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Sample records for high quality nucleic

  1. Simple, rapid and cost-effective method for high quality nucleic acids extraction from different strains of Botryococcus braunii.

    Directory of Open Access Journals (Sweden)

    Byung-Hyuk Kim

    Full Text Available This study deals with an effective nucleic acids extraction method from various strains of Botryococcus braunii which possesses an extensive extracellular matrix. A method combining freeze/thaw and bead-beating with heterogeneous diameter of silica/zirconia beads was optimized to isolate DNA and RNA from microalgae, especially from B. braunii. Eukaryotic Microalgal Nucleic Acids Extraction (EMNE method developed in this study showed at least 300 times higher DNA yield in all strains of B. braunii with high integrity and 50 times reduced working volume compared to commercially available DNA extraction kits. High quality RNA was also extracted using this method and more than two times the yield compared to existing methods. Real-time experiments confirmed the quality and quantity of the input DNA and RNA extracted using EMNE method. The method was also applied to other eukaryotic microalgae, such as diatoms, Chlamydomonas sp., Chlorella sp., and Scenedesmus sp. resulting in higher efficiencies. Cost-effectiveness analysis of DNA extraction by various methods revealed that EMNE method was superior to commercial kits and other reported methods by >15%. This method would immensely contribute to area of microalgal genomics.

  2. Direct isolation of high-quality low molecular weight RNA of pear peel from the extraction mixture containing nucleic acid.

    Science.gov (United States)

    Wang, Xin-wei; Xiong, Ai-sheng; Yao, Quan-hong; Zhang, Zhen; Qiao, Yu-shan

    2010-01-01

    Low molecular weight RNA (LMW RNA) is generally obtained either from the total RNA or from total nucleic acids solution. Many steps and chemical reagents are involved in traditional methods for LMW RNA isolation where degradation of LMW RNA often occurs, especially for plant materials with high levels of secondary catabolites. In this study, an efficient method was developed to directly isolate pure LMW RNA from pear peel, a material rich in polyphenolics that is covered with a layer of wax. The method was based on polyethylene glycol (PEG) precipitation combining CTAB buffer which is often used to isolate RNA from polysaccharide-rich and polyphenolics-rich materials. The entire procedure could be completed within 6 h and many samples could be processed at the same time. Few and common chemicals are used with this method. Hence, it could be used as an ordinary method in the laboratory. The developed method was further tested by isolating LMW RNA from Arabidopsis. Using the isolated LMW RNA samples, microRNAs were successfully detected and characterized.

  3. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Quality control material for cystic fibrosis... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a) Identification. Quality control material for cystic fibrosis nucleic acid assays. A quality control material for...

  4. Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery

    Science.gov (United States)

    McMahon, Kaylin M.; Mutharasan, R. Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K.; Luthi, Andrea J.; Helfand, Brian T.; Ardehali, Hossein; Mirkin, Chad A.; Volpert, Olga; Thaxton, C. Shad

    2014-01-01

    We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy (TEM), and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

  5. Highly fluorescent conjugated pyrenes in nucleic acid probes: (phenylethynyl)pyrenecarbonyl-functionalized locked nucleic acids.

    Science.gov (United States)

    Astakhova, Irina V; Korshun, Vladimir A; Wengel, Jesper

    2008-01-01

    In recent years, fluorescently labeled oligonucleotides have become a widely used tool in diagnostics, DNA sequencing, and nanotechnology. The recently developed (phenylethynyl)pyrenes are attractive dyes for nucleic acid labeling, with the advantages of long-wave emission relative to the parent pyrene, high fluorescence quantum yields, and the ability to form excimers. Herein, the synthesis of six (phenylethynyl)pyrene-functionalized locked nucleic acid (LNA) monomers M(1)-M(6) and their incorporation into DNA oligomers is described. Multilabeled duplexes display higher thermal stabilities than singly modified analogues. An increase in the number of phenylethynyl substituents attached to the pyrene results in decreased binding affinity towards complementary DNA and RNA and remarkable bathochromic shifts of absorption/emission maxima relative to the parent pyrene fluorochrome. This bathochromic shift leads to the bright fluorescence colors of the probes, which differ drastically from the blue emission of unsubstituted pyrene. The formation of intra- and interstrand excimers was observed for duplexes that have monomers M(1)-M(6) in both complementary strands and in numerous single-stranded probes. If more phenylethynyl groups are inserted, the detected excimer signals become more intense. In addition, (phenylethynyl)pyrenecarbonyl-LNA monomers M(4), M(5), and M(6) proved highly useful for the detection of single mismatches in DNA/RNA targets.

  6. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    Science.gov (United States)

    Cary, Robert E.

    2015-12-08

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

  7. Operating Cooperatively (OC sensor for highly specific recognition of nucleic acids.

    Directory of Open Access Journals (Sweden)

    Evan M Cornett

    Full Text Available Molecular Beacon (MB probes have been extensively used for nucleic acid analysis because of their ability to produce fluorescent signal in solution instantly after hybridization. The indirect binding of MB probe to a target analyte offers several advantages, including: improved genotyping accuracy and the possibility to analyse folded nucleic acids. Here we report on a new design for MB-based sensor, called 'Operating Cooperatively' (OC, which takes advantage of indirect binding of MB probe to a target analyte. The sensor consists of two unmodified DNA strands, which hybridize to a universal MB probe and a nucleic acid analyte to form a fluorescent complex. OC sensors were designed to analyze two human SNPs and E. coli 16S rRNA. High specificity of the approach was demonstrated by the detection of true analyte in over 100 times excess amount of single base substituted analytes. Taking into account the flexibility in the design and the simplicity in optimization, we conclude that OC sensors may become versatile and efficient tools for instant DNA and RNA analysis in homogeneous solution.

  8. Synthetic LNA/DNA nano-scaffolds for highly efficient diagnostics of nucleic acids and autoimmune antibodies

    DEFF Research Database (Denmark)

    Astakhova, Irina Kira

    2014-01-01

    of the monoclonal human autoantibody is achieved. It makes the novel "clickable" LNA/DNA complexes a very promising tool in molecular diagnostics of both nucleic acids and autoantibodies against DNA. The latter are produced under several autoimmune conditions including antiphospholipide syndrome and systemic lupus......Herein novel fluorescent oligonucleotides for homogeneous (all-in-solution) detection of nucleic acids and autoimmune antibodies (autoantibodies) are described. The probes are prepared by highly efficient copper-catalyzed click chemistry between novel alkyne-modified locked nucleic acid (LNA......) strands and a series of fluorescent azides. The multiply labeled fluorescent LNA/DNA probes prepared herein generally display high binding affinity to complementary DNA/RNA, high quantum yields and, hence, high fluorescence brightness values. With the novel fluorescent probes, specific sensing...

  9. Locked nucleic acid

    DEFF Research Database (Denmark)

    Jepsen, Jan Stenvang; Sørensen, Mads D; Wengel, Jesper

    2004-01-01

    Locked nucleic acid (LNA) is a class of nucleic acid analogs possessing very high affinity and excellent specificity toward complementary DNA and RNA, and LNA oligonucleotides have been applied as antisense molecules both in vitro and in vivo. In this review, we briefly describe the basic physioc...

  10. Nucleic acid-based assays for the detection of high-risk human papillomavirus: a technical review.

    Science.gov (United States)

    Gibson, Jane S

    2014-09-01

    Nucleic acid-based high-risk human papillomavirus (hrHPV) testing is essential to contemporary cervical cancer screening. The numbers of commercially available assays approved by the US Food and Drug Administration for HPV nucleic acid detection have increased, each offering various approaches to analysis. An understanding of the methodologies associated with HPV testing is important to the practice of laboratory medicine. An overview of instruments, chemistries, laboratory workflows, and test limitations associated with current US Food and Drug Administration-approved assays is provided. © 2014 American Cancer Society.

  11. Viral nucleic acid testing (NAT) and OPO-level disposition of high-risk donor organs.

    Science.gov (United States)

    Kucirka, L M; Alexander, C; Namuyinga, R; Hanrahan, C; Montgomery, R A; Segev, D L

    2009-03-01

    The use of Public Health Service/Centers for Disease Control and Prevention (PHS/CDC) high-risk donor (HRD) organs remains controversial, especially in light of a recent high-profile case of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) transmission. Nucleic acid testing (NAT), while more expensive and time consuming, reduces infectious risk by shortening the period between infection and detectability. The purpose of this study was to characterize HRDs and disposition of their organs by organ procurement organization (OPO), to measure NAT practices by OPO and to examine associations between NAT practices and use of HRD organs. We analyzed 29 950 deceased donors (2574 HRDs) reported to UNOS since July 1, 2004 and May 8, 2008. We then surveyed all OPO clinical directors about their use of NAT, average time to receive NAT results, locations where NAT is performed and percentage of the time NAT results are available for allocation decisions. In total, 51.7% of OPOs always perform HIV NAT, while 24.1% never do. A similar pattern is seen for HCV NAT performance, while the majority (65.6%) never perform HBV NAT. AIDS prevalence in an OPO service area is not associated with NAT practice. OPOs that perform HIV NAT are less likely to export organs outside of their region. The wide variation of current practice and the possibility that NAT would improve organ utilization support consideration for a national policy.

  12. A convenient and highly efficient synthesis of one kind of peptide nucleic acid monomer

    Directory of Open Access Journals (Sweden)

    Xuemei Tang

    2012-12-01

    Full Text Available S-Thyminyl-L-cysteine methyl ester hydrochloride (compound 1, a non-classical peptide nucleic acid monomer, was synthesized through the key intermediate, N-tert- butoxycarbonyl-S-thyminyl-L-cysteine (compound 3, which afforded from the reaction of S-thyminyl-L-cysteine hydrochloride (compound 2 with di-tert-butyl dicarbonate (Boc2O. This was followed by the esterification and deprotection of compound 3 at an overall yield of 82%. The mixture of thionyl chloride and methanol was found as an efficient reagent for simultaneous deprotection of tert-butoxycarbonyl (Boc group and esterification of carboxy group of compound 3. This high-yield two-step method was also applied to other analogues of compound 1 successfully. The chemical structures of four new compounds (5a-5d were confirmed by 1H NMR and 13C NMR.DOI: http://dx.doi.org/10.4314/bcse.v26i3.10

  13. Tsetse salivary gland proteins 1 and 2 are high affinity nucleic acid binding proteins with residual nuclease activity.

    Directory of Open Access Journals (Sweden)

    Guy Caljon

    Full Text Available Analysis of the tsetse fly salivary gland EST database revealed the presence of a highly enriched cluster of putative endonuclease genes, including tsal1 and tsal2. Tsal proteins are the major components of tsetse fly (G. morsitans morsitans saliva where they are present as monomers as well as high molecular weight complexes with other saliva proteins. We demonstrate that the recombinant tsetse salivary gland proteins 1&2 (Tsal1&2 display DNA/RNA non-specific, high affinity nucleic acid binding with K(D values in the low nanomolar range and a non-exclusive preference for duplex. These Tsal proteins exert only a residual nuclease activity with a preference for dsDNA in a broad pH range. Knockdown of Tsal expression by in vivo RNA interference in the tsetse fly revealed a partially impaired blood digestion phenotype as evidenced by higher gut nucleic acid, hematin and protein contents.

  14. Highly Stable and Sensitive Nucleic Acid Amplification and Cell-Phone-Based Readout.

    Science.gov (United States)

    Kong, Janay E; Wei, Qingshan; Tseng, Derek; Zhang, Jingzi; Pan, Eric; Lewinski, Michael; Garner, Omai B; Ozcan, Aydogan; Di Carlo, Dino

    2017-03-28

    Key challenges with point-of-care (POC) nucleic acid tests include achieving a low-cost, portable form factor, and stable readout, while also retaining the same robust standards of benchtop lab-based tests. We addressed two crucial aspects of this problem, identifying a chemical additive, hydroxynaphthol blue, that both stabilizes and significantly enhances intercalator-based fluorescence readout of nucleic acid concentration, and developing a cost-effective fiber-optic bundle-based fluorescence microplate reader integrated onto a mobile phone. Using loop-mediated isothermal amplification on lambda DNA we achieve a 69-fold increase in signal above background, 20-fold higher than the gold standard, yielding an overall limit of detection of 25 copies/μL within an hour using our mobile-phone-based platform. Critical for a point-of-care system, we achieve a >60% increase in fluorescence stability as a function of temperature and time, obviating the need for manual baseline correction or secondary calibration dyes. This field-portable and cost-effective mobile-phone-based nucleic acid amplification and readout platform is broadly applicable to other real-time nucleic acid amplification tests by similarly modulating intercalating dye performance and is compatible with any fluorescence-based assay that can be run in a 96-well microplate format, making it especially valuable for POC and resource-limited settings.

  15. Stepping towards highly flexible aptamers: enzymatic recognition studies of unlocked nucleic acid nucleotides

    DEFF Research Database (Denmark)

    Dubois, Camille; Campbell, Meghan A; Edwards, Stacey L

    2012-01-01

    Enzymatic recognition of unlocked nucleic acid (UNA) nucleotides was successfully accomplished. Therminator DNA polymerase was found to be an efficient enzyme in primer extension reactions. Polymerase chain reaction (PCR) amplification of a 81 mer UNA-modified DNA library was efficiently achieved...

  16. Highly Efficient Synthesis of Allopurinol Locked Nucleic Acid Monomer by C6 Deamination of 8-Aza-7-bromo-7-deazaadenine Locked Nucleic Acid Monomer

    DEFF Research Database (Denmark)

    Kosbar, Tamer Reda El-Saeed; Sofan, M.; Abou-Zeid, L.

    2013-01-01

    An allopurinol locked nucleic acid (LNA) monomer was prepared by a novel strategy through C6 deamination of the corresponding 8-aza-7-bromo-7-deazaadenine LNA monomer with aqueous sodium hydroxide. An 8-aza-7-deazaadenine LNA monomer was also synthesized by a modification of the new synthetic...... the required LNA monomers....

  17. Nucleic acid-based approaches to investigate microbial-related cheese quality defects

    Science.gov (United States)

    O'Sullivan, Daniel J.; Giblin, Linda; McSweeney, Paul L. H.; Sheehan, Jeremiah J.; Cotter, Paul D.

    2012-01-01

    The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors. PMID:23346082

  18. SDR-ELISA: Ultrasensitive and high-throughput nucleic acid detection based on antibody-like DNA nanostructure.

    Science.gov (United States)

    Wen, Junlin; Chen, Junhua; Zhuang, Li; Zhou, Shungui

    2017-04-15

    An ultrasensitive and high-throughput nucleic acid detection system, termed as strand displacement reaction-enzyme linked immunosorbent assay (SDR-ELISA), has been developed on the basis of antibody-like DNA nanostructures. Three digoxigenin or biotin modified hairpin probes are utilized to construct antibody-like DNA nanostructures that feature affinity toward streptavidin and anti-digoxigenin antibody via isothermal target-triggered SDR amplification. These antibody-like nanostructures have been employed to conjugate horseradish-peroxidase-labeled anti-digoxigenin antibody with streptavidin that is immobilized on microliter plate wells for enzyme-linked colorimetric assay. The resulting SDR-ELISA system is ultrasensitive for target DNA with a low detection limit of 5 fM. Moreover, the SDR-ELISA system is capable of discriminating DNA sequences with single base mutations, and do so in a high-throughput manner by detection and quantification of up to 96 or 384 DNA samples in a single shot. This detection system is further applied to detect other DNA targets such as Shewanella oneidensis specific DNA sequence, which indicates the generality of proposed SDR-ELISA system. The integration of SDR amplification and convenient ELISA technique advances an intelligent strategy for ultrasensitive and high-throughput nucleic acid detection, which may be amenable for direct visual detection and quantification using an accompanying quantitative color chart. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence.

    Science.gov (United States)

    Nejad, Maryam Imani; Shi, Ruicheng; Zhang, Xinyue; Gu, Li-Qun; Gates, Kent S

    2017-07-18

    Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

    Science.gov (United States)

    Seiler, Caroline; Sharpe, Alan; Barrett, J Carl; Harrington, Elizabeth A; Jones, Emma V; Marshall, Gayle B

    2016-01-01

    Advanced genomic techniques such as Next-Generation-Sequencing (NGS) and gene expression profiling, including NanoString, are vital for the development of personalised medicines, as they enable molecular disease classification. This has become increasingly important in the treatment of cancer, aiding patient selection. However, it requires efficient nucleic acid extraction often from formalin-fixed paraffin-embedded tissue (FFPE). Here we provide a comparison of several commercially available manual and automated methods for DNA and/or RNA extraction from FFPE cancer cell line samples from Qiagen, life Technologies and Promega. Differing extraction geometric mean yields were evaluated across each of the kits tested, assessing dual DNA/RNA extraction vs. specialised single extraction, manual silica column based extraction techniques vs. automated magnetic bead based methods along with a comparison of subsequent nucleic acid purity methods, providing a full evaluation of nucleic acids isolated. Out of the four RNA extraction kits evaluated the RNeasy FFPE kit, from Qiagen, gave superior geometric mean yields, whilst the Maxwell 16 automated method, from Promega, yielded the highest quality RNA by quantitative real time RT-PCR. Of the DNA extraction kits evaluated the PicoPure DNA kit, from Life Technologies, isolated 2-14× more DNA. A miniaturised qPCR assay was developed for DNA quantification and quality assessment. Careful consideration of an extraction kit is necessary dependent on quality or quantity of material required. Here we provide a flow diagram on the factors to consider when choosing an extraction kit as well as how to accurately quantify and QC the extracted material.

  1. Co-extraction of high-quality RNA and DNA from rubber tree (Hevea ...

    African Journals Online (AJOL)

    DR TONUKARI NYEROVWO

    2012-05-15

    May 15, 2012 ... efficient method was developed for co-extracting high-quality DNA and RNA from rubber tree (Hevea brasiliensis) in this ... ratios), agarose electrophoresis analysis and reverse transcription (RT-PCR) of isolated nucleic acids indicate that ... isolate DNA from bacterium and viruses (Lewis and. Metcalf, 1988 ...

  2. [Circulating nucleic acids and infertility].

    Science.gov (United States)

    Scalici, E; Mullet, T; Ferrières Hoa, A; Gala, A; Loup, V; Anahory, T; Belloc, S; Hamamah, S

    2015-09-01

    Circulating nucleic acids (cell-free DNA and microRNAs) have for particularity to be easily detectable in the biological fluids of the body. Therefore, they constitute biomarkers of interest in female and male infertility care. Indeed, in female, they can be used to detect ovarian reserve disorders (polycystic ovary syndrome and low functional ovarian reserve) as well as to assess follicular microenvironment quality. Moreover, in men, their expression levels can vary in case of spermatogenesis abnormalities. Finally, circulating nucleic acids have also the ability to predict successfully the quality of in vitro embryo development. Their multiple contributions during assisted reproductive technology (ART) make of them biomarkers of interest, for the development of new diagnostic and/or prognostic tests, applied to our specialty. Circulating nucleic acids would so offer the possibility of personalized medical care for infertile couples in ART. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  3. High-performance method for specific effect on nucleic acids in cells using TiO2~DNA nanocomposites

    Science.gov (United States)

    Levina, Asya S.; Repkova, Marina N.; Ismagilov, Zinfer R.; Shikina, Nadezhda V.; Malygin, Ernst G.; Mazurkova, Natalia A.; Zinov'ev, Victor V.; Evdokimov, Alexei A.; Baiborodin, Sergei I.; Zarytova, Valentina F.

    2012-10-01

    Nanoparticles are used to solve the current drug delivery problem. We present a high-performance method for efficient and selective action on nucleic acid target in cells using unique TiO2.PL-DNA nanocomposites (polylysine-containing DNA fragments noncovalently immobilized onto TiO2 nanoparticles capable of transferring DNA). These nanocomposites were used for inhibition of human influenza A (H3N2) virus replication in infected MDCK cells. They showed a low toxicity (TC50 ~ 1800 μg/ml) and a high antiviral activity (>99.9% inhibition of the virus replication). The specificity factor (antisense effect) appeared to depend on the delivery system of DNA fragments. This factor for nanocomposites is ten-times higher than for DNA in the presence of lipofectamine. IC50 for nanocomposites was estimated to be 1.5 μg/ml (30 nM for DNA), so its selectivity index was calculated as ~1200. Thus, the proposed nanocomposites are prospective for therapeutic application.

  4. The Nucleic Acid Database.

    Science.gov (United States)

    Berman, Helen M; Westbrook, John; Feng, Zukang; Iype, Lisa; Schneider, Bohdan; Zardecki, Christine

    2002-06-01

    The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about nucleic acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for nucleic acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.

  5. Highly sensitive fluorescence quantitative detection of specific DNA sequences with molecular beacons and nucleic acid dye SYBR Green I.

    Science.gov (United States)

    Xiang, Dongshan; Zhai, Kun; Xiang, Wenjun; Wang, Lianzhi

    2014-11-01

    A highly sensitive fluorescence method of quantitative detection for specific DNA sequence is developed based on molecular beacon (MB) and nucleic acid dye SYBR Green I by synchronous fluorescence analysis. It is demonstrated by an oligonucleotide sequence of wild-type HBV (target DNA) as a model system. In this strategy, the fluorophore of MB is designed to be 6-carboxyfluorescein group (FAM), and the maximum excitation wavelength and maximum emission wavelength are both very close to that of SYBR Green I. In the presence of targets DNA, the MBs hybridize with the targets DNA and form double-strand DNA (dsDNA), the fluorophore FAM is separated from the quencher BHQ-1, thus the fluorophore emit fluorescence. At the same time, SYBR Green I binds to dsDNA, the fluorescence intensity of SYBR Green I is significantly enhanced. When targets DNA are detected by synchronous fluorescence analysis, the fluorescence peaks of FAM and SYBR Green I overlap completely, so the fluorescence signal of system will be significantly enhanced. Thus, highly sensitive fluorescence quantitative detection for DNA can be realized. Under the optimum conditions, the total fluorescence intensity of FAM and SYBR Green I exhibits good linear dependence on concentration of targets DNA in the range from 2×10(-11) to 2.5×10(-9)M. The detection limit of target DNA is estimated to be 9×10(-12)M (3σ). Compared with previously reported methods of detection DNA with MB, the proposed method can significantly enhance the detection sensitivity. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Multiple sequence alignments of partially coding nucleic acid sequences

    Directory of Open Access Journals (Sweden)

    Fried Claudia

    2005-06-01

    Full Text Available Abstract Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. Results The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. Conclusion We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements.

  7. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis.

    Science.gov (United States)

    Haile, Simon; Pandoh, Pawan; McDonald, Helen; Corbett, Richard D; Tsao, Philip; Kirk, Heather; MacLeod, Tina; Jones, Martin; Bilobram, Steve; Brooks, Denise; Smailus, Duane; Steidl, Christian; Scott, David W; Bala, Miruna; Hirst, Martin; Miller, Diane; Moore, Richard A; Mungall, Andrew J; Coope, Robin J; Ma, Yussanne; Zhao, Yongjun; Holt, Rob A; Jones, Steven J; Marra, Marco A

    2017-01-01

    Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95-100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.

