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https://www.readbyqxmd.com/read/27906450/lovtrap-a-versatile-method-to-control-protein-function-with-light
#1
Hui Wang, Klaus M Hahn
We describe a detailed procedure for the use of LOVTRAP, an approach to reversibly sequester and release proteins from cellular membranes using light. In the application described here, proteins that act at the plasma membrane are held at mitochondria in the dark, and reversibly released by irradiation. The technique relies on binding of an engineered Zdk domain to a LOV2 domain, with affinity <30 nM in the dark and >500 nM upon irradiation between 400 and 500 nm. LOVTRAP can be applied to diverse proteins, as it requires attaching only one member of the Zdk/LOV2 pair to the target protein, and the other to the membrane where the target protein is to be sequestered...
December 1, 2016: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/27905549/corrigendum-egfr-tyrosine-kinase-inhibitors-versus-chemotherapy-as-first-line-therapy-for-non-small-cell-lung-cancer-patients-with-the-l858r-point-mutation
#2
Jianlin Xu, Haitang Yang, Bo Jin, Yuqing Lou, Yanwei Zhang, Xueyan Zhang, Hua Zhong, Huiming Wang, Dan Wu, Baohui Han
No abstract text is available yet for this article.
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905065/spatial-measures-of-genetic-heterogeneity-during-carcinogenesis
#3
K Storey, M D Ryser, K Leder, J Foo
In this work we explore the temporal dynamics of spatial heterogeneity during the process of tumorigenesis from healthy tissue. We utilize a spatial stochastic model of mutation accumulation and clonal expansion in a structured tissue to describe this process. Under a two-step tumorigenesis model, we first derive estimates of a non-spatial measure of diversity: Simpson's Index, which is the probability that two individuals sampled at random from the population are identical, in the premalignant population. We next analyze two new measures of spatial population heterogeneity...
November 30, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/27904766/the-role-of-pim1-in-the-ibrutinib-resistant-abc-subtype-of-diffuse-large-b-cell-lymphoma
#4
Hsu-Ping Kuo, Scott A Ezell, Sidney Hsieh, Karl J Schweighofer, Leo Wk Cheung, Shiquan Wu, Mutiah Apatira, Mint Sirisawad, Karl Eckert, Yu Liang, Jeff Hsu, Chun-Te Chen, Darrin Beaupre, Betty Y Chang
Diffuse large B cell lymphoma (DLBCL) is a heterogeneous lymphoma and the most common subtype of non-Hodgkin lymphoma, accounting for roughly 30% of newly diagnosed cases in the United States. DLBCL can be separated into the activated B cell-like (ABC) and germinal center B cell-like (GCB) subtypes, with distinct gene expression profiles, oncogenic aberrations, and clinical outcomes. ABC-DLBCL is characterized by chronically active B-cell receptor (BCR) signaling that can be modulated by Bruton's tyrosine kinase (BTK) activity...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903834/saliva-diagnostics-current-views-and-directions
#5
Karolina Elżbieta Kaczor-Urbanowicz, Carmen Martin Carreras-Presas, Katri Aro, Michael Tu, Franklin Garcia-Godoy, David Tw Wong
In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a "mirror of the body," can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term "Salivaomics" aimed to highlight the rapid development of knowledge about various "omics" constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome...
November 29, 2016: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/27903453/repair-of-8-oxo-7-8-dihydroguanine-in-prokaryotic-and-eukaryotic-cells-properties-and-biological-roles-of-the-fpg-and-ogg1-dna-n-glycosylases
#6
Serge Boiteux, Franck Coste, Bertrand Castaing
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases...
