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https://www.readbyqxmd.com/read/27919846/nucleos-t-ide-analogues-causes-hbv-s-gene-mutations-and-carcinogenesis
#1
Meng-Lan Wang, Hong Tang
BACKGROUND: The long-term use of nucleos(t)ide analogues causes drug resistance and mutations in the HBV reverse transcriptase (RT) region of the polymerase gene. The RT region overlaps the HBV surface gene (S gene) and therefore, the mutations in the RT region simultaneously modify S gene sequence. Certain mutations in the RT region bring about truncated S proteins because the corresponding changed S gene encodes a stop codon which results in the loss of a large portion of the C-terminal hydrophobic region of HBV surface protein...
December 2016: Hepatobiliary & Pancreatic Diseases International: HBPD INT
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#2
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899282/bindprofx-assessing-mutation-induced-binding-affinity-change-by-protein-interface-profiles-with-pseudo-counts
#3
Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang
Understanding how gene-level mutations affect the binding affinity of protein-protein interactions is a key issue of protein engineering. Due to the complexity of the problem, using physical force field to predict the mutation-induced binding free-energy change remains challenging. In this work, we present a renewed approach to calculate the impact of gene mutations on the binding affinity through the structure-based profiling of protein-protein interfaces, where the binding free-energy change (ΔΔG) is counted as the logarithm of relative probability of mutant amino acids over wild-type ones in the interface alignment matrix; three pseudo counts are introduced to alleviate the limit of the current interface library...
November 26, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27897175/accelerated-pseudogenization-on-the-neo-x-chromosome-in-drosophila-miranda
#4
Masafumi Nozawa, Kanako Onizuka, Mai Fujimi, Kazuho Ikeo, Takashi Gojobori
Y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes in Drosophila miranda and their autosomal orthologues in closely related species. The pseudogenization rate on the neo-X is much lower than the rate on the neo-Y, but appears to be higher than the rate on the orthologous autosome in D. pseudoobscura. Genes under less functional constraint and/or genes with male-biased expression tend to become pseudogenes on the neo-X, indicating the accumulation of slightly deleterious mutations and the feminization of the neo-X...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27891514/evidence-for-a-pathogenic-triumvirate-in-congenital-hepatic-fibrosis-in-autosomal-recessive-polycystic-kidney-disease
#5
REVIEW
Lu Jiang, Pingping Fang, James L Weemhoff, Udayan Apte, Michele T Pritchard
Autosomal recessive polycystic kidney disease (ARPKD) is a severe monogenic disorder that occurs due to mutations in the PKHD1 gene. Congenital hepatic fibrosis (CHF) associated with ARPKD is characterized by the presence of hepatic cysts derived from dilated bile ducts and a robust, pericystic fibrosis. Cyst growth, due to cyst wall epithelial cell hyperproliferation and fluid secretion, is thought to be the driving force behind disease progression. Liver fibrosis is a wound healing response in which collagen accumulates in the liver due to an imbalance between extracellular matrix synthesis and degradation...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27886338/frequency-of-the-val1016ile-mutation-on-the-kdr-gene-in-aedes-aegypti-diptera-culicidae-in-south-brazil
#6
M L Collet, C Frizzo, E Orlandin, L D P Rona, J C Nascimento, M A E Montano, G A Müller, G Wagner
Recently, the number of Aedes aegypti foci has increased in west of Santa Catarina, south Brazil, which has increased concern regarding mosquito-borne disease outbreaks such as dengue fever, Zika virus, and chikungunya. Therefore, it is important to monitor genetic resistance to insecticides through "knockdown resistance". Homozygosity (Ile/Ile) at position 1016 in the coding region of a voltage-dependent sodium channel gene (Nav) may induce resistance to pyrethroid insecticides. We evaluated the frequency of these alleles in A...
November 21, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27881736/reactive-oxygen-species-drive-evolution-of-pro-biofilm-variants-in-pathogens-by-modulating-cyclic-di-gmp-levels
#7
Song Lin Chua, Yichen Ding, Yang Liu, Zhao Cai, Jianuan Zhou, Sanjay Swarup, Daniela I Drautz-Moses, Stephan Christoph Schuster, Staffan Kjelleberg, Michael Givskov, Liang Yang
The host immune system offers a hostile environment with antimicrobials and reactive oxygen species (ROS) that are detrimental to bacterial pathogens, forcing them to adapt and evolve for survival. However, the contribution of oxidative stress to pathogen evolution remains elusive. Using an experimental evolution strategy, we show that exposure of the opportunistic pathogen Pseudomonas aeruginosa to sub-lethal hydrogen peroxide (H2O2) levels over 120 generations led to the emergence of pro-biofilm rough small colony variants (RSCVs), which could be abrogated by l-glutathione antioxidants...
