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https://www.readbyqxmd.com/read/28345860/an-instant-visual-and-instrument-free-method-for-on-site-screening-of-gts-40-3-2-soybean-based-on-body-heat-triggered-recombinase-polymerase-amplification
#1
Rui Wang, Fang Zhang, Liu Wang, Wenjuan Qian, Cheng Qian, Jian Wu, Yi-Bin Ying
On-site monitoring the plantation of genetically modified (GM) crops is of critical importance in agriculture industry throughout the world. In this paper, a simple, visual and instrument-free method for instant on-site detection of GTS 40-3-2 soybean has been developed. It is based on body-heat recombinase polymerase amplification (RPA) and followed with naked-eye detection via fluorescent DNA dye. Combining with extremely simplified sample preparation, the whole detection process can be accomplished within 10 min and the fluorescent results can be photographed by accompanied smart phone...
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345219/a-prototype-of-mathematical-treatment-of-pen-pressure-data-for-signature-verification
#2
Chi-Keung Li, Siu-Kay Wong, Lai-Chu Joyce Chim
A prototype using simple mathematical treatment of the pen pressure data recorded by a digital pen movement recording device was derived. In this study, a total of 48 sets of signature and initial specimens were collected. Pearson's correlation coefficient was used to compare the data of the pen pressure patterns. From the 820 pair comparisons of the 48 sets of genuine signatures, a high degree of matching was found in which 95.4% (782 pairs) and 80% (656 pairs) had rPA > 0.7 and rPA > 0.8, respectively...
March 26, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28342800/development-of-an-isothermal-recombinase-polymerase-amplification-assay-for-rapid-detection-of-pseudorabies-virus
#3
Yang Yang, Xiaodong Qin, Wei Zhang, Zhiyong Li, Shuaijun Zhang, Yanmin Li, Zhidong Zhang
Recombinase polymerase amplification assays using real-time fluorescent detection (real-time RPA assay) and lateral flow dipstick (RPA LFD assay) were developed targeting the gD gene of pseudorabies virus (PRV). Both assays were performed at 39 °C within 20 min. The sensitivity of the real-time RPA assay and the RPA LFD assay was 100 copies per reaction and 160 copies per reaction, respectively. Both assays did not detect DNAs from other virus or PRV negative samples. Therefore, the developed RPA assays provide a rapid, simple, sensitive and specific alternative tool for detection of PRV...
March 22, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28339256/analytic-interatomic-forces-in-the-random-phase-approximation
#4
Benjamin Ramberger, Tobias Schäfer, Georg Kresse
We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the GW approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28337424/single-institutional-experience-of-stereotactic-radiosurgery-alone-for-first-brain-metastatic-event-and-salvage-of-second-brain-metastatic-event-in-a-community-setting-with-review-of-the-literature
#5
Shaharyar Ahmad, Anthony Ricco, Royce Brown, Alexandra Hanlon, Jun Yang, Jing Feng, Michael Stanley, Richard Buonocore, Aubrey Okpaku, Steven Arrigo, John Lamond, Luther Brady, Rachelle Lanciano
PURPOSE: To document survival for patients treated with stereotactic radiosurgery (SRS) alone for brain metastases either at initial presentation or for salvage in conjunction with other known prognostic factors in a single institutional community setting with comparison to current literature. METHODS: All patients treated for brain metastases with SRS between October 2006 and October 2013 were reviewed. We identified 91 patients treated with SRS alone for first brain metastatic event (FBME) and 87 patients treated with SRS for second brain metastatic event (SBME)...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28334931/rgf1p-rho1p-gef-is-required-for-double-strand-break-repair-in-fission-yeast
#6
Elvira Manjón, Tomás Edreira, Sofía Muñoz, Yolanda Sánchez
Rho GTPases are conserved molecules that control cytoskeletal dynamics. These functions are expedited by Rho GEFs that stimulate the release of GDP to enable GTP binding, thereby allowing Rho proteins to initiate intracellular signaling. How Rho GEFs and Rho GTPases protect cells from DNA damage is unknown. Here, we explore the extreme sensitivity of a deletion mutation in the Rho1p exchange factor Rgf1p to the DNA break/inducing antibiotic phleomycin (Phl). The Rgf1p mutant cells are defective in reentry into the cell cycle following the induction of severe DNA damage...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334870/annealing-helicase-harp-closes-rpa-stabilized-dna-bubbles-non-processively
