Article
Biochemistry & Molecular Biology
Ana Hernandez-Plaza, Damian Szklarczyk, Jorge Botas, Carlos P. Cantalapiedra, Joaquin Giner-Lamia, Daniel R. Mende, Rebecca Kirsch, Thomas Rattei, Ivica Letunic, Lars J. Jensen, Peer Bork, Christian von Mering, Jaime Huerta-Cepas
Summary: The eggNOG database is a bioinformatics resource that provides orthology data and comprehensive functional information for organisms from all domains of life. The updated version 6.0 expands the number of covered organisms to 12,535 reference species, improves functional annotations, and introduces new functionality. It offers a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels and phylogenetic trees for all OGs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Anna Vlasova, Toni Hermoso Pulido, Francisco Camara, Julia Ponomarenko, Roderic Guigo
Summary: Functional annotation is essential for enhancing the biological relevance of predicted features in genomic sequences, and improving gene structural annotation. The pipeline FA-nf, implemented in Nextflow, integrates various annotation approaches for producing multiple files and reports efficiently. It can be easily parallelized and deployed in a Linux computational environment, ensuring full reproducibility through software containerization.
Article
Multidisciplinary Sciences
Luis Martinez-Liu, Rafael Hernandez-Guerrero, Nancy Rivera-Gomez, Mario Alberto Martinez-Nunez, Pedro Escobar-Turriza, Eveline Peeters, Ernesto Perez-Rueda
Summary: The study identified similarities and differences between regulatory proteins in archaea and bacteria, including differences in TF family abundances and properties like acidity and size. Despite commonalities, regulatory proteins in archaea and bacteria have undergone divergence, as indicated by these findings.
Article
Horticulture
Juventine Boaz Odoi, Emmanuel Amponsah Adjei, Michael Teye Barnor, Richard Edema, Samson Gwali, Agyemang Danquah, Thomas Lapaka Odong, Prasad Hendre
Summary: Shea tree is a significant fruit tree crop known for its oil used in cooking and cosmetic production. This study used association mapping to identify SNP markers associated with oil yield and seed-related traits in a panel of 374 shea tree accessions. The results identified 23 significant SNP markers associated with kernel oil content, kernel length, width, and weight. Sixteen candidate genes were also identified, which are involved in various processes related to seed growth, lipid biosynthesis, and stress adaptation.
Review
Genetics & Heredity
Shinya Yamamoto, Oguz Kanca, Michael F. Wangler, Hugo J. Bellen
Summary: This Review discusses the use of non-mammalian model organisms in genetic diagnosis of rare diseases, focusing on worms, flies, and zebrafish. The strategies, technologies, and approaches to using these models are explored, as well as their potential in understanding common disease mechanisms. Non-mammalian model organisms such as fruitflies, nematode worms, and zebrafish offer a quick and cost-effective way to study the effects of gene variants, which can be further validated in mammalian models and human cells. These studies have facilitated the diagnosis of numerous rare diseases and provided insights into common disease mechanisms and gene functions.
NATURE REVIEWS GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Daniela Felicio, Miguel Alves-Ferreira, Mariana Santos, Marlene Quintas, Alexandra M. Lopes, Carolina Lemos, Nadia Pinto, Sandra Martins
Summary: This study established a workflow to prioritize the functional relevance of non-coding SNPs as susceptibility loci in polygenic neurological disorders. By annotating the overlap of selected SNPs with regulatory elements and predicting their potential impact on gene expression, this study demonstrated the applicability of the workflow in prioritizing potentially relevant non-coding SNPs in multifactorial neurological diseases.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Article
Plant Sciences
Bo Xue, Seung Y. Y. Rhee
Summary: A web application has been developed to visually display and provide access to genome function annotation data for 28 species, aiding in the understanding of gene functions. The application will be regularly updated and archived to track the progress of genome function annotation efforts. This clear and simple visualization of genome function annotation status will assist in addressing the challenge of elucidating gene functions in organisms.
Article
Biochemical Research Methods
Daniel L. Cameron, Ruining Dong, Anthony T. Papenfuss
Summary: StructuralVariantAnnotation is an R/Bioconductor package that decouples downstream analysis of structural variant breakpoints and standardizes different representations into a suitable data structure. It handles both transitive breakpoints and notation differences, providing a foundation for structural variant annotation tools.
Article
Multidisciplinary Sciences
Shalini Vasan, Divya Srivastava, David Cahill, Pushplata Prasad Singh, Alok Adholeya
Summary: Genetic components regulating AM interactions in hosts and non-hosts are not completely understood. Through transcriptomic and phylogenetic analysis, genes that differentiate AM hosts from non-hosts were identified. These genes may lead to aberrations in functionality towards AM symbiosis in non-hosts. This study lays the foundation for future research on understanding genetic differences between AM hosts and non-hosts.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Yue Gao, Xin Li, Shipeng Shang, Shuang Guo, Peng Wang, Dailin Sun, Jing Gan, Jie Sun, Yakun Zhang, Junwei Wang, Xinyue Wang, Xia Li, Yunpeng Zhang, Shangwei Ning
Summary: LincSNP 3.0 is an updated comprehensive database that focuses on documenting and annotating disease or phenotype-associated variants in human long non-coding RNAs and circular RNAs, with expanded types of variants and regulatory elements, as well as identified associations among them.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Computer Science, Software Engineering
Andres Segura-Tinoco, Ivan Cantador
Summary: This paper presents ARGAEL, an open-source desktop tool designed to facilitate the manual annotation of related arguments in text documents. ARGAEL supports the use of configurable argument models, labeling of argument components and relations, and assessment of argument annotations from multiple annotators, making it suitable for large-scale, collaborative argument annotation processes.