  8. Predicting nucleic acid binding interfaces from structural models of proteins

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2011-01-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared to patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. PMID:22086767

  9. Predicting nucleic acid binding interfaces from structural models of proteins.

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

  10. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2003-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  11. Peptide Nucleic Acids (PNA)

    DEFF Research Database (Denmark)

    2002-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  12. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  13. Peptide Nucleic Acid Synthons

    DEFF Research Database (Denmark)

    2004-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  14. Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

    DEFF Research Database (Denmark)

    Kumar, Vipin; Kesavan, Venkitasamy; Gothelf, Kurt Vesterager

    2015-01-01

    Acyclic (l)-threoninol nucleic acid (aTNA) containing thymine, cytosine and adenine nucleobases were synthesized and shown to form surprisingly stable triplexes with complementary single stranded homopurine DNA or RNA targets. The triplex structures consist of two (l)-aTNA strands and one DNA...... or RNA, and these triplexes are significantly stronger than the corresponding DNA or RNA duplexes as shown in competition experiments. As a unique property the (l)-aTNAs exclusively form triplex structures with DNA and RNA and no duplex structures are observed by gel electrophoresis. The results were...... compared to the known enantiomer (d)-aTNA, which forms much weaker triplexes depending upon temperature and time. It was demonstrated that (l)-aTNA triplexes are able to stop primer extension on a DNA template, showing the potential of (l)-aTNA for antisense applications....

  15. Tadpole begging reveals high quality.

    Science.gov (United States)

    Dugas, M B; Strickler, S A; Stynoski, J L

    2017-05-01

    Parents can benefit from allocating limited resources nonrandomly among offspring, and offspring solicitation (i.e. begging) is often hypothesized to evolve because it contains information valuable to choosy parents. We tested the predictions of three 'honest begging' hypotheses - Signal of Need, Signal of Quality and Signal of Hunger - in the tadpoles of a terrestrial frog (Oophaga pumilio). In this frog, mothers provision tadpoles with trophic eggs, and when mothers visit, tadpoles perform a putative begging signal by stiffening their bodies and vibrating rapidly. We assessed the information content of intense tadpole begging with an experimental manipulation of tadpole condition (need/quality) and food deprivation (hunger). This experiment revealed patterns consistent with the Signal of Quality hypothesis and directly counter to predictions of Signal of Need and Signal of Hunger. Begging effort and performance were higher in more developed and higher condition tadpoles and declined with food deprivation. Free-living mothers were unlikely to feed tadpoles of a nonbegging species experimentally cross-fostered with their own, and allocated larger meals to more developed tadpoles and those that vibrated at higher speed. Mother O. pumilio favour their high-quality young, and because their concurrent offspring are reared in separate nurseries, must do so by making active allocation decisions. Our results suggest that these maternal choices are based at least in part on offspring signals, indicating that offspring solicitation can evolve to signal high quality. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  16. Kinetics of membrane damage to high (HNA) and low (LNA) nucleic acid bacterial clusters in drinking water by ozone, chlorine, chlorine dioxide, monochloramine, ferrate(VI), and permanganate.

    Science.gov (United States)

    Ramseier, Maaike K; von Gunten, Urs; Freihofer, Pietro; Hammes, Frederik

    2011-01-01

    Drinking water was treated with ozone, chlorine, chlorine dioxide, monochloramine, ferrate(VI), and permanganate to investigate the kinetics of membrane damage of native drinking water bacterial cells. Membrane damage was measured by flow cytometry using a combination of SYBR Green I and propidium iodide (SGI+PI) staining as indicator for cells with permeabilized membranes and SGI alone to measure total cell concentration. SGI+PI staining revealed that the cells were permeabilized upon relatively low oxidant exposures of all tested oxidants without a detectable lag phase. However, only ozonation resulted in a decrease of the total cell concentrations for the investigated reaction times. Rate constants for the membrane damage reaction varied over seven orders of magnitude in the following order: ozone > chlorine > chlorine dioxide ≈ ferrate > permanganate > chloramine. The rate constants were compared to literature data and were in general smaller than previously measured rate constants. This confirmed that membrane integrity is a conservative and therefore safe parameter for disinfection control. Interestingly, the cell membranes of high nucleic acid (HNA) content bacteria were damaged much faster than those of low nucleic acid (LNA) content bacteria during treatment with chlorine dioxide and permanganate. However, only small differences were observed during treatment with chlorine and chloramine, and no difference was observed for ferrate treatment. Based on the different reactivity of these oxidants it was suggested that HNA and LNA bacterial cell membranes have a different chemical constitution. Copyright © 2010 Elsevier Ltd. All rights reserved.

  17. An ultrasensitive photoelectrochemical nucleic acid biosensor

    Science.gov (United States)

    Gao, Zhiqiang; Tansil, Natalia C.

    2005-01-01

    A simple and ultrasensitive procedure for non-labeling detection of nucleic acids is described in this study. It is based on the photoelectrochemical detection of target nucleic acids by forming a nucleic acid/photoreporter adduct layer on an ITO electrode. The target nucleic acids were hybridized with immobilized oligonucleotide capture probes on the ITO electrode. A subsequent binding of a photoreporter—a photoactive threading bis-intercalator consisting of two N,N′-bis(3-propyl-imidazole)-1,4,5,8-naphthalene diimides (PIND) linked by a Ru(bpy)22+ (bpy = 2,2′-bipyridine) complex (PIND–Ru–PIND)—allowed for photoelectrochemical detection of the target nucleic acids. The extremely low dissociation rate of the adduct and the highly reversible photoelectrochemical response under visible light illumination (490 nm) make it possible to conduct nucleic acid detection, with a sensitivity enhancement of four orders of magnitude over voltammetry. These results demonstrate for the first time the potential of photoelectrochemical biosensors for PCR-free ultrasensitive detection of nucleic acids. PMID:16061935

  18. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2004-01-01

    A novel class of compounds known as peptide nucleic acids, bind complementary DNA and RNA strands, and generally do so more strongly than the corresponding DNA or RNA strands while exhibiting increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a...... a group consisting of naturally-occurring nucleobases and non-naturally-occurring nucleobases, including 2,6-diaminopurine, attached to a polyamide backbone, and contain alkyl amine side chains....

  19. Halogen Bonding in Nucleic Acid Complexes.

    Science.gov (United States)

    Kolář, Michal H; Tabarrini, Oriana

    2017-11-09

    Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.

  20. High-quality Indonesian condoms.

    Science.gov (United States)

    1988-06-01

    A Japanese technical team visiting the condom plant at Banjaran, Indonesia, as part of the Japanese Overseas Economic Cooperation Fund project which funded the plant, found locally produced condoms of superior quality. The marketing expert on the team predicted that family planning services provided by private practitioners and paid for by clients will account for over 50% of family planning acceptors in Indonesia by 2000. Now only 10% receive private services. Condoms are in use by 3.9% of acceptors nationwide, although as many as 15% use condoms in the capitol city. Indonesians need to be informed of the high quality of domestic condoms; marketing them for a fee will encourage this view. It is expected that in Indonesia, 2 social movements will encourage family planning, the "Posyandu" an integrated family planning and health scheme established in villages by the National Family Planning Coordinating Board, and "Arisan," a traditional system for mutual help by which villagers pool food and money to provide medicines.

  1. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    Directory of Open Access Journals (Sweden)

    Kamfai Chan

    Full Text Available Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs. Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers.

  2. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

    Science.gov (United States)

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  3. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    Science.gov (United States)

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers.

  4. Extraction of high quality DNA from seized Moroccan cannabis resin (Hashish.

    Directory of Open Access Journals (Sweden)

    Moulay Abdelaziz El Alaoui

    Full Text Available The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004 adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR amplification of tetrahydrocannabinolic acid (THCA synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances.

  5. Extraction of High Quality DNA from Seized Moroccan Cannabis Resin (Hashish)

    Science.gov (United States)

    El Alaoui, Moulay Abdelaziz; Melloul, Marouane; Alaoui Amine, Sanaâ; Stambouli, Hamid; El Bouri, Aziz; Soulaymani, Abdelmajid; El Fahime, Elmostafa

    2013-01-01

    The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish) free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004) adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR) amplification of tetrahydrocannabinolic acid (THCA) synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish) resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances. PMID:24124454

  6. Nucleic acid-based fluorescent probes and their analytical potential

    OpenAIRE

    Juskowiak, Bernard

    2010-01-01

    It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets...

  7. RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database

    OpenAIRE

    Miao, Zhichao; Westhof, Eric

    2016-01-01

    RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stan...

  8. Availability of high quality weather data measurements

    DEFF Research Database (Denmark)

    Andersen, Elsa; Johansen, Jakob Berg; Furbo, Simon

    In the period 2016-2017 the project “Availability of high quality weather data measurements” is carried out at Department of Civil Engineering at the Technical University of Denmark. The aim of the project is to establish measured high quality weather data which will be easily available...... for the building energy branch and the solar energy branch in their efforts to achieve energy savings and for researchers and students carrying out projects where measured high quality weather data are needed....

  9. Fast High-Quality Noise

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Wyvill, Geoff

    2007-01-01

    At the moment the noise functions available in a graphics programmer's toolbox are either slow to compute or they involve grid-line artifacts making them of lower quality. In this paper we present a real-time noise computation with no grid-line artifacts or other regularity problems. In other wor...

  10. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments.

    Science.gov (United States)

    Youngblut, Nicholas D; Barnett, Samuel E; Buckley, Daniel H

    2018-01-01

    Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.

  11. Utility of lab-on-a-chip technology for high-throughput nucleic acid and protein analysis

    DEFF Research Database (Denmark)

    Hawtin, Paul; Hardern, Ian; Wittig, Rainer

    2005-01-01

    samples is used to stratify gene sets for disease discovery. Finally, the applicability of a high-throughput LoaC system for assessing protein purification is demonstrated. The improvements in workflow processes, speed of analysis, data accuracy and reproducibility, and automated data analysis...

  12. Novel Biochip Platform for Nucleic Acid Analysis

    Directory of Open Access Journals (Sweden)

    Juan J. Diaz-Mochon

    2012-06-01

    Full Text Available This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top “footprint” requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market.

  13. Highly Stable Nanocontainer of APTES-Anchored Layered Titanate Nanosheet for Reliable Protection/Recovery of Nucleic Acid

    OpenAIRE

    Tae Woo Kim; In Young Kim; Dae-Hwan Park; Jin-Ho Choy; Seong-Ju Hwang

    2016-01-01

    A universal technology for the encapsulative protection of unstable anionic species by highly stable layered metal oxide has been developed via the surface modification of a metal oxide nanosheet. The surface anchoring of (3-aminopropyl)triethoxysilane (APTES) on exfoliated titanate nanosheet yields a novel cationic metal oxide nanosheet, which can be universally used for the hybridization with various biological and inorganic anions. The encapsulation of deoxyribonucleic acid (DNA) in the ca...

  14. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP experiments.

    Directory of Open Access Journals (Sweden)

    Nicholas D Youngblut

    Full Text Available Combining high throughput sequencing with stable isotope probing (HTS-SIP is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP, multi-window high-resolution stable isotope probing (MW-HR-SIP, quantitative stable isotope probing (qSIP, and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.

  15. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    Science.gov (United States)

    Esernio-Jenssen, Debra; Barnes, Marilyn

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this…

  16. MEANS AND METHODS FOR CLONING NUCLEIC ACID SEQUENCES

    NARCIS (Netherlands)

    Geertsma, Eric Robin; Poolman, Berend

    2008-01-01

    The invention provides means and methods for efficiently cloning nucleic acid sequences of interest in micro-organisms that are less amenable to conventional nucleic acid manipulations, as compared to, for instance, E.coli. The present invention enables high-throughput cloning (and, preferably,

  17. Silicon nanowires with high-k hafnium oxide dielectrics for sensitive detection of small nucleic acid oligomers.

    Science.gov (United States)

    Dorvel, Brian R; Reddy, Bobby; Go, Jonghyun; Duarte Guevara, Carlos; Salm, Eric; Alam, Muhammad Ashraful; Bashir, Rashid

    2012-07-24

    Nanobiosensors based on silicon nanowire field effect transistors offer advantages of low cost, label-free detection, and potential for massive parallelization. As a result, these sensors have often been suggested as an attractive option for applications in point-of-care (POC) medical diagnostics. Unfortunately, a number of performance issues, such as gate leakage and current instability due to fluid contact, have prevented widespread adoption of the technology for routine use. High-k dielectrics, such as hafnium oxide (HfO(2)), have the known ability to address these challenges by passivating the exposed surfaces against destabilizing concerns of ion transport. With these fundamental stability issues addressed, a promising target for POC diagnostics and SiNWFETs has been small oligonucleotides, more specifically, microRNA (miRNA). MicroRNAs are small RNA oligonucleotides which bind to mRNAs, causing translational repression of proteins, gene silencing, and expressions are typically altered in several forms of cancer. In this paper, we describe a process for fabricating stable HfO(2) dielectric-based silicon nanowires for biosensing applications. Here we demonstrate sensing of single-stranded DNA analogues to their microRNA cousins using miR-10b and miR-21 as templates, both known to be upregulated in breast cancer. We characterize the effect of surface functionalization on device performance using the miR-10b DNA analogue as the target sequence and different molecular weight poly-l-lysine as the functionalization layer. By optimizing the surface functionalization and fabrication protocol, we were able to achieve <100 fM detection levels of the miR-10b DNA analogue, with a theoretical limit of detection of 1 fM. Moreover, the noncomplementary DNA target strand, based on miR-21, showed very little response, indicating a highly sensitive and highly selective biosensing platform.

  18. Highly Stable Nanocontainer of APTES-Anchored Layered Titanate Nanosheet for Reliable Protection/Recovery of Nucleic Acid

    Science.gov (United States)

    Kim, Tae Woo; Kim, In Young; Park, Dae-Hwan; Choy, Jin-Ho; Hwang, Seong-Ju

    2016-02-01

    A universal technology for the encapsulative protection of unstable anionic species by highly stable layered metal oxide has been developed via the surface modification of a metal oxide nanosheet. The surface anchoring of (3-aminopropyl)triethoxysilane (APTES) on exfoliated titanate nanosheet yields a novel cationic metal oxide nanosheet, which can be universally used for the hybridization with various biological and inorganic anions. The encapsulation of deoxyribonucleic acid (DNA) in the cationic APTES-anchored titanate lattice makes possible the reliable long-term protection of DNA against enzymatic, chemical, and UV-vis light corrosions. The encapsulated DNA can be easily released from the titanate lattice via sonication, underscoring the functionality of the cationic APTES-anchored titanate nanosheet as a stable nanocontainer for DNA. The APTES-anchored titanate nanosheet can be also used as an efficient CO2 adsorbent and a versatile host material for various inorganic anions like polyoxometalates, leading to the synthesis of novel intercalative nanohybrids with unexplored properties and useful functionalities.

  19. Usefulness of nucleic acid testing to reduce risk of hepatitis B virus transfusion-transmitted infection in Argentina: high rate of recent infections.

    Science.gov (United States)

    Blanco, Sebastián; Balangero, Marcos César; Valle, Mildre Cledy; Montini, Oscar Luis; Carrizo, Luis Horacio; Gallego, Sandra Verónica

    2017-03-01

    Results from 10-year experience using nucleic acid test (NAT) screening in a blood bank of Córdoba are presented, showing the first data on prevalence of recent hepatitis B virus (HBV) infections and occult HBV infections (OBIs) in Argentina. Molecular screening was performed by COBAS AmpliScreen human immunodeficiency virus Type 1 (HIV-1) test Version 1.5 and COBAS AmpliScreen hepatitis C virus (HCV) test Version 2.0 and COBAS TaqScreen MPX and MPX Version 2.0 test (Roche Molecular Systems). To characterize OBI, additional molecular and serologic assays were performed. As results of NAT, 0.075% of the donors (155/205,388) tested positive for HIV, 0.05% (106/205,388) for HCV, and 0.045% (76/168,215) for HBV. Donors who tested positive for HIV or HCV by NAT were also positive by serology. There was one of 33,643 donors recently infected with HBV. At time of donation, six of 76 (7.9%) donors with confirmed HBV infection presented virologic and serologic profiles consistent with OBI. By additional studies three were OBI, two were window period infections, and one remained unclassified. NAT contributed significantly to the reduction of the potential risk of HBV transmission with a frequency of one in 56,072, detecting three in 168,215 donors without serologic evidence of infection. NAT also detected three in 168,215 OBIs. The finding of high frequency of recent infections (1/33,643), unexpected for this country, highlights the need of promoting unified effective regulations that enforce the use of NAT in all blood banks in Argentina and points out the importance of assessing the risk of HBV transmission in blood banks of other countries considered to be low-endemic. © 2016 AABB.

  20. Assessment for Melting Temperature Measurement of Nucleic Acid by HRM

    National Research Council Canada - National Science Library

    Jing Wang; Xiaoming Pan; Xingguo Liang

    2016-01-01

    High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping...

  1. Nucleic Acid Aptamers Against Proteases

    DEFF Research Database (Denmark)

    Dupont, D M; Andersen, L M; Bøtkjær, Kenneth Alrø

    2011-01-01

    Proteases are potential or realized therapeutic targets in a wide variety of pathological conditions. Moreover, proteases are classical subjects for studies of enzymatic and regulatory mechanisms. We here review the literature on nucleic acid aptamers selected with proteases as targets. Designing...... small molecule protease inhibitors of sufficient specificity has proved a daunting task. Aptamers seem to represent a promising alternative. In our review, we concentrate on biochemical mechanisms of aptamer selection, proteinaptamer recognition, protease inhibition, and advantages of aptamers...... for pharmacological intervention with pathophysiological functions of proteases. Aptamers can be selected so that they bind their targets highly specifically and with affinities corresponding to K(D) values in the nM range. Aptamers can be selected so that they recognize their targets conformation...

  2. Isolation of high quality RNA from pistachio (Pistacia vera L.) and other woody plants high in secondary metabolites.

    Science.gov (United States)

    Moazzam Jazi, Maryam; Rajaei, Saideh; Seyedi, Seyed Mahdi

    2015-10-01

    The quality and quantity of RNA are critical for successful downstream transcriptome-based studies such as microarrays and RNA sequencing (RNA-Seq). RNA isolation from woody plants, such as Pistacia vera, with very high amounts of polyphenols and polysaccharides is an enormous challenge. Here, we describe a highly efficient protocol that overcomes the limitations posed by poor quality and low yield of isolated RNA from pistachio and various recalcitrant woody plants. The key factors that resulted in a yield of 150 μg of high quality RNA per 200 mg of plant tissue include the elimination of phenol from the extraction buffer, raising the concentration of β-mercaptoethanol, long time incubation at 65 °C, and nucleic acid precipitation with optimized volume of NaCl and isopropyl alcohol. Also, the A260/A280 and A260/A230 of extracted RNA were about 1.9-2.1and 2.2-2.3, respectively, revealing the high purity. Since the isolated RNA passed highly stringent quality control standards for sensitive reactions, including RNA sequencing and real-time PCR, it can be considered as a reliable and cost-effective method for RNA extraction from woody plants.

  3. TOTAL QUALITY MANAGEMENT IN HIGH EDUCATION

    Directory of Open Access Journals (Sweden)

    Hasan SERİN, Alper AYTEKİN

    2009-01-01

    Full Text Available The approach of Total Quality Management (TQM has been even more common and most recently its use in high education has been discussed. Likewise the enterprises producing various products, universities have also inputs, processes, and outputs. Due to conditions of competition, universities have to improve the qualities of these inputs, processes, and outputs, according to satisfaction, demands, and expectations of internal and external customers. If the TQM has been implemented in the universities with a manner that aims for customer satisfaction (students, lecturers, public and private establishments, and families, supports constant development, ensures participatory approach, and encourages working in groups, it will provide universities with effectiveness, efficiency, dynamics, and economics. In this study, common problems of universities, definitions of quality and TQM in high education, customer concept at universities, and factors affecting the quality of education have been explained. Besides, in order TQM approach to be successfully implemented in the universities, various suggestions have been presented.

  4. High-quality binary interactome mapping.

    Science.gov (United States)

    Dreze, Matija; Monachello, Dario; Lurin, Claire; Cusick, Michael E; Hill, David E; Vidal, Marc; Braun, Pascal

    2010-01-01

    Physical interactions mediated by proteins are critical for most cellular functions and altogether form a complex macromolecular "interactome" network. Systematic mapping of protein-protein, protein-DNA, protein-RNA, and protein-metabolite interactions at the scale of the whole proteome can advance understanding of interactome networks with applications ranging from single protein functional characterization to discoveries on local and global systems properties. Since the early efforts at mapping protein-protein interactome networks a decade ago, the field has progressed rapidly giving rise to a growing number of interactome maps produced using high-throughput implementations of either binary protein-protein interaction assays or co-complex protein association methods. Although high-throughput methods are often thought to necessarily produce lower quality information than low-throughput experiments, we have recently demonstrated that proteome-scale interactome datasets can be produced with equal or superior quality than that observed in literature-curated datasets derived from large numbers of small-scale experiments. In addition to performing all experimental steps thoroughly and including all necessary controls and quality standards, careful verification of all interacting pairs and validation tests using independent, orthogonal assays are crucial to ensure the release of interactome maps of the highest possible quality. This chapter describes a high-quality, high-throughput binary protein-protein interactome mapping pipeline that includes these features. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Nucleic acid detection system and method for detecting influenza

    Science.gov (United States)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  6. Nucleic Acid-Based Nanoconstructs

    Science.gov (United States)

    Focuses on the design, synthesis, characterization, and development of spherical nucleic acid constructs as effective nanotherapeutic, single-entity agents for the treatment of glioblastoma multiforme and prostate cancers.

  7. Isolation of high quality DNA and RNA from cambium of the East ...

    African Journals Online (AJOL)

    The genus Warburgia belongs to the Canellaceae, a small family of tropical aromatic tree species important for their antibacterial and antifungal medicinal qualities amongst many other functions. Many published protocols for nucleic acid isolation failed to yield sufficiently good quality amounts for analysis. We have ...

  8. Effect of forage quality in faeces from different ruminant species fed high and low quality forage

    DEFF Research Database (Denmark)

    Jalali, A R; Nørgaard, P; Nielsen, M O

    2010-01-01

    Effect of forage quality in faeces from different ruminant species fed high and low quality forage......Effect of forage quality in faeces from different ruminant species fed high and low quality forage...

  9. Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential

    Directory of Open Access Journals (Sweden)

    Joel M. Harp

    2016-10-01

    Full Text Available Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cukα wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of applications of the technique to additional nucleic acid crystal structures. We have reproduced the P-SAD phasing of Z-DNA using a rotating-anode source and have attempted to phase a variety of nucleic acid crystals using P-SAD without success. A comparison of P-SAD using Z-DNA and a representative nucleic acid, the Dickerson-Drew dodecamer, is presented along with a S-SAD using only two sulfurs to phase a 2’-thio modified DNA decamer. A theoretical explanation for the limitation of P-SAD applied to nucleic acids is presented to show that the relatively high atomic displacement parameter of phosphorus in the nucleic acid backbone is responsible for the lack of success in applying P-SAD to nucleic acid diffraction data.

  10. Assuring quality in high-consequence engineering

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, Marcey L.; Kolb, Rachel R.

    2014-03-01

    In high-consequence engineering organizations, such as Sandia, quality assurance may be heavily dependent on staff competency. Competency-dependent quality assurance models are at risk when the environment changes, as it has with increasing attrition rates, budget and schedule cuts, and competing program priorities. Risks in Sandia's competency-dependent culture can be mitigated through changes to hiring, training, and customer engagement approaches to manage people, partners, and products. Sandia's technical quality engineering organization has been able to mitigate corporate-level risks by driving changes that benefit all departments, and in doing so has assured Sandia's commitment to excellence in high-consequence engineering and national service.

  11. Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges.