November 2016: Open Biology
https://www.readbyqxmd.com/read/27872178/childhood-activity-on-progression-in-limb-girdle-muscular-dystrophy-2i
#8
Brianna N Brun, Shelley R H Mockler, Katie M Laubscher, Carrie M Stephan, Julia A Collison, M Bridget Zimmerman, Katherine D Mathews
Limb girdle muscular dystrophy 2I is a slowly progressive muscular dystrophy due to mutations in the Fukutin-related protein (FKRP) gene. Clinicians are frequently asked if physical activity is harmful for pediatric patients with limb girdle muscular dystrophy 2I. The primary objective of this study was to determine if there is a relationship between self-reported childhood activity level and motor function and respiratory function in older children and adults with limb girdle muscular dystrophy 2I. We compared retrospective self-reported middle school activity level and sport participation with age at onset of weakness, 10-meter walk test, and forced vital capacity later in life in 41 participants with FKRP mutations...
November 21, 2016: Journal of Child Neurology
https://www.readbyqxmd.com/read/27870637/calcium-homeostasis-alterations-in-a-mouse-model-of-the-dynamin-2-related-centronuclear-myopathy
#9
Bodvaël Fraysse, Pascale Guicheney, Marc Bitoun
Autosomal dominant centronuclear myopathy (CNM) is a rare congenital myopathy characterized by centrally located nuclei in muscle fibers. CNM results from mutations in the gene encoding dynamin 2 (DNM2), a large GTPase involved in endocytosis, intracellular membrane trafficking, and cytoskeleton regulation. We developed a knock-in mouse model expressing the most frequent DNM2-CNM mutation; i.e. the KI-Dnm2(R465W) model. Heterozygous (HTZ) KI-Dnm2 mice progressively develop muscle atrophy, impairment of contractile properties, histopathological abnormalities, and elevated cytosolic calcium concentration...
November 15, 2016: Biology Open
https://www.readbyqxmd.com/read/27868457/the-hillary-climber-trumps-manual-testing-an-automatic-system-for-studying-drosophila-climbing
#10
Alex M Willenbrink, Margo K Gronauer, Leon F Toebben, Daniel R Kick, Madalyn Wells, Bing Zhang
Climbing or negative geotaxis is an innate behavior of the fruit fly Drosophila melanogaster. There has been considerable interest in using this simple behavior to gain insights into the changes in brain function associated with aging, influence of drugs, mutated genes, and human neurological disorders. At present, most climbing tests are conducted manually and there is a lack of a simple and automatic device for repeatable and quantitative analysis of fly climbing behavior. Here we present an automatic fly climbing system, named the Hillary Climber (after Sir Edmund Hillary), that can replace the human manual tapping of vials with a mechanical tapping mechanism to provide more consistent force and reduce variability between the users and trials...
November 21, 2016: Journal of Neurogenetics
https://www.readbyqxmd.com/read/27868255/regulatory-gene-mutation-a-driving-force-behind-group-a-streptococcus-strain-and-serotype-specific-variation
#11
Poulomee Sarkar, Paul Sumby
Data from multiple bacterial pathogens are consistent with regulator-encoding genes having higher mutation frequencies than the genome average. Such mutations drive both strain- and type- (e.g. serotype, haplotype) specific phenotypic heterogeneity, and may challenge public health due to the potential of variants to circumvent established treatment and/or preventative regimes. Here, using the human bacterial pathogen the group A Streptococcus (GAS; S. pyogenes) as a model organism, we review the types and regulatory-, phenotypic-, and disease-specific consequences of naturally occurring regulatory gene mutations...
November 21, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27859883/atomic-force-microscopy-and-lamins-a-review-study-towards-future-combined-investigations
#12
REVIEW
Ilaria Pecorari, Luca Puzzi, Orfeo Sbaizero
In the last decades, atomic force microscopy (AFM) underwent a rapid and stunning development, especially for studying mechanical properties of biological samples. The numerous discoveries relying to this approach, have increased the credit of AFM as a versatile tool, and potentially eligible as a diagnostic equipment. Meanwhile, it has become strikingly evident that lamins are involved on the onset and development of certain diseases, including cancer, Hutchinson-Gilford progeria syndrome, cardiovascular pathologies, and muscular dystrophy...