November 26, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27903277/sequence-diversity-of-dengue-virus-type-2-in-brain-and-thymus-of-infected-interferon-receptor-ko-mice-implications-for-dengue-virulence
#7
Priya Dhole, Emi E Nakayama, Akatsuki Saito, Kriengsak Limkittikul, Supranee Phanthanawiboon, Tatsuo Shioda, Takeshi Kurosu
BACKGROUND: We previously reported that a clinical isolate of dengue virus (DENV) is capable of causing acute-phase systemic infection in mice harboring knockouts of the genes encoding type-I and -II interferon IFN receptors (IFN-α/β/γR KO mice); in contrast, other virulent DENV isolates exhibited slow disease progression in this mice, yielding lethal infection around 20 days post-infection (p.i.). In the present study, we sought to clarify the dynamics of slow disease progression by examining disease progression of a type-2 DENV clinical isolate (DV2P04/08) in mice...
November 30, 2016: Virology Journal
https://www.readbyqxmd.com/read/27902963/homology-modeling-and-molecular-dynamics-simulation-of-the-hif2%C3%AE-degradation-related-hif2%C3%AE-vhl-complex
#8
Xiaotian Dong, Xiaoru Su, Jiong Yu, Jingqi Liu, Xiaowei Shi, Qiaoling Pan, Jinfeng Yang, Jiajia Chen, Lanjuan Li, Hongcui Cao
BACKGROUND: Hypoxia-inducible factor 2 alpha (HIF2α), prolyl hydroxylase domain protein 2 (PHD2), and the von Hippel Lindau tumor suppressor protein (pVHL) are three principal proteins in the oxygen-sensing pathway. Under normoxic conditions, a conserved proline in HIF2α is hydroxylated by PHD2 in an oxygen-dependent manner, and then pVHL binds and promotes the degradation of HIF2α. However, the crystal structure of the HIF2α-pVHL complex has not yet been established, and this has limited research on the interaction between HIF and pVHL...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27902775/determinants-of-trna-recognition-by-the-radical-sam-enzyme-rlmn
#9
Christina M Fitzsimmons, Danica Galonić Fujimori
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets...
2016: PloS One
https://www.readbyqxmd.com/read/27902354/humoral-immune-system-targets-clonotypic-antibody-associated-hepatitis-c-virus
#10
Amruta S Naik, Brendan A Palmer, Orla Crossbie, Elizabeth Kenny-Walsh, Liam J Fanning
Hypervariable region 1 (HVR1) is one of the potential neutralisation domains in the E2 glycoprotein of Hepatitis C virus (HCV). Point mutations of the HVR1 can lead to humoral immune escape in HCV infected patients. In this study we segregated the chronically infected viraemic sera from HCV infected patients into populations of antibody free virus (AFV) and antibody associated virus (AAV) and mapped potential epitopes within the E1E2 gene junction of AAV sequences (residues 364-430). Furthermore, we generated pseudotyped HCV particles (HCVpp) derived from AAV sequence to assess their infectivity...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27900368/whole-exome-sequencing-reveals-an-inherited-r566x-mutation-of-the-epithelial-sodium-channel-%C3%AE-subunit-in-a-case-of-early-onset-phenotype-of-liddle-syndrome
#11
Linda M Polfus, Eric Boerwinkle, Richard A Gibbs, Ginger Metcalf, Donna Muzny, Narayanan Veeraraghavan, Megan Grove, Sanjay Shete, Stephanie Wallace, Dianna Milewicz, Neil Hanchard, James R Lupski, Syed Shahrukh Hashmi, Monesha Gupta-Malhotra
To comprehensively evaluate a European-American child with severe hypertension, whole-exome sequencing (WES) was performed on the child and parents, which identified causal variation of the proband's early-onset disease. The proband's hypertension was resistant to treatment, requiring a multiple drug regimen including amiloride, spironolactone, and hydrochlorothiazide. We suspected a monogenic form of hypertension because of the persistent hypokalemia with low plasma levels of renin and aldosterone. To address this, we focused on rare functional variants and indels, and performed gene-based tests incorporating linkage scores and allele frequency and filtered on deleterious functional mutations...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27900365/genome-sequencing-in-a-case-of-niemann-pick-type-c
#12