    Science.gov (United States)

    Qing, Taiping; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Wen, Li; Shangguan, Jingfang; Mao, Zhengui; Lei, Yanli

    2016-04-01

    Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as 'nano-tools' for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

  12. Nucleic acid based molecular devices.

    Science.gov (United States)

    Krishnan, Yamuna; Simmel, Friedrich C

    2011-03-28

    In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. High Quality Virtual Reality for Architectural Exhibitions

    DEFF Research Database (Denmark)

    Kreutzberg, Anette

    2016-01-01

    This paper will summarise the findings from creating and implementing a visually high quality Virtual Reality (VR) experiment as part of an international architecture exhibition. It was the aim to represent the architectural spatial qualities as well as the atmosphere created from combining natural...... and artificial lighting in a prominent not yet built project. The outcome is twofold: Findings concerning the integration of VR in an exhibition space and findings concerning the experience of the virtual space itself. In the exhibition, an important aspect was the unmanned exhibition space, requiring the VR...... and quantitative methods at two different occasions and setups after the exhibition, both showing a high degree of immersion and experience of reality....

  14. Nucleic acid in-situ hybridization detection of infectious agents

    Science.gov (United States)

    Thompson, Curtis T.

    2000-04-01

    Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

  15. High quality transportation fuels from renewable feedstock

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Lars Peter

    2010-09-15

    Hydrotreating of vegetable oils is novel process for producing high quality renewable diesel. Hydrotreated vegetable oils (HVO) are paraffinic hydrocarbons. They are free of aromatics, have high cetane numbers and reduce emissions. HVO can be used as component or as such. HVO processes can also be modified to produce jet fuel. GHG savings by HVO use are significant compared to fossil fuels. HVO is already in commercial production. Neste Oil is producing its NExBTL diesel in two plants. Production of renewable fuels will be limited by availability of sustainable feedstock. Therefore R and D efforts are made to expand feedstock base further.

  16. Breeding and maintaining high-quality insects

    DEFF Research Database (Denmark)

    Jensen, Kim; Kristensen, Torsten Nygård; Heckmann, Lars-Henrik

    2017-01-01

    Insects have a large potential for sustainably enhancing global food and feed production, and commercial insect production is a rising industry of high economic value. Insects suitable for production typically have fast growth, short generation time, efficient nutrient utilization, high...... in a starting phase. Here, we discuss the challenges and precautions that need to be considered when breeding and maintaining high-quality insect populations for food and feed. This involves techniques typically used in domestic animal breeding programs including maintaining genetically healthy populations...... reproductive potential, and thrive at high density. Insects may cost-efficiently convert agricultural and industrial food by-products into valuable protein once the technology is finetuned. However, since insect mass production is a new industry, the technology needed to efficiently farm these animals is still...

  17. Exosomes as nucleic acid nanocarriers.

    Science.gov (United States)

    van den Boorn, Jasper G; Dassler, Juliane; Coch, Christoph; Schlee, Martin; Hartmann, Gunther

    2013-03-01

    Exosomes are nano-sized vesicles produced naturally by many cell types. They are specifically loaded with nucleic acid cargo, dependent on the exosome-producing cell and its homeostatic state. As natural intercellular shuttles of miRNA, exosomes influence an array of developmental, physiological and pathological processes in the recipient cell or tissue to which they can be selectively targeted by their tetraspanin surface-domains. By a review of current research, we illustrate here why exosomes are ideal nanocarriers for use in the targeted in vivo delivery of nucleic acids. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Nucleic acid-functionalized transition metal nanosheets for biosensing applications.

    Science.gov (United States)

    Mo, Liuting; Li, Juan; Liu, Qiaoling; Qiu, Liping; Tan, Weihong

    2017-03-15

    In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    A structure for nucleic acid has already been proposed by Pauling and Corey [1]. They kindly made'their manuscript available to us in advance of publication. Their model consists of three inter-twined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory ...

  20. Histidine-Containing Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2000-01-01

    Peptide nucleic acids containing histidine moieties are provided. These compounds have applications including diagnostics, research and potential therapeutics.......Peptide nucleic acids containing histidine moieties are provided. These compounds have applications including diagnostics, research and potential therapeutics....

  1. A guide to highly effective quality programs.

    Science.gov (United States)

    Byrnes, John; Fifer, Joe

    2010-01-01

    To dramatically improve quality while decreasing costs, hospitals should: ensure all executives are vocal and visible supporters of quality improvement; focus the board of directors on quality as a strategic priority; strategically target quality resources to improve care for the majority of patients; use the finance system as the foundation for automated quality reporting; form a strong alliance between the CFO and chief quality officer, with each playing a leadership role in the quality program; rely on a well-executed quality program to improve efficiency and decrease the cost of care.

  2. Introduction of structural affinity handles as a tool in selective nucleic acid separations

    Science.gov (United States)

    Willson, III, Richard Coale (Inventor); Cano, Luis Antonio (Inventor)

    2011-01-01

    The method is used for separating nucleic acids and other similar constructs. It involves selective introduction, enhancement, or stabilization of affinity handles such as single-strandedness in the undesired (or desired) nucleic acids as compared to the usual structure (e.g., double-strandedness) of the desired (or undesired) nucleic acids. The undesired (or desired) nucleic acids are separated from the desired (or undesired) nucleic acids due to capture by methods including but not limited to immobilized metal affinity chromatography, immobilized single-stranded DNA binding (SSB) protein, and immobilized oligonucleotides. The invention is useful to: remove contaminating genomic DNA from plasmid DNA; remove genomic DNA from plasmids, BACs, and similar constructs; selectively separate oligonucleotides and similar DNA fragments from their partner strands; purification of aptamers, (deoxy)-ribozymes and other highly structured nucleic acids; Separation of restriction fragments without using agarose gels; manufacture recombinant Taq polymerase or similar products that are sensitive to host genomic DNA contamination; and other applications.

  3. Higher Order Structure and Binding of Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2004-01-01

    Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest......, transcription initiation, and site specific cleavage of nucleic acids....

  4. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf

    2009-01-01

    toward detailed studies of the inherent dynamics of nucleic acid structures. Moreover, the placement of FRET-pair chromophores inside the base stack will be a great advantage in studies where other (biomacro)molecules interact with the nucleic acid. Lastly, our study gives possibly the first truly solid...... distances covering up to more than one turn of the DNA duplex. Importantly, we show that the rigid stacking of the two base analogs, and consequently excellent control of their exact positions and orientations, results in a high control of the orientation factor and hence very distinct FRET changes...... as the number of bases separating tCO and tC(nitro) is varied. A set of DNA strands containing the FRET-pair at wisely chosen locations will, thus, make it possible to accurately distinguish distance- from orientation-changes using FRET. In combination with the good nucleobase analog properties, this points...

  5. Method for synthesis of high quality graphene

    Science.gov (United States)

    Lanzara, Alessandra [Piedmont, CA; Schmid, Andreas K [Berkeley, CA; Yu, Xiaozhu [Berkeley, CA; Hwang, Choonkyu [Albany, CA; Kohl, Annemarie [Beneditkbeuern, DE; Jozwiak, Chris M [Oakland, CA

    2012-03-27

    A method is described herein for the providing of high quality graphene layers on silicon carbide wafers in a thermal process. With two wafers facing each other in close proximity, in a first vacuum heating stage, while maintained at a vacuum of around 10.sup.-6 Torr, the wafer temperature is raised to about 1500.degree. C., whereby silicon evaporates from the wafer leaving a carbon rich surface, the evaporated silicon trapped in the gap between the wafers, such that the higher vapor pressure of silicon above each of the wafers suppresses further silicon evaporation. As the temperature of the wafers is raised to about 1530.degree. C. or more, the carbon atoms self assemble themselves into graphene.

  6. Nucleic acid sample preparation for in vitro molecular diagnosis: from conventional techniques to biotechnology.

    Science.gov (United States)

    Rahman, Md Mahbubor; Elaissari, Abdelhamid

    2012-11-01

    Nucleic acid (DNA and RNA)-based molecular diagnosis is a promising laboratory technique because of its ability to identify disease accurately. However, one of its disadvantages is the inevitable purification and detection of nucleic acids from other contaminated entities. Different nano- and microparticles have been developed for use in an advanced, efficient high-throughput autosystem for the purification and detection of nucleic acid samples for use in molecular diagnoses. In this review, we discuss recent advances in the development of particle-based nucleic acid purification and detection. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. High Quality Data for Grid Integration Studies

    Energy Technology Data Exchange (ETDEWEB)

    Clifton, Andrew; Draxl, Caroline; Sengupta, Manajit; Hodge, Bri-Mathias

    2017-01-22

    As variable renewable power penetration levels increase in power systems worldwide, renewable integration studies are crucial to ensure continued economic and reliable operation of the power grid. The existing electric grid infrastructure in the US in particular poses significant limitations on wind power expansion. In this presentation we will shed light on requirements for grid integration studies as far as wind and solar energy are concerned. Because wind and solar plants are strongly impacted by weather, high-resolution and high-quality weather data are required to drive power system simulations. Future data sets will have to push limits of numerical weather prediction to yield these high-resolution data sets, and wind data will have to be time-synchronized with solar data. Current wind and solar integration data sets are presented. The Wind Integration National Dataset (WIND) Toolkit is the largest and most complete grid integration data set publicly available to date. A meteorological data set, wind power production time series, and simulated forecasts created using the Weather Research and Forecasting Model run on a 2-km grid over the continental United States at a 5-min resolution is now publicly available for more than 126,000 land-based and offshore wind power production sites. The National Solar Radiation Database (NSRDB) is a similar high temporal- and spatial resolution database of 18 years of solar resource data for North America and India. The need for high-resolution weather data pushes modeling towards finer scales and closer synchronization. We also present how we anticipate such datasets developing in the future, their benefits, and the challenges with using and disseminating such large amounts of data.

  8. Quality management manual for production of high quality cassava flour

    DEFF Research Database (Denmark)

    Dziedzoave, Nanam Tay; Abass, Adebayo Busura; Amoa-Awua, Wisdom K.

    and the necessary technical expertise. This quality manual was therefore developed to guide small- to medium-scale cassava in the design and implematation of Hazard Analysis Critical Control Point (HACCP) system and Good manufacturing Practices (GMP) plans for HQCF production. It describes the HQCF production...... methods, and explanins in practical terms the concept of HACCP/QACCP quality system and procedure for aplication to HQCF production. The procedures described in this manual should help cassava processing enterprises to implement the HACCP/QACCP system from the point of root delivery through every...

  9. Polysaccharide-free nucleic acids and proteins of Abelmoschus esculentus for versatile molecular studies.

    Science.gov (United States)

    Manoj-Kumar, A; Reddy, K N; Manjulatha, M; Blanco, L

    2012-01-01

    Abelmoschus esculentus (okra) is one of the polysaccharide rich crop plants. The polysaccharides interfere with nucleic acids and protein isolation thereby affecting the downstream molecular analysis. So, to understand the molecular systematics of okra, high quality DNA, RNA and proteins are essential. In this study we present a method for extracting genomic DNA, RNA and proteins from polysaccharide rich okra tissues. The conventional extraction procedures were integrated with purification treatments with pectinase, RNase and proteinase K, which improved the quality and quantity of DNA as well. Using SDS, additional washes with CIA and NaCl precipitation improved the RNA isolation both quantitatively and qualitatively. Finally, ammonium acetate mediated protein precipitation and re-solubilization increased the quality of total protein extracts from the okra leaves. All of the methods above not only eliminated the impurities but also improved the quality and quantity of nucleic acids and proteins. Further, we subjected these samples to versatile downstream molecular analyses such as restriction endonuclease digestion, RAPD, Southern, reverse transcription-PCR and Western analysis and were proved to be successful.

  10. Inorganic nanoparticles as nucleic acid transporters into eukaryotic cells

    Science.gov (United States)

    Amirkhanov, R. N.; Zarytova, V. F.; Zenkova, M. A.

    2017-02-01

    The review is concerned with inorganic nanoparticles (gold, titanium dioxide, silica, iron oxides, calcium phosphate) used as nucleic acid transporters into mammalian cells. Methods for the synthesis of nanoparticles and approaches to surface modification through covalent or noncovalent attachment of low- or high-molecular-weight compounds are considered. The data available from the literature on biological action of nucleic acids delivered into the cells by nanoparticles and on the effect of nanoparticles and their conjugates and complexes on the cell survival are summarized. Pathways of cellular internalization of nanoparticles and the mechanism of their excretion, as well as the ways of release of nucleic acids from their complexes with nanoparticles after the cellular uptake are described. The bibliography includes 161 references.

  11. Amino-containing magnetic nanoemulsions: elaboration and nucleic acid extraction

    Energy Technology Data Exchange (ETDEWEB)

    Veyret, Raphael [Unite Mixte CNRS-bioMerieux-2714, Ecole Normale Superieure de Lyon, 46 allee d' Italie, 69364 Lyon (France); Delair, Thierry [Unite Mixte CNRS-bioMerieux-2714, Ecole Normale Superieure de Lyon, 46 allee d' Italie, 69364 Lyon (France); Pichot, Christian [Unite Mixte CNRS-bioMerieux-2714, Ecole Normale Superieure de Lyon, 46 allee d' Italie, 69364 Lyon (France); Elaissari, Abdelhamid [Unite Mixte CNRS-bioMerieux-2714, Ecole Normale Superieure de Lyon, 46 allee d' Italie, 69364 Lyon (France)]. E-mail: hamid.elaissari@ens-lyon.fr

    2005-08-15

    Amino-containing magnetic colloids were prepared from highly magnetic oil-in-water (O/W) emulsions. The functionalization was performed by controlling the adsorption of polyethyleneimine onto negatively charged magnetic emulsions. The cationic magnetic nanodroplets were characterized in terms of chemical composition, particle size, size distribution, zeta potential and colloidal stability as a function of storage time. These amino-containing magnetic emulsions were assessed as a new tool for nucleic acid extraction and amplification. The adsorption of nucleic acids was mostly controlled by attractive electrostatic interactions. The adsorption efficiency of a model RNA was found to be encouraging and the captured nucleic acid molecules were directly enzymatically amplified in the presence of the magnetic particles without any elution step.

  12. Versatile phosphoramidation reactions for nucleic acid conjugations with peptides, proteins, chromophores, and biotin derivatives.

    Science.gov (United States)

    Wang, Tzu-Pin; Chiou, Yi-Jang; Chen, Yi; Wang, Eng-Chi; Hwang, Long-Chih; Chen, Bing-Hung; Chen, Yen-Hsu; Ko, Chun-Han

    2010-09-15

    successfully synthesize nucleic acid-tetraglycine conjugates. In addition, phosphoramidation reactions provided a facile approach to prepare nucleic acid-BSA conjugates with good yields. In summary, the new approach to phosphoramidation reactions offers a universal method to prepare POCs and other nucleic acid conjugates with high yields in aqueous solutions. The methods can be easily adapted to typical chemistry or biology laboratory setups which will expedite the applications of POCs for basic research and medicine.

  13. Recent Advances in Chemical Modification of Peptide Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Eriks Rozners

    2012-01-01

    Full Text Available Peptide nucleic acid (PNA has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.

  14. Self-assembling multimeric nucleic acid constructs

    Science.gov (United States)

    Cantor, C.R.; Niemeyer, C.M.; Smith, C.L.; Sano, Takeshi; Hnatowich, D.J.; Rusckowski, M.

    1996-10-01

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products. 5 figs.

  15. Establishment of a rapid, inexpensive protocol for extraction of high quality RNA from small amounts of strawberry plant tissues and other recalcitrant fruit crops.

    Science.gov (United States)

    Christou, Anastasis; Georgiadou, Egli C; Filippou, Panagiota; Manganaris, George A; Fotopoulos, Vasileios

    2014-03-01

    Strawberry plant tissues and particularly fruit material are rich in polysaccharides and polyphenolic compounds, thus rendering the isolation of nucleic acids a difficult task. This work describes the successful modification of a total RNA extraction protocol, which enables the isolation of high quantity and quality of total RNA from small amounts of strawberry leaf, root and fruit tissues. Reverse-transcription polymerase chain reaction (RT-PCR) amplification of GAPDH housekeeping gene from isolated RNA further supports the proposed protocol efficiency and its use for downstream molecular applications. This novel procedure was also successfully followed using other fruit tissues, such as olive and kiwifruit. In addition, optional treatment with RNase A following initial nucleic acid extraction can provide sufficient quality and quality of genomic DNA for subsequent PCR analyses, as evidenced from PCR amplification of housekeeping genes using extracted genomic DNA as template. Overall, this optimized protocol allows easy, rapid and economic isolation of high quality RNA from small amounts of an important fruit crop, such as strawberry, with extended applicability to other recalcitrant fruit crops. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

    National Research Council Canada - National Science Library

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures...

  17. Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

    Science.gov (United States)

    Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

    2015-12-29

    Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

  18. Uses of Nucleic Acid Analogues in the Inhibition of Nucleic Acid Amplification

    DEFF Research Database (Denmark)

    1999-01-01

    The present invention relates to the use of nucleic acid analogues in blocking nucleic acid ampli?cation procedures and to diagnostic and analytical techniques based thereon. Also included are kits for use in the conduct of nucleic acid ampli?cation reactions....

  19. Assessment for Melting Temperature Measurement of Nucleic Acid by HRM

    Directory of Open Access Journals (Sweden)

    Jing Wang

    2016-01-01

    Full Text Available High resolution melting (HRM, with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs on melting temperature (Tm measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA Tm was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher Tm, showing that the proportion of dye should be considered for precise Tm measurement of nucleic acids. Finally, HRM method was also successfully used to measure Tms of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA or secondary structural elements (even when dNTPs are present.

  20. Synthetic Procedures for Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2004-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  1. Double-Stranded Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2001-01-01

    A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  2. The Nucleic Acid Database: Present and Future

    OpenAIRE

    Berman, Helen M.; Gelbin, Anke; Clowney, Lester; Hsieh, Shu-Hsin; Zardecki, Christine; Westbrook, John

    1996-01-01

    The Nucleic Acid Database is a relational database containing information about three-dimensional nucleic acid structures. The methods used for data processing, structure validation, database management and information retrieval, as well as the various services available via the World Wide Web, are described. Plans for the future include greater reliance on the Macromolecular Crystallographic Information File for both data processing and data management.

  3. An introduction to peptide nucleic acid

    DEFF Research Database (Denmark)

    Nielsen, P E; Egholm, M

    1999-01-01

    Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful biomolec...

  4. Methods for Identifying Ligands that Target Nucleic Acid Molecules and Nucleic Acid Structural Motifs

    Science.gov (United States)

    Disney, Matthew D. (Inventor); Childs-Disney, Jessica L. (Inventor)

    2017-01-01

    Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

  5. Indoor Air Quality in High Performance Schools

    Science.gov (United States)

    High performance schools are facilities that improve the learning environment while saving energy, resources, and money. The key is understanding the lifetime value of high performance schools and effectively managing priorities, time, and budget.

  6. High Prevalence of Respiratory Viral Infections in Patients Hospitalized in an Intensive Care Unit for Acute Respiratory Infections as Detected by Nucleic Acid-Based Assays

    OpenAIRE

    Legoff, Jérôme; Guérot, Emmanuel; Ndjoyi-Mbiguino, Angélique; Matta, Mathieu; Si-Mohamed, Ali; Gutmann, Laurent; Fagon, Jean-Yves; Bélec, Laurent

    2005-01-01

    Forty-seven bronchoalveolar lavages (BAL) were obtained from 41 patients with acute pneumonia attending an intensive care unit. By molecular diagnosis, 30% of total BAL and 63% of bacteria-negative BAL were positive for respiratory viruses. Molecular detection allows for high-rate detection of respiratory viral infections in adult patients suffering from severe pneumonia.

  7. Enhancing and targeting nucleic acid delivery by magnetic force.

    Science.gov (United States)

    Plank, Christian; Anton, Martina; Rudolph, Carsten; Rosenecker, Joseph; Krötz, Florian

    2003-08-01

    Insufficient contact of inherently highly active nucleic acid delivery systems with target cells is a primary reason for their often observed limited efficacy. Physical methods of targeting can overcome this limitation and reduce the risk of undesired side effects due to non-target site delivery. The authors and others have developed a novel means of physical targeting, exploiting magnetic force acting on nucleic acid vectors associated with magnetic particles in order to mediate the rapid contact of vectors with target cells. Here, the principles of magnetic drug and nucleic acid delivery are reviewed, and the facts and potentials of the technique for research and therapeutic applications are discussed. Magnetically enhanced nucleic acid delivery - magnetofection - is universally applicable to viral and non-viral vectors, is extraordinarily rapid, simple and yields saturation level transfection at low dose in vitro. The method is useful for site-specific vector targeting in vivo. Exploiting the full potential of the technique requires an interdisciplinary research effort in magnetic field physics, magnetic particle chemistry, pharmaceutical formulation and medical application.

  8. Simulation of High Quality Ultrasound Imaging

    DEFF Research Database (Denmark)

    Hemmsen, Martin Christian; Kortbek, Jacob; Nikolov, Svetoslav Ivanov

    2010-01-01

    This paper investigates if the influence on image quality using physical transducers can be simulated with an sufficient accuracy to reveal system performance. The influence is investigated in a comparative study between Synthetic Aperture Sequential Beamformation (SASB) and Dynamic Receive Focus...... is modeled by incorporating measured element pulse echo responses into the simulation software. Validation is performed through measurements on a water phantom with three metal wires, each with a diameter of 0.07 mm. Results show that when comparing measurement and simulation, the lateral beam profile using...

  9. Achieving High-Quality Multicultural Geriatric Care.

    Science.gov (United States)

    2016-02-01

    As the ethnic diversity of the U.S. population increases, there is a growing awareness of healthcare disparities and the need to address them. This position statement that the American Geriatrics Society (AGS) Ethnogeriatrics Committee developed outlines healthcare disparities in the United States and the minimum quality indicators that healthcare organizations and healthcare providers should adopt to ensure that all older adults receive care that is culturally appropriate and takes into account level of health literacy. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

  10. Production of high-quality fish oil from herring byproducts

    NARCIS (Netherlands)

    Aidos, I.M.F.

    2002-01-01

    In this work, the feasibility of producing high-quality fish oil from herring byproducts was evaluated in various ways. With this, a contribution has been made to a more efficient usage of natural resources while yielding a high-quality product. Crude oil extracted from herring byproducts

  11. Looking for High Quality Accreditation in Higher Education in Colombia

    Science.gov (United States)

    Pérez Gama, Jesús Alfonso; Vega Vega, Anselmo

    2017-01-01

    We look for the High Quality Accreditation of tertiary education in two ways: one, involving large amount of information, including issues such as self-assessment, high quality, statistics, indicators, surveys, and field work (process engineering), during several periods of time; and the second, in relation to the information contained there about…

  12. Intumescent features of nucleic acids and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Alongi, Jenny, E-mail: jenny.alongi@polito.it; Cuttica, Fabio; Blasio, Alessandro Di; Carosio, Federico; Malucelli, Giulio

    2014-09-10

    Highlights: • The combustion resistance of DNA and caseins to different heat fluxes was studied. • Upon heating, DNA and caseins exhibited an intumescent behaviour. • The char derived from DNA was more stable and coherent than that from caseins. - Abstract: Are nucleic acids and proteins intumescent molecules? In order to get an answer, in the present manuscript, powders of deoxyribose nucleic acids (DNA) and caseins have been exposed to different heat fluxes under a cone calorimeter source and to the direct application of a propane flame. Under these conditions, DNA and caseins exhibited a typical intumescent behaviour, generating a coherent expanded cellular carbonaceous residue (char), extremely resistant to heat exposure. The resulting volumetric expansion as well as the resistance of the formed char turned out to be dependent on (i) the chemical structure of the chosen biomacromolecule, (ii) the evolution of ammonia and (iii) the adopted heat flux in cone calorimetry tests (namely, 25, 35, 50 and 75 kW/m{sup 2}). The presence of ribose units within the DNA backbone determined the formation of highly expanded and coherent residues as compared to those obtained from caseins. Indeed, under a heat flux of 35 kW/m{sup 2}, when a carbon source (i.e. common cane sugar) was added to caseins, the resulting char was similar to that formed by DNA. Furthermore, the char expansion was ascribed to the evolution of ammonia released by these biomacromolecules upon heating, as detected by thermogravimetry coupled to infrared spectroscopy, and confirmed by scanning electron microscopy experiments performed on the bubbles present in the residues of flammability tests.