#7
Daniel R Burnham, Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, Cees Dekker
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334750/ctc1-mediated-c-strand-fill-in-is-an-essential-step-in-telomere-length-maintenance
#8
Xuyang Feng, Shih-Jui Hsu, Christopher Kasbek, Mary Chaiken, Carolyn M Price
To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere replication. CST first aids in duplication of the telomeric dsDNA. Then after telomerase has extended the G-rich strand, CST facilitates fill-in synthesis of the complementary C-strand. Here, we analyze telomere structure after disruption of human CTC1 and demonstrate that functional CST is essential for telomere length maintenance due to its role in mediating C-strand fill-in...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331180/ccr5-promoter-activity-correlates-with-hiv-disease-progression-by-regulating-ccr5-cell-surface-expression-and-cd4-t-cell-apoptosis
#9
Anjali Joshi, Erin B Punke, Melina Sedano, Bethany Beauchamp, Rima Patel, Cassady Hossenlopp, Ogechika K Alozie, Jayanta Gupta, Debabrata Mukherjee, Himanshu Garg
CCR5 is the major co-receptor for HIV and polymorphisms in the CCR5 gene as well as promoter region that alter cell surface expression have been associated with disease progression. We determined the relationship between CCR5 promoter polymorphisms and CD4 decline and other immunopathological features like immune activation and CD4+ T cell apoptosis in HIV patients. CCR5 promoter haplotype HHC was significantly associated with higher CD4 counts in patients. The relative promoter activity (RPA) of each haplotype was determined in vitro and combined promoter activity based on both alleles (CRPA) was assigned to each patients...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28328604/retropharyngeal-abscess-presenting-with-sleep-apnea-syndrome
#10
Hasan Emre Koçak, Mehmet Nurettin Kiral, Harun Acipayam, Mustafa Suphi Elbistanli, Fatma Tülin Kayhan
Retropharyngeal abscess (RPA) is the second most common deep neck space infection after peritonsiller abscess in pediatric population. Major signs and symptoms on physical examination include fever, hypersalivation, odynophagia, reduced oral intake, sore throat, swelling on the neck, torticollis, limitation in neck mobility, and voice changes. In this paper, the authors present a case of RPA with unusual and interesting presenting symptoms in a 10-month-old infant that exhibit new-onset and worsening snoring and sleep apnea...
March 21, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28302331/novel-recursive-partitioning-analysis-classification-for-newly-diagnosed-glioblastoma-a-multi-institutional-study-highlighting-the-mgmt-promoter-methylation-and-idh1-gene-mutation-status
#11
Chan Woo Wee, Eunji Kim, Nalee Kim, In Ah Kim, Tae Min Kim, Yu Jung Kim, Chul-Kee Park, Jin Wook Kim, Chae-Yong Kim, Seung Hong Choi, Jae Hyoung Kim, Sung-Hye Park, Gheeyoung Choe, Soon-Tae Lee, Jong Hee Chang, Se Hoon Kim, Chang-Ok Suh, Il Han Kim
BACKGROUND AND PURPOSE: To refine the recursive partitioning analysis (RPA) classification for glioblastoma incorporating the MGMT methylation and IDH1 mutation status. METHODS AND MATERIALS: Three-hundred forty patients were treated with radiotherapy plus concurrent and adjuvant temozolomide in three tertiary-referral hospitals. MGMT methylation and IDH1 mutation status were available in all patients. Methylation of the MGMT (MGMTmeth) and mutation of IDH1 (IDH1mut) were observed in 42...
March 13, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/28301757/random-phase-approximation-methods
#12
Guo P Chen, Vamsee K Voora, Matthew M Agee, Sreeganesh Balasubramani, Filipp Furche
Random-phase approximation (RPA) methods are rapidly emerging as costeffective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed...
March 16, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28297563/spermatogenesis-associated-22-is-required-for-dna-repair-and-synapsis-of-homologous-chromosomes-in-mouse-germ-cells
#13
E Hays, N Majchrzak, V Daniel, Z Ferguson, S Brown, K Hathorne, S La Salle
Analysis of the N-ethyl-N-nitrosourea (ENU)-induced repro42 mutation previously identified spermatogenesis associated 22 (Spata22) as a gene required for meiotic progression and fertility in both male and female mice, but its specific contribution to the process was unclear. Here, we report on a novel, null allele of Spata22 (Spata22(Gt) ) and confirm its requirement for germ cell development. Similar to repro42 mutant mice, histological and mating analyses indicate that gametogenesis is profoundly affected in Spata22(Gt/Gt) males and females, resulting in infertility...
