Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes.

PubMed

Ghadessy, Farid J; Holliger, Philipp

2007-01-01

Compartmentalized self-replication (CSR) is a novel method for the directed evolution of enzymes and, in particular, polymerases. In its simplest form, CSR consists of a simple feedback loop involving a polymerase that replicates only its own encoding gene (self-replication). Self-replication occurs in discrete, spatially separate, noncommunicating compartments formed by a heat-stable water-in-oil emulsion. Compartmentalization ensures the linkage of phenotype and genotype (i.e., it ensures that each polymerase replicates only its own encoding gene to the exclusion of those in the other compartments). As a result, adaptive gains by the polymerase directly (and proportionally) translate into genetic amplification of the encoding polymerase gene. CSR has proven to be a useful strategy for the directed evolution of polymerases directly from diverse repertoires of polymerase genes. In this chapter, we describe some of the CSR protocols used successfully to evolve variants of T. aquaticus Pol I (Taq) polymerase with novel and useful properties, such as increased thermostability or resistance to the potent inhibitor, heparin, from a repertoire of randomly mutated Taq polymerase genes.

Quantitative Tetraplex Real-Time Polymerase Chain Reaction Assay with TaqMan Probes Discriminates Cattle, Buffalo, and Porcine Materials in Food Chain.

PubMed

Hossain, M A Motalib; Ali, Md Eaqub; Sultana, Sharmin; Asing; Bonny, Sharmin Quazi; Kader, Md Abdul; Rahman, M Aminur

2017-05-17

Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.

Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication.

PubMed

Aye, Seaim Lwin; Fujiwara, Kei; Ueki, Asuka; Doi, Nobuhide

2018-05-05

Although compartmentalized self-replication (CSR) and compartmentalized partnered replication (CPR) are powerful tools for directed evolution of proteins and gene circuits, limitations remain in the emulsion PCR process with the wild-type Taq DNA polymerase used so far, including long run times, low amounts of product, and false negative results due to inhibitors. In this study, we developed a high-efficiency mutant of DNA polymerase I from Thermus thermophilus HB27 (Tth pol) suited for CSR and CPR. We modified the wild-type Tth pol by (i) deletion of the N-terminal 5' to 3' exonuclease domain, (ii) fusion with the DNA-binding protein Sso7d, (iii) introduction of four known effective point mutations from other DNA polymerase mutants, and (iv) codon optimization to reduce the GC content. Consequently, we obtained a mutant that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, we performed four rounds of CSR selection with a randomly mutated library of this modified Tth pol and obtained mutants that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol. Copyright © 2018 Elsevier Inc. All rights reserved.

Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

PubMed

Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

2008-06-25

Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.

Identification and quantification of three genetically modified insect resistant cotton lines using conventional and TaqMan real-time polymerase chain reaction methods.

PubMed

Yang, Litao; Pan, Aihu; Zhang, Kewei; Guo, Jinchao; Yin, Changsong; Chen, Jianxiu; Huang, Cheng; Zhang, Dabing

2005-08-10

As the genetically modified organisms (GMOs) labeling policies are issued in many countries, qualitative and quantitative polymerase chain reaction (PCR) techniques are increasingly used for the detection of genetically modified (GM) crops in foods. Qualitative PCR and TaqMan real-time quantitative PCR methods to detect and identify three varieties of insect resistant cotton, i.e., Mon531 cotton (Monsanto Co.) and GK19 and SGK321 cottons (Chinese Academy of Agricultural Sciences), which were approved for commercialization in China, were developed in this paper. Primer pairs specific to inserted DNAs, such as Cowpea trypsin inhibitor (CpTI) gene of SGK321 cotton and the specific junction DNA sequences containing partial Cry1A(c) gene and NOS terminator of Mon531, GK19, and SGK321 cotton varieties were designed to conduct the identified PCR assays. In conventional specific identified PCR assays, the limit of detection (LOD) was 0.05% for Mon531, GK19, or SGK321 in 100 ng of cotton genomic DNA for one reaction. Also, the multiplex PCR method for screening the three GM cottons was also established, which could save time and cost in practical detection. Furthermore, a real-time quantitative PCR assay based on TaqMan chemistry for detection of insect resistant gene, Cry1A(c), was developed. This assay also featured the use of a standard plasmid as a reference molecule, which contained both a specific region of the transgene Cry1A(c) and an endogenous stearoyl-acyl carrier protein desaturase (Sad1) gene of the cotton. In quantitative PCR assay, the quantification range was from 0.01 to 100% in 100 ng of the genome DNA template, and in the detection of 1.0, 3.0, and 5.0% levels of three insect resistant cotton lines, respectively, all of the relative standard deviations (RSDs) were less than 8.2% except for the GM cotton samples with 1.0% Mon531 or GK19, which meant that our real-time PCR assays involving the use of reference molecule were reliable and practical for GM

A real-time TaqMan polymerase chain reaction for the identification of Culex vectors of West Nile and Saint Louis encephalitis viruses in North America.

PubMed

Sanogo, Yibayiri O; Kim, Chang-Hyun; Lampman, Richard; Novak, Robert J

2007-07-01

In North America, West Nile and St. Louis encephalitis viruses have been detected in a wide range of vector species, but the majority of isolations continue to be from pools of mixed mosquitoes in the Culex subgenus Culex. Unfortunately, the morphologic identification of these important disease vectors is often difficult, particularly in regions of sympatry. We developed a sensitive real-time TaqMan polymerase chain reaction assay that allows reliable identification of Culex mosquitoes including Culex pipiens pipiens, Cx. p. quinquefasciatus, Cx. restuans, Cx. salinarius, Cx. nigripalpus, and Cx. tarsalis. Primers and fluorogenic probes specific to each species were designed based on sequences of the acetylcholinesterase gene (Ace2). Both immature and adult mosquitoes were successfully identified as individuals and as mixed species pools. This identification technique provides the basis for a rapid, sensitive, and high-throughput method for expounding the species-specific contribution of vectors to various phases of arbovirus transmission.

A TaqMan-based real-time PCR assay for porcine parvovirus 4 detection and quantification in reproductive tissues of sows

USDA-ARS?s Scientific Manuscript database

Porcine parvovirus 4 (PPV4) is a DNA virus, and a member of the Parvoviridae family within the Bocavirus genera. It was recently detected in swine, but its epidemiology and pathology remain unclear. A TaqMan-based real-time polymerase chain reaction (qPCR) assay targeting a conserved region of the O...

A sensitive and high throughput TaqMan-based reverse transcription quantitative polymerase chain reaction assay efficiently discriminates ALK rearrangement from overexpression for lung cancer FFPE specimens.

PubMed

Lung, Jrhau; Lin, Yu-Ching; Hung, Ming-Szu; Jiang, Yuan Yuan; Lee, Kuan-Der; Lin, Paul Yann; Tsai, Ying Huang

2016-04-01

ALK fusion gene is an oncogenic driver in lung cancer with low prevalence, which can be ameliorated by crizotinib. Currently, ALK fusion gene can be diagnosed by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), but inconstistnt results between the two methods are encountered regularly. To make the ALK fusion gene screening more efficient and to provide a simple solution to clarify the discrepancy between FISH and IHC results, a sensitive TaqMan-based reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay was established. The 3-plex TaqMan-based RT-qPCR assay was established and performed on 102 archived formalin-fixed, paraffin-embedded (FFPE) NSCLC samples to detect ALK rearrangement and overexpression. Break-apart FISH and automatic immunohistochemistry based ALK assays were performed side by side using tissue microarray. The RT-qPCR was performed successfully for 80 samples and 10 of them showed positive signals. Three out of the 10 qPCR positive cases were further confirmed by FISH and IHC test. Two others were IHC positive and FISH negative, and expressed full-length ALK transcript. The rest were neither FISH nor IHC positive and their ALK expression level was significantly lower than those FISH or IHC positive cases. Our RT-qPCR assay demonstrates that the capability and reliability of ALK detection is comparable to FISH and IHC, but it is more effective at discriminating ALK rearrangement from overexpression. The RT-qPCR assay easily clarifies the discrepancy between FISH and IHC, and can be incorporated into routine ALK screening for lung cancer. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Comparative evaluation of new TaqMan real-time assays for the detection of hepatitis A virus.

PubMed

Houde, Alain; Guévremont, Evelyne; Poitras, Elyse; Leblanc, Danielle; Ward, Pierre; Simard, Carole; Trottier, Yvon-Louis

2007-03-01

Three novel real-time TaqMan RT-PCR assays targeting the 5'-UTR, the viral protease and the viral polymerase regions of the hepatitis A virus (HAV) were developed, evaluated and compared against a new published 5'-UTR TaqMan assay (JN) and a widely used conventional RT-PCR assay (HAVc). All conventional RT-PCR (HAV, SH-Prot and SH-Poly systems) and TaqMan (SH-Prot, SH-Poly, JN and SH-5U systems) assays evaluated were consistent for the detection of the three different HAV strains (HM-175, HAS-15 and LSH/S) used and reproducible for both RNA duplicates with the exception of two reproducibility discrepancies observed with both 5'-UTR real-time systems (JN and SH-5U). Limits of detection for conventional HAV, SH-Prot and SH-Poly RT-PCR systems were found to be equivalent when tested with serially diluted suspensions of the HM-175 strain. Although the four real-time RT-PCR TaqMan assays evaluated herein produced similar and consistent quantification data down to the level of one genomic equivalent copy with their respectively cloned amplicons, significant and important differences were observed for the detection of HAV genomic RNA. Results showed that the new real-time TaqMan SH-Poly and SH-Prot primer and probe systems were more consistent and sensitive by 5 logs as compared to both 5'-UTR designs (JN and SH-5U) used for the detection of HAV genomic RNA as well as for the detection in cell culture by cytopathic effect. Considering their higher analytical sensitivity, the proposed SH-Poly and SH-Prot amplification systems could therefore represent valuable tools for the detection of HAV in clinical, environmental and food samples.

Identification and quantification of genetically modified Moonshade carnation lines using conventional and TaqMan real-time polymerase chain reaction methods.

PubMed

Li, Peng; Jia, Junwei; Bai, Lan; Pan, Aihu; Tang, Xueming

2013-07-01

Genetically modified carnation (Dianthus caryophyllus L.) Moonshade was approved for planting and commercialization in several countries from 2004. Developing methods for analyzing Moonshade is necessary for implementing genetically modified organism labeling regulations. In this study, the 5'-transgene integration sequence was isolated using thermal asymmetric interlaced (TAIL)-PCR. Based upon the 5'-transgene integration sequence, conventional and TaqMan real-time PCR assays were established. The relative limit of detection for the conventional PCR assay was 0.05 % for Moonshade using 100 ng total carnation genomic DNA, corresponding to approximately 79 copies of the carnation haploid genome, and the limits of detection and quantification of the TaqMan real-time PCR assay were estimated to be 51 and 254 copies of haploid carnation genomic DNA, respectively. These results are useful for identifying and quantifying Moonshade and its derivatives.

Comprehensive Panel of Real-Time TaqMan™ Polymerase Chain Reaction Assays for Detection and Absolute Quantification of Filoviruses, Arenaviruses, and New World Hantaviruses

PubMed Central

Trombley, Adrienne R.; Wachter, Leslie; Garrison, Jeffrey; Buckley-Beason, Valerie A.; Jahrling, Jordan; Hensley, Lisa E.; Schoepp, Randal J.; Norwood, David A.; Goba, Augustine; Fair, Joseph N.; Kulesh, David A.

2010-01-01

Viral hemorrhagic fever is caused by a diverse group of single-stranded, negative-sense or positive-sense RNA viruses belonging to the families Filoviridae (Ebola and Marburg), Arenaviridae (Lassa, Junin, Machupo, Sabia, and Guanarito), and Bunyaviridae (hantavirus). Disease characteristics in these families mark each with the potential to be used as a biological threat agent. Because other diseases have similar clinical symptoms, specific laboratory diagnostic tests are necessary to provide the differential diagnosis during outbreaks and for instituting acceptable quarantine procedures. We designed 48 TaqMan™-based polymerase chain reaction (PCR) assays for specific and absolute quantitative detection of multiple hemorrhagic fever viruses. Forty-six assays were determined to be virus-specific, and two were designated as pan assays for Marburg virus. The limit of detection for the assays ranged from 10 to 0.001 plaque-forming units (PFU)/PCR. Although these real-time hemorrhagic fever virus assays are qualitative (presence of target), they are also quantitative (measure a single DNA/RNA target sequence in an unknown sample and express the final results as an absolute value (e.g., viral load, PFUs, or copies/mL) on the basis of concentration of standard samples and can be used in viral load, vaccine, and antiviral drug studies. PMID:20439981

TaqMan probe real-time polymerase chain reaction assay for the quantification of canine DNA in chicken nugget.

PubMed

Rahman, Md Mahfujur; Hamid, Sharifah Bee Abd; Basirun, Wan Jefrey; Bhassu, Subha; Rashid, Nur Raifana Abdul; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Ali, Md Eaqub

2016-01-01

This paper describes a short-amplicon-based TaqMan probe quantitative real-time PCR (qPCR) assay for the quantitative detection of canine meat in chicken nuggets, which are very popular across the world, including Malaysia. The assay targeted a 100-bp fragment of canine cytb gene using a canine-specific primer and TaqMan probe. Specificity against 10 different animals and plants species demonstrated threshold cycles (Ct) of 16.13 ± 0.12 to 16.25 ± 0.23 for canine DNA and negative results for the others in a 40-cycle reaction. The assay was tested for the quantification of up to 0.01% canine meat in deliberately spiked chicken nuggets with 99.7% PCR efficiency and 0.995 correlation coefficient. The analysis of the actual and qPCR predicted values showed a high recovery rate (from 87% ± 28% to 112% ± 19%) with a linear regression close to unity (R(2) = 0.999). Finally, samples of three halal-branded commercial chicken nuggets collected from different Malaysian outlets were screened for canine meat, but no contamination was demonstrated.

Specific and straightforward molecular investigation of β-thalassemia mutations in the Malaysian Malays and Chinese using direct TaqMan genotyping assays.

PubMed

Kho, S L; Chua, K H; George, E; Tan, J A M A

2013-07-15

Beta-thalassemia is a life-threatening inherited blood disorder. Rapid characterization of β-globin gene mutations is necessary because of the high frequency of Malaysian β-thalassemia carriers. A combination real-time polymerase chain reaction genotyping assay using TaqMan probes was developed to confirm β-globin gene mutations. In this study, primers and probes were designed to specifically identify 8 common β-thalassemia mutations in the Malaysian Malay and Chinese ethnic groups using the Primer Express software. "Blind tests" using DNA samples from healthy individuals and β-thalassemia patients with different genotypes were performed to determine the specificity and sensitivity of this newly designed assay. Our results showed 100% sensitivity and specificity for this novel assay. In conclusion, the TaqMan genotyping assay is a straightforward assay that allows detection of β-globin gene mutations in less than 40 min. The simplicity and reproducibility of the TaqMan genotyping assay permit its use in laboratories as a rapid and cost-effective diagnostic tool for confirmation of common β-thalassemia mutations in Malaysia.

Detection of viable Salmonella in ice cream by TaqMan real-time polymerase chain reaction assay combining propidium monoazide.

PubMed

Wang, Yuexia; Yang, Ming; Liu, Shuchun; Chen, Wanyi; Suo, Biao

2015-09-01

Real-time polymerase chain reaction (PCR) allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at -18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA) was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 10 3  CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 10 0  CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach. Copyright © 2015. Published by Elsevier B.V.

Concordance of HIV-1 RNA Values by Amplicor and TaqMan 2.0 in Patients With Confirmed Suppression in Clinical Trials

PubMed Central

Garner, Will; White, Kirsten; Szwarcberg, Javier; McCallister, Scott; Zhong, Lijie; Wulfsohn, Mike

2016-01-01

Background. The COBAS AMPLICOR HIV-1 MONITOR Test, version 1.5 (Amplicor) has been replaced with the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, version 2.0 (TaqMan 2.0), a real-time polymerase chain reaction human immunodeficiency virus type 1 (HIV-1) assay with higher sensitivity and broader dynamic range. HIV-1 RNA values at the 50 copies/mL cutoff drive major patient management decisions and clinical study outcomes. Methods. A total of 2217 samples were collected from 1922 HIV-1–infected subjects taking antiretroviral therapy for at least 48 weeks and had at least 2 consecutive samples with HIV-1 RNA <50 copies/mL by Amplicor from 7 recent clinical trials. HIV-1 RNA results were obtained from the Amplicor and TaqMan 2.0 assays in parallel by a reference laboratory. Results. The overall concordance between assay results was 96% at the cutoff of 50 copies/mL. However, statistically significant discordance at the 50 copies/mL cutoff was found between the assays for 3.9% of samples (n = 87). By TaqMan 2.0, virologic failure defined as HIV-1 RNA ≥50 copies/mL was reported for 2.8% more samples than Amplicor. Of these 87 samples, 68 samples fell within the predicted range of assay variability. Retesting of HIV-1 RNA by TaqMan 2.0 confirmed the discordance in only 28 of the 87 samples. Conclusions. The TaqMan 2.0 assay reports fewer subjects below the clinical endpoint of HIV-1 RNA <50 copies/mL in HIV clinical trials than the Amplicor assay. This difference must be considered when assessing disease progression, designing clinical trials, and comparisons with historical trials that used the Amplicor assay. PMID:26689956

TaqMan real-time polymerase chain reaction for detection of Ophidiomyces ophiodiicola, the fungus associated with snake fungal disease.

PubMed

Bohuski, Elizabeth; Lorch, Jeffrey M; Griffin, Kathryn M; Blehert, David S

2015-04-15

Fungal skin infections associated with Ophidiomyces ophiodiicola, a member of the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) complex, have been linked to an increasing number of cases of snake fungal disease (SFD) in captive snakes around the world and in wild snake populations in eastern North America. The emergence of SFD in both captive and wild situations has led to an increased need for tools to better diagnose and study the disease. We developed two TaqMan real-time polymerase chain reaction (PCR) assays to rapidly detect O. ophiodiicola in clinical samples. One assay targets the internal transcribed spacer region (ITS) of the fungal genome while the other targets the more variable intergenic spacer region (IGS). The PCR assays were qualified using skin samples collected from 50 snakes for which O. ophiodiicola had been previously detected by culture, 20 snakes with gross skin lesions suggestive of SFD but which were culture-negative for O. ophiodiicola, and 16 snakes with no clinical signs of infection. Both assays performed equivalently and proved to be more sensitive than traditional culture methods, detecting O. ophiodiicola in 98% of the culture-positive samples and in 40% of the culture-negative snakes that had clinical signs of SFD. In addition, the assays did not cross-react with a panel of 28 fungal species that are closely related to O. ophiodiicola or that commonly occur on the skin of snakes. The assays did, however, indicate that some asymptomatic snakes (~6%) may harbor low levels of the fungus, and that PCR should be paired with histology when a definitive diagnosis is required. These assays represent the first published methods to detect O. ophiodiicola by real-time PCR. The ITS assay has great utility for assisting with SFD diagnoses whereas the IGS assay offers a valuable tool for research-based applications.

Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

USGS Publications Warehouse

Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

Detection of KIT Genotype in Pigs by TaqMan MGB Real-Time Quantitative Polymerase Chain Reaction.

PubMed

Li, Xiuxiu; Li, Xiaoning; Luo, Rongrong; Wang, Wenwen; Wang, Tao; Tang, Hui

2018-05-01

The dominant white phenotype in domestic pigs is caused by two mutations in the KIT gene: a 450 kb duplication containing the entire KIT gene together with flanking sequences and one splice mutation with a G:A substitution in intron 17. The purpose of this study was to establish a simple, rapid method to determine KIT genotype in pigs. First, to detect KIT copy number variation (CNV), primers for exon 2 of the KIT gene, along with a TaqMan minor groove binder (MGB) probe, were designed. The single-copy gene, estrogen receptor (ESR), was used as an internal control. A real-time fluorescence-based quantitative PCR (FQ-PCR) protocol was developed to accurately detect KIT CNVs. Second, to detect the splice mutation ratio of the G:A substitution in intron 17, a 175 bp region, including the target mutation, was amplified from genomic DNA. Based on the sequence of the resulting amplified fragment, an MGB probe set was designed to detect the ratio of splice mutation to normal using FQ-PCR. A series of parallel amplification curves with the same internal distances were obtained using gradually diluted DNA as templates. The CT values among dilutions were significantly different (p < 0.001) and the coefficients of variation from each dilution were low (from 0.13% to 0.26%). The amplification efficiencies for KIT and ESR were approximately equal, indicating ESR was an appropriate control gene. Furthermore, use of the MGB probe set resulted in detection of the target mutation at a high resolution and stability; standard curves illustrated that the amplification efficiencies of KIT1 (G) and KIT2 (A) were approximately equal (98.8% and 97.2%). In conclusion, a simple, rapid method, with high specificity and stability, for the detection of the KIT genotype in pigs was established using TaqMan MGB probe real-time quantitative PCR.

Evolving a polymerase for hydrophobic base analogues.

PubMed

Loakes, David; Gallego, José; Pinheiro, Vitor B; Kool, Eric T; Holliger, Philipp

2009-10-21

Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.

[A novel TaqMan® MGB probe for specifically detecting Streptococcus mutans].

PubMed

Zheng, Hui; Lin, Jiu-Xiang; DU, Ning; Chen, Feng

2013-10-18

To design a new TaqMan® MGB probe for improving the specificity of Streptococcus mutans's detection. We extracted six DNA samples from different streptococcal strains for PCR reaction. Conventional nested PCR and TaqMan® MGB real-time PCR were applied independently. The first round of nested PCR was carried out with the bacterial universal primers, while a second PCR was conducted by using primers specific for the 16S rRNA gene of Streptococcus mutans. The TaqMan® MGB probe for Streptococcus mutans was designed from sequence analyses, and the primers were the same as nested PCR. Streptococcus mutans DNA with 2.5 mg/L was sequentially diluted at 5-fold intervals to 0.16 μg/L. Standard DNA samples were used to generate standard curves by TaqMan® MGB real-time PCR. In the nested PCR, the primers specific for Streptococcus mutans also detected Streptococcus gordonii with visible band of 282 bp, giving false-positive results. In the TaqMan® MGB real-time PCR reaction, only Streptococcus mutans was detected. The detection limitation of TaqMan® MGB real-time PCR for Streptococcus mutans 16S rRNA gene was 20 μg/L. We designed a new TaqMan® MGB probe, and successfully set up a PCR based method for detecting oral Streptococcus mutans. TaqMan® MGB real-time PCR is a both specific and sensitive bacterial detection method.

Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

Treesearch

Laura K Muller; Jeffrey M. Lorch; Daniel L. Lindner; Michael O' Connor; Andrea Gargas; David S. Blehert

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

Association of vitamin D receptor gene polymorphism (TaqI and Apa1) with bone mineral density in North Indian postmenopausal women.

PubMed

Ahmad, Israr; Jafar, Tabrez; Mahdi, Farzana; Ameta, Keerti; Arshad, Md; Das, Siddharth Kumar; Waliullah, Shah; Rizvi, Imran; Mahdi, Abbas Ali

2018-06-15

Vitamin D receptor (VDR) gene has an important role as a candidate gene for the regulation of bone mass in osteoporosis. However, its association with bone mineral density (BMD) is controversial and has not been established in different ethnic populations. To enhance the understanding of VDR gene polymorphism in the context of BMD, we investigated the plausible genetic association of TaqI and ApaI polymorphism with BMD in North Indian postmenopausal women with osteoporosis.254 osteoporotic women (Age 55.82 ± 6.91) and 254 postmenopausal non osteoporotic women (Age 54.76 ± 6.26) were included in the study. VDR TaqI and ApaI polymorphism were determined by PCR (polymerase chain reaction) and RFLP (restriction fragment length polymorphism). BMD was assessed by dual energy X-ray absorptiometry (DXA) at the lumbar spine (L 1 -L 4 ), hip, forearm and femoral neck. The average BMD with TT genotype was significantly lower at lumbar spine, hip and forearm. The Frequency of TT genotype and t allele was significantly high in osteoporotic women when compared with controls. The average BMD with Aa genotype was higher in ApaI. Furthermore, comparison of frequency distribution of genotype and allele for VDR ApaI between osteoporotic patients and controls did not show any significant difference. Our findings revealed that TaqI gene TT genotype was associated with low BMD in North Indian osteoporotic women. Moreover, TT genotype and t allele associated significantly with osteoporosis in postmenopausal women. Therefore, VDR TaqI gene is an important determinant of risk factor for osteoporosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Vitamin D receptor gene Alw I, Fok I, Apa I, and Taq I polymorphisms in patients with urinary stone.

PubMed

Seo, Ill Young; Kang, In-Hong; Chae, Soo-Cheon; Park, Seung Chol; Lee, Young-Jin; Yang, Yun Sik; Ryu, Soo Bang; Rim, Joung Sik

2010-04-01

To evaluate vitamin D receptor (VDR) gene polymorphisms in Korean patients so as to identify the candidate genes associated with urinary stones. Urinary stones are a multifactorial disease that includes various genetic factors. A normal control group of 535 healthy subjects and 278 patients with urinary stones was evaluated. Of 125 patients who presented stone samples, 102 had calcium stones on chemical analysis. The VDR gene Alw I, Fok I, Apa I, and Taq I polymorphisms were evaluated using the polymerase chain reaction-restriction fragment length polymorphism analysis. Allelic and genotypic frequencies were calculated to identify associations in both groups. The haplotype frequencies of the VDR gene polymorphisms for multiple loci were also determined. For the VDR gene Alw I, Fok I, Apa I, and Taq I polymorphisms, there was no statistically significant difference between the patients with urinary stones and the healthy controls. There was also no statistically significant difference between the patients with calcium stones and the healthy controls. A novel haplotype (Ht 4; CTTT) was identified in 13.5% of the patients with urinary stones and in 8.3% of the controls (P = .001). The haplotype frequencies were significantly different between the patients with calcium stones and the controls (P = .004). The VDR gene Alw I, Fok I, Apa I, and Taq I polymorphisms does not seem to be candidate genetic markers for urinary stones in Korean patients. However, 1 novel haplotype of the VDR gene polymorphisms for multiple loci might be a candidate genetic marker. Copyright 2010 Elsevier Inc. All rights reserved.

Engineering of a DNA Polymerase for Direct m6 A Sequencing.

PubMed

Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

2018-01-08

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces

NASA Astrophysics Data System (ADS)

Langer, Andreas; Schräml, Michael; Strasser, Ralf; Daub, Herwin; Myers, Thomas; Heindl, Dieter; Rant, Ulrich

2015-07-01

The engineering of high-performance enzymes for future sequencing and PCR technologies as well as the development of many anticancer drugs requires a detailed analysis of DNA/RNA synthesis processes. However, due to the complex molecular interplay involved, real-time methodologies have not been available to obtain comprehensive information on both binding parameters and enzymatic activities. Here we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes. Two measurement modes track both the dynamics of the induced switching process and the DNA extension simultaneously to quantitate binding kinetics, dissociation constants and thermodynamic energies. The high sensitivity of the method reveals previously unidentified tight binding states for Taq and Pol I (KF) DNA polymerases. Furthermore, the incorporation of label-free nucleotides can be followed in real-time and changes in the DNA polymerase conformation (finger closing) during enzymatic activity are observable.

The development of a real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay using TaqMan technology for the pan detection of bluetongue virus (BTV).

PubMed

Mulholland, Catherine; McMenamy, Michael J; Hoffmann, Bernd; Earley, Bernadette; Markey, Bryan; Cassidy, Joseph; Allan, Gordon; Welsh, Michael D; McKillen, John

2017-07-01

Bluetongue virus (BTV) is an infectious, non-contagious viral disease of domestic and wild ruminants that is transmitted by adult females of certain Culicoides species. Since 2006, several serotypes including BTV-1, 2, 4, 6, 8, 9 and 16, have spread from the Mediterranean basin into Northern Europe for the first time. BTV-8 in particular, caused a major epidemic in northern Europe. As a result, it is evident that most European countries are at risk of BTV infection. The objective of this study was to develop and validate a real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assay based on TaqMan technology for the detection of representative strains of all BTV serotypes. Primers and probes were based on genome segment 10 of the virus, the NS3 gene. The assay was tested for sensitivity, and specificity. The analytical sensitivity of the rRT-PCR assay was 200 copies of RNA per reaction. The assay did not amplify the closely related orbivirus epizootic hemorrhagic disease virus (EHDV) but successfully detected all BTV reference strains including clinical samples from animals experimentally infected with BTV-8. This real time RT-PCR assay offers a sensitive, specific and rapid alternative assay for the pan detection of BTV that could be used as part of a panel of diagnostic assays for the detection of all serotypes of BTV. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

PubMed

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods.

PubMed

Fox, C J; Taylor, M I; Pereyra, R; Villasana, M I; Rico, C

2005-03-01

Recent substantial declines in northeastern Atlantic cod stocks necessitate improved biological knowledge and the development of techniques to complement standard stock assessment methods (which largely depend on accurate commercial catch data). In 2003, an ichthyoplankton survey was undertaken in the Irish Sea and subsamples of 'cod-like' eggs were analysed using a TaqMan multiplex, PCR (polymerase chain reaction) assay (with specific probes for cod, haddock and whiting). The TaqMan method was readily applied to the large number of samples (n = 2770) generated during the survey and when combined with a manual DNA extraction protocol had a low failure rate of 6%. Of the early stage 'cod-like' eggs (1.2-1.75 mm diameter) positively identified: 34% were cod, 8% haddock and 58% whiting. As previous stock estimates based on egg surveys for Irish Sea cod assumed that the majority of 'cod-like' eggs were from cod, the TaqMan results confirm that there was probably substantial contamination by eggs of whiting and haddock that would have inflated estimates of the stock biomass.

Effects of aripiprazole and the Taq1A polymorphism in the dopamine D2 receptor gene on the clinical response and plasma monoamine metabolites level during the acute phase of schizophrenia.

PubMed

Miura, Itaru; Takeuchi, Satoshi; Katsumi, Akihiko; Mori, Azuma; Kanno, Keiko; Yang, Qiaohui; Mashiko, Hirobumi; Numata, Yoshihiko; Niwa, Shin-Ichi

2012-02-01

The Taq1A polymorphism in the dopamine D2 receptor (DRD2) gene could be related to the response to antipsychotics. We examined the effects of the Taq1A polymorphism on the plasma monoamine metabolites during the treatment of schizophrenia with aripiprazole, a DRD2 partial agonist. Thirty Japanese patients with schizophrenia were treated with aripiprazole for 6 weeks. We measured plasma levels of homovanillic acid (pHVA) and 3-methoxy-4hydroxyphenylglycol (pMHPG) before and after treatment. The Taq1A polymorphism was genotyped with polymerase chain reaction. Aripiprazole improved the acute symptoms of schizophrenia and decreased pHVA in responders (P = 0.023) but not in nonresponders (P = 0.28). Although A1 allele carriers showed a tendency to respond to aripiprazole (61.5%) compared to A1 allele noncarriers (29.4%) (P = 0.078), there was not statistically significant difference in the response between the 2 genotype groups. There were significant effect for response (P = 0.013) and genotype × response interaction (P = 0.043) on the change of pHVA. The changes of pHVA differ between responders and nonresponders in A1 allele carriers but not in A1 allele noncarriers. There were no genotype or response effects or genotype × response interaction on the changes of the plasma levels of 3-methoxy-4hydroxyphenylglycol. Our preliminary results suggest that Taq1A polymorphism may be partly associated with changes in pHVA during acute schizophrenia.

A multiplex TaqMan qPCR assay for sensitive and rapid detection of phytoplasmas infecting Rubus species.

PubMed

Linck, Holger; Krüger, Erika; Reineke, Annette

2017-01-01

Rubus stunt is an economically important disease in the production of raspberries, blackberries, and loganberries. A fast, sensitive, and reliable diagnosis of phytoplasmas, the causal agent of the disease, is of prime importance to stop its spread by vegetative propagation and by insect vectors. Therefore, multiplex qPCR assays using TaqMan probes with different kinds of fluorophores in one reaction were developed, allowing the detection of phytoplasmas in general as well as a more specific detection of phytoplasmas belonging to group 16SrV and host DNA (either plant or insect). This assay now provides a practical tool for the screening of motherplants and monitoring the presence and distribution of phytoplasmas in Rubus plants of different geographic origins, cultivars, and cultivation systems, as well as in putative insect vectors like leafhoppers.

A multiplex TaqMan qPCR assay for sensitive and rapid detection of phytoplasmas infecting Rubus species

PubMed Central

Krüger, Erika; Reineke, Annette

2017-01-01

Rubus stunt is an economically important disease in the production of raspberries, blackberries, and loganberries. A fast, sensitive, and reliable diagnosis of phytoplasmas, the causal agent of the disease, is of prime importance to stop its spread by vegetative propagation and by insect vectors. Therefore, multiplex qPCR assays using TaqMan probes with different kinds of fluorophores in one reaction were developed, allowing the detection of phytoplasmas in general as well as a more specific detection of phytoplasmas belonging to group 16SrV and host DNA (either plant or insect). This assay now provides a practical tool for the screening of motherplants and monitoring the presence and distribution of phytoplasmas in Rubus plants of different geographic origins, cultivars, and cultivation systems, as well as in putative insect vectors like leafhoppers. PMID:28545043

Acquisition of initial /s/-stop and stop-/s/ sequences in Greek

PubMed Central

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E.

2010-01-01

Previous work on children’s acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters that obey the SSP. One problem with studies that have compared the acquisition of SSP-obeying and SSP-violating clusters is that the component sounds in the two types of sequences were different. This paper examines the acquisition of initial /s/-stop and stop-/s/ sequences by sixty Greek children aged 2 through 5 years. Results showed greater accuracy for the /s/-stop relative to the stop-/s/ sequences, but no difference in accuracy between /ts/, which is usually analyzed as an affricate in Greek, and the other stop-/s/ sequences. Moreover, errors for the /s/-stop sequences and /ts/ primarily involved stop substitutions, whereas errors for /ps/ and /ks/ were more variable and often involved fricative substitutions, a pattern which may have a perceptual explanation. Finally, /ts/ showed a distinct temporal pattern relative to the stop-/s/ clusters /ps/ and /ks/, similarly to what has been reported for productions of Greek adults. PMID:22070044

Evaluation of sensitivity of TaqMan RT-PCR for rubella virus detection in clinical specimens.

PubMed

Okamoto, Kiyoko; Mori, Yoshio; Komagome, Rika; Nagano, Hideki; Miyoshi, Masahiro; Okano, Motohiko; Aoki, Yoko; Ogura, Atsushi; Hotta, Chiemi; Ogawa, Tomoko; Saikusa, Miwako; Kodama, Hiroe; Yasui, Yoshihiro; Minagawa, Hiroko; Kurata, Takako; Kanbayashi, Daiki; Kase, Tetsuo; Murata, Sachiko; Shirabe, Komei; Hamasaki, Mitsuhiro; Kato, Takashi; Otsuki, Noriyuki; Sakata, Masafumi; Komase, Katsuhiro; Takeda, Makoto

2016-07-01

An easy and reliable assay for detection of the rubella virus is required to strengthen rubella surveillance. Although a TaqMan RT-PCR assay for detection of the rubella virus has been established in Japan, its utility for diagnostic purposes has not been tested. To allow introduction of the TaqMan RT-PCR into the rubella surveillance system in Japan, the sensitivity of the assay was determined using representative strains for all genotypes and clinical specimens. The detection limits of the method for individual genotypes were examined using viral RNA extracted from 13 representative strains. The assay was also tested at 10 prefectural laboratories in Japan, designated as local reference laboratories for measles and rubella, to allow nationwide application of the assay. The detection limits and amplification efficiencies of the assay were similar among all the representative strains of the 13 genotypes. The TaqMan RT-PCR could detect approximately 90% of throat swab and urine samples taken up to 5days of illness. These samples were determined positive by a highly sensitive nested RT-PCR. The TaqMan RT-PCR could detect at least 10 pfu of rubella virus. Although the sensitivity was somewhat lower than that of the conventional nested RT-PCR, the TaqMan RT-PCR could be more practical to routine tests for rubella laboratory diagnosis and detection in view of the rapid response and reducing risks of contamination. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of polymerase chain reaction-based diagnostic tests for detection of Malsoor virus & adenovirus isolated from Rousettus species of bats in Maharashtra, India.

PubMed

Shete, Anita M; Yadav, Pragya; Kumar, Vimal; Nikam, Tushar; Mehershahi, Kurosh; Kokate, Prasad; Patil, Deepak; Mourya, Devendra T

2017-01-01

Bats are recognized as important reservoirs for emerging infectious disease and some unknown viral diseases. Two novel viruses, Malsoor virus (family Bunyaviridae, genus, Phlebovirus) and a novel adenovirus (AdV) (family, Adenoviridae genus, Mastadenovirus), were identified from Rousettus bats in the Maharashtra State of India. This study was done to develop and optimize real time reverse transcription - polymerase chain reaction (RT-PCR) assays for Malsoor virus and real time and nested PCR for adenovirus from Rousettus bats. For rapid and accurate screening of Malsoor virus and adenovirus a nested polymerase chain reaction and TaqMan-based real-time PCR were developed. Highly conserved region of nucleoprotein gene of phleboviruses and polymerase gene sequence from the Indian bat AdV isolate polyprotein gene were selected respectively for diagnostic assay development of Malsoor virus and AdV. Sensitivity and specificity of assays were calculated and optimized assays were used to screen bat samples. Molecular diagnostic assays were developed for screening of Malsoor virus and AdV and those were found to be specific. Based on the experiments performed with different parameters, nested PCR was found to be more sensitive than real-time PCR; however, for rapid screening, real-time PCR can be used and further nested PCR can be used for final confirmation or in those laboratories where real-time facility/expertise is not existing. This study reports the development and optimization of nested RT-PCR and a TaqMan-based real-time PCR for Malsoor virus and AdV. The diagnostic assays can be used for rapid detection of these novel viruses to understand their prevalence among bat population.

A universal TaqMan-based RT-PCR protocol for cost-efficient detection of small noncoding RNA.

PubMed

Jung, Ulrike; Jiang, Xiaoou; Kaufmann, Stefan H E; Patzel, Volker

2013-12-01

Several methods for the detection of RNA have been developed over time. For small RNA detection, a stem-loop reverse primer-based protocol relying on TaqMan RT-PCR has been described. This protocol requires an individual specific TaqMan probe for each target RNA and, hence, is highly cost-intensive for experiments with small sample sizes or large numbers of different samples. We describe a universal TaqMan-based probe protocol which can be used to detect any target sequence and demonstrate its applicability for the detection of endogenous as well as artificial eukaryotic and bacterial small RNAs. While the specific and the universal probe-based protocol showed the same sensitivity, the absolute sensitivity of detection was found to be more than 100-fold lower for both than previously reported. In subsequent experiments, we found previously unknown limitations intrinsic to the method affecting its feasibility in determination of mature template RISC incorporation as well as in multiplexing. Both protocols were equally specific in discriminating between correct and incorrect small RNA targets or between mature miRNA and its unprocessed RNA precursor, indicating the stem-loop RT-primer, but not the TaqMan probe, triggers target specificity. The presented universal TaqMan-based RT-PCR protocol represents a cost-efficient method for the detection of small RNAs.

Vitamin D Receptor TaqI Gene Variant in Exon 9 and Polycystic Ovary Syndrome Risk

PubMed Central

Bagheri, Morteza; Abdi Rad, Isa; Hosseini Jazani, Nima; Nanbakhsh, Fariba

2013-01-01

Background: Polycystic ovary syndrome (PCOS) is known as a metabolic disorder. The results of recent studies implied that vitamin D receptor (VDR) genetic variants may impact PCOS and insulin resistance in women with PCOS. The aim of the present study was to determine the VDR TaqI gene variant in exon 9 (T/C) (rs731236) in normal controls and patients with PCOS for the first time in Iranian Azeri women. Materials and Methods: In this case control study between April 2011 and June 2012, a total of 76 women aged 18-40 years (38 patients with PCOS and 38 healthy women as normal controls) participated. Genotypes of VDR TaqI in exon 9 (T/C) (rs731236) were determined using the PCR-RFLP method. Results: The frequencies of VDR TaqI T anc C alleles were 0.605 and 0.395 in cases and 0.697 and 0.303 in controls. Also, the genotypic frequencies of VDR TaqI were 16) (42.11), 14(36.84), and 8(21.05) in cases, and 17(44.74), 19(50), and 2(5.26) in controls for TT, TC and CC genotypes respectively. There was no difference in genotype and allele frequencies between PCOS and controls (p value>0.05) with the exception of the CC genotype (p value=0.04). Conclusion: This report, a first of its own kind in Iranian Azeri patients, suggests that the CC genotype of VDR TaqI in exon 9 (rs731236) is associated with PCOS. PMID:24520473

Development of a real-time TaqMan assay to detect mendocina sublineage Pseudomonas species in contaminated metalworking fluids.

PubMed

Saha, Ratul; Donofrio, Robert S; Bagley, Susan T

2010-08-01

A TaqMan quantitative real-time polymerase chain reaction (qPCR) assay was developed for the detection and enumeration of three Pseudomonas species belonging to the mendocina sublineage (P. oleovorans, P. pseudoalcaligenes, and P. oleovorans subsp. lubricantis) found in contaminated metalworking fluids (MWFs). These microbes are the primary colonizers and serve as indicator organisms of biodegradation of used MWFs. Molecular techniques such as qPCR are preferred for the detection of these microbes since they grow poorly on typical growth media such as R2A agar and Pseudomonas isolation agar (PIA). Traditional culturing techniques not only underestimate the actual distribution of these bacteria but are also time-consuming. The primer-probe pair developed from gyrase B (gyrB) sequences of the targeted bacteria was highly sensitive and specific for the three species. qPCR was performed with both whole cell and genomic DNA to confirm the specificity and sensitivity of the assay. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cell and 13.7 fg with genomic DNA. The primer-probe pair was successful in determining concentrations from used MWF samples, indicating levels between 2.9 x 10(3) and 3.9 x 10(6) CFU/ml. In contrast, the total count of Pseudomonas sp. recovered on PIA was in the range of <1.0 x 10(1) to 1.4 x 10(5) CFU/ml for the same samples. Based on these results from the qPCR assay, the designed TaqMan primer-probe pair can be efficiently used for rapid (within 2 h) determination of the distribution of these species of Pseudomonas in contaminated MWFs.

Development and validation of a SYBR Green I-based real-time polymerase chain reaction method for detection of haptoglobin gene deletion in clinical materials.

PubMed

Soejima, Mikiko; Tsuchiya, Yuji; Egashira, Kouichi; Kawano, Hiroyuki; Sagawa, Kimitaka; Koda, Yoshiro

2010-06-01

Anhaptoglobinemic patients run the risk of severe anaphylactic transfusion reaction because they produce serum haptoglobin (Hp) antibodies. Being homozygous for the Hp gene deletion (HP(del)) is the only known cause of congenital anhaptoglobinemia, and clinical diagnosis of HP(del) before transfusion is important to prevent anaphylactic shock. We recently developed a 5'-nuclease (TaqMan) real-time polymerase chain reaction (PCR) method. A SYBR Green I-based duplex real-time PCR assay using two forward primers and a common reverse primer followed by melting curve analysis was developed to determine HP(del) zygosity in a single tube. In addition, to obviate initial DNA extraction, we examined serially diluted blood samples as PCR templates. Allelic discrimination of HP(del) yielded optimal results at blood sample dilutions of 1:64 to 1:1024. The results from 2231 blood samples were fully concordant with those obtained by the TaqMan-based real-time PCR method. The detection rate of the HP(del) allele by the SYBR Green I-based method is comparable with that using the TaqMan-based method. This method is readily applicable due to its low initial cost and analyzability using economical real-time PCR machines and is suitable for high-throughput analysis as an alternative method for allelic discrimination of HP(del).

Quantification of measles, mumps and rubella viruses using real-time quantitative TaqMan-based RT-PCR assay.

PubMed

Ammour, Y; Faizuloev, E; Borisova, T; Nikonova, A; Dmitriev, G; Lobodanov, S; Zverev, V

2013-01-01

In this study, a rapid quantitative method using TaqMan-based real-time reverse transcription-polymerase chain reaction (qPCR-RT) has been developed for estimating the titers of measles, mumps and rubella (MMR) viruses in infected cell culture supernatants. The qPCR-RT assay was demonstrated to be a specific, sensitive, efficient and reproducible method. For MMR viral samples obtained during MMR viral propagations in Vero cells at a different multiplicity of infection, titers determined by the qPCR-RT assay have been compared with estimates of infectious virus obtained by a traditional commonly used method for MMR viruses - 50% cell culture infective dose (CCID(50)) assay, in paired samples. Pearson analysis evidenced a significant correlation between both methods for a certain period after viral inoculation. Furthermore, the established qPCR-RT assay was faster and less-laborious. The developed method could be used as an alternative method or a supplementary tool for the routine titer estimation during MMR vaccine production. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases.

PubMed

Belguise-Valladier, P; Maki, H; Sekiguchi, M; Fuchs, R P

1994-02-11

In the present work, we have studied in vitro replication of N-2-acetylaminofluorene (AAF) or cis-diamminedichloroplatinum II (cis-DDP) single modified DNA templates. We used the holoenzyme (pol III HE) or the alpha subunit of DNA polymerase III, which is involved in SOS mutagenesis, and other DNA polymerases in order to compare enzymes having different biological roles and properties. Single-stranded oligonucleotides (63-mer) bearing a single AAF adduct at one of the different guanine residues of the NarI sequence (-G1G2CG3CC-) have been used in primer extension assays. Site-specifically platinated 5'd(ApG) or 5'd(GpG) oligonucleotides were constructed and similarly used in primer extension assays. In all cases, irrespective of both the chemical nature of the lesion (i.e. AAF or cis-DDP) and its local sequence context (i.e. the 3 different sites for AAF adducts within the NarI site) replication by pol III HE and pol I Klenow fragment (pol I Kf) stops one base prior to the adduct site. Removal of the 3'-->5' proofreading activity alone was not sufficient to trigger bypass of DNA lesions. Indeed, when proofreading activity of pol I is inactivated by a point mutation (pol I Kf (exo-)), the major replication product corresponds to the position opposite the adduct site showing that incorporation across from the AAF adduct is possible. These results suggest that a polymerase with proofreading activity is actually found to stop one nucleotide before the adduct not because it is unable to insert a nucleotide opposite the adduct but most likely because elongation past the adduct is strongly impaired, giving thus an increased time frame for the proofreading exonuclease to remove the base inserted across from the adduct. These results are discussed in terms of their implications for error-free and error-prone bypass in vivo.

Association of dopamine receptor D2 gene (DRD2) Taq1 polymorphisms with eating behaviors and obesity among Chinese and Indian Malaysian university students.

PubMed

Lek, Fang-Ying; Ong, Hing-Huat; Say, Yee-How

2018-01-01

This study investigated the association of DRD2 Taq1A, Taq1B and Taq1D gene polymorphisms with eating behavior, the preference/intake frequency/craving of high-fat foods and obesity in 394 Malaysian adults (161 males, 233 females; 308 Chinese, 86 Indians; 67 obese, 327 non-obese). Eating behaviors namely Cognitive Restraint, Uncontrolled Eating and Emotional Eating scores were assessed by the Three Factor Eating Questionnaire-R18. The preference/intake frequency/craving of 26 common high-fat Malaysian foods was assessed using a 7-point hedonic scale. Anthropometric measurements were taken and Taq1 gene polymorphisms were genotyped by PCR-Restriction Fragment Length Polymorphism using DNA extracted from mouthwash samples. The overall minor allele frequencies of Taq1A, Taq1B and Taq1D according to ethnicities (Chinese/Indian) were 0.37/0.29, 0.39/0.28, 0.06/0.30, respectively; genotype and allele distributions of Taq1B and Taq1D were significantly different between ethnicities. Eating behaviorscores were not significantly different between gender and ethnicities. Those with A1 or B1 allele had lower Cognitive Restraint score and higher Uncontrolled Eating score, while those with A1/A1 or B1/B1 genotype had higher fast food preference. D1 allele was associated with increased starchy food craving and mamak (Malaysian Indian-Muslim) food preference, but not eating behavior scores. All three gene variants were not associated with obesity and adiposity. Taken together, we posit that three DRD2 Taq1 gene polymorphisms influence the eating behavior and preference/intake frequency/craving of certain high-fat foods in Malaysian adults, but their role in obesity and adiposity is still inconclusive and needs further investigation.

A novel electrochemical biosensor based on dynamic polymerase-extending hybridization for E. coli O157:H7 DNA detection.

PubMed

Wang, Lijiang; Liu, Qingjun; Hu, Zhaoying; Zhang, Yuanfan; Wu, Chunsheng; Yang, Mo; Wang, Ping

2009-05-15

A novel biosensor based on single-stranded DNA (ssDNA) probe functionalized aluminum anodized oxide (AAO) nanopore membranes was demonstrated for Escherichia coli O157:H7 DNA detection. An original and dynamic polymerase-extending (PE) DNA hybridization procedure is proposed, where hybridization happens in the existence of Taq DNA polymerase and dNTPs under controlled reaction temperature. The probe strand would be extended as long as the target DNA strand, then the capability to block the ionic flow in the pores has been prominently enhanced by the double strand complex. We have investigated the variation of ionic conductivity during the fabrication of the film and the hybridization using cyclic voltammetry and impedance spectroscopy. The present approach provides low detection limit for DNA (a few hundreds of pmol), rapid label-free and easy-to-use bacteria detection, which holds the potential for future use in various ss-DNA analyses by integrated into a self-contained biochip.

A TaqMan-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies.

PubMed

Bach, H-J; Jessen, I; Schloter, M; Munch, J C

2003-01-01

Real-time TaqMan-PCR assays were developed for detection, differentiation and absolute quantification of the pathogenic subspecies of Clavibacter michiganensis (Cm) in one single PCR run. The designed primer pair, targeting intergenic sequences of the rRNA operon (ITS) common in all subspecies, was suitable for the amplification of the expected 223-nt DNA fragments of all subspecies. Closely related bacteria were completely discriminated, except of Rathayibacter iranicus, from which weak PCR product bands appeared on agarose gel after 35 PCR cycles. Sufficient specificity of PCR detection was reached by introduction of the additional subspecies specific probes used in TaqMan-PCR. Only Cm species were detected and there was clear differentiation among the subspecies C. michiganensis sepedonicus (Cms), C. michiganensis michiganensis (Cmm), C. michiganensis nebraskensis (Cmn), C. michiganensis insidiosus (Cmi) and C. michiganensis tessellarius (Cmt). The TaqMan assays were optimized to enable a simultaneous quantification of each subspecies. Validity is shown by comparison with cell counts.

Comparison of Versant HBV DNA 3.0 and COBAS AmpliPrep-COBAS TaqMan assays for hepatitis B DNA quantitation: Possible clinical implications.

PubMed

Garbuglia, A R; Angeletti, C; Lauria, F N; Zaccaro, P; Cocca, A M; Pisciotta, M; Solmone, M; Capobianchi, M R

2007-12-01

We compared two commercial assays for HBV DNA quantitation, Versant HBV 3.0, System 340 (bDNA; Bayer Diagnostics) and COBAS AmpliPrep-COBAS TaqMan HBV Test (TaqMan; Roche Diagnostics). Analytical sensitivity, calculated on WHO International Standard, predicted 95% detection rate at 11.4 and 520.2IU/ml for TaqMan and bDNA, respectively. Specificity, established on 50 blood donor samples, was 100% and 84% for TaqMan and bDNA, respectively. When using clinical samples, HBV DNA was detected by TaqMan in 21/55 samples negative to bDNA. Mean values of HBV DNA obtained with bDNA were higher than those obtained with TaqMan (4.09log(10)+/-1.90 versus 3.39log(10)+/-2.41, p<0.001), and 24.4% of samples showed differences in viral load values >0.5log(10), without association with HBV genotype. There was a good correlation for HBV DNA concentrations measured by the two assays (r=0.94; p<0.001) within the overlapping range, and the distribution of results with respect to relevant clinical threshold recently confirmed (20,000 and 2000IU/ml) was similar. Approximately 50% of samples with low HBV DNA, appreciated by TaqMan but not by bDNA, were successfully sequenced in pol region, where drug resistance mutations are located.

Identification of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) by using polymerase chain reaction amplification and restriction analysis of the mitochondrial cytochrome b gene.

PubMed

Carrera, E; García, T; Céspedes, A; González, I; Sanz, B; Hernández, P E; Martín, R

1998-04-01

Restriction site analysis of polymerase chain reaction (PCR) products from a conserved region of the cytochrome b gene has been used for the identification of fresh and smoked samples of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Digestion of the 359-bp PCR product with the endonucleases EcoRV and TaqI yielded specific banding patterns for salmon and trout. This genetic marker can be very useful for detecting fraudulent substitution of the cheaper smoked trout for the more expensive smoked salmon.

Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay

PubMed Central

Nagy, Alexander; Vitásková, Eliška; Černíková, Lenka; Křivda, Vlastimil; Jiřincová, Helena; Sedlák, Kamil; Horníčková, Jitka; Havlíčková, Martina

2017-01-01

Ongoing evolution of viral pathogens is a significant issue in diagnostic virology employing TaqMan qPCR/RT-qPCR. Specific concerns are related to false negativity due to probe binding failure. One option for compensating for such deficiency is to integrate a second identically labelled probe in the assay. However, how this alteration influences the reaction parameters has not been comprehensively demonstrated. In the present study, we evaluate a TaqMan protocol using two identically labelled hydrolysis probes (simple, LNA (locked-nucleic-acid)) and MGB (minor-groove-binder) modified probes and combinations thereof in a single assay. Our results based on a synthetic amplicon suggest that the second probe does not compromise the TaqMan qPCR/RT-qPCR parameters, which repeatedly and reproducibly remained comparable to those of the corresponding single-probe assays, irrespective of the relative probe orientation, whether opposite or tandem, and probe modifications or combinations thereof. On the other hand, the second probe additively contributed to the overall fluorescence signal. The utility of the dual-probe approach was demonstrated on practical examples by using field specimens. We hope that the present study might serve as a theoretical basis for the development or improvement of TaqMan qPCR/RT-qPCR assays for the detection of highly variable nucleic acid templates. PMID:28120891

The Next Stop of One-Stop

ERIC Educational Resources Information Center

Bouman, Penny; Gomber, Gerri; Higgs, Ronnie; Westman, Craig

2006-01-01

This article focuses on the migration of the best practices of a one-stop setup to a communication center allowing for a one-stop shop experience via phone. Specifically, the article describes how enrollment managers at Ferris State University chose elements of their one-stop student service center to migrate into the Enrollment Services…

Prediction of striatal D2 receptor binding by DRD2/ANKK1 TaqIA allele status

PubMed Central

Eisenstein, Sarah A.; Bogdan, Ryan; Love-Gregory, Latisha; Corral-Frías, Nadia S.; Koller, Jonathan M.; Black, Kevin J.; Moerlein, Stephen M.; Perlmutter, Joel S.; Barch, Deanna M.; Hershey, Tamara

2016-01-01

In humans, the A1 (T) allele of the dopamine (DA) D2 receptor/ankyrin repeat and kinase domain containing 1 (DRD2/ANKK1) TaqIA (rs1800497) single nucleotide polymorphism has been associated with reduced striatal DA D2/D3 receptor (D2/D3R) availability. However, radioligands used to estimate D2/D3R are displaceable by endogenous DA and are non-selective for D2R, leaving the relationship between TaqIA genotype and D2R specific binding uncertain. Using the positron emission tomography (PET) radioligand, (N‐[11C]methyl)benperidol ([11C]NMB), which is highly selective for D2R over D3R and is not displaceable by endogenous DA, the current study examined whether DRD2/ANKK1 TaqIA genotype predicts D2R specific binding in 2 independent samples. Sample 1 (n = 39) was composed of obese and non-obese adults; sample 2 (n = 18) was composed of healthy controls, unmedicated individuals with schizophrenia, and siblings of individuals with schizophrenia. Across both samples, A1 allele carriers (A1+) had 5-12% less striatal D2R specific binding relative to individuals homozygous for the A2 allele (A1−), regardless of body mass index or diagnostic group. This reduction is comparable to previous PET studies of D2/D3R availability (10-14%). The pooled effect size for the difference in total striatal D2R binding between A1+ and A1− was large (0.84). In summary, in line with studies using displaceable D2/D3R radioligands, our results indicate that DRD2/ANKK1 TaqIA allele status predicts striatal D2R specific binding as measured by D2R-selective [11C]NMB. These findings support the hypothesis that DRD2/ANKK1 TaqIA allele status may modify D2R, perhaps conferring risk for certain disease states. GRAPHICAL ABSTRACT We investigated the difference in striatal dopamine D2 receptor binding, as measured by PET with (N-[11C]methyl)benperidol ([11C]NMB), between A1 allele carriers (A1+) and individuals homozygous for the A2 allele (A1−) of the DRD2/ANKK1 TaqIA single nucleotide

Detection of cashew nut DNA in spiked baked goods using a real-time polymerase chain reaction method.

PubMed

Brzezinski, Jennifer L

2006-01-01

The detection of potentially allergenic foods, such as tree nuts, in food products is a major concern for the food processing industry. A real-time polymerase chain reaction (PCR) method was designed to determine the presence of cashew DNA in food products. The PCR amplifies a 67 bp fragment of the cashew 2S albumin gene, which is detected with a cashew-specific, dual-labeled TaqMan probe. This reaction will not amplify DNA derived from other tree nut species, such as almond, Brazil nut, hazelnut, and walnut, as well as 4 varieties of peanut. This assay was sensitive enough to detect 5 pg purified cashew DNA as well as cashew DNA in a spiked chocolate cookie sample containing 0.01% (100 mg/kg) cashew.

APOE and CETP TaqIB polymorphisms influence metabolic responses to Hibiscus sabdariffa L. and Gynostemma pentaphyllum Makino tea consumption in hypercholesterolemic subjects.

PubMed

Jeenduang, Nutjaree; Sangkaew, Boonnisa; Chantaracha, Pacharee; Chanchareonsri, Sirada; Plyduang, Thunyaluk; Thitdee, Wanida; Samae, Cathaleeya; Pitumanon, Wacharaporn

2017-03-01

Hibiscus sabdariffa L. (HS) and Gynostemma pentaphyllum Makino (GP) have been used as traditional medicines to treat diabetes and hypercholesterolemia. Nevertheless, there is interindividual variation in the metabolic responses to HS and GP consumption. This may be due to genetic factors. The aim of this study was to investigate the effects of HS and GP tea consumption on anthropometric data, fasting blood glucose (FBG), and lipid concentrations in hypercholesterolemia subjects with different genotypes of the APOE and CETP TaqIB polymorphisms. Forty-eight subjects with hypercholesterolemia were given either HS or GP tea for 30 days. Anthropometric and biochemical variables were determined, and APOE and CETP TaqIB polymorphisms were analyzed using the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP). E4 (p=0.008) and homozygous B1B1 (p=0.010) carriers had significantly decreased HDL-C concentrations after HS consumption; in addition, B2 carriers who consumed HS showed significantly decreased triglyceride (TG) concentrations (p=0.039). Regarding GP consumption, non-E4 carriers had significantly decreased HDL-C (p=0.009) and FBG (p=0.042) concentrations. Furthermore, B2 carriers had significantly decreased total cholesterol (TC) (p=0.045), HDL-C (p=0.004), and FBG (p=0.026) concentrations. HS consumption may have beneficial effects with respect to TG concentrations in the B2 carriers, but it may adversely affect HDL-C concentrations in homozygous B1B1 and E4 carriers. In contrast, GP consumption may have favorable effects on TC and FBG concentrations but not on HDL-C concentrations for B2 and/or non-E4 carriers.

Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR.

PubMed

Peng, Xiujuan; Nguyen, Alex; Ghosh, Debadyuti

2018-02-01

TaqMan and SYBR Green quantitative PCR (qPCR) methods were developed as DNA-based approaches to reproducibly enumerate M13 and T7 phages from phage display selection experiments individually and simultaneously. The genome copies of M13 and T7 phages were quantified by TaqMan or SYBR Green qPCR referenced against M13 and T7 DNA standard curves of known concentrations. TaqMan qPCR was capable of quantifying M13 and T7 phage DNA simultaneously with a detection range of 2.75*10 1 -2.75*10 8 genome copies(gc)/μL and 2.66*10 1 -2.66*10 8 genome copies(gc)/μL respectively. TaqMan qPCR demonstrated an efficient amplification efficiency (E s ) of 0.97 and 0.90 for M13 and T7 phage DNA, respectively. SYBR Green qPCR was ten-fold more sensitive than TaqMan qPCR, able to quantify 2.75-2.75*10 7 gc/μL and 2.66*10 1 -2.66*10 7 gc/μL of M13 and T7 phage DNA, with an amplification efficiency E s of 1.06 and 0.78, respectively. Due to its superior sensitivity, SYBR Green qPCR was used to enumerate M13 and T7 phage display clones selected against a cell line, and quantified titers demonstrated accuracy comparable to titers from traditional double-layer plaque assay. Compared to enzyme linked immunosorbent assay, both qPCR methods exhibited increased detection sensitivity and reproducibility. These qPCR methods are reproducible, sensitive, and time-saving to determine their titers and to quantify a large number of phage samples individually or simultaneously, thus avoiding the need for time-intensive double-layer plaque assay. These findings highlight the attractiveness of qPCR for phage enumeration for applications ranging from selection to next-generation sequencing (NGS). Copyright © 2017 Elsevier B.V. All rights reserved.

A Stopped-Flow Apparatus with Light-Scattering Detection and Its Application to Biochemical Reactions

PubMed Central

Riesner, Detlev; Buenemann, Hans

1973-01-01

A stopped-flow apparatus utilizing light-scattering for following the progress of a reaction is described. The method is applicable to all reactions that result in a significant change of the average molecular weight. It was possible due to several modifications of a conventional stopped-flow system to obtain a sensitivity comparable to that of commercial instruments for static light-scattering measurements. Experiments on three reactions are reported: association and dissociation of mercury ligands with DNA, dissociation of the dimers of DNA-dependent RNA polymerase, and complex formation of tRNASer (yeast) with the cognate aminoacyl-tRNA synthetase. The changes in the intensities of the scattered light are calculated and compared with the measured amplitudes. PMID:4577138

Cortical NMDA receptor expression in human chronic alcoholism: influence of the TaqIA allele of ANKK1.

PubMed

Ridge, Justin P; Dodd, Peter R

2009-10-01

Real-time RT-PCR normalized to GAPDH was used to assay N-methyl-D-aspartate (NMDA) receptor NR1, NR2A and NR2B subunit mRNA in human autopsy cortex tissue from chronic alcoholics with and without comorbid cirrhosis of the liver and matched controls. Subunit expression was influenced by the subject's genotype. The TaqIA polymorphism selectively modulated NMDA receptor mean transcript expression in cirrhotic-alcoholic superior frontal cortex, in diametrically opposite ways in male and female subjects. Genetic make-up may differentially influence vulnerability to brain damage by altering the excitation: inhibition balance, particularly in alcoholics with comorbid cirrhosis of the liver. The TaqIA polymorphism occurs within the poorly characterised ankyrin-repeat containing kinase 1 (ANKK1) gene. Using PCR, ANKK1 mRNA transcript was detected in inferior temporal, occipital, superior frontal and primary motor cortex of control human brain. ANKK1 expression may mediate the influence of the TaqIA polymorphism on phenotype.

Comparison of culture and a novel 5' Taq nuclease assay for direct detection of Campylobacter fetus subsp. venerealis in clinical specimens from cattle.

PubMed

McMillen, Lyle; Fordyce, Geoffry; Doogan, Vivienne J; Lew, Ala E

2006-03-01

A Campylobacter fetus subsp. venerealis-specific 5' Taq nuclease PCR assay using a 3' minor groove binder-DNA probe (TaqMan MGB) was developed based on a subspecies-specific fragment of unknown identity (S. Hum, K. Quinn, J. Brunner, and S. L. On, Aust. Vet. J. 75:827-831, 1997). The assay specifically detected four C. fetus subsp. venerealis strains with no observed cross-reaction with C. fetus subsp. fetus-related Campylobacter species or other bovine venereal microflora. The 5' Taq nuclease assay detected approximately one single cell compared to 100 and 10 cells in the conventional PCR assay and 2,500 and 25,000 cells from selective culture from inoculated smegma and mucus, respectively. The respective detection limits following the enrichments from smegma and mucus were 5,000 and 50 cells/inoculum for the conventional PCR compared to 500 and 50 cells/inoculum for the 5' Taq nuclease assay. Field sampling confirmed the sensitivity and the specificity of the 5' Taq nuclease assay by detecting an additional 40 bulls that were not detected by culture. Urine-inoculated samples demonstrated comparable detection of C. fetus subsp. venerealis by both culture and the 5' Taq nuclease assay; however, urine was found to be less effective than smegma for bull sampling. Three infected bulls were tested repetitively to compare sampling tools, and the bull rasper proved to be the most suitable, as evidenced by the improved ease of specimen collection and the consistent detection of higher levels of C. fetus subsp. venerealis. The 5' Taq nuclease assay demonstrates a statistically significant association with culture (chi2 = 29.8; P < 0.001) and significant improvements for the detection of C. fetus subsp. venerealis-infected animals from crude clinical extracts following prolonged transport.

Fast real-time polymerase chain reaction for quantitative detection of Lactobacillus delbrueckii bacteriophages in milk.

PubMed

Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A

2008-12-01

One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.

A TaqI PCR-RFLP detecting a novel SNP in exon 2 of the bovine POU1F1 gene.

PubMed

Pan, Chuanying; Lan, Xianyong; Chen, Hong; Guo, Yikun; Shu, Jianhong; Lei, Chuzhao; Wang, Xinzhuang

2008-08-01

PCR-SSCP and DNA sequencing methods were applied to reveal three novel single nucleotide polymorphisms (SNPs) in exon 2 of the POU1F1 gene in 963 Chinese cattle belonging to eight breeds. Among them, a silent SNP (NM_174579:c.545G > A) detected by TaqI endonuclease is described. Frequencies of the POU1F1-G allele varied from 0.685 to 1.000. The association of TaqI polymorphism with growth traits was analyzed in 251 Nanyang cattle. No significant associations of the TaqI polymorphism with body weight and average daily gain for different growth periods (6, 12, 18, and 24 months old) were observed (P > 0.05), as well as for body sizes (P > 0.05).

MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

PubMed Central

Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

2016-01-01

In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

A new TaqMan method for the reliable diagnosis of Ehrlichia spp. in canine whole blood.

PubMed

Thomson, Kirsty; Yaaran, Tal; Belshaw, Alex; Curson, Lucia; Tisi, Laurence; Maurice, Sarah; Kiddle, Guy

2018-06-18

Ehrlichiosis is an important emerging infectious disease of the canid family and humans worldwide. To date, no extensive evaluation or validation of a molecular diagnostic test for ehrlichiosis has been published. Here, we present data for a newly designed TaqMan assay and compare its performance to a commercial technology (PCRun®). Both of these real-time methods of analysis were evaluated using a comprehensive number of prospective and retrospective samples collected from dogs exhibiting symptoms of ehrlichiosis. Whole blood samples collected from dogs, retrospectively in the United Kingdom and prospectively in Israel, were analysed for the presence of Ehrlichia canis and Ehrlichia minasensis DNA using the TaqMan PCR, developed specifically for this study. The results were compared to those of a real time commercial isothermal amplification method (PCRun® system developed by Biogal Galed Labs ACS, Galed, Israel). The sensitivity and specificity (CI: 95%) of the TaqMan PCR and PCRun® were both determined to be 100% and absolute, for all of the samples tested. Interestingly, both tests were demonstrated to be highly comparable, irrespective of differences in amplification chemistry or sequences targeted. Host differences, incidence of disease and geographical location of the isolates had little impact on the positivity recorded by each of the diagnostic methods. It was evident that both amplification methods were equally suited for diagnosing canine ehrlichiosis and while the PCRun® clearly amplified all clinically relevant Ehrlichia species known to infect dogs and humans, the TaqMan method was more specific for E. canis and E. minasensis. This work demonstrates that despite good analytical sensitivities and specificities for Ehrlichia spp. neither method could fully account for the clinical diagnosis of thrombocytopenia.

Acquisition of initial /s/-stop and stop-/s/sequences in Greek.

PubMed

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E

2011-09-01

Previous work on children's acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters that obey the SSP. One problem with studies that have compared the acquisition of SSP-obeying and SSP-violating clusters is that the component sounds in the two types of sequences were different.This paper examines the acquisition of initial /s/-stop and stop-/s/ sequences by sixty Greek children aged 2 through 5 years. Results showed greater accuracy for the /s/-stop relative to the stop-/s/ sequences, but no difference in accuracy between /ts/, which is usually analyzed as an affricate in Greek, and the other stop-/s/ sequences. Moreover, errors for the /s/-stop sequences and /ts/ primarily involved stop substitutions, whereas errors for /ps/ and /ks/ were more variable and often involved fricative substitutions, a pattern which may have a perceptual explanation. Finally, /ts/ showed a distinct temporal pattern relative to the stop-/s/ clusters /ps/ and /ks/, similar to what has been reported for productions of Greek adults.

Event specific qualitative and quantitative polymerase chain reaction detection of genetically modified MON863 maize based on the 5'-transgene integration sequence.

PubMed

Yang, Litao; Xu, Songci; Pan, Aihu; Yin, Changsong; Zhang, Kewei; Wang, Zhenying; Zhou, Zhigang; Zhang, Dabing

2005-11-30

Because of the genetically modified organisms (GMOs) labeling policies issued in many countries and areas, polymerase chain reaction (PCR) methods were developed for the execution of GMO labeling policies, such as screening, gene specific, construct specific, and event specific PCR detection methods, which have become a mainstay of GMOs detection. The event specific PCR detection method is the primary trend in GMOs detection because of its high specificity based on the flanking sequence of the exogenous integrant. This genetically modified maize, MON863, contains a Cry3Bb1 coding sequence that produces a protein with enhanced insecticidal activity against the coleopteran pest, corn rootworm. In this study, the 5'-integration junction sequence between the host plant DNA and the integrated gene construct of the genetically modified maize MON863 was revealed by means of thermal asymmetric interlaced-PCR, and the specific PCR primers and TaqMan probe were designed based upon the revealed 5'-integration junction sequence; the conventional qualitative PCR and quantitative TaqMan real-time PCR detection methods employing these primers and probes were successfully developed. In conventional qualitative PCR assay, the limit of detection (LOD) was 0.1% for MON863 in 100 ng of maize genomic DNA for one reaction. In the quantitative TaqMan real-time PCR assay, the LOD and the limit of quantification were eight and 80 haploid genome copies, respectively. In addition, three mixed maize samples with known MON863 contents were detected using the established real-time PCR systems, and the ideal results indicated that the established event specific real-time PCR detection systems were reliable, sensitive, and accurate.

The Effects of Prompting and Feedback on Drivers' Stopping at Stop Signs

PubMed Central

Austin, John; Hackett, Stacey; Gravina, Nicole; Lebbon, Angela

2006-01-01

Complete stops at a high-traffic intersection on the campus of a public university were increased with a prompting and consequence intervention. Data were collected at two opposing stop signs (Stop A and Stop B); however, the intervention was implemented only at Stop A. During the intervention, a volunteer stood next to Stop A holding a poster that read, “Please Stop—I Care,” with “Thank You For Stopping” on the reverse side. The poster was held by the volunteer so that drivers approaching Stop A could read the sign. Drivers approaching Stop B could see the volunteer but could not read the sign. When vehicles approaching Stop A made a complete stop, the volunteer flashed the “thank you” side of the poster to the driver. The strategy was evaluated using a multielement design. The intervention increased stops completed at Stop A from a baseline average of 13% to an intervention average of 52%. Stop B also showed improved stopping, from a baseline average of 6% to an intervention average of 28%. Data showed no relation between complete stops made and the drivers' use of turn signals and safety belts. PMID:16602391

DOE Office of Scientific and Technical Information (OSTI.GOV)

McInerney, Peter; Adams, Paul; Hadi, Masood Z.

As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR applications, including 3 polymerases typically used for cloning applications requiring high fidelity. Error ratemore » measurement values reported here were obtained by direct sequencing of cloned PCR products. The strategy employed here allows interrogation of error rate across a very large DNA sequence space, since 94 unique DNA targets were used as templates for PCR cloning. The six enzymes included in the study, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu , Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. Mutation spectra are reported, with the 3 high fidelity enzymes displaying broadly similar types of mutations. For these enzymes, transition mutations predominate, with little bias observed for type of transition.« less

TaqMan RT-PCR and VERSANT HIV-1 RNA 3.0 (bDNA) assay Quantification of HIV-1 RNA viral load in breast milk.

PubMed

Israel-Ballard, Kiersten; Ziermann, Rainer; Leutenegger, Christian; Di Canzio, James; Leung, Kimmy; Strom, Lynn; Abrams, Barbara; Chantry, Caroline

2005-12-01

Transmission of HIV via breast milk is a primary cause of pediatric HIV infection in developing countries. Reliable methods to detect breast milk viral load are important. To correlate the ability of the VERSANT HIV 3.0 (bDNA) assay to real-time (RT) TaqMan PCR in quantifying breast milk HIV-1 RNA. Forty-six breast milk samples that had been spiked with cell-free HIV-1 and eight samples spiked with cell-associated HIV-1 were assayed for HIV-1 RNA by both VERSANT HIV 3.0 and TaqMan RNA assays. Only assays on the cell-free samples were statistically compared. Both a Deming regression slope and a Bland-Altman slope indicated a linear relationship between the two assays. TaqMan quantitations were on average 2.6 times higher than those of HIV 3.0. A linear relationship was observed between serial dilutions of spiked cell-free HIV-1 and both the VERSANT HIV 3.0 and the TaqMan RNA assays. The two methods correlated well although the VERSANT HIV 3.0 research protocol quantified HIV-1 RNA slightly lower than TaqMan.

One-Step Reverse Transcription-Polymerase Chain Reaction for Ebola and Marburg Viruses.

PubMed

Park, Sun-Whan; Lee, Ye-Ji; Lee, Won-Ja; Jee, Youngmee; Choi, WooYoung

2016-06-01

Ebola and Marburg viruses (EBOVs and MARVs, respectively) are causative agents of severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. In 2014, there was a major Ebola outbreak in various countries in West Africa, including Guinea, Liberia, Republic of Sierra Leone, and Nigeria. EBOV and MARV are clinically difficult to diagnose and distinguish from other African epidemic diseases. Therefore, in this study, we aimed to develop a method for rapid identification of the virus to prevent the spread of infection. We established a conventional one-step reverse transcription-polymerase chain reaction (RT-PCR) assay for these pathogens based on the Superscript Reverse Transcriptase-Platinum Taq polymerase enzyme mixture. All assays were thoroughly optimized using in vitro-transcribed RNA. We designed seven primer sets of nucleocapsid protein (NP) genes based on sequences from seven filoviruses, including five EBOVs and two MARVs. To evaluate the sensitivity of the RT-PCR assay for each filovirus, 10-fold serial dilutions of synthetic viral RNA transcripts of EBOV or MARV NP genes were used to assess detection limits of viral RNA copies. The potential for these primers to cross react with other filoviruses was also examined. The results showed that the primers were specific for individual genotype detection in the examined filoviruses. The assay established in this study may facilitate rapid, reliable laboratory diagnosis in suspected cases of Ebola and Marburg hemorrhagic fevers.

STOP-IT: Windows executable software for the stop-signal paradigm.

PubMed

Verbruggen, Frederick; Logan, Gordon D; Stevens, Michaël A

2008-05-01

The stop-signal paradigm is a useful tool for the investigation of response inhibition. In this paradigm, subjects are instructed to respond as fast as possible to a stimulus unless a stop signal is presented after a variable delay. However, programming the stop-signal task is typically considered to be difficult. To overcome this issue, we present software called STOP-IT, for running the stop-signal task, as well as an additional analyzing program called ANALYZE-IT. The main advantage of both programs is that they are a precompiled executable, and for basic use there is no need for additional programming. STOP-IT and ANALYZE-IT are completely based on free software, are distributed under the GNU General Public License, and are available at the personal Web sites of the first two authors or at expsy.ugent.be/tscope/stop.html.

Dopamine Genes (DRD2/ANKK1-TaqA1 and DRD4-7R) and Executive Function: Their Interaction with Obesity

PubMed Central

Ariza, Mar; Garolera, Maite; Jurado, Maria Angeles; Garcia-Garcia, Isabel; Hernan, Imma; Sánchez-Garre, Consuelo; Vernet-Vernet, Maria; Sender-Palacios, Maria Jose; Marques-Iturria, Idoia; Pueyo, Roser; Segura, Barbara; Narberhaus, Ana

2012-01-01

Obesity is a multifactorial disease caused by the interaction between genotype and environment, and it is considered to be a type of addictive alteration. The A1 allele of the DRD2/ANKK1-TaqIA gene has been associated with addictive disorders, with obesity and with the performance in executive functions. The 7 repeat allele of the DRD4 gene has likewise been associated with the performance in executive functions, as well as with addictive behaviors and impulsivity. Participants were included in the obesity group (N = 42) if their body mass index (BMI) was equal to or above 30, and in the lean group (N = 42) if their BMI was below 25. The DRD2/ANKK1-TaqIA and DRD4 VNTR polymorphisms were obtained. All subjects underwent neuropsychological assessment. Eating behavior traits were evaluated. The ‘DRD2/ANKK1-TaqIA A1-allele status’ had a significant effect on almost all the executive variables, but no significant ‘DRD4 7R-allele status’ effects were observed for any of the executive variables analyzed. There was a significant ‘group’ x ‘DRD2/ANKK1-TaqIA A1-allele status’ interaction effect on LN and ‘group’ x ‘DRD4 7R-allele status’ interaction effect on TMT B-A score. Being obese and a carrier of the A1 allele of DRD2/ANKK1-TaqIA or the 7R allele of DRD4 VNTR polymorphisms could confer a weakness as regards the performance of executive functions. PMID:22848508

The Effects of Prompting and Feedback on Drivers' Stopping at Stop Signs

ERIC Educational Resources Information Center

Austin, John; Hackett, Stacey; Gravina, Nicole; Lebbon, Angela

2006-01-01

Complete stops at a high-traffic intersection on the campus of a public university were increased with a prompting and consequence intervention. Data were collected at two opposing stop signs (Stop A and Stop B); however, the intervention was implemented only at Stop A. During the intervention, a volunteer stood next to Stop A holding a poster…

Identification of a STOP1-like protein in Eucalyptus that regulates transcription of Al tolerance genes.

PubMed

Sawaki, Yoshiharu; Kobayashi, Yuriko; Kihara-Doi, Tomonori; Nishikubo, Nobuyuki; Kawazu, Tetsu; Kobayashi, Masatomo; Kobayashi, Yasufumi; Iuchi, Satoshi; Koyama, Hiroyuki; Sato, Shigeru

2014-06-01

Tolerance to soil acidity is an important trait for eucalyptus clones that are introduced to commercial forestry plantations in pacific Asian countries, where acidic soil is dominant in many locations. A conserved transcription factor regulating aluminum (Al) and proton (H⁺) tolerance in land-plant species, STOP1 (SENSITIVE TOPROTON RHIZOTOXICITY 1)-like protein, was isolated by polymerase chain reaction-based cloning, and then suppressed by RNA interference in hairy roots produced by Agrobacterium rhizogenes-mediated transformation. Eucalyptus STOP1-like protein complemented proton tolerance in an Arabidopsis thaliana stop1-mutant, and localized to the nucleus in a transient assay of a green fluorescent protein fusion protein expressed in tobacco leaves by Agrobacterium tumefaciens-mediated transformation. Genes encoding a citrate transporting MULTIDRUGS AND TOXIC COMPOUND EXTRUSION protein and an orthologue of ALUMINUM SENSITIVE 3 were suppressed in transgenic hairy roots in which the STOP1 orthologue was knocked down. In summary, we identified a series of genes for Al-tolerance in eucalyptus, including a gene for STOP1-like protein and the Al-tolerance genes it regulates. These genes may be useful for molecular breeding and genomic selection of elite clones to introduce into acid soil regions. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Comparison of allelic discrimination by dHPLC, HRM, and TaqMan in the detection of BRAF mutation V600E.

PubMed

Carbonell, Pablo; Turpin, María C; Torres-Moreno, Daniel; Molina-Martínez, Irene; García-Solano, José; Perez-Guillermo, Miguel; Conesa-Zamora, Pablo

2011-09-01

The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study was to compare the performance characteristics in V600E detection of denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM) with TaqMan allelic discrimination as well as direct-sequencing methods in a series of 195 colorectal paraffin-embedded specimens up to the age of 15 years. The effectiveness for obtaining results on mutation status was best using TaqMan (96.9%), followed by dHPLC (93.3%), HRM (88.7%), and sequencing (88.2%). In general, TaqMan was best for analyzing older tissues, whereas sequencing was the least efficient. Heterozygotic V600E was detected in 11.6%, 9.9%, 11.6%, and 9.9% of tissues using TaqMan, dHPLC, HRM, and sequencing, respectively. Result concordances between dHPLC and TaqMan or sequencing were excellent (κ = 0.9411 and κ = 0.8988, respectively); for HRM, the concordances were good (κ = 0.7973 and κ = 0.7488, respectively). By using DNA dilutions from tumor tissue, a minimum of 10% of V600E harboring cancer content was required for the analysis by dHPLC and HRM. dHPLC could detect four non-V600E mutations, whereas HRM detected one. Our results indicate that dHPLC and HRM are techniques that can be reliably used for the detection of the BRAFV600E mutation in archival paraffin-embedded tissues. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Associations of Cholesteryl Ester Transfer Protein TaqIB Polymorphism with the Composite Ischemic Cardiovascular Disease Risk and HDL-C Concentrations: A Meta-Analysis

PubMed Central

Guo, Shu-xia; Yao, Ming-hong; Ding, Yu-song; Zhang, Jing-yu; Yan, Yi-zhong; Liu, Jia-ming; Zhang, Mei; Rui, Dong-sheng; Niu, Qiang; He, Jia; Guo, Heng; Ma, Ru-lin

2016-01-01

Background: Previous studies have evaluated the associations between the cholesteryl ester transfer protein (CETP) TaqIB polymorphism (rs708272), the risk of developing composite ischemic cardiovascular disease (CVD) and the concentration of high-density lipoprotein cholesterol (HDL-C), but results remain controversial. The objective of this study was to investigate whether a relationship exists between these factors. Methods: We conducted a meta-analysis of available studies to clarify the associations of the CETP TaqIB polymorphism with HDL-C concentration and the composite ischemic CVD risk in both Asians and Caucasians. All statistical analyses were done with Stata 12.0. Results: Through utilization of the Cochrane Library, Embase, PubMed, Web of Science, Springer, China Science and Technology Journal Database, China National Knowledge Infrastructure, Google Scholar, and Baidu Library, a total of 45 studies from 44 papers with 20,866 cases and 21,298 controls were combined showing a significant association between the CETP TaqIB variant and composite ischemic CVD risk. Carriers of allele TaqIB-B1 were found to have a higher risk of composite ischemic CVD than non-carriers: OR = 1.15, 95% CI = 1.09–1.21, p < 0.001. Meanwhile, 28 studies with 23,959 subjects were included in the association between the CETP TaqIB polymorphism and the concentration of HDL-C. Results suggested that carriers of the B1B1 genotype had lower concentrations of HDL-C than those of the B2B2 genotype: SMD = 0.50, 95% CI = 0.36–0.65, p < 0.001. Conclusions: The synthesis of available evidence demonstrates that the CETP TaqIB polymorphism protects against composite ischemic CVD risk and is associated with a higher HDL-C concentration in both Asians and Caucasians. PMID:27608031

Real-time polymerase chain reaction-based approach for quantification of the pat gene in the T25 Zea mays event.

PubMed

Weighardt, Florian; Barbati, Cristina; Paoletti, Claudia; Querci, Maddalena; Kay, Simon; De Beuckeleer, Marc; Van den Eede, Guy

2004-01-01

In Europe, a growing interest for reliable techniques for the quantification of genetically modified component(s) of food matrixes is arising from the need to comply with the European legislative framework on novel food products. Real-time polymerase chain reaction (PCR) is currently the most powerful technique for the quantification of specific nucleic acid sequences. Several real-time PCR methodologies based on different molecular principles have been developed for this purpose. The most frequently used approach in the field of genetically modified organism (GMO) quantification in food or feed samples is based on the 5'-3'-exonuclease activity of Taq DNA polymerase on specific degradation probes (TaqMan principle). A novel approach was developed for the establishment of a TaqMan quantification system assessing GMO contents around the 1% threshold stipulated under European Union (EU) legislation for the labeling of food products. The Zea mays T25 elite event was chosen as a model for the development of the novel GMO quantification approach. The most innovative aspect of the system is represented by the use of sequences cloned in plasmids as reference standards. In the field of GMO quantification, plasmids are an easy to use, cheap, and reliable alternative to Certified Reference Materials (CRMs), which are only available for a few of the GMOs authorized in Europe, have a relatively high production cost, and require further processing to be suitable for analysis. Strengths and weaknesses of the use of novel plasmid-based standards are addressed in detail. In addition, the quantification system was designed to avoid the use of a reference gene (e.g., a single copy, species-specific gene) as normalizer, i.e., to perform a GMO quantification based on an absolute instead of a relative measurement. In fact, experimental evidences show that the use of reference genes adds variability to the measurement system because a second independent real-time PCR-based measurement

Second stop and sbottom searches with a stealth stop

NASA Astrophysics Data System (ADS)

Cheng, Hsin-Chia; Li, Lingfeng; Qin, Qin

2016-11-01

The top squarks (stops) may be the most wanted particles after the Higgs boson discovery. The searches for the lightest stop have put strong constraints on its mass. However, there is still a search gap in the low mass region if the spectrum of the stop and the lightest neutralino is compressed. In that case, it may be easier to look for the second stop since naturalness requires both stops to be close to the weak scale. The current experimental searches for the second stop are based on the simplified model approach with the decay modes {overset{˜ }{t}}_2to {overset{˜ }{t}}_1Z and {overset{˜ }{t}}_2to {overset{˜ }{t}}_1h . However, in a realistic supersymmetric spectrum there is always a sbottom lighter than the second stop, hence the decay patterns are usually more complicated than the simplified model assumptions. In particular, there are often large branching ratios of the decays {overset{˜ }{t}}_2to {overset{˜ }{b}}_1W and {overset{˜ }{b}}_1to {overset{˜ }{t}}_1W as long as they are open. The decay chains can be even more complex if there are intermediate states of additional charginos and neutralinos in the decays. By studying several MSSM benchmark models at the 14 TeV LHC, we point out the importance of the multi- W final states in the second stop and the sbottom searches, such as the same-sign dilepton and multilepton signals, aside from the traditional search modes. The observed same-sign dilepton excesses at LHC Run 1 and Run 2 may be explained by some of our benchmark models. We also suggest that the vector boson tagging and a new kinematic variable may help to suppress the backgrounds and increase the signal significance for some search channels. Due to the complex decay patterns and lack of the dominant decay channels, the best reaches likely require a combination of various search channels at the LHC for the second stop and the lightest sbottom.

Linguistic Grammar Learning and DRD2-TAQ-IA Polymorphism

PubMed Central

Wong, Patrick C. M.; Ettlinger, Marc; Zheng, Jing

2013-01-01

As research into the neurobiology of language has focused primarily on the systems level, fewer studies have examined the link between molecular genetics and normal variations in language functions. Because the ability to learn a language varies in adults and our genetic codes also vary, research linking the two provides a unique window into the molecular neurobiology of language. We consider a candidate association between the dopamine receptor D2 gene (DRD2) and linguistic grammar learning. DRD2-TAQ-IA polymorphism (rs1800497) is associated with dopamine receptor D2 distribution and dopamine impact in the human striatum, such that A1 allele carriers show reduction in D2 receptor binding relative to carriers who are homozygous for the A2 allele. The individual differences in grammatical rule learning that are particularly prevalent in adulthood are also associated with striatal function and its role in domain-general procedural memory. Therefore, we reasoned that procedurally-based grammar learning could be associated with DRD2-TAQ-IA polymorphism. Here, English-speaking adults learned artificial concatenative and analogical grammars, which have been respectively associated with procedural and declarative memory. Language learning capabilities were tested while learners’ neural hemodynamic responses were simultaneously measured by fMRI. Behavioral learning and brain activation data were subsequently compared with the learners’ DRD2 (rs1800497) genotype. Learners who were homozygous for the A2 allele were better at concatenative (but not analogical) grammar learning and had higher striatal responses relative to those who have at least one A1 allele. These results provide preliminary evidence for the neurogenetic basis of normal variations in linguistic grammar learning and its link to domain-general functions. PMID:23741438

Compartmentalized self-replication (CSR) selection of Thermococcus litoralis Sh1B DNA polymerase for diminished uracil binding.

PubMed

Tubeleviciute, Agne; Skirgaila, Remigijus

2010-08-01

The thermostable archaeal DNA polymerase Sh1B from Thermococcus litoralis has a typical uracil-binding pocket, which in nature plays an essential role in preventing the accumulation of mutations caused by cytosine deamination to uracil and subsequent G-C base pair transition to A-T during the genomic DNA replication. The uracil-binding pocket recognizes and binds uracil base in a template strand trapping the polymerase. Since DNA replication stops, the repair systems have a chance to correct the promutagenic event. Archaeal family B DNA polymerases are employed in various PCR applications. Contrary to nature, in PCR the uracil-binding property of archaeal polymerases is disadvantageous and results in decreased DNA amplification yields and lowered sensitivity. Furthermore, in diagnostics qPCR, RT-qPCR and end-point PCR are performed using dNTP mixtures, where dTTP is partially or fully replaced by dUTP. Uracil-DNA glycosylase treatment and subsequent heating of the samples is used to degrade the DNA containing uracil and prevent carryover contamination, which is the main concern in diagnostic laboratories. A thermostable archaeal DNA polymerase with the abolished uracil binding would be a highly desirable and commercially interesting product. An attempt to disable uracil binding in DNA polymerase Sh1B from T. litoralis by generating site-specific mutants did not yield satisfactory results. However, a combination of random mutagenesis of the whole polymerase gene and compartmentalized self-replication was successfully used to select variants of thermostable Sh1B polymerase capable of performing PCR with dUTP instead of dTTP.

Quantitative and specific detection of the biocontrol agent, Serratia plymuthica, in plant extracts using a real-time TaqMan® assay.

PubMed

Czajkowski, Robert; van der Wolf, Jan M

2012-11-01

A Serratia plymuthica-specific TaqMan® assay was designed based on the consensus nucleotide sequence from the 3'- end of the luxS gene present in all S. plymuthica strains tested. The specificity of the assay was demonstrated by testing 21 Serratia spp. strains and 30 isolates belonging to various species that can potentially coexist with S. plymuthica in the same environment. Positive reactions in the TaqMan® assay were observed only for S. plymuthica isolates and not for other bacteria. The TaqMan® assay could detect down to 1.95 ng of S. plymuthica DNA, down to 5 bacterial cells per reaction (100 cfu ml(-1)) in vitro, down to 50 bacterial cells per reaction (1,000 cfu ml(-1)) in spiked potato root extracts and down to 5 bacterial cells per reaction (100 cfu ml(-1)) in spiked potato haulm extracts. We used this assay to quantify S. plymuthica A30 cells in potato and tomato haulms and roots grown from S. plymuthica A30-inoculated potato seed tubers and tomato seeds. The results were comparable with the spread-plating of plant extracts on a newly developed S. plymuthica A30 selective medium (CVTR2Arif). The TaqMan® assay can be used to quantify S. plymuthica isolates in different ecosystems and in complex substrates.

Universal detection of phytoplasmas and Xylella spp. by TaqMan singleplex and multiplex real-time PCR with dual priming oligonucleotides.

PubMed

Ito, Takao; Suzaki, Koichi

2017-01-01

Phytoplasmas and Xylella spp. are bacteria that cause many economically important plant diseases worldwide. TaqMan probe-based quantitative real-time polymerase chain reaction (qPCR) assays have been utilized to universally detect phytoplasmas or Xylella fastidiosa. To develop a superior universal qPCR method, we used a dual priming oligonucleotide (DPO) with two annealing sites as a reverse primer to target the well-conserved bacterial 16S rDNA. The new qPCR assays universally detected various species of phytoplasmas and subspecies of X. fastidiosa as well as Xylella taiwanensis, and generally showed superior threshold cycle values when amplifying specific or non-specific products compared to current universal qPCR assays. The proposed qPCR assays were integrated to develop a multiplex qPCR assay that simultaneously detected phytoplasmas, Xylella spp., and an internal plant DNA positive control within 1 hour. This assay could detect a minimum of ten bacterial cells and was compatible with crude extractions used in the rapid screening of various plants. The amplicons were of sufficient lengths to be directly sequenced for preliminary identification, and the primers could be used in universal conventional PCR assays. Additionally, reverse DPO primers can be utilized to improve other probe-based qPCR assays.

Universal detection of phytoplasmas and Xylella spp. by TaqMan singleplex and multiplex real-time PCR with dual priming oligonucleotides

PubMed Central

Suzaki, Koichi

2017-01-01

Phytoplasmas and Xylella spp. are bacteria that cause many economically important plant diseases worldwide. TaqMan probe-based quantitative real-time polymerase chain reaction (qPCR) assays have been utilized to universally detect phytoplasmas or Xylella fastidiosa. To develop a superior universal qPCR method, we used a dual priming oligonucleotide (DPO) with two annealing sites as a reverse primer to target the well-conserved bacterial 16S rDNA. The new qPCR assays universally detected various species of phytoplasmas and subspecies of X. fastidiosa as well as Xylella taiwanensis, and generally showed superior threshold cycle values when amplifying specific or non-specific products compared to current universal qPCR assays. The proposed qPCR assays were integrated to develop a multiplex qPCR assay that simultaneously detected phytoplasmas, Xylella spp., and an internal plant DNA positive control within 1 hour. This assay could detect a minimum of ten bacterial cells and was compatible with crude extractions used in the rapid screening of various plants. The amplicons were of sufficient lengths to be directly sequenced for preliminary identification, and the primers could be used in universal conventional PCR assays. Additionally, reverse DPO primers can be utilized to improve other probe-based qPCR assays. PMID:28957362

An A-T linker adapter polymerase chain reaction method for chromosome walking without restriction site cloning bias.

PubMed

Trinh, Quoclinh; Xu, Wentao; Shi, Hui; Luo, Yunbo; Huang, Kunlun

2012-06-01

A-T linker adapter polymerase chain reaction (PCR) was modified and employed for the isolation of genomic fragments adjacent to a known DNA sequence. The improvements in the method focus on two points. The first is the modification of the PO(4) and NH(2) groups in the adapter to inhibit the self-ligation of the adapter or the generation of nonspecific products. The second improvement is the use of the capacity of rTaq DNA polymerase to add an adenosine overhang at the 3' ends of digested DNA to suppress self-ligation in the digested DNA and simultaneously resolve restriction site clone bias. The combination of modifications in the adapter and in the digested DNA leads to T/A-specific ligation, which enhances the flexibility of this method and makes it feasible to use many different restriction enzymes with a single adapter. This novel A-T linker adapter PCR overcomes the inherent limitations of the original ligation-mediated PCR method such as low specificity and a lack of restriction enzyme choice. Moreover, this method also offers higher amplification efficiency, greater flexibility, and easier manipulation compared with other PCR methods for chromosome walking. Experimental results from 143 Arabidopsis mutants illustrate that this method is reliable and efficient in high-throughput experiments. Copyright © 2012 Elsevier Inc. All rights reserved.

A preliminary study: novelty seeking, frontal executive function, and dopamine receptor (D2) TaqI A gene polymorphism in patients with methamphetamine dependence.

PubMed

Han, Doug Hyun; Yoon, Sujung J; Sung, Young Hoon; Lee, Young Sik; Kee, Baik Seok; Lyoo, In Kyoon; Renshaw, Perry F; Cho, Soo Churl

2008-01-01

Dopamine receptor polymorphisms have been associated with specific patterns of novelty seeking (NS) temperamental nature and frontal executive function. In addition, carriers of dopamine receptor type 2 (DRD2)-TaqI A1 have been hypothesized to be potentially vulnerable to addictive behaviors. In the present study, the association between dopamine D2 polymorphisms, NS, and frontal executive function was studied. Thirty-seven methamphetamine (MA)-dependent subjects and 40 healthy comparison subjects participated in the current study. The severity of addiction, NS temperament, and frontal executive functions were measured using the Addiction Severity Index, the NS subscale in the Temperament and Character Inventory, and the Wisconsin Card Sorting Test, respectively. All subjects were genotyped with regard to DRD2-TaqI polymorphisms. The prevalence of DRD2-TaqI A1 allele polymorphisms was greater in the MA-abuser group than in the comparison group. Patients with MA dependence also had higher NS characteristics and high scores in total trials, errors, and perseverative errors of the Wisconsin Card Sorting Test than comparison subjects. Within patients with MA dependence, the subgroup of DRD2-TaqI A1 carrier had greater NS scores relative to those without, whereas there was only a trend level of lower frontal executive function in the first subgroup. In the present study, the MA-dependent patients with DRD2-TaqI A1 allele had significantly greater NS scores and lower frontal executive function with a trend level than those without. These preliminary results suggest that MA-dependent patients may have the possibility of genetic and biogenic vulnerability to MA.

The cobas p 630 instrument: a dedicated pre-analytic solution to optimize COBAS® AmpliPrep/COBAS® TaqMan® system workflow and turn-around-time.

PubMed

Vallefuoco, L; Sorrentino, R; Spalletti Cernia, D; Colucci, G; Portella, G

2012-12-01

The cobas p 630, a fully automated pre-analytical instrument for primary tube handling recently introduced to complete the Cobas(®) TaqMan systems portfolio, was evaluated in conjunction with: the COBAS(®) AmpliPrep/COBAS(®) TaqMan HBV Test, v2.0, COBAS(®) AmpliPrep/COBAS(®) TaqMan HCV Test, v1.0 and COBAS(®) AmpliPrep/COBAS(®) TaqMan HIV Test, v2.0. The instrument performance in transferring samples from primary to secondary tubes, its impact in improving COBAS(®) AmpliPrep/COBAS(®) TaqMan workflow and hands-on reduction and the risk of possible cross-contamination were assessed. Samples from 42 HBsAg positive, 42 HCV and 42 HIV antibody (Ab) positive patients as well as 21 healthy blood donors were processed with or without automated primary tubes. HIV, HCV and HBsAg positive samples showed a correlation index of 0.999, 0.987 and of 0.994, respectively. To assess for cross-contamination, high titer HBV DNA positive samples, HCV RNA and HIV RNA positive samples were distributed in the cobas p 630 in alternate tube positions, adjacent to negative control samples within the same rack. None of the healthy donor samples showed any reactivity. Based on these results, the cobas p 630 can improve workflow and sample tracing in laboratories performing molecular tests, and reduce turnaround time, errors, and risks. Copyright © 2012 Elsevier B.V. All rights reserved.

A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases.

PubMed

Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

2008-10-04

Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases.

Stop/Start: Overview

Science.gov Websites

1 Stop/Start vehicles use a combination of regenerative and conventional friction braking to slow , The gasoline engine in a start-stop hybrid is much like those in conventional vehicles. Unlike other hybrids that use an electric motor to help power the vehicle, the engine in a start-stop hybrid is usually

Stop the top background of the stop search

NASA Astrophysics Data System (ADS)

Bai, Yang; Cheng, Hsin-Chia; Gallicchio, Jason; Gu, Jiayin

2012-07-01

The main background for the supersymmetric stop direct production search comes from Standard Model toverline t events. For the single-lepton search channel, we introduce a few kinematic variables to further suppress this background by focusing on its dileptonic and semileptonic topologies. All are defined to have end points in the background, but not signal distributions. They can substantially improve the stop signal significance and mass reach when combined with traditional kinematic variables such as the total missing transverse energy. Among them, our variable M_{{T2}}^W hasthebestoverallperformancebecause it uses all available kinematic information, including the on-shell mass of both W's. We see 20 %-30 % improvement on the discovery significance and estimate that the 8 TeV LHC run with 20 fb-1 of data would be able to reach an exclusion limit of 650-700 GeV for direct stop production, as long as the stop decays dominantly to the top quark and a light stable neutralino. Most of the mass range required for the supersymmetric solution of the naturalness problem in the standard scenario can be covered.

Development and validation of a novel hydrolysis probe real-time polymerase chain reaction for agamid adenovirus 1 in the central bearded dragon (Pogona vitticeps).

PubMed

Fredholm, Daniel V; Coleman, James K; Childress, April L; Wellehan, James F X

2015-03-01

Agamid adenovirus 1 (AgAdv-1) is a significant cause of disease in bearded dragons (Pogona sp.). Clinical manifestations of AgAdv-1 infection are variable and often nonspecific; the manifestations range from lethargy, weight loss, and inappetence, to severe enteritis, hepatitis, and sudden death. Currently, diagnosis of AgAdv-1 infection is achieved through a single published method: standard nested polymerase chain reaction (nPCR) and sequencing. Standard nPCR with sequencing provides reliable sensitivity, specificity, and validation of PCR products. However, this process is comparatively expensive, laborious, and slow. Probe hybridization, as used in a TaqMan assay, represents the best option for validating PCR products aside from the time-consuming process of sequencing. This study developed a real-time PCR (qPCR) assay using a TaqMan probe-based assay, targeting a highly conserved region of the AgAdv-1 genome. Standard curves were generated, detection results were compared with the gold standard conventional PCR and sequencing assay, and limits of detection were determined. Additionally, the qPCR assay was run on samples known to be positive for AgAdv-1 and samples known to be positive for other adenoviruses. Based on the results of these evaluations, this assay allows for a less expensive, rapid, quantitative detection of AgAdv-1 in bearded dragons. © 2015 The Author(s).

Stop codons in the hepatitis B surface proteins are enriched during antiviral therapy and are associated with host cell apoptosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colledge, Danielle; Soppe, Sally; Yuen, Lilly

Premature stop codons in the hepatitis B virus (HBV) surface protein can be associated with nucleos(t)ide analogue resistance due to overlap of the HBV surface and polymerase genes. The aim of this study was to determine the effect of the replication of three common surface stop codon variants on the hepatocyte. Cell lines were transfected with infectious HBV clones encoding surface stop codons rtM204I/sW196*, rtA181T/sW172*, rtV191I/sW182*, and a panel of substitutions in the surface proteins. HBsAg was measured by Western blotting. Proliferation and apoptosis were measured using flow cytometry. All three surface stop codon variants were defective in HBsAg secretion.more » Cells transfected with these variants were less proliferative and had higher levels of apoptosis than those transfected with variants that did not encode surface stop codons. The most cytopathic variant was rtM204I/sW196*. Replication of HBV encoding surface stop codons was toxic to the cell and promoted apoptosis, exacerbating disease progression. - Highlights: •Under normal circumstances, HBV replication is not cytopathic. •Premature stop codons in the HBV surface protein can be selected and enriched during nucleos(t)ide analogue therapy. •Replication of these variants can be cytopathic to the cell and promote apoptosis. •Inadequate antiviral therapy may actually promote disease progression.« less

A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

PubMed Central

Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

2008-01-01

Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases. This article was reviewed by Eugene Koonin and Mark Ragan. PMID:18834537

Depression - stopping your medicines

MedlinePlus

... gov/ency/patientinstructions/000570.htm Depression - stopping your medicines To use the sharing features on this page, ... no longer taking them. Before You Stop Your Medicine Stopping your medicine may be the right choice ...

Regulatory role of Cdx-2 and Taq I polymorphism of vitamin D receptor gene on chemokine expression in pulmonary tuberculosis.

PubMed

Harishankar, M; Selvaraj, P

2016-06-01

Vitamin D receptor (VDR) gene variants have been shown to be regulating the immune response in tuberculosis. We studied the regulatory role of VDR promoter Cdx-2 and 3'UTR TaqI gene variants on chemokine levels from culture filtrate antigen (CFA) stimulated with or without 1,25(OH)2D3 treated peripheral blood mononuclear cells of 50 pulmonary tuberculosis patients (PTB) and 51 normal healthy controls (HCs). In CFA with 1,25(OH)2D3 treated cultures, the MIP-1α, MIP-1β, RANTES levels were significantly decreased in Cdx-2 AA genotype compared to GG genotype, while a significantly increased MIG level was observed in Cdx-2 AA genotype (p<0.05). In TaqI polymorphism, tt genotype significantly decreased MIP-1β and RANTES levels compared to TT genotype. Moreover, a significantly increased level of IP-10 and MIG was observed in TaqI tt genotype compared with TT genotype (p<0.05). The results suggests that the 1,25(OH)2D3 may alter the chemokine response through the VDR polymorphic variants during infection. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Inhibitory motor control based on complex stopping goals relies on the same brain network as simple stopping

PubMed Central

Wessel, Jan R.; Aron, Adam R.

2014-01-01

Much research has modeled action-stopping using the stop-signal task (SST), in which an impending response has to be stopped when an explicit stop-signal occurs. A limitation of the SST is that real-world action-stopping rarely involves explicit stop-signals. Instead, the stopping-system engages when environmental features match more complex stopping goals. For example, when stepping into the street, one monitors path, velocity, size, and types of objects; and only stops if there is a vehicle approaching. Here, we developed a task in which participants compared the visual features of a multidimensional go-stimulus to a complex stopping-template, and stopped their go-response if all features matched the template. We used independent component analysis of EEG data to show that the same motor inhibition brain network that explains action-stopping in the SST also implements motor inhibition in the complex-stopping task. Furthermore, we found that partial feature overlap between go-stimulus and stopping-template lead to motor slowing, which also corresponded with greater stopping-network activity. This shows that the same brain system for action-stopping to explicit stop-signals is recruited to slow or stop behavior when stimuli match a complex stopping goal. The results imply a generalizability of the brain’s network for simple action-stopping to more ecologically valid scenarios. PMID:25270603

Interaction of the TaqIA polymorphism and poor parental socialization on changes in adolescent marijuana use.

PubMed

Vaske, Jamie

2013-02-01

The current study uses data from the genetic subsample from the National Longitudinal Study of Adolescent Health (Add Health) in waves I and II (ages of 11-19 and 12-20 respectively) to investigate the interaction of the TaqIA polymorphism and poor parental socialization on changes in adolescent marijuana use. Results reveal that TaqIA interacts with poor parental rule setting, but not quality of mother-child communication, to influence changes in marijuana use. Adolescents who are homozygous for the A1 and whose parents allow the youth to set their own curfew experience significant increases in marijuana use during adolescence. In contrast, youths with the A1/A1 genotype whose parents do not allow the adolescent to set their own curfew experience significant decreases in the frequency of marijuana use. These results suggest that direct parental social control may effectively suppress the genetic risk of the A1/A1 genotype on marijuana use in adolescence. The study's limitations are noted.

Meta-analysis of Cholesteryl Ester Transfer Protein TaqIB Polymorphism and Risk of Myocardial Infarction

PubMed Central

Cao, Min; Zhou, Zhi-Wen; Fang, Bang-Jiang; Zhao, Cheng-Gen; Zhou, Duan

2014-01-01

Abstract A number of studies have been conducted to explore the association between the cholesteryl ester transfer protein (CETP) TaqIB polymorphism and risk of myocardial infarction (MI); however, the results are inconsistent. Therefore, we conducted this meta-analysis to clarify the issue based on all the data available. Eligible studies were retrieved by searching PubMed, Embase, Web of Science, and Google Scholar. We calculated the crude odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) to assess the association between the TaqIB polymorphism and risk of MI. We included 13 studies involving 8733 MI cases and 8573 controls in the meta-analysis. The pooled results from all included studies showed decreased MI risk in the analysis of the B2B2 versus B1B1 (OR = 0.78, 95% CI = 0.68–0.91), dominant (OR = 0.88, 95% CI = 0.77–0.99), and recessive genetic models (OR = 0.84, 95% CI = 0.78–0.91). The frequency of the B2B2 genotype in MI patients was lower (OR = 0.87, 95% CI = 0.81–0.94). However, there was no significant association in the B1B2 versus B1B1 analysis (OR = 0.92, 95% CI = 0.81–1.05) and no significant difference for the B1B1 genotype (OR = 1.04, 95% CI = 0.98–1.11) and B1B2 genotype (OR = 1.03, 95% CI = 0.97–1.08). Cumulative analysis confirmed these results. Our results suggest that the B2B2 genotype of the CETP TaqIB polymorphism is a protective factor against the development of MI. PMID:25474428

Meta-analysis of cholesteryl ester transfer protein TaqIB polymorphism and risk of myocardial infarction.