  13. Quality Assurance Strategy for Existing Homes. Final Quality Management Primer for High Performing Homes

    Energy Technology Data Exchange (ETDEWEB)

    Del Bianco, M. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Taggart, J. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Sikora, J. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Wood, A. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States)

    2012-12-01

    This guide is designed to help Building America (BA) teams understand quality management and its role in transitioning from conventional to high performance home building and remodeling. It explains what quality means, the value of quality management systems, the unique need for QMS when building high performing homes, and the first steps to a implementing a comprehensive QMS. This document provides a framework and context for BA teams when they encounter builders and remodelers.

  14. Quality Assurance Strategy for Existing Homes: Final Quality Management Primer for High Performing Homes

    Energy Technology Data Exchange (ETDEWEB)

    Del Bianco, M.; Taggart, J.; Sikora, J.; Wood, A.

    2012-12-01

    This guide is designed to help Building America (BA) Teams understand quality management and its role in transitioning from conventional to high performance home building and remodeling. It explains what quality means, the value of quality management systems, the unique need for QMS when building high performing homes, and the first steps to a implementing a comprehensive QMS. This document provides a framework and context for BA teams when they encounter builders and remodelers.

  15. The use of solid supports to generate nucleic acid carriers.

    Science.gov (United States)

    Unciti-Broceta, Asier; Díaz-Mochón, Juan José; Sánchez-Martín, Rosario M; Bradley, Mark

    2012-07-17

    Nucleic acids are the foundation stone of all cellular processes. Consequently, the use of DNA or RNA to treat genetic and acquired disorders (so called gene therapy) offers enormous potential benefits. The restitution of defective genes or the suppression of malignant genes could target a range of diseases, including cancers, inherited diseases (cystic fibrosis, muscular dystrophy, etc.), and viral infections. However, this strategy has a major barrier: the size and charge of nucleic acids largely restricts their transit into eukaryotic cells. Potential strategies to solve this problem include the use of a variety of natural and synthetic nucleic acid carriers. Driven by the aim and ambition of translating this promising therapeutic approach into the clinic, researchers have been actively developing advanced delivery systems for nucleic acids for more than 20 years. A decade ago we began our investigations of solid-phase techniques to construct families of novel nucleic acid carriers for transfection. We envisaged that the solid-phase synthesis of polycationic dendrimers and derivatized polyamimes would offer distinct advantages over solution phase techniques. Notably in solid phase synthesis we could take advantage of mass action and streamlined purification procedures, while simplifying the handling of compounds with high polarities and plurality of functional groups. Parallel synthesis methods would also allow rapid access to libraries of compounds with improved purities and yields over comparable solution methodologies and facilitate the development of structure activity relationships. We also twisted the concept of the solid-phase support on its head: we devised miniaturized solid supports that provided an innovative cell delivery vehicle in their own right, carrying covalently conjugated cargos (biomolecules) into cells. In this Account, we summarize the main outcomes of this series of chemically related projects.

  16. Nucleic acid diagnostic approaches in parasitology.

    Science.gov (United States)

    Kerttula, Anne-Marie; Lavikainen, Antti

    Nucleic acid diagnostic technologies are partly replacing traditional microscopy and antigen detection methods in parasitological diagnostics. In particular, the diagnostics of parasitic diarrhea is undergoing a transformation due to the application of polymerase chain reaction (PCR) tests. Diagnostics of malaria is still based on microscopy, but rapid nucleic acid tests are emerging. Laboratories of clinical microbiology in Finland currently provide PCR tests e.g. for intestinal protozoa, Toxoplasma and Trichomonas. Nucleic acid diagnostic methods are superior in specificity and sensitivity, but may give false positive results after a treated infection.

  17. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  18. Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

    Science.gov (United States)

    Wüst, Pia K.; Nacke, Heiko; Kaiser, Kristin; Marhan, Sven; Sikorski, Johannes; Kandeler, Ellen; Daniel, Rolf

    2016-01-01

    Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actinobacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. PMID:26896137

  19. Generation of High Quality Laser Accelerated Ion Beams

    OpenAIRE

    Esirkepov, T. Zh.; Bulanov, S. V.; Nishihara, K.; Tajima, T.; Pegoraro, F.; Khoroshkov, V. S.; Mima, K.; Daido, H.; Kato, Y.; Kitagawa, Y.; Nagai, K.; Sakabe, S.

    2002-01-01

    In order to achieve a high quality, i. e. monoergetic, intense ion beam, we propose the use of a double layer target. The first layer, at the target front, consists of high-Z atoms, while the second (rear) layer is a thin coating of low-Z atoms. The high quality proton beams from the double layer target, irradiated by an ultra-intense laser pulse, are demonstrated with three dimensional Particle-in-Cell simulations.

  20. Highly Integrated Quality Assurance – An Empirical Case

    Energy Technology Data Exchange (ETDEWEB)

    Drake Kirkham; Amy Powell; Lucas Rich

    2011-02-01

    Highly Integrated Quality Assurance – An Empirical Case Drake Kirkham1, Amy Powell2, Lucas Rich3 1Quality Manager, Radioisotope Power Systems (RPS) Program, Idaho National Laboratory, P.O. Box 1625 M/S 6122, Idaho Falls, ID 83415-6122 2Quality Engineer, RPS Program, Idaho National Laboratory 3Quality Engineer, RPS Program, Idaho National Laboratory Contact: Voice: (208) 533-7550 Email: Drake.Kirkham@inl.gov Abstract. The Radioisotope Power Systems Program of the Idaho National Laboratory makes an empirical case for a highly integrated Quality Assurance function pertaining to the preparation, assembly, testing, storage and transportation of 238Pu fueled radioisotope thermoelectric generators. Case data represents multiple campaigns including the Pluto/New Horizons mission, the Mars Science Laboratory mission in progress, and other related projects. Traditional Quality Assurance models would attempt to reduce cost by minimizing the role of dedicated Quality Assurance personnel in favor of either functional tasking or peer-based implementations. Highly integrated Quality Assurance adds value by placing trained quality inspectors on the production floor side-by-side with nuclear facility operators to enhance team dynamics, reduce inspection wait time, and provide for immediate, independent feedback. Value is also added by maintaining dedicated Quality Engineers to provide for rapid identification and resolution of corrective action, enhanced and expedited supply chain interfaces, improved bonded storage capabilities, and technical resources for requirements management including data package development and Certificates of Inspection. A broad examination of cost-benefit indicates highly integrated Quality Assurance can reduce cost through the mitigation of risk and reducing administrative burden thereby allowing engineers to be engineers, nuclear operators to be nuclear operators, and the cross-functional team to operate more efficiently. Applicability of this case

  1. APPLICATION OF HIGH VOLTAGE DIVIDERS FOR POWER QUALITY INDICES MEASUREMENT

    Directory of Open Access Journals (Sweden)

    Y. L. Anokhin

    2017-12-01

    Full Text Available Introduction. Determination of power quality indices in high-voltage power grids allows to find the reasons for the deterioration of the power quality. The relevant national and International Standards for power quality contain relevant norms of quality indices and requirements for their accuracy measurement. Problem. The most complicated part in the process of measuring the power quality indices at high voltage is the selection of the corresponding high-voltage scale voltage converters. Therefore, comparing the requirements of IEC 61000-4-30 to high voltage scale voltage converters is an important task. Goal. Analysis of the International Standard IEC 61000-4-30 requirements feasibility for measuring the indices of power quality in high-voltage electrical networks using different types of high-voltage scale voltage converters. Methodology. Comparison of the requirements of IEC 61000-4-30 Standard to high-voltage scale voltage converters, when measuring power quality indices, with the characteristics of high voltage electromagnetic transformers used in Ukraine, and with promising developments of high-voltage converters of other types. Results. It is shown in the study that in order to fulfill some of the requirements for class A of IEC 61000-4-30, the characteristics of electromagnetic voltage transformers should be determined in the substation conditions using mobile calibration high-voltage laboratories. To meet all the requirements for Class A IEC 61000-4-30, it is recommended to use broadband high-voltage dividers of resistive-capacitive type. Originality. In study it is shown firstly that all the requirements of the IEC 61000-4-30 Standard for high-voltage scale voltage converters can be performed on the basis of the use of broadband resistive-capacitive damped voltage dividers. Practical value. Expositions of specific types of resistive-capacitive high-voltage dividers are presented, their parameters are confirmed by the results of state

  2. Pooled nucleic acid testing increases the diagnostic yield of acute HIV infections in a high-risk population compared to 3rd and 4th generation HIV enzyme immunoassays.

    Science.gov (United States)

    Krajden, Mel; Cook, Darrel; Mak, Annie; Chu, Ken; Chahil, Navdeep; Steinberg, Malcolm; Rekart, Michael; Gilbert, Mark

    2014-09-01

    We compared a 3rd generation (gen) and two 4th gen HIV enzyme immunoassays (EIA) to pooled nucleic acid testing (PNAT) for the identification of pre- and early seroconversion acute HIV infection (AHI). 9550 specimens from males >18 year from clinics attended by men who have sex with men were tested by Siemens ADVIA Centaur(®) HIV 1/O/2 (3rd gen) and HIV Combo (4th gen), as well as by Abbott ARCHITECT(®) HIV Ag/Ab Combo (4th gen). Third gen non-reactive specimens were also tested by Roche COBAS(®) Ampliprep/COBAS® TaqMan HIV-1 Test v.2 in pools of 24 samples. Sensitivity and specificity of the three EIAs for AHI detection were compared. 7348 persons contributed 9435 specimens and had no evidence of HIV infection, 79 (94 specimens) had established HIV infection, 6 (9 specimens) had pre-seroconversion AHI and 9 (12 specimens) had early seroconversion AHI. Pre-seroconversion AHI cases were not detected by 3rd gen EIA, whereas 2/6 (33.3%) were detected by Siemens 4th gen, 4/6 (66.7%) by Abbott 4th gen and 6/6 (100%) by PNAT. All three EIAs and PNAT detected all individuals with early seroconversion AHI. Overall sensitivity/specificity for the EIAs relative to WB or NAT resolved infection status was 93.6%/99.9% for Siemens 3rd gen, 95.7%/99.7% for Siemens 4th gen and 97.9%/99.2% for Abbott 4th gen. While both 4th gen EIAs demonstrated improved sensitivity for AHI compared to 3rd gen EIA, PNAT identified more AHI cases than either 4th gen assay. PNAT is likely to remain a useful strategy to identify AHI in high-risk populations. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

    OpenAIRE

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular f...

  4. Nanoparticulate systems for nucleic acid delivery

    NARCIS (Netherlands)

    Varkouhi, A.K.

    2011-01-01

    Development of carrier systems with controllable physicochemical and delivery properties has opened up the possibility of nanomedicines containing nucleic acids. In the last decades, much effort has been dedicated to two exciting approaches in biomedicine, namely gene and RNA interference

  5. High-quality single crystals for neutron experiments

    Indian Academy of Sciences (India)

    To make headway on any problem in physics, high-quality single crystals are required. In this talk, special emphasis ... produces crystals of superior quality, circumventing many of the problems associated with, for example, flux growth from the melt. .... In these materials, it is possible to control the electric polarization by the ...

  6. Prediction of bread-making quality using size exclusion high ...

    African Journals Online (AJOL)

    Variation in the distribution of protein molecular weight in wheat (Triticum aestivum), influences breadmaking quality of wheat cultivars, resulting in either poor or good bread. The objective of this study was to predict breadmaking quality of wheat cultivars using size exclusion high performance liquid chromatography.

  7. On-nylon membrane detection of nucleic acid molecules by rolling circle amplification.

    Science.gov (United States)

    Xu, Xinhui; Zhang, Beibei; Gan, Ping; Wu, Jian; Dai, Wei; Zhang, Ling; Wang, Jinke

    2017-09-15

    Positively-charged nylon membrane (NM) is a general solid-phase support for nucleic acid detection due to its convenient immobilization of nucleic acid materials by direct electrostatic adherence and simple UV crosslinking. Rolling circle amplification (RCA) is a widely used isothermal DNA amplification technique for nucleic acid detection. Near-infrared fluorescence (NIRF) is a new fluorescence technique with high sensitivity due to low background. This study developed a simple method for detecting nucleic acid molecules by combining the advantages of NM, RCA and NIRF, named NIRF-based solid phase RCA on nylon membrane (NM-NIRF-sRCA). The detection system of this method only need two kinds of nucleic acid molecules: target-specific probes with a RCA primer (P) at their 3' end and a rolling circle (RC). The detection procedure consists of four steps: (1) immobilizing detected nucleic acids on NM by UV crosslinking; (2) hybridizing NM with specific probes and RC; (3) amplifying by a RCA reaction containing biotin-dUTP; (4) incubating NM with NIRF-labeled streptavidin and imaging with a NIRF imager. The method was fully testified by detecting oligonucleotides, L1 fragments of various HPV subtypes cloned in plasmid, and E.coli genomic DNA. This study thus provides a new facile method for detecting nucleic acid molecules. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Perfect Strangers: Inorganic Photochemistry and Nucleic Acids

    Science.gov (United States)

    Carter, Pamela J.; Ciftan, Suzanne A.; Sistare, Mark F.; Holden Thorp, H.

    1997-06-01

    The applications of inorganic photochemistry to nucleic acid chemistry are discussed. A brief review of nucleic acid structure is given. Methods for probing DNA using emissive inorganic complexes are discussed. Photoreactions that damage DNA by hydrogen atom transfer from sugar or electron abstraction from guanine are presented. The method of photochemical footprinting using a diplatinum photocatalyst is described. The final section discusses advances in combinatorial selection experiments that increase the urgency for rapid screening methods such as those derived from inorganic photochemistry.

  9. NPIDB: nucleic acid?protein interaction database

    OpenAIRE

    Kirsanov, Dmitry D.; Zanegina, Olga N.; Aksianov, Evgeniy A.; Spirin, Sergei A.; Karyagina, Anna S.; Alexeevski, Andrei V

    2012-01-01

    The Nucleic acid?Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA?protein and RNA?protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid?Protein Interaction DataBase is an upgrade ...

  10. Carbohydrate Polymers for Nonviral Nucleic Acid Delivery

    OpenAIRE

    Sizovs, Antons; McLendon, Patrick M.; Srinivasachari, Sathya; Reineke, Theresa M.

    2010-01-01

    Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and ...

  11. Fool's Gold Footprinting: microfluidic probing of nucleic acids

    Science.gov (United States)

    Jones, Christopher D.; Schlatterer, Joerg C.; Brenowitz, Michael; Pollack, Lois

    2012-02-01

    We describe a microfluidic device containing a mineral matrix capable of rapidly generating hydroxyl radicals that enables high-resolution structural studies of nucleic acids. Hydroxyl radicals cleave the solvent accessible backbone of DNA and RNA; the cleavage products can be detected with as fine as single nucleotide resolution. Protection from hydroxyl radical cleavage (footprinting) can identify sites of protein binding or the presence of tertiary structure. Here we report preparation of micron sized particles of iron sulfide (pyrite) and fabrication of a microfluidic prototype that together generate enough hydroxyl radicals within 20 ms to cleave DNA sufficiently for a footprinting analysis to be conducted. This prototype enables the development of high-throughput and/or rapid reaction devices with which to probe nucleic acid folding dynamics and ligand binding.

  12. High Quality Education and Learning for All through Open Education

    NARCIS (Netherlands)

    Stracke, Christian M.

    2016-01-01

    Keynote at the International Lensky Education Forum 2016, Yakutsk, Republic of Sakha, Russian Federation, by Stracke, C. M. (2016, 16 August): "High Quality Education and Learning for All through Open Education"

  13. Innovative and high quality education through Open Education and OER

    NARCIS (Netherlands)

    Stracke, Christian M.

    2017-01-01

    Online presentation and webinar by Stracke, C. M. (2017, 18 December) on "Innovative and high quality education through Open Education and OER" for the Belt and Road Open Education Learning Week by the Beijing Normal University, China.

  14. IMPACT OF RESILIENCE, ICT SUPPORT AND QUALITY OF STUDENT'S LIFE ON QUALITY OF HIGH EDUCATION PROCESS

    OpenAIRE

    Zorica Lazic

    2016-01-01

    Answers to the questions of how and in what way the quality of life of students, resilience and ICT support affects the quality of high education we will get through this work where main objective is to define a network of processes and process management ensuring more quality and more innovative managing and service provision, therefore satisfying the needs of service users - in this case the students of the university. To collect the relevant data in the thematic analysis of this paper, the...

  15. Silicon Dioxide Thin Film Mediated Single Cell Nucleic Acid Isolation

    Science.gov (United States)

    Bogdanov, Evgeny; Dominova, Irina; Shusharina, Natalia; Botman, Stepan; Kasymov, Vitaliy; Patrushev, Maksim

    2013-01-01

    A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube. PMID:23874571

  16. Developing nucleic acid-based electrical detection systems.

    Science.gov (United States)

    Gabig-Ciminska, Magdalena

    2006-03-02

    Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in nucleic acid-based electrical

  17. Developing nucleic acid-based electrical detection systems

    Directory of Open Access Journals (Sweden)

    Gabig-Ciminska Magdalena

    2006-03-01

    Full Text Available Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in

  18. Developing nucleic acid-based electrical detection systems

    Science.gov (United States)

    Gabig-Ciminska, Magdalena

    2006-01-01

    Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in nucleic acid-based electrical

  19. The pattern recognition molecule deleted in malignant brain tumors 1 (DMBT1) and synthetic mimics inhibit liposomal nucleic acid delivery

    DEFF Research Database (Denmark)

    Lund Hansen, Pernille; Blaich, Stephanie; End, Caroline

    2011-01-01

    Liposomal nucleic acid delivery is a preferred option for therapeutic settings. The cellular pattern recognition molecule DMBT1, secreted at high levels in various diseases, and synthetic mimics efficiently inhibit liposomal nucleic acid delivery to human cells. These findings may have relevance ...

  20. High quality image oriented telemedicine with multimedia technology.

    Science.gov (United States)

    Takeda, H; Minato, K; Takahasi, T

    1999-07-01

    Researchers at Osaka and Kyoto University hospital performed three experiments, beginning in 1995, which looked at high quality-oriented telemedicine. This paper describes the system design for the three projects. Experiment 1 applied high-definition TV images and B-ISDN for distance learning and medical information exchange. Experiment 2 developed a super high-definition medical image filing system and the images were transmitted via B-ISDN for teleconferences and experiment 3 utilized digital, high-definition, TV images and communication satellites for teleconferences. Multimedia and communication technologies were considered to be fundamental components of telemedicine. The three projects were evaluated initially for quality of images, operability and utility. The experimental design and its implementation showed that it was possible to provide high quality image-oriented telemedicine in the health care environment. Obstacles to establishing practical telemedicine are also discussed.

  1. Nucleic acid-based fluorescent probes and their analytical potential.

    Science.gov (United States)

    Juskowiak, Bernard

    2011-03-01

    It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.

  2. Fluorescent hybridization probes for nucleic acid detection.

    Science.gov (United States)

    Guo, Jia; Ju, Jingyue; Turro, Nicholas J

    2012-04-01

    Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

  3. Banking placental tissue: An optimized collection procedure for genome-wide analysis of nucleic acids

    Science.gov (United States)

    Wolfe, L.M.; Thiagarajan, R.D.; Boscolo, F.; Taché, V.; Coleman, R.L.; Kim, J.; Kwan, W.K.; Loring, J.F.; Parast, M.; Laurent, L.C.

    2016-01-01

    Introduction Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection in a typical clinical setting are lacking. Methods To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial timepoints in a 2-h window after delivery, simultaneously comparing the traditional snap-freeze technique to commercial solutions designed to preserve RNA (RNAlater™), and DNA (DNAgard®). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide microarray profiling for gene expression and DNA methylation. Results We found that samples collected in RNAlater had higher and more consistent RINs compared to snap-frozen tissue. Similar RINs were obtained for tissue collected in RNAlater as large (1 cm3) and small (∼0.1 cm3) pieces. RNAlater appeared to better stabilize the time zero gene expression profile compared to snap-freezing for first trimester placenta. DNA methylation profiles remained quite stable over a 2 h time period after removal of the placenta from the uterus, with DNAgard being superior to other treatments. Discussion and conclusion The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is higher than samples collected using the snap-freeze method and easier to implement in busy clinical environments. PMID:24951174

  4. Gene Therapy for Advanced Melanoma: Selective Targeting and Therapeutic Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Joana R. Viola

    2013-01-01

    Full Text Available Despite recent advances, the treatment of malignant melanoma still results in the relapse of the disease, and second line treatment mostly fails due to the occurrence of resistance. A wide range of mutations are known to prevent effective treatment with chemotherapeutic drugs. Hence, approaches with biopharmaceuticals including proteins, like antibodies or cytokines, are applied. As an alternative, regimens with therapeutically active nucleic acids offer the possibility for highly selective cancer treatment whilst avoiding unwanted and toxic side effects. This paper gives a brief introduction into the mechanism of this devastating disease, discusses the shortcoming of current therapy approaches, and pinpoints anchor points which could be harnessed for therapeutic intervention with nucleic acids. We bring the delivery of nucleic acid nanopharmaceutics into perspective as a novel antimelanoma therapeutic approach and discuss the possibilities for melanoma specific targeting. The latest reports on preclinical and already clinical application of nucleic acids in melanoma are discussed.

  5. A Procedure for High Resolution Satellite Imagery Quality Assessment

    Directory of Open Access Journals (Sweden)

    Mattia Crespi

    2009-05-01

    Full Text Available Data products generated from High Resolution Satellite Imagery (HRSI are routinely evaluated during the so-called in-orbit test period, in order to verify if their quality fits the desired features and, if necessary, to obtain the image correction parameters to be used at the ground processing center. Nevertheless, it is often useful to have tools to evaluate image quality also at the final user level. Image quality is defined by some parameters, such as the radiometric resolution and its accuracy, represented by the noise level, and the geometric resolution and sharpness, described by the Modulation Transfer Function (MTF. This paper proposes a procedure to evaluate these image quality parameters; the procedure was implemented in a suitable software and tested on high resolution imagery acquired by the QuickBird, WorldView-1 and Cartosat-1 satellites.

  6. Key factors for a high-quality VR experience

    Science.gov (United States)

    Champel, Mary-Luc; Doré, Renaud; Mollet, Nicolas

    2017-09-01

    For many years, Virtual Reality has been presented as a promising technology that could deliver a truly new experience to users. The media and entertainment industry is now investigating the possibility to offer a video-based VR 360 experience. Nevertheless, there is a substantial risk that VR 360 could have the same fate as 3DTV if it cannot offer more than just being the next fad. The present paper aims at presenting the various quality factors required for a high-quality VR experience. More specifically, this paper will focus on the main three VR quality pillars: visual, audio and immersion.

  7. Process to Continuously Melt, Refine and Cast High Quality Steel

    Energy Technology Data Exchange (ETDEWEB)

    None

    2005-09-01

    The purpose of this project is to conduct research and development targeted at designing a revolutionary steelmaking process. This process will deliver high quality steel from scrap to the casting mold in one continuous process and will be safer, more productive, and less capital intensive to build and operate than conventional steelmaking. The new process will produce higher quality steel faster than traditional batch processes while consuming less energy and other resources.

