Review
Biochemistry & Molecular Biology
Xianni Zhong, Jihui Zhao, Liping Sun
Summary: A whole-cell model is an integrative approach that represents certain aspects of the cell structure and/or function. This review summarizes the workflow of whole-cell modeling into five steps, including gathering information, representing the system into modules, translating input information into scoring function, sampling the whole-cell model, and validating and interpreting the model. By combining available models, the accuracy, precision, and completeness of the integrated cell model can be maximized. The review also discusses the quantitative predictions made by existing whole-cell models and highlights the challenges, future directions, and the opportunity for establishing a community-based integrative spatiotemporal multi-scale whole-cell model.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2022)
Article
Microbiology
Jutamart Monkai, Sinang Hongsanan, Darbhe J. Bhat, Turki M. Dawoud, Saisamorn Lumyong
Summary: Five new Diaporthe species were discovered on medicinal plants in Thailand and described using morphology, culture characteristics, host association, and DNA analysis. The study revealed the first report of Diaporthe species on certain plants and provided strong evidence for the establishment of these novel species. This research expands our knowledge of taxonomy, host diversity, and the potential of medicinal plants for discovering new fungi.
Article
Respiratory System
Peifeng Ruan, Jamie L. Todd, Hongyu Zhao, Yi Liu, Richard Vinisko, Julia F. Soellner, Ramona Schmid, Robert J. Kaner, Tracy R. Luckhardt, Megan L. Neely, Imre Noth, Mary Porteous, Rishi Raj, Zeenat Safdar, Mary E. Strek, Christian Hesslinger, Scott M. Palmer, Thomas B. Leonard, Margaret L. Salisbury
Summary: This study aims to identify specific molecular subtypes of IPF and explore their clinical significance by integrating multi-omics data. Through the integration and analysis of proteomic and transcriptomic data from IPF patients, two molecular subtypes were identified, with one subtype showing more severe disease and shorter progression-free survival.
RESPIRATORY RESEARCH
(2023)
Article
Entomology
Ping Zhao, Zhenyong Du, Qian Zhao, Donghai Li, Xiaolan Shao, Hu Li, Wanzhi Cai
Summary: The genus Sclomina, a type of assassin bug endemic to China and Vietnam, includes multiple cryptic species with gradual morphological variability. Their biology and evolutionary history remain largely unknown.
Article
Biology
Elif Kubat Oktem, Ummuhan Demir, Metin Yazar, Kazim Yalcin Arga
Summary: This study examined differentially expressed genes in spinal cord samples from regenerative organisms and nonregenerative organisms. Based on these gene signatures, three small compounds were identified as potential candidates for the treatment of cancer, and they showed anticancer effects in prostate cancer cell cultures. These findings contribute to the evaluation of mechanisms and gene signatures related to cancer and the development of new cancer therapies.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Thomas Rolland, Freddy Cliquet, Richard J. L. Anney, Clara Moreau, Nicolas Traut, Alexandre Mathieu, Guillaume Huguet, Jinjie Duan, Varun Warrier, Swan Portalier, Louise Dry, Claire S. Leblond, Elise Douard, Frederique Amsellem, Simon Malesys, Anna Maruani, Roberto Toro, Anders D. Borglum, Jakob Grove, Simon Baron-Cohen, Alan Packer, Wendy K. Chung, Sebastien Jacquemont, Richard Delorme, Thomas Bourgeron
Summary: The prevalence of autism-associated genetic variants in individuals without a diagnosis of autism is explored. These variants are associated with a decrease in fluid intelligence, qualification level, income, and an increase in metrics related to material deprivation. Autism-associated genes have a larger impact on these phenotypic features than other genes with loss-of-function variants.
Article
Zoology
Dora Hlebec, Danilo Harms, Mladen Kucinic, Mark S. Harvey
Summary: Despite the use of molecular data to study invertebrates, the systematics of the pseudoscorpion family Chernetidae is still unresolved. This study provides a preliminary molecular phylogeny of chernetids, using mitochondrial and nuclear markers, to assess the subfamilial and generic relationships within the family. The results reveal the presence of a previously unrecognized subfamily and the nesting of certain genera within another subfamily. Additionally, three new subterranean species of the genus Lasiochernes are described from a karst region.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Engineering, Environmental
Fobang Liu, Taekyu Joo, Jenna C. Ditto, Maria G. Saavedra, Masayuki Takeuchi, Alexandra J. Boris, Yuhan Yang, Rodney J. Weber, Ann M. Dillner, Drew R. Gentner, Nga L. Ng
Summary: Exposure to PM2.5 is associated with millions of premature deaths annually. The overproduction of reactive oxygen species (ROS) through oxidative stress is a possible mechanism for PM2.5-induced health effects. In this study, the authors found that oxygenated organic aerosol (OOA), particularly more-oxidized OOA, is the main type of organic aerosol associated with cellular ROS production. They also identified highly unsaturated species with carbon-oxygen double bonds and aromatic rings in OOA as major contributors to cellular ROS production. These findings highlight the importance of understanding the sources and chemical characteristics of ambient OA in formulating strategies to mitigate the health impacts of PM2.5.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Forestry
Yuqian Ye, Hui Wang, Junwei Luan, Jinhao Ma, Angang Ming, Baoliang Niu, Cuiju Liu, Zac Freedman, Jingxin Wang, Shirong Liu
Summary: This study investigated the influence of tree species richness and the presence of nitrogen-fixing tree species on soil aggregate-associated organic carbon fractions. The results showed that the effects of tree species richness on organic carbon content varied depending on the presence or absence of nitrogen-fixing tree species. In the presence of nitrogen-fixing tree species, the organic carbon content increased across the gradient of tree species richness, while in the absence of nitrogen-fixing tree species, only the fine intra-aggregate particulate organic carbon in large macroaggregates showed a positive relationship with tree species richness.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Microbiology
Zi-Jian Cao, Wen-Tao Qin, Juan Zhao, Yu Liu, Shou-Xian Wang, Su-Yue Zheng
Summary: This study investigated the contamination of edible fungi substrates by Trichoderma species in North China and identified three new species. Detailed identification and classification were carried out using phenotypic features, culture characteristics, and molecular analysis. The study expands our understanding of Trichoderma species contaminating edible fungi substrates and updates knowledge of species diversity in the group.
