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Emily Koury, Kailey Harrell, Sarit Smolikove
Studies of the repair pathways associated with DNA double strand breaks (DSBs) are numerous, and provide evidence for cell-cycle specific regulation of homologous recombination (HR) by the regulation of its associated proteins. Laser microirradiation is a well-established method to examine in vitro kinetics of repair and allows for live-imaging of DSB repair from the moment of induction. Here we apply this method to whole, live organisms, introducing an effective system to analyze exogenous, microirradiation-induced breaks in the Caenorhabditis elegans germline...
December 13, 2017: Nucleic Acids Research
Kyle Kaniecki, Luisina De Tullio, Bryan Gibb, Youngho Kwon, Patrick Sung, Eric C Greene
Srs2 is a superfamily 1 (SF1) helicase and antirecombinase that is required for genome integrity. However, the mechanisms that regulate Srs2 remain poorly understood. Here, we visualize Srs2 as it acts upon single-stranded DNA (ssDNA) bound by the Rad51 recombinase. We demonstrate that Srs2 is a processive translocase capable of stripping thousands of Rad51 molecules from ssDNA at a rate of ∼50 monomers/s. We show that Srs2 is recruited to RPA clusters embedded between Rad51 filaments and that multimeric arrays of Srs2 assemble during translocation on ssDNA through a mechanism involving iterative Srs2 loading events at sites cleared of Rad51...
December 12, 2017: Cell Reports
Peili Hou, Hongmei Wang, Guimin Zhao, Chengqiang He, Hongbin He
BACKGROUND: Infectious bovine rhinotracheitis virus (IBRV) is a major pathogen in cattle and has led to significant economic losses to the dairy industry worldwide, and therefore a more optimal method for the rapid diagnosis of IBRV infection is highly needed. In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. METHODS: Distinct regions were selected as a candidate target for designing the LFD-RPA primers and probes...
December 13, 2017: BMC Veterinary Research
Ramesh Kumar, Cheok Chit Fang
RIF1 plays a key role in inhibiting DNA end resection and promoting NHEJ mediated DNA double stand break repair in G1. However, whether SUMOlyation may regulate RIF1 functions is still largely unknown. Here, we report that RIF1 is SUMOlyated in response to DNA damage. We identified PIAS4 as the primary SUMO E3 ligase required for the SUMOylation of RIF1 protein. Mammalian cells compromised of PIAS4 expression, show impaired RIF1 SUMOylation and defective for the disassembly of DNA damage responsive RIF1 foci...
December 12, 2017: Scientific Reports
Michael L Powell, Frank R Bowler, Aurore J Martinez, Catherine J Greenwood, Niall Armes, Olaf Piepenburg
Rapid, cost-effective and sensitive detection of nucleic acids has the ability to improve upon current practices employed for pathogen detection in diagnosis of infectious disease and food testing. Furthermore, if assay complexity can be reduced, nucleic acid amplification tests could be deployed in resource-limited and home use scenarios. In this study, we developed a novel Fpg (Formamidopyrimidine DNA glycosylase) probe chemistry, which allows lateral flow detection of amplification in undiluted recombinase polymerase amplification (RPA) reactions...
December 9, 2017: Analytical Biochemistry
Yukinori Takenaka, Ryohei Oya, Kengo Aoki, Hiroko Hamaguchi, Kazuya Takemura, Masayuki Nozawa, Takahiro Kitamura, Yoshifumi Yamamoto, Atsuhiko Uno
OBJECTIVES: To examine whether lactate dehydrogenase (LDH) can predict the prognosis of oral cavity squamous cell carcinoma (OSCC) and to determine the optimal cut-off values for LDH. METHODS: This retrospective study included 184 patients with OSCC, treated with surgery between 2006 and 2014. The association between LDH and T, N classification was investigated using the Mann-Whitney test. Cut-off values for LDH were determined with a recursive partitioning analysis (RPA)...
December 12, 2017: Acta Oto-laryngologica
Mona Kamal, David I Rosenthal, Stefania Volpe, Ryan P Goepfert, Adam S Garden, Katherine A Hutcheson, Karine A Al Feghali, Mohamed Ahmed Mohamed Meheissen, Salman A Eraj, Amy E Dursteler, Bowman Williams, Joshua B Smith, Jeremy M Aymard, Joel Berends, Aubrey L White, Steven J Frank, William H Morrison, Richard Cardoso, Mark S Chambers, Erich M Sturgis, Tito R Mendoza, Charles Lu, Abdallah S R Mohamed, Clifton D Fuller, G Brandon Gunn
PURPOSE: To identify a clinically meaningful cut-point for the single item dry mouth question of the MD Anderson Symptom Inventory-Head and Neck module (MDASI-HN). METHODS: Head and neck cancer survivors who had received radiation therapy (RT) completed the MDASI-HN, the University of Michigan Hospital Xerostomia Questionnaire (XQ), and the health visual analog scale (VAS) of the EuroQol Five Dimension Questionnaire (EQ-5D). The Bayesian information criteria (BIC) were used to test the prediction power of each tool for EQ-5D VAS...