PubMed

Cao, Min; Zhou, Zhi-Wen; Fang, Bang-Jiang; Zhao, Cheng-Gen; Zhou, Duan

2014-11-01

A number of studies have been conducted to explore the association between the cholesteryl ester transfer protein (CETP) TaqIB polymorphism and risk of myocardial infarction (MI); however, the results are inconsistent. Therefore, we conducted this meta-analysis to clarify the issue based on all the data available.Eligible studies were retrieved by searching PubMed, Embase, Web of Science, and Google Scholar. We calculated the crude odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) to assess the association between the TaqIB polymorphism and risk of MI.We included 13 studies involving 8733 MI cases and 8573 controls in the meta-analysis. The pooled results from all included studies showed decreased MI risk in the analysis of the B2B2 versus B1B1 (OR = 0.78, 95% CI = 0.68-0.91), dominant (OR = 0.88, 95% CI = 0.77-0.99), and recessive genetic models (OR = 0.84, 95% CI = 0.78-0.91). The frequency of the B2B2 genotype in MI patients was lower (OR = 0.87, 95% CI = 0.81-0.94). However, there was no significant association in the B1B2 versus B1B1 analysis (OR = 0.92, 95% CI = 0.81-1.05) and no significant difference for the B1B1 genotype (OR = 1.04, 95% CI = 0.98-1.11) and B1B2 genotype (OR = 1.03, 95% CI = 0.97-1.08). Cumulative analysis confirmed these results.Our results suggest that the B2B2 genotype of the CETP TaqIB polymorphism is a protective factor against the development of MI.

Inseparability of Go and Stop in Inhibitory Control: Go Stimulus Discriminability Affects Stopping Behavior.

PubMed

Ma, Ning; Yu, Angela J

2016-01-01

Inhibitory control, the ability to stop or modify preplanned actions under changing task conditions, is an important component of cognitive functions. Two lines of models of inhibitory control have previously been proposed for human response in the classical stop-signal task, in which subjects must inhibit a default go response upon presentation of an infrequent stop signal: (1) the race model, which posits two independent go and stop processes that race to determine the behavioral outcome, go or stop; and (2) an optimal decision-making model, which posits that observers decides whether and when to go based on continually (Bayesian) updated information about both the go and stop stimuli. In this work, we probe the relationship between go and stop processing by explicitly manipulating the discrimination difficulty of the go stimulus. While the race model assumes the go and stop processes are independent, and therefore go stimulus discriminability should not affect the stop stimulus processing, we simulate the optimal model to show that it predicts harder go discrimination should result in longer go reaction time (RT), lower stop error rate, as well as faster stop-signal RT. We then present novel behavioral data that validate these model predictions. The results thus favor a fundamentally inseparable account of go and stop processing, in a manner consistent with the optimal model, and contradicting the independence assumption of the race model. More broadly, our findings contribute to the growing evidence that the computations underlying inhibitory control are systematically modulated by cognitive influences in a Bayes-optimal manner, thus opening new avenues for interpreting neural responses underlying inhibitory control.

Development of a Tandem Repeat-Based Polymerase Chain Displacement Reaction Method for Highly Sensitive Detection of 'Candidatus Liberibacter asiaticus'.

PubMed

Lou, Binghai; Song, Yaqin; RoyChowdhury, Moytri; Deng, Chongling; Niu, Ying; Fan, Qijun; Tang, Yan; Zhou, Changyong

2018-02-01

Huanglongbing (HLB) is one of the most destructive diseases in citrus production worldwide. Early detection of HLB pathogens can facilitate timely removal of infected citrus trees in the field. However, low titer and uneven distribution of HLB pathogens in host plants make reliable detection challenging. Therefore, the development of effective detection methods with high sensitivity is imperative. This study reports the development of a novel method, tandem repeat-based polymerase chain displacement reaction (TR-PCDR), for the detection of 'Candidatus Liberibacter asiaticus', a widely distributed HLB-associated bacterium. A uniquely designed primer set (TR2-PCDR-F/TR2-PCDR-1R) and a thermostable Taq DNA polymerase mutant with strand displacement activity were used for TR-PCDR amplification. Performed in a regular thermal cycler, TR-PCDR could produce more than two amplicons after each amplification cycle. Sensitivity of the developed TR-PCDR was 10 copies of target DNA fragment. The sensitive level was proven to be 100× higher than conventional PCR and similar to real-time PCR. Data from the detection of 'Ca. L. asiaticus' with filed samples using the above three methods also showed similar results. No false-positive TR-PCDR amplification was observed from healthy citrus samples and water controls. These results thereby illustrated that the developed TR-PCDR method can be applied to the reliable, highly sensitive, and cost-effective detection of 'Ca. L. asiaticus'.

Automobile Stopping Distances.

ERIC Educational Resources Information Center

Logue, L. J.

1979-01-01

Discusses the effect of vehicle mass on stopping distances. Analyzes an example of a sample vehicle and tire, and calculates the braking acceleration showing the effect of different factors on the stopping performance of the tires. (GA)

T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

PubMed Central

Monnier, Stéphanie; Cox, David G; Albion, Tim; Canzian, Federico

2005-01-01

Background Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS. PMID:16221298

Association study of Toll-like receptor 5 (TLR5) and Toll-like receptor 9 (TLR9) polymorphisms in systemic lupus erythematosus.

PubMed

Demirci, F Yesim K; Manzi, Susan; Ramsey-Goldman, Rosalind; Kenney, Margaret; Shaw, Penny S; Dunlop-Thomas, Charmayne M; Kao, Amy H; Rhew, Elisa Y; Bontempo, Franklin; Kammerer, Candace; Kamboh, M Ilyas

2007-08-01

Toll-like receptors (TLR) play an important role in both adaptive and innate immunity. Variations in TLR genes have been shown to be associated with various infectious and inflammatory diseases. We investigated the association of TLR5 (Arg392Stop, rs5744168) and TLR9 (-1237T-->C, rs5743836) single nucleotide polymorphisms (SNP) with systemic lupus erythematosus (SLE) in Caucasian American subjects. We performed a case-control association study and genotyped 409 Caucasian women with SLE and 509 Caucasian healthy female controls using TaqMan allelic discrimination (rs5744168) or polymerase chain reaction-restriction fragment length polymorphism analysis (rs5743836). None of the 2 TLR SNP showed a statistically significant association with SLE risk in our cohort. Our results do not indicate a major influence of these putative functional TLR SNP on the susceptibility to (or protection from) SLE.

Diagnostic application of polymerase chain reaction for detection of Ehrlichia risticii in equine monocytic ehrlichiosis (Potomac horse fever).

PubMed

Biswas, B; Mukherjee, D; Mattingly-Napier, B L; Dutta, S K

1991-10-01

Genomic amplification by the polymerase chain reaction (PCR) was used to identify a unique genomic sequence of Ehrlichia risticii directly in DNA isolated from peripheral-blood buffy coat cells of E. risticii-infected horses (Potomac horse fever) and from infected cell cultures. A specific primer pair, selected from a cloned, species-specific, 1-kb DNA fragment of the E. risticii genome as a template, was used for the amplification of the target DNA of 247 bp. The optimal number of 40 PCR cycles, determined by analyzing an amplification profile obtained with a constant Taq polymerase concentration, was used to achieve maximum amplification of the E. risticii DNA segment. Efficient amplification of target DNA was achieved with specimens processed by either the phenol extraction or rapid lysis method. The specificity of the amplified DNA product was confirmed by the proper size (247 bp) and appropriate restriction enzyme cleavage pattern of the amplified target DNA, as well as by the specific hybridization signal obtained by using a PCR-amplified 185-bp internal DNA probe. A 10(5)- to 10(6)-fold amplification of target DNA, which allowed detection of E. risticii from as few as two to three infected cells in culture and from a very small volume of buffy coat cells from infected horses, was achieved. This PCR amplification procedure was found to be highly specific and sensitive for the detection of E. risticii for the study of Potomac horse fever.

T7-RNA Polymerase

NASA Technical Reports Server (NTRS)

1997-01-01

T7-RNA Polymerase grown on STS-81. Structure-Function Relationships of RNA Polymerase: DNA-dependent RNA polymerase is the key enzyme responsible for the biosynthesis of RNA, a process known as transcription. Principal Investigator's include Dr. Dan Carter, Dr. B.C. Wang, and Dr. John Rose of New Century Pharmaceuticals.

Clinical evaluation of a quantitative real time polymerase chain reaction assay for diagnosis of primary Epstein-Barr virus infection in children.

PubMed

Pitetti, Raymond D; Laus, Stella; Wadowsky, Robert M

2003-08-01

Epstein-Barr virus (EBV) infectious mononucleosis is often diagnosed based on characteristic clinical features and either a positive heterophil antibody test or serology, both of which can be unreliable in young children. Real time quantitative PCR assays that measure EBV DNA load in serum or plasma are highly sensitive in young children, but serum and plasma contain inhibitors of PCR which must be removed by DNA extraction techniques. A real time TaqMan PCR assay was designed and evaluated for simultaneously measuring EBV DNA load and validating the removal of PCR inhibitors from serum samples. A serum sample was available from patients classified serologically as primary EBV infection (n = 28), EBV-seronegative (n = 25) and EBV-seropositive (n = 26). Patients were classified as having EBV infectious mononucleosis if they had specified clinical findings and > or =10% atypical lymphocytes in peripheral blood or had a positive Monospot test result. DNA was purified by a spin column method and tested in PCR reactions with primers for EBV DNA polymerase gene and internal control targets. Amplification of the two PCR products was measured in real time with separate TaqMan DNA probes labeled with various fluorescent reporters. The mean age of study patients was 9 years, 4 months. Twenty-one (75%) of the patients in the primary EBV infection group, one (4%) of the seronegatives and none of the seropositives had detectable EBV DNA. Within the primary infection group, those with detectable virus were more likely than those without detectable virus to have evidence of lymphadenopathy (14 of 16 vs.1 of 5; P = 0.011), higher mean atypical (11.7 vs.0.9%; P = 0.002) and absolute atypical (1.5 vs.0.1 x 109/l; P = 0.004) lymphocyte count, higher mean absolute lymphocyte count (4.7 vs.2.3 x 109/l; P = 0.026) and higher mean aspartate aminotransferase value (119.8 vs.37.3 IU/l; P = 0.036). Ten patients, all in the primary infection group, had EBV infectious mononucleosis, and all

TaqMan PCR for Detection of Vibrio cholerae O1, O139, Non-O1, and Non-O139 in Pure Cultures, Raw Oysters, and Synthetic Seawater†

PubMed Central

Lyon, W. J.

2001-01-01

Vibrio cholerae is recognized as a leading human waterborne pathogen. Traditional diagnostic testing for Vibrio is not always reliable, because this bacterium can enter a viable but nonculturable state. Therefore, nucleic acid-based tests have emerged as a useful alternative to traditional enrichment testing. In this article, a TaqMan PCR assay is presented for quantitative detection of V. cholerae in pure cultures, oysters, and synthetic seawater. Primers and probe were designed from the nonclassical hemolysin (hlyA) sequence of V. cholerae strains. This probe was applied to DNA from 60 bacterial strains comprising 21 genera. The TaqMan PCR assay was positive for all of the strains of V. cholerae tested and negative for all other species of Vibrio tested. In addition, none of the other genera tested was amplified with the TaqMan primers and probe used in this study. The results of the TaqMan PCR with raw oysters and spiked with V. cholerae serotypes O1 and O139 were comparable to those of pure cultures. The sensitivity of the assay was in the range of 6 to 8 CFU g−1 and 10 CFU ml−1 in spiked raw oyster and synthetic seawater samples, respectively. The total assay could be completed in 3 h. Quantification of the Vibrio cells was linear over at least 6 log units. The TaqMan probe and primer set developed in this study can be used as a rapid screening tool for the presence of V. cholerae in oysters and seawater without prior isolation and characterization of the bacteria by traditional microbiological methods. PMID:11571173

Improving stopping construction to minimize leakage

PubMed Central

Grau, Roy H.; Mazzella, Andrew L.; Martikainen, Anu L.

2015-01-01

The proper sealing of stoppings is an important step in reducing leakage from the intake to the return airways. Leakage and the subsequent loss of ventilation resulting from improperly sealed stoppings can lead to unhealthy and unsafe working conditions. The research presented in this paper investigates the total leakage of a stopping, including air leakage through the stopping, at the stopping perimeter, and through the coalbed. The study also examines sealing considerations for stoppings that are constructed under roof control screen, the effects that wooden wedges had on inhibiting efficient application of polyurethane foam sealant, and airflow leakage through the surrounding coal. The work involved building a stopping in a dead end room of the NIOSH Safety Research Coal Mine and then pressurising the room using compressed air. Stopping leakage was evaluated by measuring air pressure loss in the enclosed room due to the air leakage. Part of the research utilises a diluted soap solution that was applied to the stopping and the surrounding coal to detect air leakage signified by bubble formations. The results show that stopping leakage can be minimised with proper sealing PMID:26379366

Progress in understanding heavy-ion stopping

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2016-09-01

We report some highlights of our work with heavy-ion stopping in the energy range where Bethe stopping theory breaks down. Main tools are our binary stopping theory (PASS code), the reciprocity principle, and Paul's data base. Comparisons are made between PASS and three alternative theoretical schemes (CasP, HISTOP and SLPA). In addition to equilibrium stopping we discuss frozen-charge stopping, deviations from linear velocity dependence below the Bragg peak, application of the reciprocity principle in low-velocity stopping, modeling of equilibrium charges, and the significance of the so-called effective charge.

Fluorescence resonance energy transfer analysis of escherichia coli RNA polymerase and polymerase-DNA complexes.

PubMed

Heyduk, T; Niedziela-Majka, A

Fluorescence resonance energy transfer (FRET) is a technique allowing measurements of atomic-scale distances in diluted solutions of macromolecules under native conditions. This feature makes FRET a powerful tool to study complicated biological assemblies. In this report we review the applications of FRET to studies of transcription initiation by Escherichia coli RNA polymerase. The versatility of FRET for studies of a large macromolecular assembly such as RNA polymerase is illustrated by examples of using FRET to address several different aspects of transcription initiation by polymerase. FRET has been used to determine the architecture of polymerase, its complex with single-stranded DNA, and the conformation of promoter fragment bound to polymerase. FRET has been also used as a binding assay to determine the thermodynamics of promoter DNA fragment binding to the polymerase. Functional conformational changes in the specificity subunit of polymerase responsible for the modulation of the promoter binding activity of the enzyme and the mechanistic aspects of the transition from the initiation to the elongation complex were also investigated. Copyright 2002 Wiley Periodicals, Inc.

Comparative diagnostic evaluation of OMP31 gene based TaqMan® real-time PCR assay with visual LAMP assay and indirect ELISA for caprine brucellosis.

PubMed

Saini, Suman; Gupta, V K; Gururaj, K; Singh, D D; Pawaiya, R V S; Gangwar, N K; Mishra, A K; Dwivedi, Deepak; Andani, Dimple; Kumar, Ashok; Goswami, T K

2017-08-01

Brucellosis is one of the leading causes of abortion in domestic animals that imposes costs on both economy and society. The disease is highly zoonotic and poses risk to animal handlers due to its zoonotic nature. It causes stillbirth, loss of kids and abortion in last term of pregnancy. Reproductive damage includes infertility in does and orchitis and epididymitis in breeding bucks, which result in high financial losses to farmers and the agriculture industry as a whole. It requires highly sensitive and specific assays to diagnose the disease at field level. In the current study, a visual loop-mediated isothermal amplification (LAMP) assay and the TaqMan® real-time PCR were developed with high sensitivity and specificity. For the TaqMan® probe, real-time PCR primers were developed using Omp31 gene as target and primers were designed using discontiguous conserved sequences of Omp31 gene. The Omp31 probes were designed by attaching 6-FAM reporter dye at the 5' end and BHQ-1 quencher at the 3' end. Published primers were used for visual LAMP assay targeting the Omp25 gene. Sensitivity of the standardized visual LAMP assay and TaqMan® real-time PCR assay was determined by serial dilution of positive Brucella melitensis DNA (10 2 to 10 -4  ng) obtained from standard culture. The TaqMan® probe real-time assay can detect as low as 100 fg of B. melitensis DNA, whereas culture from vaginal swab washings has a limit of detection (LOD) of only 1 cfu/ml. Similarly, the visual LAMP assay can detect as low as 10 fg of B. melitensis DNA as compared to an LOD of 30 cfu/ml from culture of vaginal swab washings. Both assays were compared with serological tests (serum tube agglutination test (STAT) and indirect enzyme-linked immunosorbent assay (iELISA)) for diagnostic sensitivity and specificity. Diagnostic sensitivities and specificities for TaqMan® real-time PCR vs. LAMP assays were 98 and 100% vs. 100 and 97.8%, respectively. Results of visual LAMP assay indicated that

A new building block for DNA network formation by self-assembly and polymerase chain reaction.

PubMed

Bußkamp, Holger; Keller, Sascha; Robotta, Marta; Drescher, Malte; Marx, Andreas

2014-01-01

The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

All in One Stop? The Accessibility of Work Support Programs at One-Stop Centers.

ERIC Educational Resources Information Center

Richer, Elise; Kubo, Hitomi; Frank, Abbey

The accessibility of work support programs at one-stop centers was examined in a study during which 33 telephone directors or managers of one-stop centers in 22 states were interviewed by telephone. The interviews established the existence of extensive differences between one-stop centers from the standpoint of all aspects of their operation,…

Luminescent beam stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryant, Diane; Morton, Simon A.

This disclosure provides systems, methods, and apparatus related to beam stops. In one aspect, a device comprises a luminescent material, a beam stop plate, and an optical fiber. The luminescent material is a parallelepiped having a first side and a second side that are squares and having a third side that is a rectangle or a square. The first side and the second side are perpendicular to the third side. The beam stop plate is attached to the first side of the luminescent material. The optical fiber has a first end and a second end, with the first end ofmore » the optical fiber attached to the third side of the luminescent material.« less

Specific Reaction Patterns to Distinct Positive Emotional Cues Related to Incentive Motivation in Dependence of the Taq1A-Polymorphism: Molecular Genetic Associations of Early and Late Event-Related Potentials.

PubMed

Munk, Aisha J L; Wielpuetz, Catrin; Osinsky, Roman; Müller, Erik M; Grant, Phillip; Hennig, Jürgen

2016-01-01

Early and late event-related potential (ERP) responses, representing early subconscious and late motivational processes, were recorded for positive emotional words related to 'wanting' and 'liking', in dependence of the dopamine-related Taq1A genotype (ANKK1/DRD2). Research suggests that 'wanting' as opposed to 'liking' is related to dopaminergic processes. Therefore, it was hypothesized that risk allele carriers of the Taq1A polymorphism exhibit late ERP changes in reaction to words representing incentive motivation, i.e. 'wanting' (word categories 'lust' and 'anticipation'), but not to words representing 'liking' ('closeness'). Seventy-two male participants performed an emotional-word Stroop task during EEG recording and were genotyped according to the Taq1A polymorphism of ANKK1/DRD2. Positive emotional words related to anticipation and lust revealed blunted responses in the late positive potential (LPP) in carriers of the A1 allele, an effect absent in response to 'liking'-related words. These differences were not evident in the earlier posterior negativity (EPN). As no differences in dependence of the Taq1A genotype were observed in reaction to 'wanting'- and 'liking'-related words in the EPN, but merely in the LPP, it can be assumed that incentive-motivational stimuli only modify motivation-related ERP responses in carriers of the A1 allele of the Taq1A polymorphism, indicating the role of dopamine in late ERP components. © 2016 S. Karger AG, Basel.

Stop/Start: Overview

Science.gov Websites

: vertical blue rule Main stage: See through car with battery, engine, and electric starter/generator visible . The car is stopped at an intersection. Main stage: See through car with battery, engine, and electric starter/generator visible. The car is stopped at an intersection. Battery: The battery is used to store

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis and TaqI polymorphism

PubMed Central

Andraos, Charlene; Koorsen, Gerrit; Knight, Julian C; Bornman, Liza

2014-01-01

The Vitamin D Receptor (VDR) gene encodes a transcription factor which, on activation by vitamin D, modulates diverse biological processes including calcium homeostasis and immune function. Genetic variation involving VDR shows striking differences in allele frequency between populations and has been associated with disease susceptibility including tuberculosis and autoimmunity, although results have often been conflicting. We hypothesized that methylation of VDR may be population specific and that the combination of differential methylation and genetic variation may characterise TB predisposition. We use bisulphite conversion and/or pyrosequencing to analyse the methylation status of 17 CpGs of VDR and to genotype 7 SNPs in the 3′ CpG Island (CGI 1060), including the commonly studied SNPs ApaI (rs7975232) and TaqI (rs731236). We show that for lymphoblastoid cell lines from two ethnically diverse populations (Yoruba from HapMap, n=30 and Caucasians, n=30) together with TB cases (n=32) and controls (n=29) from the Venda population of South Africa there are methylation variable positions (MVPs) in the 3′ end that significantly distinguish ethnicity (9/17 CpGs) and TB status (3/17 CpGs). Moreover methylation status shows complex association with TaqI genotype highlighting the need to consider both genetic and epigenetic variants in genetic studies of VDR association with disease. PMID:21168462

The Roles of Family B and D DNA Polymerases in Thermococcus Species 9°N Okazaki Fragment Maturation*

PubMed Central

Greenough, Lucia; Kelman, Zvi; Gardner, Andrew F.

2015-01-01

During replication, Okazaki fragment maturation is a fundamental process that joins discontinuously synthesized DNA fragments into a contiguous lagging strand. Efficient maturation prevents repeat sequence expansions, small duplications, and generation of double-stranded DNA breaks. To address the components required for the process in Thermococcus, Okazaki fragment maturation was reconstituted in vitro using purified proteins from Thermococcus species 9°N or cell extracts. A dual color fluorescence assay was developed to monitor reaction substrates, intermediates, and products. DNA polymerase D (polD) was proposed to function as the replicative polymerase in Thermococcus replicating both the leading and the lagging strands. It is shown here, however, that it stops before the previous Okazaki fragments, failing to rapidly process them. Instead, Family B DNA polymerase (polB) was observed to rapidly fill the gaps left by polD and displaces the downstream Okazaki fragment to create a flap structure. This flap structure was cleaved by flap endonuclease 1 (Fen1) and the resultant nick was ligated by DNA ligase to form a mature lagging strand. The similarities to both bacterial and eukaryotic systems and evolutionary implications of archaeal Okazaki fragment maturation are discussed. PMID:25814667

Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

USGS Publications Warehouse

Chase, D.M.; Elliott, D.G.; Pascho, R.J.

2006-01-01

Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

Measured values of coal mine stopping resistance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oswald, N.; Prosser, B.; Ruckman, R.

2008-12-15

As coal mines become larger, the number of stoppings in the ventilation system increases. Each stopping represents a potential leakage path which must be adequately represented in the ventilation model. Stopping resistance can be calculated using two methods, the USBM method, used to determine a resistance for a single stopping, and the MVS technique, in which an average resistance is calculated for multiple stoppings. Through MVS data collected from ventilation surveys of different subsurface coal mines, average resistances for stoppings were determined for stopping in poor, average, good, and excellent conditions. The calculated average stoppings resistance were determined for concretemore » block and Kennedy stopping. Using the average stopping resistance, measured and calculated using the MVS method, provides a ventilation modeling tool which can be used to construct more accurate and useful ventilation models. 3 refs., 3 figs.« less

Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques.

PubMed

di Rienzo, Valentina; Bubici, Giovanni; Montemurro, Cinzia; Cillo, Fabrizio

2018-01-01

In tomato, resistance to Tomato spotted wilt virus (TSWV) is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB) mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM) assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI) and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50-70 TSWV RNA copies) and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke) and summer (tomato) crops, in the same cultivated areas of Southern Italy.

14 CFR 29.675 - Stops.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Design and Construction Control Systems § 29.675 Stops. (a) Each control system must have stops that positively limit the range of motionof the pilot's controls. (b) Each stop must be located in the system so that the range of travel of its control is not appreciably...

Stop feeling: inhibition of emotional interference following stop-signal trials.

PubMed

Kalanthroff, Eyal; Cohen, Noga; Henik, Avishai

2013-01-01

Although a great deal of literature has been dedicated to the mutual links between emotion and the selective attention component of executive control, there is very little data regarding the links between emotion and the inhibitory component of executive control. In the current study we employed an emotional stop-signal task in order to examine whether emotion modulates and is modulated by inhibitory control. Results replicated previous findings showing reduced inhibitory control [longer stop-signal reaction time (SSRT)] following negative, compared to neutral pictures. Most importantly, results show decreased emotional interference following stop-signal trials. These results show that the inhibitory control component of executive control can serve to decrease emotional effects. We suggest that inhibitory control and emotion have a two-way connection in which emotion disrupts inhibitory control and activation of inhibitory control disrupts emotion.

14 CFR 27.675 - Stops.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.675 Stops. (a) Each control system must have stops that positively limit the range of motion of the pilot's controls. (b) Each stop must be located in the system so that the range of travel of its control is not appreciably...

Simultaneous detection and differentiation of three Potyviridae viruses by a multiplex TaqMan real time RT-PCR assay

USDA-ARS?s Scientific Manuscript database

A multiplex TaqMan real time RT-PCR was developed for detection and differentiation of Sweet potato virus G, Sweet potato latent virus and Sweet potato mild mottle virus in one tube. Amplification and detection of a fluorogenic cytochrome oxidase gene was included as an internal control. The assay w...

Deciding where to Stop Speaking

ERIC Educational Resources Information Center

Tydgat, Ilse; Stevens, Michael; Hartsuiker, Robert J.; Pickering, Martin J.

2011-01-01

This study investigated whether speakers strategically decide where to interrupt their speech once they need to stop. We conducted four naming experiments in which pictures of colored shapes occasionally changed in color or shape. Participants then merely had to stop (Experiment 1); or they had to stop and resume speech (Experiments 2-4). They…

14 CFR 29.675 - Stops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... stop must be located in the system so that the range of travel of its control is not appreciably...) Stops that are appropriate to the blade design must be provided to limit travel of the blade about its hinge points; and (2) There must be means to keep the blade from hitting the droop stops during any...

14 CFR 27.675 - Stops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... stop must be located in the system so that the range of travel of its control is not appreciably...) Stops that are appropriate to the blade design must be provided to limit travel of the blade about its hinge points; and (2) There must be means to keep the blade from hitting the droop stops during any...

Effects of stop-signal probability in the stop-signal paradigm: the N2/P3 complex further validated.

PubMed

Ramautar, J R; Kok, A; Ridderinkhof, K R

2004-11-01

The aim of this study was to examine the effects of frequency of occurrence of stop signals in the stop-signal paradigm. Presenting stop signals less frequently resulted in faster reaction times to the go stimulus and a lower probability of inhibition. Also, go stimuli elicited larger and somewhat earlier P3 responses when stop signals occurred less frequently. Since the amplitude effect was more pronounced on trials when go signals were followed by fast than slow reactions, it probably reflected a stronger set to produce fast responses. N2 and P3 components to stop signals were observed to be larger and of longer latency when stop signals occurred less frequently. The amplitude enhancement of these N2 and P3 components were more pronounced for unsuccessful than for successful stop-signal trials. Moreover, the successfully inhibited stop trials elicited a frontocentral P3 whereas unsuccessfully inhibited stop trials elicited a more posterior P3 that resembled the classical P3b. P3 amplitude in the unsuccessfully inhibited condition also differed between waveforms synchronized with the stop signal and waveforms synchronized with response onset whereas N2 amplitude did not. Taken together these findings suggest that N2 reflected a greater significance of failed inhibitions after low probability stop signals while P3 reflected continued processing of the erroneous response after response execution.

Protein Affinity Chromatography with Purified Yeast DNA Polymerase α Detects Proteins that Bind to DNA Polymerase

NASA Astrophysics Data System (ADS)

Miles, Jeff; Formosa, Tim

1992-02-01

We have overexpressed the POL1 gene of the yeast Saccharomyces cerevisiae and purified the resulting DNA polymerase α polypeptide in an apparently intact form. We attached the purified DNA polymerase covalently to an agarose matrix and used this matrix to chromatograph extracts prepared from yeast cells. At least six proteins bound to the yeast DNA polymerase α matrix that did not bind to a control matrix. We speculate that these proteins might be DNA polymerase α accessory proteins. Consistent with this interpretation, one of the binding proteins, which we have named POB1 (polymerase one binding), is required for normal chromosome transmission. Mutations in this gene cause increased chromosome loss and an abnormal cell morphology, phenotypes that also occur in the presence of mutations in the yeast α or δ polymerase genes. These results suggest that the interactions detected by polymerase affinity chromatography are biologically relevant and may help to illuminate the architecture of the eukaryotic DNA replication machinery.

The Influence of End-Stop Buffer Characteristics on the Severity of Suspension Seat End-Stop Impacts

NASA Astrophysics Data System (ADS)

Wu, X.; Griffin, M. J.

1998-08-01

Suspension seat end-stop impacts may be a source of increased risk of injury for the drivers of some machines and work vehicles, such as off-road vehicles. Most suspension seats use rubber buffers to reduce the severity of end-stop impacts, but they still result in a high magnitude of acceleration being transmitted to drivers when an end-stop impact occurs. An experimental study has been conducted to investigate the effect of buffer stiffness and buffer damping on the severity of end-stop impacts. The results show that the end-stop impact performance of suspension seats with only bottom buffers can be improved by the use of both top and bottom buffers. The force-deflection characteristics of rubber buffers had a significant influence on the severity of end-stop impacts. The optimum buffer should have medium stiffness which is nearly linear and occurs over a long deflection, without being compressed to its high stiffness stage. It is shown, theoretically, that buffer damping is capable of significantly reducing the severity of end-stop impacts. However, since current rubber material provides only low damping, alternative materials to those in current use, or either passive or active damping devices, are required.

Quantification of Paratrichodorus allius in DNA extracted from soil using TaqMan probe and SYBR green real-time PCR assays

USDA-ARS?s Scientific Manuscript database

The ectoparasitic stubby root nematode Paratrichodorus allius transmits Tobacco rattle virus, which causes corky ringspot disease resulting in significant economic losses in the potato industry. This study developed a diagnostic method for direct quantification of P. allius from soil DNA using a Taq...

Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes

NASA Astrophysics Data System (ADS)

Neri, Izaak; Roldán, Édgar; Jülicher, Frank

2017-01-01

We study the statistics of infima, stopping times, and passage probabilities of entropy production in nonequilibrium steady states, and we show that they are universal. We consider two examples of stopping times: first-passage times of entropy production and waiting times of stochastic processes, which are the times when a system reaches a given state for the first time. Our main results are as follows: (i) The distribution of the global infimum of entropy production is exponential with mean equal to minus Boltzmann's constant; (ii) we find exact expressions for the passage probabilities of entropy production; (iii) we derive a fluctuation theorem for stopping-time distributions of entropy production. These results have interesting implications for stochastic processes that can be discussed in simple colloidal systems and in active molecular processes. In particular, we show that the timing and statistics of discrete chemical transitions of molecular processes, such as the steps of molecular motors, are governed by the statistics of entropy production. We also show that the extreme-value statistics of active molecular processes are governed by entropy production; for example, we derive a relation between the maximal excursion of a molecular motor against the direction of an external force and the infimum of the corresponding entropy-production fluctuations. Using this relation, we make predictions for the distribution of the maximum backtrack depth of RNA polymerases, which follow from our universal results for entropy-production infima.

Acquisition of Initial /s/-Stop and Stop-/s/ Sequences in Greek

ERIC Educational Resources Information Center

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E.

2011-01-01

Previous work on children's acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters…

NcoI and TaqI RFLPs for human M creatine kinase (CKM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perryman, M.B.; Hejtmancik, J.F.; Ashizawa, Tetsuo

1988-09-12

Probe pHMCKUT contains a 135 bp cDNA fragment inserted into pGEM 3. The probe corresponds to nucleotides 1,201 to 1,336 located in the 3{prime} untranslated region of human M creatine kinase. The probe is specific for human M creatine kinase and does not hybridize to human B cretine kinase sequences. NcoI identifies a two allele polymorphism of a band at either 2.5 kb or 3.6 kb. TaqI identifies a two allele polymorphism at either 3.8 kb or 4.5 kb. Human M creatine has been localized to chromosome 19q. Autosomal co-dominant inheritance was shown in six informative Caucasian families.

Sneaky light stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eifert, Till; Nachman, Benjamin

2015-02-20

A light supersymmetric top quark partner (stop) with a mass nearly degenerate with that of the standard model (SM) top quark can evade direct searches. The precise measurement of SM top properties such as the cross-section has been suggested to give a handle for this ‘stealth stop’ scenario. We present an estimate of the potential impact a light stop may have on top quark mass measurements. The results indicate that certain light stop models may induce a bias of up to a few GeV, and that this effect can hide the shift in, and hence sensitivity from, cross-section measurements. Duemore » to the different initial states, the size of the bias is slightly different between the LHC and the Tevatron. The studies make some simplifying assumptions for the top quark measurement technique, and are based on truth-level samples.« less

Sneaky light stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eifert, Till; Nachman, Benjamin

2015-04-01

A light supersymmetric top quark partner (stop) with a mass nearly degenerate with that of the standard model (SM) top quark can evade direct searches. The precise measurement of SM top properties such as the cross-section has been suggested to give a handle for this ‘stealth stop’ scenario. We present an estimate of the potential impact a light stop may have on top quark mass measurements. The results indicate that certain light stop models may induce a bias of up to a few GeV, and that this effect can hide the shift in, and hence sensitivity from, cross-section measurements. Duemore » to the different initial states, the size of the bias is slightly different between the LHC and the Tevatron. The studies make some simplifying assumptions for the top quark measurement technique, and are based on truth-level samples.« less

New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Förster resonance energy transfer probes in 5′-nuclease assays

PubMed Central

Kutyavin, Igor V.

2010-01-01

The article describes a new technology for real-time polymerase chain reaction (PCR) detection of nucleic acids. Similar to Taqman, this new method, named Snake, utilizes the 5′-nuclease activity of Thermus aquaticus (Taq) DNA polymerase that cleaves dual-labeled Förster resonance energy transfer (FRET) probes and generates a fluorescent signal during PCR. However, the mechanism of the probe cleavage in Snake is different. In this assay, PCR amplicons fold into stem–loop secondary structures. Hybridization of FRET probes to one of these structures leads to the formation of optimal substrates for the 5′-nuclease activity of Taq. The stem–loop structures in the Snake amplicons are introduced by the unique design of one of the PCR primers, which carries a special 5′-flap sequence. It was found that at a certain length of these 5′-flap sequences the folded Snake amplicons have very little, if any, effect on PCR yield but benefit many aspects of the detection process, particularly the signal productivity. Unlike Taqman, the Snake system favors the use of short FRET probes with improved fluorescence background. The head-to-head comparison study of Snake and Taqman revealed that these two technologies have more differences than similarities with respect to their responses to changes in PCR protocol, e.g. the variations in primer concentration, annealing time, PCR asymmetry. The optimal PCR protocol for Snake has been identified. The technology’s real-time performance was compared to a number of conventional assays including Taqman, 3′-MGB-Taqman, Molecular Beacon and Scorpion primers. The test trial showed that Snake supersedes the conventional assays in the signal productivity and detection of sequence variations as small as single nucleotide polymorphisms. Due to the assay’s cost-effectiveness and simplicity of design, the technology is anticipated to quickly replace all known conventional methods currently used for real-time nucleic acid detection

The roles of family B and D DNA polymerases in Thermococcus species 9°N Okazaki fragment maturation.

PubMed

Greenough, Lucia; Kelman, Zvi; Gardner, Andrew F

2015-05-15

During replication, Okazaki fragment maturation is a fundamental process that joins discontinuously synthesized DNA fragments into a contiguous lagging strand. Efficient maturation prevents repeat sequence expansions, small duplications, and generation of double-stranded DNA breaks. To address the components required for the process in Thermococcus, Okazaki fragment maturation was reconstituted in vitro using purified proteins from Thermococcus species 9°N or cell extracts. A dual color fluorescence assay was developed to monitor reaction substrates, intermediates, and products. DNA polymerase D (polD) was proposed to function as the replicative polymerase in Thermococcus replicating both the leading and the lagging strands. It is shown here, however, that it stops before the previous Okazaki fragments, failing to rapidly process them. Instead, Family B DNA polymerase (polB) was observed to rapidly fill the gaps left by polD and displaces the downstream Okazaki fragment to create a flap structure. This flap structure was cleaved by flap endonuclease 1 (Fen1) and the resultant nick was ligated by DNA ligase to form a mature lagging strand. The similarities to both bacterial and eukaryotic systems and evolutionary implications of archaeal Okazaki fragment maturation are discussed. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

20 CFR 662.430 - Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

Code of Federal Regulations, 2013 CFR

2013-04-01

... designated to operate in a One-Stop delivery system established prior to the enactment of WIA be designated... (CONTINUED) DESCRIPTION OF THE ONE-STOP SYSTEM UNDER TITLE I OF THE WORKFORCE INVESTMENT ACT One-Stop Operators § 662.430 Under what conditions may One-Stop operators designated to operate in a One-Stop...

20 CFR 662.430 - Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

Code of Federal Regulations, 2014 CFR

2014-04-01

... designated to operate in a One-Stop delivery system established prior to the enactment of WIA be designated... (CONTINUED) DESCRIPTION OF THE ONE-STOP SYSTEM UNDER TITLE I OF THE WORKFORCE INVESTMENT ACT One-Stop Operators § 662.430 Under what conditions may One-Stop operators designated to operate in a One-Stop...

20 CFR 662.430 - Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

Code of Federal Regulations, 2012 CFR

2012-04-01

... designated to operate in a One-Stop delivery system established prior to the enactment of WIA be designated... (CONTINUED) DESCRIPTION OF THE ONE-STOP SYSTEM UNDER TITLE I OF THE WORKFORCE INVESTMENT ACT One-Stop Operators § 662.430 Under what conditions may One-Stop operators designated to operate in a One-Stop...

Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

PubMed

Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H

2015-11-01

Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence. Published by Elsevier B.V.

Development and comparison of TaqMan-based real-time PCR assays for detection and differentiation of Ralstonia solanacearum strains

USDA-ARS?s Scientific Manuscript database

Bacterial wilt caused by Ralstonia solanacearum is destructive to many plant species worldwide. The race 3 biovar 2 (r3b2) strains of R. solanacearum infect potatoes in temperature climates and are listed as select agents by the U.S. government. TaqMan-based real-time quantitative PCR (qPCR) is comm...

Stopping power: Effect of the projectile deceleration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kompaneets, Roman, E-mail: kompaneets@mpe.mpg.de; Ivlev, Alexei V.; Morfill, Gregor E.

2014-11-15

The stopping force is the force exerted on the projectile by its wake. Since the wake does not instantly adjust to the projectile velocity, the stopping force should be affected by the projectile deceleration caused by the stopping force itself. We address this effect by deriving the corresponding correction to the stopping force in the cold plasma approximation. By using the derived expression, we estimate that if the projectile is an ion passing through an electron-proton plasma, the correction is small when the stopping force is due to the plasma electrons, but can be significant when the stopping force ismore » due to the protons.« less

20 CFR 662.430 - Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

Code of Federal Regulations, 2011 CFR

2011-04-01

... designated to operate in a One-Stop delivery system established prior to the enactment of WIA be designated... DESCRIPTION OF THE ONE-STOP SYSTEM UNDER TITLE I OF THE WORKFORCE INVESTMENT ACT One-Stop Operators § 662.430 Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

20 CFR 662.430 - Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

Code of Federal Regulations, 2010 CFR

2010-04-01

... designated to operate in a One-Stop delivery system established prior to the enactment of WIA be designated... DESCRIPTION OF THE ONE-STOP SYSTEM UNDER TITLE I OF THE WORKFORCE INVESTMENT ACT One-Stop Operators § 662.430 Under what conditions may One-Stop operators designated to operate in a One-Stop delivery system...

48 CFR 42.1303 - Stop-work orders.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Stop-work orders. 42.1303... CONTRACT ADMINISTRATION AND AUDIT SERVICES Suspension of Work, Stop-Work Orders, and Government Delay of Work 42.1303 Stop-work orders. (a) Stop-work orders may be used, when appropriate, in any negotiated...

48 CFR 42.1303 - Stop-work orders.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Stop-work orders. 42.1303... CONTRACT ADMINISTRATION AND AUDIT SERVICES Suspension of Work, Stop-Work Orders, and Government Delay of Work 42.1303 Stop-work orders. (a) Stop-work orders may be used, when appropriate, in any negotiated...

Development of SYBR Green and TaqMan quantitative real-time PCR assays for hepatopancreatic parvovirus (HPV) infecting Penaeus monodon in India.

PubMed

Yadav, Reena; Paria, Anutosh; Mankame, Smruti; Makesh, M; Chaudhari, Aparna; Rajendran, K V

2015-12-01

Hepatopancreatic parvovirus (HPV) infects Penaeus monodon and causes mortality in the larval stages. Further, it has been implicated in the growth retardation in cultured P. monodon. Though different geographical isolates of HPV show large sequence variations, a sensitive PCR assay specific to Indian isolate has not yet been reported. Here, we developed a sensitive SYBR Green-based and TaqMan real-time PCR for the detection and quantification of the virus. A 441-bp PCR amplicon was cloned in pTZ57 R/T vector and the plasmid copy number was estimated. A 10-fold serial dilution of the plasmid DNA from 1 × 10(9) copies to 1 copy was prepared and used as the standard. The primers were tested initially using the standard on a conventional PCR format to determine the linearity of detection. The standards were further tested on real-time PCR format using SYBR Green and TaqMan chemistry and standard curves were generated based on the Ct values from three well replicates for each dilution. The assays were found to be sensitive, specific and reproducible with a wide dynamic range (1 × 10(9) to 10 copies) with coefficient of regression (R(2)) > 0.99, calculated average slope -3.196 for SYBR Green assay whereas, for TaqMan assay it was >0.99 and -3.367, respectively. The intra- and inter-assay variance of the Ct values ranged from 0.26% to 0.94% and 0.12% to 0.81%, respectively, for SYBR Green assay, and the inter-assay variance of the Ct values for TaqMan assay ranged from 0.07% to 1.93%. The specificity of the assays was proved by testing other DNA viruses of shrimp such as WSSV, IHHNV and MBV. Standardized assays were further tested to detect and quantify HPV in the post-larvae of P. monodon. The result was further compared with conventional PCR to test the reproducibility of the test. The assay was also used to screen Litopeneaus vannamei, Macrobrachium rosenbergii and Scylla serrata for HPV. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reducing nontemplated 3' nucleotide addition to polynucleotide transcripts

DOEpatents

Kao, C. Cheng

2000-01-01

Non-template 3' nucleotide addition to a transcript is reduced by transcribing a transcript from a template comprising an ultimate and/or penultimate 5' ribose having a C'2 substituent such as methoxy, which reduces non-template 3' nucleotide addition to the transcript. The methods are shown to be applicable to a wide variety of polymerases, including Taq, T7 RNA polymerase, etc.

TaqMan Real-Time PCR Assays To Assess Arbuscular Mycorrhizal Responses to Field Manipulation of Grassland Biodiversity: Effects of Soil Characteristics, Plant Species Richness, and Functional Traits▿ †

PubMed Central

König, Stephan; Wubet, Tesfaye; Dormann, Carsten F.; Hempel, Stefan; Renker, Carsten; Buscot, François

2010-01-01

Large-scale (temporal and/or spatial) molecular investigations of the diversity and distribution of arbuscular mycorrhizal fungi (AMF) require considerable sampling efforts and high-throughput analysis. To facilitate such efforts, we have developed a TaqMan real-time PCR assay to detect and identify AMF in environmental samples. First, we screened the diversity in clone libraries, generated by nested PCR, of the nuclear ribosomal DNA internal transcribed spacer (ITS) of AMF in environmental samples. We then generated probes and forward primers based on the detected sequences, enabling AMF sequence type-specific detection in TaqMan multiplex real-time PCR assays. In comparisons to conventional clone library screening and Sanger sequencing, the TaqMan assay approach provided similar accuracy but higher sensitivity with cost and time savings. The TaqMan assays were applied to analyze the AMF community composition within plots of a large-scale plant biodiversity manipulation experiment, the Jena Experiment, primarily designed to investigate the interactive effects of plant biodiversity on element cycling and trophic interactions. The results show that environmental variables hierarchically shape AMF communities and that the sequence type spectrum is strongly affected by previous land use and disturbance, which appears to favor disturbance-tolerant members of the genus Glomus. The AMF species richness of disturbance-associated communities can be largely explained by richness of plant species and plant functional groups, while plant productivity and soil parameters appear to have only weak effects on the AMF community. PMID:20418424

Perceptual assessment of fricative--stop coarticulation.

PubMed

Repp, B H; Mann, V A

1981-04-01

The perceptual dependence of stop consonants on preceding fricatives [Mann and Repp, J. Acoust. Soc. Am. 69, 548--558 (1981)] was further investigated in two experiments employing both natural and synthetic speech. These experiments consistently replicated our original finding that listeners, report velar stops following [s]. In addition, our data confirmed earlier reports that natural fricative noises (excerpted from utterances of [st alpha], [sk alpha], [(formula: see text)k alpha]) contain cues to the following stop consonants; this was revealed in subjects' identifications of stops from isolated fricative noises and from stimuli consisting of these noises followed by synthetic CV portions drawn from a [t alpha]--[k alpha] continuum. However, these cues in the noise portion could not account for the contextual effect of fricative identity ([formula: see text] versus [sp) on stop perception (more "k" responses following [s]). Rather, this effect seems to be related to a coarticulatory influence of a preceding fricative on stop production; Subjects' responses to excised natural CV portions (with bursts and aspiration removed) were biased towards a relatively more forward place of stop articulation when the CVs had originally been preceded by [s]; and the identification of a preceding ambiguous fricative was biased in the direction of the original fricative context in which a given CV portion had been produced. These findings support an articulatory explanation for the effect of preceding fricatives on stop consonant perception.

RNA polymerase gene, microorganism having said gene and the production of RNA polymerase by the use of said microorganism

DOEpatents

Kotani, Hirokazu; Hiraoka, Nobutsugu; Obayashi, Akira

1991-01-01

SP6 bacteriophage RNA polymerase is produced by cultivating a new microorganism (particularly new strains of Escherichia coli) harboring a plasmid that carries SP6 bacteriophage RNA polymerase gene and recovering SP6 bacteriophage RNA polymerase from the culture broth. SP6 bacteriophage RNA polymerase gene is provided as are new microorganisms harboring a plasmid that carries SP6 bacteriophage RNA polymerase gene.

Neural Architecture of Selective Stopping Strategies: Distinct Brain Activity Patterns Are Associated with Attentional Capture But Not with Outright Stopping.

PubMed

Sebastian, Alexandra; Rössler, Kora; Wibral, Michael; Mobascher, Arian; Lieb, Klaus; Jung, Patrick; Tüscher, Oliver

2017-10-04

In stimulus-selective stop-signal tasks, the salient stop signal needs attentional processing before genuine response inhibition is completed. Differential prefrontal involvement in attentional capture and response inhibition has been linked to the right inferior frontal junction (IFJ) and ventrolateral prefrontal cortex (VLPFC), respectively. Recently, it has been suggested that stimulus-selective stopping may be accomplished by the following different strategies: individuals may selectively inhibit their response only upon detecting a stop signal (independent discriminate then stop strategy) or unselectively whenever detecting a stop or attentional capture signal (stop then discriminate strategy). Alternatively, the discrimination process of the critical signal (stop vs attentional capture signal) may interact with the go process (dependent discriminate then stop strategy). Those different strategies might differentially involve attention- and stopping-related processes that might be implemented by divergent neural networks. This should lead to divergent activation patterns and, if disregarded, interfere with analyses in neuroimaging studies. To clarify this crucial issue, we studied 87 human participants of both sexes during a stimulus-selective stop-signal task and performed strategy-dependent functional magnetic resonance imaging analyses. We found that, regardless of the strategy applied, outright stopping displayed indistinguishable brain activation patterns. However, during attentional capture different strategies resulted in divergent neural activation patterns with variable activation of right IFJ and bilateral VLPFC. In conclusion, the neural network involved in outright stopping is ubiquitous and independent of strategy, while different strategies impact on attention-related processes and underlying neural network usage. Strategic differences should therefore be taken into account particularly when studying attention-related processes in stimulus

Cholesterol ester transfer protein (CETP) Taq1B polymorphism influences the effect of a standardized cardiac rehabilitation program on lipid risk markers.

PubMed

Ayyobi, Amir F; Hill, John S; Molhuizen, Henri O F; Lear, Scott A

2005-08-01

Cardiac rehabilitation programs (CR) are standard treatment for patients with coronary artery disease (CAD), yet a large variation in risk factor and lipoprotein changes exists. We investigated the role of three common genetic polymorphisms (CETP Taq1B, LIPC -514 and apo E) associated with alterations of lipoprotein metabolism, in patients before and after standardized CR. Three-hundred and seven patients were recruited for this study. DNA samples were collected and all three genotypes were determined for every patient. While the hepatic lipase LIPC promoter polymorphism and apo E genotype showed little or no correlation with response to CR, CETP Taq1B showed significant association with changes in plasma lipid and lipoproteins. The B1 homozygotes for CETP Taq1B genotype showed significant reduction in TC (-0.25+/-0.07, p < 0.01), LDL-C (-0.15+/-0.06, p < 0.050) and TG (-0.20+/-0.08, p < 0.05). B2 carriers showed no significant change in these parameters. HDL-C, exercise capacity and BMI improved independent of genotype. Individuals with the B1B1 genotype appear to respond well to CR, whereas B2 carriers exhibit marginal gains in lipoprotein risk factors. Although the B2 carriers had similar benefits in exercise capacity and weight reduction, long-term consequences of little or no change in lipoprotein risk factors require further investigation to establish appropriate management strategies.

High resolution TaqMan real-time PCR approach to detect hazelnut DNA encoding for ITS rDNA in foods.

PubMed

López-Calleja, Inés María; de la Cruz, Silvia; Pegels, Nicolette; González, Isabel; García, Teresa; Martín, Rosario

2013-12-01

A broad range of foods have been described as causing allergies, but the majority of allergic reactions can be ascribed to a limited number of food components. Recent extensive surveys showed how tree nuts, particularly hazelnut (Corylus avellana L.) seeds, rank amongst the most important sources of food allergy. In order to protect the allergic consumer, efficient and reliable methods are required for the detection of allergenic ingredients. For this purpose, we have developed a real-time polymerase chain reaction (PCR) for detection of hazelnut in commercial food products. In this way a specific hazelnut primer pair based on the ITS marker (70 bp) and a nuclease (TaqMan) probe labelled with FAM and BHQ were designed. Sensibility of real-time PCR was determined by analysis of raw and heat treated hazelnut-wheat flour mixtures with a range of detection of 0.1-100,000 ppm. Practical applicability of the real-time PCR assay developed for determining hazelnut in different food matrices was investigated by analyzing 179 commercial foodstuffs comprising snacks, biscuits, chocolates, bonbons, creams, nut bars, ice creams, precooked meals, breads, beverages, yogurts, cereals, meat products, rice cake and nougat. From the total of samples analyzed, 40 commercial food products that didn't declare hazelnut nor traces on the label were found to contain hazelnut. The real-time PCR method proposed herein due to its high sensitivity facilitates the detection of hazelnut traces in commercial food products and can also be useful for monitoring the effectiveness of cleaning processes and as consequence, can help to prevent the food allergic consumer from unintentional ingestion of hidden allergens. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection.

PubMed

Dacheux, Laurent; Larrous, Florence; Lavenir, Rachel; Lepelletier, Anthony; Faouzi, Abdellah; Troupin, Cécile; Nourlil, Jalal; Buchy, Philippe; Bourhy, Herve

2016-07-01

The definitive diagnosis of lyssavirus infection (including rabies) in animals and humans is based on laboratory confirmation. The reference techniques for post-mortem rabies diagnosis are still based on direct immunofluorescence and virus isolation, but molecular techniques, such as polymerase chain reaction (PCR) based methods, are increasingly being used and now constitute the principal tools for diagnosing rabies in humans and for epidemiological analyses. However, it remains a key challenge to obtain relevant specificity and sensitivity with these techniques while ensuring that the genetic diversity of lyssaviruses does not compromise detection. We developed a dual combined real-time reverse transcription polymerase chain reaction (combo RT-qPCR) method for pan-lyssavirus detection. This method is based on two complementary technologies: a probe-based (TaqMan) RT-qPCR for detecting the RABV species (pan-RABV RT-qPCR) and a second reaction using an intercalating dye (SYBR Green) to detect other lyssavirus species (pan-lyssa RT-qPCR). The performance parameters of this combined assay were evaluated with a large panel of primary animal samples covering almost all the genetic variability encountered at the viral species level, and they extended to almost all lyssavirus species characterized to date. This method was also evaluated for the diagnosis of human rabies on 211 biological samples (positive n = 76 and negative n = 135) including saliva, skin and brain biopsies. It detected all 41 human cases of rabies tested and confirmed the sensitivity and the interest of skin biopsy (91.5%) and saliva (54%) samples for intra-vitam diagnosis of human rabies. Finally, this method was successfully implemented in two rabies reference laboratories in enzootic countries (Cambodia and Morocco). This combined RT-qPCR method constitutes a relevant, useful, validated tool for the diagnosis of rabies in both humans and animals, and represents a promising tool for lyssavirus

Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection

PubMed Central

Lavenir, Rachel; Lepelletier, Anthony; Faouzi, Abdellah; Troupin, Cécile; Nourlil, Jalal; Buchy, Philippe; Bourhy, Herve

2016-01-01

The definitive diagnosis of lyssavirus infection (including rabies) in animals and humans is based on laboratory confirmation. The reference techniques for post-mortem rabies diagnosis are still based on direct immunofluorescence and virus isolation, but molecular techniques, such as polymerase chain reaction (PCR) based methods, are increasingly being used and now constitute the principal tools for diagnosing rabies in humans and for epidemiological analyses. However, it remains a key challenge to obtain relevant specificity and sensitivity with these techniques while ensuring that the genetic diversity of lyssaviruses does not compromise detection. We developed a dual combined real-time reverse transcription polymerase chain reaction (combo RT-qPCR) method for pan-lyssavirus detection. This method is based on two complementary technologies: a probe-based (TaqMan) RT-qPCR for detecting the RABV species (pan-RABV RT-qPCR) and a second reaction using an intercalating dye (SYBR Green) to detect other lyssavirus species (pan-lyssa RT-qPCR). The performance parameters of this combined assay were evaluated with a large panel of primary animal samples covering almost all the genetic variability encountered at the viral species level, and they extended to almost all lyssavirus species characterized to date. This method was also evaluated for the diagnosis of human rabies on 211 biological samples (positive n = 76 and negative n = 135) including saliva, skin and brain biopsies. It detected all 41 human cases of rabies tested and confirmed the sensitivity and the interest of skin biopsy (91.5%) and saliva (54%) samples for intra-vitam diagnosis of human rabies. Finally, this method was successfully implemented in two rabies reference laboratories in enzootic countries (Cambodia and Morocco). This combined RT-qPCR method constitutes a relevant, useful, validated tool for the diagnosis of rabies in both humans and animals, and represents a promising tool for lyssavirus

Tourette Syndrome: Help Stop Bullying

MedlinePlus

... Submit Button Past Emails Tourette Syndrome: Help Stop Bullying Language: English (US) Español (Spanish) Recommend on Facebook ... you can increase acceptance by helping to stop bullying of children with TS. Bullying doesn’t just ...

