Article
Veterinary Sciences
Christine Thomas, Ulrich Methner, Manja Marz, Joerg Linde
Summary: Bacteria of the genus Salmonella are a major risk to livestock, the food economy, and public health. Traditional slide agglutination has been used for Salmonella serotyping, but whole-genome sequencing (WGS) followed by in silico serotyping has emerged as an alternative method. This study compared the performance of in silico serotyping tools and traditional slide agglutination tests using ONT sequencing data of 28 Salmonella strains. The results showed high accuracy for in silico serotyping and identified similar genetic markers with both sequencing technologies.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Plant Sciences
Chen Tan, Haimei Zhang, Haidong Chen, Miaotian Guan, Zhenzhi Zhu, Xueying Cao, Xianhong Ge, Bo Zhu, Daozong Chen
Summary: Potential SSR molecular markers were successfully developed for 40 Matthiola incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.
Article
Cell Biology
Estelle Colin, Yannis Duffourd, Emilie Tisserant, Raissa Relator, Ange-Line Bruel, Frederic Tran Mau-Them, Anne-Sophie Denomme-Pichon, Hana Safraou, Julian Delanne, Nolwenn Jean-Marcais, Boris Keren, Bertrand Isidor, Marie Vincent, Cyril Mignot, Delphine Heron, Alexandra Afenjar, Solveig Heide, Anne Faudet, Perrine Charles, Sylvie Odent, Yvan Herenger, Arthur Sorlin, Sebastien Moutton, Jennifer Kerkhof, Haley McConkey, Martin Chevarin, Charlotte Poe, Victor Couturier, Valentin Bourgeois, Patrick Callier, Anne Boland, Robert Olaso, Christophe Philippe, Bekim Sadikovic, Christel Thauvin-Robinet, Laurence Faivre, Jean-Francois Deleuze, Antonio Vitobello
Summary: This study utilized multiple molecular analysis techniques, including genome sequencing, RNA sequencing, and DNA methylation analysis, to diagnose cases of rare neurodevelopmental disorders with negative exome sequencing results. The study found that integrating these techniques can solve some cases and identify potential candidate genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Carolina Penaloza, Alejandro P. Gutierrez, Lel Eory, Shan Wang, Ximing Guo, Alan L. Archibald, Tim P. Bean, Ross D. Houston
Summary: A chromosome-level assembly for the Pacific oyster (C. gigas) was created and annotated, providing a valuable resource for genetics and genomics studies, as well as selective breeding in aquaculture.
Article
Cell Biology
Estelle Colin, Yannis Duffourd, Martin Chevarin, Emilie Tisserant, Simon Verdez, Julien Paccaud, Ange-Line Bruel, Frederic Tran Mau-Them, Anne-Sophie Denomme-Pichon, Julien Thevenon, Hana Safraou, Thomas Besnard, Alice Goldenberg, Benjamin Cogne, Bertrand Isidor, Julian Delanne, Arthur Sorlin, Sebastien Moutton, Melanie Fradin, Christele Dubourg, Magali Gorce, Dominique Bonneau, Salima El Chehadeh, Francois-Guillaume Debray, Martine Doco-Fenzy, Kevin Uguen, Nicolas Chatron, Bernard Aral, Nathalie Marle, Paul Kuentz, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Damien Sanlaville, Patrick Callier, Christophe Philippe, Christel Thauvin-Robinet, Laurence Faivre, Antonio Vitobello
Summary: Multi-omics technologies provide valuable and increasingly accessible tools for diagnostic laboratories to help patients with unresolved rare diseases, especially those clinically diagnosed with rare OMIM diseases. However, there is currently no consensus on the optimal diagnostic care pathway to follow after negative results with standard approaches.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Chuner Cai, Kai Gu, Hui Zhao, Sophie Steinhagen, Peimin He, Thomas Wichard
Summary: This study sequenced and annotated the complete chloroplast genome of Ulva compressa, compared it with the mitogenome, and analyzed evolutionary trends through phylogenetic analyses. The findings identified potential genetic markers in the chloroplast genes and highlighted differences in repeat features among different Ulva subspecies.
