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https://www.readbyqxmd.com/read/28720700/hitchhiking-and-epistasis-give-rise-to-cohort-dynamics-in-adapting-populations
#1
Sean W Buskirk, Ryan Emily Peace, Gregory I Lang
Beneficial mutations are the driving force of adaptive evolution. In asexual populations, the identification of beneficial alleles is confounded by the presence of genetically linked hitchhiker mutations. Parallel evolution experiments enable the recognition of common targets of selection; yet these targets are inherently enriched for genes of large target size and mutations of large effect. A comprehensive study of individual mutations is necessary to create a realistic picture of the evolutionarily significant spectrum of beneficial mutations...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28714588/cellular-force-assay-detects-altered-contractility-caused-by-a-nephritis-associated-mutation-in-nonmuscle-myosin-iia
#2
Shota P Fukuda, Tsubasa S Matsui, Takafumi Ichikawa, Taichi Furukawa, Noriyuki Kioka, Shuichiro Fukushima, Shinji Deguchi
Recent progress in understanding the essential roles of mechanical forces in regulating various cellular processes expands the field of biology to one where interdisciplinary approaches with engineering techniques become indispensable. Contractile forces or contractility-inherently present in proliferative cells due to the activity of ubiquitous nonmuscle myosin II (NMII)-are one of such mechano-regulators, but because NMII works downstream of diverse signaling pathways, it is often difficult to predict how the inherent cellular forces change upon perturbations to particular molecules...
July 17, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/28701314/cux1-promotes-cell-proliferation-and-polycystic-kidney-disease-progression-in-an-adpkd-mouse-model
#3
Binu Porath, Safia Livingston, Erica L Andres, Alexandra M Petrie, Joshua C Wright, Anna E Woo, Carol G Carlton, Richard Baybutt, Gregory B Vanden Heuvel
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common monogenic hereditary disorders in humans characterized by fluid-filled cysts, primarily in the kidneys. Cux1, a cell cycle regulatory gene highly expressed during kidney development, is elevated in the cyst-lining cells of Pkd1 mutant mice, and in human ADPKD cells. However, forced expression of Cux1 is insufficient to induce cystic disease in transgenic mice, or to induce rapid cyst formation after cilia disruption in the kidneys of adult mice...
July 12, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28699086/estimating-direct-cost-of-cystic-fibrosis-care-using-irish-registry-healthcare-resource-utilisation-data-2008-2012
#4
Abaigeal D Jackson, Andrew L Jackson, Godfrey Fletcher, Gerardine Doyle, Mary Harrington, Shijun Zhou, Fiona Cullinane, Charles Gallagher, Edward McKone
BACKGROUND: Understanding the determinants of cost of cystic fibrosis (CF) care and health outcomes may be useful for financial planning for the delivery of CF services. Registries contain information otherwise unavailable to healthcare activity/cost monitoring systems. We estimated the direct medical cost of CF care using registry data and examined how cost was affected by patient characteristics and CF gene (CF Transmembrane Conductance Regulator [CFTR]) mutation. METHODS: Healthcare resource utilisation data (2008-2012) were obtained for CF patients enrolled with the Irish CF Registry by 2013 from linked registry and national hospitalisation database records...