  8. The High Flying Leadership Qualities: What Matters the Most

    Science.gov (United States)

    2016-04-01

    which is an important leadership quality … If it’s important to the supervisor to develop skills and education in both them- selves and employees, it...IATIO N THE HIGH FLYING Leadership Qualities: What Matters the Most? Col Robert L. Tremaine, USAF (Ret.) Like many U.S. companies, the Department...every DoD organization invests in leadership development the same way. The ones that do think more deeply about their future have thoughtful and

  9. Next Generation High Quality Videoconferencing Service for the LHC

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    In recent times, we have witnessed an explosion of video initiatives in the industry worldwide. Several advancements in video technology are currently improving the way we interact and collaborate. These advancements are forcing tendencies and overall experiences: any device in any network can be used to collaborate, in most cases with an overall high quality. To cope with this technology progresses, CERN IT Department has taken the leading role to establish strategies and directions to improve the user experience in remote dispersed meetings and remote collaboration at large in the worldwide LHC communities. Due to the high rate of dispersion in the LHC user communities, these are critically dependent of videoconferencing technology, with a need of robustness and high quality for the best possible user experience. We will present an analysis of the factors that influenced the technical and strategic choices to improve the reliability, efficiency and overall quality of the LHC remote sessions. In particular, ...

  10. Two open access, high-quality datasets from anesthetic records.

    Science.gov (United States)

    Cumin, David; Newton-Wade, Vanessa; Harrison, Michael J; Merry, Alan F

    2013-01-01

    To provide a set of high-quality time-series physiologic and event data from anesthetic cases formatted in an easy-to-use structure. With ethics committee approval, data from surgical operations under general anesthesia were collected, including physiologic data, drug administrations, events, and clinicians' comments. These data were de-identified, formatted in a combined CSV/XML structure and made publicly available. Two separate datasets were collected containing physiologic time-series data and time-stamped events for 34 patients. For 20 patients, the data included 400 physiologic signals collected over 20 h, 274 events, and 597 drug administrations. For 14 patients, the data included 23 physiologic signals collected over 69 h, with 286 time stamped comments. Data reuse potentially saves significant time and financial costs. However, there are few high-quality repositories for accessible physiologic data and clinical interventions from surgical cases. De-identifying records assists with overcoming problems of privacy and storing the data in a format which is easily manipulated with computing resources facilitates access by the wider research community. It is hoped that additional high-quality data will be added. Future work includes developing tools to explore and visualize the data more efficiently, and establishing quality control measures. An approach to collecting and storing high-quality datasets from surgical operations under anesthesia such that they can be easily accessed by others for use in research has been demonstrated.

  11. Production of high-quality fish oil from herring byproducts

    OpenAIRE

    Aidos, I.M.F.

    2002-01-01

    In this work, the feasibility of producing high-quality fish oil from herring byproducts was evaluated in various ways. With this, a contribution has been made to a more efficient usage of natural resources while yielding a high-quality product. Crude oil extracted from herring byproducts is relatively rich in essentialw-3 PUFAs such as EPA and DHA, and is relatively stable during storage. The main conclusions of this study were: herring byprodu...

  12. IMPACT OF RESILIENCE, ICT SUPPORT AND QUALITY OF STUDENT'S LIFE ON QUALITY OF HIGH EDUCATION PROCESS

    Directory of Open Access Journals (Sweden)

    Zorica Lazic

    2016-12-01

    Full Text Available Answers to the questions of how and in what way the quality of life of students, resilience and ICT support affects the quality of high education we will get through this work where main objective is to define a network of processes and process management ensuring more quality and more innovative managing and service provision, therefore satisfying the needs of service users - in this case the students of the university. To collect the relevant data in the thematic analysis of this paper, the method of interviewing by questionnaires was applied. The sample survey was conducted among undergraduate students, teachers and staff of the Teacher Training Faculty in Uzice.

  13. Imaging Functional Nucleic Acid Delivery to Skin.

    Science.gov (United States)

    Kaspar, Roger L; Hickerson, Robyn P; González-González, Emilio; Flores, Manuel A; Speaker, Tycho P; Rogers, Faye A; Milstone, Leonard M; Contag, Christopher H

    2016-01-01

    Monogenic skin diseases arise from well-defined single gene mutations, and in some cases a single point mutation. As the target cells are superficial, these diseases are ideally suited for treatment by nucleic acid-based therapies as well as monitoring through a variety of noninvasive imaging technologies. Despite the accessibility of the skin, there remain formidable barriers for functional delivery of nucleic acids to the target cells within the dermis and epidermis. These barriers include the stratum corneum and the layered structure of the skin, as well as more locally, the cellular, endosomal and nuclear membranes. A wide range of technologies for traversing these barriers has been described and moderate success has been reported for several approaches. The lessons learned from these studies include the need for combinations of approaches to facilitate nucleic acid delivery across these skin barriers and then functional delivery across the cellular and nuclear membranes for expression (e.g., reporter genes, DNA oligonucleotides or shRNA) or into the cytoplasm for regulation (e.g., siRNA, miRNA, antisense oligos). The tools for topical delivery that have been evaluated include chemical, physical and electrical methods, and the development and testing of each of these approaches has been greatly enabled by imaging tools. These techniques allow delivery and real time monitoring of reporter genes, therapeutic nucleic acids and also triplex nucleic acids for gene editing. Optical imaging is comprised of a number of modalities based on properties of light-tissue interaction (e.g., scattering, autofluorescence, and reflectance), the interaction of light with specific molecules (e.g., absorbtion, fluorescence), or enzymatic reactions that produce light (bioluminescence). Optical imaging technologies operate over a range of scales from macroscopic to microscopic and if necessary, nanoscopic, and thus can be used to assess nucleic acid delivery to organs, regions, cells

  14. Multifunctional Nucleic Acids for Tumor Cell Treatment

    DEFF Research Database (Denmark)

    Pofahl, Monika; Wengel, Jesper; Mayer, Günter

    2014-01-01

    -proliferative and antimiR function in one 37-nucleotide nucleic acid molecule. It inhibits cancer cell growth and induces gene expression that is pathologically damped by an oncomir. These findings will have a strong impact on future developments regarding aptamer- and antimiR-related applications for tumor targeting......We report on a multifunctional nucleic acid, termed AptamiR, composed of an aptamer domain and an antimiR domain. This composition mediates cell specific delivery of antimiR molecules for silencing of endogenous micro RNA. The introduced multifunctional molecule preserves cell targeting, anti...

  15. Nucleic acid purification from plants, animals and microbes in under 30 seconds.

    Directory of Open Access Journals (Sweden)

    Yiping Zou

    2017-11-01

    Full Text Available Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling, means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.

  16. Nucleic Acid-Passivated Semiconductor Nanocrystals: Biomolecular Templating of Form and Function

    Science.gov (United States)

    Ma, Nan; Tikhomirov, Grigory; Kelley, Shana O.

    2009-01-01

    Conspectus Bright, photostable luminescent labels are powerful tools for the imaging of biological events in vitro and in vivo. Semiconductor nanocrystals have emerged as attractive alternatives to commonly used organic lumophores due to their high quantum yields and the spectral tunability that can be achieved through synthetic control. While conventional synthetic methods generally yield high-quality nanocrystals with excellent properties for biological imaging, ligand exchange and biological conjugation are necessary to make nanocrystals biocompatible and biospecific. These steps can result in substantial deterioration of optical characteristic of these nanocrystals. Moreover, the complexity of multistep nanocrystal synthesis, typically requiring inert and anhydrous conditions, prohibits many end users of these lumiphores from generating their own custom materials. We sought to streamline semiconductor nanocrystal synthesis and develop synthetic routes that would be accessible to scientists from all disciplines. In search of such an approach we turned to nucleic acids as a programmable and versatile ligand set, and found that these biomolecules are indeed appropriate for biocompatible semiconductor nanocrystals preparation. In this account we present a summary of our work on nucleic acids-programmed nanocrystal synthesis that has resulted in the successful development of a one-step synthesis of biofunctionalized nanocrystals in aqueous solution. We first discuss results obtained with nucleotide-capped cadmium and lead chalcogenide-based nanocrystals that served to guide further investigation of polynucleotide-assisted synthesis. We investigate the roles of individual nucleobases and their structures in passivation of the surfaces of nanocrystals and modulating morphology and optical characteristics. We show that nanocrystals’ optical properties and morphologies are highly influenced by nucleic acid structures and sequences, as well as by reaction conditions

  17. Negative Binomial charts for monitoring high-quality processes

    NARCIS (Netherlands)

    Albers, Willem/Wim

    Good control charts for high quality processes are often based on the number of successes between failures. Geometric charts are simplest in this respect, but slow in recognizing moderately increased failure rates p. Improvement can be achieved by waiting until r > 1 failures have occurred, i.e. by

  18. Learning Disabilities and Achieving High-Quality Education Standards

    Science.gov (United States)

    Gartland, Debi; Strosnider, Roberta

    2017-01-01

    This is an official document of the National Joint Committee on Learning Disabilities (NJCLD), of which Council for Learning Disabilities is a long-standing, active member. With this position paper, NJCLD advocates for the implementation of high-quality education standards (HQES) for students with learning disabilities (LD) and outlines the…

  19. Coming soon to your clinic: high-quality ART.

    NARCIS (Netherlands)

    Empel, IW van; Nelen, W.L.D.M.; Hermens, R.P.M.G.; Kremer, J.A.M.

    2008-01-01

    The concept of 'patient-friendly' medically assisted reproduction includes a robust set of clinical practice principles, to improve the quality of subfertility care. This concept is an important move away from the sole focus on effectiveness and high pregnancy rates in assisted reproduction

  20. The High-Quality School: Thoughtful vs. Technocratic Leadership. Draft.

    Science.gov (United States)

    Webb, Clark

    Four ideas or theses about schooling and leadership together form a coherent approach to teaching and learning in the high-quality school. They form the basis, if not for large-scale reform, at least for individual consideration and adoption. The first thesis is that humans are creatures of perspective or viewpoint. The second thesis is that the…

  1. 36 CFR 910.31 - High architectural quality.

    Science.gov (United States)

    2010-07-01

    ... architectural quality. Development must maintain a uniformly high standard of architecture, representative of the best contemporary design and planning concepts. Great care and sensitivity must be shown in the... GENERAL GUIDELINES AND UNIFORM STANDARDS FOR URBAN PLANNING AND DESIGN OF DEVELOPMENT WITHIN THE...

  2. Improving high quality, equitable maternal health services in Malawi ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Malawi has high rates of maternal mortality despite concerted efforts to increase the rate of births at health facilities. In response, the Ministry of Health implemented a Standards-Based Management and Recognition for Reproductive Health initiative to improve the quality of health services. Similar initiatives have proven ...

  3. Supplementation of quality protein to high producing Jersey cows ...

    African Journals Online (AJOL)

    Evelen

    The milk yield potential of 500 kg cows grazing ryegrass pasture, with no supplementation, is 16 to. 17 litres a day (Dugmore, 1995). The aim of the study was to determine whether grazing cows that are receiving maize supplementation, with minerals included, would respond to the addition of a high quality protein source,.

  4. The Nature of Spontaneity in High Quality Mathematics Learning Experiences

    Science.gov (United States)

    Williams, Gaye

    2004-01-01

    Spontaneity has been linked to high quality learning experiences in mathematics (Csikszentmihalyi & Csikszentmihalyi, 1992; Williams, 2002).This paper shows how spontaneity can be identified by attending to the nature of social elements in the process of abstracting (Dreyfus, Hershkowitz, & Schwarz, 2001). This process is elaborated…

  5. Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications.

    Science.gov (United States)

    Peña-Llopis, Samuel; Brugarolas, James

    2013-11-01

    Genomic technologies have revolutionized our understanding of complex Mendelian diseases and cancer. Solid tumors present several challenges for genomic analyses, such as tumor heterogeneity and tumor contamination with surrounding stroma and infiltrating lymphocytes. We developed a protocol to (i) select tissues of high cellular purity on the basis of histological analyses of immediately flanking sections and (ii) simultaneously extract genomic DNA (gDNA), mRNA, noncoding RNA (ncRNA; enriched in miRNA) and protein from the same tissues. After tissue selection, about 12-16 extractions of DNA, RNA or protein can be obtained per day. Compared with other similar approaches, this fast and reliable methodology allowed us to identify mutations in tumors with remarkable sensitivity and to perform integrative analyses of whole-genome and exome data sets, DNA copy numbers (by single-nucleotide polymorphism (SNP) arrays), gene expression data (by transcriptome profiling and quantitative PCR (qPCR)) and protein levels (by western blotting and immunohistochemical analysis) from the same samples. Although we focused on renal cell carcinoma, this protocol may be adapted with minor changes to any human or animal tissue to obtain high-quality and high-yield nucleic acids and proteins.

  6. Highly qualified does not equal high quality: A study of urban stakeholders' perceptions of quality in science teaching

    Science.gov (United States)

    Miranda, Rommel Joseph

    By employing qualitative methods, this study sought to determine the perceptions that urban stakeholders hold about what characteristics should distinguish a high school science teacher whom they would consider to demonstrate high quality in science teaching. A maximum variation sample of six science teachers, three school administrators, six parents and six students from a large urban public school district were interviewed using semi-structured, in-depth interview techniques. From these data, a list of observable characteristics which urban stakeholders hold as evidence of high quality in science teaching was generated. Observational techniques were utilized to determine the extent to which six urban high school science teachers, who meet the NCLB Act criteria for being "highly qualified", actually possessed the characteristics which these stakeholders hold as evidence of high quality in science teaching. Constant comparative analysis was used to analyze the data set. The findings suggest that urban stakeholders perceive that a high school science teacher who demonstrates high quality in science teaching should be knowledgeable about their subject matter, their student population, and should be resourceful; should possess an academic background in science and professional experience in science teaching; should exhibit professionalism, a passion for science and teaching, and a dedication to teaching and student learning; should be skillful in planning and preparing science lessons and in organizing the classroom, in presenting the subject matter to students, in conducting a variety of hands-on activities, and in managing a classroom; and should assess whether students complete class goals and objectives, and provide feedback about grades for students promptly. The findings further reveal that some of the urban high school science teachers who were deemed to be "highly qualified", as defined by the NCLB Act, engaged in practices that threatened quality in science

  7. High quality digital holographic reconstruction on analog film

    Science.gov (United States)

    Nelsen, B.; Hartmann, P.

    2017-05-01

    High quality real-time digital holographic reconstruction, i.e. at 30 Hz frame rates, has been at the forefront of research and has been hailed as the holy grail of display systems. While these efforts have produced a fascinating array of computer algorithms and technology, many applications of reconstructing high quality digital holograms do not require such high frame rates. In fact, applications such as 3D holographic lithography even require a stationary mask. Typical devices used for digital hologram reconstruction are based on spatial-light-modulator technology and this technology is great for reconstructing arbitrary holograms on the fly; however, it lacks the high spatial resolution achievable by its analog counterpart, holographic film. Analog holographic film is therefore the method of choice for reconstructing highquality static holograms. The challenge lies in taking a static, high-quality digitally calculated hologram and effectively writing it to holographic film. We have developed a theoretical system based on a tunable phase plate, an intensity adjustable high-coherence laser and a slip-stick based piezo rotation stage to effectively produce a digitally calculated hologram on analog film. The configuration reproduces the individual components, both the amplitude and phase, of the hologram in the Fourier domain. These Fourier components are then individually written on the holographic film after interfering with a reference beam. The system is analogous to writing angularly multiplexed plane waves with individual component phase control.

  8. ABIOGENIC INFORMATION COUPLING BETWEEN NUCLEIC ACID AND PROTEIN,OR, HOW PROTEIN AND DNA WERE MARRIED

    Energy Technology Data Exchange (ETDEWEB)

    Calvin, Melvin

    1968-12-01

    There is now experimental evidence for selectivity between the amino acid and the nucleic acid base which is the beginning of the chemical translation process from one linear system to the other. The linear system of the nucleic acid is, of course, an excellent place to store the information, whereas the linear system of the polypeptide, on the other hand, is the versatile system which can perform many different types of reactions but is unable to store information reliably. The experiments the author has described here may represent the beginning of the method of coupling of those two essential qualities which are required for the generation and evolution of a living organism.

  9. A locked nucleic Acid-based nanocrawler

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Pasternak, Karol; Campbell, Meghan A

    2013-01-01

    Herein we introduce a novel fluorescent LNA/DNA machine, a nanocrawler, which reversibly moves along a directionally polar complementary road controlled by affinity-enhancing locked nucleic acid (LNA) monomers and additional regulatory strands. Polyaromatic hydrocarbon (PAH) dyes attached to 2...

  10. Thermodynamic Analysis of Nylon Nucleic Acids

    Science.gov (United States)

    Liu, Yu; Wang, Risheng; Ding, Liang; Sha, Ruojie; Lukeman, Philip S.

    2010-01-01

    The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides containing nylon nucleic acids (1 to 5 amide linkages) revealed that the amide linkage enhanced significantly the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26°C increase in the thermal transition temperature (Tm) for 5 linkages) and RNA (around 15°C increase in Tm for 5 linkages) when compared with non-amide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2′ position of ribose, and recovery of stability upon linkage of the side chains. PMID:18543259

  11. Recent progress in nucleic acids isotachophoresis

    Czech Academy of Sciences Publication Activity Database

    Datinská, Vladimíra; Voráčová, Ivona; Schlecht, U.; Berka, J.; Foret, František

    2018-01-01

    Roč. 41, č. 1 (2018), s. 236-247 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GBP206/12/G014 Institutional support: RVO:68081715 Keywords : isotachophoresis * nucleic acids * sample preparation Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 2.557, year: 2016

  12. Compact pulley-type microring resonator with high quality factor

    Science.gov (United States)

    Cai, Dong-Po; Lu, Jyun-Hong; Chen, Chii-Chang; Lee, Chien-Chieh; Lin, Chu-En; Yen, Ta-Jen

    2014-11-01

    A pulley-type microring resonator with ultra-small dimensions and ultra-high quality factor on a silicon-on-insulator wafer is fabricated and characterized. Simulation results show that the bending loss of the pulley-type microring resonator can be diminished by wrapping the curved waveguide around the microring, and that the energy loss from the output port can be decreased by tuning the width of the bus waveguide to achieve destructive interference. A quality factor of 1.73 × 105 is obtained in this experiment. The compact size of the pulley-type microring resonator with low bending loss is suitable for an integrated optical circuit.

  13. Integration study of high quality teaching resources in universities

    Directory of Open Access Journals (Sweden)

    Honglu Liu

    2012-12-01

    Full Text Available Purpose: The development level and quality of education depend on the merits and efficiency in the use of teaching resources, especially in the case of obvious contradiction between the demand and supply of teaching resources. So to integrate teaching resources, improve the efficiency in the use of high quality teaching resources, and take the road of content development to enhance the competitiveness of education has become very important and urgent.Design/methodology/approach: On the basis of analysis on the teaching resources of universities and the problems they faced, this paper introduced the basic concepts of cloud storage, and built the integration architecture of high quality teaching resources in universities based on the cloud storage.Findings and Originality/value: The HDFS-based cloud storage proposed in this paper is a dynamically adjustable and Internet-based storage solution, and the users can access storage targets using the network through a common and easy-to-use protocol and application programming interfaces. This new technology is useful for end users benefits. With the continuous development and improvement of cloud storage, it will necessarily result in more and more applications in the institutions of higher learning and education network.Originality/value: This paper introduced the cloud storage into the integration of high quality teaching resources in universities first and as a new form of service, it can be a good solution.

  14. Locked and unlocked nucleosides in functional nucleic acids

    DEFF Research Database (Denmark)

    Doessing, Holger; Vester, Birte

    2011-01-01

    Nucleic acids are able to adopt a plethora of structures, many of which are of interest in therapeutics, bio- or nanotechnology. However, structural and biochemical stability is a major concern which has been addressed by incorporating a range of modifications and nucleoside derivatives. This rev....... This review summarizes the use of locked nucleic acid (LNA) and un-locked nucleic acid (UNA) monomers in functional nucleic acids such as aptamers, ribozymes, and DNAzymes....

  15. The Nucleic Acid Database: new features and capabilities

    OpenAIRE

    Coimbatore Narayanan, Buvaneswari; Westbrook, John; Ghosh, Saheli; Petrov, Anton I.; Sweeney, Blake; Zirbel, Craig L.; Leontis, Neocles B.; Berman, Helen M.

    2013-01-01

    The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D nucleic acid structures and their complexes. In addition to primary data, the NDB contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. This article descri...

  16. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    Science.gov (United States)

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-09

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths.

  17. Examination of Operation Quality for High-frequent Railway Operation

    DEFF Research Database (Denmark)

    Landex, Alex; Kaas, Anders H.

    2009-01-01

    The examination of operation quality for high-frequent operation requires other approaches than the typical evaluation of punctuality (trains on time) and reliability (operated trains). This is because passengers in high-frequent railway systems do not necessarily notice train delays as they just...... take the first train in their direction. The article examines four different approaches to examine operation quality for high-frequent operation that are based on the experiences of the passengers. These approaches are the service frequency of the operation, travel time extension, a combination...... operation simulation software. Combining the passenger delay model with simulation software gives the possibility to forecast future infrastructure and operation scenarios which make it possible to improve the planning....

  18. High quality early childhood education in the United States

    Directory of Open Access Journals (Sweden)

    Mercedes Varona Alabern

    2015-06-01

    Full Text Available The United States education system, K-12 produced impressive results for most of the 20th century. We trace its origins back to the end of the 19th century, when the America’s social and economical needs and its circumstances were very different from the ones today. Nowadays, American society is far more complex and demands highly qualified citizens, a requirement which inevitably starts with high quality early childhood education, as we will illustrate below. Therefore, experts are currently requesting all public administrations and private sector to take further steps to ensure high quality preschool education for everyone in order to improve Americans’ skills and the United States’ economy, as well as to overcome the existing inequalities.

  19. Conducting high quality writing intervention research: Twelve recommendations

    Directory of Open Access Journals (Sweden)

    Steve Graham

    2014-10-01

    Full Text Available Writing intervention research can enhance our knowledge about writing, its development, and how to teach it effectively. Despite the importance of such research, many of the writing intervention studies conducted previously were of poor quality, as documented by Graham and colleagues in a series of meta-analyses (Graham, McKeown, Kiuhara, & Harris, 2012; Graham & Perin, 2007; Rogers & Graham, 2008. In this article, we offer 12 recommendations for conducting high quality intervention research, recommendations that draw on those meta-analyses as well as previous work on improving the quality of intervention research (Pressley & Harris, 1994a, 1994b and our experiences as writing intervention researchers and editors of journals that publish intervention research (including the Journal of Writing Research . The recommendations address issues and actions involved in designing, conducting, and reporting such research.