Article
Environmental Sciences
Haining Wang, Xiaoxue Fu, Chengqian Zhao, Zhendong Luan, Chaolun Li
Summary: This paper presents a deep learning model for the fast and accurate recognition and classification of substrates and the dominant associated species in cold seeps, which improves the recognition accuracy of substrates by utilizing different classifiers. The model's results were manually verified using images obtained in the Formosa cold seep, showing potential for application.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Endocrinology & Metabolism
Daniel G. Whitney, Michelle S. Caird, Cathleen L. Raggio, Edward A. Hurvitz, Gregory A. Clines, Karl J. Jepsen
Summary: Bone development is essential for bone strength, but certain factors can lead to abnormal development and lower strength. Current guidelines for assessing bone strength are inadequate for abnormal bone development, and a multi-trait, integrative approach is needed. This Perspective emphasizes the importance of translational research to optimize bone growth and prevent fragility fractures in pediatric conditions.
Article
Environmental Sciences
Olivier Laroche, Sonnich Meier, Svein A. Mjos, Nigel Keeley
Summary: This study examined the impact of salmon farming on several epibenthic suspension-feeders and identified potential molecular indicators of this impact. The results showed species-specific effects and differences in fatty acid profiles and host microbiome communities.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Physiology
Christian L. Cox, Michael L. Logan
Summary: In studies comparing only a few populations or species, the principle of severity can be applied to generate strong inferences about adaptation. This approach involves ensuring closely related species in the study system, formulating clear hypotheses, collecting data that avoid statistical underdetermination, and refining alternative hypotheses systematically to differentiate potential agents of selection.
PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY
(2021)
Article
Ecology
Jinlong Liu, Han Yan, Guopan Li, Shaobin Li
Summary: The study found strong and positive associations between nest concealment and clutch size, incubation period, nestling period, and nest success across 21 sympatric bird species living on the Tibet Plateau at 3,400m altitude. This suggests that nest-site characteristics, such as concealment, play a crucial role in reproductive performance in alpine bird communities.
ECOLOGY AND EVOLUTION
(2021)
Review
Chemistry, Medicinal
Sebastien Duperron, Mehdi A. Beniddir, Sylvain Durand, Arlette Longeon, Charlotte Duval, Olivier Gros, Cecile Bernard, Marie-Lise Bourguet-Kondracki
Article
Microbiology
Berenice Piquet, Francois H. Lallier, Coralie Andre, Bruce Shillito, Ann C. Andersen, Sebastien Duperron
Article
Microbiology
Sigmund Jensen, Jeremy A. Frank, Magnus O. Arntzen, Sebastien Duperron, Gustav Vaaje-Kolstad, Martin Hovland
Summary: The study uncovered the functions encoded in the genome of Gammaproteobacteria from the family Endozoicomonadaceae, which live inside deep-water coral reef clams and are associated with symbiotic relationships and nutritional systems. The research suggests a nutritional symbiosis fueled by enzymatic products from extracellular degradation processes.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Naema S. Beziat, Sebastien Duperron, Sebastien Halary, Catherine Azede, Olivier Gros
Summary: This study investigates the interactions between bacterial ectosymbionts and two Caribbean mangrove crabs, showing that different bacterial morphotypes colonize the gills of Aratus pisonii and Minuca rapax. Molecular analysis revealed the dominance of Alphaproteobacteria and Bacteroidetes in both host species, with specific bacterial phylotypes not shared between the two crab species. Further investigations are needed to confirm the specificity and nature of the symbiosis.