July 11, 2017: PharmacoEconomics
https://www.readbyqxmd.com/read/28698407/ccctc-binding-factor-inhibits-breast-cancer-cell-proliferation-and-metastasis-via-inactivation-of-the-nuclear-factor-kappab-pathway
#5
Jie Wu, Peng-Chang Li, Jun-Yi Pang, Guo-You Liu, Xue-Min Xie, Jia-Yao Li, Yi-Cong Yin, Jian-Hua Han, Xiu-Zhi Guo, Ling Qiu
CCCTC-binding factor (CTCF) is an important epigenetic regulator implicated in multiple cellular processes, including growth, proliferation, differentiation, and apoptosis. Although CTCF deletion or mutation has been associated with human breast cancer, the role of CTCF in breast cancer is questionable. We investigated the biological functions of CTCF in breast cancer and the underlying mechanism. The results showed that CTCF expression in human breast cancer cells and tissues was significantly lower than that in normal breast cells and tissues...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28696257/transient-and-dynamic-dna-supercoiling-potently-stimulates-the-leu-500-promoter-in-escherichia-coli
#6
Xiaoduo Zhi, Samantha Dages, Kelley Dages, Yingting Liu, Zi-Chun Hua, John Makemson, Fenfei Leng
The inactive prokaryotic leu-500 promoter (Pleu-500) contains a single A-to-G point mutation in the -10 region of the leucine operon promoter, which causes leucine auxotrophy. This promoter can be activated by (-) DNA supercoiling in Escherichia coli topA strains. However, whether this activation arises from global, permanent or transient, dynamic supercoiling is still not fully understood. In this article, using a newly established in vivo system carrying a pair of divergently coupled promoters, i.e., an IPTG-inducible promoter and Pleu-500 that control the expression of lacZ and luc (the firefly luciferase gene) respectively, we demonstrate that transient, dynamic (-) DNA supercoiling provided by divergent transcription in both wild-type and topA strains can potently activate Pleu-500...
July 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28690787/the-effects-of-historical-fragmentation-on-major-histocompatibility-complex-class-ii-%C3%AE-and-microsatellite-variation-in-the-aegean-island-reptile-podarcis-erhardii
#7
Trent Santonastaso, Jackie Lighten, Cock van Oosterhout, Kenneth L Jones, Johannes Foufopoulos, Nicola M Anthony
The major histocompatibility complex (MHC) plays a key role in disease resistance and is the most polymorphic gene region in vertebrates. Although habitat fragmentation is predicted to lead to a loss in MHC variation through drift, the impact of other evolutionary forces may counter this effect. Here we assess the impact of selection, drift, migration, and recombination on MHC class II and microsatellite variability in 14 island populations of the Aegean wall lizard Podarcis erhardii. Lizards were sampled from islands within the Cyclades (Greece) formed by rising sea levels as the last glacial maximum approximately 20,000 before present...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28689197/nkl-homeobox-gene-msx1-acts-like-a-tumor-suppressor-in-nk-cell-leukemia
#8
Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Maren Kaufmann, Roderick A F MacLeod, Hans G Drexler
NKL homeobox gene MSX1 is physiologically expressed in lymphoid progenitors and subsequently downregulated in developing T- and B-cells. In contrast, elevated expression levels of MSX1 persist in mature natural killer (NK)-cells, indicating a functional role in this compartment. While T-cell acute lymphoblastic leukemia (T-ALL) subsets exhibit aberrant overexpression of MSX1, we show here that in malignant NK-cells the level of MSX1 transcripts is aberrantly downregulated. Chromosomal deletions at 4p16 hosting the MSX1 locus have been described in NK-cell leukemia patients...
June 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28659438/linker-proteins-restore-basement-membrane-and-correct-lama2-related-muscular-dystrophy-in-mice
#9
Judith R Reinhard, Shuo Lin, Karen K McKee, Sarina Meinen, Stephanie C Crosson, Maurizio Sury, Samantha Hobbs, Geraldine Maier, Peter D Yurchenco, Markus A Rüegg
LAMA2-related muscular dystrophy (LAMA2 MD or MDC1A) is the most frequent form of early-onset, fatal congenital muscular dystrophies. It is caused by mutations in LAMA2, the gene encoding laminin-α2, the long arm of the heterotrimeric (α2, β1, and γ1) basement membrane protein laminin-211 (Lm-211). We establish that despite compensatory expression of laminin-α4, giving rise to Lm-411 (α4, β1, and γ1), muscle basement membrane is labile in LAMA2 MD biopsies. Consistent with this deficit, recombinant Lm-411 polymerized and bound to cultured myotubes only weakly...
