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https://www.readbyqxmd.com/read/28625161/recombinase-polymerase-amplification-rpa-an-isothermal-technique-suitable-for-a-range-of-applications-evaluation-of-rpa-volume-tolerance
#1
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No abstract text is available yet for this article.
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28607004/rpa-activates-the-xpf-ercc1-endonuclease-to-initiate-processing-of-dna-interstrand-crosslinks
#2
Ummi B Abdullah, Joanna F McGouran, Sanja Brolih, Denis Ptchelkine, Afaf H El-Sagheer, Tom Brown, Peter J McHugh
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity...
June 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28604711/the-anaphase-promoting-complex-impacts-repair-choice-by-protecting-ubiquitin-signalling-at-dna-damage-sites
#3
Kyungsoo Ha, Chengxian Ma, Han Lin, Lichun Tang, Zhusheng Lian, Fang Zhao, Ju-Mei Li, Bei Zhen, Huadong Pei, Suxia Han, Marcos Malumbres, Jianping Jin, Huan Chen, Yongxiang Zhao, Qing Zhu, Pumin Zhang
Double-strand breaks (DSBs) are repaired through two major pathways, homology-directed recombination (HDR) and non-homologous end joining (NHEJ). While HDR can only occur in S/G2, NHEJ can happen in all cell cycle phases (except mitosis). How then is the repair choice made in S/G2 cells? Here we provide evidence demonstrating that APC(Cdh1) plays a critical role in choosing the repair pathways in S/G2 cells. Our results suggest that the default for all DSBs is to recruit 53BP1 and RIF1. BRCA1 is blocked from being recruited to broken ends because its recruitment signal, K63-linked poly-ubiquitin chains on histones, is actively destroyed by the deubiquitinating enzyme USP1...
June 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28598461/acute-retropharyngeal-abscess-masquerading-as-meningitis
#4
P Sakthivel, R Yogal, H Verma, A Saini, A Chandran
Retropharyngeal abscess is a potentially serious deep neck space infection occurring more frequently in children than in adults. The clinical picture of RPA is highly variable with paucity of physical findings. Prompt diagnosis of RPA especially in infants is mandatory to prevent potential fatal complications including airway obstruction. The diagnosis of RPA should be based on high index of clinical suspicion with supportive imaging studies like lateral X-ray of neck and CT. We present a case of acute retropharyngeal abscess which was initially misdiagnosed as meningitis and led to airway obstruction...
January 2017: JNMA; Journal of the Nepal Medical Association
https://www.readbyqxmd.com/read/28594346/interactive-roles-of-dna-helicases-and-translocases-with-the-single-stranded-dna-binding-protein-rpa-in-nucleic-acid-metabolism
#5
REVIEW
Sanket Awate, Robert M Brosh
Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress...
June 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28592488/dna-damage-induced-atr-kinase-activation-in-non-replicating-cells-is-regulated-by-the-xpb-subunit-of-transcription-factor-ii-h-tfiih
#6
Michael G Kemp
The role of the DNA damage response protein kinase ataxia telangiectasia and Rad-3-related (ATR) in the cellular response to DNA damage during the replicative phase of the cell cycle has been extensively studied. However, little is known about ATR kinase function in cells that are not actively replicating DNA and which constitute most cells in the human body. Using small-molecule inhibitors of ATR kinase and overexpression of a kinase-inactive form of the enzyme, I show here that ATR promotes cell death in non-replicating/non-cycling cultured human cells exposed to N-acetoxy-2-acetylaminofluorene (NA-AAF), which generates bulky DNA adducts that block RNA polymerase movement...
June 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28581776/achieving-stable-radiation-pressure-acceleration-of-heavy-ions-via-successive-electron-replenishment-from-ionization-of-a-high-z-material-coating
#7
X F Shen, B Qiao, H Zhang, S Kar, C T Zhou, H X Chang, M Borghesi, X T He
A method to achieve stable radiation pressure acceleration (RPA) of heavy ions from laser-irradiated ultrathin foils is proposed, where a high-Z material coating in front is used. The coated high-Z material, acting as a moving electron repository, continuously replenishes the accelerating heavy ion foil with comoving electrons in the light-sail acceleration stage due to its successive ionization under laser fields with Gaussian temporal profile. As a result, the detrimental effects such as foil deformation and electron loss induced by the Rayleigh-Taylor-like and other instabilities in RPA are significantly offset and suppressed so that stable acceleration of heavy ions are maintained...
