Genetics gene

Thomas Badet, Daniel Croll
Plant pathogens can rapidly overcome resistance of their hosts by mutating key pathogenicity genes encoding for effectors. Pathogen adaptation is fuelled by extensive genetic variability in populations and different strains may not share the same set of genes. Recently, such an intra-specific variation in gene content became formalized as pangenomes distinguishing core genes (i.e. shared) and accessory genes (i.e. lineage or strain-specific). Across pathogens species, key effectors tend to be part of the rapidly evolving accessory genome...
May 29, 2020: Current Opinion in Plant Biology
Arnaud Beddok, Sophie Krieger, Laurent Castera, Dominique Stoppa-Lyonnet, Juliette Thariat
Fanconi anemia (FA) is a rare genetic disease that is mostly transmitted, according to a recessive model with biallelic germline alterations in one of the 22 genes of the FA pathway, or monoallelic alteration of the 23rd FA gene (RAD51). The FA pathway is implicated in interstrand DNA crosslink repair, induces genome stability, and is a potent driver of tumorigenesis. Patients with FA have a 500 to 1000-fold increased risk of developing head and neck squamous cell carcinoma (HNSCC). Patients with FA developing an HNSCC, usually have severe radiation toxicities...
May 29, 2020: Oral Oncology
Michael Schulz, Birgitta Michels, Katja Niesel, Stefan Stein, Henner Farin, Franz Rödel, Lisa Sevenich
Brain-resident microglia and bone marrow-derived macrophages represent the most abundant non-cancerous cells in the brain tumor microenvironment with critical functions in disease progression and therapeutic response. To date little is known about genetic programs that drive disease-associated phenotypes of microglia and macrophages in brain metastases. Here we used cytometric and transcriptomic analyses to define cellular and molecular changes of the myeloid compartment at distinct stages of brain metastasis and in response to radiotherapy...
May 18, 2020: IScience
Johanna C Herkert, Judith M A Verhagen, Raquel Yotti, Alireza Haghighi, Dean G Phelan, Paul A James, Natasha J Brown, Chloe Stutterd, Ivan Macciocca, Kai'En Leong, Marian L C Bulthuis, Yolande van Bever, Marjon A van Slegtenhorst, Ludolf G Boven, Amy E Roberts, Radhika Agarwal, Jonathan Seidman, Neal K Lakdawala, Francisco Fernández-Avilés, Michael A Burke, Mary Ella Pierpont, Elizabeth Braunlin, Ahmet Okay Ḉağlayan, Daniela Q C M Barge-Schaapveld, Erwin Birnie, Lennie van Osch-Gevers, Irene M van Langen, Jan D H Jongbloed, Paul J Lockhart, David J Amor, Christine E Seidman, Ingrid M B H van de Laar
INTRODUCTION: Biallelic damaging variants in ALPK3, encoding alpha-protein kinase 3, cause pediatric-onset cardiomyopathy with manifestations that are incompletely defined. METHODS AND RESULTS: We analyzed clinical manifestations of damaging biallelic ALPK3 variants in 19 pediatric patients, including nine previously published cases. Among these, 11 loss-of-function (LoF) variants, seven compound LoF and deleterious missense variants, and one homozygous deleterious missense variant were identified...
April 21, 2020: American Heart Journal
Peggy Hiu Ying Chan, Kathy Yuen Yee Chan, Catherine Mary Schooling, Lai Ling Hui, Michael Ho Ming Chan, Albert Martin Li, Robert Chi Keung Cheung, Hugh Simon Lam
BACKGROUND: Genetic variations in glutathione (GSH)-related and metallothionein (MT) genes, which are involved in producing enzymes in the methylmercury (MeHg) metabolism pathway, have been proposed as one of the reasons for the individual variability in MeHg toxicokinetics. OBJECTIVE: To investigate the impact of genetic variations in MT and GSH-related genes on the association of fish consumption with body burden of MeHg, as measured by hair Hg concentrations among young children and women of childbearing age...
May 20, 2020: Environmental Research
Joel Henrique Ellwanger, Bruna Kulmann-Leal, Valéria de Lima Kaminski, Andressa Gonçalves Rodrigues, Marcelo Alves de Souza Bragatte, José Artur Bogo Chies
The interactions between chemokine receptors and their ligands may affect susceptibility to infectious diseases as well as their clinical manifestations. These interactions mediate both the traffic of inflammatory cells and virus-associated immune responses. In the context of viral infections, the human C-C chemokine receptor type 5 (CCR5) receives great attention from the scientific community due to its role as an HIV-1 co-receptor. The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals...
May 29, 2020: Virus Research
Louise Roer, Frank Hansen, Henrik Hasman, Anette M Hammerum, Lina Maria Cavaco
The aim of the study was to investigate recurrent infections within individual patients caused by Extended-spectrum beta-lactamase and plasmid-AmpC-producing Escherichia coli (ESBL/pAmpC Ec) isolates, with more than one year interval. The national collection of ESBL/pAmpC Ec isolates collected from January 2014 through June 2017, where screened for patients with multiple isolates with more than one year between the episodes. The isolates were whole genome sequenced and analysed for resistance genes, virulence genes and MLST...
