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https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#1
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28918231/highly-sensitive-surface-plasmon-resonance-biosensor-for-the-detection-of-hiv-related-dna-based-on-dynamic-and-structural-dna-nanodevices
#2
Wei Diao, Min Tang, Shijia Ding, Xinmin Li, Wenbin Cheng, Fei Mo, Xiaoyu Yan, Hongmin Ma, Yurong Yan
Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products...
September 9, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28918132/assessing-precision-bias-and-sigma-metrics-of-53-measurands-of-the-alinity-ci-system
#3
Sten Westgard, Victoria Petrides, Sharon Schneider, Marvin Berman, Jörg Herzogenrath, Anthony Orzechowski
Assay performance is dependent on the accuracy and precision of a given method. These attributes can be combined into an analytical Sigma-metric, providing a simple value for laboratorians to use in evaluating a test method's capability to meet its analytical quality requirements. Sigma-metrics were determined for 37 clinical chemistry assays, 13 immunoassays, and 3 ICT methods on the Alinity ci system. METHODS: Analytical Performance Specifications were defined for the assays, following a rationale of using CLIA goals first, then Ricos Desirable goals when CLIA did not regular the method, and then other sources if the Ricos Desirable goal was unrealistic...
September 13, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28916783/differential-regulation-of-vaginal-lipocalins-obp-mup-during-the-estrous-cycle-of-the-house-mouse
#4
Martina Černá, Barbora Kuntová, Pavel Talacko, Romana Stopková, Pavel Stopka
Female house mice produce pheromone-carrying major urinary proteins (MUPs) in a cycling manner, thus reaching the maximum urinary production just before ovulation. This is thought to occur to advertise the time of ovulation via deposited urine marks. This study aimed to characterize the protein content from the house mouse vaginal flushes to detect putative vaginal-advertising molecules for a direct identification of reproductive states. Here we show that the mouse vaginal discharge contains lipocalins including those from the odorant binding (OBP) and major urinary (MUP) protein families...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916651/escherichia-coli-and-neisseria-gonorrhoeae-uvrd-helicase-unwinds-g4-dna-structures
#5
Kaustubh Shukla, Roshan Thakur, Debayan Ganguli, Desirazu Rao, Ganesh Nagaraju
G-quadruplex (G4) secondary structures have been implicated in various biological processes including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination...
September 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28916620/the-anthracycline-metabolite-doxorubicinol-abolishes-ryr2-sensitivity-to-physiological-changes-in-luminal-ca-2-through-an-interaction-with-calsequestrin
#6
Amy Hanna, Alexander Lam, Chris Thekkedam, Hermia Willemse, Angela Fay Dulhunty, Nicole Beard
The chemotherapeutic anthracycline metabolite doxorubicinol (doxOL) has been shown to interact with and disrupt the function of the cardiac ryanodine receptor Ca2+ release channel (RyR2) in the sarcoplasmic reticulum (SR) membrane and the SR Ca2+ binding protein calsequestrin2 (CSQ2). Normal increases in RyR2 activity in response to increasing diastolic SR [Ca2+] are influenced by CSQ2 and are disrupted in arrhythmic conditions. Therefore we explored the action of doxOL on RyR2's response to changes in luminal [Ca2+] seen during diastole...
September 15, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28915787/mmquant-how-to-count-multi-mapping-reads
#7
Matthias Zytnicki
BACKGROUND: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results. RESULTS: We provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene...
September 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28915229/the-optimal-night-time-home-blood-pressure-monitoring-schedule-agreement-with-ambulatory-blood-pressure-and-association-with-organ-damage
#8
Anastasios Kollias, Emmanuel Andreadis, Gerasimos Agaliotis, George N Kolyvas, Apostolos Achimastos, George S Stergiou
OBJECTIVE: Night-time home blood pressure (HBP) monitoring has emerged as a feasible, reliable and low-cost alternative to ambulatory blood pressure (ABP) monitoring. This study evaluated the optimal schedule of night-time HBP monitoring in terms of agreement with night-time ABP and association with preclinical target-organ damage. METHODS: Untreated hypertensive adults were evaluated with ABP (24-h) and HBP monitoring (daytime: six days, duplicate morning and evening measurements; night-time: three nights, three-hourly automated measurements/night), and determination of left ventricular mass index, common carotid intima-media thickness and urinary albumin excretion...
