: This study compares the gene expression profiles of susceptible native European noble crayfish and invasive disease-resistant marbled crayfish challenged with two different strains of Aphanomyces astaci. The results show distinct immune responses in the two crayfish species, indicating that the coevolutionary history of the crayfish with specific A. astaci strains influences the type and strength of the host immune response to the pathogen.
Article
Plant Sciences
Gregoire Le Provost, Benjamin Brachi, Isabelle Lesur, Celine Lalanne, Karine Labadie, Jean-Marc Aury, Corinne Da Silva, Dragos Postolache, Thibault Leroy, Christophe Plomion
Summary: By combining RNA-seq and a genome scan of genetic divergence between two closely related oak species, researchers identified potentially adaptive genes related to drought and waterlogging responses, as well as intrinsic reproductive barriers in oak trees.
Article
Biology
Ljudevit Luka Bostjancic, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklos Balint, Klaus Schwenk, Odile Lecompte, Kathrin Theissinger
Summary: This data article provides a detailed description of the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with the pathogen Aphanomyces astaci. The transcriptomes were obtained through RNA sequencing and differential gene expression analysis was performed. These data are of great importance for future expression studies.
BMC RESEARCH NOTES
(2022)
Article
Microbiology
Arthur Monjot, Gisele Bronner, Damien Courtine, Corinne Cruaud, Corinne Da Silva, Jean-Marc Aury, Frederick Gavory, Anne Mone, Agnes Vellet, Ivan Wawrzyniak, Jonathan Colombet, Hermine Billard, Didier Debroas, Cecile Lepere
Summary: The advent of high-throughput sequencing has revealed the diverse microbial eukaryotes in aquatic ecosystems, but their function and contribution to the trophic food web in freshwater ecosystems are not well understood. This study used a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes and analysed metatranscriptomic data to assess their metabolic potential. The analysis showed a high diversity of microbial eukaryotes in the deep water layer, with saprotrophs expressing transcripts related to sulfur and nitrate metabolism, as well as organic matter degradation. Seasonal variations were observed in the mixolimnion, particularly for parasites and mixoplankton. Water mixing during spring and autumn promoted the dissemination of parasitic fungi and over-expression of genes involved in the parasitic cycle. Mixoplanktonic haptophytes showed an advantage in phagotrophy under nutrient limitation.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Christelle Rutz, Lena Bonassin, Arnaud Kress, Caterina Francesconi, Ljudevit Luka Bostjancic, Dorine Merlat, Kathrin Theissinger, Odile Lecompte
Summary: Repetitive elements play a significant role in the evolution of Decapoda genomes. However, current analysis pipelines fail to identify these elements completely. In this study, we developed a new standardized pipeline that accurately annotates repetitive elements in Decapoda and other Crustacea genomes. Our results show that Decapoda species have a higher abundance of repetitive elements compared to other Crustacea. The patterns of these elements reflect the phylogenetic relationships of Decapoda and the different evolutionary trajectories within Crustacea.
Article
Biotechnology & Applied Microbiology
Yannis Nevers, Natasha M. Glover, Christophe Dessimoz, Odile Lecompte
Summary: By comparing protein length distribution across 2326 species, it was found that proteins are slightly longer on average in eukaryotes than in bacteria or archaea, but the variation of length distribution across species is low, especially compared to other genomic features. Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting that the actual variation of protein length distribution across species is even smaller.
Article
Biotechnology & Applied Microbiology
Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-Lopez, Laura Capasso, Julie Poulain, Emilie Boissin, Melanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Le-Hoang, Sylvie Tambutte, Valerie Barbe, Clementine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J. Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Denis Allemand, Serge Planes, Eric Gilson, Didier Zoccola, Patrick Wincker, Christian R. Voolstra, Jean-Marc Aury
Summary: In the Tara Pacific expedition, we assembled two coral genomes, Porites lobata and Pocillopora cf. effusa, with greatly improved contiguity. We annotated their gene catalog and found a relatively high number of genes, 43,000 and 32,000, respectively. These duplicated genes are mainly related to the immune system and disease resistance, providing insights into the stress resilience of reef-building corals.
Article
Fisheries
Ljudevit Luka Bostjancic, Caterina Francesconi, Lena Bonassin, Sandra Hudina, Romana Gracan, Ivana Maguire, Christelle Rutz, Ana Beck, Ana Dobrovic, Odile Lecompte, Kathrin Theissinger
Summary: Alien invasive species are one of the main drivers of biodiversity loss in freshwater ecosystems. In Europe, the pathogen Aphanomyces astaci is considered one of the most problematic invasive species, as its introduction has severely reduced European freshwater crayfish stocks, particularly the noble crayfish population. However, the temporal dynamics of the noble crayfish immune response during Ap. astaci infection remains poorly understood.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Mathematical & Computational Biology
Arnaud Kress, Olivier Poch, Odile Lecompte, Julie D. Thompson
Summary: Protein annotation errors can have significant consequences in various fields. In this study, researchers developed an automated fact-checking approach to identify true domain loss/gain events from false events caused by annotation errors. Using genome-wide ortholog sets and high-quality genome annotations, they analyzed domain gain and loss events in predicted proteomes of non-human primates and fungi. The study revealed that errors in protein annotations led to an over-estimation of domain losses and gains in these organisms. This highlights the need to critically examine protein annotations and develop scalable computational fact-checking methods to mitigate the propagation of wrong information in protein databases.
FRONTIERS IN BIOINFORMATICS
(2023)
Article
Environmental Sciences
Cedric Boulart, Olivier Rouxel, Carla Scalabrin, Pierre Le Meur, Ewan Pelleter, Camille Poitrimol, Eric Thiebaut, Marjolaine Matabos, Jade Castel, Adrien Tran Y. Lu, Loic N. Michel, Cecile Cathalot, Sandrine Cheron, Audrey Boissier, Yoan Germain, Vivien Guyader, Sophie Arnaud-Haond, Francois Bonhomme, Thomas Broquet, Valerie Cueff-Gauchard, Victor Le Layec, Stephane L'Haridon, Jean Mary, Anne-Sophie Le Port, Aurelie Tasiemski, Darren C. Kuama, Stephane Hourdez, Didier Jollivet
Summary: The discovery of a high-temperature hydrothermal vent field on the Woodlark Ridge is reported, showing evidence of an active and stable hydrothermal circulation for a long period of time. This vent field may act as a dispersing center for hydrothermal fauna in nearby basins.
COMMUNICATIONS EARTH & ENVIRONMENT
(2022)