May 29, 2020: International Journal of Antimicrobial Agents
Anne-Louise Ponsonby, Christos Symeonides, Richard Saffery, Jochen F Mueller, Martin O'Hely, Peter D Sly, Nicole Wardrop, Angela Pezic, Toby Mansell, Fiona Collier, David Burgner, Kristie Thompson, Soumini Vijayasarathy, Eva J Sugeng, Terence Dwyer, Sarath Ranganathan, Peter J Anderson, Vicki Anderson, Peter Vuillermin
Prenatal phthalate chemicals may have adverse effects on brain development by various mechanisms including oxidant damage. However, birth cohort findings have been conflicting. This study aimed to (i) investigate the interplay between maternal prenatal phthalate levels, infant genetic vulnerability to oxidative stress, and child neurodevelopment and (ii) examine combined putative oxidant exposures. A population-based birth cohort of 1064 women with prenatal recruitment in Victoria, Australia. Maternal urine was collected at 36 weeks of pregnancy and phthalate metabolite concentrations measured...
May 29, 2020: Neurotoxicology
Fan Wu, Jiyoung Shim, Cheemeng Tan
The control of gene expression noise is important for improving drug treatment and the performance of synthetic biological systems. Previous work has tuned gene expression noise by changing the rate of transcription initiation, mRNA degradation, and mRNA translation. However, these methods are invasive: they require changes to the target genetic components. Here, we create an orthogonal system based on CRISPR-dCas9 to tune gene expression noise. Specifically, we modulate the gene expression noise of a reporter gene in Escherichia coli by incorporating CRISPR activation and repression (CRISPRar) simultaneously in a single cell...
June 1, 2020: Nucleic Acids Research
Jack Humphrey, Nicol Birsa, Carmelo Milioto, Martha McLaughlin, Agnieszka M Ule, David Robaldo, Andrea B Eberle, Rahel Kräuchi, Matthew Bentham, Anna-Leigh Brown, Seth Jarvis, Cristian Bodo, Maria G Garone, Anny Devoy, Gianni Soraru, Alessandro Rosa, Irene Bozzoni, Elizabeth M C Fisher, Oliver Mühlemann, Giampietro Schiavo, Marc-David Ruepp, Adrian M Isaacs, Vincent Plagnol, Pietro Fratta
Mutations in the RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease. FUS plays a role in numerous aspects of RNA metabolism, including mRNA splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterized, as most disease models have been based on overexpressing mutant FUS, which will alter RNA processing due to FUS autoregulation. We and others have recently created knockin models that overcome the overexpression problem, and have generated high depth RNA-sequencing on FUS mutants in parallel to FUS knockout, allowing us to compare mutation-induced changes to genuine loss of function...
June 1, 2020: Nucleic Acids Research
Julia B Carleton, Matthew Ginley-Hidinger, Kristofer C Berrett, Ryan M Layer, Aaron R Quinlan, Jason Gertz
The human genome encodes an order of magnitude more gene expression enhancers than promoters, suggesting that most genes are regulated by the combined action of multiple enhancers. We have previously shown that neighboring estrogen-responsive enhancers exhibit complex synergistic contributions to the production of an estrogenic transcriptional response. Here we sought to determine the molecular underpinnings of this enhancer cooperativity. We generated genetic deletions of four estrogen receptor α (ER) bound enhancers that regulate two genes and found that enhancers containing full estrogen response element (ERE) motifs control ER binding at neighboring sites, while enhancers with pre-existing histone acetylation/accessibility confer a permissible chromatin environment to the neighboring enhancers...
June 1, 2020: Nucleic Acids Research
Nicholas J Kooyers, Abigail Donofrio, Benjamin K Blackman, Liza Holeski
Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a QTL mapping experiment involving a cross between two populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs)...
June 1, 2020: Journal of Heredity
Yi Wang, Chen Wang, Mamy Jayne Nelly Rajaofera, Li Zhu, Wenbo Liu, Fucong Zheng, Weiguo Miao
Promoters are very important for transcriptional regulation and gene expression, and have become invaluable tools for genetic engineering. Owing to the characteristics of obligate biotrophs, molecular research into obligate biotrophic fungi is seriously lagging behind, and very few of their endogenous promoters have been developed. In this study, a WY7 fragment was predicted in the genome of Oidium heveae Steinmann using PromoterScan. Its promoter function was verified with transient transformations (Agrobacterium tumefaciens-mediated transformation, ATMT) in Nicotiana tabacum cv...
2020: PloS One
Jerry L Spivak, Akil Merchant, Donna M Williams, Ophelia Rogers, Wanke Zhao, Amy Duffield, Linda S Resar, Alison R Moliterno, Zhizhuang J Zhao
The myeloproliferative neoplasms, polycythemia vera, essential thrombocytosis and primary myelofibrosis are hematopoietic stem cell disorders and share driver mutations that either directly activate the thrombopoietin receptor, MPL, or activate it indirectly through gain-of-function mutations in the gene for JAK2, its cognate tyrosine kinase. Paradoxically, MPL surface expression in hematopoietic stem cells is also reduced in the myeloproliferative neoplasms due to abnormal post-translational glycosylation and premature destruction of JAK2, suggesting that the myeloproliferative neoplasms are disorders of MPL processing since MPL is the only hematopoietic growth factor receptor in hematopoietic stem cells...