Evaluating the Effects of Traffic on Driver Stopping and Turn Signal Use at a Stop Sign: A Systematic Replication

ERIC Educational Resources Information Center

Lebbon, Angela R.; Austin, John; Van Houten, Ron; Malenfant, Louis E.

2007-01-01

The current analyses of observational data found that oncoming traffic substantially affected driver stopping patterns and turn signal use at the target stop sign. The percentage of legal stops and turn signal use by drivers in the presence and absence of traffic was analyzed using a multi-element design. The results showed that legal stops were…

Field trip stop descriptions

NASA Technical Reports Server (NTRS)

Nummedal, D.

1978-01-01

Fifteen sites within the channeled scabland were selected as stops with the dual aim of visiting locations critical to the arguments for a catastrophic flood origin of the scablands, as well as permitting an examination of the variability in both erosional and depositional features. The stop locations are plotted on a generalized geologic map and their coordinates are given in table form.

The Applicability of TaqMan-Based Quantitative Real-Time PCR Assays for Detecting and Enumerating Cryptosporidium spp. Oocysts in the Environment

PubMed Central

Staggs, Sarah E.; Beckman, Erin M.; Keely, Scott P.; Mackwan, Reena; Ware, Michael W.; Moyer, Alan P.; Ferretti, James A.; Sayed, Abu; Xiao, Lihua; Villegas, Eric N.

2013-01-01

Quantitative real-time polymerase chain reaction (qPCR) assays to detect Cryptosporidium oocysts in clinical samples are increasingly being used to diagnose human cryptosporidiosis, but a parallel approach for detecting and identifying Cryptosporidium oocyst contamination in surface water sources has yet to be established for current drinking water quality monitoring practices. It has been proposed that Cryptosporidium qPCR-based assays could be used as viable alternatives to current microscopic-based detection methods to quantify levels of oocysts in drinking water sources; however, data on specificity, analytical sensitivity, and the ability to accurately quantify low levels of oocysts are limited. The purpose of this study was to provide a comprehensive evaluation of TaqMan-based qPCR assays, which were developed for either clinical or environmental investigations, for detecting Cryptosporidium oocyst contamination in water. Ten different qPCR assays, six previously published and four developed in this study were analyzed for specificity and analytical sensitivity. Specificity varied between all ten assays, and in one particular assay, which targeted the Cryptosporidium 18S rRNA gene, successfully detected all Cryptosporidium spp. tested, but also cross-amplified T. gondii, fungi, algae, and dinoflagellates. When evaluating the analytical sensitivity of these qPCR assays, results showed that eight of the assays could reliably detect ten flow-sorted oocysts in reagent water or environmental matrix. This study revealed that while a qPCR-based detection assay can be useful for detecting and differentiating different Cryptosporidium species in environmental samples, it cannot accurately measure low levels of oocysts that are typically found in drinking water sources. PMID:23805235

Design principles of a microtubule polymerase

PubMed Central

Geyer, Elisabeth A; Miller, Matthew P; Brautigam, Chad A; Biggins, Sue

2018-01-01

Stu2/XMAP215 microtubule polymerases use multiple tubulin-binding TOG domains and a lattice-binding basic region to processively promote faster elongation. How the domain composition and organization of these proteins dictate polymerase activity, end localization, and processivity is unknown. We show that polymerase activity does not require different kinds of TOGs, nor are there strict requirements for how the TOGs are linked. We identify an unexpected antagonism between the tubulin-binding TOGs and the lattice-binding basic region: lattice binding by the basic region is weak when at least two TOGs engage tubulins, strong when TOGs are empty. End-localization of Stu2 requires unpolymerized tubulin, at least two TOGs, and polymerase competence. We propose a ‘ratcheting’ model for processivity: transfer of tubulin from TOGs to the lattice activates the basic region, retaining the polymerase at the end for subsequent rounds of tubulin binding and incorporation. These results clarify design principles of the polymerase. PMID:29897335

DNA polymerase preference determines PCR priming efficiency.

PubMed

Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

2014-01-30

Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially

Rapid polymerase chain reaction-based screening assay for bacterial biothreat agents.

PubMed

Yang, Samuel; Rothman, Richard E; Hardick, Justin; Kuroki, Marcos; Hardick, Andrew; Doshi, Vishal; Ramachandran, Padmini; Gaydos, Charlotte A

2008-04-01

To design and evaluate a rapid polymerase chain reaction (PCR)-based assay for detecting Eubacteria and performing early screening for selected Class A biothreat bacterial pathogens. The authors designed a two-step PCR-based algorithm consisting of an initial broad-based universal detection step, followed by specific pathogen identification targeted for identification of the Class A bacterial biothreat agents. A region in the bacterial 16S rRNA gene containing a highly variable sequence flanked by clusters of conserved sequences was chosen as the target for the PCR assay design. A previously described highly conserved region located within the 16S rRNA amplicon was selected as the universal probe (UniProbe, Integrated DNA Technology, Coralville, IA). Pathogen-specific TaqMan probes were designed for Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Performance of the assay was assessed using genomic DNA extracted from the aforementioned biothreat-related organisms (inactivated or surrogate) and other common bacteria. The UniProbe detected the presence of all tested Eubacteria (31/31) with high analytical sensitivity. The biothreat-specific probes accurately identified organisms down to the closely related species and genus level, but were unable to discriminate between very close surrogates, such as Yersinia philomiragia and Bacillus cereus. A simple, two-step PCR-based assay proved capable of both universal bacterial detection and identification of select Class A bacterial biothreat and biothreat-related pathogens. Although this assay requires confirmatory testing for definitive species identification, the method has great potential for use in ED-based settings for rapid diagnosis in cases of suspected Category A bacterial biothreat agents.

A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples.

PubMed

Claus, C; Bergs, S; Emmrich, N C; Hübschen, J M; Mankertz, A; Liebert, U G

2017-02-01

Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.

Stop-catalyzed baryogenesis beyond the MSSM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katz, Andrey; Perelstein, Maxim; Ramsey-Musolf, Michael J.

2015-11-19

Nonminimal supersymmetric models that predict a tree-level Higgs mass above the minimal supersymmetric standard model (MSSM) bound are well motivated by naturalness considerations. Indirect constraints on the stop sector parameters of such models are significantly relaxed compared to the MSSM; in particular, both stops can have weak-scale masses. We revisit the stop-catalyzed electroweak baryogenesis (EWB) scenario in this context. We find that the LHC measurements of the Higgs boson production and decay rates already rule out the possibility of stop-catalyzed EWB. Here, we also introduce a gauge-invariant analysis framework that may generalize to other scenarios in which interactions outside themore » gauge sector drive the electroweak phase transition.« less

14 CFR 25.675 - Stops.

Code of Federal Regulations, 2014 CFR

2014-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.675 Stops. (a) Each control system must have stops that positively limit the range of motion of each movable aerodynamic... adjustments will not adversely affect the control characteristics of the airplane because of a change in the...

14 CFR 23.675 - Stops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... STANDARDS: NORMAL, UTILITY, ACROBATIC, AND COMMUTER CATEGORY AIRPLANES Design and Construction Control Systems § 23.675 Stops. (a) Each control system must have stops that positively limit the range of motion... loads corresponding to the design conditions for the control system. [Amdt. 23-17, 41 FR 55464, Dec. 20...

14 CFR 25.675 - Stops.

Code of Federal Regulations, 2011 CFR

2011-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.675 Stops. (a) Each control system must have stops that positively limit the range of motion of each movable aerodynamic... adjustments will not adversely affect the control characteristics of the airplane because of a change in the...

14 CFR 25.675 - Stops.

Code of Federal Regulations, 2012 CFR

2012-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.675 Stops. (a) Each control system must have stops that positively limit the range of motion of each movable aerodynamic... adjustments will not adversely affect the control characteristics of the airplane because of a change in the...

14 CFR 23.675 - Stops.

Code of Federal Regulations, 2014 CFR

2014-01-01

... STANDARDS: NORMAL, UTILITY, ACROBATIC, AND COMMUTER CATEGORY AIRPLANES Design and Construction Control Systems § 23.675 Stops. (a) Each control system must have stops that positively limit the range of motion... loads corresponding to the design conditions for the control system. [Amdt. 23-17, 41 FR 55464, Dec. 20...

14 CFR 23.675 - Stops.

Code of Federal Regulations, 2011 CFR

2011-01-01

... STANDARDS: NORMAL, UTILITY, ACROBATIC, AND COMMUTER CATEGORY AIRPLANES Design and Construction Control Systems § 23.675 Stops. (a) Each control system must have stops that positively limit the range of motion... loads corresponding to the design conditions for the control system. [Amdt. 23-17, 41 FR 55464, Dec. 20...

14 CFR 25.675 - Stops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.675 Stops. (a) Each control system must have stops that positively limit the range of motion of each movable aerodynamic... adjustments will not adversely affect the control characteristics of the airplane because of a change in the...

14 CFR 23.675 - Stops.

Code of Federal Regulations, 2012 CFR

2012-01-01

... STANDARDS: NORMAL, UTILITY, ACROBATIC, AND COMMUTER CATEGORY AIRPLANES Design and Construction Control Systems § 23.675 Stops. (a) Each control system must have stops that positively limit the range of motion... loads corresponding to the design conditions for the control system. [Amdt. 23-17, 41 FR 55464, Dec. 20...

14 CFR 23.675 - Stops.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS: NORMAL, UTILITY, ACROBATIC, AND COMMUTER CATEGORY AIRPLANES Design and Construction Control Systems § 23.675 Stops. (a) Each control system must have stops that positively limit the range of motion... loads corresponding to the design conditions for the control system. [Amdt. 23-17, 41 FR 55464, Dec. 20...

On the Natural History of Preaspirated Stops

ERIC Educational Resources Information Center

Clayton, Ian D.

2010-01-01

This dissertation makes two contributions, one empirical, the other theoretical. Empirically, the dissertation deepens our understanding of the lifecycle and behavior of the preaspirated stop, an extremely rare phonological feature. I show that in most confirmed cases, preaspirated stops develop from earlier voiceless geminate stops, less commonly…

Optimally Stopped Optimization

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel

We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known, and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time, optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark the performance of a D-Wave 2X quantum annealer and the HFS solver, a specialized classical heuristic algorithm designed for low tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N = 1098 variables, the D-Wave device is between one to two orders of magnitude faster than the HFS solver.

Simulating fail-stop in asynchronous distributed systems

NASA Technical Reports Server (NTRS)

Sabel, Laura; Marzullo, Keith

1994-01-01

The fail-stop failure model appears frequently in the distributed systems literature. However, in an asynchronous distributed system, the fail-stop model cannot be implemented. In particular, it is impossible to reliably detect crash failures in an asynchronous system. In this paper, we show that it is possible to specify and implement a failure model that is indistinguishable from the fail-stop model from the point of view of any process within an asynchronous system. We give necessary conditions for a failure model to be indistinguishable from the fail-stop model, and derive lower bounds on the amount of process replication needed to implement such a failure model. We present a simple one-round protocol for implementing one such failure model, which we call simulated fail-stop.

Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene.

PubMed Central

Earl, P L; Jones, E V; Moss, B

1986-01-01

A 5400-base-pair segment of the vaccinia virus genome was sequenced and an open reading frame of 938 codons was found precisely where the DNA polymerase had been mapped by transfer of a phosphonoacetate-resistance marker. A single nucleotide substitution changing glycine at position 347 to aspartic acid accounts for the drug resistance of the mutant vaccinia virus. The 5' end of the DNA polymerase mRNA was located 80 base pairs before the methionine codon initiating the open reading frame. Correspondence between the predicted Mr 108,577 polypeptide and the 110,000 purified enzyme indicates that little or no proteolytic processing occurs. Extensive homology, extending over 435 amino acids, was found upon comparing the DNA polymerase of vaccinia virus and DNA polymerase of Epstein-Barr virus. A highly conserved sequence of 14 amino acids in the carboxyl-terminal regions of the above DNA polymerases is also present at a similar location in adenovirus DNA polymerase. This structure, which is predicted to form a turn flanked by beta-pleated sheets, may form part of an essential binding or catalytic site that accounts for its presence in DNA polymerases of poxviruses, herpesviruses, and adenoviruses. Images PMID:3012524

Distinguishing Heterodera filipjevi and H. avenae using polymerase chain reaction-restriction fragment length polymorphism and cyst morphology.

PubMed

Yan, Guiping; Smiley, Richard W

2010-03-01

The cereal cyst nematodes Heterodera filipjevi and H. avenae impede wheat production in the Pacific Northwest (PNW). Accurate identification of cyst nematode species and awareness of high population density in affected fields are essential for designing effective control measures. Morphological methods for differentiating these species are laborious. These species were differentiated using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS)-ribosomal (r)DNA with up to six restriction endonucleases (TaqI, HinfI, PstI, HaeIII, RsaI, and AluI). The method was validated by inspecting underbridge structures of cyst vulval cones. Grid soil sampling of an Oregon field infested by both species revealed that H. filipjevi was present at most of the infested grid sites but mixtures of H. avenae and H. filipjevi also occurred. These procedures also detected and differentiated H. filipjevi and H. avenae in soil samples from nearby fields in Oregon and H. avenae in samples from Idaho and Washington. Intraspecific polymorphism was not observed within H. filipjevi or PNW H. avenae populations based on the ITS-rDNA. However, intraspecific variation was observed between H. avenae populations occurring in the PNW and France. Methods described here will improve detection and identification efficiencies for cereal cyst nematodes in wheat fields.

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay.

PubMed

Pegels, N; González, I; Fernández, S; García, T; Martín, R

2012-01-01

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.

Quality of "Glottal" Stops in Tracheoesophageal Speakers

ERIC Educational Resources Information Center

van Rossum, M. A.; van As-Brooks, C. J.; Hilgers, F. J. M.; Roozen, M.

2009-01-01

Glottal stops are conveyed by an abrupt constriction at the level of the glottis. Tracheoesophageal (TE) speakers are known to have poor control over the new voice source (neoglottis), and this might influence the production of "glottal" stops. This study investigated how TE speakers realized "glottal" stops in abutting words…

The DRD2 Taq1A A1 Allele May Magnify the Risk of Alzheimer's in Aging African-Americans.

PubMed

Blum, Kenneth; Badgaiyan, Rajendra D; Dunston, Georgia M; Baron, David; Modestino, Edward J; McLaughlin, Thomas; Steinberg, Bruce; Gold, Mark S; Gondré-Lewis, Marjorie C

2017-09-30

Alzheimer's disease is an irreversible, progressive brain disorder that slowly destroys cognitive skills and the ability to perform the simplest tasks. More than 5 million Americans are afflicted with Alzheimer's; a disorder which ranks third, just behind heart disease and cancer, as a cause of death for older people. With no real cure and in spite of enormous efforts worldwide, the disease remains a mystery in terms of treatment. Importantly, African-Americans are two times as likely as Whites to develop late-onset Alzheimer's disease and less likely to receive timely diagnosis and treatment. Dopamine function is linked to normal cognition and memory and carriers of the DRD2 Taq1A A1 allele have significant loss of D2 receptor density in the brain. Recent research has shown that A1 carriers have worse memory performance during long-term memory (LTM) updating, compared to non-carriers or A2-carriers. A1carriers also show less blood oxygen level-dependent (BOLD) activation in the left caudate nucleus which is important for LTM updating. This latter effect was only seen in older adults, suggesting magnification of genetic effects on brain functioning in the elderly. Moreover, the frequency of the A1 allele is 0.40 in African-Americans, with an approximate prevalence of the DRD2 A1 allele in 50% of an African-American subset of individuals. This is higher than what is found in a non-screened American population (≤ 28%) for reward deficiency syndrome (RDS) behaviors. Based on DRD2 known genetic polymorphisms, we hypothesize that the DRD2 Taq1A A1 allele magnifies the risk of Alzheimer's in aging African-Americans. Research linking this high risk for Alzheimer's in the African-American population, with DRD2/ANKK1-TaqIA polymorphism and neurocognitive deficits related to LTM, could pave the way for novel, targeted pro-dopamine homeostatic treatment.

33 CFR 183.528 - Fuel stop valves.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Fuel stop valves. 183.528 Section...) BOATING SAFETY BOATS AND ASSOCIATED EQUIPMENT Fuel Systems Equipment Standards § 183.528 Fuel stop valves. (a) Each electrically operated fuel stop valve in a fuel line between the fuel tank and the engine...

Stopping Speech Suppresses the Task-Irrelevant Hand

ERIC Educational Resources Information Center

Cai, Weidong; Oldenkamp, Caitlin L.; Aron, Adam R.

2012-01-01

Some situations require one to quickly stop an initiated response. Recent evidence suggests that rapid stopping engages a mechanism that has diffuse effects on the motor system. For example, stopping the hand dampens the excitability of the task-irrelevant leg. However, it is unclear whether this "global suppression" could apply across wider motor…

46 CFR 64.41 - Stop valve closure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Stop valve closure. 64.41 Section 64.41 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MARINE PORTABLE TANKS AND CARGO HANDLING SYSTEMS Standards for an MPT § 64.41 Stop valve closure. A stop valve that operates by a screwed...

Mixing stops at the LHC

DOE PAGES

Agrawal, Prateek; Frugiuele, Claudia

2014-01-01

We study the phenomenology of a light stop NLSP in the presence of large mixing with either the first or the second generation. R-symmetric models provide a prime setting for this scenario, but our discussion also applies to the MSSM when a significant amount of mixing can be accommodated. In our framework the dominant stop decay is through the flavor violating mode into a light jet and the LSP in an extended region of parameter space. There are currently no limits from ATLAS and CMS in this region. We emulate shape-based hadronic SUSY searches for this topology, and find thatmore » they have potential sensitivity. If the extension of these analyses to this region is robust, we find that these searches can set strong exclusion limits on light stops. If not, then the flavor violating decay mode is challenging and may represent a blind spot in stop searches even at 13 TeV. Thus, an experimental investigation of this scenario is well motivated.« less

RNA Polymerase in Mumps Virion

PubMed Central

Bernard, Jacqueline P.; Northrop, Robert L.

1974-01-01

Mumps virions of the Enders' strain were examined for polymerase activity in vitro. An RNA-dependent RNA polymerase was found to be associated with the virion. The general properties of the reaction appear to be similar to those described for other paramyxoviruses. PMID:4836602

Basal forebrain neuronal inhibition enables rapid behavioral stopping

PubMed Central

Mayse, Jeffrey D.; Nelson, Geoffrey M.; Avila, Irene; Gallagher, Michela; Lin, Shih-Chieh

2015-01-01

Cognitive inhibitory control, the ability to rapidly suppress responses inappropriate for the context, is essential for flexible and adaptive behavior. While most studies on inhibitory control have focused on the fronto-basal-ganglia circuit, here we explore a novel hypothesis and show that rapid behavioral stopping is enabled by neuronal inhibition in the basal forebrain (BF). In rats performing the stop signal task, putative noncholinergic BF neurons with phasic bursting responses to the go signal were inhibited nearly completely by the stop signal. The onset of BF neuronal inhibition was tightly coupled with and temporally preceded the latency to stop, the stop signal reaction time. Artificial inhibition of BF activity in the absence of the stop signal was sufficient to reproduce rapid behavioral stopping. These results reveal a novel subcortical mechanism of rapid inhibitory control by the BF, which provides bidirectional control over the speed of response generation and inhibition. PMID:26368943

DNA Polymerase Eta and Chemotherapeutic Agents

PubMed Central

2011-01-01

Abstract The discovery of human DNA polymerase eta (pol η) has a major impact on the fields of DNA replication/repair fields. Since the discovery of human pol η, a number of new DNA polymerases with the ability to bypass various DNA lesions have been discovered. Among these polymerases, pol η is the most extensively studied lesion bypass polymerase with a defined major biological function, that is, to replicate across the cyclobutane pyrimidine dimers introduced by UV irradiation. Cyclobutane pyrimidine dimer is a major DNA lesion that causes distortion of DNA structure and block the replicative DNA polymerases during DNA replication process. Genetic defects in the pol η gene, Rad30, results in a disease called xeroderma pigmentosum variant. This review focuses on the overall properties of pol η and the mechanism that involved in regulating its activity in cells. In addition, the role of pol η in the action of DNA-targeting anticancer compounds is also discussed. Antioxid. Redox Signal. 14, 2521–2529. PMID:21050139

Kinetic Analysis of the Bypass of a Bulky DNA Lesion Catalyzed by Human Y-family DNA Polymerases

PubMed Central

Sherrer, Shanen M.; Sanman, Laura E.; Xia, Cynthia X.; Bolin, Eric R.; Malik, Chanchal K.; Efthimiopoulos, Georgia; Basu, Ashis K.; Suo, Zucai

2012-01-01

1-Nitropyrene (1-NP), a mutagen and potential carcinogen, is the most abundant nitro polyaromatic hydrocarbon in diesel exhaust, which reacts with DNA to form predominantly N-(deoxyguanosin-8-yl)-1-aminopyrene (dGAP). If not repaired, this DNA lesion is presumably bypassed in vivo by any of human Y-family DNA polymerases kappa (hPolκ), iota (hPolτ), eta (hPolη), and Rev1 (hRev1). Our running start assays demonstrated that each of these enzymes was indeed capable of traversing a site-specifically placed dGAP on a synthetic DNA template but hRev1 was stopped after lesion bypass. The time required to bypass 50% of the dGAP sites (t50bypass ) encountered by hPolη, hPolκ and hPolτ was determined to be 2.5 s, 4.1 s, and 106.5 s, respectively. The efficiency order of catalyzing translesion synthesis of dGAP (hPolη > hPolκ > hPolτ >> hRev1) is the same as the order for these human Y-family enzymes to elongate undamaged DNA. Although hPolη bypassed dGAP efficiently, replication by both hPolκ and hPolτ was strongly stalled at the lesion site and at a site immediately downstream from dGAP. By employing pre-steady state kinetic methods, a kinetic basis was established for polymerase pausing at these DNA template sites. Besides efficiency of bypass, the fidelity of those low-fidelity polymerases at these pause sites was also significantly decreased. Thus, if the translesion DNA synthesis of dGAP in vivo is catalyzed by a human Y-family DNA polymerase, e.g. hPolη, the process is certainly mutagenic. PMID:22324639

Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene.

PubMed

Horvath, Rita; Hudson, Gavin; Ferrari, Gianfrancesco; Fütterer, Nancy; Ahola, Sofia; Lamantea, Eleonora; Prokisch, Holger; Lochmüller, Hanns; McFarland, Robert; Ramesh, V; Klopstock, Thomas; Freisinger, Peter; Salvi, Fabrizio; Mayr, Johannes A; Santer, Rene; Tesarova, Marketa; Zeman, Jiri; Udd, Bjarne; Taylor, Robert W; Turnbull, Douglass; Hanna, Michael; Fialho, Doreen; Suomalainen, Anu; Zeviani, Massimo; Chinnery, Patrick F

2006-07-01

Mutations in the gene coding for the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (POLG1) have recently been described in patients with diverse clinical presentations, revealing a complex relationship between genotype and phenotype in patients and their families. POLG1 was sequenced in patients from different European diagnostic and research centres to define the phenotypic spectrum and advance understanding of the recurrence risks. Mutations were identified in 38 cases, with the majority being sporadic compound heterozygotes. Eighty-nine DNA sequence changes were identified, including 2 predicted to alter a splice site, 1 predicted to cause a premature stop codon and 13 predicted to cause novel amino acid substitutions. The majority of children had a mutation in the linker region, often 1399G-->A (A467T), and a mutation affecting the polymerase domain. Others had mutations throughout the gene, and 11 had 3 or more substitutions. The clinical presentation ranged from the neonatal period to late adult life, with an overlapping phenotypic spectrum from severe encephalopathy and liver failure to late-onset external ophthalmoplegia, ataxia, myopathy and isolated muscle pain or epilepsy. There was a strong gender bias in children, with evidence of an environmental interaction with sodium valproate. POLG1 mutations cause an overlapping clinical spectrum of disease with both dominant and recessive modes of inheritance. 1399G-->A (A467T) is common in children, but complete POLG1 sequencing is required to identify multiple mutations that can have complex implications for genetic counselling.

Proactive and Reactive Stopping When Distracted: An Attentional Account

PubMed Central

2014-01-01

Performance in response inhibition paradigms is typically attributed to inhibitory control. Here we examined the idea that stopping may largely depend on the outcome of a sensory detection process. Subjects performed a speeded go task, but they were instructed to withhold their response when a visual stop signal was presented. The stop signal could occur in the center of the screen or in the periphery. On half of the trials, perceptual distractors were presented throughout the trial. We found that these perceptual distractors impaired stopping, especially when stop signals could occur in the periphery. Furthermore, the effect of the distractors on going was smallest in the central stop-signal condition, medium in a condition in which no signals could occur, and largest in the condition in which stop signals could occur in the periphery. The results show that an important component of stopping is finding a balance between ignoring irrelevant information in the environment and monitoring for the occurrence of occasional stop signals. These findings highlight the importance of sensory detection processes when stopping and could shed new light on a range of phenomena and findings in the response inhibition literature. PMID:24842070

Lifespan Changes in Global and Selective Stopping and Performance Adjustments

PubMed Central

van de Laar, Maria C.; van den Wildenberg, Wery P. M.; van Boxtel, Geert J. M.; van der Molen, Maurits W.

2011-01-01

This study examined stopping and performance adjustments in four age groups (M ages: 8, 12, 21, and 76 years). All participants performed on three tasks, a standard two-choice task and the same task in which stop-signal trials were inserted requiring either the suppression of the response activated by the choice stimulus (global stop task) or the suppression of the response when one stop-signal was presented but not when the other stop-signal occurred (selective stop task). The results showed that global stopping was faster than selective stopping in all age groups. Global stopping matured more rapidly than selective stopping. The developmental gain in stopping was considerably more pronounced compared to the loss observed during senescence. All age groups slowed the response on trials without a stop-signal in the stop task compared to trials in the choice task, the elderly in particular. In addition, all age groups slowed on trials following stop-signal trials, except the elderly who did not slow following successful inhibits. By contrast, the slowing following failed inhibits was disproportionally larger in the elderly compared to young adults. Finally, sequential effects did not alter the pattern of performance adjustments. The results were interpreted in terms of developmental change in the balance between proactive and reactive control. PMID:22180746

The expanding polymerase universe.

PubMed

Goodman, M F; Tippin, B

2000-11-01

Over the past year, the number of known prokaryotic and eukaryotic DNA polymerases has exploded. Many of these newly discovered enzymes copy aberrant bases in the DNA template over which 'respectable' polymerases fear to tread. The next step is to unravel their functions, which are thought to range from error-prone copying of DNA lesions, somatic hypermutation and avoidance of skin cancer, to restarting stalled replication forks and repairing double-stranded DNA breaks.

Why stop self-injuring? Development of the reasons to stop self-injury questionnaire.

PubMed

Turner, Brianna J; Chapman, Alexander L; Gratz, Kim L

2014-01-01

We developed a measure of reasons to refrain from nonsuicidal self-injury (NSSI), the Reasons to Stop Self-Injury Questionnaire (RSSIQ), and examined how such reasons are associated with vulnerability versus resiliency for NSSI. Following qualitative item generation, we explored the factor structure, reliability, and convergent validity of the RSSIQ in 218 self-injuring undergraduates. In Study 2, we confirmed the hierarchical factor structure in 146 self-injuring individuals. In Study 3, we examined the incremental predictive validity of the RSSIQ. These studies resulted in a 40-item inventory with nine subscales and two higher-order factors. Resiliency-related reasons to stop NSSI were associated with greater hopefulness, social support, and adaptive coping, and prospectively protected against NSSI 3 months later, while vulnerability-related reasons were associated with greater psychopathology and dysfunctional coping, and predicted more chronic and severe NSSI. These studies, and the RSSIQ, can enhance the assessment and treatment of NSSI by clarifying motivations to stop NSSI.

Inhibitory Effects on Response Force in the Stop-Signal Paradigm

ERIC Educational Resources Information Center

Ko, Yao-Ting; Alsford, Toni; Miller, Jeff

2012-01-01

The forcefulness of key press responses was measured in stop-all and selective stopping versions of the stop-signal paradigm. When stop signals were presented too late for participants to succeed in stopping their responses, response force was nonetheless reduced relative to trials in which no stop signal was presented. This effect shows that…

Severe Hemophilia A in a Male Old English Sheep Dog with a C→T Transition that Created a Premature Stop Codon in Factor VIII

PubMed Central

Lozier, Jay N; Kloos, Mark T; Merricks, Elizabeth P; Lemoine, Nathaly; Whitford, Margaret H; Raymer, Robin A; Bellinger, Dwight A; Nichols, Timothy C

2016-01-01

Animals with hemophilia are models for gene therapy, factor replacement, and inhibitor development in humans. We have actively sought dogs with severe hemophilia A that have novel factor VIII mutations unlike the previously described factor VIII intron 22 inversion. A male Old English Sheepdog with recurrent soft-tissue hemorrhage and hemarthrosis was diagnosed with severe hemophilia A (factor VIII activity less than 1% of normal). We purified genomic DNA from this dog and ruled out the common intron 22 inversion; we then sequenced all 26 exons. Comparing the results with the normal canine factor VIII sequence revealed a C→T transition in exon 12 of the factor VIII gene that created a premature stop codon at amino acid 577 in the A2 domain of the protein. In addition, 2 previously described polymorphisms that do not cause hemophilia were present at amino acids 909 and 1184. The hemophilia mutation creates a new TaqI site that facilitates rapid genotyping of affected offspring by PCR and restriction endonuclease analyses. This mutation is analogous to the previously described human factor VIII mutation at Arg583, which likewise is a CpG dinucleotide transition causing a premature stop codon in exon 12. Thus far, despite extensive treatment with factor VIII, this dog has not developed neutralizing antibodies (‘inhibitors’) to the protein. This novel mutation in a dog gives rise to severe hemophilia A analogous to a mutation seen in humans. This model will be useful for studies of the treatment of hemophilia. PMID:27780008

Note on measuring electronic stopping of slow ions

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2017-11-01

Extracting stopping cross sections from energy-loss measurements requires careful consideration of the experimental geometry. Standard procedures for separating nuclear from electronic stopping treat electronic energy loss as a friction force, ignoring its dependence on impact parameter. In the present study we find that incorporating this dependence has a major effect on measured stopping cross sections, in particular for light ions at low beam energies. Calculations have been made for transmission geometry, nuclear interactions being quantified by Bohr-Williams theory of multiple scattering on the basis of a Thomas-Fermi-Molière potential, whereas electronic interactions are characterized by Firsov theory or PASS code. Differences between the full and the restricted stopping cross section depend on target thickness and opening angle of the detector and need to be taken into account in comparisons with theory as well as in applications of stopping data. It follows that the reciprocity principle can be violated when checked on restricted instead of full electronic stopping cross sections. Finally, we assert that a seeming gas-solid difference in stopping of low-energy ions is actually a metal-insulator difference. In comparisons with experimental results we mostly consider proton data, where nuclear stopping is only a minor perturbation.

Evaluation of bus emissions generated near bus stops

NASA Astrophysics Data System (ADS)

Yu, Qian; Li, Tiezhu

2014-03-01

The purpose of this research is to demonstrate a methodology for quantification of bus emissions generated near bus stops based on the real-world on-road emissions data collected by the Portable Emission Measurement System (PEMS). Data collection was carried out on an urban diesel bus throughout a bus line under normal operation condition on four work days. Stop influence zone is defined as the area in which the normal bus driving is interrupted by bus stops. The second-by-second data were screened out within the stop influence zone. And the bus running state near a stop was classified into three driving modes, deceleration, idling, and acceleration. Then emission characteristics were analyzed for each mode. Under the idling condition, the emission rates (g s-1) were not constant all the time. The NOX emission rate decreased in the first 4-6 s while the corresponding emission rates of CO2, CO, NOX, and HC increased in the last 4 s of idling. Besides, the influence of bus stop characteristics on emissions was investigated using statistical methods. Platform type, length and location of bus stops showed significant effects on the length of the stop influence zone. However, there were no significant effects on distance-based emission factors.

[Comparative analysis of real-time quantitative PCR-Sanger sequencing method and TaqMan probe method for detection of KRAS/BRAF mutation in colorectal carcinomas].

PubMed

Zhang, Xun; Wang, Yuehua; Gao, Ning; Wang, Jinfen

2014-02-01

To compare the application values of real-time quantitative PCR-Sanger sequencing and TaqMan probe method in the detection of KRAS and BRAF mutations, and to correlate KRAS/BRAF mutations with the clinicopathological characteristics in colorectal carcinomas. Genomic DNA of the tumor cells was extracted from formalin fixed paraffin embedded (FFPE) tissue samples of 344 colorectal carcinomas by microdissection. Real-time quantitative PCR-Sanger sequencing and TaqMan probe method were performed to detect the KRAS/BRAF mutations. The frequency and types of KRAS/BRAF mutations, clinicopathological characteristics and survival time were analyzed. KRAS mutations were detected in 39.8% (137/344) and 38.7% (133/344) of 344 colorectal carcinomas by using real-time quantitative PCR-Sanger sequencing and TaqMan probe method, respectively. BRAF mutation was detected in 4.7% (16/344) and 4.1% (14/344), respectively. There was no significant correlation between the two methods. The frequency of the KRAS mutation in female was higher than that in male (P < 0.05). The frequency of the BRAF mutation in colon was higher than that in rectum. The frequency of the BRAF mutation in stage III-IV cases was higher than that in stageI-II cases. The frequency of the BRAF mutation in signet ring cell carcinoma was higher than that in mucinous carcinoma and nonspecific adenocarcinoma had the lowest mutation rate. The frequency of the BRAF mutation in grade III cases was higher than that in grade II cases (P < 0.05). The overall concordance for the two methods of KRAS/BRAF mutation detection was 98.8% (kappa = 0.976). There was statistic significance between BRAF and KRAS mutations for the survival time of colorectal carcinomas (P = 0.039). There were no statistic significance between BRAF mutation type and BRAF/KRAS wild type (P = 0.058). (1) Compared with real-time quantitative PCR-Sanger sequencing, TaqMan probe method is better with regard to handling time, efficiency, repeatability, cost

Stopping eating and drinking.

PubMed

Schwarz, Judith K

2009-09-01

Voluntarily stopping eating and drinking, in which death occurs within one to three weeks of beginning the fast, is increasingly explored in the literature and mainstream media as an option to be discussed with "decisionally capable," suffering patients who want to hasten their dying. The author uses an example from her experience to describe stopping eating and drinking, as well as other clinical practices associated with hastening dying; explores whether this practice can or should be distinguished from suicide; and discusses the ethical and legal implications for nurses.

Sweet Spots and Door Stops

ERIC Educational Resources Information Center

Thompson, Michael; Tsui, Stella; Leung, Chi Fan

2011-01-01

A sweet spot is referred to in sport as the perfect place to strike a ball with a racquet or bat. It is the point of contact between bat and ball where maximum results can be produced with minimal effort from the hand of the player. Similar physics can be applied to the less inspiring examples of door stops; the perfect position of a door stop is…

IDENTIFYING POTENTIAL SOURCES OF BACKGROUND CONTAMINATION IN RT-PCR

EPA Science Inventory

Extraction of nucleic acids from low biomass samples, such as drinking water, is particularly sensitive to potential background contamination because the contaminating material is minimally diluted by the sample. The presence of bacterial DNA in Taq DNA polymerase is wel...

Association of vitamin D receptor BsmI, TaqI, FokI, and ApaI polymorphisms with susceptibility of chronic periodontitis: A systematic review and meta-analysis based on 38 case -control studies.

PubMed

Mashhadiabbas, Fatemeh; Neamatzadeh, Hossein; Nasiri, Rezvan; Foroughi, Elnaz; Farahnak, Soudabeh; Piroozmand, Parisa; Mazaheri, Mahta; Zare-Shehneh, Masoud

2018-01-01

There has been increasing interest in the study of the association between Vitamin D receptor (VDR) gene polymorphisms and risk of chronic periodontitis. However, the results remain inconclusive. To better understand the roles of VDR polymorphisms (BsmI, TaqI, FokI, and ApaI) in chronic periodontitis susceptibility, we conducted this systematic review and meta-analysis. The PubMed, Google Scholar, and Web of Science database were systemically searched to determine all the eligible studies about VDR polymorphisms and risk of chronic periodontitis up to April 2017. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the associations between VDR polymorphisms and chronic periodontitis risk. All the statistical analyses were performed by Comprehensive Meta-Analysis. All P values were two-tailed with a significant level at 0.05. Finally, a total of 38 case-control studies in 19 publications were identified which met our inclusion criteria. There are ten studies with 866 chronic periodontitis cases and 786 controls for BsmI, 16 studies with 1570 chronic periodontitis cases and 1676 controls for TaqI, five studies with 374 chronic periodontitis cases and 382 controls for FokI, and seven studies with 632 chronic periodontitis cases and 604 controls for ApaI. Overall, no significant association was observed between VDR gene BsmI, TaqI, FokI, and ApaI polymorphisms and risk of chronic periodontitis in any genetic model. Subgroup analysis stratified by ethnicity suggested a significant association between BsmI polymorphism and chronic periodontitis risk in the Caucasian subgroup under allele model (A vs. G: OR = 1.747, 95% CI = 1.099-2.778, P = 0.018). Further, no significant associations were observed when stratified by Hardy-Weinberg equilibrium status for BsmI, TaqI, and ApaI. Our results suggest that BsmI, TaqI, FokI, and ApaI polymorphisms in the VDR gene might not be associated with risk of chronic periodontitis in overall population.

Identification of Patients with Sleep Disordered Breathing: Comparing the Four-Variable Screening Tool, STOP, STOP-Bang, and Epworth Sleepiness Scales

PubMed Central

Silva, Graciela E.; Vana, Kimberly D.; Goodwin, James L.; Sherrill, Duane L.; Quan, Stuart F.

2011-01-01

Study Objective: The Epworth Sleepiness Scale (ESS) has been used to detect patients with potential sleep disordered breathing (SDB). Recently, a 4-Variable screening tool was proposed to identify patients with SDB, in addition to the STOP and STOP-Bang questionnaires. This study evaluated the abilities of the 4-Variable screening tool, STOP, STOP-Bang, and ESS questionnaires in identifying subjects at risk for SDB. Methods: A total of 4,770 participants who completed polysomnograms in the baseline evaluation of the Sleep Heart Health Study (SHHS) were included. Subjects with RDIs ≥ 15 and ≥ 30 were considered to have moderate-to-severe or severe SDB, respectively. Variables were constructed to approximate those in the questionnaires. The risk of SDB was calculated by the 4-Variable screening tool according to Takegami et al. The STOP and STOP-Bang questionnaires were evaluated including variables for snoring, tiredness/sleepiness, observed apnea, blood pressure, body mass index, age, neck circumference, and gender. Sleepiness was evaluated using the ESS questionnaire and scores were dichotomized into < 11 and ≥ 11. Results: The STOP-Bang questionnaire had higher sensitivity to predict moderate-to-severe (87.0%) and severe (70.4%) SDB, while the 4-Variable screening tool had higher specificity to predict moderate-to-severe and severe SDB (93.2% for both). Conclusions: In community populations such as the SHHS, high specificities may be more useful in excluding low-risk patients, while avoiding false positives. However, sleep clinicians may prefer to use screening tools with high sensitivities, like the STOP-Bang, in order to avoid missing cases that may lead to adverse health consequences and increased healthcare costs. Citation: Silva GE; Vana KD; Goodwin JL; Sherrill DL; Quan SF. Identification of patients with sleep disordered breathing: comparing the Four-Variable screening tool, STOP, STOP-Bang, and Epworth Sleepiness Scales. J Clin Sleep Med 2011

Optimally Stopped Optimization

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel A.

2016-11-01

We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark simulated annealing on a class of maximum-2-satisfiability (MAX2SAT) problems. We also compare the performance of a D-Wave 2X quantum annealer to the Hamze-Freitas-Selby (HFS) solver, a specialized classical heuristic algorithm designed for low-tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N =1098 variables, the D-Wave device is 2 orders of magnitude faster than the HFS solver, and, modulo known caveats related to suboptimal annealing times, exhibits identical scaling with problem size.

The Stop Transmission of Polio Data Management (STOP DM) assignment and its role in polio eradication and immunization data improvement in Africa

PubMed Central

Benke, Amalia; Williams, Alford Joseph; MacNeil, Adam

2017-01-01

The availability and use of high quality immunization and surveillance data are crucial for monitoring all components of the Global Polio Eradication Program (GPEI). The Stop Transmission of Polio (STOP) program was initiated in 1999 to train and mobilize human resources to provide technical support to polio endemic and at-risk countries and in 2002 the STOP data management (STOP DM) deployment was created to provide capacity development in the area of data management for immunization and surveillance data for these countries. Since 2002, Africa has received the majority of support from the STOP DM program, with almost 80% of assignments being placed in African countries. The STOP DM program has played a valuable role in improving the quality and use of data for the GPEI and has increasingly supported other immunization program data needs. In this report we provide an overview of the history, current status, and future of the STOP DM program, with a specific focus on the African continent. PMID:29296155

The Stop Transmission of Polio Data Management (STOP DM) assignment and its role in polio eradication and immunization data improvement in Africa.

PubMed

Benke, Amalia; Williams, Alford Joseph; MacNeil, Adam

2017-01-01

The availability and use of high quality immunization and surveillance data are crucial for monitoring all components of the Global Polio Eradication Program (GPEI). The Stop Transmission of Polio (STOP) program was initiated in 1999 to train and mobilize human resources to provide technical support to polio endemic and at-risk countries and in 2002 the STOP data management (STOP DM) deployment was created to provide capacity development in the area of data management for immunization and surveillance data for these countries. Since 2002, Africa has received the majority of support from the STOP DM program, with almost 80% of assignments being placed in African countries. The STOP DM program has played a valuable role in improving the quality and use of data for the GPEI and has increasingly supported other immunization program data needs. In this report we provide an overview of the history, current status, and future of the STOP DM program, with a specific focus on the African continent.

The TaqIA RFLP is associated with attenuated intervention-induced body weight loss and increased carbohydrate intake in post-menopausal obese women.

PubMed

Cameron, Jameason D; Riou, Marie-Ève; Tesson, Frédérique; Goldfield, Gary S; Rabasa-Lhoret, Rémi; Brochu, Martin; Doucet, Éric

2013-01-01

Polymorphisms of the dopamine receptor D2 (DRD2) gene have been associated with obesity phenotypes. Our aim was to examine if the genotype of TaqIA Restriction Fragment Length Polymorphism (RFPL) was related to an attenuated weight loss response or to changes in energy expenditure (EE) and food preference before and after weight loss. methods: Obese post-menopausal women (age=57.1 ± 4.6 yr, weight=85.4 ± 15.4 kg and BMI=32.8 ± 4.5 kg/m(2)) were genotyped for TaqIA (n=127) by using PCR-RFLP analysis and categorized as possessing at least one copy of the A1 allele (A1(+)) or no copy (A1(-)). Women were randomized into two groups, caloric restriction (CR) and caloric restriction+resistance training (CRRT) and in this study were further classified as follows: A1(+)CR, A1(+)CRRT, A1-(-)CR and (-)A1(-)CRRT. Body composition, total daily EE, physical activity EE, Resting EE (REE), and energy intake were obtained at baseline and post-intervention using DXA, doubly-labeled water, indirect calorimetry, and 3-day dietary records, respectively. Overall, all of the anthropometric variables and REE significantly decreased post-intervention (p<0.001). Women in the CRRT group lost significantly more fat mass (FM) than the CR women (p<0.05). There were significant time by group by allele interactions for attenuated body weight (BW), BMI, and FM loss for A1(+) (vs. A1(-)) in CRRT (p<0.05) and for increased % carbohydrate intake (p<0.01). TaqIA genotype was associated with body weight loss post-intervention; more specifically, carriers of the A1 allele lost significantly less BW and FM than the A1(-) and had increased carbohydrate intake in the CRRT group. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development of a Real-Time, TaqMan Reverse Transcription-PCR Assay for Detection and Differentiation of Lyssavirus Genotypes 1, 5, and 6

PubMed Central

Wakeley, P. R.; Johnson, N.; McElhinney, L. M.; Marston, D.; Sawyer, J.; Fooks, A. R.

2005-01-01

Several reverse transcription-PCR (RT-PCR) methods have been reported for the detection of rabies and rabies-related viruses. These methods invariably involve multiple transfers of nucleic acids between different tubes, with the risk of contamination leading to the production of false-positive results. Here we describe a single, closed-tube, nonnested RT-PCR with TaqMan technology that distinguishes between classical rabies virus (genotype 1) and European bat lyssaviruses 1 and 2 (genotypes 5 and 6) in real time. The TaqMan assay is rapid, sensitive, and specific and allows for the genotyping of unknown isolates concomitant with the RT-PCR. The assay can be applied quantitatively and the use of an internal control enables the quality of the isolated template to be assessed. Despite sequence heterogeneity in the N gene between the different genotypes, a universal forward and reverse primer set has been designed, allowing for the simplification of previously described assays. We propose that within a geographically constrained area, this assay will be a useful tool for the detection and differentiation of members of the Lyssavirus genus. PMID:15956398

Vaccines Stop Illness

MedlinePlus

Skip Navigation Bar Home Current Issue Past Issues Vaccines Stop Illness Past Issues / Spring 2008 Table of ... meningitis won't infect, cripple, or kill children. Vaccine Safety In light of recent questions about vaccine ...

14 CFR 398.8 - Number of intermediate stops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Number of intermediate stops. 398.8 Section 398.8 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION... Number of intermediate stops. (a) Except in Alaska, no more than one intermediate stop is permitted in...

14 CFR 398.8 - Number of intermediate stops.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 4 2014-01-01 2014-01-01 false Number of intermediate stops. 398.8 Section 398.8 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION... Number of intermediate stops. (a) Except in Alaska, no more than one intermediate stop is permitted in...

Vitamin-D receptor (VDR) gene polymorphisms (Taq-I & Apa-I) in Syrian healthy population.

PubMed

Haddad, Shaden

2014-12-01

The vitamin D endocrine system regulates bone metabolism and calcium homeostasis as well as cellular proliferation and differentiation. Vitamin D receptor (VDR) mediates Vit-D activity, thus VDR gene polymorphisms may correlate with different diseases. This study aimed to determine the distribution of VDR gene (Taq-I and Apa-I) polymorphisms using a RFLP in unrelated normal healthy individuals of Syrian population. Allelic frequencies were 65% vs 35% and 66% vs 34% for T vs t and A vs a alleles, respectively. Genotype distribution was 36%, 58% and 6% for TT, Tt and tt and 42%, 47% and 10% for AA, Aa and aa, respectively. These results demonstrate that the frequency and distribution of the VDR polymorphisms in Syrian population are different from other populations worldwide.

Evaluation of the clinical sensitivity for the quantification of human immunodeficiency virus type 1 RNA in plasma: Comparison of the new COBAS TaqMan HIV-1 with three current HIV-RNA assays--LCx HIV RNA quantitative, VERSANT HIV-1 RNA 3.0 (bDNA) and COBAS AMPLICOR HIV-1 Monitor v1.5.

PubMed

Katsoulidou, Antigoni; Petrodaskalaki, Maria; Sypsa, Vana; Papachristou, Eleni; Anastassopoulou, Cleo G; Gargalianos, Panagiotis; Karafoulidou, Anastasia; Lazanas, Marios; Kordossis, Theodoros; Andoniadou, Anastasia; Hatzakis, Angelos

2006-02-01

The COBAS TaqMan HIV-1 test (Roche Diagnostics) was compared with the LCx HIV RNA quantitative assay (Abbott Laboratories), the Versant HIV-1 RNA 3.0 (bDNA) assay (Bayer) and the COBAS Amplicor HIV-1 Monitor v1.5 test (Roche Diagnostics), using plasma samples of various viral load levels from HIV-1-infected individuals. In the comparison of TaqMan with LCx, TaqMan identified as positive 77.5% of the 240 samples versus 72.1% identified by LCx assay, while their overall agreement was 94.6% and the quantitative results of samples that were positive by both methods were strongly correlated (r=0.91). Similarly, in the comparison of TaqMan with bDNA 3.0, both methods identified 76.3% of the 177 samples as positive, while their overall agreement was 95.5% and the quantitative results of samples that were positive by both methods were strongly correlated (r=0.95). Finally, in the comparison of TaqMan with Monitor v1.5, TaqMan identified 79.5% of the 156 samples as positive versus 80.1% identified by Monitor v1.5, while their overall agreement was 95.5% and the quantitative results of samples that were positive by both methods were strongly correlated (r=0.96). In conclusion, the new COBAS TaqMan HIV-1 test showed excellent agreement with other widely used commercially available tests for the quantitation of HIV-1 viral load.

Dembo polymerase chain reaction technique for detection of bovine abortion, diarrhea, and respiratory disease complex infectious agents in potential vectors and reservoirs.

PubMed

Rahpaya, Sayed Samim; Tsuchiaka, Shinobu; Kishimoto, Mai; Oba, Mami; Katayama, Yukie; Nunomura, Yuka; Kokawa, Saki; Kimura, Takashi; Kobayashi, Atsushi; Kirino, Yumi; Okabayashi, Tamaki; Nonaka, Nariaki; Mekata, Hirohisa; Aoki, Hiroshi; Shiokawa, Mai; Umetsu, Moeko; Morita, Tatsushi; Hasebe, Ayako; Otsu, Keiko; Asai, Tetsuo; Yamaguchi, Tomohiro; Makino, Shinji; Murata, Yoshiteru; Abi, Ahmad Jan; Omatsu, Tsutomu; Mizutani, Tetsuya

2018-05-31

Bovine abortion, diarrhea, and respiratory disease complexes, caused by infectious agents, result in high and significant economic losses for the cattle industry. These pathogens are likely transmitted by various vectors and reservoirs including insects, birds, and rodents. However, experimental data supporting this possibility are scarce. We collected 117 samples and screened them for 44 bovine abortive, diarrheal, and respiratory disease complex pathogens by using Dembo polymerase chain reaction (PCR), which is based on TaqMan real-time PCR. Fifty-seven samples were positive for at least one pathogen, including bovine viral diarrhea virus, bovine enterovirus, Salmonella enterica ser. Dublin, Salmonella enterica ser. Typhimurium, and Neospora caninum ; some samples were positive for multiple pathogens. Bovine viral diarrhea virus and bovine enterovirus were the most frequently detected pathogens, especially in flies, suggesting an important role of flies in the transmission of these viruses. Additionally, we detected the N. caninum genome from a cockroach sample for the first time. Our data suggest that insects (particularly flies), birds, and rodents are potential vectors and reservoirs of abortion, diarrhea, and respiratory infectious agents, and that they may transmit more than one pathogen at the same time.

Vitamin-D Receptor (VDR) Gene Polymorphisms (TaqI, FokI) in Turkish Patients with Hashimoto's Thyroiditis: Relationship to the Levels of Vit-D and Cytokines.

PubMed

Guleryuz, Bedia; Akin, Fulya; Ata, Melek Tunc; Dalyanoglu, Mukaddes Mergen; Turgut, Sebahat

2016-01-01

Hashimoto's thyroiditis (HT) is a common autoimmune disease. Vitamin D is an important regulator of immune system. It has been shown in several studies that vitamin D prevents the development of lots of autoimmune diseases. There are some studies that prove vitamin D receptor (VDR) gene polymorphism increases the risk of Hashimoto's thyroiditis. In this study, we aimed to investigate the association between HT and level of 25(OH)D3, IL-2, IL-4, IL-5, TNF-α and IFN-γ and VDR FokI and TaqI gene polymorphism. Moreover, to find out whether low levels of vitamin D affect HT pathogenesis over inflammatory parameters. We performed a case-control study that included 136 cases with HT (49 euthyroid, 49 subclinical hypothyroid, 38 hypothyroid patients) and 50 healthy control. Serum levels of 25(OH)D3, glucose, insulin, parathyroid hormone, calcium, phosphorus, alkaline phosphatase were measured and IL-4, IL-5, TNF-α, IFN-γ analysis were performed with ELISA kits in all 186 subjects. Genetic analysis for VDR FokI and TaqI gene polymorphisms were done by RFLP in all subjects. Mean serum 25(OH)D levels were 14.88±8.23 ng/ml in patient with HT and 15.52±1.34 ng/ml in healthy controls. There were no statically significant differences between the groups in terms of vitamin D levels (P=0.977). Prevalence of vitamin D insufficiency in HT cases was significantly higher than controls (p=0.02). Although serum IL-2, IL-4, TNF-α and IFN-γ were significantly higher in HT patients, there were no significant differences regarding IL-5 levels. Significant differences were observed between the groups regarding the genotype of TaqI but no differences regarding FokI genotype. Vitamin D insufficiency is associated with HT. There is a relationship between VDR TaqI gene polymorphism and HT. Although vitamin D levels are low in both patient and control group, detection of high level of inflammatory parameters in HT group makes us think that low level of vitamin D does not affect HT

"Stop Diabetes Now!"