May 19, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28575658/rfwd3-mediated-ubiquitination-promotes-timely-removal-of-both-rpa-and-rad51-from-dna-damage-sites-to-facilitate-homologous-recombination
#8
Shojiro Inano, Koichi Sato, Yoko Katsuki, Wataru Kobayashi, Hiroki Tanaka, Kazuhiro Nakajima, Shinichiro Nakada, Hiroyuki Miyoshi, Kerstin Knies, Akifumi Takaori-Kondo, Detlev Schindler, Masamichi Ishiai, Hitoshi Kurumizaka, Minoru Takata
RFWD3 is a recently identified Fanconi anemia protein FANCW whose E3 ligase activity toward RPA is essential in homologous recombination (HR) repair. However, how RPA ubiquitination promotes HR remained unknown. Here, we identified RAD51, the central HR protein, as another target of RFWD3. We show that RFWD3 polyubiquitinates both RPA and RAD51 in vitro and in vivo. Phosphorylation by ATR and ATM kinases is required for this activity in vivo. RFWD3 inhibits persistent mitomycin C (MMC)-induced RAD51 and RPA foci by promoting VCP/p97-mediated protein dynamics and subsequent degradation...
June 1, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28575657/rpa-mediated-recruitment-of-the-e3-ligase-rfwd3-is-vital-for-interstrand-crosslink-repair-and-human-health
#9
Laura Feeney, Ivan M Muñoz, Christophe Lachaud, Rachel Toth, Paul L Appleton, Detlev Schindler, John Rouse
Defects in the repair of DNA interstrand crosslinks (ICLs) are associated with the genome instability syndrome Fanconi anemia (FA). Here we report that cells with mutations in RFWD3, an E3 ubiquitin ligase that interacts with and ubiquitylates replication protein A (RPA), show profound defects in ICL repair. An amino acid substitution in the WD40 repeats of RFWD3 (I639K) found in a new FA subtype abolishes interaction of RFWD3 with RPA, thereby preventing RFWD3 recruitment to sites of ICL-induced replication fork stalling...
June 1, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28573472/new-nucleic-acid-testing-devices-to-diagnose-infectious-diseases-in-resource-limited-settings
#10
REVIEW
P Maffert, S Reverchon, W Nasser, C Rozand, H Abaibou
Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification...
June 1, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28560661/outcome-and-prognostic-factors-in-patients-with-brain-metastases-from-small-cell-lung-cancer-treated-with-whole-brain-radiotherapy
#11
Denise Bernhardt, Sebastian Adeberg, Farastuk Bozorgmehr, Nils Opfermann, Juliane Hoerner-Rieber, Laila König, Jutta Kappes, Michael Thomas, Felix Herth, Claus Peter Heußel, Arne Warth, Jürgen Debus, Martin Steins, Stefan Rieken
The purpose of this study was to evaluate prognostic factors associated with overall survival (OS) and neurological progression free survival (nPFS) in small-cell lung cancer (SCLC) patients with brain metastases who received whole-brain radiotherapy (WBRT). From 2003 to 2015, 229 SCLC patients diagnosed with brain metastases who received WBRT were analyzed retrospectively. In this cohort 219 patients (95%) received a total photon dose of 30 Gy in 10 fractions. The prognostic factors evaluated for OS and nPFS were: age, Karnofsky Performance Status (KPS), number of brain metastases, synchronous versus metachronous disease, initial response to chemotherapy, the Radiation Therapy Oncology Group recursive partitioning analysis (RPA) class and thoracic radiation...
May 30, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28551686/human-rad52-interactions-with-replication-protein-a-and-the-rad51-presynaptic-complex
#12
Chu Jian Ma, YoungHo Kwon, Patrick Sung, Eric C Greene
Rad52 is a highly-conserved protein involved in the repair of DNA damage. Human RAD52 has been shown to mediate ssDNA annealing and is synthetic lethal with mutations in other key recombination proteins. Here, we use single-molecule imaging and ssDNA curtains to examine the binding interactions of human RAD52 with RPA-coated ssDNA, and we monitor the fate of RAD52 during assembly of the presynaptic complex. We show that RAD52 binds tightly to the RPA-ssDNA complex and imparts an inhibitory effect on RPA turnover...
May 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28546384/systematic-analysis-of-the-dna-damage-response-network-in-telomere-defective-budding-yeast
#13
Eva-Maria Holstein, Greg Ngo, Conor Lawless, Peter Banks, Matthew Greetham, Darren Wilkinson, David Lydall
Functional telomeres are critically important to eukaryotic genetic stability. Scores of proteins and pathways are known to affect telomere function. Here, we report a series of related genome-wide genetic interaction screens performed on budding yeast cells with acute or chronic telomere defects. Genetic interactions were examined in cells defective in Cdc13 and Stn1, affecting two components of CST, a single stranded DNA (ssDNA) binding complex that binds telomeric DNA. For comparison, genetic interactions were also examined in cells with defects in Rfa3, affecting the major ssDNA binding protein, RPA, which has overlapping functions with CST at telomeres...
