Article
Biochemical Research Methods
Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir, Aaron R. Quinlan
Summary: This study presents a new metric that combines genetic variation and splice predictions to discern whether a genetic variant leads to deleterious alternative splicing. Based on this metric, a machine learning approach called ConSpliceML is developed to accurately predict deleterious splice variants in protein-coding genes, especially in cryptic splicing regions beyond canonical splice sites.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Si Qi, Shuisen Chen, Wei Wang, Wenhan Li, Xueliang Xu, Ming Zhong, Jingwei Lin, Yueying Yu, Yongsheng Chen, Haoge Li
Summary: Research has shown that alternative splicing and duplication of MADS-box genes in maize lead to functional divergence. While Zmm16 plays a new role in flower development, the duplicated genes Zmm18/29 have not shown typical B class gene function. The study also analyzed the transcripts of these genes, examining their effects on protein-protein interactions and phylogenetic relationships.
Article
Agricultural Engineering
Yifan Jiang, Fei Chen, Aixia Song, Yiyong Zhao, Xinlu Chen, Yuan Gao, Guo Wei, Wanbo Zhang, Yaqin Guan, Jianyu Fu, Junhao Chen, Wenlei Guo, Zhengjia Wang, Tobias G. Koellner, Zhineng Li, Ning Liu, Shunzhao Sui, Liangsheng Zhang, Feng Chen
Summary: Wintersweet is a winter-blooming magnoliids species with diverse varieties, including Concolor, Patens, and Rubrum groups, with the most variation in tepal color. The genome assembly of C. praecox var. concolor revealed its relationship with eudicots and experienced two rounds of whole genome duplication. Several gene families related to floral development were expanded and retained. The identification of genes responsible for floral scent biosynthesis provides valuable insights for molecular breeding in wintersweet.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Grant W. de Jong, Keith L. Adams
Summary: Polyploidy has had a significant impact on the evolution of flowering plants. Allopolyploids, particularly Brassica napus, show extensive changes in gene expression and alternative splicing patterns when infected with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses reveal these differences and their role in enhancing the defense response against the pathogen.
Article
Gastroenterology & Hepatology
Ming Zhang, Can Chen, Zequn Lu, Yimin Cai, Yanmin Li, Fuwei Zhang, Yizhuo Liu, Shuoni Chen, Heng Zhang, Shuhui Yang, Hui Gen, Yuan Jiang, Caibo Ning, Jinyu Huang, Wenzhuo Wang, Linyun Fan, Yi Zhang, Meng Jin, Jinxin Han, Zhen Xiong, Ming Cai, Jiuyang Liu, Chaoqun Huang, Xiaojun Yang, Bin Xu, Heng Li, Bin Li, Xu Zhu, Yongchang Wei, Ying Zhu, Jianbo Tian, Xiaoping Miao
Summary: This study provides a comprehensive functional analysis of splicing quantitative trait loci (sQTLs) in cancer and specifically in colorectal cancer (CRC). The researchers identified genetic variants that control messenger RNA splicing and examined their association with CRC risk. They also conducted biological experiments to investigate the potential mechanisms of these sQTLs and target genes. The study highlights the role of sQTLs in cancer susceptibility and suggests their potential as biomarkers and therapeutic targets.
Article
Biochemistry & Molecular Biology
Lili Xiang, Xiaofen Liu, Yanna Shi, Yajing Li, Weidong Li, Fang Li, Kunsong Chen
Summary: The research found that CmbHLH2 and CmbHLH2.1 play important roles in flower color alteration in 'Jimba' chrysanthemums, with the former playing a predominant role in the process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biodiversity Conservation
Luis Santos-del-Blanco, Sanna Olsson, Katharina B. Budde, Delphine Grivet, Santiago C. Gonzalez-Martinez, Ricardo Alia, Juan J. Robledo-Arnuncio
Summary: Estimating contemporary effective population size (N-e) is crucial for genetic conservation and monitoring. However, commonly used genetic estimators may have limitations when applied to widespread forest tree populations. Factors such as genetic isolation, small and restricted samples, gene flow between populations, and overlapping generations can affect the accuracy of these estimators.