MedlinePlus

... of this page please turn Javascript on. Feature: Diabetes "Stop Diabetes Now!" Past Issues / Fall 2009 Table of Contents ... Tips for Seniors at Risk for Type 2 Diabetes Lifestyle changes that lead to weight loss—such ...

Effect of variability of sequence length of go trials preceding a stop trial on ability of response inhibition in stop-signal task.

PubMed

Hiraoka, Koichi; Kinoshita, Atsushi; Kunimura, Hiroshi; Matsuoka, Masakazu

2018-05-31

This study investigated whether the variability of the sequence length of the go trials preceding a stop trial enhanced or interfered with inhibitory control. The hypotheses tested were either inhibitory control improves when the sequence length of the go trials varies as a consequence of increased preparatory effort or it degrades as a consequence of the switching cost from the go trial to the stop trial. The right-handed participants abducted the left or right index finger in response to a go cue during the go trials. A stop cue was given at 50, 90, or 130 ms after the go cue, with 0.25 probability in the stop trial. In the less variable session, a stop trial was presented after two, three, or four consecutive go trials. In the variable session, a stop trial was presented after one, two, three, four, or five consecutive go trials. The reaction time and stop-signal reaction time were not significantly different between the sessions and between the response sides. Nevertheless, the probability of successful inhibition of the right-hand response in the variable session was higher than that in the less variable session when the stop cue was given 50 ms after a go cue. This finding supports the view that preparatory effort due to less predictability of the chance of a forthcoming response inhibition enhances the ability of the right-hand response inhibition when the stop process begins earlier.

Association of vitamin D receptor BsmI, TaqI, FokI, and ApaI polymorphisms with susceptibility of chronic periodontitis: A systematic review and meta-analysis based on 38 case –control studies

PubMed Central

Mashhadiabbas, Fatemeh; Neamatzadeh, Hossein; Nasiri, Rezvan; Foroughi, Elnaz; Farahnak, Soudabeh; Piroozmand, Parisa; Mazaheri, Mahta; Zare-Shehneh, Masoud

2018-01-01

Background: There has been increasing interest in the study of the association between Vitamin D receptor (VDR) gene polymorphisms and risk of chronic periodontitis. However, the results remain inconclusive. To better understand the roles of VDR polymorphisms (BsmI, TaqI, FokI, and ApaI) in chronic periodontitis susceptibility, we conducted this systematic review and meta-analysis. Materials and Methods: The PubMed, Google Scholar, and Web of Science database were systemically searched to determine all the eligible studies about VDR polymorphisms and risk of chronic periodontitis up to April 2017. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the associations between VDR polymorphisms and chronic periodontitis risk. All the statistical analyses were performed by Comprehensive Meta-Analysis. All P values were two-tailed with a significant level at 0.05. Results: Finally, a total of 38 case–control studies in 19 publications were identified which met our inclusion criteria. There are ten studies with 866 chronic periodontitis cases and 786 controls for BsmI, 16 studies with 1570 chronic periodontitis cases and 1676 controls for TaqI, five studies with 374 chronic periodontitis cases and 382 controls for FokI, and seven studies with 632 chronic periodontitis cases and 604 controls for ApaI. Overall, no significant association was observed between VDR gene BsmI, TaqI, FokI, and ApaI polymorphisms and risk of chronic periodontitis in any genetic model. Subgroup analysis stratified by ethnicity suggested a significant association between BsmI polymorphism and chronic periodontitis risk in the Caucasian subgroup under allele model (A vs. G: OR = 1.747, 95% CI = 1.099–2.778, P = 0.018). Further, no significant associations were observed when stratified by Hardy–Weinberg equilibrium status for BsmI, TaqI, and ApaI. Conclusion: Our results suggest that BsmI, TaqI, FokI, and ApaI polymorphisms in the VDR gene might not be associated with risk of

Delayed vaccine virus replication in chickens vaccinated subcutaneously with an immune complex infectious bursal disease vaccine: Quantification of vaccine virus by real-time polymerase chain reaction

PubMed Central

2005-01-01

Abstract The distribution of the immune complex vaccine virus for infectious bursal disease (IBD) in tissue was examined and the viral loads of the organs were quantitatively compared. One-day-old specific pathogen free (SPF) and maternally immune broiler chickens were injected subcutaneously with the vaccine. Lymphoid and non-lymphoid tissues were collected at various time intervals during the experiment to test for infectious bursal disease virus (IBDV)-RNA by using reverse transcriptase-polymerase chain reaction (RT-PCR). Only the bursa of Fabricius was found to be positive with unusually long viral persistence in the broiler group. The positive bursa samples were further investigated by using real-time PCR coupled with a TaqMan probe. The highest amounts of the virus were detected at its first appearance in the bursa: on day 14 post vaccination (PV) in the SPF chickens and on day 17 and day 21 PV in the maternally immune broiler group. The virus then gradually cleared, most likely due to the parallel appearance of the active immune response indicated by seroconversion. PMID:15971678

DNA polymerase ζ cooperates with polymerases κ and ι in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients

PubMed Central

Ziv, Omer; Geacintov, Nicholas; Nakajima, Satoshi; Yasui, Akira; Livneh, Zvi

2009-01-01

Human cells tolerate UV-induced cyclobutane pyrimidine dimers (CPD) by translesion DNA synthesis (TLS), carried out by DNA polymerase η, the POLH gene product. A deficiency in DNA polymerase η due to germ-line mutations in POLH causes the hereditary disease xeroderma pigmentosum variant (XPV), which is characterized by sunlight sensitivity and extreme predisposition to sunlight-induced skin cancer. XPV cells are UV hypermutable due to the activity of mutagenic TLS across CPD, which explains the cancer predisposition of the patients. However, the identity of the backup polymerase that carries out this mutagenic TLS was unclear. Here, we show that DNA polymerase ζ cooperates with DNA polymerases κ and ι to carry out error-prone TLS across a TT CPD. Moreover, DNA polymerases ζ and κ, but not ι, protect XPV cells against UV cytotoxicity, independently of nucleotide excision repair. This presents an extreme example of benefit-risk balance in the activity of TLS polymerases, which provide protection against UV cytotoxicity at the cost of increased mutagenic load. PMID:19564618

DNA polymerase zeta cooperates with polymerases kappa and iota in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients.

PubMed

Ziv, Omer; Geacintov, Nicholas; Nakajima, Satoshi; Yasui, Akira; Livneh, Zvi

2009-07-14

Human cells tolerate UV-induced cyclobutane pyrimidine dimers (CPD) by translesion DNA synthesis (TLS), carried out by DNA polymerase eta, the POLH gene product. A deficiency in DNA polymerase eta due to germ-line mutations in POLH causes the hereditary disease xeroderma pigmentosum variant (XPV), which is characterized by sunlight sensitivity and extreme predisposition to sunlight-induced skin cancer. XPV cells are UV hypermutable due to the activity of mutagenic TLS across CPD, which explains the cancer predisposition of the patients. However, the identity of the backup polymerase that carries out this mutagenic TLS was unclear. Here, we show that DNA polymerase zeta cooperates with DNA polymerases kappa and iota to carry out error-prone TLS across a TT CPD. Moreover, DNA polymerases zeta and kappa, but not iota, protect XPV cells against UV cytotoxicity, independently of nucleotide excision repair. This presents an extreme example of benefit-risk balance in the activity of TLS polymerases, which provide protection against UV cytotoxicity at the cost of increased mutagenic load.

[Application of transcription mediated amplification and real-time reverse transcription polymerase chain reaction in detection of human immunodeficiency virus RNA].

PubMed

Wu, Daxian; Tao, Shuhui; Liu, Shuiping; Zhou, Jiebin; Tan, Deming; Hou, Zhouhua

2017-07-28

To observe the sensitivity of transcription mediated amplification (TMA), and to compare its performance with real-time reverse transcription polymerase chain reaction (real-time RT-PCR) in detecting human immunodeficiency virus RNA (HIV RNA).
 Methods: TMA system was established with TaqMan probes, specific primers, moloney murine leukemia virus (MMLV) reverse transcriptase, T7 RNA polymerase, and reaction substrates. The sensitivity of TMA was evaluated by amplifying a group of 10-fold diluted HIV RNA standards which were transcribed in vitro. A total of 60 plasma of HIV infected patients were measured by TMA and Cobas Amplicor HIV-1 Monitor test to observe the positive rate. The correlation and concordance of the above two technologies were investigated by linear regression and Bland-Altman analysis.
 Results: TMA system was established successfully and HIV RNA transcribed standards at concentration of equal or more than 10 copies/mL could be detected by TMA technology. Among 60 samples of plasma from HIV infected patients, 46 were positively detected and 12 were negatively amplified by both TMA and Cobas reagents; 2 samples were positively tested by Cobas reagent but negatively tested by TMA system. The concordance rate of the two methods was 97.1% and the difference of positive detection rate between the two methods was not statistically significant (P>0.05). Linear regression was used for 46 samples which were positively detected by both TMA and Cobas reagents and showed an excellent correlation between the two reagents (r=0.997, P<0.001). Bland-Altma analysis revealed that the mean different value of HIV RNA levels for denary logarithm was 0.02. Forty-four samples were included in 95% of credibility interval of concordance.
 Conclusion: TMA system has the potential of high sensitivity. TMA and real-time RT-PCR keep an excellent correlation and consistency in detecting HIV RNA.

Post-Stop-Signal Adjustments: Inhibition Improves Subsequent Inhibition

ERIC Educational Resources Information Center

Bissett, Patrick G.; Logan, Gordon D.

2012-01-01

Performance in the stop-signal paradigm involves a balance between going and stopping, and one way that this balance is struck is through shifting priority away from the go task, slowing responses after a stop signal, and improving the probability of inhibition. In 6 experiments, the authors tested whether there is a corresponding shift in…

Multi-arm group sequential designs with a simultaneous stopping rule.

PubMed

Urach, S; Posch, M

2016-12-30

Multi-arm group sequential clinical trials are efficient designs to compare multiple treatments to a control. They allow one to test for treatment effects already in interim analyses and can have a lower average sample number than fixed sample designs. Their operating characteristics depend on the stopping rule: We consider simultaneous stopping, where the whole trial is stopped as soon as for any of the arms the null hypothesis of no treatment effect can be rejected, and separate stopping, where only recruitment to arms for which a significant treatment effect could be demonstrated is stopped, but the other arms are continued. For both stopping rules, the family-wise error rate can be controlled by the closed testing procedure applied to group sequential tests of intersection and elementary hypotheses. The group sequential boundaries for the separate stopping rule also control the family-wise error rate if the simultaneous stopping rule is applied. However, we show that for the simultaneous stopping rule, one can apply improved, less conservative stopping boundaries for local tests of elementary hypotheses. We derive corresponding improved Pocock and O'Brien type boundaries as well as optimized boundaries to maximize the power or average sample number and investigate the operating characteristics and small sample properties of the resulting designs. To control the power to reject at least one null hypothesis, the simultaneous stopping rule requires a lower average sample number than the separate stopping rule. This comes at the cost of a lower power to reject all null hypotheses. Some of this loss in power can be regained by applying the improved stopping boundaries for the simultaneous stopping rule. The procedures are illustrated with clinical trials in systemic sclerosis and narcolepsy. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

Pulling out all the stops: searching for RPV SUSY with stop-jets

NASA Astrophysics Data System (ADS)

Bai, Yang; Katz, Andrey; Tweedie, Brock

2014-01-01

If the lighter stop eigenstate decays directly to two jets via baryonic R-parity violation, it could have escaped existing LHC and Tevatron searches in four-jet events, even for masses as small as 100 GeV. In order to recover sensitivity in the face of increasingly harsh trigger requirements at the LHC, we propose a search for stop pairs in the highly-boosted regime, using the approaches of jet substructure. We demonstrate that the four-jet triggers can be completely bypassed by using inclusive jet- H T triggers, and that the resulting QCD continuum background can be processed by substructure methods into a featureless spectrum suitable for a data-driven bump-hunt down to 100 GeV. We estimate that the LHC 8 TeV run is sensitive to 100 GeV stops with decays of any flavor at better than 5σ-level, and could place exclusions up to 300 GeV or higher. Assuming Minimal Flavor Violation and running a b-tagged analysis, exclusion reach may extend up to nearly 400 GeV. Longer-term, the 14 TeV LHC at 300 fb-1 could extend these mass limits by a factor of two, while continuing to improve sensitivity in the 100 GeV region.

Aptamer Selection Express: A Novel Method for Rapid Single-Step Selection and Sensing of Aptamers

DTIC Science & Technology

2008-12-01

sample) was as follows: 5 µL buffer, 2 µL MgCl2, 2.5 µL DMSO, 1 µL betaine , 1 µL each dNTP, 2.5 µL F primer, 2.5 µL R primer, 0.54 µL taq polymerase...and 25.1 µL H2O. Betaine and increased DMSO were added to the master mix to eliminate polymerase jumping during PCR ampli- fication.10 Using the

48 CFR 52.242-15 - Stop-Work Order.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 2 2010-10-01 2010-10-01 false Stop-Work Order. 52.242-15... Stop-Work Order. As prescribed in 42.1305(b), insert the following clause. The 90-day period stated in the clause may be reduced to less than 90 days. Stop-Work Order (AUG 1989) (a) The Contracting Officer...

48 CFR 52.242-15 - Stop-Work Order.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 2 2011-10-01 2011-10-01 false Stop-Work Order. 52.242-15... Stop-Work Order. As prescribed in 42.1305(b), insert the following clause. The 90-day period stated in the clause may be reduced to less than 90 days. Stop-Work Order (AUG 1989) (a) The Contracting Officer...

Higgs-stoponium mixing near the stop-antistop threshold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodwin, Geoffrey T.; Chung, Hee Sok; Wagner, Carlos E. M.

Supersymmetric extensions of the standard model contain additional heavy neutral Higgs bosons that are coupled to heavy scalar top quarks (stops). This system exhibits interesting field theoretic phenomena when the Higgs mass is close to the stop-antistop production threshold. Existing work in the literature has examined the digluon-to-diphoton cross section near threshold and has focused on enhancements in the cross section that might arise either from the perturbative contributions to the Higgs-to-digluon and Higgs-to-diphoton form factors or from mixing of the Higgs boson with stoponium states. Near threshold, enhancements in the relevant amplitudes that go as inverse powers of themore » stop-antistop relative velocity require resummations of perturbation theory and/or nonperturbative treatments. We present a complete formulation of threshold effects at leading order in the stop-antistop relative velocity in terms of nonrelativistic effective field theory. We give detailed numerical calculations for the case in which the stop-antistop Green’s function is modeled with a Coulomb-Schr¨odinger Green’s function. We find several general effects that do not appear in a purely perturbative treatment. Higgs-stop-antistop mixing effects displace physical masses from the threshold region, thereby rendering the perturbative threshold enhancements inoperative. In the case of large Higgs-stop-antistop couplings, the displacement of a physical state above threshold substantially increases its width, owing to its decay width to a stop-antistop pair, and greatly reduces its contribution to the cross section.« less

A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity.

PubMed

Freemont, P S; Ollis, D L; Steitz, T A; Joyce, C M

1986-09-01

The Klenow fragment of DNA polymerase I from Escherichia coli has two enzymatic activities: DNA polymerase and 3'-5' exonuclease. The crystal structure showed that the fragment is folded into two distinct domains. The smaller domain has a binding site for deoxynucleoside monophosphate and a divalent metal ion that is thought to identify the 3'-5' exonuclease active site. The larger C-terminal domain contains a deep cleft that is believed to bind duplex DNA. Several lines of evidence suggested that the large domain also contains the polymerase active site. To test this hypothesis, we have cloned the DNA coding for the large domain into an expression system and purified the protein product. We find that the C-terminal domain has polymerase activity (albeit at a lower specific activity than the native Klenow fragment) but no measurable 3'-5' exonuclease activity. These data are consistent with the hypothesis that each of the three enzymatic activities of DNA polymerase I from E. coli resides on a separate protein structural domain.

Persisting roughness when deposition stops.

PubMed

Schwartz, Moshe; Edwards, S F

2004-12-01

Useful theories for growth of surfaces under random deposition of material have been developed by several authors. The simplest theory is that introduced by Edwards and Wilkinson (EW), which is linear and soluble. Its nonlinear generalization by Kardar, Parisi, and Zhang (KPZ) resulted in many subsequent studies. Yet both EW and KPZ theories contain an unphysical feature. When deposition of material is stopped, both theories predict that as time tends to infinity, the surface becomes flat. In fact, of course, the final surface is not flat, but simply has no gradients larger than the gradient related to the angle of repose. We modify the EW and KPZ theories to accommodate this feature and study the consequences for the simpler system which is a modification of the EW equation. In spite of the fact that the equation describing the evolution of the surface is not linear, we find that the steady state in the presence of noise is not very different in the long-wavelength limit from that of the linear EW equation. The situation is quite different from that of EW when deposition stops. Initially there is still some rearrangement of the surface, but that stops as everywhere on the surface the gradient is less than that related to the angle of repose. The most interesting feature observed after deposition stops is the emergence of history-dependent steady-state distributions.

Development and validation of a real-time TaqMan assay for the detection and enumeration of Pseudomonas fluorescens ATCC 13525 used as a challenge organism in testing of food equipments.

PubMed

Saha, Ratul; Bestervelt, Lorelle L; Donofrio, Robert S

2012-02-01

Pseudomonas fluorescens ATCC 13525 is used as the challenge organism to evaluate the efficacy of the clean-in-place (CIP) process of food equipment (automatic ice-maker) as per NSF/ANSI Standard 12. Traditional culturing methodology is presently used to determine the concentration of the challenge organism, which takes 48 h to confirm the cell density. Storage of the challenge preparation in the refrigerator might alter the cell density as P. fluorescens is capable of growing at 4 °C. Also, background organism can grow on the Pseudomonas F agar (PFA) used for the recovery of P. fluorescens thus affecting the results of the test. Real-time TaqMan assay targeting the cpn60 gene was developed for the enumeration and the identification of P. fluorescens because of its specificity, accuracy, and shorter turnaround time. The TaqMan primer-probe pair developed using the Allele ID® 7.0 probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10 colony forming units (CFU)/mL. The assay was also successful in determining the concentration of the challenge preparation within 2 h. Based on these observations, TaqMan assay targeting the cpn60 gene can be efficiently used for strain level identification and enumeration of bacteria. Pseudomonas fluorescens ATCC 13525 is used as a challenge organism in the efficacy testing of clean-in-place process of food equipments. Currently, culturing technique is used for its identification and estimation, which is not only time-consuming but also prone to error. Real-time TaqMan assay is more specific, sensitive, and accurate along with a shorter turnaround time compared to culturing techniques, thereby increasing the overall quality of the testing methodology to evaluate the clean-in-place process critical for the food industry to protect public health and safety. © 2012 Institute of Food Technologists®

Stop/Start: Driving

Science.gov Websites

gasoline engine does not run when the vehicle is at rest. When pulling out, the electric starter/generator the gasoline engine when pulling out from a stop and generating electricity which is stored in the

RNA binding and replication by the poliovirus RNA polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to {sup 32}P-labeled ribohomopolymeric RNAs wasmore » examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K{sub a} for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 {times} 10{sup 9} M{sup {minus}1}. The polymerase binds to a subgenomic RNAs which contain the 3{prime} end of the genome with a K{sub a} similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3{prime} noncoding region.« less

Long-lived stops in MSSM scenarios with a neutralino LSP

NASA Astrophysics Data System (ADS)

Johansen, M.; Edsjö, J.; Hellman, S.; Milstead, D.

2010-08-01

This work investigates the possibility of a long-lived stop squark in supersymmetric models with the neutralino as the lightest supersymmetric particle (LSP). We study the implications of meta-stable stops on the sparticle mass spectra and the dark matter density. We find that in order to obtain a sufficiently long stop lifetime so as to be observable as a stable R-hadron at an LHC experiment, we need to fine tune the mass degeneracy between the stop and the LSP considerably. This increases the stop-neutralino co-anihilation cross section, leaving the neutralino relic density lower than what is expected from the WMAP results for stop masses ≲1.5 TeV/ c 2. However, if such scenarios are realised in nature we demonstrate that the long-lived stops will be produced at the LHC and that stop-based R-hadrons with masses up to 1 TeV/c2 can be detected after one year of running at design luminosity.

Stop the Violence: Overcoming Self-Destruction.

ERIC Educational Resources Information Center

George, Nelson, Ed.

The story of the Stop the Violence movement among rap music artists and music industry colleagues is told, along with the story of a video that was produced as part of this initiative. The Stop the Violence project grew out of the reaction to violence among concert goers at a 1987 rap concert on Long Island (New York). Rap musicians have joined…

Using all-way stop control for residential traffic management.

DOT National Transportation Integrated Search

1995-01-01

All-way, or multiway, stop signs are perhaps the most controversial form of residential traffic control. Residents are likely to request all-way stop signs more frequently than any other form of control. Stop signs are thought of as panaceas for many...

Pseudomonas aeruginosa phage PaP1 DNA polymerase is an A-family DNA polymerase demonstrating ssDNA and dsDNA 3'-5' exonuclease activity.

PubMed

Liu, Binyan; Gu, Shiling; Liang, Nengsong; Xiong, Mei; Xue, Qizhen; Lu, Shuguang; Hu, Fuquan; Zhang, Huidong

2016-08-01

Most phages contain DNA polymerases, which are essential for DNA replication and propagation in infected host bacteria. However, our knowledge on phage-encoded DNA polymerases remains limited. This study investigated the function of a novel DNA polymerase of PaP1, which is the lytic phage of Pseudomonas aeruginosa. PaP1 encodes its sole DNA polymerase called Gp90 that was predicted as an A-family DNA polymerase with polymerase and 3'-5' exonuclease activities. The sequence of Gp90 is homologous but not identical to that of other A-family DNA polymerases, such as T7 DNA polymerases (Pol) and DNA Pol I. The purified Gp90 demonstrated a polymerase activity. The processivity of Gp90 in DNA replication and its efficiency in single-dNTP incorporation are similar to those of T7 Pol with processive thioredoxin (T7 Pol/trx). Gp90 can degrade ssDNA and dsDNA in 3'-5' direction at a similar rate, which is considerably lower than that of T7 Pol/trx. The optimized conditions for polymerization were a temperature of 37 °C and a buffer consisting of 40 mM Tris-HCl (pH 8.0), 30 mM MgCl2, and 200 mM NaCl. These studies on DNA polymerase encoded by PaP1 help advance our knowledge on phage-encoded DNA polymerases and elucidate PaP1 propagation in infected P. aeruginosa.

Inferring Stop-Locations from WiFi.

PubMed

Wind, David Kofoed; Sapiezynski, Piotr; Furman, Magdalena Anna; Lehmann, Sune

2016-01-01

Human mobility patterns are inherently complex. In terms of understanding these patterns, the process of converting raw data into series of stop-locations and transitions is an important first step which greatly reduces the volume of data, thus simplifying the subsequent analyses. Previous research into the mobility of individuals has focused on inferring 'stop locations' (places of stationarity) from GPS or CDR data, or on detection of state (static/active). In this paper we bridge the gap between the two approaches: we introduce methods for detecting both mobility state and stop-locations. In addition, our methods are based exclusively on WiFi data. We study two months of WiFi data collected every two minutes by a smartphone, and infer stop-locations in the form of labelled time-intervals. For this purpose, we investigate two algorithms, both of which scale to large datasets: a greedy approach to select the most important routers and one which uses a density-based clustering algorithm to detect router fingerprints. We validate our results using participants' GPS data as well as ground truth data collected during a two month period.

Inferring Stop-Locations from WiFi

PubMed Central

Wind, David Kofoed; Sapiezynski, Piotr; Furman, Magdalena Anna; Lehmann, Sune

2016-01-01

Human mobility patterns are inherently complex. In terms of understanding these patterns, the process of converting raw data into series of stop-locations and transitions is an important first step which greatly reduces the volume of data, thus simplifying the subsequent analyses. Previous research into the mobility of individuals has focused on inferring ‘stop locations’ (places of stationarity) from GPS or CDR data, or on detection of state (static/active). In this paper we bridge the gap between the two approaches: we introduce methods for detecting both mobility state and stop-locations. In addition, our methods are based exclusively on WiFi data. We study two months of WiFi data collected every two minutes by a smartphone, and infer stop-locations in the form of labelled time-intervals. For this purpose, we investigate two algorithms, both of which scale to large datasets: a greedy approach to select the most important routers and one which uses a density-based clustering algorithm to detect router fingerprints. We validate our results using participants’ GPS data as well as ground truth data collected during a two month period. PMID:26901663

Polymerase Gamma Disease through the Ages

ERIC Educational Resources Information Center

Saneto, Russell P.; Naviaux, Robert K.

2010-01-01

The most common group of mitochondrial disease is due to mutations within the mitochondrial DNA polymerase, polymerase gamma 1 ("POLG"). This gene product is responsible for replication and repair of the small mitochondrial DNA genome. The structure-function relationship of this gene product produces a wide variety of diseases that at times, seems…

Light stops and fine-tuning in MSSM

NASA Astrophysics Data System (ADS)

Çiçi, Ali; Kırca, Zerrin; Ün, Cem Salih

2018-01-01

We discuss the fine-tuning issue within the MSSM framework. Following the idea that the fine-tuning can measure effects of some missing mechanism, we impose non-universal gaugino masses at the GUT scale, and explore the low scale implications. We realize that the fine-tuning parametrized with Δ _{EW} can be as low as zero. We consider the stop mass with a special importance and focus on the mass scales as m_{\\tilde{t}} ≤ 700 GeV, which are excluded by the current experiments when the stop decays into a neutralino along with a top quark or a chargino along with a bottom quark. We find that the stop mass can be as low as about 250 GeV with Δ _{EW} ˜ 50. We find that the solutions in this region can be exluded only up to 60% when stop decays into a neutralino-top quark, and 50% when it decays into a chargino-b quark. Setting 65% CL to be potential exclusion and 95% to be pure exclusion limit such solutions will be tested in near future experiments, which are conducted with higher luminosity. In addition to stop, the region with low fine-tuning and light stops predicts masses for the other supersymmetric particles such as m_{\\tilde{b}} ≳ 700 GeV, m_{\\tilde{τ }} ≳ 1 TeV, m_{\\tilde{χ }1^{± }} ≳ 120 GeV. The details for the mass scales and decay rates are also provided by tables of benchmark points.

Effect of oxygen-breathing during a decompression-stop on bubble-induced platelet activation after an open-sea air dive: oxygen-stop decompression.

PubMed

Pontier, J-M; Lambrechts, K

2014-06-01

We highlighted a relationship between decompression-induced bubble formation and platelet micro-particle (PMP) release after a scuba air-dive. It is known that decompression protocol using oxygen-stop accelerates the washout of nitrogen loaded in tissues. The aim was to study the effect of oxygen deco-stop on bubble formation and cell-derived MP release. Healthy experienced divers performed two scuba-air dives to 30 msw for 30 min, one with an air deco-stop and a second with 100% oxygen deco-stop at 3 msw for 9 min. Bubble grades were monitored with ultrasound and converted to the Kisman integrated severity score (KISS). Blood samples for cell-derived micro-particle analysis (AnnexinV for PMP and CD31 for endothelial MP) were taken 1 h before and after each dive. Mean KISS bubble score was significantly lower after the dive with oxygen-decompression stop, compared to the dive with air-decompression stop (4.3 ± 7.3 vs. 32.7 ± 19.9, p < 0.001). After the dive with an air-breathing decompression stop, we observed an increase of the post-dive mean values of PMP (753 ± 245 vs. 381 ± 191 ng/μl, p = 0.003) but no significant change in the oxygen-stop decompression dive (329 ± 215 vs. 381 +/191 ng/μl, p = 0.2). For the post-dive mean values of endothelial MP, there was no significant difference between both the dives. The Oxygen breathing during decompression has a beneficial effect on bubble formation accelerating the washout of nitrogen loaded in tissues. Secondary oxygen-decompression stop could reduce bubble-induced platelet activation and the pro-coagulant activity of PMP release preventing the thrombotic event in the pathogenesis of decompression sickness.

Picornaviral Polymerase Structure, Function, and Fidelity Modulation

PubMed Central

Peersen, Olve B.

2017-01-01

Like all positive strand RNA viruses, the picornaviruses replicate their genomes using a virally encoded RNA-dependent RNA polymerase enzyme known as 3Dpol. Over the past decade we have made tremendous advances in our understanding of 3Dpol structure and function, including the discovery of a novel mechanism for closing the active site that allows these viruses to easily fine tune replication fidelity and quasispecies distributions. This review summarizes current knowledge of picornaviral polymerase structure and how the enzyme interacts with RNA and other viral proteins to form stable and processive elongation complexes. The picornaviral RdRPs are among the smallest viral polymerases, but their fundamental molecular mechanism for catalysis appears to be generally applicable as a common feature of all positive strand RNA virus polymerases. PMID:28163093

Yeast Cells Expressing the Human Mitochondrial DNA Polymerase Reveal Correlations between Polymerase Fidelity and Human Disease Progression*

PubMed Central

Qian, Yufeng; Kachroo, Aashiq H.; Yellman, Christopher M.; Marcotte, Edward M.; Johnson, Kenneth A.

2014-01-01

Mutations in the human mitochondrial polymerase (polymerase-γ (Pol-γ)) are associated with various mitochondrial disorders, including mitochondrial DNA (mtDNA) depletion syndrome, Alpers syndrome, and progressive external opthamalplegia. To correlate biochemically quantifiable defects resulting from point mutations in Pol-γ with their physiological consequences, we created “humanized” yeast, replacing the yeast mtDNA polymerase (MIP1) with human Pol-γ. Despite differences in the replication and repair mechanism, we show that the human polymerase efficiently complements the yeast mip1 knockouts, suggesting common fundamental mechanisms of replication and conserved interactions between the human polymerase and other components of the replisome. We also examined the effects of four disease-related point mutations (S305R, H932Y, Y951N, and Y955C) and an exonuclease-deficient mutant (D198A/E200A). In haploid cells, each mutant results in rapid mtDNA depletion, increased mutation frequency, and mitochondrial dysfunction. Mutation frequencies measured in vivo equal those measured with purified enzyme in vitro. In heterozygous diploid cells, wild-type Pol-γ suppresses mutation-associated growth defects, but continuous growth eventually leads to aerobic respiration defects, reduced mtDNA content, and depolarized mitochondrial membranes. The severity of the Pol-γ mutant phenotype in heterozygous diploid humanized yeast correlates with the approximate age of disease onset and the severity of symptoms observed in humans. PMID:24398692

Electronic stopping in oxides beyond Bragg additivity

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2018-01-01

We present stopping cross sections calculated by our PASS code for several ions in metal oxides and SiO2 over a wide energy range. Input takes into account changes in the valence structure by assigning two additional electrons to the 2p shell of oxygen and removing the appropriate number of electrons from the outer shells of the metal atom. Results are compared with tabulated experimental values and with two versions of Bragg's additivity rule. Calculated stopping cross sections are applied in testing a recently-proposed scaling rule, which relates the stopping cross section to the number of oxygen atoms per molecule.

75 FR 19878 - Retroactive Stop Loss Special Pay Compensation

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-16

... 0790-AI59] Retroactive Stop Loss Special Pay Compensation AGENCY: Office of the Under Secretary of... Stop Loss Special Pay as authorized and appropriated in The Supplemental Appropriations Act, 2009. This... claims to the Secretaries of the Military Departments for Retroactive Stop Loss Special Pay is October 21...

Visualizing polynucleotide polymerase machines at work

PubMed Central

Steitz, Thomas A

2006-01-01

The structures of T7 RNA polymerase (T7 RNAP) captured in the initiation and elongation phases of transcription, that of φ29 DNA polymerase bound to a primer protein and those of the multisubunit RNAPs bound to initiating factors provide insights into how these proteins can initiate RNA synthesis and synthesize 6–10 nucleotides while remaining bound to the site of initiation. Structural insight into the translocation of the product transcript and the separation of the downstream duplex DNA is provided by the structures of the four states of nucleotide incorporation. Single molecule and biochemical studies show a distribution of primer terminus positions that is altered by the binding of NTP and PPi ligands. This article reviews the insights that imaging the structure of polynucleotide polymerases at different steps of the polymerization reaction has provided on the mechanisms of the polymerization reaction. Movies are shown that allow the direct visualization of the conformational changes that the polymerases undergo during the different steps of polymerization. PMID:16900098

Rapid and Specific Detection of Salmonella spp. in Animal Feed Samples by PCR after Culture Enrichment

PubMed Central

Löfström, Charlotta; Knutsson, Rickard; Axelsson, Charlotta Engdahl; Rådström, Peter

2004-01-01

A PCR procedure has been developed for routine analysis of viable Salmonella spp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymerase Tth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStart Taq, Platinum Taq, Pwo, rTth, Taq, and Tfl. The specificity of the Tth assay was confirmed by testing 101 Salmonella and 43 non-Salmonella strains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification with Tth DNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain. PMID:14711627

Multiple two-polymerase mechanisms in mammalian translesion DNA synthesis.

PubMed

Livneh, Zvi; Ziv, Omer; Shachar, Sigal

2010-02-15

The encounter of replication forks with DNA lesions may lead to fork arrest and/or the formation of single-stranded gaps. A major strategy to cope with these replication irregularities is translesion DNA synthesis (TLS), in which specialized error-prone DNA polymerases bypass the blocking lesions. Recent studies suggest that TLS across a particular DNA lesion may involve as many as four different TLS polymerases, acting in two-polymerase reactions in which insertion by a particular polymerase is followed by extension by another polymerase. Insertion determines the accuracy and mutagenic specificity of the TLS reaction, and is carried out by one of several polymerases such as poleta, polkappa or poliota. In contrast, extension is carried out primarily by polzeta. In cells from XPV patients, which are deficient in TLS across cyclobutane pyrimidine dimers (CPD) due to a deficiency in poleta, TLS is carried out by at least two backup reactions each involving two polymerases: One reaction involves polkappa and polzeta, and the other poliota and polzeta. These mechanisms may also assist poleta in normal cells under an excessive amount of UV lesions.

Lack of association between TaqI A1 Allele of dopamine D2 receptor gene and alcohol-use disorders in Atayal natives of Taiwan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chia-Hsiang Chen; Shih-Hsiang Chien; Hai-Gwo Hwu

1996-09-20

Association studies between the A1 allele of the dopamine D2 receptor (DRD2) gene TaqI A polymorphism and alcoholism remain controversial. A recent study from Japan demonstrated that the A1 allele is associated with severe alcoholism in the Japanese population. We were interested in knowing if this association also exists in the Atayals of Taiwan, who were found to have a higher prevalence of alcohol-use disorders than the Han Chinese in Taiwan. Genotype and allele frequencies were determined in alcohol-abusing, alcohol-dependent, and nonalcoholic control Atayal natives in Taiwan. A1 allele frequencies in alcohol-dependent, alcohol-abusing, and normal control Atayals were 0.39, 0.42,more » and 0.39, respectively. No difference in A1 allele frequency was found among these three groups. Our data do not support the hypothesis that the A1 allele of the TaqI A polymorphism of the DRD2 gene increases susceptibility to alcohol-use disorders in the Atayals of Taiwan. 18 refs., 1 tab.« less

Using the Stop Transmission of Polio (STOP) Program to Develop a South Sudan Expanded Program on Immunization Workforce.

PubMed

Tchoualeu, Dieula D; Hercules, Margaret A; Mbabazi, William B; Kirbak, Anthony L; Usman, Abdulmumini; Bizuneh, Ketema; Sandhu, Hardeep S

2017-07-01

In 2009, the international Stop Transmission of Polio (STOP) program began supporting the Global Polio Eradication Initiative in the Republic of South Sudan to address shortages of human resources and strengthen acute flaccid paralysis surveillance. Workforce capacity support is provided to the South Sudan Expanded Program on Immunization by STOP volunteers, implementing partners, and non-governmental organizations. In 2013, the Polio Technical Advisory Group recommended that South Sudan transition key technical support from external partners to national staff as part of the Polio Eradication and Endgame Strategic Plan, 2013-2018. To assist in this transition, the South Sudan Expanded Program on Immunization human resources development project was launched in 2015. This 3-year project aims to build national workforce capacity as a legacy of the STOP program by training 56 South Sudanese at national and state levels with the intent that participants would become Ministry of Health staff on their successful completion of the project. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Investigation of nuclear stopping observable in heavy ion collisions

NASA Astrophysics Data System (ADS)

Deepshikha; Kumar, Suneel

2018-07-01

Detailed analysis has been made on nuclear stopping using various observable. Transport model, isospin dependent quantum molecular dynamics model (IQMD) has been used to study stopping over the whole mass range at incident energies between 10 MeV/nucleon and 1000 MeV/nucleon. Our study proves that ratio of width of transverse to longitudinal rapidity distribution i.e., < varxz > is the most suitable parameter to study nuclear stopping. Also, it has been observed that light mass fragments (LMF's) emitted from participant region can be used as barometer to study nuclear stopping.

Innovative Municipal Transport Stops for Opole

NASA Astrophysics Data System (ADS)

Kozłowski, Wojciech

2017-10-01

There were presented the conceptual design of innovative municipal transport stops for Opole in Poland. In Opole buses are the most commonly used means of transport. Their popularity is because they use a generally available road infrastructure. Unfortunately, municipal transport is still the weak point of the city. Thus, a project of innovative municipal transport stops for Opole has been conceived which you can learn more about here.

Light Stops at Exceptional Points

NASA Astrophysics Data System (ADS)

Goldzak, Tamar; Mailybaev, Alexei A.; Moiseyev, Nimrod

2018-01-01

Almost twenty years ago, light was slowed down to less than 10-7 of its vacuum speed in a cloud of ultracold atoms of sodium. Upon a sudden turn-off of the coupling laser, a slow light pulse can be imprinted on cold atoms such that it can be read out and converted into a photon again. In this process, the light is stopped by absorbing it and storing its shape within the atomic ensemble. Alternatively, the light can be stopped at the band edge in photonic-crystal waveguides, where the group speed vanishes. Here, we extend the phenomenon of stopped light to the new field of parity-time (P T ) symmetric systems. We show that zero group speed in P T symmetric optical waveguides can be achieved if the system is prepared at an exceptional point, where two optical modes coalesce. This effect can be tuned for optical pulses in a wide range of frequencies and bandwidths, as we demonstrate in a system of coupled waveguides with gain and loss.

46 CFR 58.25-50 - Rudder stops.

Code of Federal Regulations, 2012 CFR

2012-10-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MAIN AND AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-50 Rudder stops. (a) Power-operated steering gear must have arrangements for cutting off power to the gear before the rudder reaches the stops. These arrangements must be...

46 CFR 58.25-50 - Rudder stops.

Code of Federal Regulations, 2013 CFR

2013-10-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MAIN AND AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-50 Rudder stops. (a) Power-operated steering gear must have arrangements for cutting off power to the gear before the rudder reaches the stops. These arrangements must be...

46 CFR 58.25-50 - Rudder stops.

Code of Federal Regulations, 2010 CFR

2010-10-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MAIN AND AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-50 Rudder stops. (a) Power-operated steering gear must have arrangements for cutting off power to the gear before the rudder reaches the stops. These arrangements must be...

46 CFR 58.25-50 - Rudder stops.

Code of Federal Regulations, 2014 CFR

2014-10-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MAIN AND AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-50 Rudder stops. (a) Power-operated steering gear must have arrangements for cutting off power to the gear before the rudder reaches the stops. These arrangements must be...

46 CFR 58.25-50 - Rudder stops.

Code of Federal Regulations, 2011 CFR

2011-10-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING MAIN AND AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-50 Rudder stops. (a) Power-operated steering gear must have arrangements for cutting off power to the gear before the rudder reaches the stops. These arrangements must be...

Higgs and Z assisted stop searches at hadron colliders

NASA Astrophysics Data System (ADS)

Su, Shufang; Zhang, Huanian

2018-05-01

Current searches for the light top squark (stop) mostly focus on the decay channels of \\tilde{t}\\to t{χ}_1^0 or \\tilde{t}\\to b{χ}_1^{±}\\to bW{χ}_1^0 , leading to [InlineMediaObject not available: see fulltext.] final states for stop pair productions at the LHC. However, in supersymmetric scenarios with light neutralinos and charginos other than the neutralino lightest supersymmetric particle (LSP), more than one decay mode of the stop could be dominant. While those new decay modes could significantly weaken the current stop search limits at the LHC, they also offer alternative discovery channels for stop searches. In this paper, we studied the scenario with light Higgsino next-to-LSPs (NLSPs) and Bino LSP. The light stop decays primarily via {\\tilde{t}}_1\\to t{χ}_2^0/{χ}_3^0 , with the neutralinos subsequent decaying to a Z boson or a Higgs boson: χ 2 0 / χ 3 0 → χ 1 0 h/ Z. Pair production of light stops at the LHC leads to final states of [InlineMediaObject not available: see fulltext.] or [InlineMediaObject not available: see fulltext.] . We consider three signal regions: one charged lepton (1 ℓ), two opposite sign charged leptons (2 OS ℓ) and at least three charged leptons (≥3 ℓ). We found that the 1 ℓ signal region of channel [InlineMediaObject not available: see fulltext.] has the best reach sensitivity for light stop searches. For 14 TeV LHC with 300 fb-1 integrated luminosity, a stop mass up to 900 GeV can be discovered at 5 σ significance, or up to 1050 GeV can be excluded at 95% C.L. Combining all three decay channels for 1 ℓ signal region extends the reach for about 100-150 GeV. We also studied the stop reach at the 100 TeV pp collider with 3 ab-1 luminosity, with discovery and exclusion reach being 6 TeV and 7 TeV, respectively.

To Stop or Not to Stop--Kinematics and the Yellow Light.

ERIC Educational Resources Information Center

Watts, J. Fred

1981-01-01

Describes an exercise involving the use of kinematics to decide if one should stop or try and get through an intersection when the traffic light turns yellow. Gives students' experience in recording data, doing simple calculations and connecting classroom studies to real world experiences. (Author/SK)

Nonlinear effects contributing to hand-stopping tones in a horn.

PubMed

Ebihara, Takayasu; Yoshikawa, Shigeru

2013-05-01

Hand stopping is a technique for playing the French horn while closing the bell relatively tightly using the right hand. The resulting timbre is called "penetrating" and "metallic." The effect of hand stopping on the horn input impedance has been studied, but the tone quality has hardly ever been considered. In the present paper, the dominant physical cause of the stopped-tone quality is discussed in detail. Numerical calculations of the transmission function of the stopped-horn model and the measurements of both sound pressure and wall vibration in hand stopping are carried out. They strongly suggest that the metallicness of the stopped tone is characterized by the generation of higher harmonics extending over 10 kHz due to the rapidly corrugating waveform and that the associated wall vibration on the bell may be responsible for this higher harmonic generation. However, excitation experiments and immobilization experiments performed to elucidate the relationship between sound radiation and wall vibration deny their correlation. Instead, the measurement result of the mouthpiece pressure in hand stopping suggests that minute wave corrugations peculiar to the metallic stopped tones are probably formed by nonlinear sound propagation along the bore.

DNA polymerase gamma from Xenopus laevis. I. The identification of a high molecular weight catalytic subunit by a novel DNA polymerase photolabeling procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Insdorf, N.F.; Bogenhagen, D.F.

1989-12-25

DNA polymerase gamma has been purified over 10,000-fold from mitochondria of Xenopus laevis ovaries. We have developed a novel technique which specifically photolabels DNA polymerases. This procedure, the DNA polymerase trap, was used to identify a catalytic subunit of 140,000 Da from X. laevis DNA polymerase gamma. Additional catalytically active polypeptides of 100,000 and 55,000 Da were identified in the highly purified enzyme. These appear to be products of degradation of the 140,000-Da subunit. The DNA polymerase trap, which does not require large amounts of enzyme or renaturation from sodium dodecyl sulfate, is an alternative to the classic activity gel.

Can I Stop Myself From Having a Wet Dream? (For Teens)

MedlinePlus

... Can I Stop Myself From Having a Wet Dream? KidsHealth / For Teens / Can I Stop Myself From Having a Wet Dream? Print Can I stop myself from having a wet dream? – Tom* You really can't stop wet dreams, ...

Development and psychometric properties of the Suicidality: Treatment Occurring in Paediatrics (STOP) Suicidality Assessment Scale (STOP-SAS) in children and adolescents.

PubMed

Flamarique, I; Santosh, P; Zuddas, A; Arango, C; Purper-Ouakil, D; Hoekstra, P J; Coghill, D; Schulze, U; Dittmann, R W; Buitelaar, J K; Lievesley, K; Frongia, R; Llorente, C; Méndez, I; Sala, R; Fiori, F; Castro-Fornieles, J

2016-12-13

To create a self-reported, internet-based questionnaire for the assessment of suicide risk in children and adolescents. As part of the EU project 'Suicidality: Treatment Occurring in Paediatrics' (STOP project), we developed web-based Patient Reported Outcome Measures (PROMs) for children and adolescents and for proxy reports by parents and clinicians in order to assess suicidality. Based on a literature review, expert panels and focus groups of patients, we developed the items of the STOP Suicidality Assessment Scale (STOP-SAS) in Spanish and English, translated it into four more languages, and optimized it for web-based presentation using the HealthTracker TM platform. Of the total 19 questions developed for the STOP-SAS, four questions that assess low-level suicidality were identified as screening questions (three of them for use with children, and all four for use with adolescents, parents and clinicians). A total of 395 adolescents, 110 children, 637 parents and 716 clinicians completed the questionnaire using the HealthTracker TM , allowing us to evaluate the internal consistency and convergent validity of the STOP-SAS with the clinician-rated Columbia Suicide Severity Rating Scale (C-SSRS). Validity was also assessed with the receiver operating characteristic (ROC) area of the STOP-SAS with the C-SSRS. The STOP-SAS comprises 19 items in its adolescent, parent, and clinician versions, and 14 items in its children's version. Good internal consistency was found for adolescents (Cronbach's alpha: 0.965), children (Cronbach's alpha: 0.922), parents (Cronbach's alpha: 0.951) and clinicians (Cronbach's alpha: 0.955) versions. A strong correlation was found between the STOP-SAS and the C-SSRS for adolescents (r:0.670), parents (r:0.548), clinicians (r:0.863) and children (r:0.654). The ROC area was good for clinicians' (0.917), adolescents' (0.834) and parents' (0.756) versions but only fair (0.683) for children's version. The STOP-SAS is a comprehensive, web

Stopped nucleons in configuration space

DOE PAGES

Bialas, Andrzej; Bzdak, Adam; Koch, Volker

2017-05-09

In this note, using the colour string model, we study the configuration space distribution of stopped nucleons in heavy-ion collisions. We find that the stopped nucleons from the target and the projectile end up separated from each other by the distance increasing with the collision energy. In consequence, for the center of mass energies larger than 6 or 10 GeV (depending on the details of the model) it appears that the system created is not in thermal and chemical equilibrium, and the net baryon density reached is likely not much higher than that already present in the colliding nuclei.

Stopping hormone replacement therapy: were women ill advised?

PubMed

Cumming, Grant P; Currie, Heather D; Panay, Nick; Moncur, Rik; Lee, Amanda J

2011-09-01

To survey women who stopped hormone replacement therapy (HRT) after 2002, including those who later restarted. A questionnaire on the UK-based menopause website www.menopausematters.co.uk evaluating how women are influenced by HRT advice. Main outcome measures Answers to questions regarding stopping/restarting HRT in response to the advice in the early 2000s and advice given today. A total of 1100 responses were obtained. Of those who made the decision to stop HRT themselves, 56.4% (n = 425/754) said that they were influenced by the media. In those who would potentially most benefit from HRT, 72.8% (n = 220/302) stopped without medical advice. Overall, women aged under 50 years were significantly more likely to stop HRT themselves than women over 50 (P < 0.001). In women in whom symptoms returned, 37.5% (n = 362/966) said these affected their ability to work, 45.1% (n = 436) had problems with decision-making, 53.6% (n = 518) admitted to relationships being negatively affected and 29.2% (n = 286) said that symptoms affected their social relationships. Overall 46.5% of women (n = 485/1044) would not have stopped HRT given the current understanding of risk. Compared with women over 50, significantly more women under the age of 50 said that they would not have previously stopped their HRT based on their current understanding of risk (P < 0.001). The negative impact of published research and its reporting from the early 2000s are being mitigated by current press coverage. Media reports appear to influence the younger woman more than the older woman. Health professionals and media must learn the lessons from the past.

Stop coannihilation in the CMSSM and SubGUT models

NASA Astrophysics Data System (ADS)

Ellis, John; Evans, Jason L.; Luo, Feng; Olive, Keith A.; Zheng, Jiaming

2018-05-01

Stop coannihilation may bring the relic density of heavy supersymmetric dark matter particles into the range allowed by cosmology. The efficiency of this process is enhanced by stop-antistop annihilations into the longitudinal (Goldstone) modes of the W and Z bosons, as well as by Sommerfeld enhancement of stop annihilations and the effects of bound states. Since the couplings of the stops to the Goldstone modes are proportional to the trilinear soft supersymmetry-breaking A-terms, these annihilations are enhanced when the A-terms are large. However, the Higgs mass may be reduced below the measured value if the A-terms are too large. Unfortunately, the interpretation of this constraint on the stop coannihilation strip is clouded by differences between the available Higgs mass calculators. For our study, we use as our default calculator FeynHiggs 2.13.0, the most recent publicly available version of this code. Exploring the CMSSM parameter space, we find that along the stop coannihilation strip the masses of the stops are severely split by the large A-terms. This suppresses the Higgs mass drastically for μ and A_0 > 0, whilst the extent of the stop coannihilation strip is limited for A_0 < 0 and either sign of μ . However, in sub-GUT models, reduced renormalization-group running mitigates the effect of the large A-terms, allowing larger LSP masses to be consistent with the Higgs mass calculation. We give examples where the dark matter particle mass may reach ≳ 8 TeV.

Evaluation of the Cobas TaqMan MTB Test for the Detection of Mycobacterium tuberculosis Complex According to Acid-Fast-Bacillus Smear Grades in Respiratory Specimens

PubMed Central

Huh, Hee Jae; Koh, Won-Jung; Song, Dong Joon

2014-01-01

We evaluated the performance of the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), stratified by acid-fast bacilli (AFB) smear grades. The sensitivity of this test in smear-positive specimens was >95% in all grades, while that in trace and negative specimens was 85.3% and 34.4%, respectively. PMID:25428157

Measurement of electron angle at MABE beam stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanford, T.W.L.; Coleman, P.D.; Poukey, J.W.

1984-01-01

The mean angle of incidence at the beam stop of a 60 KA, 7 MV annular electron beam, in the 20 kg guide field of the MABE accelerator, is determined. Radiation measured in TLD arrays mounted downstream of the stop is compared with the radiation expected using a CYLTRAN Monte Carlo simulation of the electron/photon transport in the stop as a function of incident angles and energies. All radiation profiles measured are well fit, if the electrons are assumed to be incident with a polar angle theta of 15/sup 0/ +- 2/sup 0/. Comparing theta with that expected from themore » Adler-Miller model, and a MAGIC code simulation of beam behavior at the stop enables the mean transverse beam velocity to be estimated.« less

An outbreak of West Nile Virus infection in the region of Monastir, Tunisia, 2003

PubMed Central

Riabi, Samira; Gaaloul, Imed; Mastouri, Maha; Hassine, Mohsen; Aouni, Mahjoub

2014-01-01

Background A West Nile (WN) fever epidemic occurred in the region of Monastir, Tunisia, between August and October 2003. Aim of the study We attempt to describe the epidemiology, clinical presentation, and outcome of patients with confirmed West Nile virus (WNV) infection. Methods Three groups of specimens were prepared. One was made up of serum only (n  =  43), the other of cerebrospinal fluid (CSF) only (n  =  30), and the third group was made up of both (n  =  40). These specimens were obtained from 113 patients. A serological diagnosis and evidence of WNV genome by nested reverse-transcriptase polymerase chain reaction (nRT-PCR) and TaqMan reverse transcription-polymerase chain reaction (RT-PCR) were carried out. Results Thirty-eight cases (33.6%) were serologically positive. Results of nRT-PCR showed a total of 10 positive cases of WNV (8.8%) detected in group 1 (n  =  1/43), group 2 (n  =  5/30), and group 3 (n  =  4/40) whereas the PCR TaqMan showed 18 positive samples (15.9%) found in group 1 (n  =  3/43), group 2 (n  =  9/30), and group 3 (n  =  6/40). All TaqMan PCR positive cases were nRT-PCR positive. In addition, four serologically probable cases were confirmed by TaqMan PCR. The attempts to isolate WNV by cell culture were unsuccessful. Considering the results of TaqMan assay and the serological diagnosis, WNV infection was confirmed in a total of 42 patients. The main clinical presentations were meningoencephalitis (40%), febrile disease (95%), and meningitis (36%). Eight patients (19%) died. The highest case-fatality rates occurred among patients aged ≧55 years. The phylogenetic analysis revealed that isolates of WNV were closely related to the Tunisian strain 1997 (PAH001) and the Israeli one (Is-98). Conclusions West Nile virus is a reemerging global pathogen that remains an important public health challenge in the next decade. PMID:24766339

75 FR 21505 - Retroactive Stop Loss Special Pay Compensation; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

... 0790-AI59] Retroactive Stop Loss Special Pay Compensation; Correction AGENCY: Office of the Under... Retroactive Stop Loss Special Pay Compensation that was authorized and appropriated in the Supplemental... the Act. The change of eligibility for Retroactive Stop Loss [[Page 21506

Are one-stop shops acceptable? Community perspectives on one-stop shop models of sexual health service provision in the UK.

PubMed

Griffiths, C; Gerressu, M; French, R S

2008-10-01

Traditionally, genitourinary medicine (GUM) and contraceptive services have been provided separately. Providing these services on one site, as a one-stop shop, has been suggested as a way of improving access to care. There is little evidence about the acceptability of such an approach. We aimed to assess acceptability of different one-stop shop models (a young people's, an all ages (mainstream) and a general practice service) of sexual health provision among different community groups. Between April and December 2005, 19 semi-structured interviews and 14 focus groups were conducted with young heterosexual men (n = 48), men who have sex with men (MSM; n = 46) and minority ethnic men and women (n = 28) across England. Knowledge of one-stop shops was limited. The concept was acceptable to participants (except MSM), although there was variation as to the preferred model. Young men and African individuals described distrust of general practice confidentiality, preferring young people's or mainstream models, respectively. South Asians associated stigma with GUM, preferring instead a general practice one-stop shop. Regardless of model, respondents expressed preference for one provider/one session to provide GUM and contraceptive care. In terms of acceptability there can be no blue print one-stop shop model. Local assessments should determine whether a one-stop shop would have public health benefit and if so how best one should be set up to maximise access. To accommodate client preference for one provider/session for their sexual health needs it may be that the development of "integrated training" for providers across clinical specialties is a more realistic way forward.

Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples.

PubMed

Wood, Susanna A; Zaiko, Anastasija; Richter, Ingrid; Inglis, Graeme J; Pochon, Xavier

2017-07-01

The Mediterranean fanworm, Sabella spallanzanii Gmelin 1791, was first detected in the Southern Hemisphere in the 1990s and is now abundant in many parts of southern Australia and in several locations around northern New Zealand. Once established, it can proliferate rapidly, reaching high densities with potential ecological and economic impacts. Early detection of new S. spallanzanii incursions is important to prevent its spread, guide eradication or control efforts and to increase knowledge on the species' dispersal pathways. In this study, we developed a TaqMan probe real-time polymerase chain reaction assay targeting a region of the mitochondrial cytochrome oxidase I gene. The assay was validated in silico and in vitro using DNA from New Zealand and Australian Sabellidae with no cross-reactivity detected. The assay has a linear range of detection over seven orders of magnitude with a limit of detection reached at 12.4 × 10 -4  ng/μL of DNA. We analysed 145 environmental (water, sediment and biofouling) samples and obtained positive detections only from spiked samples and those collected at a port where S. spallanzanii is known to be established. This assay has the potential to enhance current morphological and molecular-based methods, through its ability to rapidly and accurately identify S. spallanzanii in environmental samples.

Modeling level-of-safety for bus stops in China.

PubMed

Ye, Zhirui; Wang, Chao; Yu, Yongbo; Shi, Xiaomeng; Wang, Wei

2016-08-17

Safety performance at bus stops is generally evaluated by using historical traffic crash data or traffic conflict data. However, in China, it is quite difficult to obtain such data mainly due to the lack of traffic data management and organizational issues. In light of this, the primary objective of this study is to develop a quantitative approach to evaluate bus stop safety performance. The concept of level-of-safety for bus stops is introduced and corresponding models are proposed to quantify safety levels, which consider conflict points, traffic factors, geometric characteristics, traffic signs and markings, pavement conditions, and lighting conditions. Principal component analysis and k-means clustering methods were used to model and quantify safety levels for bus stops. A case study was conducted to show the applicability of the proposed model with data collected from 46 samples for the 7 most common types of bus stops in China, using 32 of the samples for modeling and 14 samples for illustration. Based on the case study, 6 levels of safety for bus stops were defined. Finally, a linear regression analysis between safety levels and the number of traffic conflicts showed that they had a strong relationship (R(2) value of 0.908). The results indicated that the method was well validated and could be practically used for the analysis and evaluation of bus stop safety in China. The proposed model was relatively easy to implement without the requirement of traffic crash data and/or traffic conflict data. In addition, with the proposed method, it was feasible to evaluate countermeasures to improve bus stop safety (e.g., exclusive bus lanes).

DNA polymerase having modified nucleotide binding site for DNA sequencing

DOEpatents

Tabor, Stanley; Richardson, Charles

1997-01-01

Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.

PubMed

Chan, Yi-Wah; Mohr, Remus; Millard, Andrew D; Holmes, Antony B; Larkum, Anthony W; Whitworth, Anna L; Mann, Nicholas H; Scanlan, David J; Hess, Wolfgang R; Clokie, Martha R J

2011-08-01

DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.

Stop identity cue as a cue to language identity

NASA Astrophysics Data System (ADS)

Castonguay, Paula Lisa

The purpose of the present study was to determine whether language membership could potentially be cued by the acoustic-phonetic detail of word-initial stops and retained all the way through the process of lexical access to aid in language identification. Of particular interest were language-specific differences in CE and CF word-initial stops. Experiment 1 consisted of an interlingual homophone production task. The purpose of this study was to examine how word-initial stop consonants differ in terms of acoustic properties in Canadian English (CE) and Canadian French (CF) interlingual homophones. The analyses from the bilingual speakers in Experiment 1 indicate that bilinguals do produce language-specific differences in CE and CF word-initial stops, and that closure duration, voice onset time, and burst spectral SD may provide cues to language identity in CE and CF stops. Experiment 2 consisted of a Phoneme and Language Categorization task. The purpose of this study was to examine how stop identity cues, such as VOT and closure duration, influence a listener to identify word-initial stop consonants as belonging to Canadian English (CE) or Canadian French (CF). The RTs from the bilingual listeners in this study indicate that bilinguals do perceive language-specific differences in CE and CF word-initial stops, and that voice onset time may provide cues to phoneme and language membership in CE and CF stops. Experiment 3 consisted of a Phonological-Semantic priming task. The purpose of this study was to examine how subphonetic variations, such as changes in the VOT, affect lexical access. The results of Experiment 3 suggest that language-specific cues, such as VOT, affects the composition of the bilingual cohort and that the extent to which English and/or French words are activated is dependent on the language-specific cues present in a word. The findings of this study enhanced our theoretical understanding of lexical structure and lexical access in bilingual speakers

Detection of hepatitis C virus RNA using ligation-dependent polymerase chain reaction in formalin-fixed, paraffin-embedded liver tissues.

PubMed Central

Park, Y. N.; Abe, K.; Li, H.; Hsuih, T.; Thung, S. N.; Zhang, D. Y.

1996-01-01

Reverse transcription polymerase chain reaction (RT-PCR) has been used to detect hepatitis C virus (HCV) sequences in liver tissue. However, RT-PCR has a variable detection sensitivity, especially on routinely processed formalin-fixed, paraffin-embedded (FFPE) specimens. RNA-RNA and RNA-protein cross-links formed during formalin fixation is the major limiting factor preventing reverse trans criptase from extending the primers. To overcome this problem, we applied the ligation-dependent PCR (LD-PCR) for the detection of HCV RNA in FFPE liver tissue. This method uses two capture probes for RNA isolation and two hemiprobes for the subsequent PCR. Despite cross-links, the capture probes and the hemiprobes are able to form hybrids with HCV RNAs released from the FFPE tissue. The hybrids are isolated through binding of the capture probes to paramagnetic beads. The hemiprobes are then ligated by a T4 DNA ligase to form a full probe that serves as a template for the Taq DNA polymerase. A total of 22 FFPE liver specimens, 21 with hepatocellular carcinoma (HCC) and 1 with biliary cirrhosis secondary to bile duct atresia were selected for this study, of which 13 patients were HCV seropositive and 9 seronegative. HCV RNA was detectable by ID-PCR from all 13 HCV-seropositive HCCs and from 5 of 8 HCV-seronegative HCCs but not from the HCV-seronegative liver with biliary atresia. By contrast, RT-PCR detected HCV sequences in only 5 of the HCV-sero-positive and in 1 of the HCV-seronegative HCCs. To resolve the discordance between the LD-PCR and RT-PCR results, RT-PCR was performed on frozen liver tissue of the discrepant specimens, which confirmed the LD-PCR positive results. In conclusion, LD-PCR is a more sensitive method than RT-PCR for the detection of HCV sequences in routinely processed liver tissues. A high rate of HCV infection (86%) is found in HCC specimens, indicating a previously underestimated role of HCV in HCC pathogenesis. Images Figure 2 PMID:8909238

D2 Dopamine receptor Taq1A polymorphism, body weight, and dietary intake in type 2 diabetes

PubMed Central

Barnard, Neal D.; Noble, Ernest P.; Ritchie, Terry; Cohen, Joshua; Jenkins, David J.A.; Turner-McGrievy, Gabrielle; Gloede, Lise; Ferdowsian, Hope

2008-01-01

OBJECTIVE Certain D2 dopamine receptor Taq 1A genotypes (A1A1, A1A2) have been associated with obesity and substance abuse. We hypothesized that their presence would be associated with reduced efficacy of dietary interventions in individuals with type 2 diabetes. RESEARCH METHODS & PROCEDURES In the course of a randomized clinical trial in an outpatient research center in which 93 adults with type 2 diabetes were assigned to a low-fat vegan diet or a diet following 2003 American Diabetes Association guidelines for 74 weeks, Taq 1A genotype was determined. Nutrient intake, body weight, and hemoglobin A1c (A1c) were measured over 74 weeks. RESULTS The A1 allele was highly prevalent, occurring in 47% of white participants (n = 49), which was significantly higher than the 29% prevalence previously reported in nondiabetic whites (P=0.01). The A1 allele was found in 55% of black participants (n = 44). Black participants with A1+ genotypes had significantly greater mean body weight (11.2 kg heavier, P=0.05), and greater intake of fat (P=0.002), saturated fat (P=0.01) and cholesterol (P=0.02), compared with A2A2 (A1-) individuals; dietary changes during the study did not favor one genotype group. Among whites, baseline anthropometric and nutrient differences between gene groups were small. However, among whites in the vegan group, A1+ individuals reduced fat intake (P=0.04) and A1c (P=0.01) significantly less than did A1- individuals. CONCLUSIONS The A1 allele appears to be highly prevalent among individuals with type 2 diabetes. Potential influences on diet, weight, and glycemic control merit further exploration. PMID:18834717

Electron and Positron Stopping Powers of Materials

National Institute of Standards and Technology Data Gateway

SRD 7 NIST Electron and Positron Stopping Powers of Materials (PC database for purchase)   The EPSTAR database provides rapid calculations of stopping powers (collisional, radiative, and total), CSDA ranges, radiation yields and density effect corrections for incident electrons or positrons with kinetic energies from 1 keV to 10 GeV, and for any chemically defined target material.

The stopping rules for winsorized tree

NASA Astrophysics Data System (ADS)

Ch'ng, Chee Keong; Mahat, Nor Idayu

2017-11-01

Winsorized tree is a modified tree-based classifier that is able to investigate and to handle all outliers in all nodes along the process of constructing the tree. It overcomes the tedious process of constructing a classical tree where the splitting of branches and pruning go concurrently so that the constructed tree would not grow bushy. This mechanism is controlled by the proposed algorithm. In winsorized tree, data are screened for identifying outlier. If outlier is detected, the value is neutralized using winsorize approach. Both outlier identification and value neutralization are executed recursively in every node until predetermined stopping criterion is met. The aim of this paper is to search for significant stopping criterion to stop the tree from further splitting before overfitting. The result obtained from the conducted experiment on pima indian dataset proved that the node could produce the final successor nodes (leaves) when it has achieved the range of 70% in information gain.

Epoxy bond and stop etch fabrication method

DOEpatents

Simmons, Jerry A.; Weckwerth, Mark V.; Baca, Wes E.

2000-01-01

A class of epoxy bond and stop etch (EBASE) microelectronic fabrication techniques is disclosed. The essence of such techniques is to grow circuit components on top of a stop etch layer grown on a first substrate. The first substrate and a host substrate are then bonded together so that the circuit components are attached to the host substrate by the bonding agent. The first substrate is then removed, e.g., by a chemical or physical etching process to which the stop etch layer is resistant. EBASE fabrication methods allow access to regions of a device structure which are usually blocked by the presence of a substrate, and are of particular utility in the fabrication of ultrafast electronic and optoelectronic devices and circuits.

DNA polymerase having modified nucleotide binding site for DNA sequencing

DOEpatents

Tabor, S.; Richardson, C.

1997-03-25

A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

The Lower Extremity Biomechanics of Single- and Double-Leg Stop-Jump Tasks

PubMed Central

2011-01-01

The anterior cruciate ligament (ACL) injury is a common occurrence in sports requiring stop-jump tasks. Single- and double-leg stop-jump techniques are frequently executed in sports. The higher risk of ACL injury in single-leg drop landing task compared to a double-leg drop landing task has been identified. However the injury bias between single- and double-leg landing techniques has not been investigated for stop-jump tasks. The purpose of this study was to determine the differences between single- and double-leg stop-jump tasks in knee kinetics that were influenced by the lower extremity kinematics during the landing phase. Ground reaction force, lower extremity kinematics, and knee kinetics data during the landing phase were obtained from 10 subjects performing single- and double-leg stop-jump tasks, using motion-capture system and force palates. Greater peak posterior and vertical ground reaction forces, and peak proximal tibia anterior and lateral shear forces (p < 0.05) during landing phase were observed of single-leg stop-jump. Single-leg stop-jump exhibited smaller hip and knee flexion angle, and knee flexion angular velocity at initial foot contact with the ground (p < 0.05). We found smaller peak hip and knee flexion angles (p < 0.05) during the landing phase of single-leg stop-jump. These results indicate that single-leg landing may have higher ACL injury risk than double-leg landing in stop-jump tasks that may be influenced by the lower extremity kinematics during the landing phase. Key points Non-contact ACL injuries are more likely to occur during the single-leg stop-jump task than during the double-leg stop-jump task. Single-leg stop-jump exhibited greater peak proximal tibia anterior and lateral shear forces, and peak posterior and vertical ground reaction forces during the landing phase than the double-leg stop-jump task. Single-leg stop-jump exhibited smaller hip flexion angle, knee flexion angle, and knee flexion angular velocity at initial foot

Acoustic characteristics of Punjabi retroflex and dental stops.

PubMed

Hussain, Qandeel; Proctor, Michael; Harvey, Mark; Demuth, Katherine

2017-06-01

The phonological category "retroflex" is found in many Indo-Aryan languages; however, it has not been clearly established which acoustic characteristics reliably differentiate retroflexes from other coronals. This study investigates the acoustic phonetic properties of Punjabi retroflex /ʈ/ and dental /ʈ̪/ in word-medial and word-initial contexts across /i e a o u/, and in word-final context across /i a u/. Formant transitions, closure and release durations, and spectral moments of release bursts are compared in 2280 stop tokens produced by 30 speakers. Although burst spectral measures and formant transitions do not consistently differentiate retroflexes from dentals in some vowel contexts, stop release duration, and total stop duration reliably differentiate Punjabi retroflex and dental stops across all word contexts and vocalic environments. These results suggest that Punjabi coronal place contrasts are signaled by the complex interaction of temporal and spectral cues.

Stopping mechanism for capsule endoscope using electrical stimulus.

PubMed

Woo, Sang Hyo; Kim, Tae Wan; Cho, Jin Ho

2010-01-01

An ingestible capsule, which has the ability to stop at certain locations in the small intestine, was designed and implemented to monitor intestinal diseases. The proposed capsule can contract the small intestine by using electrical stimuli; this contraction causes the capsule to stop when the maximum static frictional force (MSFF) is larger than the force of natural peristalsis. In vitro experiments were carried out to verify the feasibility of the capsule, and the results showed that the capsule was successfully stopped in the small intestine. Various electrodes and electrical stimulus parameters were determined on the basis of the MSFF. A moderate increment of the MSFF (12.7 +/- 4.6 gf at 5 V, 10 Hz, and 5 ms) and the maximum increment of the MSFF (56.5 +/- 9.77 gf at 20 V, 10 Hz, and 5 ms) were obtained, and it is sufficient force to stop the capsule.

One-stop endoscopic hernia surgery: efficient and satisfactory.

PubMed

Voorbrood, C E H; Burgmans, J P J; Clevers, G J; Davids, P H P; Verleisdonk, E J M M; Schouten, N; van Dalen, T

2015-06-01

One-stop surgery offers patients diagnostic work-up and subsequent surgical treatment on the same day. In the present study, patient satisfaction and efficiency from an institutional perspective were evaluated in patients who were referred for one-stop endoscopic inguinal hernia repair. In a high-volume inguinal hernia clinic, all consecutive patients referred for one-stop surgical treatment, were registered prospectively. An instructed secretary screened patients for eligibility for the one-stop option when the appointment was made. Totally extraperitoneal hernia repair under general anaesthesia was the preferred operative technique. Patient's satisfaction, successful day surgery and institutional efficiency were evaluated. Between January 2010 and January 2012 a total of 349 patients (17 % of all patients in the hernia clinic) were referred for one-stop hernia repair. Mean age was 47.5 years and 96.3 % were males. Three hundred thirty-six patients underwent hernia surgery on the same day (96.3 %). In thirteen patients (3.7 %) no operative repair was done on the day of presentation due to an incorrect diagnosis (n = 7), a watchful waiting policy for asymptomatic hernia (n = 3), rescheduling due to a large scrotal hernia, and there were two "no shows". Following hernia repair 97 % of the patients were discharged on the same day, while ten patients required hospitalization. Based on the questionnaires the main satisfaction score among patients was 9.0 (8.89-9.17 95 % CI) on a scale ranging from 0 to 10. One-stop hernia surgery is feasible and satisfactory from an institutional as well as from a patient's perspective.

Stopping decisions: information order effects on nonfocal evaluations.

PubMed

Yu, Michael; Gonzalez, Cleotilde

2013-08-01

We investigated how the order in which information is presented affects when a person decides to stop performing a task. A stopping decision is a decision to stop performing a task on the basis of a sequence of cues. Previous order-effects models do not account for how these contexts limit available working memory for making such decisions. Participants decided how long to perform a task known as the Work Hazard Game that began by rewarding points but later cost points if work continued after an unannounced "emergency." An additive sequence of cues indicated the probability of an emergency. Study I involved a three-group design with cue sequences that indicated the same risk at each decision point but whose final cue presented a high, medium, or low probability. Study 2 had a 2 x 2 design with high or low final cues and an easy or a challenging task. In Study I, participants stopped sooner when the most recent cue presented a high rather than low probability (p = .09), despite the same emergency risk. In Study 2, participants stopped sooner when the most recent cue presented a high rather than low probability for the challenging task but not for the easy task (p = .08). Stopping decisions appear sensitive to the most recent cue observed while experiencing task load. Participants responded to the same risks differently only on the basis of a change in presentation. Findings may be relevant for research and training for hazardous jobs, such as subsurface coal mining, fishing, and trucking.

Multicentre study of Y chromosome microdeletions in 1,808 Chinese infertile males using multiplex and real-time polymerase chain reaction.

PubMed

Zhu, X-B; Gong, Y-H; He, J; Guo, A-L; Zhi, E-L; Yao, J-E; Zhu, B-S; Zhang, A-J; Li, Z

2017-06-01

Azoospermia factor (AZF) genes on the long arm of the human Y chromosome are involved in spermatogenesis, and microdeletions in the AZF region have been recognised to be the second major genetic cause of spermatogenetic failure resulting in male infertility. While screening for these microdeletions can avoid unnecessary medical and surgical treatments, current methods are generally time-consuming. Therefore, we established a new method to detect and analyse microdeletions in the AZF region quickly, safely and efficiently. In total, 1,808 patients with spermatogenetic failure were recruited from three hospitals in southern China, of which 600 patients were randomly selected for screening for Y chromosome microdeletions in AZF regions employing real-time polymerase chain reaction with a TaqMan probe. In our study, of 1,808 infertile patients, 150 (8.3%) were found to bear microdeletions in the Y chromosome using multiplex PCR, while no deletions were found in the controls. Among the AZF deletions detected, two were in AZFa, three in AZFb, 35 in AZFc, three in AZFb+c and two in AZFa+b+c. Our method is fast-it permits the scanning of DNA from a patient in one and a half hours-and reliable, minimising the risk of cross-contamination and false-positive and false-negative results. © 2016 Blackwell Verlag GmbH.

Rapid detection of Enterovirus and Coxsackievirus A10 by a TaqMan based duplex one-step real time RT-PCR assay.

PubMed

Chen, Jingfang; Zhang, Rusheng; Ou, Xinhua; Yao, Dong; Huang, Zheng; Li, Linzhi; Sun, Biancheng

2017-06-01

A TaqMan based duplex one-step real time RT-PCR (rRT-PCR) assay was developed for the rapid detection of Coxsackievirus A10 (CV-A10) and other enterovirus (EVs) in clinical samples. The assay was fully evaluated and found to be specific and sensitive. When applied in 115 clinical samples, a 100% diagnostic sensitivity in CV-A10 detection and 97.4% diagnostic sensitivity in other EVs were found. Copyright © 2017 Elsevier Ltd. All rights reserved.

Human DNA polymerase η accommodates RNA for strand extension.

PubMed

Su, Yan; Egli, Martin; Guengerich, F Peter

2017-11-03

Ribonucleotides are the natural analogs of deoxyribonucleotides, which can be misinserted by DNA polymerases, leading to the most abundant DNA lesions in genomes. During replication, DNA polymerases tolerate patches of ribonucleotides on the parental strands to different extents. The majority of human DNA polymerases have been reported to misinsert ribonucleotides into genomes. However, only PrimPol, DNA polymerase α, telomerase, and the mitochondrial human DNA polymerase (hpol) γ have been shown to tolerate an entire RNA strand. Y-family hpol η is known for translesion synthesis opposite the UV-induced DNA lesion cyclobutane pyrimidine dimer and was recently found to incorporate ribonucleotides into DNA. Here, we report that hpol η is able to bind DNA/DNA, RNA/DNA, and DNA/RNA duplexes with similar affinities. In addition, hpol η, as well as another Y-family DNA polymerase, hpol κ, accommodates RNA as one of the two strands during primer extension, mainly by inserting dNMPs opposite unmodified templates or DNA lesions, such as 8-oxo-2'-deoxyguanosine or cyclobutane pyrimidine dimer, even in the presence of an equal amount of the DNA/DNA substrate. The discovery of this RNA-accommodating ability of hpol η redefines the traditional concept of human DNA polymerases and indicates potential new functions of hpol η in vivo . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Balancing Cognitive Demands: Control Adjustments in the Stop-Signal Paradigm

ERIC Educational Resources Information Center

Bissett, Patrick G.; Logan, Gordon D.

2011-01-01

Cognitive control enables flexible interaction with a dynamic environment. In 2 experiments, the authors investigated control adjustments in the stop-signal paradigm, a procedure that requires balancing speed (going) and caution (stopping) in a dual-task environment. Focusing on the slowing of go reaction times after stop signals, the authors…

Stop/Start: Overview

Science.gov Websites

/Start technology conserves energy by shutting off the gasoline engine when the vehicle is at rest, such as at a traffic light, and automatically re-starting it when the driver pushes the gas pedal to go engine when pulling out from a stop and generating electricity which is stored in the battery. Main stage

CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations.

PubMed

Kuscu, Cem; Parlak, Mahmut; Tufan, Turan; Yang, Jiekun; Szlachta, Karol; Wei, Xiaolong; Mammadov, Rashad; Adli, Mazhar

2017-07-01

CRISPR-Cas9-induced DNA damage may have deleterious effects at high-copy-number genomic regions. Here, we use CRISPR base editors to knock out genes by changing single nucleotides to create stop codons. We show that the CRISPR-STOP method is an efficient and less deleterious alternative to wild-type Cas9 for gene-knockout studies. Early stop codons can be introduced in ∼17,000 human genes. CRISPR-STOP-mediated targeted screening demonstrates comparable efficiency to WT Cas9, which indicates the suitability of our approach for genome-wide functional screenings.

Messenger RNA transcripts

Treesearch

Dan Cullen

2004-01-01

In contrast to DNA, messenger RNA (mRNA) in complex substrata is rarely analyzed, in large part because labile RNA molecules are difficult to purify. Nucleic acid extractions from fungi that colonize soil are particularly difficult and plagued by humic substances that interfere with Taq polymerase (Tebbe and Vahjen 1993 and references therein). Magnetic capture...

Post-Stop-Signal Slowing: Strategies Dominate Reflexes and Implicit Learning

ERIC Educational Resources Information Center

Bissett, Patrick G.; Logan, Gordon D.

2012-01-01

Control adjustments are necessary to balance competing cognitive demands. One task that is well-suited to explore control adjustments is the stop-signal paradigm, in which subjects must balance initiation and inhibition. One common adjustment in the stop-signal paradigm is post-stop-signal slowing. Existing models of sequential adjustments in the…

Seismic stops for nuclear power plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cloud, R.L.; Leung, J.S.M.; Anderson, P.H.

1989-10-01

In the regulated world of nuclear power, the need to have analytical proof of performance in hypothetical design-basis events such as earth quakes has placed a premium on design configurations that are mathematically tractable and easily analyzed. This is particularly true for the piping design. Depending on how the piping analyses are organized and on how old the plant is, there may be from 200 to 1000 separate piping runs to be designed, analyzed, and qualified. In this situation, the development of snubbers seemed like the answer to a piping engineer's prayer. At any place where seismic support was requiredmore » but thermal motion had to be accommodated, a snubber could be specified. But, as experience has now shown, the program was solved only on paper. This article presents an alternative to conventional snubbers. These new devices, termed Seismic Stops are designed to replace snubbers directly and look like snubbers on the outside. But their design is based on a completely different principle. The original concept has adapted from early seismic-resistant pipe support designs used on fossil power plants in California. The fundamental idea is to provide a space envelope in which the pipe can expand freely between the hot and cold positions, but cannot move outside the envelope. Seismic Stops are designed to transmit any possible impact load, as would occur in an earthquake, away from the pipe itself to the Seismic Stop. The Seismic Stop pipe support is shown.« less

Investigation of Influenza Virus Polymerase Activity in Pig Cells

PubMed Central

Moncorgé, Olivier; Long, Jason S.; Cauldwell, Anna V.; Zhou, Hongbo; Lycett, Samantha J.

2013-01-01

Reassortant influenza viruses with combinations of avian, human, and/or swine genomic segments have been detected frequently in pigs. As a consequence, pigs have been accused of being a “mixing vessel” for influenza viruses. This implies that pig cells support transcription and replication of avian influenza viruses, in contrast to human cells, in which most avian influenza virus polymerases display limited activity. Although influenza virus polymerase activity has been studied in human and avian cells for many years by use of a minigenome assay, similar investigations in pig cells have not been reported. We developed the first minigenome assay for pig cells and compared the activities of polymerases of avian or human influenza virus origin in pig, human, and avian cells. We also investigated in pig cells the consequences of some known mammalian host range determinants that enhance influenza virus polymerase activity in human cells, such as PB2 mutations E627K, D701N, G590S/Q591R, and T271A. The two typical avian influenza virus polymerases used in this study were poorly active in pig cells, similar to what is seen in human cells, and mutations that adapt the avian influenza virus polymerase for human cells also increased activity in pig cells. In contrast, a different pattern was observed in avian cells. Finally, highly pathogenic avian influenza virus H5N1 polymerase activity was tested because this subtype has been reported to replicate only poorly in pigs. H5N1 polymerase was active in swine cells, suggesting that other barriers restrict these viruses from becoming endemic in pigs. PMID:23077313

Development and in-house validation of the event-specific polymerase chain reaction detection methods for genetically modified soybean MON89788 based on the cloned integration flanking sequence.

PubMed

Liu, Jia; Guo, Jinchao; Zhang, Haibo; Li, Ning; Yang, Litao; Zhang, Dabing

2009-11-25

Various polymerase chain reaction (PCR) methods were developed for the execution of genetically modified organism (GMO) labeling policies, of which an event-specific PCR detection method based on the flanking sequence of exogenous integration is the primary trend in GMO detection due to its high specificity. In this study, the 5' and 3' flanking sequences of the exogenous integration of MON89788 soybean were revealed by thermal asymmetric interlaced PCR. The event-specific PCR primers and TaqMan probe were designed based upon the revealed 5' flanking sequence, and the qualitative and quantitative PCR assays were established employing these designed primers and probes. In qualitative PCR, the limit of detection (LOD) was about 0.01 ng of genomic DNA corresponding to 10 copies of haploid soybean genomic DNA. In the quantitative PCR assay, the LOD was as low as two haploid genome copies, and the limit of quantification was five haploid genome copies. Furthermore, the developed PCR methods were in-house validated by five researchers, and the validated results indicated that the developed event-specific PCR methods can be used for identification and quantification of MON89788 soybean and its derivates.

StopApp: Using the Behaviour Change Wheel to Develop an App to Increase Uptake and Attendance at NHS Stop Smoking Services.

PubMed

Fulton, Emily Anne; Brown, Katherine E; Kwah, Kayleigh L; Wild, Sue

2016-06-08

Smokers who attend NHS Stop Smoking Services (SSS) are four times more likely to stop smoking; however, uptake has been in decline. We report the development of an intervention designed to increase uptake of SSS, from a more motivated self-selected sample of smokers. In Phase 1 we collected data to explore the barriers and facilitators to people using SSS. In Phase 2, data from extant literature and Phase 1 were subject to behavioural analysis, as outlined by the Behaviour Change Wheel (BCW) framework. Relevant Behaviour Change Techniques (BCTs) were identified in order to address these, informing the content of the StopApp intervention. In Phase 3 we assessed the acceptability of the StopApp. Smokers and ex-smokers identified a number of barriers to attending SSS, including a lack of knowledge about what happens at SSS (Capability); the belief that SSS is not easy to access (Opportunity); that there would be 'scare tactics' or 'nagging'; and not knowing anyone who had been and successfully quit (Motivation). The 'StopApp' is in development and will link in with the commissioned SSS booking system. Examples of the content and functionality of the app are outlined. The next phase will involve a full trial to test effectiveness.

Velocity dependence of heavy-ion stopping below the maximum

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2015-01-01

In the slowing-down of heavy ions in materials, the standard description by Lindhard and Scharff assumes the electronic stopping cross section to be proportional to the projectile speed v up to close to a stopping maximum, which is related to the Thomas-Fermi speed vTF . It is well known that strict proportionality with v is rarely observed, but little is known about the systematics of observed deviations. In this study we try to identify factors that determine positive or negative curvature of stopping cross sections on the basis of experimental data and of binary stopping theory. We estimate the influence of shell structure of the target and of the equilibrium charge of the ion and comment the role of dynamic screening.

Proactive Adjustments of Response Strategies in the Stop-Signal Paradigm

ERIC Educational Resources Information Center

Verbruggen, Frederick; Logan, Gordon D.

2009-01-01

In the stop-signal paradigm, fast responses are harder to inhibit than slow responses, so subjects must balance speed is the go task with successful stopping in the stop task. In theory, subjects achieve this balance by adjusting response thresholds for the go task, making proactive adjustments in response to instructions that indicate that…

49 CFR 392.22 - Emergency signals; stopped commercial motor vehicles.

Code of Federal Regulations, 2011 CFR

2011-10-01

... is stopped upon the traveled portion of a highway or the shoulder of a highway for any cause other... commercial motor vehicle is stopped upon the traveled portion or the shoulder of a highway for any cause... 100 feet) from the stopped commercial motor vehicle in the center of the traffic lane or shoulder...

49 CFR 392.22 - Emergency signals; stopped commercial motor vehicles.

Code of Federal Regulations, 2014 CFR

2014-10-01

... is stopped upon the traveled portion of a highway or the shoulder of a highway for any cause other... commercial motor vehicle is stopped upon the traveled portion or the shoulder of a highway for any cause... 100 feet) from the stopped commercial motor vehicle in the center of the traffic lane or shoulder...

49 CFR 392.22 - Emergency signals; stopped commercial motor vehicles.

Code of Federal Regulations, 2013 CFR

2013-10-01

... is stopped upon the traveled portion of a highway or the shoulder of a highway for any cause other... commercial motor vehicle is stopped upon the traveled portion or the shoulder of a highway for any cause... 100 feet) from the stopped commercial motor vehicle in the center of the traffic lane or shoulder...

49 CFR 392.22 - Emergency signals; stopped commercial motor vehicles.

Code of Federal Regulations, 2012 CFR

2012-10-01

... is stopped upon the traveled portion of a highway or the shoulder of a highway for any cause other... commercial motor vehicle is stopped upon the traveled portion or the shoulder of a highway for any cause... 100 feet) from the stopped commercial motor vehicle in the center of the traffic lane or shoulder...

49 CFR 392.22 - Emergency signals; stopped commercial motor vehicles.

Code of Federal Regulations, 2010 CFR

2010-10-01

... is stopped upon the traveled portion of a highway or the shoulder of a highway for any cause other... commercial motor vehicle is stopped upon the traveled portion or the shoulder of a highway for any cause... 100 feet) from the stopped commercial motor vehicle in the center of the traffic lane or shoulder...

Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection.

PubMed

Hernández, Marta; Rodríguez-Lázaro, David; Esteve, Teresa; Prat, Salomé; Pla, Maria

2003-12-15

Commercialization of several genetically modified crops has been approved worldwide to date. Uniplex polymerase chain reaction (PCR)-based methods to identify these different insertion events have been developed, but their use in the analysis of all commercially available genetically modified organisms (GMOs) is becoming progressively insufficient. These methods require a large number of assays to detect all possible GMOs present in the sample and thereby the development of multiplex PCR systems using combined probes and primers targeted to sequences specific to various GMOs is needed for detection of this increasing number of GMOs. Here we report on the development of a multiplex real-time PCR suitable for multiple GMO identification, based on the intercalating dye SYBR Green I and the analysis of the melting curves of the amplified products. Using this method, different amplification products specific for Maximizer 176, Bt11, MON810, and GA21 maize and for GTS 40-3-2 soybean were obtained and identified by their specific Tm. We have combined amplification of these products in a number of multiplex reactions and show the suitability of the methods for identification of GMOs with a sensitivity of 0.1% in duplex reactions. The described methods offer an economic and simple alternative to real-time PCR systems based on sequence-specific probes (i.e., TaqMan chemistry). These methods can be used as selection tests and further optimized for uniplex GMO quantification.

49 CFR 236.826 - System, automatic train stop.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false System, automatic train stop. 236.826 Section 236..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.826 System, automatic train stop. A system so arranged that its operation will automatically...

49 CFR 236.826 - System, automatic train stop.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false System, automatic train stop. 236.826 Section 236..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.826 System, automatic train stop. A system so arranged that its operation will automatically...

46 CFR 111.103-7 - Ventilation stop stations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Case of Fire Break Glass and Operate Switch to Stop Ventilation;” (c) Have the “stop” position of the switch clearly identified; (d) Have a nameplate that identifies the system controlled; and (e) Be arranged so that damage to the switch or cable automatically stops the equipment controlled. ...

46 CFR 111.103-7 - Ventilation stop stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Case of Fire Break Glass and Operate Switch to Stop Ventilation;” (c) Have the “stop” position of the switch clearly identified; (d) Have a nameplate that identifies the system controlled; and (e) Be arranged so that damage to the switch or cable automatically stops the equipment controlled. ...

46 CFR 111.103-7 - Ventilation stop stations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Case of Fire Break Glass and Operate Switch to Stop Ventilation;” (c) Have the “stop” position of the switch clearly identified; (d) Have a nameplate that identifies the system controlled; and (e) Be arranged so that damage to the switch or cable automatically stops the equipment controlled. ...

46 CFR 111.103-7 - Ventilation stop stations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Case of Fire Break Glass and Operate Switch to Stop Ventilation;” (c) Have the “stop” position of the switch clearly identified; (d) Have a nameplate that identifies the system controlled; and (e) Be arranged so that damage to the switch or cable automatically stops the equipment controlled. ...

Evaluation of the Cobas TaqMan MTB test for the detection of Mycobacterium tuberculosis complex according to acid-fast-bacillus smear grades in respiratory specimens.

PubMed

Huh, Hee Jae; Koh, Won-Jung; Song, Dong Joon; Ki, Chang-Seok; Lee, Nam Yong

2015-02-01

We evaluated the performance of the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), stratified by acid-fast bacilli (AFB) smear grades. The sensitivity of this test in smear-positive specimens was >95% in all grades, while that in trace and negative specimens was 85.3% and 34.4%, respectively. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Identification of four squid species by quantitative real-time polymerase chain reaction.

PubMed

Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

2016-02-01

Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. Copyright © 2016 Elsevier Ltd. All rights reserved.

New Deoxyribonucleic Acid Polymerase Induced by Bacillus subtilis Bacteriophage PBS2

PubMed Central

Price, Alan R.; Cook, Sandra J.

1972-01-01

The deoxyribonucleic acid (DNA) of Bacillus subtilis phage PBS2 has been confirmed to contain uracil instead of thymine. PBS2 phage infection of wild-type cells or DNA polymerase-deficient cells results in an increase in the specific activity of DNA polymerase. This induction of DNA polymerase activity is prevented by actinomycin D and chloramphenicol. In contrast to the major B. subtilis DNA polymerase, which prefers deoxythymidine triphosphate (dTTP) to deoxyuridine triphosphate (dUTP), the DNA polymerase in crude extracts of PBS2-infected cells is equally active whether dTTP or dUTP is employed. This phage-induced polymerase may be responsible for the synthesis of uracil-containing DNA during PBS2 phage infection. PMID:4623224

Control of trunk motion following sudden stop perturbations during cart pushing.

PubMed

Lee, Yun-Ju; Hoozemans, Marco J M; van Dieën, Jaap H

2011-01-04

External perturbations during pushing tasks have been suggested to be a risk factor for low-back symptoms. An experiment was designed to investigate whether self-induced and externally induced sudden stops while pushing a high inertia cart influence trunk motions, and how flexor and extensor muscles counteract these perturbations. Twelve healthy male participants pushed a 200 kg cart at shoulder height and hip height. Pushing while walking was compared to situations in which participants had to stop the cart suddenly (self-induced stop) or in which the wheels of the cart were unexpectedly blocked (externally induced stop). For the perturbed conditions, the peak values and the maximum changes from the reference condition (pushing while walking) of the external moment at L5/S1, trunk inclination and electromyographic amplitudes of trunk muscles were determined. In the self-induced stop, a voluntary trunk extension occurred. Initial responses in both stops consisted of flexor and extensor muscle cocontraction. In self-induced stops this was followed by sustained extensor activity. In the externally induced stops, an external extension moment caused a decrease in trunk inclination. The opposite directions of the internal moment and trunk motion in the externally induced stop while pushing at shoulder height may indicate insufficient active control of trunk posture. Consequently, sudden blocking of the wheels in pushing at shoulder height may put the low back at risk of mechanical injury. Copyright © 2010 Elsevier Ltd. All rights reserved.

Substorm onset: Current sheet avalanche and stop layer

NASA Astrophysics Data System (ADS)

Haerendel, Gerhard

2015-03-01

A new scenario is presented for the onset of a substorm and the nature of the breakup arc. There are two main components, current sheet avalanche and stop layer. The first refers to an earthward flow of plasma and magnetic flux from the central current sheet of the tail, triggered spontaneously or by some unknown interaction with an auroral streamer or a suddenly appearing eastward flow at the end of the growth phase. The second offers a mechanism to stop the flow abruptly at the interface between magnetosphere and tail and extract momentum and energy to be partially processed locally and partially transmitted as Poynting flux toward the ionosphere. The stop layer has a width of the order of the ion inertial length. The different dynamics of the ions entering freely and the magnetized electrons create an electric polarization field which stops the ion flow and drives a Hall current by which flow momentum is transferred to the magnetic field. A simple formalism is used to describe the operation of the process and to enable quantitative conclusions. An important conclusion is that by necessity the stop layer is also highly structured in longitude. This offers a natural explanation for the coarse ray structure of the breakup arc as manifestation of elementary paths of energy and momentum transport. The currents aligned with the rays are balanced between upward and downward directions. While the avalanche is invoked for explaining the spontaneous substorm onset at the inner edge of the tail, the expansion of the breakup arc for many minutes is taken as evidence for a continued formation of new stop layers by arrival of flow bursts from the near-Earth neutral line. This is in line with earlier conclusions about the nature of the breakup arc. Small-scale structure, propagation speed, and energy flux are quantitatively consistent with observations. However, the balanced small-scale currents cannot constitute the substorm current wedge. The source of the latter must be

A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

PubMed

Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-30

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

The stability of locus equation slopes across stop consonant voicing/aspiration

NASA Astrophysics Data System (ADS)

Sussman, Harvey M.; Modarresi, Golnaz

2004-05-01

The consistency of locus equation slopes as phonetic descriptors of stop place in CV sequences across voiced and voiceless aspirated stops was explored in the speech of five male speakers of American English and two male speakers of Persian. Using traditional locus equation measurement sites for F2 onsets, voiceless labial and coronal stops had significantly lower locus equation slopes relative to their voiced counterparts, whereas velars failed to show voicing differences. When locus equations were derived using F2 onsets for voiced stops that were measured closer to the stop release burst, comparable to the protocol for measuring voiceless aspirated stops, no significant effects of voicing/aspiration on locus equation slopes were observed. This methodological factor, rather than an underlying phonetic-based explanation, provides a reasonable account for the observed flatter locus equation slopes of voiceless labial and coronal stops relative to voiced cognates reported in previous studies [Molis et al., J. Acoust. Soc. Am. 95, 2925 (1994); O. Engstrand and B. Lindblom, PHONUM 4, 101-104]. [Work supported by NIH.

DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis.

PubMed

Barnes, Ryan P; Hile, Suzanne E; Lee, Marietta Y; Eckert, Kristin A

2017-09-01

Common fragile sites (CFSs) are inherently unstable genomic loci that are recurrently altered in human tumor cells. Despite their instability, CFS are ubiquitous throughout the human genome and associated with large tumor suppressor genes or oncogenes. CFSs are enriched with repetitive DNA sequences, one feature postulated to explain why these loci are inherently difficult to replicate, and sensitive to replication stress. We have shown that specialized DNA polymerases (Pols) η and κ replicate CFS-derived sequences more efficiently than the replicative Pol δ. However, we lacked an understanding of how these enzymes cooperate to ensure efficient CFS replication. Here, we designed a model of lagging strand replication with RFC loaded PCNA that allows for maximal activity of the four-subunit human Pol δ holoenzyme, Pol η, and Pol κ in polymerase mixing assays. We discovered that Pol η and κ are both able to exchange with Pol δ stalled at repetitive CFS sequences, enhancing Normalized Replication Efficiency. We used this model to test the impact of PCNA mono-ubiquitination on polymerase exchange, and found no change in polymerase cooperativity in CFS replication compared with unmodified PCNA. Finally, we modeled replication stress in vitro using aphidicolin and found that Pol δ holoenzyme synthesis was significantly inhibited in a dose-dependent manner, preventing any replication past the CFS. Importantly, Pol η and κ were still proficient in rescuing this stalled Pol δ synthesis, which may explain, in part, the CFS instability phenotype of aphidicolin-treated Pol η and Pol κ-deficient cells. In total, our data support a model wherein Pol δ stalling at CFSs allows for free exchange with a specialized polymerase that is not driven by PCNA. Copyright © 2017 Elsevier B.V. All rights reserved.

49 CFR 37.201 - Intermediate and rest stops.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Intermediate and rest stops. 37.201 Section 37.201 Transportation Office of the Secretary of Transportation TRANSPORTATION SERVICES FOR INDIVIDUALS WITH DISABILITIES (ADA) Over-the-Road Buses (OTRBs) § 37.201 Intermediate and rest stops. (a) Whenever an OTRB makes...

The global polio eradication initiative Stop Transmission of Polio (STOP) program - 1999-2013.

PubMed

2013-06-21

In 1988, the Global Polio Eradication Initiative (GPEI) was established through a partnership between the World Health Organization (WHO), Rotary International, CDC, and the United Nations Children's Fund (UNICEF). By 2012, the annual incidence of polio had decreased by >99%, compared with 1988, and the number of countries in which wild poliovirus (WPV) circulation has never been interrupted was reduced to three: Afghanistan, Nigeria, and Pakistan. However, because of the persistence of endemic WPV transmission and recurring outbreaks in polio-free countries after the original polio eradication target date of 2000, the World Health Assembly in 2012 declared the completion of polio eradication a programmatic emergency. A key component of GPEI is the Stop Transmission of Polio (STOP) program, which was developed and initiated by CDC with WHO in 1999 to mobilize additional human resources and technical assistance for countries affected by WPV transmission. During 1999-2013, 1,563 volunteers were identified, trained, and deployed for 2,221 assignments in 69 countries. The number of volunteers increased from 90-120 per year during 1999-2011 to 287 in 2012 and 378 in 2013, and the number of volunteer person-months in the field per year increased from 273 in 1999 to 1,456 in 2012. The STOP program has aided GPEI by strengthening the capacity of country-level immunization programs and by allowing a large cohort of volunteers to gain valuable field experience that prepares them well for subsequent work as staff members of WHO, UNICEF, and other public health agencies.

Modified pseudomonas oleovorans phaC1 nucleic acids encoding bispecific polyhydroxyalkanoate polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srienc, Friedrich; Jackson, John K.; Somers, David A.

A genetically engineered Pseudomonas oleovorans phaC1 polyhydroxyalkanoate (PHA) polymerase having tailored substrate specificity is provided. The modified PHA polymerase is preferably a "bispecific" PHA polymerase capable of copolymerizing a short chain length monomer and a medium chain length monomer is provided. Methods for making the modified PHA polymerase and for making nucleic acids encoding the modified PHA polymerase are also disclosed, as are methods of producing PHA using the modified PHA polymerase. The invention further includes methods to assay for altered substrate specificity.

Effect of bus-stop spacing on mobile emissions in urban areas.

DOT National Transportation Integrated Search

2003-01-01

The operational effect of bus-stop spacing has been a critical issue. Closely spaced bus stops : disrupt the traffic flow on the bus route, particularly during peak hours because buses make frequent stops : to provide services to customers. The disru...

Apparatus for stopping a vehicle

DOEpatents

Wattenburg, Willard H [Walnut Creek, CA; McCallen, David B [Livermore, CA

2007-03-20

An apparatus for externally controlling one or more brakes on a vehicle having a pressurized fluid braking system. The apparatus can include a pressurizable vessel that is adapted for fluid-tight coupling to the braking system. Impact to the rear of the vehicle by a pursuit vehicle, shooting a target mounted on the vehicle or sending a signal from a remote control can all result in the fluid pressures in the braking system of the vehicle being modified so that the vehicle is stopped and rendered temporarily inoperable. A control device can also be provided in the driver's compartment of the vehicle for similarly rendering the vehicle inoperable. A driver or hijacker of the vehicle preferably cannot overcome the stopping action from the driver's compartment.

The origin and early evolution of nucleic acid polymerases

NASA Technical Reports Server (NTRS)

Lazcano, A.; Cappello, R.; Valverde, V.; Llaca, V.; Oro, J.

1992-01-01

The hypothesis that vestiges of the ancestral RNA-dependent RNA polymerase involved in the replication of RNA genomes of Archean cells are present in the eubacterial RNA-polymerase beta-prime subunit and its homologues is discussed. It is shown that, in the DNA-dependent RNA polymerases from three cellular lineages, a very conserved sequence of eight amino acids, also found in a small RNA-binding site previously described for the E. coli polynucleotide phosphorylase and the S1 ribosomal protein, is present. The optimal conditions for the replicase activity of the avian-myeloblastosis-virus reverse transcriptase are presented. The evolutionary significance of the in vitro modifications of substrate and template specificities of RNA polymerases and reverse transcriptases is discussed.

Should I Stop or Should I Go? The Role of Associations and Expectancies

PubMed Central

2015-01-01

Following exposure to consistent stimulus–stop mappings, response inhibition can become automatized with practice. What is learned is less clear, even though this has important theoretical and practical implications. A recent analysis indicates that stimuli can become associated with a stop signal or with a stop goal. Furthermore, expectancy may play an important role. Previous studies that have used stop or no-go signals to manipulate stimulus–stop learning cannot distinguish between stimulus-signal and stimulus-goal associations, and expectancy has not been measured properly. In the present study, participants performed a task that combined features of the go/no-go task and the stop-signal task in which the stop-signal rule changed at the beginning of each block. The go and stop signals were superimposed over 40 task-irrelevant images. Our results show that participants can learn direct associations between images and the stop goal without mediation via the stop signal. Exposure to the image-stop associations influenced task performance during training, and expectancies measured following task completion or measured within the task. But, despite this, we found an effect of stimulus–stop learning on test performance only when the task increased the task-relevance of the images. This could indicate that the influence of stimulus–stop learning on go performance is strongly influenced by attention to both task-relevant and task-irrelevant stimulus features. More generally, our findings suggest a strong interplay between automatic and controlled processes. PMID:26322688

46 CFR 111.103-9 - Machinery stop stations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... fan, induced draft fan, blower of an inert gas system, fuel oil transfer pump, fuel oil unit, fuel oil service pump, and any other fuel oil pumps must have a stop control that is outside of the space containing the pump or fan. (b) Each stop control must meet § 111.103-7. ...

46 CFR 111.103-9 - Machinery stop stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... fan, induced draft fan, blower of an inert gas system, fuel oil transfer pump, fuel oil unit, fuel oil service pump, and any other fuel oil pumps must have a stop control that is outside of the space containing the pump or fan. (b) Each stop control must meet § 111.103-7. ...

46 CFR 111.103-9 - Machinery stop stations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... fan, induced draft fan, blower of an inert gas system, fuel oil transfer pump, fuel oil unit, fuel oil service pump, and any other fuel oil pumps must have a stop control that is outside of the space containing the pump or fan. (b) Each stop control must meet § 111.103-7. ...

46 CFR 111.103-9 - Machinery stop stations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... fan, induced draft fan, blower of an inert gas system, fuel oil transfer pump, fuel oil unit, fuel oil service pump, and any other fuel oil pumps must have a stop control that is outside of the space containing the pump or fan. (b) Each stop control must meet § 111.103-7. ...

46 CFR 111.103-9 - Machinery stop stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... fan, induced draft fan, blower of an inert gas system, fuel oil transfer pump, fuel oil unit, fuel oil service pump, and any other fuel oil pumps must have a stop control that is outside of the space containing the pump or fan. (b) Each stop control must meet § 111.103-7. ...

Prototype Stop Bar System Evaluation at John F. Kennedy International Airport

DTIC Science & Technology

1992-09-01

2 Red Stop Bar Visual Presentation 4 3 Green Stop Bar Visual Presentation 5 4 Photographs of Red and Green Inset Stop Bar Lights 6 5 Photographs of...to green. This provides pilots with a visual confirmation of the controller’s verbal clearance and is intended to prevent runway incursions. The Port...34 colocated with the red lights. The visual presentation of an individual stop bar appears as either five red lights (see figure 2), or five green

Stopping Distances: An Excellent Example of Empirical Modelling.

ERIC Educational Resources Information Center

Lawson, D. A.; Tabor, J. H.

2001-01-01

Explores the derivation of empirical models for the stopping distance of a car being driven at a range of speeds. Indicates that the calculation of stopping distances makes an excellent example of empirical modeling because it is a situation that is readily understood and particularly relevant to many first-year undergraduates who are learning or…

Tongue-Palate Contact of Perceptually Acceptable Alveolar Stops

ERIC Educational Resources Information Center

Lee, Alice; Gibbon, Fiona E.; O'Donovan, Cliona

2013-01-01

Increased tongue-palate contact for perceptually acceptable alveolar stops has been observed in children with speech sound disorders (SSD). This is a retrospective study that further investigated this issue by using quantitative measures to compare the target alveolar stops /t/, /d/ and /n/ produced in words by nine children with SSD (20 tokens of…

Design Considerations for a Stopped-Rotor Cyclocopter for Venus Exploration

NASA Technical Reports Server (NTRS)

Husseyin, S.; Warmbrodt, William G.

2016-01-01

This paper considers the use of a cycloidal blade system as a means of providing lift and propulsive thrust as well as combined with a stopped rotor system, to create a stopped-rotor cyclocopter vehicle, during a mission to Venus. This stopped-rotor cyclocopter will be capable of flying at all atmospheric levels of Venus as well as landing on the surface for scientific investigation. Three reference conceptual designs with different stopped-rotor cyclocopter yaw angles are tested in RotCFD as well as a model of a hovering cyclorotor for comparison with past work in the literature and innovative study for future projects.

Repair of Clustered Damage and DNA Polymerase Iota.

PubMed

Belousova, E A; Lavrik, O I

2015-08-01

Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase.

PubMed

Jordan, Paul C; Liu, Cheng; Raynaud, Pauline; Lo, Michael K; Spiropoulou, Christina F; Symons, Julian A; Beigelman, Leo; Deval, Jerome

2018-02-01

Paramyxoviruses represent a family of RNA viruses causing significant human diseases. These include measles virus, the most infectious virus ever reported, in addition to parainfluenza virus, and other emerging viruses. Paramyxoviruses likely share common replication machinery but their mechanisms of RNA biosynthesis activities and details of their complex polymerase structures are unknown. Mechanistic and functional details of a paramyxovirus polymerase would have sweeping implications for understanding RNA virus replication and for the development of new antiviral medicines. To study paramyxovirus polymerase structure and function, we expressed an active recombinant Nipah virus (NiV) polymerase complex assembled from the multifunctional NiV L protein bound to its phosphoprotein cofactor. NiV is an emerging highly pathogenic virus that causes severe encephalitis and has been declared a global public health concern due to its high mortality rate. Using negative-stain electron microscopy, we demonstrated NiV polymerase forms ring-like particles resembling related RNA polymerases. We identified conserved sequence elements driving recognition of the 3'-terminal genomic promoter by NiV polymerase, and leading to initiation of RNA synthesis, primer extension, and transition to elongation mode. Polyadenylation resulting from NiV polymerase stuttering provides a mechanistic basis for transcription termination. It also suggests a divergent adaptation in promoter recognition between pneumo- and paramyxoviruses. The lack of available antiviral therapy for NiV prompted us to identify the triphosphate forms of R1479 and GS-5734, two clinically relevant nucleotide analogs, as substrates and inhibitors of NiV polymerase activity by delayed chain termination. Overall, these findings provide low-resolution structural details and the mechanism of an RNA polymerase from a previously uncharacterized virus family. This work illustrates important functional differences yet remarkable

The IAEA stopping power database, following the trends in stopping power of ions in matter

NASA Astrophysics Data System (ADS)

Montanari, C. C.; Dimitriou, P.

2017-10-01

The aim of this work is to present an overview of the state of art of the energy loss of ions in matter, based on the new developments in the stopping power database of the International Atomic Energy Agency (IAEA). This exhaustive collection of experimental data, graphs, programs and comparisons, is the legacy of Helmut Paul, who made it accessible to the global scientific community, and has been extensively employed in theoretical and experimental research during the last 25 years. The field of stopping power in matter is evolving, with new trends in materials of interest, including oxides, nitrides, polymers, and biological targets. Our goal is to identify areas of interest and emerging data needs to meet the requirements of a continuously developing user community.