June 2, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28535142/srs2-promotes-synthesis-dependent-strand-annealing-by-disrupting-dna-polymerase-%C3%AE-extending-d-loops
#14
Jie Liu, Christopher Ede, William D Wright, Steven K Gore, Shirin S Jenkins, Bret D Freudenthal, M Todd Washington, Xavier Veaute, Wolf-Dietrich Heyer
Synthesis-dependent strand annealing (SDSA) is the preferred mode of homologous recombination in somatic cells leading to an obligatory non-crossover outcome, thus avoiding the potential for chromosomal rearrangements and loss of heterozygosity. Genetic analysis identified the Srs2 helicase as a prime candidate to promote SDSA. Here, we demonstrate that Srs2 disrupts D-loops in an ATP-dependent fashion and with a distinct polarity. Specifically, we partly reconstitute the SDSA pathway using Rad51, Rad54, RPA, RFC, DNA Polymerase δ with different forms of PCNA...
May 23, 2017: ELife
https://www.readbyqxmd.com/read/28534480/molecular-basis-for-primpol-recruitment-to-replication-forks-by-rpa
#15
Thomas A Guilliam, Nigel C Brissett, Aaron Ehlinger, Benjamin A Keen, Peter Kolesar, Elaine M Taylor, Laura J Bailey, Howard D Lindsay, Walter J Chazin, Aidan J Doherty
DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase-polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28528216/prognostic-factors-in-patients-treated-with-surgery-for-brain-metastases-a-single-center-retrospective-analysis-of-125-patients
#16
Zhenghao Liu, Bingxi Lei, Meiguang Zheng, Zhongjun Li, Shuaibin Huang, Yuefei Deng
BACKGROUD: Brain metastases are the most common malignant intracranial tumors,however, the prognosis of patients is still poor despite multiple treatment have been applicated.The aim of this study was to analyse parameters influence overall survival from patient, tumor and treatment. Summarized characteristics of long-time(>2 years) survivors furtherly. MATERIALS AND METHODS: In total, clinical data of 125patients between 2004 and 2015 were collected and the parameters from patients, tumor and treatment were evaluated...
May 17, 2017: International Journal of Surgery
https://www.readbyqxmd.com/read/28527442/inhomogeneous-fluid-of-penetrable-spheres-application-of-the-random-phase-approximation
#17
Yan Xiang, Derek Frydel
The focus of the present work is the application of the random phase approximation (RPA), derived for inhomogeneous fluids [Frydel and Ma, Phys. Rev. E 93, 062112 (2016)], to penetrable-spheres. As penetrable-spheres transform into hard-spheres with increasing interactions, they provide an interesting case for exploring the RPA, its shortcomings, and limitations, the weak- versus the strong-coupling limit. Two scenarios taken up by the present study are a one-component and a two-component fluid with symmetric interactions...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28510991/development-of-a-panel-of-recombinase-polymerase-amplification-assays-for-detection-of-common-bacterial-urinary-tract-infection-pathogens
#18
Balakrishnan Raja, Heather J Goux, Archana Marapadaga, Sri Rajagopalan, Katerina Kourentzi, Richard C Willson
AIMS: To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. METHODS AND RESULTS: The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, and Enterococcus faecalis. All five RPAs required reaction times of under 12 minutes to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of non-target bacterial genomic DNA...
May 16, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28510759/an-intact-mcm10-coiled-coil-interaction-surface-is-important-for-origin-melting-helicase-assembly-and-the-recruitment-of-pol-%C3%AE-to-mcm2-7
#19
Patricia Perez-Arnaiz, Irina Bruck, Max K Colbert, Daniel L Kaplan
Mcm10 is an essential eukaryotic factor required for DNA replication. The replication fork helicase is composed of Cdc45, Mcm2-7 and GINS (CMG). DDK is an S-phase-specific kinase required for replication initiation, and the DNA primase-polymerase in eukaryotes is pol α. Mcm10 forms oligomers in vitro, mediated by the coiled-coil domain at the N-terminal region of the protein. We characterized an Mcm10 mutant at the N-terminal Domain (NTD), Mcm10-4A, defective for self-interaction. We found that the Mcm10-4A mutant was defective for stimulating DDK phosphorylation of Mcm2, binding to eighty-nucleotide ssDNA, and recruiting pol α to Mcm2-7 in vitro...
May 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28505562/ultra-fast-electronic-detection-of-antimicrobial-resistance-genes-using-isothermal-amplification-and-thin-film-transistor-sensors
#20
Chunxiao Hu, Sumit Kalsi, Ioannis Zeimpekis, Kai Sun, Peter Ashburn, Carrie Turner, J Mark Sutton, Hywel Morgan
A low cost thin-film transistor (TFT) nanoribbon (NR) sensor has been developed for rapid real-time detection of DNA amplification using an isothermal Recombinase Polymerase Amplification (RPA) method. The semiconductor chip measures DNA amplification through a pH change, rather than via fluorescence. The utility of the method was demonstrated by amplifying CTX-M and NDM, two genes that confer bacterial resistance to cephalosporins and carbapenems, respectively. It is shown that this approach provides extremely fast and sensitive detection...
May 9, 2017: Biosensors & Bioelectronics
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