Max Dougherty, John Lazar, Jason C Klein, Karina Diaz, Theodore Gobillot, Eli Grunblatt, Nicholas Hasle, Daniel Lawrence, Megan Maurano, Maria Nelson, Gregory Olson, Sanjay Srivatsan, Jay Shendure, C Dirk Keene, Thomas Bird, Marshall S Horwitz, Desiree A Marshall
Adult-onset Niemann-Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical ("variant" level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899967/heteroplasmy-of-mutant-mitochondrial-dna-a10398g-and-analysis-of-its-prognostic-value-in-non-small-cell-lung-cancer
#13
Yuexiao Qi, Yuehua Wei, Qiaoli Wang, Hui Xu, You Wang, Anqi Yao, Hui Yang, Yan Gao, Fuxiang Zhou
Mitochondrial dysfunction is associated with pathogenic mitochondrial (mt)DNA mutations. The majority of mtDNA point mutations have a heteroplasmic status, which is defined as the coexistence of wild-type and mutated DNA within a cell or tissue. Previous findings demonstrated that certain mtDNA heteroplasmic mutations contribute to widely spread chronic diseases, including cancer, and alterations in the heteroplasmy level are associated with the clinical phenotype and severity of cancer. In the present study, the proportions of mutant mtDNA 10398G were assessed using amplification-refractory mutation system-quantitative polymerase chain reaction (PCR) assay in 129 non-small cell lung cancer (NSCLC) tissue samples...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27898095/efficient-generation-of-orthologous-point-mutations-in-pigs-via-crispr-assisted-ssodn-mediated-homology-directed-repair
#14
Kankan Wang, Xiaochun Tang, Yan Liu, Zicong Xie, Xiaodong Zou, Mengjing Li, Hongming Yuan, Hongsheng Ouyang, Huping Jiao, Daxin Pang
Precise genome editing in livestock is of great value for the fundamental investigation of disease modeling. However, genetically modified pigs carrying subtle point mutations were still seldom reported despite the rapid development of programmable endonucleases. Here, we attempt to investigate single-stranded oligonucleotides (ssODN) mediated knockin by introducing two orthologous pathogenic mutations, p.E693G for Alzheimer's disease and p.G2019S for Parkinson's disease, into porcine APP and LRRK2 loci, respectively...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27895626/a-proposal-for-formation-of-archaean-stromatolites-before-the-advent-of-oxygenic-photosynthesis
#15
John F Allen
Stromatolites are solid, laminar structures of biological origin. Living examples are sparsely distributed and formed by cyanobacteria, which are oxygenic phototrophs. However, stromatolites were abundant between 3.4 and 2.4 Gyr, prior to the advent of cyanobacteria and oxygenic photosynthesis. Here I propose that many Archaean stromatolites were seeded at points of efflux of hydrogen sulfide from hydrothermal fields into shallow water, while their laminar composition arose from alternating modes of strictly anoxygenic photosynthetic metabolism...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27894751/polymerase-%C3%AE%C2%B5-pole-ultra-mutation-in-uterine-tumors-correlates-with-t-lymphocyte-infiltration-and-increased-resistance-to-platinum-based-chemotherapy-in-vitro
#16
Stefania Bellone, Eliana Bignotti, Silvia Lonardi, Francesca Ferrari, Floriana Centritto, Alice Masserdotti, Francesca Pettinella, Jonathan Black, Gulden Menderes, Gary Altwerger, Pei Hui, Salvatore Lopez, Christopher de Haydu, Elena Bonazzoli, Federica Predolini, Luca Zammataro, Emiliano Cocco, Federico Ferrari, Antonella Ravaggi, Chiara Romani, Fabio Facchetti, Enrico Sartori, Franco E Odicino, Dan-Arin Silasi, Babak Litkouhi, Elena Ratner, Masoud Azodi, Peter E Schwartz, Alessandro D Santin
OBJECTIVE: Up to 12% of all endometrial-carcinomas (EC) harbor DNA-polymerase-ε-(POLE) mutations. It is currently unknown whether the favorable prognosis of POLE-mutated EC is derived from their low metastatic capability, extraordinary number of somatic mutations thus imparting immunogenicity, or a high sensitivity to chemotherapy. METHODS: Polymerase-chain-reaction-amplification and Sanger-sequencing were used to test for POLE exonuclease-domain-mutations (exons 9-14) 131 EC...