BIOLOGICAL CONSERVATION
(2022)
Article
Biochemistry & Molecular Biology
Kofi Amoah, Yun-Hua Esther Hsiao, Jae Hoon Bahn, Yiwei Sun, Christina Burghard, Boon Xin Tan, Ei-Wen Yang, Xinshu Xiao
Summary: Alternative splicing is a RNA processing mechanism that affects most genes in human, and can be modulated by genetic variants. Utilizing GTEx data, the study of genetically modulated alternative splicing (GMAS) reveals that GMAS events are shared more frequently across tissues and individuals than expected by chance, indicating a genetically driven nature.
Article
Biochemistry & Molecular Biology
Yukihiro Kinjo, Nathan Lo, Paula Villa Martin, Gaku Tokuda, Simone Pigolotti, Thomas Bourguignon
Summary: This study identified three mechanisms leading to gene loss in the intracellular endosymbiont Blattabacterium: gene loss rates increase exponentially with the accumulation of substitutions, genes involved in vitamin and amino acid metabolism undergo relaxed selection in certain lineages, and interactions among genes result in a domino effect of gene loss within pathways.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Immunology
Elena Putscher, Michael Hecker, Brit Fitzner, Nina Boxberger, Margit Schwartz, Dirk Koczan, Peter Lorenz, Uwe Klaus Zettl
Summary: This study found that genetic variants from MS risk loci affect pre-mRNA splicing. These findings substantiate the role of alternative splicing events in the genetics of MS. Further research on how disease-causing genetic variants modify the interactions between splicing regulatory sequence elements and RNA-binding proteins can help deepen our understanding of the genetic susceptibility to MS.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
William T. Sloan, Chioma F. Nnaji, Mary Lunn, Thomas P. Curtis, Sean D. Colloms, Jillian M. Couto, Ameet J. Pinto, Stephanie Connelly, Susan J. Rosser
Summary: The structure and dynamics of microbial communities are influenced by individual events like births, deaths, speciation, and immigration, with randomness manifesting as ecological drift. Despite theoretical reasons suggesting imperceptibility of drift in large microbial communities, evidence shows its effects can be seen even in complex communities. To reconcile this contradiction, observation of dynamics in simple systems is needed to understand demographic stochasticity and the 'effective community size' required to reproduce observed dynamics in mathematical models.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Irene Novo, Noelia Perez-Pereira, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The availability of high-density markers allows the estimation of historical effective population size. Recent refinement methods have been shown to be accurate with simulation data and have been applied to real data of various species. An experimental design with Drosophila melanogaster was carried out to test the method, which showed generally good performance. The limitations of the method and its application were discussed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Xiaoli Ren, Liya Zhi, Lei Liu, Deyuan Meng, Qiannan Su, Aamana Batool, Jun Ji, Liqiang Song, Na Zhang, Lin Guo, Xigang Liu, Junming Li, Wei Zhang
Summary: The study identified five splicing variants of the G(gamma) subunit gene TaGS3 in wheat, showing different functions in regulating grain weight and size during wheat polyploidization. TaGS3.1 overexpression reduces grain weight and length, while TaGS3.5 overexpression increases them significantly. Biochemical assays revealed the interaction of TaGS3 isoforms with different proteins, suggesting a differential regulation of grain size via alternative splicing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Evolutionary Biology
Langqing Liu, Mirte Bosse, Hendrik-Jan Megens, Manon de Visser, Martien A. M. Groenen, Ole Madsen
Summary: Human disturbance and climate change have a negative impact on habitat integrity and size, leading to population decline and habitat fragmentation for wild fauna and flora. Analysis of the genomic data of the pygmy hog reveals a very small historical population size with no recent inbreeding, but evidence of harmful mutation accumulation exceeding purifying selection. Care must be taken in conservation efforts to prevent further inbreeding depression and mitigate potential environmental changes.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Ecology
Shunsuke Kanamori, Luis M. Diaz, Antonio Cadiz, Katsushi Yamaguchi, Shuji Shigenobu, Masakado Kawata
Summary: This study assembled and compared the genomes of six Cuban Anolis lizards, revealing genetic changes that occurred during their diversification, including transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The study also estimated changes in past effective population size using Pairwise Sequentially Markovian Coalescent analysis.
