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https://www.readbyqxmd.com/read/29055159/genomics-of-natural-populations-evolutionary-forces-that-establish-and-maintain-gene-arrangements-in-drosophila-pseudoobscura
#1
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/29054934/radiation-induced-dna-damage-in-operators-performing-endovascular-aortic-repair
#2
Tamer El-Sayed, Ashish S Patel, Jun S Cho, James A Kelly, Francesca E Ludwinski, Prakash Saha, Oliver T Lyons, Alberto Smith, Bijan Modarai
Background -Radiation exposure during fluoroscopically-guided interventions such as endovascular aortic repair (EVAR) is a growing concern for operators. This study aimed to measure DNA damage/repair markers in operators perfoming EVAR. Methods -Expression of the DNA damage/repair marker, gamma-H2AX (γ-H2AX) and DNA damage response (DDR) marker, phosphorylated ataxia telangiectasia mutated (pATM), were quantified in circulating lymphocytes in operators during the peri-operative period of endovascular (infra-renal [IEVAR], branched [BEVAR] and fenestrated [FEVAR]) and open aortic repair using flow cytometry...
October 20, 2017: Circulation
https://www.readbyqxmd.com/read/29053826/induction-of-somatic-mutations-by-low-dose-x-rays-the-challenge-in-recognizing-radiation-induced-events
#3
Haruki Nagashima, Kumiko Shiraishi, Saori Ohkawa, Yuki Sakamoto, Kenshi Komatsu, Shinya Matsuura, Akira Tachibana, Hiroshi Tauchi
It is difficult to distinguish radiation-induced events from spontaneous events during induction of stochastic effects, especially in the case of low-dose or low-dose-rate exposures. By using a hypersensitive system for detecting somatic mutations at the HPRT1 locus, we investigated the frequency and spectrum of mutations induced by low-dose X-rays. The mutant frequencies induced by doses of >0.15 Gy were statistically significant when compared with the spontaneous frequency, and a clear dose dependency was also observed for mutant frequencies at doses of >0...
October 19, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/29053425/association-of-mannose-binding-lectin-rs1800450-and-tumor-necrotic-factor-%C3%AE-rs1800620-polymorphism-with-helicobacter-pylori-in-type-ii-diabetes-mellitus
#4
Elnaz Mortazavi, Behnaz Eslami, Parisa Aghahosseini, Fatemeh Ahron, Armagan Amininejad, Sepideh Mahmoodi, Hadis Satarpour, Nilofar Radmanesh, Hossein Rassi
Type II diabetes mellitus (T2DM) is the prevalent type of diabetes, including 90% of the cases world-wide. Helicobacter pylori plays a pathogenic role in the development of T2DM. The host genetic factors have a significant impact on the clinical outcome and anatomical distribution of H. pylori infection and polymorphisms in several genes such as tumor necrotic factor (TNF)-α and mannose-binding lectin (MBL) and are considered to increase the risk for the development of T2DM. In this study, we investigate the prevalence rate of H...
October 2017: Monoclonal Antibodies in Immunodiagnosis and Immunotherapy
https://www.readbyqxmd.com/read/29053361/artificial-selection-to-increase-the-phenotypic-variance-in-gmax-fails
#5
Jacqueline L Sztepanacz, Mark W Blows
Stabilizing selection is important in evolutionary theories of the maintenance of genetic variance and has been invoked as the key process determining macroevolutionary patterns of trait evolution. However, manipulative evidence for the extent of stabilizing selection, particularly on multivariate traits, is lacking. We used artificial disruptive selection in Drosophila serrata as a tool to determine the relative strength of stabilizing selection experienced by multivariate trait combinations with contrasting levels of genetic and mutational variance...
November 2017: American Naturalist
https://www.readbyqxmd.com/read/29050768/single-nucleotide-polymorphisms-in-efflux-pumps-genes-in-extensively-drug-resistant-mycobacterium-tuberculosis-isolates-from-pakistan
#6
Akbar Kanji, Rumina Hasan, Asho Ali, Ambreen Zaver, Ying Zhang, Kehkashan Imtiaz, Wanliang Shi, Taane G Clark, Ruth McNerney, Jody Phelan, Shoaib Rao, Samreen Shafiq, Zahra Hasan
It is challenging to understand mechanisms of drug resistance in Mycobacterium tuberculosis (MTB) due to the large variability in resistance associated genes. Efflux pump genes contribute to drug resistance and thus add to this complexity. Efflux pump gene protein superfamilies have been characterized by genome analysis of drug resistant strains and through in vitro transcriptional studies. However, there is limited information regarding efflux pump genes in extensively drug resistant (XDR) tuberculosis (TB) isolates...