June 28, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28652603/skeletal-dysplasia-mutations-effect-on-human-filamins-structure-and-mechanosensing
#10
Jonne Seppälä, Rafael C Bernardi, Tatu J K Haataja, Maarit Hellman, Olli T Pentikäinen, Klaus Schulten, Perttu Permi, Jari Ylänne, Ulla Pentikäinen
Cells' ability to sense mechanical cues in their environment is crucial for fundamental cellular processes, leading defects in mechanosensing to be linked to many diseases. The actin cross-linking protein Filamin has an important role in the conversion of mechanical forces into biochemical signals. Here, we reveal how mutations in Filamin genes known to cause Larsen syndrome and Frontometaphyseal dysplasia can affect the structure and therefore function of Filamin domains 16 and 17. Employing X-ray crystallography, the structure of these domains was first solved for the human Filamin B...
June 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28652417/k-ras-mutations-as-the-earliest-driving-force-in-a-subset-of-colorectal-carcinomas
#11
REVIEW
Nikolaos Margetis, Myrsini Kouloukoussa, Kyriaki Pavlou, Spyridon Vrakas, Theodoros Mariolis-Sapsakos
K-ras oncogene is a key factor in colorectal cancer. Based on published and our data we propose that K-ras could be the oncogene responsible for the inactivation of the tumor-suppressor gene APC, currently considered as the initial step in colorectal tumorigenesis. K-ras fulfills the criteria of the oncogene-induced DNA damage model, as it can provoke well-established causes for inactivating tumor-suppressors, i.e. DNA double-strand breaks (causing allele deletion) and ROS production (responsible for point mutation)...
July 2017: In Vivo
https://www.readbyqxmd.com/read/28646116/tonic-b-cell-receptor-signaling-in-diffuse-large-b-cell-lymphoma
#12
Ondrej Havranek, Jingda Xu, Stefan Köhrer, Zhiqiang Wang, Lisa Becker, Justin M Comer, Jared Henderson, Wencai Ma, John Man Chun Ma, Jason R Westin, Dipanjan Ghosh, Nicholas Shinners, Luhong Sun, Allen F Yi, Anusha R Karri, Jan A Burger, Tomasz Zal, R Eric Davis
We used CRISPR/Cas9-mediated genomic modification to investigate B-cell receptor (BCR) signaling in cell lines of diffuse large B-cell lymphoma (DLBCL). Three manipulations that altered BCR genes without affecting surface BCR levels showed that BCR signaling differs between the germinal center B-cell (GCB) subtype, which is insensitive to BTK inhibition by ibrutinib, and the activated B-cell (ABC) subtype. Replacing antigen-binding BCR regions had no effect on BCR signaling in GCB-DLBCL lines, reflecting this subtype's exclusive use of tonic BCR signaling...
June 23, 2017: Blood
https://www.readbyqxmd.com/read/28630351/evolutionary-radiation-of-lanthipeptides-in-marine-cyanobacteria
#13
Andres Cubillos-Ruiz, Jessie W Berta-Thompson, Jamie W Becker, Wilfred A van der Donk, Sallie W Chisholm
Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus Unlike other lanthipeptide-producing bacteria, picocyanobacteria use an unprecedented mechanism of substrate promiscuity for the production of numerous and diverse lanthipeptides using a single lanthionine synthetase. Through a cross-scale analysis of prochlorosin biosynthesis genes-from genomes to oceanic populations-we show that marine picocyanobacteria have the collective capacity to encode thousands of different cyclic peptides, few of which would display similar ring topologies...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28623921/genome-wide-analysis-of-codon-usage-bias-in-bovine-coronavirus
#14
Matías Castells, Matías Victoria, Rodney Colina, Héctor Musto, Juan Cristina
BACKGROUND: Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host's immune system and evolution. METHODS: We performed a comprehensive analysis of codon usage and composition of BCoV...