2020: PloS One
Zhihui Huang, Xiaofei Liu, Aijun Ma, Xin-An Wang, Xiaoli Guo, Tingting Zhao, Jinsheng Zhang, Shuangshuang Yang, Rongjing Xu
The tumor suppressor protein, p53 plays a crucial role in protecting genetic integrity. Once activated by diverse cell stresses, p53 reversibly activates downstream target genes to regulate cell cycle and apoptosis. However, few studies have investigated the effects of thermal stress in turbot, specifically the p53 signaling pathway. In this study, the rapid amplification of cDNA ends was used to obtain a full-length cDNA of the turbot p53 gene (Sm-p53) and perform bioinformatics analysis. The results showed that the cDNA of the Sm-p53 gene was 2928 bp in length, encoded a 381 amino acid protein, with a theoretical isoelectric point of 6...
May 2020: Journal of Thermal Biology
Gernot Wolf, Alberto de Iaco, Ming-An Sun, Melania Bruno, Matthew Tinkham, Don Hoang, Apratim Mitra, Sherry Ralls, Didier Trono, Todd S Macfarlan
The Krüppel-associated box zinc finger protein (KRAB-ZFP) family diversified in mammals. The majority of human KRAB-ZFPs bind transposable elements (TEs), however, since most TEs are inactive in humans it is unclear whether KRAB-ZFPs emerged to suppress TEs. We demonstrate that many recently emerged murine KRAB-ZFPs also bind to TEs, including the active ETn, IAP, and L1 families. Using a CRISPR/Cas9-based engineering approach, we genetically deleted five large clusters of KRAB-ZFPs and demonstrate that target TEs are de-repressed, unleashing TE-encoded enhancers...
June 1, 2020: ELife
Marine Feyereisen, Jennifer Mahony, Tadhg O'Sullivan, Viktor Boer, Douwe van Sinderen
AIMS: Beer is a harsh medium for bacteria to survive, however, lactic acid bacteria (LAB) including Lactobacillus brevis have evolved the ability to grow in beer. Here, the influence of environmental factors such as low pH, ethanol or hop content was assessed. METHODS AND RESULTS: A transcriptomic analysis of two Lb. brevis beer-spoiling strains was performed comparing growth in nutritive media with or without the imposition of a stressor related to the beer environment...
June 1, 2020: Journal of Applied Microbiology
Nicole D Facompre, Pavithra Rajagopalan, Varun Sahu, Alexander T Pearson, Kathleen T Montone, Claire D James, Frederico O Gleber-Netto, Gregory S Weinstein, Jalal Jalaly, Alexander Lin, Anil K Rustgi, Hiroshi Nakagawa, Joseph A Califano, Curtis R Pickering, Elizabeth A White, Brad Windle, Iain M Morgan, Roger B Cohen, Phyllis A Gimotty, Devraj Basu
Therapeutic innovation for human papilloma virus-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) is impaired by inadequate preclinical models and absence of accurate biomarkers. This study establishes the first well-characterized panel of patient-derived xenografts (PDXs) and organoids from HPV+ HNSCCs while determining fidelity of the models to the distinguishing genetic features of this cancer type. Despite low engraftment rates, whole exome sequencing showed that PDXs retain multiple distinguishing features of HPV+ HNSCC lost in existing cell lines, including PIK3CA mutations, TRAF3 deletion, and absence of EGFR amplifications...
June 1, 2020: International Journal of Cancer. Journal International du Cancer
Denis Awany, Imane Allali, Emile R Chimusa
Despite the meteoric rise in genome-wide association studies for metabolic diseases (MetD) over the last few years, our understanding of the pathogenesis of these diseases is still far from complete. Recent developments have established that MetD arises from complex interactions between host genetics, the gut microbiome, and the environment. However, our knowledge of the genetic and microbiome components involved, and the underlying molecular mechanisms remains limited. Here, we review and summarize recent studies investigating the genetic and microbiome basis of MetD...
June 1, 2020: Human Molecular Genetics
Gabriela Waskow, Mirelen Moura de Oliveira Rodrigues, Gabriela Höher, Tor Onsten, Juliana Dal-Ri Lindenau, Marilu Fiegenbaum, Silvana Almeida
We evaluated genetic variability among the blood groups Kell (c.578C > T and c.1790T > C), Kidd (c.838A > G), Duffy (c.125A > G, c.265C > T and c.1-67T > C), Diego (c.2561C > T), MNS (c.143T > C) and Rh (c.676G > C) in Rio Grande do Sul in southern Brazil. Genetic profiling from 382 volunteer blood donors was performed through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a real-time PCR system. The sample was divided into two groups: Euro-Brazilian and Afro-Brazilian...
2020: Genetics and Molecular Biology
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