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https://www.readbyqxmd.com/read/29132312/genomic-analysis-of-endemic-clones-of-toxigenic-and-non-toxigenic-corynebacterium-diphtheriae-in-belarus-during-and-after-the-major-epidemic-in-1990s
#1
Steffen Grosse-Kock, Valentina Kolodkina, Edward C Schwalbe, Jochen Blom, Andreas Burkovski, Paul A Hoskisson, Sylvain Brisse, Darren Smith, Iain C Sutcliffe, Leonid Titov, Vartul Sangal
BACKGROUND: Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. In this study, we analysed the genome sequences of a collection of 93 C. diphtheriae strains collected during and after this outbreak (1996 - 2014) in a former Soviet State, Belarus to understand the evolutionary dynamics and virulence capacities of these strains...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29123983/evaluation-of-sox2-binding-affinities-for-distinct-dna-patterns-using-steered-molecular-dynamics-simulation
#2
Dhanusha Yesudhas, Muhammad Ayaz Anwar, Suresh Panneerselvam, Han-Kyul Kim, Sangdun Choi
Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence-specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF-binding pattern in DNA. Sox2 recognizes a 6- to 7-base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2-DNA during simulation to study the behavior of a complex under nonequilibrium conditions...
November 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29109707/genomic-comparisons-reveal-microevolutionary-differences-in-mycobacterium-abscessus-subspecies
#3
Joon L Tan, Kee P Ng, Chia S Ong, Yun F Ngeow
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29109227/the-impact-of-recombination-on-human-mutation-load-and-disease
#4
REVIEW
Isabel Alves, Armande Ang Houle, Julie G Hussin, Philip Awadalla
Recombination promotes genomic integrity among cells and tissues through double-strand break repair, and is critical for gamete formation and fertility through a strict regulation of the molecular mechanisms associated with proper chromosomal disjunction. In humans, congenital defects and recurrent structural abnormalities can be attributed to aberrant meiotic recombination. Moreover, mutations affecting genes involved in recombination pathways are directly linked to pathologies including infertility and cancer...
December 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29109226/the-red-queen-model-of-recombination-hot-spot-evolution-a-theoretical-investigation
#5
Thibault Latrille, Laurent Duret, Nicolas Lartillot
In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs...
December 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29099333/tezacaftor-ivacaftor-in-residual-function-heterozygotes-with-cystic-fibrosis
#6
Steven M Rowe, Cori Daines, Felix C Ringshausen, Eitan Kerem, John Wilson, Elizabeth Tullis, Nitin Nair, Christopher Simard, Linda Han, Edward P Ingenito, Charlotte McKee, Julie Lekstrom-Himes, Jane C Davies
Background Cystic fibrosis is an autosomal recessive disease caused by mutations in the CFTR gene that lead to progressive respiratory decline. Some mutant CFTR proteins show residual function and respond to the CFTR potentiator ivacaftor in vitro, whereas ivacaftor alone does not restore activity to Phe508del mutant CFTR. Methods We conducted a randomized, double-blind, placebo-controlled, phase 3, crossover trial to evaluate the efficacy and safety of ivacaftor alone or in combination with tezacaftor, a CFTR corrector, in 248 patients 12 years of age or older who had cystic fibrosis and were heterozygous for the Phe508del mutation and a CFTR mutation associated with residual CFTR function...
November 3, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/29099062/mutational-biases-and-gc-biased-gene-conversion-affect-gc-content-in-the-plastomes-of-dendrobium-genus
#7
Zhitao Niu, Qingyun Xue, Hui Wang, Xuezhu Xie, Shuying Zhu, Wei Liu, Xiaoyu Ding
The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus...
November 2, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29096703/regulatory-and-evolutionary-signatures-of-sex-biased-genes-on-both-the-x-chromosome-and-the-autosomes
#8
Jiangshan J Shen, Ting-You Wang, Wanling Yang
BACKGROUND: Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. METHODS: In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs)...