November 17, 2016: Microscopy Research and Technique
https://www.readbyqxmd.com/read/27852226/genomic-differentiation-among-wild-cyanophages-despite-widespread-horizontal-gene-transfer
#13
Ann C Gregory, Sergei A Solonenko, J Cesar Ignacio-Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa Dos Santos, Joshua S Weitz, Alexandra Z Worden, Tanja Woyke, Matthew B Sullivan
BACKGROUND: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27849586/origins-of-the-current-seventh-cholera-pandemic
#14
Dalong Hu, Bin Liu, Lu Feng, Peng Ding, Xi Guo, Min Wang, Boyang Cao, Peter R Reeves, Lei Wang
Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27847329/the-genetic-profile-of-susceptibility-to-infectious-diseases-in-roman-period-populations-from-central-poland
#15
Magda Lewandowska, Krystyna Jędrychowska-Dańska, Alicja Zamerska, Tomasz Płoszaj, Henryk W Witas
For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 -196 to -174 ins/del) related to susceptibility to infections in humans...
November 12, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27846237/integrated-genomics-identifies-mir-32-mcl-1-pathway-as-a-critical-driver-of-melanomagenesis-implications-for-mir-replacement-and-combination-therapy
#16
Prasun J Mishra, Pravin J Mishra, Glenn Merlino
AIMS: Cutaneous malignant melanoma is among the deadliest human cancers, broadly resistant to most clinical therapies. A majority of patients with BRAFV600E melanomas respond well to inhibitors such as vemurafenib, but all ultimately relapse. Moreover, there are no viable treatment options available for other non-BRAF melanoma subtypes in the clinic. A key to improving treatment options lies in a better understanding of mechanisms underlying melanoma progression, which are complex and heterogeneous...
2016: PloS One
https://www.readbyqxmd.com/read/27822534/long-term-evolution-of-burkholderia-multivorans-during-a-chronic-cystic-fibrosis-infection-reveals-shifting-forces-of-selection
#17
Inês N Silva, Pedro M Santos, Mário R Santos, James E A Zlosnik, David P Speert, Sean W Buskirk, Eric L Bruger, Christopher M Waters, Vaughn S Cooper, Leonilde M Moreira
Burkholderia multivorans is an opportunistic pathogen capable of causing severe disease in patients with cystic fibrosis (CF). Patients may be chronically infected for years, during which the bacterial population evolves in response to unknown forces. Here we analyze the genomic and functional evolution of a B. multivorans infection that was sequentially sampled from a CF patient over 20 years. The population diversified into at least four primary, coexisting clades with distinct evolutionary dynamics. The average substitution rate was only 2...
May 2016: MSystems
https://www.readbyqxmd.com/read/27820829/co-operation-between-polymerases-and-nucleotide-synthetases-in-the-rna-world
#18
Ye Eun Kim, Paul G Higgs
It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs (ribozymes). The two most obvious types of ribozymes are a polymerase, which uses a neighbouring strand as a template to make a complementary sequence to the template, and a nucleotide synthetase, which synthesizes monomers for use by the polymerase. When a chemical source of monomers is available, the polymerase can survive on its own. When the chemical supply of monomers is too low, nucleotide production by the synthetase is essential and the two ribozymes can only survive when they are together...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27802374/genetic-variations-leading-to-familial-dilated-cardiomyopathy
#19
REVIEW
Kae Won Cho, Jongsung Lee, Youngjo Kim
Cardiomyopathy is a major cause of death worldwide. Based on pathohistological abnormalities and clinical manifestation, cardiomyopathies are categorized into several groups: hypertrophic, dilated, restricted, arrhythmogenic right ventricular, and unclassified. Dilated cardiomyopathy, which is characterized by dilation of the left ventricle and systolic dysfunction, is the most severe and prevalent form of cardiomyopathy and usually requires heart transplantation. Its etiology remains unclear. Recent genetic studies of single gene mutations have provided significant insights into the complex processes of cardiac dysfunction...
October 2016: Molecules and Cells
https://www.readbyqxmd.com/read/27775859/tissue-selective-expression-of-a-conditionally-active-rock2-estrogen-receptor-fusion-protein
#20
Michael S Samuel, Nicola Rath, Siti F Masre, Sarah T Boyle, David A Greenhalgh, Marina Kochetkova, Sheila Bryson, David Stevenson, Michael F Olson
The serine/threonine kinases ROCK1 and ROCK2 are central mediators of actomyosin contractile force generation that act downstream of the RhoA small GTP-binding protein. As a result, they have key roles in regulating cell morphology and proliferation, and have been implicated in numerous pathological conditions and diseases including hypertension and cancer. Here we describe the generation of a gene-targeted mouse line that enables CRE-inducible expression of a conditionally-active fusion between the ROCK2 kinase domain and the hormone-binding domain of a mutated estrogen receptor (ROCK2:ER)...
October 24, 2016: Genesis: the Journal of Genetics and Development
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