Article
Biochemistry & Molecular Biology
Lingyu Qiu, Chen Liang, Yidong Zheng, Huayu Kang, Aiyue Chen, Chunlin Chen, Xinlong Wang, Jielin Yang, Qiongfang Fang, Xinjie Hui, Yueming Hu, Zewei Chen, Ou Sha, Wei-Guo Zhu, Yejun Wang
Summary: This research systematically investigates stable expressed genes (SEGs) in humans at the single-cell level and observes their specificity in development, tissue, and cell types. The study identifies a list of 408 spatial-temporal SEGs and finds development-specific SEGs as well as tissue-specific SEGs with immune and RNA splicing functions. The research also explores the application of SEGs in cell decomposition and accurately predicts the proportions of major immune cells in peripheral blood samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Owais R. Hakiem, Syed M. A. Rizvi, Cuper Ramirez, Ming Tan
Summary: In this study, we used DNA immunoprecipitation-seq and RNA-seq analyses to investigate the role of the transcription factor Euo in Chlamydia trachomatis. We found that Euo represses late chlamydial genes and activates a subset of midcycle genes, as well as regulating its own expression. Our findings highlight the important role of Euo as a developmental regulator in C. trachomatis and demonstrate a correlative approach that can be used to study transcription factors in other pathogenic bacteria.
Article
Biochemistry & Molecular Biology
Rakan Naboulsi, Jakub Cieslak, Denis Headon, Ahmad Jouni, Juan J. Negro, Goran Andersson, Gabriella Lindgren
Summary: Gene expression differences can help understand important genetic mechanisms between phenotypic traits. Choosing an appropriate sample collection method can enhance the specificity of results. In this study, RNA-seq was performed on plucked-hair and skin biopsy samples, and cell-type enrichment was compared between the two methods using cell-specific marker genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Clinical Neurology
Ainara Elorza, Yamile Marquez, Jorge R. Cabrera, Jose Luis Sanchez-Trincado, Maria Santos-Galindo, Ivo H. Hernandez, Sara Pico, Juan Diaz-Hernandez, Ramon Garcia-Escudero, Manuel Irimia, Jose J. Lucas
Summary: Correction of mis-splicing events is a promising therapeutic approach for neurological diseases caused by splicing-affecting mutations. Next-generation RNA sequencing has enabled the investigation of global mis-splicing in diseased tissue to identify key pathogenic mis-spliced genes. Our new intersect-RNA-seq approach captures pathogenic global mis-splicing in the Huntington's disease striatum.
Article
Biotechnology & Applied Microbiology
Federico Agostini, Julian Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Summary: The study investigates the transcriptional activity of unannotated regions in the human genome, revealing that most transcripts originate from fuzzy transcription of known genes and a small portion from putative long non-coding RNA loci. The transcriptional activity and sensitivity of intergenic RNAs were validated using various methods, providing insights into their processing and degradation pathways.
Article
Biochemistry & Molecular Biology
Tiankun Hui, Hongyang Jing, Xinsheng Lai
Summary: This study identified novel proteins and pathways that may be crucial for neuromuscular junction (NMJ) development and maintenance through RNA-seq analysis of synaptic regions in diaphragm samples from newborn and adult mice. The dataset provides insights into the molecular mechanisms underlying NMJ development and the pathogenesis of NMJ disorders.
CELL AND BIOSCIENCE
(2021)
Article
Fisheries
Li-jun He, Zhen Yang, Zhao-wei Zhong, Yan Xu, Yan Feng, Zhen Ding, Hong-wei Liu, Yong-hua Jiang
Summary: The distribution of pigment cells in the fins and scales of pearlscale angelfish was observed, and genes related to skin coloration were annotated and screened. The results indicated that melanocytes were more concentrated in the tail scales, melanocytes and yellow pigment cells were mainly present in the anal fin, tail fin, and dorsal fin, and xanthophore with a few melanocytes were mainly present in the pectoral fin and abdominal fin. Through KEGG pathway enrichment analysis, it was found that tyrosine metabolism, MAPK, Wnt, and melanin production were involved in the regulation of skin coloration in C. vrolikii.