Article
Computer Science, Interdisciplinary Applications
Hans Friedrich Stabenau, Jonathan W. Waks
Summary: This article introduces an open-source software package called BRAVEHEART for scientific analysis of digital standard 12-lead ECGs. The software provides automatic processing of ECG and VCG signals, customizable measurements, and output of results. It aims to facilitate the development of ECG/VCG analysis and improve the reproducibility of future studies.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Genetics & Heredity
Zehra Koeksal, Claus Borsting, Leonor Gusmao, Vania Pereira
Summary: SNPtotree v1.0 is a software that can uniquely determine the hierarchical order of variants on non-recombining DNA without the need for manual sorting. The software infers the relationships between variants using pairwise comparisons and integrates the combined information into a phylogenetic tree. In benchmark testing, SNPtotree outperforms traditional methods in the accuracy of phylogenetic trees for sequencing data with high amounts of missing information.
Article
Biochemistry & Molecular Biology
Qiangwei Zhou, Sheng Cheng, Shanshan Zheng, Zhenji Wang, Pengpeng Guan, Zhixian Zhu, Xingyu Huang, Cong Zhou, Guoliang Li
Summary: The study developed a comprehensive database called ChromLoops, which integrated 1030 ChIA-PET, HiChIP, and PLAC-Seq datasets from 13 species, and documented 1,491,416,813 high-quality chromatin loops. The database provided annotations for genes and regions overlapping with chromatin loop anchors, and included rich functional annotations. Additionally, it identified genes with high-frequency chromatin interactions in different species and cancer samples.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Genetics & Heredity
James M. Alfieri, Guosong Wang, Michelle M. Jonika, Clare A. Gill, Heath Blackmon, Giridhar N. Athrey
Summary: Single-cell sequencing has revolutionized our understanding of cell diversity, organizational connections, and genotype-phenotype relationships. While most research has been focused on model organisms, applying this technology to non-model organisms can uncover new insights that are inaccessible using traditional model organisms.
Article
Biochemical Research Methods
Samuel M. Nicholls, Wayne Aubrey, Kurt De Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare
Summary: This study discusses the challenges of recovering genomic sequences from microbial communities, introducing the metagenomic individual haplotyping problem and providing software implementations for it. By extending the single individual haplotype problem to microbial communities, the authors have made progress in understanding the evolution and ecology of microbial ecosystems.
Article
Microbiology
Lucy A. Onime, Linda B. Oyama, Benjamin J. Thomas, Jurnorain Gani, Peter Alexander, Kate E. Waddams, Alan Cookson, Narcis Fernandez-Fuentes, Christopher J. Creevey, Sharon A. Huws
Summary: The study identified a potentially novel antimicrobial peptide, Lubelisin, from the rumen eukaryotic metatranscriptomic library, which exhibited killing activity against methicillin-resistant Staphylococcus aureus (MRSA) with low cytotoxicity against human and sheep erythrocytes. Membrane permeabilization assays suggested that the antimicrobial activity of Lubelisin may be due to cytoplasmic membrane damage.
Article
Biochemical Research Methods
Nicholas J. Dimonaco, Wayne Aubrey, Kim Kenobi, Amanda Clare, Christopher J. Creevey
Summary: This article presents an evaluation framework for assessing the performance of CDS prediction tools based on a comprehensive set of primary and secondary metrics. The research found that no individual tool ranked as the most accurate across all genomes or metrics analyzed, and even top-ranked tools produced conflicting gene collections.
Article
Multidisciplinary Sciences
Geoffrey N. Gobert, Donald P. McManus, Geoff McMullan, Christopher J. Creevey, Jack Carson, Malcolm K. Jones, Sujeevi S. K. Nawaratna, Kosala G. Weerakoon, Hong You
Summary: This study used FISH and microbial profiling techniques to demonstrate for the first time the presence of bacteria on the epithelial surfaces of adult schistosomes, which differ from the host blood and bile. These schistosome surface-associated bacteria are considered an important component of the host-parasite interaction.