Ball Screw Actuator Including an Axial Soft Stop

NASA Technical Reports Server (NTRS)

Forrest, Steven Talbert (Inventor); Woessner, George (Inventor); Abel, Steve (Inventor); Wingett, Paul T. (Inventor); Hanlon, Casey (Inventor)

2016-01-01

An actuator includes an actuator housing, a ball screw, and an axial soft stop assembly. The ball screw extends through the actuator housing and has a first end and a second end. The ball screw is coupled to receive a drive force and is configured, upon receipt of the drive force, to selectively move in a retract direction and an extend direction. The axial soft stop assembly is disposed within the actuator housing. The axial soft stop assembly is configured to be selectively engaged by the ball screw and, upon being engaged thereby, to translate, with compliance, a predetermined distance in the extend direction, and to prevent further movement of the ball screw upon translating the predetermined distance.

Light stops and observation of supersymmetry at LHC run II

NASA Astrophysics Data System (ADS)

Kaufman, Bryan; Nath, Pran; Nelson, Brent D.; Spisak, Andrew B.

2015-11-01

Light stops consistent with the Higgs boson mass of ˜126 GeV are investigated within the framework of minimal supergravity. It is shown that models with light stops which are also consistent with the thermal relic density constraints require stop coannihilation with the neutralino LSP. The analysis shows that the residual set of parameter points with light stops satisfying both the Higgs mass and the relic density constraints lie within a series of thin strips in the m0-m1 /2 plane for different values of A0/m0. Consequently, this region of minimal supergravity parameter space makes a number of very precise predictions. It is found that light stops of mass down to 400 GeV or lower can exist consistent with all constraints. A signal analysis for this class of models at LHC run II is carried out and the dominant signals for their detection identified. Also computed is the minimum integrated luminosity for 5 σ discovery of the models analyzed. If supersymmetry is realized in this manner, the stop masses can be as low as 400 GeV or lower, and the mass gap between the lightest neutralino and lightest stop will be approximately 30-40 GeV. We have optimized the ATLAS signal regions specifically for stop searches in the parameter space and find that a stop with mass ˜375 GeV can be discovered with as little as ˜60 fb-1 of integrated luminosity at run II of the LHC; the integrated luminosity needed for discovery could be further reduced with more efficient signature analyses. The direct detection of dark matter in this class of models is also discussed. It is found that dark matter cross sections lie close to, but above, coherent neutrino scattering and would require multiton detectors such as LZ to see a signal of dark matter for this class of models.

Mammalian proliferating cell nuclear antigen stimulates the processivity of two wheat embryo DNA polymerases.

PubMed Central

Laquel, P; Litvak, S; Castroviejo, M

1993-01-01

Multiple DNA polymerases have been described in all organisms studied to date. Their specific functions are not easy to determine, except when powerful genetic and/or biochemical tools are available. However, the processivity of a DNA polymerase could reflect the physiological role of the enzyme. In this study, analogies between plant and animal DNA polymerases have been investigated by analyzing the size of the products synthesized by wheat DNA polymerases A, B, CI, and CII as a measure of their processivity. Thus, incubations have been carried out with poly(dA)-oligo(dT) as a template-primer under varying assay conditions. In the presence of MgCl2, DNA polymerase A was highly processive, whereas DNA polymerases B, CI, and CII synthesized much shorter products. With MnCl2 instead of MgCl2, DNA polymerase A was highly processive, DNA polymerases B and CII were moderately processive, and DNA polymerase CI remained strictly distributive. The effect of calf thymus proliferating cell nuclear antigen (PCNA) on wheat polymerases was studied as described for animal DNA polymerases. The high processivity of DNA polymerase A was PCNA independent, whereas both enzyme activity and processivity of wheat DNA polymerases B and CII were significantly stimulated by PCNA. On the other hand, DNA polymerase CI was not stimulated by PCNA and, like animal DNA polymerase beta, was distributive in all cases. From these results, we propose that wheat DNA polymerase A could correspond to a DNA polymerase alpha, DNA polymerases B and CII could correspond to the delta-like enzyme, and DNA polymerase CI could correspond to DNA polymerase beta. PMID:7906418

Stopping for School Buses. Traffic Laws Commentary Series.

ERIC Educational Resources Information Center

Yaw, E. Eugene

The degree of uniformity among State laws requiring drivers to stop for school buses receiving or discharging children is not such that drivers could reasonably be expected to know these laws. Because of the wide variation of State laws and the inherent vulnerability of school children and of any vehicle stopping on a highway, there can be no…

Mapping DNA polymerase errors by single-molecule sequencing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, David F.; Lu, Jenny; Chang, Seungwoo

Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replicationmore » product is tagged with a unique nucleotide sequence before amplification. Here, this allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.« less

Mapping DNA polymerase errors by single-molecule sequencing

DOE PAGES

Lee, David F.; Lu, Jenny; Chang, Seungwoo; ...

2016-05-16

Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replicationmore » product is tagged with a unique nucleotide sequence before amplification. Here, this allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.« less

DNA Polymerase in Virions of a Reptilian Type C Virus

PubMed Central

Twardzik, Daniel R.; Papas, Takis S.; Portugal, Frank H.

1974-01-01

A study was made of the DNA polymerase of reptilian type C virus isolated from Russell's viper spleen cells. Simultaneous detection experiments demonstrated the presence of 70S RNA and RNA-dependent DNA polymerase activity in reptilian type C virions. The endogenous activity was dependent on the addition of all four deoxynucleotide triphosphates and demonstrated an absolute requirement for a divalent cation. The reptilian viral DNA polymerase elutes from phosphocellulose at 0.22 M salt. In this respect, it is similar to the avian (avian myeloblastosis virus; AMV) viral enzyme but is different from the mammalian (Rauscher leukemia virus; RLV) viral enzyme which elutes at 0.4 M salt. The molecular weight of the viper DNA polymerase as estimated from glycerol gradient centrifugation is 109,000. It is a smaller enzyme than the AMV DNA polymerase (180,000 daltons) and somewhat larger than the RLV enzyme (70,000 daltons). A comparison of other properties of the type C reptilian DNA polymerase with the enzyme found in other type C oncogenic viruses is made. PMID:4129837

Development and Evaluation of a Multiplex Real-Time Polymerase Chain Reaction Procedure to Clinically Type Prevalent Salmonella enterica Serovars

PubMed Central

Muñoz, Nélida; Diaz-Osorio, Miguel; Moreno, Jaime; Sánchez-Jiménez, Miryan; Cardona-Castro, Nora

2010-01-01

A multiplex real-time polymerase chain reaction procedure was developed to identify the most prevalent clinical isolates of Salmonella enterica subsp. enterica. Genes from the rfb, fliC, fljB, and viaB groups that encode the O, H, and Vi antigens were used to design 15 primer pairs and TaqMan probes specific for the genes rfbJ, wzx, fliC, fljB, wcdB, the sdf-l sequence, and invA, which was used as an internal amplification control. The primers and probes were variously combined into six sets. The first round of reactions used two of these sets to detect Salmonella O:4, O:9, O:7, O:8, and O:3,10 serogroups. Once the serogroups were identified, the results of a second round of reactions that used primers and probes for the flagellar antigen l genes, 1,2; e,h; g,m; d; e,n,x; and z10, and the Vi gene were used to identify individual serovars. The procedure was standardized using 18 Salmonella reference strains and other enterobacteria. The procedure's reliability and sensitivity was evaluated using 267 randomly chosen serotyped Salmonella clinical isolates. The procedure had a sensitivity of 95.5% and was 100% specific. Thus, our technique is a quick, sensitive, reliable, and specific means of identifying S. enterica serovars and can be used in conjunction with traditional serotyping. Other primer and probe combinations could be used to increase the number of identifiable serovars. PMID:20110454

49 CFR 236.335 - Dogs, stops and trunnions of mechanical locking.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Dogs, stops and trunnions of mechanical locking..., AND APPLIANCES Interlocking Rules and Instructions § 236.335 Dogs, stops and trunnions of mechanical locking. Driving pieces, dogs, stops and trunnions shall be rigidly secured to locking bars. Swing dogs...

49 CFR 236.335 - Dogs, stops and trunnions of mechanical locking.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Dogs, stops and trunnions of mechanical locking..., AND APPLIANCES Interlocking Rules and Instructions § 236.335 Dogs, stops and trunnions of mechanical locking. Driving pieces, dogs, stops and trunnions shall be rigidly secured to locking bars. Swing dogs...

49 CFR 236.335 - Dogs, stops and trunnions of mechanical locking.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Dogs, stops and trunnions of mechanical locking..., AND APPLIANCES Interlocking Rules and Instructions § 236.335 Dogs, stops and trunnions of mechanical locking. Driving pieces, dogs, stops and trunnions shall be rigidly secured to locking bars. Swing dogs...

49 CFR 236.335 - Dogs, stops and trunnions of mechanical locking.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Dogs, stops and trunnions of mechanical locking..., AND APPLIANCES Interlocking Rules and Instructions § 236.335 Dogs, stops and trunnions of mechanical locking. Driving pieces, dogs, stops and trunnions shall be rigidly secured to locking bars. Swing dogs...

49 CFR 236.335 - Dogs, stops and trunnions of mechanical locking.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Dogs, stops and trunnions of mechanical locking..., AND APPLIANCES Interlocking Rules and Instructions § 236.335 Dogs, stops and trunnions of mechanical locking. Driving pieces, dogs, stops and trunnions shall be rigidly secured to locking bars. Swing dogs...

Polymerase chain displacement reaction.

PubMed

Harris, Claire L; Sanchez-Vargas, Irma J; Olson, Ken E; Alphey, Luke; Fu, Guoliang

2013-02-01

Quantitative PCR assays are now the standard method for viral diagnostics. These assays must be specific, as well as sensitive, to detect the potentially low starting copy number of viral genomic material. We describe a new technique, polymerase chain displacement reaction (PCDR), which uses multiple nested primers in a rapid, capped, one-tube reaction that increases the sensitivity of normal quantitative PCR (qPCR) assays. Sensitivity was increased by approximately 10-fold in a proof-of-principle test on dengue virus sequence. In PCDR, when extension occurs from the outer primer, it displaces the extension strand produced from the inner primer by utilizing a polymerase that has strand displacement activity. This allows a greater than 2-fold increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Increased sensitivity in PCDR would be useful in nucleic acid detection for viral diagnostics.

The Phenomenon of Unduly Hardening [C] (Palatal Stop) to [K] (Velar Stop) in Turkish Speech and Its Remedy through Minimal Pairs

ERIC Educational Resources Information Center

Yurtbasi, Metin

2016-01-01

The voiceless allophones of (alveolo) palatal stop consonant [c] and velar stop consonant [k] of the phoneme /k/ represented by the letter "K" exists in almost all languages of the world. Which of these will be sounded in speech is determined by the type of the vowel that are adjacent to them. In Turkish, the dark variant [k] occurs…

A meiotic DNA polymerase from a mushroom, Agaricus bisporus.

PubMed Central

Takami, K; Matsuda, S; Sono, A; Sakaguchi, K

1994-01-01

A meiotic DNA polymerase [DNA nucleotidyltransferase (DNA-directed), EC 2.7.7.7], which likely has a role in meiotic DNA repair, was isolated from a mushroom, Agaricus bisporus. The purified fraction displays three bands in SDS/PAGE, at molecular masses of 72 kDa, 65 kDa and 36 kDa. Optimal activity is at pH 7.0-8.0 in the presence of 5 mM Mg2+ and 50 mM KCl and at 28-30 degrees C, which is the temperature for meiosis. This enzyme is resistant to N-ethylmaleimide and sensitive to 2',3'-dideoxythymidine 5'-triphosphate, suggesting that it is a beta-like DNA polymerase. These characteristics are similar to those of Coprinus DNA polymerase beta [Sakaguchi and Lu (1982) Mol. Cell. Biol. 2, 752-757]. In Western-blot analysis, the antiserum against the Coprinus polymerase reacts only with the 65 kDa band, which coincides with the molecular mass of the Coprinus polymerase. Western-blot analysis also showed that the antiserum could react with crude extracts not only from the Agaricales family, to which Agaricus and Coprinus belong, but also from different mushroom families and Saccharomyces. The Agaricus polymerase activity can be found only in the meiotic-cell-rich fraction, but the enzyme is also present in the somatic cells in an inactive state. Images Figure 2 Figure 5 Figure 6 PMID:8172591

Functional Architecture of T7 RNA Polymerase Transcription Complexes

PubMed Central

Nayak, Dhananjaya; Guo, Qing; Sousa, Rui

2007-01-01

Summary T7 RNA polymerase is the best-characterized member of a widespread family of single-subunit RNA polymerases. Crystal structures of T7 RNA polymerase initiation and elongation complexes have provided a wealth of detailed information on RNA polymerase interactions with the promoter and transcription bubble, but the absence of DNA downstream of the melted region of the template in the initiation complex structure, and the absence of DNA upstream of the transcription bubble in the elongation complex structure means that our picture of the functional architecture of T7 RNA polymerase transcription complexes remains incomplete. Here we use the site-specifically tethered chemical nucleases and functional characterization of directed T7 RNAP mutants to both reveal the architecture of the duplex DNA that flanks the transcription bubble in the T7 RNAP initiation and elongation complexes, and to define the function of the interactions made by these duplex elements. We find that downstream duplex interactions made with a cluster of lysines (K711/K713/K714) are present during both elongation and initiation where they contribute to stabilizing a bend in the downstream DNA that is important for promoter opening. The upstream DNA in the elongation complex is also found to be sharply bent at the upstream edge of the transcription bubble, thereby allowing formation of upstream duplex:polymerase interactions that contribute to elongation complex stability. PMID:17580086

Results of the Abbott RealTime HIV-1 assay for specimens yielding "target not detected" results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test.

PubMed

Babady, N Esther; Germer, Jeffrey J; Yao, Joseph D C

2010-03-01

No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding "target not detected" results by CTM.

Putting it All Together: Has One-Stop Shopping Arrived?

ERIC Educational Resources Information Center

Flanagan, Patrick

1997-01-01

Reviews the current state of "one-stop shopping" for telecom services. Discusses regulatory obstacles; administrative problems with single billing; and resistance of telecom providers to change. Concludes that the leading one-stop shopping providers will be individual carriers who offer cost savings. (AEF)

Stopping while Going! Response Inhibition Does Not Suffer Dual-Task Interference

ERIC Educational Resources Information Center

Yamaguchi, Motonori; Logan, Gordon D.; Bissett, Patrick G.

2012-01-01

Although dual-task interference is ubiquitous in a variety of task domains, stop-signal studies suggest that response inhibition is not subject to such interference. Nevertheless, no study has directly examined stop-signal performance in a dual-task setting. In two experiments, stop-signal performance was examined in a psychological refractory…

BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription

PubMed Central

Grierson, Patrick M.; Lillard, Kate; Behbehani, Gregory K.; Combs, Kelly A.; Bhattacharyya, Saumitri; Acharya, Samir; Groden, Joanna

2012-01-01

Bloom's syndrome (BS) is an autosomal recessive disorder that is invariably characterized by severe growth retardation and cancer predisposition. The Bloom's syndrome helicase (BLM), mutations of which lead to BS, localizes to promyelocytic leukemia protein bodies and to the nucleolus of the cell, the site of RNA polymerase I-mediated ribosomal RNA (rRNA) transcription. rRNA transcription is fundamental for ribosome biogenesis and therefore protein synthesis, cellular growth and proliferation; its inhibition limits cellular growth and proliferation as well as bodily growth. We report that nucleolar BLM facilitates RNA polymerase I-mediated rRNA transcription. Immunofluorescence studies demonstrate the dependance of BLM nucleolar localization upon ongoing RNA polymerase I-mediated rRNA transcription. In vivo protein co-immunoprecipitation demonstrates that BLM interacts with RPA194, a subunit of RNA polymerase I. 3H-uridine pulse-chase assays demonstrate that BLM expression is required for efficient rRNA transcription. In vitro helicase assays demonstrate that BLM unwinds GC-rich rDNA-like substrates that form in the nucleolus and normally inhibit progression of the RNA polymerase I transcription complex. These studies suggest that nucleolar BLM modulates rDNA structures in association with RNA polymerase I to facilitate RNA polymerase I-mediated rRNA transcription. Given the intricate relationship between rDNA metabolism and growth, our data may help in understanding the etiology of proportional dwarfism in BS. PMID:22106380

BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription.

PubMed

Grierson, Patrick M; Lillard, Kate; Behbehani, Gregory K; Combs, Kelly A; Bhattacharyya, Saumitri; Acharya, Samir; Groden, Joanna

2012-03-01

Bloom's syndrome (BS) is an autosomal recessive disorder that is invariably characterized by severe growth retardation and cancer predisposition. The Bloom's syndrome helicase (BLM), mutations of which lead to BS, localizes to promyelocytic leukemia protein bodies and to the nucleolus of the cell, the site of RNA polymerase I-mediated ribosomal RNA (rRNA) transcription. rRNA transcription is fundamental for ribosome biogenesis and therefore protein synthesis, cellular growth and proliferation; its inhibition limits cellular growth and proliferation as well as bodily growth. We report that nucleolar BLM facilitates RNA polymerase I-mediated rRNA transcription. Immunofluorescence studies demonstrate the dependance of BLM nucleolar localization upon ongoing RNA polymerase I-mediated rRNA transcription. In vivo protein co-immunoprecipitation demonstrates that BLM interacts with RPA194, a subunit of RNA polymerase I. (3)H-uridine pulse-chase assays demonstrate that BLM expression is required for efficient rRNA transcription. In vitro helicase assays demonstrate that BLM unwinds GC-rich rDNA-like substrates that form in the nucleolus and normally inhibit progression of the RNA polymerase I transcription complex. These studies suggest that nucleolar BLM modulates rDNA structures in association with RNA polymerase I to facilitate RNA polymerase I-mediated rRNA transcription. Given the intricate relationship between rDNA metabolism and growth, our data may help in understanding the etiology of proportional dwarfism in BS.

Polymerase chain reaction system

DOEpatents

Benett, William J.; Richards, James B.; Stratton, Paul L.; Hadley, Dean R.; Milanovich, Fred P.; Belgrader, Phil; Meyer, Peter L.

2004-03-02

A portable polymerase chain reaction DNA amplification and detection system includes one or more chamber modules. Each module supports a duplex assay of a biological sample. Each module has two parallel interrogation ports with a linear optical system. The system is capable of being handheld.

Who stops selling? A systematic analysis of ex-tobacco retailers.

PubMed

Feletto, Eleonora; Burton, Suzan; Williams, Kelly; Fry, Rae; Sutton, Clare; Bagus, Lachlan; Egger, Sam

2016-03-09

There is evidence that wide distribution of cigarettes contributes to smoking, and multiple commentators have called for a review of tobacco retailing. This study analyses retailers who stop selling cigarettes, why they do so, and discusses the implications for tobacco control. An audit of tobacco retailers in the Australian state of NSW was used to identify retailers who had stopped selling tobacco, and they were then compared with current retailers to determine how many, and what types of outlets stop selling tobacco. Attempts were made to contact and interview all former tobacco retailers identified in three audited regions. In-depth interviews were conducted with 13 ex-tobacco retailers, or 31% of the subset of ex-tobacco retailers. Low-volume outlet types were over-represented as a proportion of retailers exiting the market, and some had resumed selling within 18 months of the audit. Low profits were often cited as a contributor to stopping; however, in all but one case, the decision to stop selling was also influenced by a significant change in business circumstances-either legislative or other business changes. Few retailers stop selling tobacco while continuing in the same business, and those who stop disproportionately represent retailer types with low sales volume. The results suggest that legislative changes provide a window where retailers could be prompted to exit the market. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ

PubMed Central

Ma, Emilie; Veaute, Xavier; Coïc, Eric

2017-01-01

Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by specialized translesion DNA synthesis (TLS) polymerases to allow DNA replication completion in the presence of DNA damage. In eukaryotes, Rad6- and Rad18-mediated PCNA ubiquitination at lysine 164 promotes recruitment of TLS polymerases, allowing cells to efficiently cope with DNA damage. However, several studies showed that TLS polymerases can be recruited also in the absence of PCNA ubiquitination. We hypothesized that the stability of the interactions between DNA polymerase δ (Pol δ) subunits and/or between Pol δ and PCNA at the primer/template junction is a crucial factor to determine the requirement of PCNA ubiquitination. To test this hypothesis, we used a structural mutant of Pol δ in which the interaction between Pol3 and Pol31 is inhibited. We found that in yeast, rad18Δ-associated UV hypersensitivity is suppressed by pol3-ct, a mutant allele of the POL3 gene that encodes the catalytic subunit of replicative Pol δ. pol3-ct suppressor effect was specifically dependent on the Rev1 and Pol ζ TLS polymerases. This result strongly suggests that TLS polymerases could rely much less on PCNA ubiquitination when Pol δ interaction with PCNA is partially compromised by mutations. In agreement with this model, we found that the pol3-FI allele suppressed rad18Δ-associated UV sensitivity as observed for pol3-ct. This POL3 allele carries mutations within a putative PCNA Interacting Peptide (PIP) motif. We then provided molecular and genetic evidence that this motif could contribute to Pol δ-PCNA interaction indirectly, although it is not a bona fide PIP. Overall, our results suggest that the primary role of PCNA ubiquitination is to allow TLS polymerases to outcompete Pol δ for PCNA access upon DNA damage. PMID:29281621

Independent Structural Domains in Paramyxovirus Polymerase Protein*

PubMed Central

Dochow, Melanie; Krumm, Stefanie A.; Crowe, James E.; Moore, Martin L.; Plemper, Richard K.

2012-01-01

All enzymatic activities required for genomic replication and transcription of nonsegmented negative strand RNA viruses (or Mononegavirales) are believed to be concentrated in the viral polymerase (L) protein. However, our insight into the organization of these different enzymatic activities into a bioactive tertiary structure remains rudimentary. Fragments of Mononegavirales polymerases analyzed to date cannot restore bioactivity through trans-complementation, unlike the related L proteins of segmented NSVs. We investigated the domain organization of phylogenetically diverse Paramyxovirus L proteins derived from measles virus (MeV), Nipah virus (NiV), and respiratory syncytial virus (RSV). Through a comprehensive in silico and experimental analysis of domain intersections, we defined MeV L position 615 as an interdomain candidate in addition to the previously reported residue 1708. Only position 1708 of MeV and the homologous positions in NiV and RSV L also tolerated the insertion of epitope tags. Splitting of MeV L at residue 1708 created fragments that were unable to physically interact and trans-complement, but strikingly, these activities were reconstituted by the addition of dimerization tags to the fragments. Equivalently split fragments of NiV, RSV, and MeV L oligomerized with comparable efficiency in all homo- and heterotypic combinations, but only the homotypic pairs were able to trans-complement. These results demonstrate that synthesis as a single polypeptide is not required for the Mononegavirales polymerases to adopt a proper tertiary conformation. Paramyxovirus polymerases are composed of at least two truly independent folding domains that lack a traditional interface but require molecular compatibility for bioactivity. The functional probing of the L domain architecture through trans-complementation is anticipated to be applicable to all Mononegavirales polymerases. PMID:22215662

Poly(A) polymerase contains multiple functional domains.

PubMed Central

Raabe, T; Murthy, K G; Manley, J L

1994-01-01

Poly(A) polymerase (PAP) contains regions of similarity with several known protein domains. Through site-directed mutagenesis, we provide evidence that PAP contains a functional ribonucleoprotein-type RNA binding domain (RBD) that is responsible for primer binding, making it the only known polymerase to contain such a domain. The RBD is adjacent to, and probably overlaps with, an apparent catalytic region responsible for polymerization. Despite the presence of sequence similarities, this catalytic domain appears to be distinct from the conserved polymerase module found in a large number of RNA-dependent polymerases. PAP contains two nuclear localization signals (NLSs) in its C terminus, each by itself similar to the consensus bipartite NLS found in many nuclear proteins. Mutagenesis experiments indicate that both signals, which are separated by nearly 140 residues, play important roles in directing PAP exclusively to the nucleus. Surprisingly, basic amino acids in the N-terminal-most NLS are also essential for AAUAAA-dependent polyadenylation but not for nonspecific poly(A) synthesis, suggesting that this region of PAP is involved in interactions both with nuclear targeting proteins and with nuclear polyadenylation factors. The serine/threonine-rich C terminus is multiply phosphorylated, including at sites affected by mutations in either NLS. Images PMID:8164653

Fricative-stop coarticulation: acoustic and perceptual evidence.

PubMed

Repp, B H; Mann, V A

1982-06-01

Eight native speakers of American English each produced ten tokens of all possible CV, FCV, and VFCV utterances with V = [a] or [u], F = [s] or [integral of], and C = [t] or [k]. Acoustic analysis showed that the formant transition onsets following the stop consonant release were systematically influenced by the preceding fricative, although there were large individual differences. In particular, F3 and F4 tended to be higher following [s] than following [integral of]. The coarticulatory effects were equally large in FCV (e.g.,/sta/) and VFCV (e.g.,/asda/) utterances; that is, they were not reduced when a syllable boundary intervened between fricative and stop. In a parallel perceptual study, the CV portions of these utterances (with release bursts removed to provoke errors) were presented to listeners for identification of the stop consonant. The pattern of place-of-articulation confusions, too, revealed coarticulatory effects due to the excised fricative context.

Exploring the nearly degenerate stop region with sbottom decays

DOE PAGES

An, Haipeng; Gu, Jiayin; Wang, Lian-Tao

2017-04-13

A light stop with mass almost degenerate with the lightest neutralino has important connections with both naturalness and dark matter relic abundance. This region is also very hard to probe at colliders. In this paper, we demonstrate the potential of searching for such stop particles at the LHC from sbottom decays, focusing on two channels with final states 2ℓ+EmissT2ℓ+ETmiss and 1b1ℓ+Emore » $$miss\\atop{T}$$1b1ℓ+E$$miss\\atop{T}$$. We also found that, if the lightest sbottom has mass around or below 1 TeV and has a significant branching ratio to decay to stop and W($$\\tilde{b}$$→$$\\tilde{t}$$W), a stop almost degenerate with neutralino can be excluded up to about 500-600 GeV at the 13 TeV LHC with 300 fb -1 data. The searches we propose are complementary to other SUSY searches at the LHC and could have the best sensitivity to the stop-bino coannihilation region. Finally, since they involve final states which have already been used in LHC searches, a reinterpretation of the search results already has sensitivity. Further optimization could deliver the full potential of these channels.« less

IMPACTS OF BUS STOP IMPROVEMENTS

DOT National Transportation Integrated Search

2018-03-23

Improving bus stops by providing shelters, seating, signage, and sidewalks is relatively inexpensive and popular among riders and local officials. Making such improvements, however, is not often a priority for U.S. transit providers because of compet...

General misincorporation frequency: Re-evaluation of the fidelity of DNA polymerases.

PubMed

Yang, Jie; Li, Bianbian; Liu, Xiaoying; Tang, Hong; Zhuang, Xiyao; Yang, Mingqi; Xu, Ying; Zhang, Huidong; Yang, Chun

2018-02-19

DNA replication in cells is performed in the presence of four dNTPs and four rNTPs. In this study, we re-evaluated the fidelity of DNA polymerases using the general misincorporation frequency consisting of three incorrect dNTPs and four rNTPs but not using the traditional special misincorporation frequency with only the three incorrect dNTPs. We analyzed both the general and special misincorporation frequencies of nucleotide incorporation opposite dG, rG, or 8-oxoG by Pseudomonas aeruginosa phage 1 (PaP1) DNA polymerase Gp90 or Sulfolobus solfataricus DNA polymerase Dpo4. Both misincorporation frequencies of other DNA polymerases published were also summarized and analyzed. The general misincorporation frequency is obviously higher than the special misincorporation frequency for many DNA polymerases, indicating the real fidelity of a DNA polymerase should be evaluated using the general misincorporation frequency. Copyright © 2018 Elsevier Inc. All rights reserved.

Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions

PubMed Central

Shanbhag, Vinit; Sachdev, Shrikesh; Flores, Jacqueline A.; Modak, Mukund J.; Singh, Kamalendra

2018-01-01

DNA polymerases are essential for genome replication, DNA repair and translesion DNA synthesis (TLS). Broadly, these enzymes belong to two groups: replicative and non-replicative DNA polymerases. A considerable body of data suggests that both groups of DNA polymerases are associated with cancer. Many mutations in cancer cells are either the result of error-prone DNA synthesis by non-replicative polymerases, or the inability of replicative DNA polymerases to proofread mismatched nucleotides due to mutations in 3′-5′ exonuclease activity. Moreover, non-replicative, TLS-capable DNA polymerases can negatively impact cancer treatment by synthesizing DNA past lesions generated from treatments such as cisplatin, oxaliplatin, etoposide, bleomycin, and radiotherapy. Hence, the inhibition of DNA polymerases in tumor cells has the potential to enhance treatment outcomes. Here, we review the association of DNA polymerases in cancer from the A and B families, which participate in lesion bypass, and conduct gene replication. We also discuss possible therapeutic interventions that could be used to maneuver the role of these enzymes in tumorigenesis. PMID:29301327

Selection and stopping in voluntary action: A meta-analysis and combined fMRI study☆

PubMed Central

Rae, Charlotte L.; Hughes, Laura E.; Weaver, Chelan; Anderson, Michael C.; Rowe, James B.

2014-01-01

Voluntary action control requires selection of appropriate responses and stopping of inappropriate responses. Selection and stopping are often investigated separately, but they appear to recruit similar brain regions, including the pre-supplementary motor area (preSMA) and inferior frontal gyrus. We therefore examined the evidence for overlap of selection and stopping using two approaches: a meta-analysis of existing studies of selection and stopping, and a novel within-subject fMRI study in which action selection and a stop signal task were combined factorially. The novel fMRI study also permitted us to investigate hypotheses regarding a common mechanism for selection and stopping. The preSMA was identified by both methods as common to selection and stopping. However, stopping a selected action did not recruit preSMA more than stopping a specified action, nor did stop signal reaction times differ significantly across the two conditions. These findings suggest that the preSMA supports both action selection and stopping, but the two processes may not require access to a common inhibition mechanism. Instead, the preSMA might represent information about potential actions that is used in both action selection and stopping in order to resolve conflict between competing available responses. PMID:24128740

Safer stops for vulnerable customers

DOT National Transportation Integrated Search

2003-03-01

This synthesis report presents a brief synopsis of the current literature and technologies being used in the development of safer and more secure bus stops. While the focus is more specifically with regard to vulnerable populations - women, children,...

Eukaryotic DNA polymerase ζ

PubMed Central

Makarova, Alena V.; Burgers, Peter M.

2015-01-01

This review focuses on eukaryotic DNA polymerase ζ (Pol ζ), the enzyme responsible for the bulk of mutagenesis in eukaryotic cells in response to DNA damage. Pol ζ is also responsible for a large portion of mutagenesis during normal cell growth, in response to spontaneous damage or to certain DNA structures and other blocks that stall DNA replication forks. Novel insights in mutagenesis have been derived from recent advances in the elucidation of the subunit structure of Pol ζ. The lagging strand DNA polymerase δ shares the small Pol31 and Pol32 subunits with the Rev3-Rev7 core assembly giving a four subunit Pol ζ complex that is the active form in mutagenesis. Furthermore, Pol ζ forms essential interactions with the mutasome assembly factor Rev1 and with proliferating cell nuclear antigen (PCNA). These interactions are modulated by posttranslational modifications such as ubiquitination and phosphorylation that enhance translesion synthesis (TLS) and mutagenesis. PMID:25737057

A fluorescence-based alkaline phosphatase-coupled polymerase assay for identification of inhibitors of dengue virus RNA-dependent RNA polymerase.

PubMed

Niyomrattanakit, Pornwaratt; Abas, Siti Nurdiana; Lim, Chin Chin; Beer, David; Shi, Pei-Yong; Chen, Yen-Liang

2011-02-01

The flaviviral RNA-dependent RNA polymerase (RdRp) is an attractive drug target. To discover new inhibitors of dengue virus RdRp, the authors have developed a fluorescence-based alkaline phosphatase-coupled polymerase assay (FAPA) for high-throughput screening (HTS). A modified nucleotide analogue (2'-[2-benzothiazoyl]-6'-hydroxybenzothiazole) conjugated adenosine triphosphate (BBT-ATP) and 3'UTR-U(30) RNA were used as substrates. After the polymerase reaction, treatment with alkaline phosphatase liberates the BBT fluorophore from the polymerase reaction by-product, BBT(PPi), which can be detected at excitation and emission wavelengths of 422 and 566 nm, respectively. The assay was evaluated by examining the time dependency, assay reagent effects, reaction kinetics, and signal stability and was validated with 3'dATP and an adenosine-nucleotide triphosphate inhibitor, giving IC(50) values of 0.13 µM and 0.01 µM, respectively. A pilot screen of a diverse compound library of 40,572 compounds at 20 µM demonstrated good performance with an average Z factor of 0.81. The versatility and robustness of FAPA were evaluated with another substrate system, BBT-GTP paired with 3'UTR-C(30) RNA. The FAPA method presented here can be readily adapted for other nucleotide-dependent enzymes that generate PPi.

Stress, social support, and stopping smoking after myocardial infarction in England.

PubMed Central

Greenwood, D C; Muir, K R; Packham, C J; Madeley, R J

1995-01-01

STUDY OBJECTIVE--To examine the effect on mortality of stopping smoking after myocardial infarction and the psychosocial factors that influence the decision to stop. DESIGN--Analysis of smokers in a large prospective study. Self completed questionnaires provided information on psychosocial factors. SETTING--Coronary care units at six English hospitals participating in a multicentre clinical trial. SUBJECTS--These comprised consenting myocardial infarction survivors who had been identified as smokers and who completed questionnaires within seven days of infarct at six hospitals participating in the Anglo-Scandinavian study of early thrombolysis. The 532 patients identified have been followed for over five and a half years. The main outcome measure was five year all cause mortality. MAIN RESULTS--Smokers who stopped within one month showed significantly reduced mortality compared with those who persisted, adjusting for other prognostic indicators (odds ratio 0.56, 95% confidence interval 0.33, 0.98). Overall, 74% stopped smoking. Being married, low life stress levels before infarct, and higher social class were associated with stopping smoking but the differentials were small. Of the clinical variables, a final diagnosis of definite myocardial infarction was associated with stopping smoking. All associations remained after multiple logistic regression. CONCLUSION--Smoking cessation can halve the smokers' odds of dying after myocardial infarction and psychosocial factors play a small but important role in the important decision to stop smoking. Health professionals should continue to stress the importance of stopping smoking to all patients as there is little evidence to support specific directing of advice to relatively "stress or "socially isolated" groups. PMID:8596092

A Pause-then-Cancel model of stopping: evidence from basal ganglia neurophysiology.

PubMed

Schmidt, Robert; Berke, Joshua D

2017-04-19

Many studies have implicated the basal ganglia in the suppression of action impulses ('stopping'). Here, we discuss recent neurophysiological evidence that distinct hypothesized processes involved in action preparation and cancellation can be mapped onto distinct basal ganglia cell types and pathways. We examine how movement-related activity in the striatum is related to a 'Go' process and how going may be modulated by brief epochs of beta oscillations. We then describe how, rather than a unitary 'Stop' process, there appear to be separate, complementary 'Pause' and 'Cancel' mechanisms. We discuss the implications of these stopping subprocesses for the interpretation of the stop-signal reaction time-in particular, some activity that seems too slow to causally contribute to stopping when assuming a single Stop processes may actually be fast enough under a Pause-then-Cancel model. Finally, we suggest that combining complementary neural mechanisms that emphasize speed or accuracy respectively may serve more generally to optimize speed-accuracy trade-offs.This article is part of the themed issue 'Movement suppression: brain mechanisms for stopping and stillness'. © 2017 The Author(s).

DNA Carrier Testing and Newborn Screening for Maple Syrup Urine Disease in Old Order Mennonite Communities

PubMed Central

Carleton, Stephanie M.; Peck, Dawn S.; Grasela, Julie; Dietiker, Kristin L.

2010-01-01

Maple syrup urine disease (MSUD) is an inherited metabolic disorder caused by mutations in the branched chain α-keto acid dehydrogenase complex. Worldwide incidence of MSUD is 1:225,000 live births. However, within Old Order Mennonite communities, the incidence is 1:150 live births and results from a common tyrosine to asparagine substitution (Y438N) in the E1α subunit of branched chain α-keto acid dehydrogenase. We developed a new DNA diagnostic assay utilizing TaqMan® technology and compared its efficacy, sensitivity, and duration with an existing polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) assay. Carrier testing was performed by both TaqMan technology and PCR-RFLP on DNA isolated from buccal swabs of 160 individuals as well as from buccal swabs and blood spots of nine at-risk newborns; assay time, sensitivity, and reliability were also evaluated. The TaqMan assay, like the PCR-RFLP assay, accurately determined Y438N E1α allele status. However, the TaqMan assay appeared (1) more sensitive than the PCR-RFLP assay, requiring 10-fold less DNA (10 ng) to reliably determine genotype status and (2) faster, reducing the assay time required for diagnosis from ∼12 to 5 h. TaqMan technology allowed more rapid DNA diagnoses of MSUD in the neonate, thereby reducing the likelihood of neurological impairment while enhancing health and prognosis for affected infants. PMID:20136525

Stochastic resetting in backtrack recovery by RNA polymerases

NASA Astrophysics Data System (ADS)

Roldán, Édgar; Lisica, Ana; Sánchez-Taltavull, Daniel; Grill, Stephan W.

2016-06-01

Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random walk along the DNA template. Recovery of polymerases from the transcriptionally inactive backtracked state is determined by a kinetic competition between one-dimensional diffusion and RNA cleavage. Here we describe backtrack recovery as a continuous-time random walk, where the time for a polymerase to recover from a backtrack of a given depth is described as a first-passage time of a random walker to reach an absorbing state. We represent RNA cleavage as a stochastic resetting process and derive exact expressions for the recovery time distributions and mean recovery times from a given initial backtrack depth for both continuous and discrete-lattice descriptions of the random walk. We show that recovery time statistics do not depend on the discreteness of the DNA lattice when the rate of one-dimensional diffusion is large compared to the rate of cleavage.

A Conceptual Approach for Optimising Bus Stop Spacing

NASA Astrophysics Data System (ADS)

Johar, Amita; Jain, S. S.; Garg, P. k.

2017-06-01

An efficient public transportation system is essential of any country. The growth, development and shape of the urban areas are mainly due to availability of good transportation (Shah et al. in Inst Town Plan India J 5(3):50-59, 1). In developing countries, like India, travel by local bus in a city is very common. The accidents, congestion, pollution and appropriate location of bus stops are the major problems arising in metropolitan cities. Among all the metropolitan cities in India, Delhi has highest percentage of growth of population and vehicles. Therefore, it is important to adopt efficient and effective ways to improve mobility in different metropolitan cities in order to overcome the problem and to reduce the number of private vehicles on the road. The primary objective of this paper is to present a methodology for developing a model for optimum bus stop spacing (OBSS). It describes the evaluation of existing urban bus route, data collection, development of model for optimizing urban bus route and application of model. In this work, the bus passenger generalized cost method is used to optimize the spacing between bus stops. For the development of model, a computer program is required to be written. The applicability of the model has been evaluated by taking the data of urban bus route of Delhi Transport Corporation (DTC) in Excel sheet in first phase. Later on, it is proposed to develop a programming in C++ language. The developed model is expected to be useful to transport planner for rational design of the spacing of bus stops to save travel time and to generalize operating cost. After analysis it is found that spacing between the bus stop comes out to be between 250 and 500 m. The Proposed Spacing of bus stops is done considering the points that they don't come nearer to metro/rail station, entry or exit of flyover and near traffic signal.

Stopping power measurements with the Time-of-Flight (ToF) technique

DOE PAGES

Fontana, Cristiano L.; Chen, Chien-Hung; Crespillo, Miguel L.; ...

2015-11-10

In our review of measurements of the stopping power of ions in matter is presented along with new measurements of the stopping powers of O, Si, Ti, and Au ions in self-supporting thin foils of SiO 2, Nb 2O 5, and Ta 2O 5. Moreover, a Time-of-Flight system at the Ion Beam Materials Laboratory at the University of Tennessee, Knoxville, was used in transmission geometry in order to reduce experimental uncertainties. Finally, the resulting stopping powers show good precision and accuracy and corroborate previously quoted values in the literature. New stopping data are determined.

Stopping power measurements with the Time-of-Flight (ToF) technique

NASA Astrophysics Data System (ADS)

Fontana, Cristiano L.; Chen, Chien-Hung; Crespillo, Miguel L.; Graham, Joseph T.; Xue, Haizhou; Zhang, Yanwen; Weber, William J.

2016-01-01

A review of measurements of the stopping power of ions in matter is presented along with new measurements of the stopping powers of O, Si, Ti, and Au ions in self-supporting thin foils of SiO2, Nb2O5, and Ta2O5. A Time-of-Flight system at the Ion Beam Materials Laboratory at the University of Tennessee, Knoxville, was used in transmission geometry in order to reduce experimental uncertainties. The resulting stopping powers show good precision and accuracy and corroborate previously quoted values in the literature. New stopping data are determined.

PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates.

PubMed Central

Barnes, W M

1994-01-01

A target length limitation to PCR amplification of DNA has been identified and addressed. Concomitantly, the base-pair fidelity, the ability to use PCR products as primers, and the maximum yield of target fragment were increased. These improvements were achieved by the combination of a high level of an exonuclease-free, N-terminal deletion mutant of Taq DNA polymerase, Klentaq1, with a very low level of a thermostable DNA polymerase exhibiting a 3'-exonuclease activity (Pfu, Vent, or Deep Vent). At least 35 kb can be amplified to high yields from 1 ng of lambda DNA template. Images PMID:8134376

Detection of adulterated murine components in meat products by TaqMan© real-time PCR.

PubMed

Fang, Xin; Zhang, Chi

2016-02-01

Using murine meat to substitute mutton has been identified as a new type of meat fraud in China, yet no detection method for murine species has been reported. Here, three kinds of rodent were used as target species to establish a murine-specific real-time PCR method of detection. The mitochondrial cytochrome b gene (cytb) of each target was sequenced and a TaqMan probe was designed based on the cytb. Simultaneously, an internal positive control (IPC) plasmid along with its respective probe were designed to monitor the PCR reaction. As a result, the duplex real-time PCR system was verified to be specific. The limit of detection (LOD) was lower than 1 pg of DNA per reaction and 0.1% murine contamination in meat mixtures. Standard curves were generated for a quantitative analysis. Thus, this study provided a new tool to control the quality of meat products for official and third-party laboratories. Copyright © 2015. Published by Elsevier Ltd.

Big Data Discovery and Access Services through NOAA OneStop

NASA Astrophysics Data System (ADS)

Casey, K. S.; Neufeld, D.; Ritchey, N. A.; Relph, J.; Fischman, D.; Baldwin, R.

2017-12-01

The NOAA OneStop Project was created as a pathfinder effort to to improve the discovery of, access to, and usability of NOAA's vast and diverse collection of big data. OneStop is led by the NOAA/NESDIS National Centers for Environmental Information (NCEI), and is seen as a key NESDIS contribution to NOAA's open data and data stewardship efforts. OneStop consists of an entire framework of services, from storage and interoperable access services at the base, through metadata and catalog services in the middle, to a modern user interface experience at the top. Importantly, it is an open framework where external tools and services can connect at whichever level is most appropriate. Since the beta release of the OneStop user interface at the 2016 Fall AGU meeting, significant progress has been made improving and modernizing many NOAA data collections to optimize their use within the framework. In addition, OneStop has made progress implementing robust metadata management and catalog systems at the collection and granule level and improving the user experience with the web interface. This progress will be summarized and the results of extensive user testing including professional usability studies will be reviewed. Key big data technologies supporting the framework will be presented and a community input sought on the future directions of the OneStop Project.

Effect of Weight Transfer on a Vehicle's Stopping Distance.

ERIC Educational Resources Information Center

Whitmire, Daniel P.; Alleman, Timothy J.

1979-01-01

An analysis of the minimum stopping distance problem is presented taking into account the effect of weight transfer on nonskidding vehicles and front- or rear-wheels-skidding vehicles. Expressions for the minimum stopping distances are given in terms of vehicle geometry and the coefficients of friction. (Author/BB)

Stopping epilepsy treatment in seizure remission: Good or bad or both?

PubMed

Schmidt, Dieter; Sillanpää, Matti

2017-01-01

To review the outcome of epilepsy after stopping antiepileptic drugs in remission. Stopping antiepileptic drugs (AEDs) in remission is routinely done in many patients. Although the consequences of an unexpected relapse seizure in the 2 years after stopping AEDs may cause anguish and social issues, the impact on the long term seizure outlook of the epilepsy is minimal, if any. Discontinuation of drug treatment does not seem to affect the long-term prognosis but exposes patients who were seizure-free for years to a transient two-fold risk of seizures for the first 2 years after stopping AEDs. In addition, 20% of patients who were seizure-free for years, do not become seizure-free immediately after restarting AED treatment after relapse. The list of potential pitfalls is long. Patients with juvenile myoclonic epilepsy, those with prior withdrawal attempts and late remission have a higher risk of relapse. Stopping AEDs in remission does not affect the long-term patterns of epilepsy and some patients report a better general health in a life without AEDs. High-risk patients should not be generally encouraged to stop their AEDs in remission. We need new drugs that combine anti-seizure and antiepileptogenic effects to prevent seizure relapse and flare up of epilepsy after stopping AEDs in remission. Copyright © 2016 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Modeling the effect of bus stops on capacity of curb lane

NASA Astrophysics Data System (ADS)

Luo, Qingyu; Zheng, Tianyao; Wu, Wenjing; Jia, Hongfei; Li, Jin

With the increase of buses and bus lines, a negative effect on road section capacity is made by the prolonged delay and queuing time at bus stops. However, existing methods of measuring the negative effect pay little attention to different bus stop types in the curb lanes. This paper uses Gap theory and Queuing theory to build models for effect-time and potential capacity in different conditions, including curbside bus stops, bus bays with overflow and bus bays without overflow. In order to make the effect-time models accurate and reliable, two types of probabilities are introduced. One is the probability that the dwell time is less than the headway of curb lane at curbside bus stops; the other is the overflow probability at bus bays. Based on the fundamental road capacity model and effect-time models, potential capacity models of curb lane are designed. The new models are calibrated by the survey data from Changchun City, and verified by the simulation software of VISSIM. Furthermore, with different arrival rates of vehicles, the setting conditions of bus stops are researched. Results show that the potential capacity models have high precision. They can offer a reference for recognizing the effect of bus stops on the capacity of curb lane, which can provide a basis for planning, design and management of urban roads and bus stops.

Polymerase III transcription factor B activity is reduced in extracts of growth-restricted cells.

PubMed Central

Tower, J; Sollner-Webb, B

1988-01-01

Extracts of cells that are down-regulated for transcription by RNA polymerase I and RNA polymerase III exhibit a reduced in vitro transcriptional capacity. We have recently demonstrated that the down-regulation of polymerase I transcription in extracts of cycloheximide-treated and stationary-phase cells results from a lack of an activated subform of RNA polymerase I which is essential for rDNA transcription. To examine whether polymerase III transcriptional down-regulation occurs by a similar mechanism, the polymerase III transcription factors were isolated and added singly and in pairs to control cell extracts and to extracts of cells that had reduced polymerase III transcriptional activity due to cycloheximide treatment or growth into stationary phase. These down-regulations result from a specific reduction in TFIIIB; TFIIIC and polymerase III activities remain relatively constant. Thus, although transcription by both polymerase III and polymerase I is substantially decreased in extracts of growth-arrested cells, this regulation is brought about by reduction of different kinds of activities: a component of the polymerase III stable transcription complex in the former case and the activated subform of RNA polymerase I in the latter. Images PMID:3352599

A TaqMan real-time PCR method based on alternative oxidase genes for detection of plant species in animal feed samples.

PubMed

Campos, Maria Doroteia; Valadas, Vera; Campos, Catarina; Morello, Laura; Braglia, Luca; Breviario, Diego; Cardoso, Hélia G

2018-01-01

Traceability of processed food and feed products has been gaining importance due to the impact that those products can have on human/animal health and to the associated economic and legal concerns, often related to adulterations and frauds as it can be the case for meat and milk. Despite mandatory traceability requirements for the analysis of feed composition, few reliable and accurate methods are presently available to enforce the legislative frame and allow the authentication of animal feeds. In this study, nine sensitive and species-specific real-time PCR TaqMan MGB assays are described for plant species detection in animal feed samples. The method is based on selective real-time qPCR (RT-qPCR) amplification of target genes belonging to the alternative oxidase (AOX) gene family. The plant species selected for detection in feed samples were wheat, maize, barley, soybean, rice and sunflower as common components of feeds, and cotton, flax and peanut as possible undesirable contaminants. The obtained results were compared with end-point PCR methodology. The applicability of the AOX TaqMan assays was evaluated through the screening of commercial feed samples, and by the analysis of plant mixtures with known composition. The RT-qPCR methodology allowed the detection of the most abundant species in feeds but also the identification of contaminant species present in lower amounts, down to 1% w/w. AOX-based methodology provides a suitable molecular marker approach to ascertain plant species composition of animal feed samples, thus supporting feed control and enforcement of the feed sector and animal production.

Integrated microfluidic card with TaqMan probes and high-resolution melt analysis to detect tuberculosis drug resistance mutations across 10 genes.

PubMed

Pholwat, Suporn; Liu, Jie; Stroup, Suzanne; Gratz, Jean; Banu, Sayera; Rahman, S M Mazidur; Ferdous, Sara Sabrina; Foongladda, Suporn; Boonlert, Duangjai; Ogarkov, Oleg; Zhdanova, Svetlana; Kibiki, Gibson; Heysell, Scott; Houpt, Eric

2015-02-24

Genotypic methods for drug susceptibility testing of Mycobacterium tuberculosis are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations. Twenty-seven primer pairs and 40 probes were designed to interrogate 3,200 base pairs of critical regions of the inhA, katG, rpoB, embB, rpsL, rrs, eis, gyrA, gyrB, and pncA genes. The method was evaluated on 230 clinical M. tuberculosis isolates from around the world, and it yielded 96.1% accuracy (2,431/2,530) in comparison to that of Sanger sequencing and 87% accuracy in comparison to that of the slow culture-based susceptibility testing. This TAC-HRM method integrates assays for 10 genes to yield fast, comprehensive, and accurate drug susceptibility results for the 9 major antibiotics used to treat TB and could be deployed to improve treatment outcomes. Multidrug-resistant tuberculosis threatens global tuberculosis control efforts. Optimal therapy utilizes susceptibility test results to guide individualized treatment regimens; however, the susceptibility testing methods in use are technically difficult and slow. We developed an integrated TaqMan array card method with high-resolution melt analysis that interrogates 10 genes to yield a fast, comprehensive, and accurate drug susceptibility result for the 9 major antituberculosis antibiotics. Copyright © 2015 Pholwat et al.

Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement

NASA Astrophysics Data System (ADS)

Yuce, Meral; Budak, Hikmet

2014-12-01

Impact of dispersion quality of NH2-MWCNTs (13-18 nm in diameter with a length between 1 and 12 µm, >99 % purity) in the amplification efficiency of a random DNA oligonucleotide library (96 bp) was investigated. Amplification yield in the presence of non-filtered NH2-MWCNT dispersion, filtered NH2-MWCNT dispersion and surface-attached NH2-MWCNTs was explored, and physical interactions between NH2-MWCNTs and major PCR reagents including DNA template, wild type Taq DNA polymerase enzyme and primers were determined using high resolution polyacrylamide gel electrophoresis, dynamic light scattering, UV-Vis-NIR spectroscopy and scanning electron microscopy techniques. The results revealed that presence of NH2-MWCNT dispersion which was sonicated, centrifuged and filtered, enhanced the total PCR efficiency up to 70 % while the presence of NH2-MWCNT only centrifuged after sonication, inhibited the reaction significantly at similar concentrations. Furthermore, the NH2-MWCNTs coupled covalently onto magnetic microspheres, contributed for the specificity enhancement whilst decreasing the amplification efficiency by 30 % at the maximum concentration, which suggests a removable enhancement system for sensitive applications. On the other hand, the relative hydrodynamic size distribution measurements displayed a clear difference between the filtered NH2 and non-filtered NH2-MWCNT water dispersions, which justifies the inhibition of the amplification by the non-filtered NH2-MWCNTs containing big agglomerates and bundles. Finally, we demonstrated that major PCR components adsorb onto the NH2-MWCNTs with diverse affinities, and maintain their functions after adsorption, which provides a good framework to further develop tunable NH2-MWCNT-carriers to be utilized in various nanobiotechnology and material science applications.

Measurement and interpretation of electron angle at MABE beam stop

NASA Astrophysics Data System (ADS)

Sanford, T. W. L.; Coleman, P. D.; Poukey, J. W.

1985-02-01

The mean angle of incidence at the beam stop of a 60 kA, 7 MV annular electron beam, in the 20 kG guide field of the MABE accelerator, was determined. Radiation dose measured in TLD arrays mounted downstream of the stop is compared with the radiation dose expected using a CYLTRAN Monte Carlo simulation of the electron/photon transport in the stop as a function of incident angles and energies. All radiation profiles measured are well fit, if the electrons are assumed to be incident with a polar angle theta of 15(0) + or - 2(0). A comparison of theta with that expected from the Adler-Miller model, and a MAGIC code simulation of beam behavior at the stop enables the mean transverse beam velocity to be estimated.

Measurement and interpretation of electron angle at MABE beam stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanford, T.W.L.; Coleman, P.D.; Poukey, J.W.

1985-01-01

This analysis shows that radiation measurements combined with a sophisticated simulation provides a simple but powerful tool for estimating beam temperature in intense pulsed annular electron-beam accelerators. Specifically, the mean angle of incidence of a 60 kA, 7 MeV annular electron-beam at the beam stop of the MABE accelerator and the transverse beam temperature are determined. The angle is extracted by comparing dose profiles measured downstream of the stop with that expected from a simulation of the electron/photon transport in the stop. By calculating and removing the effect on the trajectories due to the change in electric field near themore » stop, the beam temperature is determined. Such measurements help give insight to beam generation and propagation within the accelerator. 9 refs., 6 figs., 1 tab.« less

Measurement and interpretation of electron angle at mabe beam stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanford, T.W.L.; Coleman, P.D.; Poukey, J.W.