BMC ECOLOGY AND EVOLUTION
(2022)
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
Multidisciplinary Sciences
Androniki Psifidi, Andreas Kranis, Lisa M. Rothwell, Abi Bremner, Kay Russell, Diego Robledo, Stephen J. Bush, Mark Fife, Paul M. Hocking, Georgios Banos, David A. Hume, Jim Kaufman, Richard A. Bailey, Santiago Avendano, Kellie A. Watson, Pete Kaiser, Mark. P. Stevens
Summary: This study identified quantitative trait loci associated with Campylobacter load in commercial broilers, including on chromosomes 14, 16, 19, and 26. RNA-Seq analysis revealed differentially transcribed genes near the key QTL on chromosome 16. Strong cis-QTLs within the MHC gene region were identified, implicating pathways related to antigen presentation, immune responses, and signaling. Despite the potential for breeding selection, high frequency of resistance alleles and non-genetic factors significantly influenced Campylobacter colonization.
SCIENTIFIC REPORTS
(2021)
Review
Immunology
David A. Hume, Melanie Caruso, Sahar Keshvari, Omkar L. Patkar, Anuj Sehgal, Stephen J. Bush, Kim M. Summers, Clare Pridans, Katharine M. Irvine
Summary: The laboratory rat remains a preferred model for studies in physiology, behavior, and complex human diseases, with the mononuclear phagocyte system playing a crucial role in regulating various bodily functions. Recruitment and proliferation of MPS cells are essential in the initiation and resolution of inflammation. Despite most knowledge in MPS biology originating from studies of inbred mice, advances in technology have made the rat model increasingly valuable.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Neurosciences
Omkar L. Patkar, Melanie Caruso, Ngari Teakle, Sahar Keshvari, Stephen J. Bush, Clare Pridans, Arnauld Belmer, Kim M. Summers, Katharine M. Irvine, David A. Hume
Summary: Mutations in the human CSF1R gene have been associated with neurodegenerative diseases. Results from rat models with Csf1r mutations show reduced fiber tracts and microglial markers, with minimal impact on other neuronal markers. Defects in dendritic arborization and expression of specific neural cell adhesion molecules were also observed. These findings suggest that microglia may play a significant role in brain development, while CSF1R haploinsufficiency is unlikely to cause leukoencephalopathy.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Genetics & Heredity
Sahar Keshvari, Melanie Caruso, Ngari Teakle, Lena Batoon, Anuj Sehgal, Omkar L. Patkar, Michelle Ferrari-Cestari, Cameron E. Snell, Chen Chen, Alex Stevenson, Felicity M. Davis, Stephen J. Bush, Clare Pridans, Kim M. Summers, Allison R. Pettit, Katharine M. Irvine, David A. Hume
Summary: Homozygous mutation of the Csf1r locus leads to various postnatal developmental abnormalities in mice, rats, and humans. In a rat model, the Csf1rko allele resulted in a nearly complete loss of embryonic macrophages and affected early growth and development of multiple organs. Transfer of normal bone marrow cells rescued the mutant phenotypes, indicating the importance of tissue macrophages for normal postnatal development.
Article
Cell Biology
Iveta Gazova, Lucas Lefevre, Stephen J. Bush, Rocio Rojo, David A. Hume, Andreas Lengeling, Kim M. Summers
Summary: Mutation of the USP16 gene affects cell differentiation and proliferation, allowing cells to survive in the absence of USP16, indicating potential redundancy in the functions attributed to USP16.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Stephen J. Bush
Summary: Minimizing false positives is crucial in variant calling, and using Snippy is found to be the most direct way to achieve this. The study also highlights the issue of a disproportionate number of false calls near indels in variant calling pipelines.
MICROBIAL GENOMICS
(2021)
Article
Genetics & Heredity
Jose O. Valdebenito, Kathryn H. Maher, Gergely Zachar, Qin Huang, Zhengwang Zhang, Larry J. Young, Tamas Szekely, Pinjia Que, Yang Liu, Araxi O. Urrutia
Summary: This study investigates sex differences in the expression of immune genes in the brain of adult males and females in two wild populations of Kentish plovers breeding in different habitats. The results show a significant male-biased immune gene upregulation, and no difference in upregulation between coastal and inland populations. The study calls for further research on gene expression in wild populations to understand the implications of immune function for life histories and demography in natural systems.
