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https://www.readbyqxmd.com/read/28545270/-correlation-between-mutation-of-p53-gene-2-4-exons-from-peripheral-blood-and-hpv16-positive-cervical-cancer-susceptibility-and-clinical-significance
#1
C M Yin, Y F Yao, Z L Yan, H Y Yang
Objective: To detect mutations of p53 gene 2-4 exons from peripheral blood and to explore their relevance in HPV16-positive cervical cancer susceptibility and clinical significance. Methods: Collected firstly cases from the Third Affiliated Hospital of Kunming Medical University from October 2012 to April 2014, included 167 cases HPV16-postive cervical cancer and 160 cases HPV-negative healthy women. Genomic DNA from the host peripheral venous blood was taken, mutations of p53 gene 2-4 exons were analyzed with software DNAstar after PCR and bidirectional sequencing...
May 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28544821/predictive-model-for-high-frequency-microsatellite-instability-in-colorectal-cancer-patients-over-50%C3%A2-years-of-age
#2
Kenji Fujiyoshi, Tatsuro Yamaguchi, Miho Kakuta, Akemi Takahashi, Yoshiko Arai, Mina Yamada, Gou Yamamoto, Sachiko Ohde, Misato Takao, Shin-Ichiro Horiguchi, Soichiro Natsume, Shinsuke Kazama, Yusuke Nishizawa, Yoji Nishimura, Yoshito Akagi, Hirohiko Sakamoto, Kiwamu Akagi
Microsatellite instability (MSI) is an important biomarker for screening for Lynch syndrome, and also of response to immune checkpoint inhibitors. The aim of this study is to create a predictive model to determine which elderly patients with colorectal cancer (CRC) should undergo MSI and/or immunohistochemistry testing on the basis of clinicopathological data. We analyzed a test cohort of CRC patients aged ≥50 years (n = 2219) by multivariate logistic regression analyses to identify predictors of high-frequency MSI (MSI-H)...
May 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28542905/perfecting-prediction-of-mutational-impact-on-the-aggregation-propensity-of-the-als-associated-hnrnpa2-prion-like-protein
#3
Cristina Batlle, María Rosario Fernández, Valentin Iglesias, Salvador Ventura
An increasing number of human proteins are being found to bear a prion-like domain (PrLD) driving the formation of membraneless compartments through liquid-liquid phase separation. Point mutations in these PrLDs promote the transition to an amyloid-like state. There has been much debate on whether this aberrant aggregation is caused by compositional or sequential changes. A recent extensive mutational study of the ALS-associated prion-like hnRNPA2 protein provides a framework to discriminate the molecular determinants behind pathogenic PrLDs aggregation...
May 25, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542837/phenotype-and-natural-history-of-variant-late-infantile-ceroid-lipofuscinosis-5
#4
Alessandro Simonati, Ruth E Williams, Nardo Nardocci, Minna Laine, Roberta Battini, Angela Schulz, Barbara Garavaglia, Francesca Moro, Francesco Pezzini, Filippo M Santorelli
AIM: To characterize the phenotypic profile of a cohort of children affected with CLN5, a rare form of neuronal ceroid-lipofuscinosis (NCL), and to trace the features of the natural history of the disease. METHOD: Records of 15 children (nine males, six females) were obtained from the data sets of the DEM-CHILD International NCL Registry. Disease progression was measured by rating six functional domains at different time points along the disease course. All patients underwent mutation analysis of the CLN5 gene and ultrastructural investigations of peripheral tissues...