  20. Quality and efficiency in high dimensional Nearest neighbor search

    KAUST Repository

    Tao, Yufei

    2009-01-01

    Nearest neighbor (NN) search in high dimensional space is an important problem in many applications. Ideally, a practical solution (i) should be implementable in a relational database, and (ii) its query cost should grow sub-linearly with the dataset size, regardless of the data and query distributions. Despite the bulk of NN literature, no solution fulfills both requirements, except locality sensitive hashing (LSH). The existing LSH implementations are either rigorous or adhoc. Rigorous-LSH ensures good quality of query results, but requires expensive space and query cost. Although adhoc-LSH is more efficient, it abandons quality control, i.e., the neighbor it outputs can be arbitrarily bad. As a result, currently no method is able to ensure both quality and efficiency simultaneously in practice. Motivated by this, we propose a new access method called the locality sensitive B-tree (LSB-tree) that enables fast highdimensional NN search with excellent quality. The combination of several LSB-trees leads to a structure called the LSB-forest that ensures the same result quality as rigorous-LSH, but reduces its space and query cost dramatically. The LSB-forest also outperforms adhoc-LSH, even though the latter has no quality guarantee. Besides its appealing theoretical properties, the LSB-tree itself also serves as an effective index that consumes linear space, and supports efficient updates. Our extensive experiments confirm that the LSB-tree is faster than (i) the state of the art of exact NN search by two orders of magnitude, and (ii) the best (linear-space) method of approximate retrieval by an order of magnitude, and at the same time, returns neighbors with much better quality. © 2009 ACM.

  1. Family Perspectives on High-Quality Pediatric Subspecialty Referrals.

    Science.gov (United States)

    Ray, Kristin N; Ashcraft, Laura Ellen; Kahn, Jeremy M; Mehrotra, Ateev; Miller, Elizabeth

    2016-08-01

    Although children are frequently referred to subspecialist physicians, many inadequacies in referral processes have been identified from physician and system perspectives. Little is known, however, about how to comprehensively measure or improve the quality of the referral systems from a family-centered perspective. To foster family-centered improvements to pediatric subspecialty referrals, we sought to develop a framework for high-quality, patient-centered referrals from the perspectives of patients and their families. We used stakeholder-informed qualitative analysis of parent, caregiver, and patient interviews to identify outcomes, processes, and structures of high-quality pediatric subspecialty referrals as perceived by patients and their family members. We interviewed 21 informants. Informants identified 5 desired outcomes of subspecialty referrals: improved functional status or symptoms; improved long-term outcomes; improved knowledge of their disease; informed expectations; and reduced anxiety about the child's health status. Processes that informants identified as supporting these outcomes centered around 6 key steps in subspecialty referrals, including the referral decision, previsit information transfer, appointment scheduling, subspecialist visit, postvisit information transfer, and ongoing care integration and communication. Health care delivery structures identified by informants as supporting these processes included physical infrastructure, human resources, and information technology systems. We identified family-centered outcomes, processes, and structures of high-quality pediatric subspecialty referrals. These domains can be used not only to improve measurement of the quality of existing referral systems but also to inform future interventions to improve patient-centered outcomes for children in need of specialty care. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

  2. Auto Spell Suggestion for High Quality Speech Synthesis in Hindi

    Science.gov (United States)

    Kabra, Shikha; Agarwal, Ritika

    2014-02-01

    The goal of Text-to-Speech (TTS) synthesis in a particular language is to convert arbitrary input text to intelligible and natural sounding speech. However, for a particular language like Hindi, which is a highly confusing language (due to very close spellings), it is not an easy task to identify errors/mistakes in input text and an incorrect text degrade the quality of output speech hence this paper is a contribution to the development of high quality speech synthesis with the involvement of Spellchecker which generates spell suggestions for misspelled words automatically. Involvement of spellchecker would increase the efficiency of speech synthesis by providing spell suggestions for incorrect input text. Furthermore, we have provided the comparative study for evaluating the resultant effect on to phonetic text by adding spellchecker on to input text.

  3. Wellbeing Understanding in High Quality Healthcare Informatics and Telepractice.

    Science.gov (United States)

    Fiorini, Rodolfo A; De Giacomo, Piero; L'Abate, Luciano

    2016-01-01

    The proper use of healthcare informatics technology and multidimensional conceptual clarity are fundamental to create and boost outstanding clinical and telepractice results. Avoiding even terminology ambiguities is mandatory for high quality of care service. For instance, well-being or wellbeing is a different way to write the same concept only, or there is a good deal of ambiguity around the meanings of these terms the way they are written. In personal health, healthcare and healthcare informatics, this kind of ambiguity and lack of conceptual clarity has been called out repeatedly over the past 50 years. It is time to get the right, terse scenario. We present a brief review to develop and achieve ultimate wellbeing understanding for practical high quality healthcare informatics and telepractice application. This article presents an innovative point of view on deeper wellbeing understanding towards its increased clinical effective application.

  4. A high throughput DNA extraction method with high yield and quality

    Directory of Open Access Journals (Sweden)

    Xin Zhanguo

    2012-07-01

    Full Text Available Abstract Background Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome, and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L. Moench] leaves and dry seeds with high yield, high quality, and affordable cost. Results We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. Conclusion A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

  5. A high throughput DNA extraction method with high yield and quality.

    Science.gov (United States)

    Xin, Zhanguo; Chen, Junping

    2012-07-28

    Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome), and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L.) Moench] leaves and dry seeds with high yield, high quality, and affordable cost. We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

  6. CD 116: A vigorous wheat cultivar with high industrial quality

    OpenAIRE

    Francisco de Assis Franco; Volmir Sergio Marchioro; Tatiane Dalla Nora; Ivan Schuster; Edson Feliciano de Oliveira; Elisa Serra Negra Vieira; Fábio Júnior Alcantara de Lima

    2009-01-01

    Cultivar CD 116 was developed by the Cooperativa Central de Pesquisa Agrícola (COODETEC) and issuitable for cultivation in the states of Paraná, São Paulo, Mato Grosso do Sul, Mato Grosso, Minas Gerais, Goiás, andDistrito Federal. CD 116 is tolerant to the major diseases, particularly blast, has a high industrial grain quality and meanyield of 3908 kg ha-1, exceeding the control cultivars by 6%.

  7. Origin of Overstretching Transitions in Single-Stranded Nucleic Acids

    Science.gov (United States)

    Scholl, Zackary N.; Rabbi, Mahir; Lee, David; Manson, Laura; S-Gracz, Hanna; Marszalek, Piotr E.

    2013-11-01

    We combined single-molecule force spectroscopy with nuclear magnetic resonance measurements and molecular mechanics simulations to examine overstretching transitions in single-stranded nucleic acids. In single-stranded DNA and single-stranded RNA there is a low-force transition that involves unwinding of the helical structure, along with base unstacking. We determined that the high-force transition that occurs in polydeoxyadenylic acid single-stranded DNA is caused by the cooperative forced flipping of the dihedral angle formed between four atoms, O5’-C5’-C4’-C3’ (γ torsion), in the nucleic acid backbone within the canonical B-type helix. The γ torsion also flips under force in A-type helices, where the helix is shorter and wider as compared to the B-type helix, but this transition is less cooperative than in the B type and does not generate a high-force plateau in the force spectrums of A-type helices. We find that a similar high-force transition can be induced in polyadenylic acid single-stranded RNA by urea, presumably due to disrupting the intramolecular hydrogen bonding in the backbone. We hypothesize that a pronounced high-force transition observed for B-type helices of double stranded DNA also involves a cooperative flip of the γ torsion. These observations suggest new fundamental relationships between the canonical structures of single-and double-stranded DNA and the mechanism of their molecular elasticity.

  8. Convenient synthesis and application of versatile nucleic acid lipid membrane anchors in the assembly and fusion of liposomes

    DEFF Research Database (Denmark)

    Ries, Oliver; Löffler, Philipp M. G.; Vogel, Stefan

    2015-01-01

    Hydrophobic moieties like lipid membrane anchors are highly demanded modifications for nucleic acid oligomers. Membrane-anchor modified oligonucleotides are applicable in biomedicine leading to new delivery strategies as well as in biophysical investigations towards assembly and fusion of liposom...

  9. Spectrofluorimetric study of the binding of codeine to nucleic acids

    Science.gov (United States)

    Wang, Feng; Huang, Wei; Su, Liang; Dong, Zijia; Zhang, Shuai

    2009-06-01

    The characteristics of the interaction between codeine (CD) and nucleic acids were studied by ultraviolet-visible spectra and fluorescent spectra. It shows that there is a powerful ability in nucleic acids to quench the fluorescence intensity of codeine. The fluorescence quenching data were analyzed according to Stern-Volmer equation and Förster's nonradiative energy transfer mechanism. Thus the binding constant and the thermodynamic parameters between codeine and nucleic acids were obtained. The results show that codeine interacts with nucleic acids in a mode of groove binding and -OCH 3 of the codeine molecular combines with the groove of nucleic acids through hydrogen bond or van der Waals force.

  10. High quality fuel gas from biomass pyrolysis with calcium oxide.

    Science.gov (United States)

    Zhao, Baofeng; Zhang, Xiaodong; Chen, Lei; Sun, Laizhi; Si, Hongyu; Chen, Guanyi

    2014-03-01

    The removal of CO2 and tar in fuel gas produced by biomass thermal conversion has aroused more attention due to their adverse effects on the subsequent fuel gas application. High quality fuel gas production from sawdust pyrolysis with CaO was studied in this paper. The results of pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) experiments indicate that the mass ratio of CaO to sawdust (Ca/S) remarkably affects the behavior of sawdust pyrolysis. On the basis of Py-GC/MS results, one system of a moving bed pyrolyzer coupled with a fluid bed combustor has been developed to produce high quality fuel gas. The lower heating value (LHV) of the fuel gas was above 16MJ/Nm(3) and the content of tar was under 50mg/Nm(3), which is suitable for gas turbine application to generate electricity and heat. Therefore, this technology may be a promising route to achieve high quality fuel gas for biomass utilization. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. High quality mask storage in an advanced Logic-Fab

    Science.gov (United States)

    Jähnert, Carmen; Fritsche, Silvio

    2012-02-01

    High efficient mask logistics as well as safe and high quality mask storage are essential requirements within an advanced lithography area of a modern logic waferfab. Fast operational availability of the required masks at the exposure tool with excellent mask condition requires a safe mask handling, safeguarding of high mask quality over the whole mask usage time without any quality degradation and an intelligent mask logistics. One big challenge is the prevention of haze on high advanced phase shift masks used in a high volume production line for some thousands of 248nm or 193nm exposures. In 2008 Infineon Dresden qualified a customer specific developed semi-bare mask storage system from DMSDynamic Micro Systems in combination with a high advanced mask handling and an interconnected complex logistic system. This high-capacity mask storage system DMS M1900.22 for more than 3000 masks with fully automated mask and box handling as well as full-blown XCDA purge has been developed and adapted to the Infineon Lithotoollandscape using Nikon and SMIF reticle cases. Advanced features for ESD safety and mask security, mask tracking via RFID and interactions with the exposure tools were developed and implemented. The stocker is remote controlled by the iCADA-RSM system, ordering of the requested mask directly from the affected exposure tool allows fast access. This paper discusses the advantages and challenges for this approach as well as the practical experience gained during the implementation of the new system which improves the fab performance with respect to mask quality, security and throughput. Especially the realization of an extremely low and stable humidity level in addition with a well controlled air flow at each mask surface, preventing masks from haze degradation and particle contamination, turns out to be a notable technical achievement. The longterm stability of haze critical masks has been improved significantly. Relevant environmental parameters like

  12. Methods and systems for fabricating high quality superconducting tapes

    Energy Technology Data Exchange (ETDEWEB)

    Majkic, Goran; Selvamanickam, Venkat

    2018-02-13

    An MOCVD system fabricates high quality superconductor tapes with variable thicknesses. The MOCVD system can include a gas flow chamber between two parallel channels in a housing. A substrate tape is heated and then passed through the MOCVD housing such that the gas flow is perpendicular to the tape's surface. Precursors are injected into the gas flow for deposition on the substrate tape. In this way, superconductor tapes can be fabricated with variable thicknesses, uniform precursor deposition, and high critical current densities.

  13. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification.

    Science.gov (United States)

    Borysiak, Mark D; Kimura, Kevin W; Posner, Jonathan D

    2015-04-07

    Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications.

  14. Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Yan

    Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.

  15. High quality factor resonance at room temperature with nanostrings under high tensile stress

    Science.gov (United States)

    Verbridge, Scott S.; Parpia, Jeevak M.; Reichenbach, Robert B.; Bellan, Leon M.; Craighead, H. G.

    2006-06-01

    Quality factors as high as 207 000 are demonstrated at room temperature for radio-frequency silicon nitride string resonators with cross sectional dimensions on the scale of 100 nm, made with a nonlithographic technique. A product of quality factor and surface to volume ratio greater than 6000 nm-1 is presented, the highest yet reported. Doubly clamped nanostring resonators are fabricated in high tensile-stress silicon nitride using a nonlithographic electrospinning process. We fabricate devices with an electron beam process, and demonstrate frequency and quality factor results identical to those obtained with the nonlithographic technique. We also compare high tensile-stress doubly clamped beams with doubly clamped and cantilever resonators made of a lower stress material, as well as cantilever beams made of the high stress material. In all cases, the doubly clamped high stress beams have the highest quality factors. We therefore attribute the high quality factors to high tensile stress. Potential dominant loss mechanisms are discussed, including surface and clamping losses, and thermoelastic dissipation. Some practical advantages offered by these nanostrings for mass sensing are discussed.

  16. Exonuclease III-boosted cascade reactions for ultrasensitive SERS detection of nucleic acids.

    Science.gov (United States)

    Sun, Yudie; Peng, Pai; Guo, Ruiyan; Wang, Huihui; Li, Tao

    2018-05-01

    A variety of nucleic acid amplification techniques have been integrated into different detection methods to promote the development of sensitive and convenient analysis of nucleic acids. However, it is still in urgent need to develop amplified nucleic acid biosensors for the analysis of susceptible gene and even distinguishing single-base mismatched DNA in complex biological samples. Benefiting from the achieved detection strategies, here we boost isothermal nucleic acid amplification by resorting to enzyme amplification, and combine this two-stage amplification method with surface-enhanced Raman spectroscopy (SERS) to develop a signal-on nucleic acid detection platform. Due to the high cleavage efficiency of Exonuclease III (Exo III), a large amount of trigger DNA are produced to initiate multiple hybridization chain reaction circles. The product structure tagged with Tamra is then anchored onto the plasmonic SERS substrate and meanwhile enriched. It is demonstrated that this detection platform is sensitive toward the myocardial infarction disease related gene. A detection limit of 1 fM for the gene analysis in a linear relationship in the wide range from 1 fM to 10nM is achieved, better than most of previous counterparts. Meanwhile, our developed detection platform exhibits a high selectivity for the target gene over mismatched analogues. Our strategy provides a robust tool for signal amplification of gene detection even in blood samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein.

    Science.gov (United States)

    Martin, Sandra L; Cruceanu, Margareta; Branciforte, Dan; Wai-Lun Li, Patrick; Kwok, Stanley C; Hodges, Robert S; Williams, Mark C

    2005-05-06

    LINE-1 is a highly successful, non-LTR retrotransposon that has played a leading role in shaping mammalian genomes. These elements move autonomously through an RNA intermediate using target-primed reverse transcription (TPRT). L1 encodes two essential polypeptides for retrotransposition, the products of its two open reading frames, ORF1 and ORF2. The exact function of the ORF1 protein (ORF1p) in L1 retrotransposition is unknown, although it is an RNA-binding protein that can act as a nucleic acid chaperone. Here, we investigate the requirements for these two activities in L1 retrotransposition by examining the consequences of mutating two adjacent and highly conserved arginine residues in the ORF1p from mouse L1. Substitution of both arginine residues with alanine strongly reduces the affinity of the protein for single-stranded nucleic acid, whereas substitution of one or both with lysine has only minimal effects on this feature. Rather, the lysine substitutions alter the delicate balance between the ORF1 protein's melting and reannealing activities, thereby reducing its nucleic acid chaperone activity. These findings establish the importance of the nucleic acid chaperone activity of ORF1p to successful L1 retrotransposition, and provide insight into the essential properties of nucleic acid chaperones.

  18. Efficacy Assessment of Nucleic Acid Decontamination Reagents Used in Molecular Diagnostic Laboratories.

    Science.gov (United States)

    Fischer, Melina; Renevey, Nathalie; Thür, Barbara; Hoffmann, Donata; Beer, Martin; Hoffmann, Bernd

    2016-01-01

    The occurrence of nucleic acid cross contamination in the laboratory resulting in false positive results of diagnostic samples is seriously problematic. Despite precautions to minimize or even avoid nucleic acid cross contaminations, it may appear anyway. Until now, no standardized strategy is available to evaluate the efficacy of commercially offered decontamination reagents. Therefore, a protocol for the reliable determination of nucleic acid decontamination efficacy using highly standardized solution and surface tests was established and validated. All tested sodium hypochlorite-based reagents proved to be highly efficient in nucleic acid decontamination even after short reaction times. For DNA Away, a sodium hydroxide-based decontamination product, dose- and time-dependent effectiveness was ascertained. For two other commercial decontamination reagents, the phosphoric acid-based DNA Remover and the non-enzymatic reagent DNA-ExitusPlus™ IF, no reduction of amplifiable DNA/RNA was observed. In conclusion, a simple test procedure for evaluation of the elimination efficacy of decontamination reagents against amplifiable nucleic acid is presented.

  19. Digital Microfluidics for Nucleic Acid Amplification.

    Science.gov (United States)

    Coelho, Beatriz; Veigas, Bruno; Fortunato, Elvira; Martins, Rodrigo; Águas, Hugo; Igreja, Rui; Baptista, Pedro V

    2017-06-25

    Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  20. Digital Microfluidics for Nucleic Acid Amplification

    Directory of Open Access Journals (Sweden)

    Beatriz Coelho

    2017-06-01

    Full Text Available Digital Microfluidics (DMF has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  1. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  2. Detection of nucleic acids by multiple sequential invasive cleavages

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

    2012-10-16

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  3. Quality Assessment of Some High Consumption Foods in Zanjan City

    Directory of Open Access Journals (Sweden)

    Hassan Hassanzad Azar

    2016-06-01

    Full Text Available Background: Foods go through many changes from production to table and continuous control is necessary to maintain food safety and supply foods with good quality. The aim of this study was to evaluate the quality of some foods with high consumption in Zanjan city within 5 years from 2009 to 2013. Methods: In a case-control descriptive study with an annually- controlled program within 5 years from 2009 to 2014, some food samples including pasteurized milk, vegetable oils, flour, kebab, salt, confectionary products and a special cookie called nan-chay were collected and analyzed in food control laboratory of Zanjan university of medical sciences. Results: According to national standard of Iran, of Nan-chay, salt, vegetable oils, kebab, confectionary products, and pasteurized milk samples 68.4%, 46%, 24.3%, 10.4%, 9.3%, 5% were out of national standard limits and unacceptable, respectively. All flour samples had good standard quality. Mean± sd values of pH in Nan-chay samples were 7.5 and 1.19, respectively. Mean± sd values of the degree of purity in salt samples were 98.21 and 1.75, respectively. Conclusion: Results showed that among the 7 types of collected foods in Zanjan city, the most nonstandard cases were of Nan-chay samples and the best quality was seen in flour samples.

  4. NAPP: the Nucleic Acid Phylogenetic Profile Database

    OpenAIRE

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2017-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to ...

  5. Prediction of protein and nucleic acid interactions

    OpenAIRE

    Cirillo, Davide

    2016-01-01

    The purpose of my doctoral studies has been the development of bioinformatics methods to quantitatively evaluate associations between proteins and nucleic acids (NAs). This thesis aims at providing insights into molecular features and still relatively unknown mechanisms of protein-NAs associations, such as RNA-binding proteins and long noncoding RNAs as well as transcription factors and regulatory DNA elements. In this work, I present two algorithms, catRAPID omics express and PAnDA, for the ...

  6. Carbohydrate Polymers for Nonviral Nucleic Acid Delivery

    Science.gov (United States)

    Sizovs, Antons; McLendon, Patrick M.; Srinivasachari, Sathya

    2014-01-01

    Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and these results are discussed with the focus on facile synthetic routes and favorable performance in biological systems. Many of these carbohydrates have been used to develop alternative types of biomaterials for nucleic acid delivery to typical polyplexes, and these novel materials are discussed. Also presented are polymeric vehicles that incorporate copolymerized carbohydrates into polymer backbones based on polyethylenimine and polylysine and their effect on transfection and biocompatibility. Unique scaffolds, such as clusters and polymers based on cyclodextrin (CD), are also discussed, with the focus on recent successes in vivo and in the clinic. These results are presented with the emphasis on the role of carbohydrate and charge on transfection. Use of carbohydrates as molecular recognition ligands for cell-type specific delivery is also briefly reviewed. We contend that carbohydrates have contributed significantly to progress in the field of non-viral DNA delivery, and these new discoveries are impactful for developing new vehicles and materials for treatment of human disease. PMID:21504102

  7. Construction of High-Quality Camel Immune Antibody Libraries.

    Science.gov (United States)

    Romão, Ema; Poignavent, Vianney; Vincke, Cécile; Ritzenthaler, Christophe; Muyldermans, Serge; Monsion, Baptiste

    2018-01-01

    Single-domain antibodies libraries of heavy-chain only immunoglobulins from camelids or shark are enriched for high-affinity antigen-specific binders by a short in vivo immunization. Thus, potent binders are readily retrieved from relatively small-sized libraries of 10(7)-10(8) individual transformants, mostly after phage display and panning on a purified target. However, the remaining drawback of this strategy arises from the need to generate a dedicated library, for nearly every envisaged target. Therefore, all the procedures that shorten and facilitate the construction of an immune library of best possible quality are definitely a step forward. In this chapter, we provide the protocol to generate a high-quality immune VHH library using the Golden Gate Cloning strategy employing an adapted phage display vector where a lethal ccdB gene has to be substituted by the VHH gene. With this procedure, the construction of the library can be shortened to less than a week starting from bleeding the animal. Our libraries exceed 10(8) individual transformants and close to 100% of the clones harbor a phage display vector having an insert with the length of a VHH gene. These libraries are also more economic to make than previous standard approaches using classical restriction enzymes and ligations. The quality of the Nanobodies that are retrieved from immune libraries obtained by Golden Gate Cloning is identical to those from immune libraries made according to the classical procedure.

  8. Adsorption and isolation of nucleic acids on cellulose magnetic beads using a three-dimensional printed microfluidic chip.

    Science.gov (United States)

    Zhang, Lei; Deraney, Rachel N; Tripathi, Anubhav

    2015-11-01

    While advances in genomics have enabled sensitive and highly parallel detection of nucleic acid targets, the isolation and extraction of the nucleic acids remain a critical bottleneck in the workflow. We present here a simple 3D printed microfluidic chip that allows for the vortex and centrifugation free extraction of nucleic acids. This novel microfluidic chip utilizes the presence of a water and oil interface to filter out the lysate contaminants. The pure nucleic acids, while bound on cellulose particles, are magnetically moved across the oil layer. We demonstrated efficient and rapid extraction of spiked Human Papillomavirus (HPV) 18 plasmids in specimen transport medium, in under 15 min. An overall extraction efficiency of 61% is observed across a range of HPV plasmid concentrations (5 × 10(1) to 5 × 10(6) copies/100 μl). The magnetic, interfacial, and viscous drag forces inside the microgeometries of the chip are modeled. We have also developed a kinetics model for the adsorption of nucleic acids on cellulose functionalized superparamagnetic beads. We also clarify here the role of carrier nucleic acids in the adsorption and isolation of nucleic acids. Based on the various mechanistic insights detailed here, customized microfluidic devices can be designed to meet the range of current and emerging point of care diagnostics needs.