Review
Medicine, Research & Experimental
Fang Liu, Yunfei Wang, Hongcang Gu, Xiaoxue Wang
Summary: DNA methylation is a stable epigenetic modification occurring at CpG dinucleotides, playing essential roles in both physiological and pathological processes. In human diseases, especially cancer, aberrant DNA methylation has been observed. However, conventional methods for DNA methylation profiling require a large amount of DNA from heterogeneous cell populations, making it impractical for rare or circulating tumor cells. Therefore, the development of sequencing technologies that can accurately profile DNA methylation using small numbers of cells, or even single cells, is crucial. Excitingly, various single-cell DNA methylation sequencing and omics sequencing technologies have been developed, greatly advancing our understanding of the molecular mechanisms of DNA methylation. In this review, we summarize these methods, their applications in biomedical sciences, discuss technical challenges, and provide prospects for future research directions.
Article
Ecology
Sonia Boughattas, Dana Albatesh, Albandari Al-Khater, Bruno W. Giraldes, Asma A. Althani, Fatiha M. Benslimane
Summary: This study presented an optimized DNA isolation method that significantly improved sequencing yield for different marine species compared to commonly reported protocols or commercial kits. The method proved to be successful regardless of the shape, consistency, and sample preservation of the marine species, demonstrating a 39-fold increase in Oxford Nanopore Technologies sequencing yield for Spirobranchus sp., and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples.
ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Alessia Russo, Baptiste Mayjonade, Daniel Frei, Giacomo Potente, Roman T. Kellenberger, Lea Frachon, Dario Copetti, Bruno Studer, Juerg E. Frey, Ueli Grossniklaus, Philipp M. Schluter
Summary: This article describes a method for extracting high molecular weight (HMW) DNA from low input plant material, which is easy to follow and quick. It successfully enables HMW DNA extraction from different plant species and is suitable for long-read sequencing on the Oxford Nanopore Technologies PromethION(R) platform.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hilke Schroeder, Birgit Kersten
Summary: European oak and European white oak, along with European beech, are the main economically used deciduous tree species in Europe. Identification of these two species is important due to their ecological differences. A marker set of six markers from four nuclear regions has been identified as a cost-efficient and widely applicable method for distinguishing between these two species.
Review
Neurosciences
Evan Udine, Angita Jain, Marka van Blitterswijk
Summary: ALS is a progressive and fatal disease caused by motor neuron loss. Despite the discovery of numerous ALS-linked genes, there are still cases that cannot be explained. Various technologies have been used to identify regions of interest and investigate candidate genes, including traditional methods like linkage analysis and Sanger sequencing, as well as more recent methods like whole-exome and whole-genome sequencing. The complex genetics of ALS have led to the development of novel sequencing technologies, such as long-read sequencing, which can uncover the contribution of repeat expansions and other types of structural variation. These advancements are crucial for our understanding of ALS and the discovery of new genes associated with the disease.
MOLECULAR NEURODEGENERATION
(2023)
Article
Biotechnology & Applied Microbiology
Jidong Lang, Yanju Li, Wenjuan Yang, Ruyi Dong, Yuebin Liang, Jia Liu, Lanyou Chen, Weiwei Wang, Binbin Ji, Geng Tian, Nanying Che, Bo Meng
Summary: This study identified and annotated the genome sequence and ARGs of the newly isolated bacterium A. faecalis PGB1.
Article
Fisheries
Shiyan Liu, Chong Han, Jingjun Huang, Qiaoying Zhu, Dingrui Liu, Linqiang Han, Shuisheng Li, Guifeng Li, Haoran Lin, Yong Zhang
Summary: Four X chromosome-specific markers were identified and validated by genome sequencing and PCR, promoting the development of all-male breeding of mandarin fish.
Article
Biochemistry & Molecular Biology
Matteo Martina, Alberto Acquadro, Lorenzo Barchi, Davide Gulino, Fabio Brusco, Mario Rabaglio, Flavio Portis, Ezio Portis, Sergio Lanteri
Summary: This study obtained the first draft genome of Anemone coronaria and developed a set of microsatellite markers specific for this species. The results of this study provide valuable tools for Breeding Rights disputes, breeding strategies, and phylogenetic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Infectious Diseases
Irene Bianconi, Richard Aschbacher, Elisabetta Pagani
Summary: Recent advancements in sequencing technology and data analytics have revolutionized pathogen detection and typing, making the process faster and more cost-effective. Genomic analysis is becoming the standard for pathogen analysis and control, providing insights into pathogen epidemiology and antimicrobial resistance. Integrated genomic data can accurately predict resistance phenotypes and aid in the investigation and control of hospital outbreaks. When combined with epidemiological data, genomic data can provide profound insights into the evolution and genetic relationships of antimicrobial resistance in pathogens, hosts, and the environment.