AQUACULTURE INTERNATIONAL
(2023)
Article
Cell Biology
Xuelin He, Li Liu, Baode Chen, Chao Wu
Summary: The study identified 46 cell type-specific gene clusters for 83 mouse cell types and proposed a simple method called CTSFinder to distinguish different cell types in bulk RNA-Seq samples. This method was successfully applied to various organs, different stages of mouse liver development, and long-term neural progenitor cell culture system, revealing the dynamics of different cell types.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Alexander Gerniers, Orian Bricard, Pierre Dupont
Summary: This study presents a data mining method, MicroCellClust, to identify small subpopulations of cells with highly specific expression profiles. Through controlled experiments, it is shown to achieve a high F-1 score in identifying rare subpopulations of human T cells, specific CD4 T cells from breast cancer samples, and a subpopulation related to a specific stage in the cell cycle. Additionally, three rare subpopulations in mouse embryonic stem cells are successfully identified with MicroCellClust, demonstrating its effectiveness in identifying small subsets of cells with highly specific expression profiles.
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Biotechnology & Applied Microbiology
Yao Dai, Yumeng Cao, Jens Kohler, Aiping Lu, Shaohua Xu, Haiyun Wang
Summary: This study identified OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification in cancer exosomes. A combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses is recommended for superior accuracy.
Article
Agronomy
Xiaoling Niu, Nanxin Zhai, Xinsen Yang, Meng Su, Caiyue Liu, Liu Wang, Pengzheng Qu, Wuge Liu, Qianhua Yuan, Xinwu Pei
Summary: This study identified differentially expressed genes in Shanlan upland rice through transcriptome sequencing and gene expression analysis, providing a basis for studying its drought-resistant mechanism.
Article
Fisheries
Camilla A. Santos, Sonia C. S. Andrade, Ana K. Teixeira, Flavio Farias, Ana C. Guerrelhas, Joao L. Rocha, Patricia D. Freitas
Summary: This study used RNA-seq data to analyze gene expression patterns related to growth performance and weight gain in Litopenaeus vannamei shrimp. The results show that certain genes are up-regulated in higher growth families, potentially involved in weight gain and immune response.
Article
Biochemistry & Molecular Biology
Dong Liu, Zhenzhen Hong, Lang Gui, Li Zhao, Yude Wang, Shengming Sun, Mingyou Li
Summary: In this study, PacBio RNA-seq was utilized to analyze the full-length transcriptomes of the brains and thoracic ganglia of Macrobrachium rosenbergii. The results revealed sexual dimorphism in the growth of this aquaculture prawn. Genes associated with protein processing pathways were also identified, and their regulation by multiple LncRNAs in different organs and sexes of the prawn was observed. These findings provide new theories and insights for studying the nervous system, sexual control, and growth dimorphism.
Article
Multidisciplinary Sciences
Yanshuo Chen, Yixuan Wang, Yuelong Chen, Yuqi Cheng, Yumeng Wei, Yunxiang Li, Jiuming Wang, Yingying Wei, Ting-Fung Chan, Yu Li
Summary: The authors developed TAPE, a deep learning method that connects bulk RNA-seq and single-cell RNA-seq, to analyze cell type fractions and cell-type-specific gene expression in clinical data. TAPE achieved precise deconvolution in a short time and showed better overall performance and comparable accuracy compared to popular methods. It also demonstrated robustness, speed, and the ability to provide biologically meaningful predictions across different cell types. Additionally, TAPE successfully predicted cell-type-specific gene expression profiles with biological significance in clinical data analysis.
NATURE COMMUNICATIONS
(2022)
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
Biochemistry & Molecular Biology
Maria Torres-Sanchez, Jennifer Villate, Sarah McGrath-Blaser, Ana Longo
Summary: This study examines the functional machinery driving the invasion of the pathogen Batrachochytrium dendrobatidis (Bd) in multiple hosts. Through a meta-analysis of Bd gene expression, the researchers identified plastic infection strategies of Bd in hosts with varying disease susceptibility. They also found that certain genes were differentially expressed in hosts with similar infection outcomes. The study provides insights into the eco-evolutionary dynamics of host-pathogen systems.
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)
Article
Biochemistry & Molecular Biology
Maria Torres-Sanchez, Ana Longo
Summary: The study found evolutionary pressures driven by pathogens and candidate beneficial symbionts, shaping the genetics of the host, and revealed knowledge about multipartite symbiotic relationships in amphibians.
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)
Article
Biochemical Research Methods
Hector Lorente-Martinez, Ainhoa Agorreta, Diego San Mauro
Summary: This study introduces a comprehensive and versatile workflow that provides convenience for molecular evolution research based on genomic data. The workflow involves steps such as searching and capturing gene sequences of interest, processing and purifying the sequences, generating multiple sequence alignments, selecting the best-fit model of evolution, and reconstructing a reliable phylogenetic tree.
METHODS AND PROTOCOLS
(2022)