  9. Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

    Science.gov (United States)

    Behzadi, Payam; Ranjbar, Reza; Alavian, Seyed Moayed

    2014-01-01

    Context: To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. Results: Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. Conclusions: Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages. PMID:25789132

  10. Biotransformation of Organic Waste into High Quality Fertilizer

    DEFF Research Database (Denmark)

    Bryndum, Sofie

    Agriculture faces several challenges of future provision of nutrients such as limited P reserves and increasing prices of synthetic fertilizers and recycling of nutrients from organic waste can be an important strategy for the long-term sustainability of the agricultural systems. Organically...... and S, is often low; and (3) the unbalanced composition of nutrients rarely matches crop demands. Therefore the objective of this project was to investigate the potential for (1) recycling nutrients from agro-industrial wastes and (2) compost biotransformation into high-quality organic fertilizers......, including three succeeding compost experiments, conducted in Denmark (Paper II). The composting studies investigated three management interventions to enhance the compost fertilizer quality and accelerate compost turnover: (1) the addition of nutrient rich material, (2) the compost turning frequency and (3...

  11. Efficient high-quality volume rendering of SPH data.

    Science.gov (United States)

    Fraedrich, Roland; Auer, Stefan; Westermann, Rüdiger

    2010-01-01

    High quality volume rendering of SPH data requires a complex order-dependent resampling of particle quantities along the view rays. In this paper we present an efficient approach to perform this task using a novel view-space discretization of the simulation domain. Our method draws upon recent work on GPU-based particle voxelization for the efficient resampling of particles into uniform grids. We propose a new technique that leverages a perspective grid to adaptively discretize the view-volume, giving rise to a continuous level-of-detail sampling structure and reducing memory requirements compared to a uniform grid. In combination with a level-of-detail representation of the particle set, the perspective grid allows effectively reducing the amount of primitives to be processed at run-time. We demonstrate the quality and performance of our method for the rendering of fluid and gas dynamics SPH simulations consisting of many millions of particles.

  12. Characterization of a crosslinked nucleic acid - helix destabilizing protein complex

    Energy Technology Data Exchange (ETDEWEB)

    Karpel, R.L.; Levin, V.Y.; Haley, B.E.

    1986-05-01

    They have enzymatically synthesized /sup 3/H- and /sup 32/P-poly(A,8N/sub 3/A) from 8-N/sub 3/ADP and radiolabeled ADP, and have used this polynucleotide to photoaffinity label T4 gene 32 protein, as well as several other helix-destabilizing proteins (HDPs). Irradiation of /sup 32/P-/sup 3/H-poly(A,N/sub 3/A) mixtures for short durations produces a covalent complex, seen as a high molecular weight, radioactive band on SDS-polyacrylamide gels. Preliminary experiments on other HDPs, from prokaryotic, eukaryotic and animal viral sources, show analogous results. Several successful control experiments indicate that this system is suitable for binding site localization on /sup 32/P. Single-stranded nucleic acids competitively inhibit photolabeling. The effect of NaCl on photolabeling parallels the salt-dependence of /sup 32/P-poly(A,N/sub 3/A) binding. Photolabeling reaches a plateau after approx.1 min, and the formation of the high molecular weight complex parallels the reduction of free /sup 32/P on SDS gels. Staph. nuclease digestion of crosslinked complexes produces a diffuse, radioactive band on SDS gels, migrating just behind free /sup 32/P. When these digested complexes are subjected to reverse-phase HPLC on a C3 Ultrapore column, the nucleic acid /sup 32/P-label is seen to coelute with protein. They are currently employing RP-HPLC methods to locate the label on tryptic peptides of nuclease-digested complexes.

  13. [Study on the feasibility of human papilloma virus subtypes detection by automatic nucleic acid extraction workstation].

    Science.gov (United States)

    Zhang, Rui; Ye, Ali; Dou, Yaling; Gan, Yong; Kong, Lingjun; Chen, Yu; Xu, Yingchun

    2015-12-08

    To verify the feasibility of human papilloma virus(HPV) subtypes detection by AUTRAX automatic nucleic acid extraction workstation. A total of 183 HPV test samples (2 562 types) were collected during August 2014 in Peking Union Medical College Hospital. Nucleic acid determination kit of high-risk HPV types (16, 18, 35, 39, 58, 31, 33, 68, 56, 45, 59, 51, 52) and 6 , 11 type (real-time PCR) were applied for detection. Each sample was divided into two parts. One part was treated with manual extraction, which entailed manually preparing PCR reaction system and added the sample to the PCR plate. Another was treated with the AUTRAX automatic nucleic acid extraction workstation, which automatically prepared the reaction system and added to the PCR board. These two parts proceeded to the real-time PCR detection. The result of manual extraction was set as the golden standard and the Kappa consistency analysis was conducted. Meanwhile, precision and pollution prevention of the AUTRAX were verified. The sensitivity of AUTRAX automatic nucleic acids extraction workstation was 97.12% (101/104). The specificity was 99.51% (2 446/2 458). The accuracy was 99.42% (2 547/2 562). The result of Kappa consistency analysis showed that the two parts were the same (Kappa=0.926). Coefficient of variation (CV) of each HPV types was less than 5%.No pollution phenomenon was found. AUTRAX automatic nucleic acids extraction workstation can be used for the HPV subtypes detection in clinical settings.

  14. High Quality Test Pattern Generation and Boolean Satisfiability

    CERN Document Server

    Eggersglüß, Stephan

    2012-01-01

    This book provides an overview of automatic test pattern generation (ATPG) and introduces novel techniques to complement classical ATPG, based on Boolean Satisfiability (SAT).  A fast and highly fault efficient SAT-based ATPG framework is presented which is also able to generate high-quality delay tests such as robust path delay tests, as well as tests with long propagation paths to detect small delay defects. The aim of the techniques and methodologies presented in this book is to improve SAT-based ATPG, in order to make it applicable in industrial practice. Readers will learn to improve the performance and robustness of the overall test generation process, so that the ATPG algorithm reliably will generate test patterns for most targeted faults in acceptable run time to meet the high fault coverage demands of industry. The techniques and improvements presented in this book provide the following advantages: Provides a comprehensive introduction to test generation and Boolean Satisfiability (SAT); Describes a...

  15. Fat Quality Influences the Obesogenic Effect of High Fat Diets

    Science.gov (United States)

    Crescenzo, Raffaella; Bianco, Francesca; Mazzoli, Arianna; Giacco, Antonia; Cancelliere, Rosa; di Fabio, Giovanni; Zarrelli, Armando; Liverini, Giovanna; Iossa, Susanna

    2015-01-01

    High fat and/or carbohydrate intake are associated with an elevated risk for obesity and chronic diseases such as diabetes and cardiovascular diseases. The harmful effects of a high fat diet could be different, depending on dietary fat quality. In fact, high fat diets rich in unsaturated fatty acids are considered less deleterious for human health than those rich in saturated fat. In our previous studies, we have shown that rats fed a high fat diet developed obesity and exhibited a decrease in oxidative capacity and an increase in oxidative stress in liver mitochondria. To investigate whether polyunsaturated fats could attenuate the above deleterious effects of high fat diets, energy balance and body composition were assessed after two weeks in rats fed isocaloric amounts of a high-fat diet (58.2% by energy) rich either in lard or safflower/linseed oil. Hepatic functionality, plasma parameters, and oxidative status were also measured. The results show that feeding on safflower/linseed oil diet attenuates the obesogenic effect of high fat diets and ameliorates the blood lipid profile. Conversely, hepatic steatosis and mitochondrial oxidative stress appear to be negatively affected by a diet rich in unsaturated fatty acids. PMID:26580650

  16. Fat Quality Influences the Obesogenic Effect of High Fat Diets

    Directory of Open Access Journals (Sweden)

    Raffaella Crescenzo

    2015-11-01

    Full Text Available High fat and/or carbohydrate intake are associated with an elevated risk for obesity and chronic diseases such as diabetes and cardiovascular diseases. The harmful effects of a high fat diet could be different, depending on dietary fat quality. In fact, high fat diets rich in unsaturated fatty acids are considered less deleterious for human health than those rich in saturated fat. In our previous studies, we have shown that rats fed a high fat diet developed obesity and exhibited a decrease in oxidative capacity and an increase in oxidative stress in liver mitochondria. To investigate whether polyunsaturated fats could attenuate the above deleterious effects of high fat diets, energy balance and body composition were assessed after two weeks in rats fed isocaloric amounts of a high-fat diet (58.2% by energy rich either in lard or safflower/linseed oil. Hepatic functionality, plasma parameters, and oxidative status were also measured. The results show that feeding on safflower/linseed oil diet attenuates the obesogenic effect of high fat diets and ameliorates the blood lipid profile. Conversely, hepatic steatosis and mitochondrial oxidative stress appear to be negatively affected by a diet rich in unsaturated fatty acids.

  17. Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2011-01-01

    Full Text Available Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

  18. High Quality Acquisition of Surface Electromyography - Conditioning Circuit Design

    Science.gov (United States)

    Shobaki, Mohammed M.; Malik, Noreha Abdul; Khan, Sheroz; Nurashikin, Anis; Haider, Samnan; Larbani, Sofiane; Arshad, Atika; Tasnim, Rumana

    2013-12-01

    The acquisition of Surface Electromyography (SEMG) signals is used for many applications including the diagnosis of neuromuscular diseases, and prosthesis control. The diagnostic quality of the SEMG signal is highly dependent on the conditioning circuit of the SEMG acquisition system. This paper presents the design of an SEMG conditioning circuit that can guarantee to collect high quality signal with high SNR such that it is immune to environmental noise. The conditioning circuit consists of four stages; consisting of an instrumentation amplifier that is used with a gain of around 250; 4th order band pass filter in the 20-500Hz frequency range as the two initial stages. The third stage is an amplifier with adjustable gain using a variable resistance; the gain could be changed from 1000 to 50000. In the final stage the signal is translated to meet the input requirements of data acquisition device or the ADC. Acquisition of accurate signals allows it to be analyzed for extracting the required characteristic features for medical and clinical applications. According to the experimental results, the value of SNR for collected signal is 52.4 dB which is higher than the commercial system, the power spectrum density (PSD) graph is also presented and it shows that the filter has eliminated the noise below 20 Hz.

  19. Sleep quality and its relationship with quality of life among high-risk pregnant women (gestational diabetes and hypertension).

    Science.gov (United States)

    Saadati, Fatemeh; Sehhatiei Shafaei, Fahimeh; Mirghafourvand, Mozhgan

    2018-01-01

    Sleep is one of the most basic human requirements. This research aims at determining the status of sleep quality and its relationship with quality of life among high-risk pregnant women in Tabriz, Iran, in 2015. This research was a sectional study done on 364 qualified women in 28-36 weeks of pregnancy suffering from mild preeclampsia and gestational diabetes. The sampling was done as convenience. Personal-social-midwifery questionnaire, Pittsburg sleep quality, and quality of life in pregnancy (QOL-ORAV) were used for gathering data. Multivariate linear regression model was used for determining the relationship between sleep quality and its subsets with quality of life and controlling confounders. In the current study, the prevalence of sleep disturbance was 96.4%. Mean (SD) of the total score of sleep quality was 10.1 (4.1) and the total score of quality of life was 61.7 (17.3). According to Pearson's correlation test, there was statistically significant relationship between quality of life and sleep quality and all its subsets except sleep duration and use of sleep medication (p quality of life. The findings of current research show that sleep quality is low among high-risk pregnant women and quality of life is medium. So, it is necessary that required training is given by health cares for improving sleep quality and quality of life to mothers.

  20. Performing High-Quality Science on CubeSats

    DEFF Research Database (Denmark)

    H. Zurbuchen, Thomas; von Steiger, Rudolf; Bartalev, Sergey

    2016-01-01

    January 2016 the International Space Science Institute in Berne, Switzerland,hosted a two-day Forum to focus on the rapid evolution of CubeSats as an enabling technology platform, with special emphasis on their promise to perform high-quality science.The Forum was initiated in coordination...... in this area of research. Our discussions focused on four themes characteristic of CubeSats and their evolution: 1) identification of appropriate science in avariety of research disciplines, 2) technology development, 3) international vs. national approaches, and 4) educational benefits. These discussions...

  1. Stress and sleep quality in high school brazilian adolescents.

    Science.gov (United States)

    Mesquita, Gema; Reimão, Rubens

    2010-06-01

    The objective of the present study is to analyze the effect of stress on sleep quality in a group of adolescents. Two high schools in Alfenas, southern Minas Gerais State, Brazil, were chosen to participate in the study. The sample consisted of both genders (n=160) with 65.63% females. The age range of participants was 15 to18 years. The Pittsburgh Sleep Quality Index (PSQI) was applied for collection of data to quantify sleep quality. The Lipp Inventory of Stress Symptoms that objectively identifies symptoms of stress was applied. It was observed that 23.53% of stressed students and 45.33% of unstressed ones sleep well; 76.47% of stressed pupils and 54.67% of those unstressed do not sleep well. With regard to school performance, a mean of 0.65 was found for stressed students and 0.60 for those without stress, Mann-Whitney (p=0.0596). Stress contributed to raising the percentage of poor sleepers, as ell as increasing ean school performance.

  2. CCD Astrophotography High-Quality Imaging from the Suburbs

    CERN Document Server

    Stuart, Adam

    2006-01-01

    This is a reference book for amateur astronomers who have become interested in CCD imaging. Those glorious astronomical images found in astronomy magazines might seem out of reach to newcomers to CCD imaging, but this is not the case. Great pictures are attainable with modest equipment. Adam Stuart’s many beautiful images, reproduced in this book, attest to the quality of – initially – a beginner’s efforts. Chilled-chip astronomical CCD-cameras and software are also wonderful tools for cutting through seemingly impenetrable light-pollution. CCD Astrophotography from the Suburbs describes one man’s successful approach to the problem of getting high-quality astronomical images under some of the most light-polluted conditions. Here is a complete and thoroughly tested program that will help every CCD-beginner to work towards digital imaging of the highest quality. It is equally useful to astronomers who have perfect observing conditions, as to those who have to observe from light-polluted city skies.

  3. Scaffolding along Nucleic Acid Duplexes Using 2'-Amino-Locked Nucleic Acids

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Wengel, Jesper

    2014-01-01

    Conspectus Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined...... depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing...... functionalized 2'-amino-LNA scaffolds offer great opportunities for material science, diagnostics, and medicine of the future....

  4. Design Considerations for RNA Spherical Nucleic Acids (SNAs).

    Science.gov (United States)

    Barnaby, Stacey N; Perelman, Grant A; Kohlstedt, Kevin L; Chinen, Alyssa B; Schatz, George C; Mirkin, Chad A

    2016-09-21

    Ribonucleic acids (RNAs) are key components in many cellular processes such as cell division, differentiation, growth, aging, and death. RNA spherical nucleic acids (RNA-SNAs), which consist of dense shells of double-stranded RNA on nanoparticle surfaces, are powerful and promising therapeutic modalities because they confer advantages over linear RNA such as high cellular uptake and enhanced stability. Due to their three-dimensional shell of oligonucleotides, SNAs, in comparison to linear nucleic acids, interact with the biological environment in unique ways. Herein, the modularity of the RNA-SNA is used to systematically study structure-function relationships in order to understand how the oligonucleotide shell affects interactions with a specific type of biological environment, namely, one that contains serum nucleases. We use a combination of experiment and theory to determine the key architectural properties (i.e., sequence, density, spacer moiety, and backfill molecule) that affect how RNA-SNAs interact with serum nucleases. These data establish a set of design parameters for SNA architectures that are optimized in terms of stability.

  5. High Quality Factor Fano-Resonant All-Dielectric Metamaterials

    CERN Document Server

    Yang, Yuanmu; Briggs, Dayrl P; Valentine, Jason

    2014-01-01

    Fano-resonant plasmonic metamaterials and nanostructures have become a major focus of the nanophotonics fields over the past several years due their ability to produce high quality factor (Q-factor) resonances. The origin of such resonances is the interference between a broad and narrow resonance, ultimately allowing suppression of radiative damping. However, Fano-resonant plasmonic structures still suffer non-radiative damping due to Ohmic loss, ultimately limiting the achievable Q-factors to values less than 10. Here, we report experimental demonstration of Fano-resonant silicon-based metamaterials that have a response that mimics the electromagnetically induced transparency (EIT) found in atomic systems. Due to extremely low absorption loss, a record-high Q-factor of 306 was experimentally observed. Furthermore, the unit cell of the metamaterial was designed with a feed-gap which results in strong local field enhancement in the surrounding medium resulting in strong light-matter interaction. This allows th...

  6. Percutaneous vertebroplasty with a high-quality rotational angiographic unit

    Energy Technology Data Exchange (ETDEWEB)

    Pedicelli, Alessandro [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: apedicelli@rm.unicatt.it; Rollo, Massimo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mrollo@rm.unicatt.it; Piano, Mariangela [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mariangela.piano@gmail.com; Re, Thomas J. [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: tomjre@gmail.com; Cipriani, Maria C. [Department of Gerontology, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: alexped@yahoo.com; Colosimo, Cesare [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: colosimo@rm.unicatt.it; Bonomo, Lorenzo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: lbonomo@rm.unicatt.it

    2009-02-15

    We evaluated the reliability of a rotational angiographic unit (RA) with flat-panel detector as a single technique to guide percutaneous vertebroplasty (PVP) and for post-procedure assessment by 2D and 3D reformatted images. Fifty-five consecutive patients (104 vertebral bodies) were treated under RA fluoroscopy. Rotational acquisitions with 2D and 3D reconstruction were obtained in all patients for immediate post-procedure assessment. In complex cases, this technique was also used to evaluate the needle position during the procedure. All patients underwent CT scan after the procedure. RA and CT findings were compared. In all cases, a safe trans-pedicular access and an accurate control of the bone-cement injection were successfully performed with high-quality fluoroscopy, even at the thoracic levels and in case of vertebra plana. 2D and 3D rotational reconstructions permitted CT-like images that clearly showed needle position and were similar to CT findings in depicting intrasomatic implant-distribution. RA detected 40 cement leakages compared to 42 demonstrated by CT and showed overall 95% sensitivity and 100% specificity compared to CT for final post-procedure assessment. Our preliminary results suggest that high-quality RA is reliable and safe as a single technique for PVP guidance, control and post-procedure assessment. It permits fast and cost-effective procedures avoiding multi-modality imaging.

  7. High Framingham risk score decreases quality of life in adults

    Directory of Open Access Journals (Sweden)

    Christian Yosaputra

    2010-04-01

    Full Text Available Cardiovascular disease (CVD risk factors, such as diabetes, hypertension, hypercholesterolemia, smoking, and obesity tend to occur together in the general population. Increasing prevalence of multiple CVD risk factors has been related to increased risk of death from coronary heart disease and stroke. Studies have suggested that people with several risk factors of CVD may have impaired health-related quality of life. The objective of this study was to assess the association of CVD risk factors with quality of life (QOL among adults aged 40 to 65 years. A cross-sectional study was conducted involving 220 subjects 40 - 65 years of age at a health center. The CVD risk factors were assessed using the Framingham risk score that is the standard instrument for assessment of the risk of a first cardiac event. The risk factors assessed were age, smoking, blood pressure, total cholesterol and high density lipoprotein cholesterol concentrations. QOL was assessed by means of the WHOQOL-BREF instrument that had been prevalidated. The results of the study showed that 28.2% of subjects were smokers, 56.4% had stage 1 hypertension, 42.8% high total cholesterol and 13.6% low HDL cholesterol. The high risk group amounted to 45.5% and 42.3% constitued an intermediate risk group. High CVD risk scores were significantly associated with a low QOL for all domains (physical, psychological, social and environment (p=0.000. Preventing or reducing the multiple CVD risk factors to improve QOL is necessary among adults.

  8. Disposable nucleic acid biosensors based on gold nanoparticle probes and lateral flow strip.

    Science.gov (United States)

    Mao, Xun; Ma, Yunqing; Zhang, Aiguo; Zhang, Lurong; Zeng, Lingwen; Liu, Guodong

    2009-02-15

    In this article, we describe a disposable nucleic acid biosensor (DNAB) for low-cost and sensitive detection of nucleic acid samples in 15 min. Combining the unique optical properties of gold nanoparticles (Au-NP) and the high efficiency of chromatographic separation, sandwich-type DNA hybridization reactions were realized on the lateral flow strips, which avoid multiple incubation, separation, and washing steps in the conventional nucleic acid biosensors. The captured Au-NP probes on the test zone and control zone of the biosensor produced the characteristic red bands, enabling visual detection of nucleic acid samples without instrumentation. The quantitative detection was performed by reading the intensities of the produced red bands with a portable strip reader. The parameters (e.g., the concentration of reporter probe, the size of Au-NP, the amount of Au-NP-DNA probe, lateral flow membranes, and the concentration of running buffer) that govern the sensitivity and reproducibility of the sensor were optimized. The response of the optimized device is highly linear over the range of 1-100 nM target DNA, and the limit of detection is estimated to be 0.5 nM in association with a 15 min assay time. The sensitivity of the biosensor was further enhanced by using horseradish peroxidase (HRP)-Au-NP dual labels which ensure a quite low detection limit of 50 pM. The DNAB has been applied for the detection of human genomic DNA directly with a detection limit of 2.5 microg/mL (1.25 fM) by adopting well-designed DNA probes. The new nucleic acid biosensor thus provides a rapid, sensitive, low cost, and quantitative tool for the detection of nucleic acid samples. It shows great promise for in-field and point-of-care diagnosis of genetic diseases and detection of infectious agents or warning against biowarfare agents.

  9. High quality yarns from high speed roller ginning of upland cotton

    Science.gov (United States)

    The highest quality yarns from upland cotton are typically produced by using combing in the textile mill. Combing is a resource-intensive process in which short fibers are removed from cotton before spinning. The improvement in fiber length and length uniformity of upland cotton when high speed ro...

  10. The Nucleic Acid Database: new features and capabilities.

    Science.gov (United States)

    Coimbatore Narayanan, Buvaneswari; Westbrook, John; Ghosh, Saheli; Petrov, Anton I; Sweeney, Blake; Zirbel, Craig L; Leontis, Neocles B; Berman, Helen M

    2014-01-01

    The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D nucleic acid structures and their complexes. In addition to primary data, the NDB contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities.

  11. Robert Feulgen Prize Lecture 1995. New approaches to in situ detection of nucleic acids.

    Science.gov (United States)

    Thiry, M

    1995-08-01

    The present paper reviews recent results obtained by different molecular biology-based, immunocytological approaches to the localization and identification of nucleic acids in sections of biological material. Examples of sensitive, high-resolution detection methods for RNA, DNA or specialized DNA regions are presented. Special emphasis is placed on the potential values and limitations of these new methods.

  12. Single-molecule pull-down for investigating protein–nucleic acid interactions

    NARCIS (Netherlands)

    Fareh, M.; Loeff, L.; Szczepaniak, M.; Haagsma, Anna C.; Yeom, K.H.; Joo, C.

    2016-01-01

    The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein

  13. Modulation of CpG oligodeoxynucleotide-mediated immune stimulation by locked nucleic acid (LNA)

    DEFF Research Database (Denmark)

    Vollmer, Jörg; Jepsen, Jan Stenvang; Uhlmann, Eugen

    2004-01-01

    Locked nucleic acid (LNA) is an RNA derivative that when introduced into oligodeoxynucleotides (ODN), mediates high efficacy and stability. CpG ODNs are potent immune stimulators and are recognized by toll-like receptor-9 (TLR9). Some phosphorothioate antisense ODNs bearing CpG dinucleotides have...

  14. Modification of nucleic acids by azobenzene derivatives and their applications in biotechnology and nanotechnology.

    Science.gov (United States)

    Li, Jing; Wang, Xingyu; Liang, Xingguo

    2014-12-01

    Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well-organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light-switching biosystems or light-driven nanomachines. Here we review recent advances in azobenzene-modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Synthetic Nucleic Acid Analogues in Gene Therapy: An Update for Peptide–Oligonucleotide Conjugates

    DEFF Research Database (Denmark)

    Taskova, Maria; Mantsiou, Anna; Astakhova, Kira

    2017-01-01

    The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide–oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described...