Article
Environmental Sciences
Melissa Hanafi-Portier, Sarah Samadi, Laure Corbari, Tin-Yam Chan, Wei-Jen Chen, Jhen-Nien Chen, Mao-Ying Lee, Christopher Mah, Thomas Saucede, Catherine Borremans, Karine Olu
Summary: Imagery has become an important tool for assessing deep-sea biodiversity, providing quantitative and repeatable estimates. Taxon identification from images is challenging, especially in regions where faunal knowledge is limited. The efficiency of imagery and physical sampling may vary among different habitat types.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Zoology
Hsin Lee, Nicolas Puillandre, Yasunori Kano, Wei-Jen Chen, Sarah Samadi
Summary: This study investigates the species diversity of the family Cocculinidae using an integrated approach. The results reveal high diversity in the Indo-West Pacific region, with many species not assigned to known names. Additionally, a previously unknown copulatory structure and ten main clades in the family were discovered.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Chemistry, Medicinal
Andrea Castaldi, Roberta Teta, Germana Esposito, Mehdi A. Beniddir, Nicole J. De Voogd, Sebastien Duperron, Valeria Costantino, Marie-Lise Bourguet-Kondracki
Summary: This study examined a unique molecular family restricted to the Callyspongia genus, discovering a series of rare linear peptides. The structure of one peptide was determined through various analyses, and proposed structures for several other peptides were also suggested. Interestingly, similar substances were found in the molecular network of cyanobacteria strains, indicating that sponge-associated cyanobacteria might be the true producers of these peptides.
Article
Marine & Freshwater Biology
Pierre Foucault, Alison Gallet, Charlotte Duval, Benjamin Marie, Sebastien Duperron
Summary: This study investigates the response of gut microbiota and the metabolome of a model fish species to exposure to cyanobacterial blooms. The results indicate that even short-lived blooms can cause significant changes in microbiota composition and holobiont metabolome. The study highlights the relevance of multi-omics approaches in ecotoxicology research.
AQUATIC TOXICOLOGY
(2022)
Article
Microbiology
Charlotte Duval, Benjamin Marie, Pierre Foucault, Sebastien Duperron
Summary: This study provides the first insights into the establishment of bacterial microbiota during early developmental stages of laboratory-reared medaka using a 16S-rRNA-sequencing-based approach. Major shifts in community compositions are observed, from a Proteobacteria-dominated community in larvae and juveniles to a more phylum-diverse community towards adulthood.
Article
Microbiology
Sebastien Halary, Sebastien Duperron, Justine Demay, Charlotte Duval, Sahima Hamlaoui, Berenice Piquet, Anita Reinhardt, Cecile Bernard, Benjamin Marie
Summary: Cyanobacteria are pioneer colonizers in specific environments, and their settlement in new habitats precedes the establishment of complex microbial consortia. Some heterotrophic bacteria are considered as cyanobacterial partners, forming their cyanosphere and potentially involved in mutualistic relationships through nutrient exchange and sharing of common goods. This study isolated non-axenic cyanobacterial strains and their associated cyanospheres from thermal mud and biofilms in a retention basin, and used metagenomic analysis to characterize the community structure and relationships. The results provided insights into the potential roles and metabolic capabilities of the microorganisms in thermal mud-associated cyanobacterial biofilms. The study also highlighted the influence of reference protein database selection for functional annotation and the challenge of finding a single database that covers both autotroph and heterotroph metabolic specificities.
Article
Microbiology
Anais Masse, Juliette Detang, Charlotte Duval, Sebastien Duperron, Anthony C. C. Woo, Isabelle Domart-Coulon
Summary: This study analyzed the composition and plasticity of bacterial communities associated with the green algae Ostreobium in response to varying salinities. The results showed that the host genotype of Ostreobium determined the structure of the bacterial community, with different genotypes having different dominant bacterial strains. The abundance of Rhizobiales also shifted in response to an increase in salinity. Additionally, a small core microbiota was found across all salinities, suggesting an important functional role in the coral holobiont.
Article
Ecology
Sebastien Halary, Sebastien Duperron, Sandra Kim Tiam, Charlotte Duval, Cecile Bernard, Benjamin Marie
Summary: Cyanobacteria play a significant role in global primary production but can also cause harmful events called blooms. However, the study of genetic diversity in bloom development and the ecology of harmful cyanobacteria has been underestimated. A comparative study of Aphanizomenon gracile revealed extensive heterogeneity in gene contents, suggesting the potential for essential metabolite exchanges among individuals in a bloom.
ISME COMMUNICATIONS
(2023)
Article
Microbiology
Sebastien Duperron, Pierre Foucault, Charlotte Duval, Midoli Goto, Alison Gallet, Simon Colas, Benjamin Marie
Summary: Massive sequencing of the 16S rRNA gene is a standard method for describing and comparing microbial communities. Nontargeted metabolomics can complement this by providing information on community functioning. This study validates a method of extracting metabolites followed by DNA extraction, which allows for the combination of 16S rRNA sequencing with metabolome characterization from a single sample.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Microbiology
Sebastien Halary, Charlotte Duval, Alison Gallet, Sebastien Duperron, Berenice Piquet, Justine Demay, Cecile Bernard, Benjamin Marie
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Geochemistry & Geophysics
Germain Bayon, Nolwenn Lemaitre, Jean-Alix Barrat, Xudong Wang, Dong Feng, Sebastien Duperron