December 2017: Tuberculosis
https://www.readbyqxmd.com/read/29050270/kit-performed-as-a-driver-gene-candidate-affecting-the-survival-status-of-patients-with-stomach-adenocarcinoma
#7
Shengli Pan, Jin Tan, Yingying Deng, Ben-Hai Wan, Xiao-Yu Zhang, Bu-Gao Guan
Stomach adenocarcinoma is estimated to cause 10,000 deaths in the US in 2016 and is the third most deadly cancer in China. We aim to identify the proteins and the genes that have impact on the prognosis of patients with stomach adenocarcinoma. Data of patients with stomach adenocarcinoma were retrieved from The Cancer Genome Atlas (TCGA). Proteins whose expression levels were highly correlated with survival status of patients were figured out. The expression levels of their mRNAs and their roles in the pathway were used to determine the driver gene candidates...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049607/dose-response-association-of-cd8-tumor-infiltrating-lymphocytes-and-survival-time-in-high-grade-serous-ovarian-cancer
#8
Ellen L Goode, Matthew S Block, Kimberly R Kalli, Robert A Vierkant, Wenqian Chen, Zachary C Fogarty, Aleksandra Gentry-Maharaj, Aleksandra Toloczko, Alexander Hein, Aliecia L Bouligny, Allan Jensen, Ana Osorio, Andreas D Hartkopf, Andy Ryan, Anita Chudecka-Glaz, Anthony M Magliocco, Arndt Hartmann, Audrey Y Jung, Bo Gao, Brenda Y Hernandez, Brooke L Fridley, Bryan M McCauley, Catherine J Kennedy, Chen Wang, Chloe Karpinskyj, Christiani B de Sousa, Daniel G Tiezzi, David L Wachter, Esther Herpel, Florin Andrei Taran, Francesmary Modugno, Gregg Nelson, Jan Lubinski, Janusz Menkiszak, Jennifer Alsop, Jenny Lester, Jesús García-Donas, Jill Nation, Jillian Hung, José Palacios, Joseph H Rothstein, Joseph L Kelley, Jurandyr M de Andrade, Luis Robles-Díaz, Maria P Intermaggio, Martin Widschwendter, Matthias W Beckmann, Matthias Ruebner, Mercedes Jimenez-Linan, Naveena Singh, Oleg Oszurek, Paul R Harnett, Peter F Rambau, Peter Sinn, Philipp Wagner, Prafull Ghatage, Raghwa Sharma, Robert P Edwards, Roberta B Ness, Sandra Orsulic, Sara Y Brucker, Sharon E Johnatty, Teri A Longacre, Ursula Eilber, Valerie McGuire, Weiva Sieh, Yanina Natanzon, Zheng Li, Alice S Whittemore, Anna deFazio, Annette Staebler, Beth Y Karlan, Blake Gilks, David D Bowtell, Estrid Høgdall, Francisco J Candido Dos Reis, Helen Steed, Ian G Campbell, Jacek Gronwald, Javier Benítez, Jennifer M Koziak, Jenny Chang-Claude, Kirsten B Moysich, Linda E Kelemen, Linda S Cook, Marc T Goodman, María José García, Peter A Fasching, Stefan Kommoss, Suha Deen, Susanne K Kjaer, Usha Menon, James D Brenton, Paul D P Pharoah, Georgia Chenevix-Trench, David G Huntsman, Stacey J Winham, Martin Köbel, Susan J Ramus
Importance: Cytotoxic CD8+ tumor-infiltrating lymphocytes (TILs) participate in immune control of epithelial ovarian cancer; however, little is known about prognostic patterns of CD8+ TILs by histotype and in relation to other clinical factors. Objective: To define the prognostic role of CD8+ TILs in epithelial ovarian cancer. Design, Setting, and Participants: This was a multicenter observational, prospective survival cohort study of the Ovarian Tumor Tissue Analysis Consortium...