March 2017: Andrology
https://www.readbyqxmd.com/read/28280701/renoportal-anastomosis-in-living-donor-liver-transplantation-with-prior-proximal-splenorenal-shunt
#14
Fatih Ozdemir, Koray Kutluturk, Bora Barut, Perviz Abbasov, Ramazan Kutlu, Cuneyt Kayaalp, Sezai Yılmaz
For transplant surgeons, end-stage liver disease with portal venous thrombosis and a previous splenorenal shunt (SRS) is a significant challenge during liver transplantation. Thrombosis of the portal vein can be corrected by surgical interventions, such as portal venous thrombectomy or surgical removal of the thrombosed portal vein. Even also placement of a graft between the mesenteric vein and the graft portal vein can be performed. If these maneuvers fail, a renoportal anastomosis (RPA) can be performed to achieve adequate graft inflow...
February 24, 2017: World Journal of Transplantation
https://www.readbyqxmd.com/read/28272886/first-principles-models-for-van-der-waals-interactions-in-molecules-and-materials-concepts-theory-and-applications
#15
Jan Hermann, Robert A DiStasio, Alexandre Tkatchenko
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches)...
March 8, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28272471/dynamics-of-laser-driven-proton-acceleration-exhibited-by-measured-laser-absorptivity-and-reflectivity
#16
J H Bin, K Allinger, K Khrennikov, S Karsch, P R Bolton, J Schreiber
Proton acceleration from nanometer thin foils with intense laser pulses is investigated experimentally. We analyzed the laser absorptivity by parallel monitoring of laser transmissivity and reflectivity with different laser intensities when moving the targets along the laser axis. A direct correlation between laser absorptivity and maximum proton energy is observed. Experimental results are interpreted in analytical estimation, exhibiting a coexistence of plasma expansion and light-sail form of radiation pressure acceleration (RPA-LS) mechanisms during the entire proton acceleration process based on the measured laser absorptivity and reflectivity...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265089/reconstitution-of-saccharomyces-cerevisiae-dna-polymerase-%C3%AE%C2%B5-dependent-mismatch-repair-with-purified-proteins
#17
Nikki Bowen, Richard D Kolodner
Mammalian and Saccharomyces cerevisiae mismatch repair (MMR) proteins catalyze two MMR reactions in vitro. In one, mispair binding by either the MutS homolog 2 (Msh2)-MutS homolog 6 (Msh6) or the Msh2-MutS homolog 3 (Msh3) stimulates 5' to 3' excision by exonuclease 1 (Exo1) from a single-strand break 5' to the mispair, excising the mispair. In the other, Msh2-Msh6 or Msh2-Msh3 activate the MutL homolog 1 (Mlh1)-postmeiotic segregation 1 (Pms1) endonuclease in the presence of a mispair and a nick 3' to the mispair, to make nicks 5' to the mispair, allowing Exo1 to excise the mispair...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28263577/vanishing-overhead-linear-scaling-random-phase-approximation-by-cholesky-decomposition-and-an-attenuated-coulomb-metric
#18
Arne Luenser, Henry F Schurkus, Christian Ochsenfeld
A reformulation of the random phase approximation within the resolution-of-the-identity (RI) scheme is presented, that is competitive to canonical molecular orbital RI-RPA already for small- to medium-sized molecules. For electronically sparse systems drastic speedups due to the reduced scaling behavior compared to the molecular orbital formulation are demonstrated. Our reformulation is based on two ideas, which are independently useful: First, a Cholesky decomposition of density matrices that reduces the scaling with basis set size for a fixed-size molecule by one order, leading to massive performance improvements...
March 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28258182/annealing-of-complementary-dna-sequences-during-double-strand-break-repair-in-drosophila-is-mediated-by-the-ortholog-of-smarcal1
#19
Julie Korda Holsclaw, Jeff Sekelsky
DNA double-strand breaks (DSBs) pose a serious threat to genomic integrity. If unrepaired, they can lead to chromosome fragmentation and cell death. If repaired incorrectly, they can cause mutations and chromosome rearrangements. DSBs are repaired using end-joining or homology-directed repair strategies, with the predominant form of homology-directed repair being synthesis-dependent strand annealing (SDSA). SDSA is the first defense against genomic rearrangements and information loss during DSB repair, making it a vital component of cell health and an attractive target for chemotherapeutic development...
March 3, 2017: Genetics
https://www.readbyqxmd.com/read/28257700/functions-of-replication-protein-a-as-a-sensor-of-r-loops-and-a-regulator-of-rnaseh1
#20
Hai Dang Nguyen, Tribhuwan Yadav, Sumanprava Giri, Borja Saez, Timothy A Graubert, Lee Zou
R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops...
March 2, 2017: Molecular Cell
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