November 25, 2016: Gynecologic Oncology
https://www.readbyqxmd.com/read/27894601/treatment-rationale-and-study-design-for-the-relay-study-a-multicenter-randomized-double-blind-study-of-erlotinib-with-ramucirumab-or-placebo-in-patients-with-epidermal-growth-factor-receptor-mutation-positive-metastatic-non-small-cell-lung-cancer
#17
Edward B Garon, Martin Reck, Luis Paz-Ares, Santiago Ponce, Jesus Corral Jaime, Oscar Juan, Ernest Nadal, Pablo Lee, Rita Dalal, Jingyi Liu, Shuang He, Joseph Treat, Kazuhiko Nakagawa
INTRODUCTION: We present the treatment rationale and study design for the RELAY study (NCT02411448 ). This phase Ib/III study will assess safety, tolerability, and efficacy of the combination of ramucirumab with erlotinib in previously untreated stage IV non-small-cell lung cancer patients with an activating epidermal growth factor receptor (EGFR) mutation. PATIENTS AND METHODS: The study is being conducted in approximately 120 sites in North America, Europe, and Asia and is currently open for enrollment...
June 8, 2016: Clinical Lung Cancer
https://www.readbyqxmd.com/read/27894357/new-insights-into-the-generation-and-role-of-de-novo-mutations-in-health-and-disease
#18
REVIEW
Rocio Acuna-Hidalgo, Joris A Veltman, Alexander Hoischen
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases...
November 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/27892483/down-regulation-of-coasy-the-gene-associated-with-nbia-vi-reduces-bmp-signaling-perturbs-dorso-ventral-patterning-and-alters-neuronal-development-in-zebrafish
#19
Deepak Khatri, Daniela Zizioli, Natascia Tiso, Nicola Facchinello, Sara Vezzoli, Alessandra Gianoncelli, Maurizio Memo, Eugenio Monti, Giuseppe Borsani, Dario Finazzi
Mutations in Pantothenate kinase 2 and Coenzyme A (CoA) synthase (COASY), genes involved in CoA biosynthesis, are associated with rare neurodegenerative disorders with brain iron accumulation. We showed that zebrafish pank2 gene plays an essential role in brain and vasculature development. Now we extended our study to coasy. The gene has high level of sequence identity with the human ortholog and is ubiquitously expressed from the earliest stages of development. The abrogation of its expression led to strong reduction of CoA content, high lethality and a phenotype resembling to that of dorsalized mutants...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27892470/vertical-magnetic-separation-of-circulating-tumor-cells-for-somatic-genomic-alteration-analysis-in-lung-cancer-patients
#20
Chang Eun Yoo, Jong-Myeon Park, Hui-Sung Moon, Je-Gun Joung, Dae-Soon Son, Hyo-Jeong Jeon, Yeon Jeong Kim, Kyung-Yeon Han, Jong-Mu Sun, Keunchil Park, Donghyun Park, Woong-Yang Park
Efficient isolation and genetic analysis of circulating tumor cells (CTCs) from cancer patients' blood is a critical step for clinical applications using CTCs. Here, we report a novel CTC-isolation method and subsequent genetic analysis. CTCs from the blood were complexed with magnetic beads coated with antibodies against the epithelial cell adhesion molecule (EpCAM) and separated vertically on a density-gradient medium in a modified well-plate. The recovery rate of model CTCs was reasonable and the cell purity was enhanced dramatically when compared to those parameters obtained using a conventional magnetic isolation method...
November 28, 2016: Scientific Reports
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