October 12, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/29047188/the-predictive-value-of-brca1-2-mrna-expression-for-response-to-neoadjuvant-chemotherapy-in-brca-negative-breast-cancers
#9
Ye Xu, Tao Ouyang, Jinfeng Li, Tianfeng Wang, Zhaoqing Fan, Tie Fan, Benyao Lin, Yuntao Xie
It is well known that BRCA1 and BRCA2 play a central role in DNA repair, but the relationship between BRCA1 and BRCA2 mRNA expression and response to neoadjuvant chemotherapy in sporadic breast cancer patients has not been well established. Here, we investigate the association between BRCA1 or BRCA2 mRNA expression levels and pathological response in 674 BRCA1/2 mutation-negative breast cancer patients who received neoadjuvant chemotherapy. BRCA1and BRCA2 mRNA expression were assessed using quantitative real-time polymerase chain reaction in core biopsy breast cancer tissue obtained prior to the initiation of neoadjuvant chemotherapy...
October 19, 2017: Cancer Science
https://www.readbyqxmd.com/read/29046514/protein-phosphatase-magnesium-dependent-1%C3%AE-ppm1d-expression-as-a-prognostic-marker-in-adult-supratentorial-diffuse-astrocytic-and-oligodenroglial-tumors
#10
Hui Jeong Jeong, Chang Gok Woo, Bora Lee, Shin Kwang Khang, Soo Jeong Nam, Jene Choi
Background: Protein phosphatase magnesium-dependent 1δ (PPM1D) is a p53-induced serine/threonine phosphatase, which is overexpressed in various human cancers. A recent study reported that the mutation in the PPM1D gene is associated with poor prognosis in brainstem gliomas. In this study, we evaluate the utility of PPM1D as a prognostic biomarker of adult supratentorial diffuse astrocytic and oligodenroglial tumors. Materials and Methods: To investigate PPM1D protein expression, mRNA expression, and copy number changes, immunohistochemistry, RNAscope in situ hybridization, and fluorescence in situ hybridization in 84 adult supratentorial diffuse gliomas were performed, respectively...
October 18, 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/29046437/modulation-of-global-transcriptional-regulatory-networks-as-a-strategy-for-increasing-kanamycin-resistance-of-the-translational-elongation-factor-g-mutants-in-escherichia-coli
#11
Aalap Mogre, Reshma T V, Aswin Sai Narain Seshasayee
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we had used short term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via  different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD / cpxA / topA / cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance...
October 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29046204/-clinical-features-and-vps33b-mutations-in-a-family-affected-by-arthrogryposis-renal-dysfunction-and-cholestasis-syndrome
#12
Da-Gui Huang, Jia-Jia Liu, Li Guo, Yuan-Zong Song
Arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome is an autosomal recessive disorder caused by mutations in the VPS33B or VIPAS39 gene. The aim of this study was to investigate the clinical features and VPS33B gene mutations of an infant with ARC syndrome. A 47-day-old female infant was referred to the hospital with the complaint of jaundiced skin and sclera for 45 days and abnormal liver function for 39 days. The patient had been managed in different hospitals, but the therapeutic effects were unsatisfactory due to undetermined diagnosis...
October 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/29045954/-pulmonary-arterial-hypertension-as-leading-manifestation-of-methylmalonic-aciduria-clinical-characteristics-and-gene-testing-in-15-cases
#13
X Q Liu, H Yan, J X Qiu, C Y Zhang, J G Qi, X Zhang, H J Xiao, Y L Yang, Y H Chen, J B DU
OBJECTIVE: To deepen our understanding of Methylmalonic aciduria (MMA) associated pulmonary hypertension (PH) by analyzing the characteristics of clinical presentation, pulmonary high resolusion CT(HRCT), treatment response and gene mutation. METHODS: This study includes 15 cases of pediatric patients with MMA associated PH diagnosed and treated in Peking University First Hospital pediatric department between May 2012 and May 2016 with symptoms of PH as their leading presentation...
October 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/29043376/enhanced-rhamnolipid-production-in-burkholderia-thailandensis-transposon-knockout-strains-deficient-in-polyhydroxyalkanoate-pha-synthesis
#14
Scott J Funston, Konstantina Tsaousi, Thomas J Smyth, Matthew S Twigg, Roger Marchant, Ibrahim M Banat
Microbially produced rhamnolipids have significant commercial potential; however, the main bacterial producer, Pseudomonas aeruginosa, is an opportunistic human pathogen, which limits biotechnological exploitation. The non-pathogenic species Burkholderia thailandensis produces rhamnolipids; however, yield is relatively low. The aim of this study was to determine whether rhamnolipid production could be increased in Burkholderia thailandensis through mutation of genes responsible for the synthesis of the storage material polyhydroxyalkanoate (PHA), thereby increasing cellular resources for the production of rhamnolipids...