May 25, 2017: Developmental Medicine and Child Neurology
https://www.readbyqxmd.com/read/28542550/a-spatio-temporal-assessment-of-simian-human-immunodeficiency-virus-shiv-evolution-reveals-a-highly-dynamic-process-within-the-host
#5
Alison F Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela D M Kashuba, Brandon F Keele, Shiu-Lok Hu, Dmitri A Petrov, Pleuni S Pennings, Zandrea Ambrose
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542489/d-helix-influences-dimerization-of-the-atp-binding-cassette-abc-transporter-associated-with-antigen-processing-1-tap1-nucleotide-binding-domain
#6
Ahmet S Vakkasoglu, Sriram Srikant, Rachelle Gaudet
ATP-binding cassette (ABC) transporters form a large family of transmembrane importers and exporters. Using two nucleotide-binding domains (NBDs), which form a canonical ATP-sandwich dimer at some point within the transport cycle, the transporters harness the energy from ATP binding and hydrolysis to drive substrate transport. However the structural elements that enable and tune the dimerization propensity of the NBDs have not been fully elucidated. Here we compared the biochemical properties of the NBDs of human and rat TAP1, a subunit of the heterodimeric transporter associated with antigen processing (TAP)...
2017: PloS One
https://www.readbyqxmd.com/read/28542371/whole-genome-sequencing-of-spermatocytic-tumors-provides-insights-into-the-mutational-processes-operating-in-the-male-germline
#7
Eleni Giannoulatou, Geoffrey J Maher, Zhihao Ding, Ad J M Gillis, Lambert C J Dorssers, Alexander Hoischen, Ewa Rajpert-De Meyts, Gilean McVean, Andrew O M Wilkie, Leendert H J Looijenga, Anne Goriely
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases...
2017: PloS One
https://www.readbyqxmd.com/read/28542229/thermodynamic-framework-to-assess-low-abundance-dna-mutation-detection-by-hybridization
#8
Hanny Willems, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform...
2017: PloS One
https://www.readbyqxmd.com/read/28542170/human-mutations-in-integrator-complex-subunits-link-transcriptome-integrity-to-brain-development
#9
Renske Oegema, David Baillat, Rachel Schot, Leontine M van Unen, Alice Brooks, Sima Kheradmand Kia, A Jeannette M Hoogeboom, Zheng Xia, Wei Li, Matteo Cesaroni, Maarten H Lequin, Marjon van Slegtenhorst, William B Dobyns, Irenaeus F M de Coo, Frans W Verheijen, Andreas Kremer, Peter J van der Spek, Daphne Heijsman, Eric J Wagner, Maarten Fornerod, Grazia M S Mancini
Integrator is an RNA polymerase II (RNAPII)-associated complex that was recently identified to have a broad role in both RNA processing and transcription regulation. Importantly, its role in human development and disease is so far largely unexplored. Here, we provide evidence that biallelic Integrator Complex Subunit 1 (INTS1) and Subunit 8 (INTS8) gene mutations are associated with rare recessive human neurodevelopmental syndromes. Three unrelated individuals of Dutch ancestry showed the same homozygous truncating INTS1 mutation...
May 25, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28542039/role-of-the-uridine-cytidine-kinase-2-mutation-in-cellular-sensitiveness-toward-3-ethynylcytidine-treatment-of-human-cancer-cells
#10
Akira Sato, Takeshi Takano, Akiko Hiramoto, Tomoharu Naito, Akira Matsuda, Masakazu Fukushima, Yusuke Wataya, Hye-Sook Kim
A nucleosidic medicine, 1-(3-C-ethynyl-β-D-ribo-pentofuranosyl)cytosine [3'-ethynylcytidine (ECyd)], is a potent inhibitor of RNA polymerase I and shows anticancer activity to various human solid tumors in vitro and in vivo. ECyd is phosphorylated to 3'-ethyntlcytidine 5'-monophosphate by uridine/cytidine kinase 2 (UCK2) and subsequently further to diphosphate and triphosphate (3'-ethyntlcytidine 5'-diphosphate, 3'-ethyntlcytidine 5'-triphosphate). 3'-Ethyntlcytidine 5'-triphosphate is an active metabolite that can inhibit RNA polymerase I competitively, causing cancer cell death...