December 8, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
Mary E Natoli, Brittany A Rohrman, Carolina de Santiago, Gert U van Zyl, Rebecca R Richards-Kortum
Regular HIV-1 viral load monitoring is the standard of care to assess antiretroviral therapy effectiveness in resource-rich settings. Persistently elevated viral loads indicate virologic failure (VF), which warrants HIV drug resistance testing (HIVDRT) to allow individualized regimen switches. However, in settings lacking access to HIVDRT, clinical decisions are often made based on symptoms, leading to unnecessary therapy switches and increased costs of care. This work presents a proof-of-concept assay to detect M184V, the most common drug resistance mutation after first-line antiretroviral therapy failure, in a paper format...
December 8, 2017: Analytical Biochemistry
Maria-Nefeli Tsaloglou, Alex Nemiroski, Gulden Camci-Unal, Dionysios C Christodouleas, Lara P Murray, John T Connelly, George M Whitesides
This paper demonstrates a new method for electrochemical detection of specific sequences of DNA present in trace amounts in serum or blood. This method is designed for use at the point-of-care (particularly in resource-limited settings). By combining recombinase polymerase amplification (RPA)- an isothermal alternative to the polymerase chain reaction - with an electroactive mediator, this electrochemical methodology enables accurate detection of DNA in the field using a low-cost, portable electrochemical analyzer (specifically designed for this type of analysis)...
December 7, 2017: Analytical Biochemistry
Zeljana Bonacic Losic
The surface plasmon excitation spectrum is calculated for the semi-infinite three-dimensional Dirac semimetal. We used the random phase approximation (RPA) for the calculation of the surface dielectric function, from which we derived the dynamical structure factor. The surface excitation spectrum shows a well-defined strong surface plasmon peak due to the plasmon mode in the bulk, with a noticeable influence of electron-hole excitations at large wave vectors parallel to the surface. The obtained spectrum will be useful for exploring experimentally the surface spectral properties of three-dimensional topological Dirac semimetals...
December 8, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Roshan S Prabhu, Robert H Press, Danielle M Boselli, Katherine R Miller, Scott P Lankford, Robert J McCammon, Benjamin J Moeller, John H Heinzerling, Carolina E Fasola, Kirtesh R Patel, Anthony L Asher, Ashley L Sumrall, Walter J Curran, Hui-Kuo G Shu, Stuart H Burri
Patients treated with stereotactic radiosurgery (SRS) for brain metastases (BM) are at increased risk of distant brain failure (DBF). Two nomograms have been recently published to predict individualized risk of DBF after SRS. The goal of this study was to assess the external validity of these nomograms in an independent patient cohort. The records of consecutive patients with BM treated with SRS at Levine Cancer Institute and Emory University between 2005 and 2013 were reviewed. Three validation cohorts were generated based on the specific nomogram or recursive partitioning analysis (RPA) entry criteria: Wake Forest nomogram (n = 281), Canadian nomogram (n = 282), and Canadian RPA (n = 303) validation cohorts...
December 7, 2017: Journal of Neuro-oncology
Ana Teixeira-Silva, Anissia Ait Saada, Julien Hardy, Ismail Iraqui, Marina Charlotte Nocente, Karine Fréon, Sarah A E Lambert
Replication requires homologous recombination (HR) to stabilize and restart terminally arrested forks. HR-mediated fork processing requires single stranded DNA (ssDNA) gaps and not necessarily double strand breaks. We used genetic and molecular assays to investigate fork-resection and restart at dysfunctional, unbroken forks in Schizosaccharomyces pombe. Here, we report that fork-resection is a two-step process regulated by the non-homologous end joining factor Ku. An initial resection mediated by MRN-Ctp1 removes Ku from terminally arrested forks, generating ~110 bp sized gaps obligatory for subsequent Exo1-mediated long-range resection and replication restart...