November 2, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/29093449/abnormal-contractility-in-human-heart-myofibrils-from-patients-with-dilated-cardiomyopathy-due-to-mutations-in-ttn-and-contractile-protein-genes
#9
Petr G Vikhorev, Natalia Smoktunowicz, Alex B Munster, O'Neal Copeland, Sawa Kostin, Cecile Montgiraud, Andrew E Messer, Mohammad R Toliat, Amy Li, Cristobal G Dos Remedios, Sean Lal, Cheavar A Blair, Kenneth S Campbell, Maya Guglin, Ralph Knoll, Steven B Marston
Dilated cardiomyopathy (DCM) is an important cause of heart failure. Single gene mutations in at least 50 genes have been proposed to account for 25-50% of DCM cases and up to 25% of inherited DCM has been attributed to truncating mutations in the sarcomeric structural protein titin (TTNtv). Whilst the primary molecular mechanism of some DCM-associated mutations in the contractile apparatus has been studied in vitro and in transgenic mice, the contractile defect in human heart muscle has not been studied. In this study we isolated cardiac myofibrils from 3 TTNtv mutants, and 3 with contractile protein mutations (TNNI3 K36Q, TNNC1 G159D and MYH7 E1426K) and measured their contractility and passive stiffness in comparison with donor heart muscle as a control...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089018/rapid-turnover-of-effectors-in-grass-powdery-mildew-blumeria-graminis
#10
Fabrizio Menardo, Coraline R Praz, Thomas Wicker, Beat Keller
BACKGROUND: Grass powdery mildew (Blumeria graminis, Ascomycota) is a major pathogen of cereal crops and has become a model organism for obligate biotrophic fungal pathogens of plants. The sequenced genomes of two formae speciales (ff.spp.), B.g. hordei and B.g. tritici (pathogens of barley and wheat), were found to be enriched in candidate effector genes (CEGs). Similar to other filamentous pathogens, CEGs in B. graminis are under positive selection. Additionally, effectors are more likely to have presence-absence polymorphisms than other genes among different strains...
October 31, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29074702/respiratory-consequences-of-targeted-losses-of-hoxa5-gene-function-in-mice
#11
Kim Landry-Truchon, Stéphanie Fournier, Nicolas Houde, Jean-Philippe Rousseau, Lucie Jeannotte, Richard Kinkead
Fetal development of the respiratory tract and diaphragm requires strict coordination between genetically controlled signals and mechanical forces produced by the neural network that generates breathing. Being expressed in the mesenchyme of trachea, lung and diaphragm, and in phrenic motoneurons HOXA5 is a key transcription factor regulating lung development and function. Consequently, most Hoxa5(-/-) mutants die at birth from respiratory failure. However, the extensive effect of the null mutation makes it difficult to identify the origins of respiratory dysfunction in newborns...
October 26, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29070483/research-progress-of-myosin-heavy-chain-genes-in-human-genetic-diseases
#12
Yi-Min He, Ming-Min Gu
Myosins constitute a large superfamily proteins, which convert chemical energy, through ATP hydrolysis, to mechanical force for diverse cellular movements, such as cell migration and muscle contraction. The class Ⅱ myosin forms the filaments in muscle and non-muscle cells as a hexameric protein complex, consisting of two myosin heavy chain (MyHC) subunits and two pairs of non-identical light chain subunits. There are several MyHC isoforms encoded by different genes of the MYH family in humans. At present, distinct mutations in different genes of the MYH family are associated with various human genetic diseases...