1985-10-01

This analysis shows that radiation measurements combined with a sophisticated simulation provides a simple but powerful tool for estimating beam temperature in intense pulsed annular electron-beam accelerators. Specifically, the mean angle of incidence of a 60 kA, 7 MeV annular electron-beam at the beam stop of the MABE accelerator and the transverse beam temperature are determined. The angle is extracted by comparing dose profiles measured downstream of the stop with that expected from a simulation of the electron/photon transport in the stop. By calculating and removing the effect on the trajectories due to the change in electric field near themore » stop, the beam temperature is determined. Such measurements help give insight to beam generation and propagation within the accelerator.« less

Measurement and interpretation of electron angle at MABE beam stop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanford, T.W.L.; Coleman, P.D.; Poukey, J.W.

1985-02-01

The mean angle of incidence at the beam stop of a 60 kA, 7 MV annular electron beam, in the 20 kG guide field of the MABE accelerator, is determined. Radiation dose measured in TLD arrays mounted downstream of the stop is compared with the radiation dose expected using a CYLTRAN Monte Carlo simulation of the electron/photon transport in the stop as a function of incident angles and energies. All radiation profiles measured are well fit, if the electrons are assumed to be incident with a polar angle theta of 15/sup 0/ +- 2/sup 0/. Comparing this theta with thatmore » expected from the Adler-Miller model, and a MAGIC code simulation of beam behavior at the stop enables the mean transverse beam velocity to be estimated.« less

Alternative Fuels Data Center: Truck Stop Electrification Site Data

Science.gov Websites

Collection Methods Tools Printable Version Share this resource Send a link to Alternative Fuels Data Center: Truck Stop Electrification Site Data Collection Methods to someone by E-mail Share Alternative Fuels Data Center: Truck Stop Electrification Site Data Collection Methods on Facebook Tweet about

Stopping power beyond the adiabatic approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caro, M.; Correa, A. A.; Artacho, E.

2017-06-01

Energetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on themore » time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. Particularly, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons.« less

Stopped-Rotor Cyclocopter for Venus Exploration

NASA Technical Reports Server (NTRS)

Husseyin, Sema; Warmbrodt, William G.

2016-01-01

The cyclocopter system can use two or more rotating blades to create lift, propulsion and control. This system is explored for its use in a mission to Venus. Cyclocopters are not limited to speed and altitude and can provide 360 degrees of vector thrusting which is favorable for good maneuverability. The novel aspect of this study is that no other cyclocopter configuration has been previously proposed for Venus or any (terrestrial or otherwise) exploration application where the cyclocopters rotating blades are stopped, and act as fixed wings. The design considerations for this unique planetary aerial vehicle are discussed in terms of implementing the use of a cyclorotor blade system combined with a fixed wing and stopped rotor mechanism. This proposed concept avoids many of the disadvantages of conventional-rotor stopped-rotor concepts and accounts for the high temperature, pressure and atmospheric density present on Venus while carrying out the mission objectives. The fundamental goal is to find an ideal design that implements the combined use of cyclorotors and fixed wing surfaces. These design concepts will be analyzed with the computational fluid dynamics tool RotCFD for aerodynamic assessment. Aspects of the vehicle design is 3D printed and tested in a small water tunnel or wind tunnel.

Towards a model-based cognitive neuroscience of stopping - a neuroimaging perspective.

PubMed

Sebastian, Alexandra; Forstmann, Birte U; Matzke, Dora

2018-07-01

Our understanding of the neural correlates of response inhibition has greatly advanced over the last decade. Nevertheless the specific function of regions within this stopping network remains controversial. The traditional neuroimaging approach cannot capture many processes affecting stopping performance. Despite the shortcomings of the traditional neuroimaging approach and a great progress in mathematical and computational models of stopping, model-based cognitive neuroscience approaches in human neuroimaging studies are largely lacking. To foster model-based approaches to ultimately gain a deeper understanding of the neural signature of stopping, we outline the most prominent models of response inhibition and recent advances in the field. We highlight how a model-based approach in clinical samples has improved our understanding of altered cognitive functions in these disorders. Moreover, we show how linking evidence-accumulation models and neuroimaging data improves the identification of neural pathways involved in the stopping process and helps to delineate these from neural networks of related but distinct functions. In conclusion, adopting a model-based approach is indispensable to identifying the actual neural processes underlying stopping. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

RNA Polymerase II Elongation Control

PubMed Central

Zhou, Qiang; Li, Tiandao; Price, David H.

2014-01-01

Regulation of the elongation phase of transcription by RNA Polymerase II (Pol II) is utilized extensively to generate the pattern of mRNAs needed to specify cell types and to respond to environmental changes. After Pol II initiates, negative elongation factors cause it to pause in a promoter proximal position. These polymerases are poised to respond to the positive transcription elongation factor, P-TEFb, and then enter productive elongation only under the appropriate set of signals to generate full length properly processed mRNAs. Recent global analyses of Pol II and elongation factors, mechanisms that regulate P-TEFb involving the 7SK snRNP, factors that control both the negative and positive elongation properties of Pol II and the mRNA processing events that are coupled with elongation are discussed. PMID:22404626

Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets.

PubMed

Babu, Binoy; Jeyaprakash, Ayyamperumal; Jones, Debra; Schubert, Timothy S; Baker, Carlye; Washburn, Brian K; Miller, Steven H; Poduch, Kristina; Knox, Gary W; Ochoa-Corona, Francisco M; Paret, Mathews L

2016-09-01

Rose rosette virus (RRV), belonging to the genus Emaravirus, is a highly destructive pathogen that causes rose rosette disease. The disease is a major concern for the rose industry in the U.S. due to the lack of highly sensitive methods for early detection of RRV. This is critical, as early identification of the infected plants and eradication is necessary in minimizing the risks associated with the spread of the disease. A highly reliable, specific and sensitive detection assay is thus required to test and confirm the presence of RRV in suspected plant samples. In this study a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of RRV from infected roses, utilizing multiple gene targets. Four pairs of primers and probes; two of them (RRV_2-1 and RRV_2-2) based on the consensus sequences of the glycoprotein gene (RNA2) and the other two (RRV_3-2 and RRV_3-5) based on the nucleocapsid gene (RNA3) were designed. The specificity of the primers and probes was evaluated against other representative viruses infecting roses, belonging to the genera Alfamovirus, Cucumovirus, Ilarvirus, Nepovirus, Tobamovirus, and Tospovirus and one Emaravirus (Wheat mosaic virus). Dilution assays using the in vitro transcripts (spiked with total RNA from healthy plants, and non-spiked) showed that all the primers and probes are highly sensitive in consistently detecting RRV with a detection limit of 1 fg. Testing of the infected plants over a period of time (three times in monthly intervals) indicated high reproducibility, with the primer/probe RRV_3-5 showing 100% positive detection, while RRV_2-1, RRV_2-2 and RRV_3-2 showed 90% positive detection. The developed real-time RT-PCR assay is reliable, highly sensitive, and can be easily used in diagnostic laboratories for testing and confirmation of RRV. Copyright © 2016 Elsevier B.V. All rights reserved.

Using stop signals to reduce impulsive choices for palatable unhealthy foods.

PubMed

Veling, Harm; Aarts, Henk; Stroebe, Wolfgang

2013-05-01

Exposure to palatable foods in the environment can trigger impulsive reactions to obtain them, which may lead to unhealthy food choices and eating behaviour. Two studies tested the fundamental question whether impulsive unhealthy food choices can be altered by means of linking unhealthy palatable foods to behavioural stop signals. Study 1 adopted a 2 (signal condition: stop signal vs. control) by 2 (appetite: low vs. high) between-subjects design. Study 2 adopted a 2 (signal condition: stop signal vs. control) between-subjects design with frequency to consume unhealthy palatable foods as a continuous factor. Participants performed a task in which behavioural stop signals were either consistently (or not) presented in close temporal proximity to unhealthy palatable snack foods. Next, participants were given the opportunity to select snacks that they would like to consume. Two studies showed that participants were less likely to select unhealthy palatable foods that had been presented near stop signals, and that they selected healthy foods instead. Importantly, this reduction in choices for palatable foods was especially observed when participants' appetite was relatively high (Study 1), or when this food was part of their habit to frequently consume this food (Study 2). These findings show that a short stop signal intervention in which palatable foods are presented in close temporal proximity of stop signals can reduce palatable food choices by modifying an impulsive determinant of eating behaviour. What is already known on this subject? Exposure to unhealthy palatable foods in the environment can lead to impulsive food choices. People's habits towards unhealthy palatable foods and their current state of appetite are important determinants of such impulsive food choices. This impulsive behaviour is hard to change. What this study add? Linking unhealthy palatable foods to behavioural stop signals reduces choices for these foods, and increases healthy food choices

Development and evaluation of a Quadruplex Taq Man real-time PCR assay for simultaneous detection of clinical isolates of Enterococcus faecalis, Enterococcus faecium and their vanA and vanB genotypes.

PubMed

Naserpour Farivar, Taghi; Najafipour, Reza; Johari, Pouran; Aslanimehr, Masoumeh; Peymani, Amir; Jahani Hashemi, Hoasan; Mirzaui, Baman

2014-10-01

We developed and evaluated the utility of a quadruplex Taqman real-time PCR assay that allows simultaneous identification of vancomycin-resistant genotypes and clinically relevant enterococci. The specificity of the assay was tested using reference strains of vancomycin-resistant and susceptible enterococci. In total, 193 clinical isolates were identified and subsequently genotyped using a Quadruplex Taqman real-time PCR assay and melting curve analysis. Representative Quadruplex Taqman real-time PCR amplification curve were obtained for Enterococcus faecium, Enterococcus faecalis, vanA-containing E. faecium, vanB-containing E. faecalis. Phenotypic and genotypic analysis of the isolates gave same results for 82 enterococcal isolates, while in 5 isolates, they were inconsistent. We had three mixed strains, which were detected by the TaqMan real-time PCR assay and could not be identified correctly using phenotypic methods. Vancomycin resistant enterococci (VRE) genotyping and identification of clinically relevant enterococci were rapidly and correctly performed using TaqMan real-time multiplex real-time PCR assay.

Bucket shaking stops bunch dancing in Tevatron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burov, A.; Tan, C.Y.; /Fermilab

2011-03-01

Bunches in Tevatron are known to be longitudinally unstable: their collective oscillations, also called dancing bunches, persist without any signs of decay. Typically, a damper is used to stop these oscillations, but recently, it was theoretically predicted that the oscillations can be stabilized by means of small bucket shaking. Dedicated measurements in Tevatron have shown that this method does stop the dancing. According to predictions of Refs. [2,3], the flattening of the bunch distribution at low amplitudes should make the bunch more stable against LLD. An experiment has been devised to flatten the distribution by modulating the RF phase atmore » the low-amplitude synchrotron frequency for a few degrees of amplitude. These beam studies show that stabilisation really happens. After several consecutive shakings, the dancing disappears and the resulting bunch profile becomes smoother at the top. Although not shown in this report, sometimes a little divot forms at the centre of the distribution. These experiments confirm that resonant RF shaking flattens the bunch distribution at low amplitudes, and the dancing stops.« less

The frequentist implications of optional stopping on Bayesian hypothesis tests.

PubMed

Sanborn, Adam N; Hills, Thomas T

2014-04-01

Null hypothesis significance testing (NHST) is the most commonly used statistical methodology in psychology. The probability of achieving a value as extreme or more extreme than the statistic obtained from the data is evaluated, and if it is low enough, the null hypothesis is rejected. However, because common experimental practice often clashes with the assumptions underlying NHST, these calculated probabilities are often incorrect. Most commonly, experimenters use tests that assume that sample sizes are fixed in advance of data collection but then use the data to determine when to stop; in the limit, experimenters can use data monitoring to guarantee that the null hypothesis will be rejected. Bayesian hypothesis testing (BHT) provides a solution to these ills because the stopping rule used is irrelevant to the calculation of a Bayes factor. In addition, there are strong mathematical guarantees on the frequentist properties of BHT that are comforting for researchers concerned that stopping rules could influence the Bayes factors produced. Here, we show that these guaranteed bounds have limited scope and often do not apply in psychological research. Specifically, we quantitatively demonstrate the impact of optional stopping on the resulting Bayes factors in two common situations: (1) when the truth is a combination of the hypotheses, such as in a heterogeneous population, and (2) when a hypothesis is composite-taking multiple parameter values-such as the alternative hypothesis in a t-test. We found that, for these situations, while the Bayesian interpretation remains correct regardless of the stopping rule used, the choice of stopping rule can, in some situations, greatly increase the chance of experimenters finding evidence in the direction they desire. We suggest ways to control these frequentist implications of stopping rules on BHT.

7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7IdTP incorporation during PCR-amplification and protection from endodeoxyribonuclease hydrolysis.

PubMed Central

Seela, F; Röling, A

1992-01-01

The enzymatic synthesis of 7-deazapurine nucleoside containing DNA (501 bp) is performed by PCR-amplification (Taq polymerase) using a pUC18 plasmid DNA as template and the triphosphates of 7-deaza-2'-deoxyguanosine (c7Gd), -adenosine (c7Ad) and -inosine (c7Id). c7GdTP can fully replace dGTP resulting in a completely modified DNA-fragment of defined size and sequence. The other two 7-deazapurine triphosphates (c7AdTP) and (c7IdTP) require the presence of the parent purine 2'-deoxyribonucleotides. In purine/7-deazapurine nucleotide mixtures Taq polymerase prefers purine over 7-deazapurine nucleotides but accepts c7GdTP much better than c7AdTP or c7IdTP. As incorporation of 7-deazapurine nucleotides represents a modification of the major groove of DNA it can be used to probe DNA/protein interaction. Regioselective phosphodiester hydrolysis of the modified DNA-fragments was studied with 28 endodeoxyribonucleases. c7Gd is able to protect the DNA from the phosphodiester hydrolysis in more than 20 cases, only a few enzymes (Mae III, Rsa I, Hind III, Pvu II or Taq I) do still hydrolyze the modified DNA. c7Ad protects DNA less efficiently, as this DNA could only be modified in part. The absence of N-7 as potential binding position or a geometric distortion of the recognition duplex caused by the 7-deazapurine base can account for protection of hydrolysis. Images PMID:1738604

Uncover compressed supersymmetry via boosted bosons from the heavier stop/sbottom

NASA Astrophysics Data System (ADS)

Kang, Zhaofeng; Li, Jinmian; Zhang, Mengchao

2017-06-01

A light stop around the weak scale is a hopeful messenger of natural supersymmetry (SUSY), but it has not shown up at the current stage of LHC. Such a situation raises the question of the fate of natural SUSY. Actually, a relatively light stop can easily be hidden in a compressed spectra such as mild mass degeneracy between stop and neutralino plus top quark. Searching for such a stop at the LHC is a challenge. On the other hand, in terms of the argument of natural SUSY, other members in the stop sector, including a heavier stop \\tilde{t}_2 and lighter sbottom \\tilde{b}_1 (both assumed to be left-handed-like), are also supposed to be relatively light and therefore searching for them would provide an alternative method to probe natural SUSY with a compressed spectra. In this paper we consider quasi-natural SUSY which tolerates relatively heavy colored partners near the TeV scale, with a moderately large mass gap between the heavier members and the lightest stop. Then W / Z / h as companions of \\tilde{t}_2 and \\tilde{b}_1 decaying into \\tilde{t}_1 generically are well boosted, and they, along with other visible particles from \\tilde{t}_1 decay, are a good probe to study compressed SUSY. We find that the resulting search strategy with boosted bosons can have better sensitivity than those utilizing multi-leptons.

[Causes of stopping subcutaneous specific immunotherapy in asthmatic children].

PubMed

Huang, Ya-Na; Huang, Ying; Dai, Ji-Hong; Yang, Fang-Fang

2012-09-01

To improve the compliance with subcutaneous specific immunotherapy (SCIT) by analyzing the causes of stopping SCIT in asthmatic children. A telephone follow-up was conducted in the asthmatic children who received SCIT but did not finished the 3-year course of treatment from June 2005 to October 2010, so as to analyze the causes of stopping SCIT. A total of 616 asthmatic children received SCIT, and 322 (52.2%) of them stopped SCIT.A total of 127 cases (39.4%) of the 322 children received telephone follow-up. In the 127 children, 53 (41.8%) stopped the SCIT for the reason of bad effecacy, 29 (22.8%) for remission of asthma,12 (9.4%) for expensive fees, 10 (7.9%) for complex process of treatment, 10 (7.9%) for adverse reaction, 9 (7.1%) for long distance from the hospital, and 4 (3.1%) for having no time for treatment. And 69 (54.3%) of them stopped SCIT in the first year, 28 (22.1%) in the second year, and 30 (23.6%) in the third year. Currently, 85 cases (66.9%) of the 127 asthmatic children were up to the control level, and the other 42 cases were not. There was significant difference in the control level of asthma berween the group receiving treatment with regular inhaled corticosteroids (ICS) and the group receiving treatment with irregular ICS (P<0.01). Bad efficacy, remission of asthma, expensive fees, complex process of treatment, and adverse reaction are the main reasons contributing to the stop of SCIT in asthmatic children. To improve the compliance with SCIT, It is important to make the patients and their parents understand the long treatment course and slow effect of SCIT, encourage them to use objective indices for evaluating the state of asthma, and effectively prevent and treat the adverse reactions.

Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

DOEpatents

Studier, F. William; Dubendorff, John W.

1998-01-01

This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods.

Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

DOEpatents

Studier, F.W.; Dubendorff, J.W.

1998-10-20

This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods. 12 figs.

Cloning and expression of autogenes encoding RNA polymerases of T7-like bacteriophages

DOEpatents

Studier, F.W.; Dubendorff, J.W.

1998-11-03

This invention relates to the cloning and expression of autogenes encoding RNA polymerases of T7 and T7-like bacteriophages, in which the RNA polymerase gene is transcribed from a promoter which is recognized by the encoded RNA polymerase. Cloning of T7 autogenes was achieved by reducing the activity of the RNA polymerase sufficiently to permit host cell growth. T7 RNA polymerase activity was controlled by combining two independent methods: lac-repression of the recombinant lac operator-T7 promoter in the autogene and inhibition of the polymerase by T7 lysozyme. Expression systems for producing the RNA polymerases of T7 and other T7-like bacteriophages, and expression systems for producing selected gene products are described, as well as other related materials and methods. 12 figs.

Effect of pH on the Misincorporation Rate of DNA Polymerase η.

PubMed

Nishimoto, Naomi; Suzuki, Motoshi; Izuta, Shunji

2016-01-01

The many known eukaryotic DNA polymerases are classified into four families; A, B, X, and Y. Among them, DNA polymerase η, a Y family polymerase, is a low fidelity enzyme that contributes to translesional synthesis and somatic hypermutation. Although a high mutation frequency is observed in immunoglobulin genes, translesional synthesis occurs with a high accuracy. We determined whether the misincorporation rate of DNA polymerase η varies with ambient conditions. It has been reported that DNA polymerase η is unable to exclude water molecules from the active site. This finding suggests that some ions affect hydrogen bond formation at the active site. We focused on the effect of pH and evaluated the misincorporation rate of deoxyguanosine triphosphate (dGTP) opposite template T by DNA polymerase η at various pH levels with a synthetic template-primer. The misincorporation rate of dGTP by DNA polymerase η drastically increased at pH 8.0-9.0 compared with that at pH 6.5-7.5. Kinetic analysis revealed that the Km value for dGTP on the misincorporation opposite template T was markedly affected by pH. However, this drastic change was not seen with the low fidelity DNA polymerase α.

Stop-like modification of the dental fricative ∕ð∕: An acoustic analysis

PubMed Central

Zhao, Sherry Y.

2010-01-01

This study concentrates on one of the commonly occurring phonetic variations in English: the stop-like modification of the dental fricative ∕ð∕. The variant exhibits a drastic change from the canonical ∕ð∕; the manner of articulation is changed from one that is fricative to one that is stop-like. Furthermore, the place of articulation of stop-like ∕ð∕ has been a point of uncertainty, leading to confusion between stop-like ∕ð∕ and ∕d/. In this study, acoustic and spectral moment measures were taken from 100 stop-like ∕ð∕ and 102 ∕d/ tokens produced by 59 male and 23 female speakers in the TIMIT corpus. Data analysis indicated that stop-like ∕ð∕ is significantly different from ∕d/ in burst amplitude, burst spectrum shape, burst peak frequency, second formant at following-vowel onset, and spectral moments. Moreover, the acoustic differences from ∕d/ are consistent with those expected for a dental stop-like ∕ð∕. Automatic classification experiments involving these acoustic measures suggested that they are salient in distinguishing stop-like ∕ð∕ from ∕d/. PMID:20968372

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

PubMed Central

Jeruzalmi, D; Steitz, T A

1998-01-01

The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex reveals that lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerase structure with that of the homologous pol I family of DNA polymerases reveals identities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantly from a previously published structure. Sequence similarities between phage RNA polymerases and those from mitochondria and chloroplasts, when interpreted in the context of our revised model of T7 RNA polymerase, suggest a conserved fold. PMID:9670025

Purine inhibitors of protein kinases, G proteins and polymerases

DOEpatents

Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

2001-07-03

The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

Intersection Detection Based on Qualitative Spatial Reasoning on Stopping Point Clusters

NASA Astrophysics Data System (ADS)

Zourlidou, S.; Sester, M.

2016-06-01

The purpose of this research is to propose and test a method for detecting intersections by analysing collectively acquired trajectories of moving vehicles. Instead of solely relying on the geometric features of the trajectories, such as heading changes, which may indicate turning points and consequently intersections, we extract semantic features of the trajectories in form of sequences of stops and moves. Under this spatiotemporal prism, the extracted semantic information which indicates where vehicles stop can reveal important locations, such as junctions. The advantage of the proposed approach in comparison with existing turning-points oriented approaches is that it can detect intersections even when not all the crossing road segments are sampled and therefore no turning points are observed in the trajectories. The challenge with this approach is that first of all, not all vehicles stop at the same location - thus, the stop-location is blurred along the direction of the road; this, secondly, leads to the effect that nearby junctions can induce similar stop-locations. As a first step, a density-based clustering is applied on the layer of stop observations and clusters of stop events are found. Representative points of the clusters are determined (one per cluster) and in a last step the existence of an intersection is clarified based on spatial relational cluster reasoning, with which less informative geospatial clusters, in terms of whether a junction exists and where its centre lies, are transformed in more informative ones. Relational reasoning criteria, based on the relative orientation of the clusters with their adjacent ones are discussed for making sense of the relation that connects them, and finally for forming groups of stop events that belong to the same junction.

46 CFR 32.56-45 - Draft stops-T/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Draft stops-T/ALL. 32.56-45 Section 32.56-45 Shipping....56-45 Draft stops—T/ALL. (a) Where ceilings or linings are fitted in accommodation, service, or... if draft stops of “B” Class construction are fitted between the ceiling or lining and the deck or...

46 CFR 32.56-45 - Draft stops-T/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Draft stops-T/ALL. 32.56-45 Section 32.56-45 Shipping....56-45 Draft stops—T/ALL. (a) Where ceilings or linings are fitted in accommodation, service, or... if draft stops of “B” Class construction are fitted between the ceiling or lining and the deck or...

46 CFR 32.56-45 - Draft stops-T/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Draft stops-T/ALL. 32.56-45 Section 32.56-45 Shipping....56-45 Draft stops—T/ALL. (a) Where ceilings or linings are fitted in accommodation, service, or... if draft stops of “B” Class construction are fitted between the ceiling or lining and the deck or...

Terminal iterative learning control based station stop control of a train

NASA Astrophysics Data System (ADS)

Hou, Zhongsheng; Wang, Yi; Yin, Chenkun; Tang, Tao

2011-07-01

The terminal iterative learning control (TILC) method is introduced for the first time into the field of train station stop control and three TILC-based algorithms are proposed in this study. The TILC-based train station stop control approach utilises the terminal stop position error in previous braking process to update the current control profile. The initial braking position, or the braking force, or their combination is chosen as the control input, and corresponding learning law is developed. The terminal stop position error of each algorithm is guaranteed to converge to a small region related with the initial offset of braking position with rigorous analysis. The validity of the proposed algorithms is verified by illustrative numerical examples.

Role of disulfide bridges in archaeal family-B DNA polymerases.

PubMed

Killelea, Tom; Connolly, Bernard A

2011-06-14

The family-B DNA polymerases obtained from the order Thermococcales, for example, Pyrococcus furiosus (Pfu-Pol) are commonly used in the polymerase chain reaction (PCR) because of their high thermostability and low error rates. Most of these polymerases contain four cysteines, arranged as two disulfide bridges. With Pfu-Pol C429-C443 forms one of the disulfides (DB1) and C507-C510 (DB2) the other. Although the disulfides are well conserved in the enzymes from the hyperthermophilic Thermococcales, they are less prevalent in euryarchaeal polymerases from other orders, and tend to be only found in other hyperthermophiles. Here, we report on the effects of deleting the disulfide bridges by mutating the relevant cysteines to serines. A variety of techniques, including differential scanning calorimetry and differential scanning fluorimetry, have shown that both disulfides make a contribution to thermostability, with DB1 being more important than DB2. However, even when both disulfides are removed, sufficient thermostability remains for normal (identical to the wild type) performance in PCR and quantitative (real-time) PCR. Therefore, polymerases totally lacking cysteine are fully compatible with most PCR-based applications. This observation opens the way to further engineering of polymerases by introduction of a single cysteine followed by appropriate chemical modification. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development a of multiplex TaqMan real-time RT-PCR assay for simultaneous detection of Asian prunus viruses, plum bark necrosis stem pitting associated virus, and peach latent mosaic virus

USDA-ARS?s Scientific Manuscript database

Asian prunus viruses (APV 1, APV 2 and APV 3) and Plum bark necrosis stem pitting associated virus (PBNSPaV) are two recently described viruses infecting Prunus spp., and Peach latent mosaic viroid (PLMVd) is a viroid that infects the same species. A single-tube multiplex, TaqMan real-time RT-PCR as...

Evidence for interaction between the stop signal and the Stroop task conflict.

PubMed

Kalanthroff, Eyal; Goldfarb, Liat; Henik, Avishai

2013-04-01

Performance of the Stroop task reflects two conflicts--informational (between the incongruent word and ink color) and task (between relevant color naming and irrelevant word reading). The task conflict is usually not visible, and is only seen when task control is damaged. Using the stop-signal paradigm, a few studies demonstrated longer stop-signal reaction times for incongruent trials than for congruent trials. This indicates interaction between stopping and the informational conflict. Here we suggest that "zooming in" on task-control failure trials will reveal another interaction--between stopping and task conflict. To examine this suggestion, we combined stop-signal and Stroop tasks in the same experiment. When participants' control failed and erroneous responses to a stop signal occurred, a reverse facilitation emerged in the Stroop task (Experiment 1) and this was eliminated using methods that manipulated the emergence of the reverse facilitation (Experiment 2). Results from both experiments were replicated when all stimuli were used in the same task (Experiment 3). In erroneous response trials, only the task conflict increased, not the informational conflict. These results indicate that task conflict and stop-signal inhibition share a common control mechanism that is dissociable from the control mechanism activated by the informational conflict.

Accurate atomistic first-principles calculations of electronic stopping

DOE PAGES

Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

2015-01-20

In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

17. DETAIL OF STEEL STOPS AT WEST END OF MOBILE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. DETAIL OF STEEL STOPS AT WEST END OF MOBILE SERVICE STRUCTURE RAIL WITH STEEL STOPS AND CONCRETE TIE-DOWN BLOCK; VIEW TO NORTHWEST. - Cape Canaveral Air Station, Launch Complex 17, Facility 28416, East end of Lighthouse Road, Cape Canaveral, Brevard County, FL

Modeling RNA polymerase interaction in mitochondria of chordates

PubMed Central

2012-01-01

Background In previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA secondary structures during transcription, including transcription initiation and termination. The model accurately reproduces changes of gene transcription level observed in polymerase sigma-subunit knockout and heat shock experiments in plant plastids. The corresponding computer program and a user guide are available at http://lab6.iitp.ru/en/rivals. Here we apply the model to the analysis of transcription and (partially) translation processes in the mitochondria of frog, rat and human. Notably, mitochondria possess only phage-type polymerases. We consider the entire mitochondrial genome so that our model allows RNA polymerases to complete more than one circle on the DNA strand. Results Our model of RNA polymerase interaction during transcription initiation and elongation accurately reproduces experimental data obtained for plastids. Moreover, it also reproduces evidence on bulk RNA concentrations and RNA half-lives in the mitochondria of frog, human with or without the MELAS mutation, and rat with normal (euthyroid) or hyposecretion of thyroid hormone (hypothyroid). The transcription characteristics predicted by the model include: (i) the fraction of polymerases terminating at a protein-dependent terminator in both directions (the terminator polarization), (ii) the binding intensities of the regulatory protein factor (mTERF) with the termination site and, (iii) the transcription initiation intensities (initiation frequencies) of all promoters in all five conditions (frog, healthy human, human with MELAS syndrome, healthy rat, and hypothyroid rat with aberrant mtDNA methylation). Using the model, absolute levels of all gene transcription can be inferred from an arbitrary array of the three transcription characteristics, whereas, for selected genes only

Primate community of the tropical rain forests of Saracá-Taqüera National Forest, Pará, Brazil.

PubMed

Oliveira, L C; Loretto, D; Viana, L R; Silva, J S; Fernandes, W G

2009-11-01

Brazil is the richest country in the world in terms of primate species and the Amazonian rain forest is one of the richest biomes containing 15 (ca. 90%) of the Neotropical primate genera. Although considered key elements in conservation strategies, there is only anecdotal information on primates for several protected areas within the region. Here we present new data on the community composition of the primates in the Saracá-Taqüera National Forest (429,600 ha), an actively mined, bauxite rich area, in Pará, Brazil. We used information from the literature, technical reports, museum data, and interviews conducted with agents from the Brazilian Institute of the Environment and Natural Renewable Resources (Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis - IBAMA) and members of the local 'Quilombo' community. In addition, from July 2003 to June 2007, we carried out 19 field trips ranging from 10 to15 days each, amounting to a total effort of 1,230 hours and 1,420 km of censuses, resulting in 1,034 records of eight primate species (Saguinus martinsi, Saguinus midas, Saimiri sciureus, Cebus apella, Pithecia pithecia, Chiropotes sagulatus, Ateles paniscus, and Alouatta macconelli). Two other species (Cebus olivaceus and Aotus trivirgatus) were recorded only indirectly, through interviews and literature data. In all, Alouatta macconelli was the most frequently recorded species (43% of all records); while Saguinus midas and P. pithecia were the least (ca. 0.4 and 0.6% of all records). Based on our results, we discuss group sizes as well as taxonomic problems concerning the genera Pithecia and Chiropotes, for which we registered individuals displaying phenotypic geographical variation and two different forms, respectively. Despite the deforestation inherent in bauxite mining, the Saracá-Taqüera National Forest still has a remarkable richness of primate species. Our study results place this National Forest amongst the richest reserves, in terms

GPs have key role in helping patients to stop smoking.

PubMed

Brown, Jamie; Raupach, Tobias; West, Robert

2012-05-01

Eighteen per cent of all deaths in adults aged 35 or over in England are still attributable to smoking. Almost all these premature deaths could be avoided if smokers stopped before their mid-thirties but only a quarter of people who have ever smoked regularly manage to quit by this age. Advice from the patient's GP is one of the most important triggers to a smoker making an attempt to quit. All patients attending a surgery for any reason who have smoked within the past three years should be offered advice on stopping smoking. Smokers without smoking-related diseases are just as likely to respond to advice as those with them. It is also important to re-assess the status of former smokers who were recorded as having stopped within the past three years. Half of those who stopped six months ago will relapse at some point as will 40% of those who stopped a year ago. Offer help with stopping to all smokers. The National Centre for Smoking Cessation and Training has launched a new online training module on how GPs can best deliver smoking cessation support to their patients. Optimum treatment involves behavioural support plus one of the smoking cessation medications. Behavioural support includes a number of specific behaviour change techniques that enhance the smoker's chances of remaining abstinent. These include: measurement of carbon monoxide in expired air; advice on best use of medication and helping smokers to put in place a clear 'not a puff' rule.

Reasons for starting and stopping electronic cigarette use.

PubMed

Pepper, Jessica K; Ribisl, Kurt M; Emery, Sherry L; Brewer, Noel T

2014-10-03

The aim of our study was to explore reasons for starting and then stopping electronic cigarette (e-cigarette) use. Among a national sample of 3878 U.S. adults who reported ever trying e-cigarettes, the most common reasons for trying were curiosity (53%); because a friend or family member used, gave, or offered e-cigarettes (34%); and quitting or reducing smoking (30%). Nearly two-thirds (65%) of people who started using e-cigarettes later stopped using them. Discontinuation was more common among those whose main reason for trying was not goal-oriented (e.g., curiosity) than goal-oriented (e.g., quitting smoking) (81% vs. 45%, p < 0.001). The most common reasons for stopping e-cigarette use were that respondents were just experimenting (49%), using e-cigarettes did not feel like smoking cigarettes (15%), and users did not like the taste (14%). Our results suggest there are two categories of e-cigarette users: those who try for goal-oriented reasons and typically continue using and those who try for non-goal-oriented reasons and then typically stop using. Research should distinguish e-cigarette experimenters from motivated users whose decisions to discontinue relate to the utility or experience of use. Depending on whether e-cigarettes prove to be effective smoking cessation tools or whether they deter cessation, public health programs may need distinct strategies to reach and influence different types of users.

In Defence of Thought Stopping

ERIC Educational Resources Information Center

Bakker, Gary Maria

2009-01-01

Thought stopping (TS) has a long and established history as an effective mental control technique among the cognitive behavioural therapies (CBT). Recent claims have arisen, particularly from acceptance and mindfulness-based authors, that thought suppression--and therefore TS--is counterproductive. These claims take the syllogistic form: TS is a…

Complementation between polymerase- and exonuclease-deficient mitochondrial DNA polymerase mutants in genomically engineered flies

PubMed Central

Bratic, Ana; Kauppila, Timo E. S.; Macao, Bertil; Grönke, Sebastian; Siibak, Triinu; Stewart, James B.; Baggio, Francesca; Dols, Jacqueline; Partridge, Linda; Falkenberg, Maria; Wredenberg, Anna; Larsson, Nils-Göran

2015-01-01

Replication errors are the main cause of mitochondrial DNA (mtDNA) mutations and a compelling approach to decrease mutation levels would therefore be to increase the fidelity of the catalytic subunit (POLγA) of the mtDNA polymerase. Here we genomically engineer the tamas locus, encoding fly POLγA, and introduce alleles expressing exonuclease- (exo−) and polymerase-deficient (pol−) POLγA versions. The exo− mutant leads to accumulation of point mutations and linear deletions of mtDNA, whereas pol− mutants cause mtDNA depletion. The mutant tamas alleles are developmentally lethal but can complement each other in trans resulting in viable flies with clonally expanded mtDNA mutations. Reconstitution of human mtDNA replication in vitro confirms that replication is a highly dynamic process where POLγA goes on and off the template to allow complementation during proofreading and elongation. The created fly models are valuable tools to study germ line transmission of mtDNA and the pathophysiology of POLγA mutation disease. PMID:26554610

Objectification of Public Bus Stop's Pavement Surface Morphology

NASA Astrophysics Data System (ADS)

Decký, Martin; Kováč, Matúš; Mužík, Juraj; Mičechová, Lenka; Ďuriš, Lukáš

2018-06-01

The article deals with the road pavement surface morphology objectification in term of the surface unevenness degradation during the life cycle of bus stop pavements. The article presents the results of long-term rut depth measurements performed during 25 years on selected bus stops which were intended to determine correlation dependences of pavement rut depth on a number of design axles. The article also presents different methods for rut depth measurements including the straightedge test, Profilograph GE, TRIMBLE CX, and dynamic Road Scanner.

Imagine stopping the progression of Alzheimer's

MedlinePlus

... Issue Past Issues Imagine stopping the progression of Alzheimer's Past Issues / Fall 2006 Table of Contents For ... I have friends and loved ones suffering from Alzheimer's. But I can imagine… and hope for… a ...

No association between the TaqI A1 RFLP of the D2 receptor gene and alcoholism in a Mexican population

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cruz-Fuentes, C.; Carmarena, B.; Eroza, V.

1994-09-01

The suggested association of the A1 allele of the D2 dopamine receptor (DRD2) human gene with alcoholism was studied by comparing the DRD2/TaqI genotypes of 36 healthy controls and 38 individuals who met the DSM-III-R diagnostic criteria for alcohol dependence. All subjects were unrelated, with parents and grandparents of Mexican origin. The alcoholics in our sample suffered one of the following conditions: delirium tremens (16.6%), alcohol hallucinosis (56.6%) or uncomplicated alcohol withdrawal (26.4%). Eight-eight percent of the controls carried the A1 allele. The frequency of the DRD2 A1 allele in the Mexican urban sample (pA1 = 0.61) was 2 tomore » 3-fold higher than reported in Caucasian populations from the USA and Europe, but similar to the allele frequencies found in defined Amerindian populations. There were not significant differences in the prevalence or allele frequency between alcoholics (pA1 = 0.64) and controls, regardless if the alcoholics were subtyped accordingly to severity, age of onset or positive family history. Alcoholics had higher scores than controls in the neuroticism (N) and psychoticism (P) subscales on the Eysenck personality test: alcoholics P = 6.2 {+-} 2.9, N = 16.0 {+-} 4.2 vs. controls P = 2.5 {+-} 2.3, N = 5.7 {+-} 5.1; p<0.001 and p<0.001, respectively. However, no relationship between personality traits and genotypes was found. Our results do not support a consistent association between the TaqI A1 RFLP for the DRD2 gene and alcoholism.« less

Development of a TaqMan Array Card for Acute-Febrile-Illness Outbreak Investigation and Surveillance of Emerging Pathogens, Including Ebola Virus.

PubMed

Liu, Jie; Ochieng, Caroline; Wiersma, Steve; Ströher, Ute; Towner, Jonathan S; Whitmer, Shannon; Nichol, Stuart T; Moore, Christopher C; Kersh, Gilbert J; Kato, Cecilia; Sexton, Christopher; Petersen, Jeannine; Massung, Robert; Hercik, Christine; Crump, John A; Kibiki, Gibson; Maro, Athanasia; Mujaga, Buliga; Gratz, Jean; Jacob, Shevin T; Banura, Patrick; Scheld, W Michael; Juma, Bonventure; Onyango, Clayton O; Montgomery, Joel M; Houpt, Eric; Fields, Barry

2016-01-01

Acute febrile illness (AFI) is associated with substantial morbidity and mortality worldwide, yet an etiologic agent is often not identified. Convalescent-phase serology is impractical, blood culture is slow, and many pathogens are fastidious or impossible to cultivate. We developed a real-time PCR-based TaqMan array card (TAC) that can test six to eight samples within 2.5 h from sample to results and can simultaneously detect 26 AFI-associated organisms, including 15 viruses (chikungunya, Crimean-Congo hemorrhagic fever [CCHF] virus, dengue, Ebola virus, Bundibugyo virus, Sudan virus, hantaviruses [Hantaan and Seoul], hepatitis E, Marburg, Nipah virus, o'nyong-nyong virus, Rift Valley fever virus, West Nile virus, and yellow fever virus), 8 bacteria (Bartonella spp., Brucella spp., Coxiella burnetii, Leptospira spp., Rickettsia spp., Salmonella enterica and Salmonella enterica serovar Typhi, and Yersinia pestis), and 3 protozoa (Leishmania spp., Plasmodium spp., and Trypanosoma brucei). Two extrinsic controls (phocine herpesvirus 1 and bacteriophage MS2) were included to ensure extraction and amplification efficiency. Analytical validation was performed on spiked specimens for linearity, intra-assay precision, interassay precision, limit of detection, and specificity. The performance of the card on clinical specimens was evaluated with 1,050 blood samples by comparison to the individual real-time PCR assays, and the TAC exhibited an overall 88% (278/315; 95% confidence interval [CI], 84% to 92%) sensitivity and a 99% (5,261/5,326, 98% to 99%) specificity. This TaqMan array card can be used in field settings as a rapid screen for outbreak investigation or for the surveillance of pathogens, including Ebola virus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Stopping distance for high energy jets in weakly coupled quark-gluon plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold, Peter; Cantrell, Sean; Xiao Wei

2010-02-15

We derive a simple formula for the stopping distance for a high-energy quark traveling through a weakly coupled quark-gluon plasma. The result is given to next-to-leading order in an expansion in inverse logarithms ln(E/T), where T is the temperature of the plasma. We also define a stopping distance for gluons and give a leading-log result. Discussion of stopping distance has a theoretical advantage over discussion of energy loss rates in that stopping distances can be generalized to the case of strong coupling, where one may not speak of individual partons.

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

DOEpatents

Studier, F.W.; Davanloo, P.; Rosenberg, A.H.; Moffatt, B.A.; Dunn, J.J.

1997-12-02

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells. 10 figs.

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

DOEpatents

Studier, F. William; Davanloo, Parichehre; Rosenberg, Alan H.; Moffatt, Barbara A.; Dunn, John J.

1999-02-09

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

DOEpatents

Studier, F. William; Davanloo, Parichehre; Rosenberg, Alan H.; Moffatt, Barbara A.; Dunn, John J.

1997-12-02

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

DOEpatents

Studier, F. William; Davanloo, Parichehre; Rosenberg, Alan H.; Moffatt, Barbara A.; Dunn, John J.

1990-01-01

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the T7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

DOEpatents

Studier, F.W.; Davanloo, P.; Rosenberg, A.H.; Moffatt, B.A.; Dunn, J.J.

1999-02-09

This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells. 10 figs.

Human DNA polymerase θ grasps the primer terminus to mediate DNA repair

DOE PAGES

Zahn, Karl E.; Averill, April M.; Aller, Pierre; ...

2015-03-16

DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break–inducing agents, including ionizing radiation. Reported in this paper are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contactsmore » to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. Finally, these observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.« less

Revealing compressed stops using high-momentum recoils

DOE PAGES

Macaluso, Sebastian; Park, Michael; Shih, David; ...

2016-03-22

In this study, searches for supersymmetric top quarks at the LHC have been making great progress in pushing sensitivity out to higher mass, but are famously plagued by gaps in coverage around lower-mass regions where the decay phase space is closing off. Within the common stop-NLSP/neutralino-LSP simplified model, the line in the mass plane where there is just enough phase space to produce an on-shell top quark remains almost completely unconstrained. Here, we show that is possible to define searches capable of probing a large patch of this difficult region, with S/B ~ 1 and significances often well beyond 5σ.more » The basic strategy is to leverage the large energy gain of LHC Run 2, leading to a sizable population of stop pair events recoiling against a hard jet. The recoil not only re-establishes a E T, but also leads to a distinctive anti-correlation between the E T and the recoil jet transverse vectors when the stops decay all-hadronically. Accounting for jet combinatorics, backgrounds, and imperfections in E T measurements, we estimate that Run 2 will already start to close the gap in exclusion sensitivity with the first few 10s of fb –1. By 300 fb –1, exclusion sensitivity may extend from stop masses of 550 GeV on the high side down to below 200 GeV on the low side, approaching the “stealth” point at m t¯ = m t and potentially overlapping with limits from tt¯ cross section and spin correlation measurements.« less

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.

PubMed

Zhou, Katherine I; Clark, Wesley C; Pan, David W; Eckwahl, Matthew J; Dai, Qing; Pan, Tao

2018-05-11

The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity and specificity, in part due to the use of reverse transcription stops. We sought to use mutations rather than just stops in sequencing data to identify pseudouridine sites. Here, we identify reverse transcription conditions that allow read-through of carbodiimide-modified pseudouridine (CMC-Ψ), and we show that pseudouridines in carbodiimide-treated human ribosomal RNA have context-dependent mutation and stop rates in high-throughput sequencing libraries prepared under these conditions. Furthermore, accounting for the context-dependence of mutation and stop rates can enhance the detection of pseudouridine sites. Similar approaches could contribute to the sequencing-based detection of many RNA modifications.

Enzyme kinetics above denaturation temperature: a temperature-jump/stopped-flow apparatus.

PubMed

Kintses, Bálint; Simon, Zoltán; Gyimesi, Máté; Tóth, Júlia; Jelinek, Balázs; Niedetzky, Csaba; Kovács, Mihály; Málnási-Csizmadia, András

2006-12-15

We constructed a "temperature-jump/stopped-flow" apparatus that allows us to study fast enzyme reactions at extremely high temperatures. This apparatus is a redesigned stopped-flow which is capable of mixing the reactants on a submillisecond timescale concomitant with a temperature-jump even as large as 60 degrees C. We show that enzyme reactions that are faster than the denaturation process can be investigated above denaturation temperatures. In addition, the temperature-jump/stopped-flow enables us to investigate at physiological temperature the mechanisms of many human enzymes, which was impossible until now because of their heat instability. Furthermore, this technique is extremely useful in studying the progress of heat-induced protein unfolding. The temperature-jump/stopped-flow method combined with the application of structure-specific fluorescence signals provides novel opportunities to study the stability of certain regions of enzymes and identify the unfolding-initiating regions of proteins. The temperature-jump/stopped-flow technique may become a breakthrough in exploring new features of enzymes and the mechanism of unfolding processes.

Effect of STOP technique on safety climate in a construction company.

PubMed

Darvishi, Ebrahim; Maleki, Afshin; Dehestaniathar, Saeed; Ebrahemzadih, Mehrzad

2015-01-01

Safety programs are a core part of safety management in workplaces that can reduce incidents and injuries. The aim of this study was to investigate the influence of Safety Training Observation Program (STOP) technique as a behavior modification program on safety climate in a construction company. This cross-sectional study was carried out on workers of the Petrochemical Construction Company, western Iran. In order to improve safety climate, an unsafe behavior modification program entitled STOP was launched among workers of project during 12 months from April 2013 and April 2014. The STOP technique effectiveness in creating a positive safety climate was evaluated using the Safety Climate Assessment Toolkit. 76.78% of total behaviors were unsafe. 54.76% of total unsafe acts/ at-risk behaviors were related to the fall hazard. The most cause of unsafe behaviors was associated with habit and unavailability of safety equipment. After 12 month of continuous implementation the STOP technique, 55.8% of unsafe behaviors reduced among workers. The average score of safety climate evaluated using of the Toolkit, before and after the implementation of the STOP technique was 5.77 and 7.24, respectively. The STOP technique can be considered as effective approach for eliminating at-risk behavior, reinforcing safe work practices, and creating a positive safety climate in order to reduction incidents/injuries.

New Stopping Criteria for Segmenting DNA Sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wentian

2001-06-18

We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian information criterion in the model selection framework. When this criterion is applied to telomere of S.cerevisiae and the complete sequence of E.coli, borders of biologically meaningful units were identified, and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genomemore » sequences.« less

Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution.

PubMed

Gahlon, Hailey L; Romano, Louis J; Rueda, David

2017-11-20

Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.

Stashing the stops in multijet events at the LHC

NASA Astrophysics Data System (ADS)

Diglio, Sara; Feligioni, Lorenzo; Moultaka, Gilbert

2017-09-01

While the presence of a light stop is increasingly disfavored by the experimental limits set on R-parity conserving scenarios, the naturalness of supersymmetry could still be safely concealed in the more challenging final states predicted by the existence of non-null R-parity violating couplings. Although R-parity violating signatures are extensively looked for at the Large Hadron Collider, these searches mostly assume 100% branching ratios for the direct decays of supersymmetric particles into Standard Model ones. In this paper we scrutinize the implications of relaxing this assumption by focusing on one motivated scenario where the lightest stop is heavier than a chargino and a neutralino. Considering a class of R-parity baryon number violating couplings, we show on general grounds that while the direct decay of the stop into Standard Model particles is dominant for large values of these couplings, smaller values give rise, instead, to the dominance of a plethora of longer decay chains and richer final states that have been so far barely analyzed at the LHC, thus weakening the impact of the present experimental stop mass limits. We characterize the case for R-parity baryon number violating couplings in the 10-7-10-1 range, in two different benchmark points scenarios within the model-independent setting of the low-energy phenomenological Minimal Supersymmetric Standard Model. We identify the different relevant experimental signatures from stop pair production and decays, estimate the corresponding proton-proton cross sections at √{s }=14 TeV and discuss signal versus background issues.

Isolation and characterization of high affinity aptamers against DNA polymerase iota.

PubMed

Lakhin, Andrei V; Kazakov, Andrei A; Makarova, Alena V; Pavlov, Yuri I; Efremova, Anna S; Shram, Stanislav I; Tarantul, Viacheslav Z; Gening, Leonid V

2012-02-01

Human DNA-polymerase iota (Pol ι) is an extremely error-prone enzyme and the fidelity depends on the sequence context of the template. Using the in vitro systematic evolution of ligands by exponential enrichment (SELEX) procedure, we obtained an oligoribonucleotide with a high affinity to human Pol ι, named aptamer IKL5. We determined its dissociation constant with homogenous preparation of Pol ι and predicted its putative secondary structure. The aptamer IKL5 specifically inhibits DNA-polymerase activity of the purified enzyme Pol ι, but did not inhibit the DNA-polymerase activities of human DNA polymerases beta and kappa. IKL5 suppressed the error-prone DNA-polymerase activity of Pol ι also in cellular extracts of the tumor cell line SKOV-3. The aptamer IKL5 is useful for studies of the biological role of Pol ι and as a potential drug to suppress the increase of the activity of this enzyme in malignant cells.

Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

PubMed Central

2015-01-01

The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and allow for efficient lesion bypass. Their promiscuous active sites, however, also lead to fidelities that are much lower than those observed for other DNA polymerases and give rise to interesting mechanistic properties. Additionally, the Y-family DNA polymerases have several other unique structural features and undergo a set of conformational changes during substrate binding and catalysis different from those observed for replicative DNA polymerases. In recent years, pre-steady-state kinetic methods have been extensively employed to reveal a wealth of information about the catalytic properties of these fascinating noncanonical DNA polymerases. Here, we review many of the recent findings on the kinetic mechanisms of DNA polymerization with undamaged and damaged DNA substrates by the Y-family DNA polymerases, and the conformational dynamics employed by these error-prone enzymes during catalysis. PMID:24716482

Genetic polymorphisms of cytochrome p4502E1 and susceptibility to alcoholic liver disease and hepatocellular carcinoma in a white population: a study and literature review, including meta-analysis

PubMed Central

Wong, N A C S; Rae, F; Simpson, K J; Murray, G D; Harrison, D J

2000-01-01

Aims—To investigate the associations between the Rsa I, Dra I, and Taq I genetic polymorphisms of cytochrome p4502E1 and susceptibility to alcoholic liver disease or to hepatocellular carcinoma. Methods—DNA samples isolated from 61 patients with alcoholic liver disease, 46 patients with hepatocellular carcinoma, and 375 healthy controls were subjected to polymerase chain reaction amplification followed by digestion with the endonucleases Rsa I, Dra I, or Taq I. Meta-analysis was performed using data from previous studies of Rsa I polymorphism and the risk of alcoholic liver disease. Results—No association was found between any of the three polymorphisms and susceptibility to hepatocellular carcinoma. The distributions of Rsa I and Dra I alleles among the patients with alcoholic liver disease were not significantly different from those among the control group. Meta-analysis of this data and previous data concerning Rsa I polymorphism and alcoholic liver disease risk failed to demonstrate any significant association between the two. However, the alcoholic liver disease group in this study showed a significantly lower frequency of the less common Taq I allele compared with the healthy control group (odds ratio, 0.33; 95% confidence interval, 0.12 to 0.78). Conclusions—Possession of the less common Taq I cytochrome p4502E1 allele is associated with reduced susceptibility to alcoholic liver disease. There is no existing evidence that the Taq I polymorphism is directly associated with altered alcohol metabolism, but it might be in linkage disequilibrium with as yet unidentified protective factors. PMID:10889908

A movable stop mechanism for the SIRE telescope

NASA Technical Reports Server (NTRS)

Tweedt, R. E.; Poulsen, R. N.

1982-01-01

A movable stop mechanism (MSM) designed to activate flaps that change the size and shape of a telescope aperture stop on command is described. Operating at the cryogenic temperatures of the optical system, it consists primarily of a rotary solenoid that drives (activates) dual four-bar linkages in synchronism that in turn rotate the butterfly flaps into position. The design, performance characteristics, and testing of this mechanism are discussed. Specific problems that occurred during testing and the solutions that were adopted are also described.

A novel duplex real-time reverse transcriptase-polymerase chain reaction assay for the detection of hepatitis C viral RNA with armored RNA as internal control

PubMed Central

2010-01-01

Background The hepatitis C virus (HCV) genome is extremely heterogeneous. Several HCV infections can not be detected using currently available commercial assays, probably because of mismatches between the template and primers/probes. By aligning the HCV sequences, we developed a duplex real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using 2 sets of primers/probes and a specific armored RNA as internal control. The 2 detection probes were labelled with the same fluorophore, namely, 6-carboxyfluorescein (FAM), at the 5' end; these probes could mutually combine, improving the power of the test. Results The limit of detection of the duplex primer/probe assay was 38.99 IU/ml. The sensitivity of the assay improved significantly, while the specificity was not affected. All HCV genotypes in the HCV RNA Genotype Panel for Nucleic Acid Amplification Techniques could be detected. In the testing of 109 serum samples, the performance of the duplex real-time RT-PCR assay was identical to that of the COBAS AmpliPrep (CAP)/COBAS TaqMan (CTM) assay and superior to 2 commercial HCV assay kits. Conclusions The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection. PMID:20529244

Identification of stopping ions in a silicon Timepix detector

NASA Astrophysics Data System (ADS)

Stoffle, Nicholas; Pinsky, Lawrence

2018-02-01

Timepix detectors are increasingly used in space-based applications. Such detectors are low power, low mass, and provide a wealth of information necessary for characterizing the ionizing radiation environment in space for both humans and hardware. Stopping ions are shown to contribute to the energy loss spectrum in a thin, pixelated, Timepix detector, and this energy loss is shown to contribute to the LET spectrum near 14 keV/micron. Bulk data also indicates the presence of Hydrogen isotopes in the energy loss spectra. Individual track analysis can be used to identify the stopping ions and the related energy and isotope through comparison with theoretical energy loss curves. While this calculation is specific to the Timepix, the impact of stopping ions on other instruments can be estimated using the insight gained from this approach.

Purine inhibitors of protein kinases, G proteins and polymerases

DOEpatents

Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

2004-10-12

The present invention relates to 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

Low-bias flat band-stop filter based on velocity modulated gaussian graphene superlattice