September 14, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28914656/charcot-marie-tooth-disease-type-1a-influence-of-body-mass-index-on-nerve-conduction-studies-and-on-the-charcot-marie-tooth-examination-score
#9
Nivedita U Jerath, Michael E Shy
PURPOSE: Charcot-Marie-Tooth Disease type 1A (CMT1A) is caused by a duplication of the peripheral myelin protein gene 22 at chromosome 17p11.2-12. There is limited data regarding whether body mass index (BMI) affects electrophysiological or clinical data in those with CMT1A. METHODS: Electrophysiological data, the Charcot-Marie-Tooth examination score (CMTES) and BMI from 101 patients with known CMT1A were obtained and analyzed. RESULTS: When controlling for age, a higher BMI does not affect ulnar motor nerve conduction studies in those with CMT1A, but rather components of the CMTES (loss of pinprick and motor strength in the lower extremities)...
September 11, 2017: Journal of Clinical Neurophysiology: Official Publication of the American Electroencephalographic Society
https://www.readbyqxmd.com/read/28914273/patterns-and-appropriateness-of-thrombophilia-testing-in-an-academic-medical-center
#10
Nicholas Cox, Stacy A Johnson, Sara Vazquez, Ryan P Fleming, Matthew T Rondina, David Kaplan, Stephanie Chauv, Gabriel V Fontaine, Scott M Stevens, Scott Woller, Daniel M Witt
BACKGROUND: Clinical guidelines recommend against routine use of thrombophilia testing in patients with acute thromboembolism. Thrombophilia testing rarely changes acute management of a thrombotic event. OBJECTIVE: To determine appropriateness of thrombophilia testing in a teaching hospital. DESIGN: Retrospective cohort study. SETTING: One academic medical center in Utah. PARTICIPANTS: All patients who received thrombophilia testing between July 1, 2014, and December 31, 2014...
September 2017: Journal of Hospital Medicine: An Official Publication of the Society of Hospital Medicine
https://www.readbyqxmd.com/read/28914269/looking-beyond-the-exome-a-phenotype-first-approach-to-molecular-diagnostic-resolution-in-rare-and-undiagnosed-diseases
#11
Loren D M Pena, Yong-Hui Jiang, Kelly Schoch, Rebecca C Spillmann, Nicole Walley, Nicholas Stong, Sarah Rapisardo Horn, Jennifer A Sullivan, Allyn McConkie-Rosell, Sujay Kansagra, Edward C Smith, Mays El-Dairi, Jane Bellet, Martha Ann Keels, Joan Jasien, Peter G Kranz, Richard Noel, Shashi K Nagaraj, Robert K Lark, Daniel S G Wechsler, Daniela Del Gaudio, Marco L Leung, Laura G Hendon, Collette C Parker, Kelly L Jones, David B Goldstein, Vandana Shashi
PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914261/rsk2-is-a-new-pim2-target-with-pro-survival-functions-in-flt3-itd-positive-acute-myeloid-leukemia
#12
M-A Hospital, A Jacquel, F Mazed, E Saland, C Larrue, J Mondesir, R Birsen, A S Green, M Lambert, P Sujobert, E-F Gautier, V Salnot, M Le Gall, J Decroocq, L Poulain, N Jacque, M Fontenay, O Kosmider, C Récher, P Auberger, P Mayeux, D Bouscary, J-E Sarry, J Tamburini
Acute myeloid leukemia (AML) with the FLT3 internal tandem duplication (FLT3-ITD AML) accounts for 20-30% of AML cases. This subtype usually responds poorly to conventional therapies, and might become resistant to FLT3 tyrosine kinase inhibitors (TKIs) due to molecular bypass mechanisms. New therapeutic strategies focusing on resistance mechanisms are therefore urgently needed. Pim kinases are FLT3-ITD oncogenic targets that have been implicated in FLT3 TKI resistance. However, their precise biological function downstream of FLT3-ITD requires further investigation...
September 15, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28913705/variable-park2-mutations-cause-early-onset-parkinson-s-disease-in-a-small-restricted-population
#13
Shay Ben-Shachar, Zaid Afawi, Rafik Masalha, Samih Badarny, Tova Neiman, Dina Pavzner, Anat Bar-Shira, Avi Orr-Urtreger
Early-onset Parkinson's disease (EOPD) is less common than the typical adult-onset PD and may be associated with a genetic etiology. Mutations in several genes are known to cause autosomal recessive (AR) PD. This study aimed to detect the etiology of EOPD in consanguineous families or families living in a specific small geographic region in Israel. Six families with EOPD affecting more than a single individual were recruited. Homozygous mapping analysis using a single-nucleotide polymorphism-based array was performed in all families, followed by Sanger sequencing of related genes based on the mapping results...