Article
Multidisciplinary Sciences
Elizabeth H. Hart, Sarah R. Christofides, Teri E. Davies, Pauline Rees Stevens, Christopher J. Creevey, Carsten T. Mueller, Hilary J. Rogers, Alison H. Kingston-Smith
Summary: This study investigated how the plant response to climate change affects forage quality and subsequent rumen fermentation. The results indicate that breeding future forage varieties should target tolerance of acute stress rather than long term climate.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Isabela Maria Fernandes de Oliveira, Fernanda Godoy-Santos, Linda Boniface Oyama, Sofia Magalhaes Moreira, Rodrigo Goncalves Dias, Sharon Ann Huws, Christopher J. Creevey, Hilario Cuquetto Mantovani
Summary: This study characterized the genetic features of Streptococcus lutetiensis through whole-genome sequencing, revealing its antimicrobial activity and adaptation to the rumen environment. The genome of S. lutetiensis UFV80 contained a putative CRISPR-Cas9 system, while all bacterial genomes harbored genetic clusters related to the biosynthesis of bacteriocins. SDS-PAGE confirmed the predicted class II bacteriocins. These findings highlight the importance of this research.
Article
Microbiology
Katie Lawther, Fernanda Godoy Santos, Linda Boniface Oyama, Francesco Rubino, Steven Morrison, Chris J. Creevey, John W. McGrath, Sharon Ann Huws
Summary: This study reveals the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes, highlighting the significant risks to human and animal health. The analysis of a large number of samples from various countries provides a global insight into resistomes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Linda B. Oyama, Hamza Olleik, Ana Carolina Nery Teixeira, Matheus M. Guidini, James A. Pickup, Brandon Yeo Pei Hui, Nicolas Vidal, Alan R. Cookson, Hannah Vallin, Toby Wilkinson, Denise M. S. Bazzolli, Jennifer Richards, Mandy Wootton, Ralf Mikut, Kai Hilpert, Marc Maresca, Josette Perrier, Matthias Hess, Hilario C. Mantovani, Narcis Fernandez-Fuentes, Christopher J. Creevey, Sharon A. Huws
Summary: This study identified two antimicrobial peptides, HG2 and HG4, from a rumen microbiome metagenomic dataset. These peptides showed activity against methicillin-resistant Staphylococcus aureus (MRSA) strains, including anti-biofilm and anti-inflammatory activities. In addition, they demonstrated low toxicity to human cells and were effective in a mouse model of MRSA infection.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Meeting Abstract
Agriculture, Dairy & Animal Science
Mohsen Davoudkhani, Francesco Rubino, Christopher J. Creevey, Rafael Munoz-Tamayo
JOURNAL OF ANIMAL SCIENCE
(2022)
Correction
Multidisciplinary Sciences
Elizabeth H. Hart, Sarah R. Christofides, Teri E. Davies, Pauline Rees Stevens, Christopher J. Creevey, Carsten T. Muller, Hilary J. Rogers, Alison H. Kingston-Smith
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Adam J. Mulkern, Linda B. Oyama, Alan R. Cookson, Christopher J. Creevey, Toby J. Wilkinson, Hamza Olleik, Marc Maresca, Giarla C. da Silva, Patricia P. Fontes, Denise M. S. Bazzolli, Hilario C. Mantovani, Bamu F. Damaris, Luis A. J. Mur, Sharon A. Huws
Summary: This study evaluated the therapeutic potential of antimicrobial peptides (AMPs) from the rumen microbiome against Pseudomonas aeruginosa infections. All AMPs exhibited antimicrobial activity against the strains tested, with no decrease in activity. The AMPs Lynronne 1 and 2 showed efficacy in an in vivo infection model. These findings highlight the potential of microbiome-derived AMPs for the treatment of Pseudomonas aeruginosa infections.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biochemistry & Molecular Biology
Peter O. Mulhair, Charley G. P. McCarthy, Karen Siu-Ting, Christopher J. Creevey, Mary J. O'Connell
Summary: Conflicting studies have placed the Xenacoelomorpha in two different positions within the animal tree, either as the primary emerging bilaterian phylum or within Deuterostomia. Recent studies also question the monophyly of Deuterostomia. Hidden paralogy and low phylogenetic signal are challenges in reconstructing species phylogenies.
Article
Biochemistry & Molecular Biology
Charley G. P. McCarthy, Peter O. Mulhair, Karen Siu-Ting, Christopher J. Creevey, Mary J. O'Connell
Summary: There is conflicting evidence regarding whether sponges or comb jellies are at the root of the animal phylogeny, and dataset size, construction, and model fit all influence animal root inference.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Lorenzo A. Santorelli, Toby Wilkinson, Ronke Abdulmalik, Yuma Rai, Christopher J. Creevey, Sharon Huws, Jorge Gutierrez-Merino
Summary: This study investigates the bacterial communities in different beehives and finds that each hive has its own distinct microbiome, which is influenced by plants, beekeeping methods, and the bacterial communities in the surrounding environment. Therefore, the microbiome of beehives can be used as a valuable biosensor to inform the health of honeybees and their surrounding environment.
ENVIRONMENTAL MICROBIOME
(2023)
Meeting Abstract
Infectious Diseases
Lucy Dillon, Nicholas J. Dimonaco, Christopher J. Creevey
JAC-ANTIMICROBIAL RESISTANCE
(2023)