Article
Biochemistry & Molecular Biology
Stephen J. Bush, Courtney J. Murren, Araxi O. Urrutia, Paula X. Kover
Summary: Selection leaves signatures in the DNA sequence of genes, but the effect these genes have on reproductive fitness is rarely quantified experimentally. Using Arabidopsis as a model, the study found that essential genes were more likely to be classified as negatively selected, but genes predicted to be positively selected did not have a significantly different effect on fitness.
Article
Biology
Alberto H. Orta, Stephen J. Bush, Mariana Gutierrez-Mariscal, Susana Castro-Obregon, Lorraine Jaimes-Hoy, Ricardo Grande, Gloria Vazquez, Elisa Gorostieta-Salas, Monica Martinez-Pacheco, Karina Diaz-Barba, Paola Cornejo-Paramo, Alejandro Sanchez-Flores, Tamas Szekely, Araxi O. Urrutia, Diego Cortez
Summary: Research showed that frequent mosaic loss of chromosome Y (LOY) observed in aging men might also be present in rats. This suggests that LOY may be a natural process in placental mammals.
COMMUNICATIONS BIOLOGY
(2021)
Article
Immunology
Bernadette C. Young, Stephen J. Bush, Sam Lipworth, Sophie George, Kate E. Dingle, Nick Sanderson, Alice Brankin, Timothy Walker, Srilakshmi Sharma, James Leong, Puneet Plaha, Monika Hofer, Peter Chiodini, B. Gottstein, Lavinia Furrer, Derrick Crook, Andrew Brent
Summary: Direct pathogen DNA sequencing offers flexible solutions for diagnosis of difficult pathogens, as demonstrated in this study where infections with mycobacteria (leprosy) and parasites (coenurosis) were diagnosed by sequencing directly from tissue.
OPEN FORUM INFECTIOUS DISEASES
(2022)
Review
Endocrinology & Metabolism
Kim M. Summers, Stephen J. Bush, Margaret R. Davis, David A. Hume, Sahar Keshvari, Jennifer A. West
Summary: Fibrillin-1 serves as a component of extracellular microfibrils and plays a role in connective tissues' elasticity. It has been found that a peptide derived from fibrillin-1, called asprosin, functions as a glucogenic hormone during fasting and stimulates appetite in the hypothalamus. Asprosin levels are associated with metabolic syndrome-related pathologies. The relationship between the generation of asprosin and the expression of fibrillin-1 protein needs further exploration.
MOLECULAR GENETICS AND METABOLISM
(2023)
Article
Multidisciplinary Sciences
Marie Bernkopf, Ummi B. Abdullah, Stephen J. Bush, Katherine A. Wood, Sahar Ghaffari, Eleni Giannoulatou, Nils Koelling, Geoffrey J. Maher, Loic M. Thibaut, Jonathan Williams, Edward M. Blair, Fiona Blanco Kelly, Angela Bloss, Emma Burkitt-Wright, Natalie Canham, Alexander T. Deng, Abhijit Dixit, Jacqueline Eason, Frances Elmslie, Alice Gardham, Eleanor Hay, Muriel Holder, Tessa Homfray, Jane A. Hurst, Diana Johnson, Wendy D. Jones, Usha Kini, Emma Kivuva, Ajith Kumar, Melissa M. Lees, Harry G. Leitch, Jenny E. V. Morton, Andrea H. Nemeth, Shwetha Ramachandrappa, Katherine Saunders, Deborah J. Shears, Lucy Side, Miranda Splitt, Alison Stewart, Helen Stewart, Mohnish Suri, Penny Clouston, Robert W. Davies, Andrew O. M. Wilkie, Anne Goriely
Summary: This study presents a systematic approach to providing individualized recurrence risk, which can stratify most couples into seven discrete categories associated with substantially different risks to future offspring. It offers the prospect of driving a major transformation in the practice of genetic counselling.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Kim M. Summers, Stephen J. Bush, Chunlei Wu, David A. Hume
Summary: The researchers generated a comprehensive rat transcriptomic atlas by curating and downloading a large number of rat RNA-seq datasets. Through gene co-expression network analysis, they identified tissue and cell type specific transcript clusters and found transcription factors associated with lineage determination. The atlas provides a valuable resource for analyzing the transcriptomes of unexplored cell types and tissues.
NAR GENOMICS AND BIOINFORMATICS
(2022)