September 15, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28912486/the-homologous-recombination-machinery-orchestrates-post-replication-dna-repair-during-self-renewal-of-mouse-embryonic-stem-cells
#14
Eui-Hwan Choi, Seobin Yoon, Kyung-Soon Park, Keun P Kim
Embryonic stem (ES) cells require homologous recombination (HR) to cope with genomic instability caused during self-renewal. Here, we report expression dynamics and localization of endogenous HR factors in DNA break repair of ES cells. In addition, we analyzed gene expression patterns of HR-related factors at the transcript level with RNA-sequencing experiments. We showed that ES cells constitutively expressed diverse HR proteins throughout the cell cycle and that HR protein expression was not significantly changed even in the DNA damaging conditions...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912176/anexelekto-mer-tyrosine-kinase-inhibitor-ono-7475-growth-arrests-and-kills-fms-like-tyrosine-kinase-3-internal-tandem-duplication-mutant-acute-myeloid-leukemia-cells-by-diverse-mechanisms
#15
Peter P Ruvolo, Huaxian Ma, Vivian R Ruvolo, Xiaorui Zhang, Hong Mu, Wendy Schober, Ivonne Hernandez, Miguel Gallardo, Joseph Khoury, Jorge Cortes, Michael Andreeff, Sean M Post
Nearly one-third of patients with acute myeloid leukemia have FMS-Like Tyrosine Kinase 3 mutations and thus have poor survival prospects. Receptor tyrosine kinase Anexelekto is critical for FMS-Like Tyrosine Kinase 3 signaling and participates in FMS-Like Tyrosine Kinase 3 inhibitor resistance mechanisms. Thus, strategies targeting Anexelekto could prove useful for acute myeloid leukemia therapy. ONO-7475 is an inhibitor with high specificity for Anexelekto and MER Tyrosine Kinase. Here we report that ONO-7475 potently arrested growth and induced apoptosis in acute myeloid leukemia with internal tandem duplication mutation of FMS-Like Tyrosine Kinase 3...
September 14, 2017: Haematologica
https://www.readbyqxmd.com/read/28912110/the-genetics-of-congenitally-small-brains
#16
REVIEW
Sarah Duerinckx, Marc Abramowicz
Primary microcephaly (PM) refers to a congenitally small brain, resulting from insufficient prenatal production of neurons, and serves as a model disease for brain volumic development. Known PM genes delineate several cellular pathways, among which the centriole duplication pathway, which provide interesting clues about the cellular mechanisms involved. The general interest of the genetic dissection of PM is illustrated by the convergence of Zika virus infection and PM gene mutations on congenital microcephaly, with CENPJ/CPAP emerging as a key target...
September 11, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28911668/determination-of-multiresidue-analysis-of-%C3%AE-agonists-in-muscle-and-viscera-using-liquid-chromatograph-tandem-mass-spectrometry-with-quick-easy-cheap-effective-rugged-and-safe-methodologies
#17
Yen-Ping Lin, Ying-Lin Lee, Chien-Ya Hung, Wen-Jeng Huang, Sheng-Che Lin
The official analytical method of the Taiwan Food and Drug Administration, Ministry of Health and Welfare for testing for veterinary drug residues in foods is the multiresidue analysis of β-agonists. Samples are pretreated through liquid-liquid extraction and solid-phase extraction. This method is time consuming and requires the intensive use of solvents. To improve analytical efficiency and reduce costs, our study incorporated QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) techniques to establish a new method of multiresidue analysis of β-agonists in animal muscle and viscera...
April 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28911105/a-novel-nucleoid-associated-protein-coordinates-chromosome-replication-and-chromosome-partition
#18
James A Taylor, Gaël Panis, Patrick H Viollier, Gregory T Marczynski
We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein (GapR) that selectively aids the initiation of chromosome replication and the initial steps of chromosome partitioning. The protein binds the chromosome origin of replication (Cori) and has higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. gapR gene expression is essential for normal rapid growth and sufficient GapR levels are required for the correct timing of chromosome replication...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911102/fancj-helicase-controls-the-balance-between-short-and-long-tract-gene-conversions-between-sister-chromatids
#19
Sarmi Nath, Kumar Somyajit, Anup Mishra, Ralph Scully, Ganesh Nagaraju
The FANCJ DNA helicase is linked to hereditary breast and ovarian cancers as well as bone marrow failure disorder Fanconi anemia (FA). Although FANCJ has been implicated in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR), the molecular mechanism underlying the tumor suppressor functions of FANCJ remains obscure. Here, we demonstrate that FANCJ deficient human and hamster cells exhibit reduction in the overall gene conversions in response to a site-specific chromosomal DSB induced by I-SceI endonuclease...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910985/yeast-bacteria-competition-induced-new-metabolic-traits-through-large-scale-genomic-rearrangements-in-lachancea-kluyveri
#20
Nerve Zhou, Samuele Bottagisi, Michael Katz, Joseph Schacherer, Anne Friedrich, Zoran Gojkovic, Krishna B S Swamy, Wolfgang Knecht, Concetta Compagno, Jure Piškur
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations...
September 1, 2017: FEMS Yeast Research
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