Article
Fisheries
N. Kareem, E. Yates, M. Skidmore, D. Hoole
FISH & SHELLFISH IMMUNOLOGY
(2018)
Article
Biochemistry & Molecular Biology
T. Olivier Amoussou, Issaka Youssao Abdou Karim, Guiguigbaza-Kossigan Dayo, Ibrahim Imorou Toko, Modou Sere, Antoine Chikou, Aboubacar Toguyeni
MOLECULAR BIOLOGY REPORTS
(2018)
Meeting Abstract
Toxicology
N. L. Guedegba, I. Imorou Toko, P. T. Agbohessi, N. Oreins, L. Francois, O. Palluel, S. N. M. Mandiki, J. -M. Porcher, B. Schiffers, M. -L. Scippo, P. Kestemont
TOXICOLOGY LETTERS
(2018)
Article
Environmental Sciences
Berny's G. Y. M. Zoumenou, Martin P. Aina, Ibrahim Imorou Toko, Ahmed Igout, Caroline Douny, Francois Brose, Bruno Schiffers, Ibrachi Gouda, Kisito Chabi Sika, Patrick Kestemont, Marie-Louise Scippo
BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
(2019)
Article
Environmental Sciences
Nicresse L. Guedegba, Ibrahim Imorou Toko, Prudencio T. Agbohessi, Berny's Zoumenou, Caroline Douny, Syaghalirwa N. M. Mandiki, Bruno Schiffers, Marie-Louise Scippo, Patrick Kestemont
JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART B-PESTICIDES FOOD CONTAMINANTS AND AGRICULTURAL WASTES
(2019)
Article
Environmental Sciences
Nicresse Lea Guedegba, Ibrahim Imorou Toko, Imen Ben Ammar, Loic Francois, Noelle Oreins, Olivier Palluel, Syaghalirwa N. M. Mandiki, Thierry Jauniaux, Jean-Marc Porcher, Marie-Louise Scippo, Patrick Kestemont
Summary: The study revealed that exposure to Acer 35 EC affects biomarkers and physiological functions in Nile tilapia juveniles, including reduced cholinesterase activity in muscles, intercellular superoxide anion production in both sexes, and disruption of female steroidogenesis and gametogenesis.
Article
Agriculture, Dairy & Animal Science
Rodrigue O. E. Pelebe, Ibrahim Imorou Toko, Issa N. Ouattara, Ulbad P. Tougan, Eloi Y. Attakpa, Jean Fall, Elie Montchowui
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2020)
Article
Environmental Sciences
Caroline Douny, Y. M. Berny's G. Zoumenou, Martin Aina, Ibrahim Imorou Toko, Ahmed Igout, Lea Guedegba, Sika K. Chabi, Patrick Kestemont, Marie-Louise Scippo
Summary: In Northern Benin, insecticide residues were detected in water, sediments, and fish samples, with organochlorine pesticides being the primary contaminants. Although estimated daily intakes were below acceptable levels for consumers in the North of Benin, the presence of multiple pesticide residues in a single fish sample indicates a potential risk due to exposure to pesticide mixtures.
ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
(2021)
Article
Biodiversity Conservation
Rodrigue Orobiyi Edeya Pelebe, Ibrahim Imorou Toko, Erik Verheyen, Maarten Van Steenberge
Summary: The study revealed that the population of Sarotherodon melanotheron in the Atchakpa reservoir may have resulted from a natural range extension within Benin. The subspecies S. m. melanotheron has also been previously introduced in the Philippines. Further research is necessary to investigate the socioeconomic, ecological, and environmental impacts of this species in the reservoir.
Article
Environmental Sciences
Nicresse Lea Guedegba, Imen Ben Ammar, Alexis Houndji, Ibrahim Imorou Toko, Lara Van De Merckt, Prudencio Tachegnon Agbohessi, Syaghalirwa N. M. Mandiki, Marie-Louise Scippo, Patrick Kestemont
Summary: An in-situ study combined with an integrated biomarker response was conducted to evaluate the impact of agricultural effluents on the physiological responses of Nile tilapia in North Benin. The results showed that the Batran water reservoir was more harmful to fish than the Songhai reservoir, with higher levels of pesticide contamination depressing immune and reproductive functions. Additionally, the study found that fish contact with sediments in enclosures exacerbated the pesticide burden on fish.
Article
Agronomy
Abdoul-Ibrachi Gouda, Mahodjegbe Hermas Luc Mehoba, Ibrahim Imorou Toko, Marie-Louise Scippo, Patrick Kestemont, Bruno Schiffers
BIOTECHNOLOGIE AGRONOMIE SOCIETE ET ENVIRONNEMENT
(2018)