October 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29062102/arrhythmogenic-cardiomyopathy-related-dsg2-mutations-affect-desmosomal-cadherin-binding-kinetics
#13
Mareike Dieding, Jana Davina Debus, Raimund Kerkhoff, Anna Gaertner-Rommel, Volker Walhorn, Hendrik Milting, Dario Anselmetti
Cadherins are calcium dependent adhesion proteins that establish the intercellular mechanical contact by bridging the gap to adjacent cells. Desmoglein-2 (Dsg2) is a specific cadherin of the cell-cell contact in cardiac desmosomes. Mutations in the DSG2-gene are regarded to cause arrhythmogenic (right ventricular) cardiomyopathy (ARVC) which is a rare but severe heart muscle disease. The molecular pathomechanisms of the vast majority of DSG2 mutations, however, are unknown. Here, we investigated the homophilic binding of wildtype Dsg2 and two mutations which are associated with ARVC...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29061997/improved-detection-of-braf-v600e-using-allele-specific-pcr-coupled-with-external-and-internal-controllers
#14
Zhao Yang, Na Zhao, Dong Chen, Kun Wei, Ning Su, Jun-Fu Huang, Han-Qing Xu, Guang-Jie Duan, Wei-Ling Fu, Qing Huang
Although traditional allele-specific PCR (tAS-PCR) is a common screening method for BRAF V600E mutations, its lower amplification specificity and mutation selectivity have limited its clinical applications. We hypothesize that these limitations are associated with the weaker specificities of allele-specific primers and the thermodynamic driving forces of DNA polymerase. We used three strategies to circumvent these limitations, namely, modifying allele-specific primers, introducing a competitive external allele-specific controller (i...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29055159/genomics-of-natural-populations-evolutionary-forces-that-establish-and-maintain-gene-arrangements-in-drosophila-pseudoobscura
#15
Zachary L Fuller, Gwilym D Haynes, Stephen Richards, Stephen W Schaeffer
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29048530/population-genomic-analysis-of-a-pitviper-reveals-microevolutionary-forces-underlying-venom-chemistry
#16
Steven D Aird, Jigyasa Arora, Agneesh Barua, Lijun Qiu, Kouki Terada, Alexander S Mikheyev
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29037158/genomic-divergence-and-cohesion-in-a-species-of-pelagic-freshwater-bacteria
#17
Matthias Hoetzinger, Martin W Hahn
BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29018970/andersen-s-syndrome-mutants-produce-a-knockdown-of-inwardly-rectifying-k-channel-in-mouse-skeletal-muscle-in-vivo
#18
Dina Simkin, Gaëlle Robin, Serena Giuliano, Ana Vukolic, Pamela Moceri, Nicolas Guy, Kay-Dietrich Wagner, Alain Lacampagne, Bruno Allard, Saïd Bendahhou
Andersen's syndrome (AS) is a rare autosomal disorder that has been defined by the triad of periodic paralysis, cardiac arrhythmia, and developmental anomalies. AS has been directly linked to over 40 different autosomal dominant negative loss-of-function mutations in the KCNJ2 gene, encoding for the tetrameric strong inward rectifying K(+) channel KIR2.1. While KIR2.1 channels have been suggested to contribute to setting the resting membrane potential (RMP) and to control the duration of the action potential (AP) in skeletal and cardiac muscle, the mechanism by which AS mutations produce such complex pathophysiological symptoms is poorly understood...
October 10, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28991908/mitochondrial-dual-coding-genes-in-trypanosoma-brucei
#19
Laura E Kirby, Donna Koslowsky
Trypanosoma brucei is transmitted between mammalian hosts by the tsetse fly. In the mammal, they are exclusively extracellular, continuously replicating within the bloodstream. During this stage, the mitochondrion lacks a functional electron transport chain (ETC). Successful transition to the fly, requires activation of the ETC and ATP synthesis via oxidative phosphorylation. This life cycle leads to a major problem: in the bloodstream, the mitochondrial genes are not under selection and are subject to genetic drift that endangers their integrity...
October 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28978154/novel-sox17-frameshift-mutations-in-endometrial-cancer-are-functionally-distinct-from-recurrent-missense-mutations
#20
Christopher J Walker, Matthew J O'Hern, Vanida A Serna, Takeshi Kurita, Mario A Miranda, Caroline E Sapp, David G Mutch, David E Cohn, Paul J Goodfellow
Extensive genomic profiling for endometrioid endometrial carcinoma (EEC) has pointed to genes and pathways important in uterine development as critical mediators of endometrial tumorigenesis. SOX17 is a developmental transcription factor necessary for proper endoderm formation that has been implicated as a tumor suppressor and shown to modulate WNT signaling. SOX17 mutation analysis in 539 primary EECs revealed frequent missense and frameshift mutations with an overall 11.5% mutation rate. More than half the mutations identified were frameshifts (32 of 62), and the hotspot missense changes, p...
September 15, 2017: Oncotarget
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