May 24, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28541743/rarevar-a-framework-for-detecting-low-frequency-single-nucleotide-variants
#11
Yangyang Hao, Xiaoling Xuei, Lang Li, Harikrishna Nakshatri, Howard J Edenberg, Yunlong Liu
Accurate identification of low-frequency somatic point mutations in tumor samples has important clinical utilities. Although high-throughput sequencing technology enables capturing such variants while sequencing primary tumor samples, our ability for accurate detection is compromised when the variant frequency is close to the sequencer error rate. Most current experimental and bioinformatic strategies target mutations with ≥5% allele frequency, which limits our ability to understand the cancer etiology and tumor evolution...
May 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28541300/splicing-modulators-act-at-the-branch-point-adenosine-binding-pocket-defined-by-the-phf5a-sf3b-complex
#12
Teng Teng, Jennifer Hc Tsai, Xiaoling Puyang, Michael Seiler, Shouyong Peng, Sudeep Prajapati, Daniel Aird, Silvia Buonamici, Benjamin Caleb, Betty Chan, Laura Corson, Jacob Feala, Peter Fekkes, Baudouin Gerard, Craig Karr, Manav Korpal, Xiang Liu, Jason T Lowe, Yoshiharu Mizui, James Palacino, Eunice Park, Peter G Smith, Vanitha Subramanian, Zhenhua Jeremy Wu, Jian Zou, Lihua Yu, Agustin Chicas, Markus Warmuth, Nicholas Larsen, Ping Zhu
Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates with the differential GC content between adjacent introns and exons...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28540979/alcohol-consumption-aldehyde-dehydrogenase-2-gene-polymorphisms-and-cardiovascular-health-in-korea
#13
REVIEW
Min Jeong Shin, Yoonsu Cho, George Davey Smith
Alcohol consumption is a serious health issue in Korea in terms of the amount consumed and the behavior related to its consumption. Aldehyde dehydrogenase 2 (ALDH2) is a key enzyme in alcohol metabolism that degrades acetaldehyde to nontoxic acetic acid. The enzyme is coded by the ALDH2 gene, which is commonly polymorphic in East Asian populations. A point mutation in the ALDH2 gene (the rs671 allele) yields an inactive form of ALDH2 that causes acetaldehyde accumulation in the body after alcohol consumption, thereby inhibiting normal alcohol metabolism...
July 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28540711/pcr-in-the-analysis-of-clinical-samples-prenatal-and-postnatal-diagnosis-of-inborn-errors-of-metabolism
#14
Laura Vilarinho, Célia Nogueira
Inborn errors of metabolism (IEMs) are individually rare but collectively common. As more and more genes are cloned and specific disease-causing mutations are identified, the diagnosis of IEMs is becoming increasingly confirmed by mutation analysis. Diagnosis is important not only for treatment and prognosis but also for genetic counselling and prenatal diagnosis in subsequent pregnancies. A wide range of molecular methods is available for the identification of mutations and other DNA variants, most of which are based on the Polymerase Chain Reaction (PCR)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540701/inverse-pcr-for-point-mutation-introduction
#15
Diogo Silva, Gustavo Santos, Mário Barroca, Tony Collins
Inverse PCR is a powerful tool for the rapid introduction of desired mutations at desired positions in a circular double-stranded DNA sequence. Here, custom-designed mutant primers oriented in the inverse direction are used to amplify the entire circular template with incorporation of the required mutation(s). By careful primer design it can be used to perform such diverse modifications as the introduction of point mutations and multiple mutations, the insertion of new sequences, and even sequence deletions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540421/yeast-env9-encodes-a-conserved-lipid-droplet-ld-short-chain-dehydrogenase-involved-in-ld-morphology
#16
Ikha M Siddiqah, Surya P Manandhar, Stephanie M Cocca, Teli Hsueh, Vanessa Cervantes, Editte Gharakhanian
Lipid droplets (LDs) have emerged as dynamic and interactive organelles with important roles in lipid metabolism and membrane biogenesis. Here, we report that Saccharomyces cerevisiae Env9 is a novel conserved oxidoreductase involved in LD morphology. Microscopic and biochemical studies confirm localization of tagged Env9 to LDs and implicate its C-terminal hydrophobic domain (aa241-265) in its membrane association and stability. Confocal studies reveal a role for Env9 in LD morphology. Env9 positively affects both formation of large LDs upon overexpression and LD proliferation under poor carbon source...