October 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29039873/tillf%C3%A3-rlitliga-referensintervall-kr%C3%A3-vs-f%C3%A3-r-v%C3%A3-rdering-av-p-alp-nya-pediatriska-referensintervall-f%C3%A3-r-alkaliskt-fosfatas-har-klinisk-betydelse-f%C3%A3-r-att-hitta-r%C3%A3-tt-till-diagnosen
#15
Per Magnusson
Age- and gender-specific reference intervals are pivotal to ensure appropriate interpretation of plasma alkaline phosphatase activities in the lower range Hypophosphatasia (HPP) is an inborn error of metabolism caused by loss-of-function mutations of the ALPL gene that mainly express alkaline phosphatase (ALP) in bone and liver. The clinical expression of HPP is highly variable and is classified into six different forms mainly affecting bone and tooth mineralization. The prognosis for each of these HPP forms depends upon the severity of the skeletal disease which reflects the age at presentation...
October 16, 2017: Läkartidningen
https://www.readbyqxmd.com/read/29036671/crispr-cas9-mediated-gene-knockout-is-insensitive-to-target-copy-number-but-is-dependent-on-guide-rna-potency-and-cas9-sgrna-threshold-expression-level
#16
Garmen Yuen, Fehad J Khan, Shaojian Gao, Jayne M Stommel, Eric Batchelor, Xiaolin Wu, Ji Luo
CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036491/transcription-associated-compositional-skews-in-drosophila-genes
#17
Juraj Bergman, Andrea J Betancourt, Claus Vogl
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome dataset of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared to somatic expression, consistent with the process of transcription-associated mutation bias...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036232/rare-and-common-variants-of-apob-and-pcsk9-in-korean-patients-with-extremely-low-low-density-lipoprotein-cholesterol-levels
#18
Chan Joo Lee, Yunbeom Lee, Sungha Park, Seok-Min Kang, Yangsoo Jang, Ji Hyun Lee, Sang-Hak Lee
BACKGROUND: Screening of variants, related to lipid metabolism in patients with extreme cholesterol levels, is a tool used to identify targets affecting cardiovascular outcomes. The aim of this study was to examine the prevalence and characteristics of rare and common variants of APOB and PCSK9 in Korean patients with extremely low low-density lipoprotein-cholesterol (LDL-C) levels. METHODS: Among 13,545 participants enrolled in a cardiovascular genome cohort, 22 subjects, whose LDL-C levels without lipid-lowering agents were ≤1 percentile (48 mg/dL) of Korean population, were analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/29035868/comparative-analysis-of-codon-usage-pattern-and-its-influencing-factors-in-schistosoma-japonicum-and-ascaris-suum
#19
Gulshana A Mazumder, Arif Uddin, Supriyo Chakraborty
Schistosoma japonicum and Ascaris suum are considered as the major parasites of human which cause various life threatening diseases such as schistomiasis and ascariasis. The codon usage bias (CUB) is known as the phenomenon of more usage of a specific codon than the other synonymous codons for an amino acid. The factors that influence the codon usage bias are mutation pressure, natural selection, gene expression, gene length, GC content, RNA stability, recombination rates, codon position etc. Here we had used various bioinformatic tools and statistical analyses to understand the compositional features, expression level and codon usage bias in the genes of these two species...
December 20, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/29035360/ezh2-promotes-degradation-of-stalled-replication-forks-by-recruiting-mus81-through-histone-h3-trimethylation
#20
Beatrice Rondinelli, Ewa Gogola, Hatice Yücel, Alexandra A Duarte, Marieke van de Ven, Roxanne van der Sluijs, Panagiotis A Konstantinopoulos, Jos Jonkers, Raphaël Ceccaldi, Sven Rottenberg, Alan D D'Andrea
The emergence of resistance to poly-ADP-ribose polymerase inhibitors (PARPi) poses a threat to the treatment of BRCA1 and BRCA2 (BRCA1/2)-deficient tumours. Stabilization of stalled DNA replication forks is a recently identified PARPi-resistance mechanism that promotes genomic stability in BRCA1/2-deficient cancers. Dissecting the molecular pathways controlling genomic stability at stalled forks is critical. Here we show that EZH2 localizes at stalled forks where it methylates Lys27 on histone 3 (H3K27me3), mediating recruitment of the MUS81 nuclease...
October 16, 2017: Nature Cell Biology
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