December 7, 2017: Nature Communications
J Biau, E Chautard, E De Schlichting, G Dupic, B Pereira, A Fogli, M Müller-Barthélémy, P Dalloz, T Khalil, A F Dillies, X Durando, C Godfraind, P Verrelle
BACKGROUND: The optimization of the management for elderly glioblastoma patients is crucial given the demographics of aging in many countries. We report the outcomes for a "real-life" patient cohort (i.e. unselected) comprising consecutive glioblastoma patients aged 70 years or more, treated with different radiotherapy +/- temozolomide regimens. METHODS: From 2003 to 2016, 104 patients ≥ 70 years of age, consecutively treated by radiotherapy for glioblastoma, were included in this study...
December 6, 2017: Radiation Oncology
David O Onyango, Gabriella Lee, Jeremy M Stark
Disruption of RNA splicing causes genome instability, which could contribute to cancer etiology. Furthermore, RNA splicing is an emerging anti-cancer target. Thus, we have evaluated the influence of the spliceosome factor PRPF8 and the splicing inhibitor Pladienolide B (PlaB) on homologous recombination (HR). We find that PRPF8 depletion and PlaB treatment cause a specific defect in homology-directed repair (HDR), and single strand annealing (SSA), which share end resection as a common intermediate, and BRCA1 as a required factor...
November 7, 2017: Oncotarget
Yuancong Xu, Yujun Wei, Nan Cheng, Kunlun Huang, Weiran Wang, Li Zhang, Wentao Xu, Yunbo Luo
In this study, a whole-course nucleic acid constructed biosensor that combines the all-in-one concepts of the Universal Blocking Linker Recombinase Polymerase Amplification (UBLRPA) and a PNA-based lateral flow device (PLFD) has been developed for the on-site ultra-sensitive detection of food pathogens. Using the pre-amplification UBLRPA principle, a universal linker and C3 space blocker was applied to produce the universal linker single-duplex DNA products. The developed amplification system was employed to realize the conversion from duplex products to a single strand...
December 4, 2017: Analytical Chemistry
Matthias Beuerle, Christian Ochsenfeld
Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors...
November 28, 2017: Journal of Chemical Physics
Astrid Lancrey, Layal Safa, Jean Chatain, Emmanuelle Delagoutte, Jean-François Riou, Patrizia Alberti, Carole Saintomé
Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s...
November 27, 2017: Biochimie
Luiz M Oliveira, Thiago S Moreira, Ana C Takakura
Central chemoreceptors are primarily sensitive to changes in CO2/H+, and such changes lead to intense breathing activity. Medullary raphe and retrotrapezoid nucleus (RTN) neurons are candidates for central chemoreceptors because they are unusually pH sensitive. The pathophysiology of Parkinson's disease (PD) is related to the reduction of neurons in the substantia nigra pars compacta (SNpc) that express dopamine, although other neurons can also be degenerated in this pathology. In rodent models of PD, we showed an impairment of the hypercapnia ventilatory response due to a reduction in the number of RTN chemosensitive neurons...
November 27, 2017: Neuroscience
Sarah E Abbott, Fabian Camacho, Lauren C Peres, Anthony J Alberg, Elisa V Bandera, Melissa Bondy, Michele L Cote, Ellen Funkhouser, Patricia G Moorman, Edward S Peters, Bo Qin, Ann G Schwartz, Jill Barnholtz-Sloan, Paul Terry, Joellen M Schildkraut
PURPOSE: While recreational physical activity (RPA) has been associated with reduced mortality in breast, colorectal, and prostate cancers, evidence for epithelial ovarian cancer (EOC) is limited. Most EOC studies have been in predominantly white populations, although inactivity is more prevalent and survival is poorer among African-American (AA) women. We examined RPA before and after EOC diagnosis and associations with survival among AA women. METHODS: We analyzed data from 264 EOC survivors enrolled in a population-based, case-control study who completed surveys that included questions about pre- and post-diagnosis RPA...
November 29, 2017: Cancer Causes & Control: CCC
Mirza Pojskic, Miriam H A Bopp, Markus Schymalla, Christopher Nimsky, Barbara Carl
Background: Metastases are the most frequent tumors in the brain. Most often used scoring systems to predict the outcome are the RPA (Recursive Partitioning Analysis) classification and the DS-GPA (Diagnosis-Specific Graded Prognostic Assessment) score. The goal of our study was to determine prognostic factors which influence outcome in patients who undergo surgery for brain metastases and to compare different outcome scores. Methods: Two hundred and twenty-nine patients who underwent surgery for brain metastases in our institution between January 2005 and December 2014 were included in the study...
2017: Surgical Neurology International
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