May 24, 2017: Current Genetics
https://www.readbyqxmd.com/read/28540352/dataset-on-galanin-receptor-3-mutants-that-improve-recombinant-receptor-expression-and-stability-in-an-agonist-and-antagonist-bound-form
#17
Thao T Ho, Jasmine T Nguyen, Juping Liu, Pawel Stanczak, Aaron A Thompson, Yingzhuo G Yan, Jasmine Chen, Charles K Allerston, Charles L Dillard, Hao Xu, Nicholas J Shoger, Jill S Cameron, Mark E Massari, Kathleen Aertgeerts
Galanin Receptor 3 (GALR3) is a G-protein-coupled receptor with a widespread distribution in the brain and plays a role in a variety of physiologic processes including cognition/memory, sensory/pain processing, hormone secretion, and feeding behavior. Therefore, GALR3 is considered an attractive CNS drug target (Freimann et al., 2015) [1]. This dataset contains GALR3 point mutants that improve recombinant protein expression and thermal stability of the receptor contained in virus-like particles (VLPs) or obtained by detergent-purification of baculovirus-infected insect cells...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28539463/braf-fusion-as-a-novel-mechanism-of-acquired-resistance-to-vemurafenib-in-braf-v600e-mutant-melanoma
#18
Atul Kulkarni, Husam Al-Hraishawi, Srilatha Simhadri, Kim M Hirshfield, Suzie Chen, Sharon R Pine, Chandrika Jeyamohan, Levi Sokol, Siraj M Ali, Man Lung Teo, Eileen White, Lorna Rodriguez-Rodriguez, Janice M Mehnert, Shridar Ganesan
Many patients with BRAF (V)(600E) mutant melanoma treated with BRAF inhibitors experience a rapid response, but ultimately develop resistance. Insight into the mechanism of resistance is critical for development of more effective treatment strategies. <br /><br />Experimental Design: Comprehensive genomic profiling of serial biopsies was performed in a patient with a BRAF(V600E) mutant metastatic melanoma who developed resistance to vemurafenib. An AGAP3-BRAF fusion gene, identified in the vemurafenib-resistant tumor, was expressed in BRAF(V600E) melanoma cell lines and its effect on drug sensitivity was evaluated...
May 24, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28538155/structure-and-intermolecular-interactions-between-l-type-straight-flagellar-filaments
#19
Daniel Louzon, Avi Ginsburg, Walter Schwenger, Tom Dvir, Zvonimir Dogic, Uri Raviv
Bacterial mobility is powered by rotation of helical flagellar filaments driven by rotary motors. Flagellin isolated from the Salmonella Typhimurium SJW1660 strain, which differs by a point mutation from the wild-type strain, assembles into straight filaments in which flagellin monomers are arranged in a left-handed helix. Using small-angle x-ray scattering and osmotic stress methods, we investigated the structure of SJW1660 flagellar filaments as well as the intermolecular forces that govern their assembly into dense hexagonal bundles...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28537891/multiplex-pcr-approach-to-simultaneously-identify-several-mutations-in-fine-needle-cytology-thyroid-samples
#20
Emilia Vuttariello, Marco Borra, Elvira Mauriello, Celeste Calise, Barbara D'Andrea, Anna Capiluongo, Franco Fulciniti, Anna Cipolletta, Mario Monaco, Luciano Pezzullo, Gennaro Chiappetta
The most frequent initial manifestation of thyroid cancer is the appearance of a nodule. More than 20% of the general population has a palpable thyroid nodule and the percentage rises to 70% based on ultrasound identification. In 95% of cases the nodule is simply a hyperplastic or benign lesion. The most reliable diagnostic test for thyroid nodules is fine needle aspiration (FNA), but cytological discrimination between malignant and benign follicular neoplasms remains difficult. Cytological analysis is now, almost routinely, being combined with molecular genetics to enable the pathologist to make a more objective diagnosis...
May 7, 2017: Oncotarget
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