June 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/28611399/homozygous-truncating-mutation-in-nrap-gene-identified-by-whole-exome-sequencing-in-a-patient-with-dilated-cardiomyopathy
#15
Grażyna T Truszkowska, Zofia T Bilińska, Angelika Muchowicz, Agnieszka Pollak, Anna Biernacka, Katarzyna Kozar-Kamińska, Piotr Stawiński, Piotr Gasperowicz, Joanna Kosińska, Tomasz Zieliński, Rafał Płoski
The genetic background of dilated cardiomyopathy is highly heterogeneous, with close to 100 known genes and a number of candidates described to date. Nebulin-related-anchoring protein (NRAP) is an actin-binding cytoskeletal protein expressed predominantly in striated and cardiac muscles, and is involved in myofibrillar assembly in the foetal heart and in force transmission in the adult heart. The homozygous NRAP truncating variant (rs201084642), which is predicted to introduce premature stop codon into all NRAP isoforms, was revealed in the dilated cardiomyopathy patient using whole exome sequencing...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28608966/next-generation-sequencing-and-clinical-outcomes-of-patients-with-lung-adenocarcinoma-treated-with-stereotactic-body-radiotherapy
#16
Richard J Cassidy, Xinyan Zhang, Pretesh R Patel, Joseph W Shelton, Chase E Escott, Gabriel L Sica, Michael R Rossi, Charles E Hill, Conor E Steuer, Rathi N Pillai, Suresh S Ramalingam, Taofeek K Owonikoko, Madhusmita Behera, Seth D Force, Felix G Fernandez, Walter J Curran, Kristin A Higgins
BACKGROUND: Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population...
June 13, 2017: Cancer
https://www.readbyqxmd.com/read/28607159/mechanisms-of-pyocyanin-toxicity-and-genetic-determinants-of-resistance-in-staphylococcus-aureus
#17
Michael J Noto, William J Burns, William N Beavers, Eric P Skaar
Pseudomonas aeruginosa and Staphylococcus aureus are commonly isolated from polymicrobial infections, such as wound infections and chronic respiratory infections of persons with cystic fibrosis. Despite their co-isolation, P. aeruginosa produces substances toxic to S. aureus, including pyocyanin, a blue pigmented molecule that functions in P. aeruginosa virulence. Pyocyanin inhibits S. aureus respiration, forcing it to derive energy from fermentation and adopt a small colony variant (SCV) phenotype. The mechanisms by which S...
June 12, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28595038/bio-electric-field-enhancement-the-influence-on-hyaluronan-mediated-motility-receptors-in-human-breast-carcinoma
#18
Marcy C Purnell
Mechanisms that regulate cancer cell metastasis are often intricately linked to mechanisms that control cell migration in wound repair. Hyaluronan Mediated Motility Receptor (HMMR) encodes a receptor for hyaluronan-mediated motility (RHAMM), a non-integral cell surface hyaluronan receptor and intracellular protein that promotes mitotic spindle formation and cell motility. RHAMM has been found to have increased expression in both cancers and wounds, and when cancers show increased RHAMM expression poor outcomes have occurred...
April 2017: Discovery Medicine
https://www.readbyqxmd.com/read/28592659/mitochondrial-dna-3243a-g-heteroplasmy-is-associated-with-changes-in-cytoskeletal-protein-expression-and-cell-mechanics
#19
Judith Kandel, Martin Picard, Douglas C Wallace, David M Eckmann
Mitochondrial and mechanical alterations in cells have both been shown to be hallmarks of human disease. However, little research has endeavoured to establish connections between these two essential features of cells in both functional and dysfunctional situations. In this work, we hypothesized that a specific genetic alteration in mitochondrial function known to cause human disease would trigger changes in cell mechanics. Using a previously characterized set of mitochondrial cybrid cell lines, we examined the relationship between heteroplasmy for the mitochondrial DNA (mtDNA) 3243A>G mutation, the cell cytoskeleton, and resulting cellular mechanical properties...
June 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28575451/intra-and-inter-specific-variations-of-gene-expression-levels-in-yeast-are-largely-neutral
#20
Jian-Rong Yang, Calum J Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments...
May 29, 2017: Molecular Biology and Evolution
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