  16. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time.

    Science.gov (United States)

    Gandelman, Olga A; Church, Vicki L; Moore, Cathy A; Kiddle, Guy; Carne, Christopher A; Parmar, Surendra; Jalal, Hamid; Tisi, Laurence C; Murray, James A H

    2010-11-30

    The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs) enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART) continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi) produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi) produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a simple light detector, the iNAAT-BART combination is ideal

  17. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time.

    Directory of Open Access Journals (Sweden)

    Olga A Gandelman

    Full Text Available BACKGROUND: The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. PRINCIPAL FINDINGS: Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. CONCLUSIONS: The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a

  18. Determination of saffron quality by high-performance liquid chromatography.

    Science.gov (United States)

    Valle García-Rodríguez, M; Serrano-Díaz, Jéssica; Tarantilis, Petros A; López-Córcoles, Horacio; Carmona, Manuel; Alonso, Gonzalo L

    2014-08-13

    The aim of this work was to propose a high-performance liquid chromatography with diode array detection (HPLC-DAD) method for determining the three main compounds responsible for determining the quality of saffron (crocetin esters, picrocrocin, and safranal) by preparing an aqueous extract according to the ISO 3632 standard to solve the difficulty that this standard has for aroma and taste determination by ultraviolet-visible spectroscopy. Toward this aim, laboratory-isolated picrocrocin, a safranal standard with a purity of ≥ 88%, trans-crocetin di(β-D-gentiobiosyl) ester (trans-4-GG) and trans-crocetin (β-D-glucosyl)-(β-D-gentiobiosyl) ester (trans-3-Gg) standards, both with a purity of ≥ 99%, and 50 different saffron spice samples from Italy, Iran, Greece, and Spain were used in the intralaboratory validation of the HPLC method. The analytical method proposed was adequate in terms of linearity, selectivity, sensitivity, and accuracy for determining the three foremost parameters that define the quality of saffron using only a saffron solution prepared according to the ISO 3632 standard.

  19. Improving eggshell quality at high temperatures with dietary sodium bicarbonate.

    Science.gov (United States)

    Balnave, D; Muheereza, S K

    1997-04-01

    Two experiments were conducted that confirmed the hypothesis that a dietary bicarbonate supplement will improve eggshell quality in hens at high temperatures as long as feed is consumed during the period of eggshell formation. End-of-lay hens were maintained on continuous light at temperatures of 30 and 35 C. Individual egg weights and shell quality measures for each hen were calculated as a proportion of the initial values determined during an acclimatization period at 25 C. Improvements in shell breaking strength in both experiments were observed as a result of supplementing control diets with 1% sodium bicarbonate (NaHCO3). This response to NaHCO3 was not a reflection of a reduced rate of lay or egg mass output, as these were similar or inferior on the control diets. Similar feed intakes on the control and NaHCO3 diets indicated that the response was not related to differences in calcium intakes. Supplements of zinc methionine and ascorbic acid proved to be inferior to NaHCO3. Improvements in egg weight were associated with the introduction of continuous lighting.

  20. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

    Science.gov (United States)

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

  1. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

    Science.gov (United States)

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. © The Author(s) 2016. Published by Oxford University Press.

  2. Nucleic acid delivery: the missing pieces of the puzzle?

    Science.gov (United States)

    Nguyen, Juliane; Szoka, Francis C

    2012-07-17

    The delivery of genes or RNA interference (RNAi) agents can increase or decrease the expression of virtually any protein in a cell, and this process opens the path for cures to most diseases that afflict humans. However, the high molecular weight, anionic nature, and instability of nucleic acids in the presence of enzymes pose major obstacles to their delivery and frustrates their use as human therapies. This Account describes current ideas about the mechanisms in nonviral nucleic acid delivery and how lipidic and polymeric carriers can overcome some of the critical barriers to delivery. Over the last 20 years, researchers have developed a multitude of polymeric and lipidic vectors, but only a small fraction of these have progressed into clinical trials. None of these vectors has received FDA approval, which indicates that the current vectors do not yet have suitable properties for effective in vivo nucleic acid delivery. Nucleic acid delivery is a multistep process and inefficiencies at any stage result in a dramatic decrease in gene delivery or gene silencing. However, the majority of studies investigating synthetic vectors focus solely on optimization of endosomal escape. A small number of studies address how to improve uptake via targeted delivery, and an even smaller fraction examine the intracellular fate of the delivery systems and nucleic acid cargo. The internalization of genes into the cell nucleus remains an inefficient and mysterious process. In the case of DNA delivery, strategies are needed to increase and accelerate the migration of DNA through the cytoplasm and transport it through the nuclear membrane. siRNA delivery involves fewer barriers. siRNA is more readily released from the carrier and more resistant to enzymatic degradation, and its target is in the cytoplasm; hence, siRNA delivery systems are becoming a clinical reality. With regard to siRNA therapy, the exact cytoplasmic location of RNA-induced silencing complex (RISC) formation and

  3. (Collection of high quality acoustical records for honeybees)

    Energy Technology Data Exchange (ETDEWEB)

    Kerr, H.T.; Buchanan, M.E.

    1987-02-19

    High quality acoustical data records were collected for both European and Africanized honeybees under various field conditions. This data base was needed for more rigorous evaluation of a honeybee identification technique previously developed by the travelers from preliminary data sets. Laboratory-grade recording equipment was used to record sounds made by honeybees in and near their nests and during foraging flights. Recordings were obtained from European and Africanized honeybees in the same general environment. Preliminary analyses of the acoustical data base clearly support the general identification algorithm: Africanized honeybee noise has significantly higher frequency content than does European honeybee noise. As this algorithm is refined, it may result in the development of a simple field-portable device for identifying subspecies of honeybees. Further, the honeybee's acoustical signals appear to be correlated with specific colony conditions. Understanding these variations may have enormous benefit for entomologists and for the beekeeping industry.

  4. High Quality Rapeseed Products as Feed for Sensitive Monogastrics

    DEFF Research Database (Denmark)

    Frandsen, Heidi Blok

    . Glucosinolates can be transformed enzymatic by the enzyme myrosinase (EC. 3.2.1.147), or non-enzymatic by heat treatment or under the acidic and reducing conditions in the stomach of monogastrics. The type of transformation product depends on the parent glucosinolate and of the chemical conditions, and in some...... for cheaper protein rapeseed meal has been considered as an alternative to soya-protein. Rapeseed (Brassica napus L. spp. oleifera) has a well-balanced amino acid profile for monogastrics, but it contains several compounds which are anti-nutritional and might lower the protein quality and limit the amount...... cake was included, while losses up to 88% were observed when cold-pressed rapeseed caked was used. N-balance trials with rats clearly demonstrated effects on the biologic value caused by high glucosinolate concentrations, active myrosinase and long temperature treatments. The second study (manuscript...

  5. Towards organizational development for sustainable high-quality medical teaching.

    Science.gov (United States)

    Engbers, Rik; de Caluwé, Léon I A; Stuyt, Paul M J; Fluit, Cornelia R M G; Bolhuis, Sanneke

    2013-02-01

    Literature shows that faculty development programmes are not organizationally embedded in academic hospitals. This leaves medical teaching a low and informal status. The purpose of this article is to explore how organizational literature can strengthen our understanding of embedding faculty development in organizational development, and to provide a useful example of organizational development with regards to medical teaching and faculty development. Constructing a framework for organizational development from the literature, based on expert brainstorming. This framework is applied to a case study. A framework for organizational development is described. Applied in a context of medical teaching, these organizational insights show the process (and progress) of embedding faculty development in organizational development. Organizational development is a necessary condition for assuring sustainable faculty development for high-quality medical teaching. Organizational policies can only work in an organization that is developing. Recommendations for further development and future research are discussed.

  6. Power quality in high-tech campus: a case study

    Energy Technology Data Exchange (ETDEWEB)

    Moreno-Munoz, A.; Redel, M.; Gonzalez, M. [Universidad de Cordoba (Spain). Departamento de Electrotecnia y Electronica

    2006-07-01

    This paper presents preliminary results from a power-quality audit conducted at a high-tech campus over the last year. Voltage and current were measured at various R and D buildings; it was found that the main problems for the equipment installed were voltage sags and surges. The paper examines the causes and effects of power disturbances that affect computer or any other microprocessor-based equipment and analyses the auto-protection capabilities of modern power supplies. The convenience of 'enhanced power supply' or 'low-cost customer-side' protection solutions is also discussed. Finally, it addresses the role of the standards on the protection of electronic equipment and the implications for the final customer. (author)

  7. High-quality stable electron beams from laser wakefield acceleration in high density plasma

    Directory of Open Access Journals (Sweden)

    B. S. Rao

    2014-01-01

    Full Text Available High-quality, stable electron beams are produced from self-injected laser wakefield acceleration using the interaction of moderate 3 TW, 45 fs duration Ti:sapphire laser pulses with high density (>5×10^{19}   cm^{−3} helium gas jet plasma. The electron beam has virtually background-free quasimonoenergetic distribution with energy 35.6_{−2.5}^{+3.9}  MeV, charge 3.8_{−1.2}^{+2.8}  pC, divergence and pointing variation ∼10  mrad. The stable and high quality of the electron beam opens an easy way for applications of the laser wakefield accelerator in the future, particularly due to the widespread availability of sub-10 TW class lasers with a number of laser plasma laboratories around the world.

  8. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  9. The structure of high-quality aluminium cast iron

    Directory of Open Access Journals (Sweden)

    D. Kopyciński

    2012-01-01

    Full Text Available In this study presents the analyse of aluminium iron cast structure (as-cast condition which are used in high temperature. While producing the casts of aluminium iron major influence has been preserve the structure of technological process parameters. The addition to Fe-C-Al alloy V, Ti, Cr leads to the improvement of functional and mechanical cast qualities. In this study, a method was investigated to eliminate the presence of undesirable Al4C3 phases in a aluminium cast iron structure and thus improve the production process. V and Ti additions in aluminium cast iron allows to development of FeAl - VC or TiC alloys. In particular, V or Ti contents above 5 wt.% were found to totally eliminate the presence of Al4C3. In addition, preliminary work indicates that the alloy with the FeAl - VC or TiC structure reveals high oxidation resistance. The introduction of 5 wt.% chromium to aluminium cast iron strengthened Al4C3 precipitate. Thus, the resultant alloy can be considered an intermetallic FeAl matrix strengthened by VC and TiC or modified Al4C3 reinforcements.

  10. Stress and sleep quality in high school brazilian adolescents

    Directory of Open Access Journals (Sweden)

    Gema Mesquita

    2010-06-01

    Full Text Available OBJECTIVE: The objective of the present study is to analyze the effect of stress on sleep quality in a group of adolescents. METHOD: Two high schools in Alfenas, southern Minas Gerais State, Brazil, were chosen to participate in the study. The sample consisted of both genders (n=160 with 65.63% females. The age range of participants was 15 to18 years. The Pittsburgh Sleep Quality Index (PSQI was applied for collection of data to quantify sleep quality. The Lipp Inventory of Stress Symptoms that objectively identifies symptoms of stress was applied. RESULTS: It was observed that 23.53% of stressed students and 45.33% of unstressed ones sleep well; 76.47% of stressed pupils and 54.67% of those unstressed do not sleep well. With regard to school performance, a mean of 0.65 was found for stressed students and 0.60 for those without stress, Mann-Whitney (p=0.0596. CONCLUSION: Stress contributed to raising the percentage of poor sleepers, as ell as increasing ean school performance.OBJETIVO: O objetivo do presente estudo foi analisar a influência do stress sobre a qualidade do sono em um grupo de adolescentes. MÉTODO: Foram escolhidas duas instituições educacionais do ensino médio, na cidade de Alfenas, sul de Minas Gerais, Brasil. A amostra foi composta por ambos os sexos (n=160, com 65,63% do sexo feminino. A faixa etária dos participantes foi de 15 a 18 anos. Para a coleta de dados aplicou-se: Índice de Qualidade de Sono de Pittsburgh (IQSP utilizado para quantificar a qualidade do sono; o Inventário de Sintomas de Stress para Adultos de Lipp (ISSL que identifica de modo objetivo a sintomatologia de stress foi aplicado. RESULTADOS: Observou-se que 23,53% dos estressados dormem bem e 45,33% dos não estressados dormem bem; 76,47% dos estressados não dormem bem e 54,67% dos não estressados não dormem bem. Quanto ao rendimento escolar têm-se as médias 0,65 para os alunos estressados e 0,60 para aqueles que não sofrem de stress, Mann

  11. Approaches in breeding for high quality protein maize

    Directory of Open Access Journals (Sweden)

    Denić Miloje

    2008-01-01

    Full Text Available Maize is the principal crop and major staple food in the most African and South American countries. The main problem in human nutrition in developing countries, and in livestock feed in developed countries, is insufficient production and poor quality of cereal proteins. In the case of maize, due to the very low content of essential amino acids lysine and tryptophan in grain endosperm, biological value is very low, which is main limiting factor of common maize in human nutrition and feeding of monogastric animals. Quality protein maize (QPM can help in solving of this problem. Maize production also faces serious constraints caused by agro-ecological conditions and poor socio-economic situation. To alleviate the effect of the constraints, selected genotypes with more desirable traits and appropriate field-plot techniques to create multiple-stress conditions, were used. It was found that, in downy mildew nursery distance up to 35 m from spreader plot is providing sufficient down load of spores for plant infection, provided that the testing breeding materials are planted towards to down-stream direction of the dominant wind. Using these breeding approaches large number of early, white and flint synthetics, composites and inbred lines were created with resistance or tolerance to downy mildew (DMR, maize streak virus (SR and drought (DT. Created genotypes exhibited very good kernel modification and yield potential under low and normal inputs. In the case of synthetics and composites, besides tolerance to multiple stress factors, they were competing in yield with local QPM and normal maize checks. In the case of created inbred lines high combining ability was exhibited both in non-conventional and conventional maize hybrids. Trial data revealed that in the most cases the best entries were over-yielding the best checks.

  12. High-quality endoscope reprocessing decreases endoscope contamination.

    Science.gov (United States)

    Decristoforo, Petra; Kaltseis, Josef; Fritz, Andreas; Edlinger, Michael; Posch, Wilfried; Wilflingseder, Doris; Lass-Flörl, Cornelia; Orth-Höller, Dorothea

    2018-02-02

    Several outbreaks of severe infections due to contamination of gastrointestinal (GI) endoscopes, mainly duodenoscopes have been described previously. The rate of microbial endoscope contamination is varying dramatically in literature. Thus, the aim of this multicentre prospective study was to evaluate the hygiene quality of endoscopes and automated endoscope reprocessors (AERs) in Tyrol/Austria. In 2015 and 2016, a total of 463 GI endoscopes and 105 AERs from 29 endoscopy centres were analysed by a routine (R) and a combined routine and advanced (CRA) sampling procedure and investigated for microbial contamination by culture- and molecular-based analyses. The contamination rate of GI endoscopes was 1.3-4.6% according to national guideline, suggesting that 1.3-4.6 patients out of 100 could have had contacts with hygiene relevant microorganisms through an endoscopic intervention. Comparison of R and CRA sampling showed 1.8% of R versus 4.6% of CRA failing the acceptance criteria in phase I and 1.3% of R versus 3.0% of CRA samples in phase II. The most commonly identified indicator organism was Pseudomonas spp., mainly P. oleovorans. None of the tested viruses were detected in 40 samples. While AERs in phase I failed (n=9, 17.6%) mainly due to technical faults, phase II revealed lapses (n=6, 11.5%) only on account to microbial contamination of the last rinsing water, mainly with Pseudomonas spp. In the present study the contamination rate of endoscopes was low compared to results from other European countries, possibly due to high quality of endoscope reprocessing, drying and storage. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  13. Locked nucleic acid: modality, diversity, and drug discovery

    DEFF Research Database (Denmark)

    Hagedorn, Peter H.; Persson, Robert; Funder, Erik D.

    2017-01-01

    (LNA), which exhibits high binding affinity and potency, is widely used. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide compound is a unique entity, and small...... structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.......Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with pharmacological properties in vivo. Locked nucleic acid...

  14. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya

    2013-01-01

    We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific...... is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (... geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection...

  15. Intriguing nucleic-acid-binding features of mammalian prion protein.

    Science.gov (United States)

    Silva, Jerson L; Lima, Luís Maurício T R; Foguel, Debora; Cordeiro, Yraima

    2008-03-01

    In transmissible spongiform encephalopathies, the infectious material consists chiefly of a protein, the scrapie prion protein PrP(Sc), that carries no genetic coding material; however, prions are likely to have accomplices that chaperone their activity and promote the conversion of the cellular prion protein PrP(C) into the disease-causing isoform (PrP(Sc)). Recent studies from several laboratories indicate that PrP(C) recognizes many nucleic acids (NAs) with high affinities, and we correlate these findings with a possible pathophysiological role for this interaction. Thus, of the chaperones, NA is the most likely candidate for prions. The participation of NAs in prion propagation opens new avenues for developing new diagnostic tools and therapeutics to target prion diseases, as well as for understanding the function of PrP(C), probably as a NA chaperone.

  16. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-05

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  17. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-12

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  18. Molecular Structure of Nucleic Acids–A Structure for Deoxyribose ...

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 11. Molecular Structure of Nucleic Acids – A Structure for Deoxyribose Nucleic Acid. J D Watson F H C Crick. Classics Volume 9 Issue 11 November 2004 pp 96-98 ...

  19. Unlocked nucleic acid - an RNA modification with broad potential

    DEFF Research Database (Denmark)

    Pasternak, Anna; Wengel, Jesper

    2011-01-01

    The first unlocked nucleic acid (UNA) monomer was described more than a decade ago, but only recent reports have revealed the true potential applications of this acyclic RNA mimic. UNA monomers enable the modulation of the thermodynamic stability of various nucleic acid structures such as RNA and...

  20. Nucleic acid drugs: a novel approach | Jarald | African Journal of ...

    African Journals Online (AJOL)

    Nucleic acid base sequence of proteins plays a crucial role in the expression of gene. The gene is responsible for the synthesis of proteins and these proteins, which are synthesized, are responsible for the biological process and also for dreadful diseases as well. Once if the nucleic acid sequence is altered, we would be ...

  1. Nucleic Acid Therapy: from humble beginnings a dynamic technology

    CSIR Research Space (South Africa)

    Millroy, L

    2011-02-01

    Full Text Available The term “nucleic acid therapy” encompasses a wide range of technologies for the treatment of a range of plant and animal ailments. As the name implies, it makes use of nucleic acid (either DNA or RNA) as a therapeutic agent. There are six branches...

  2. Gene Targeting and Expression Modulation by Peptide Nucleic Acids (PNA)

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    Peptide nucleic acids (PNA) are artificial structural mimics of nucleic acids capable of sequence specific hybridization to both RNA and DNA. Thus they have obvious potential as gene targeting agents for drug discovery approaches. An overview with emphasis on recent progress on RNA "interference"...

  3. Detecting Microbial Nucleic Acids within Nematode Bodies: A Photo Essay

    Science.gov (United States)

    We developed a taxa-specific, fluorescence in situ hybridization (FISH) technique to localize microbial nucleic acids within nematode bodies. This technique involves hybridization of a nucleic acid probe to target microbial sequences. Hybridization is detected microscopically, as the probes have f...

  4. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic acids...

  5. Nucleic acid based fluorescent sensor for mercury detection

    Science.gov (United States)

    Lu, Yi; Liu, Juewen

    2013-02-05

    A nucleic acid enzyme comprises an oligonucleotide containing thymine bases. The nucleic acid enzyme is dependent on both Hg.sup.2+and a second ion as cofactors, to produce a product from a substrate. The substrate comprises a ribonucleotide, a deoxyribonucleotide, or both.

  6. Circulating nucleic acids damage DNA of healthy cells by integrating ...

    Indian Academy of Sciences (India)

    Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored. We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their own that are deleterious to healthy cells of the body. Fragmented DNA and ...

  7. EGVI endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2008-04-01

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  8. EGVII endoglucanase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2009-05-05

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  9. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2012-02-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  10. Use of Nucleic Acid Analogues in Diagnostics and Analytical Procedures

    DEFF Research Database (Denmark)

    2002-01-01

    Methods of capture, recognition, detection, identification or quantitation of nucleic acids and diagnostics uses generally are described in which are used: (a) a peptide nucleic acid (PNA) comprising a polyamide backbone bearing a plurality of ligands at respective spaced locations along said...

  11. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

    DEFF Research Database (Denmark)

    Bag, Satyabrata; Saha, Bipasa; Mehta, Ojasvi

    2016-01-01

    methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved...

  12. Cytosolic nucleic acid sensors and innate immune regulation.

    Science.gov (United States)

    Ori, Daisuke; Murase, Motoya; Kawai, Taro

    2017-03-04

    During viral and bacterial infections, pathogen-derived cytosolic nucleic acids are recognized by the intracellular RNA sensors retinoic acid-inducible gene I and melanoma-differentiated gene 5 and intracellular DNA sensors, including cyclic-di-GMP-AMP synthase, absent in melanoma 2, interferon (IFN)-gamma inducible protein 16, polymerase III, and so on. Binding of intracellular nucleic acids to these sensors activates downstream signaling cascades, resulting in the production of type I IFNs and pro-inflammatory cytokines to induce appropriate systematic immune responses. While these sensors also recognize endogenous nucleic acids and activate immune responses, they can discriminate between self- and non-self-nucleic acids. However, dysfunction of these sensors or failure of regulatory mechanisms causes aberrant activation of immune response and autoimmune disorders. In this review, we focus on how intracellular immune sensors recognize exogenous nucleic acids and activate the innate immune system, and furthermore, how autoimmune diseases result from dysfunction of these sensors.

  13. Nucleic Acid Aptamers for Living Cell Analysis

    Science.gov (United States)

    Xiong, Xiangling; Lv, Yifan; Chen, Tao; Zhang, Xiaobing; Wang, Kemin; Tan, Weihong

    2014-06-01

    Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as “chemical antibodies,” have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

  14. Electrical properties of nucleic acid bases

    Science.gov (United States)

    Basch, Harold; Garmer, D. R.; Jasien, P. G.; Krauss, M.; Stevens, W. J.

    1989-11-01

    The dipole polarizabilities for the five nucleic acid bases, uracil, cytosine, thymine, guanine, and adenine have been determined by the coupled perturbed Hartree-Fock (CPHF) method using a polarized double-zeta basis set. Electronic correlation corrections from second-order Møller-Plesset (MP2) perturbation theory are given. The treatment required to obtain accurate polarizabilities of these π systems was estimated from calculations on imidazole, benzene, and pyridine, giving results that are in good agreement with experiment. Similarly, optimal basis sets for static electrical properties were determined and applied to calculations of the dipole moments of the bases. With correlation corrections, these agree with experiment within 5% for all molecules except adenine.

  15. Low-quality birds do not display high-quality signals: The cysteine-pheomelanin mechanism of honesty

    Science.gov (United States)

    Galván, Ismael; Wakamatsu, Kazumasa; Camarero, Pablo R; Mateo, Rafael; Alonso-Alvarez, Carlos

    2015-01-01

    The mechanisms that make that the costs of producing high-quality signals are unaffordable to low-quality signalers are a current issue in animal communication. The size of the melanin-based bib of male house sparrows Passer domesticus honestly signals quality. We induced the development of new bibs while treating males with buthionine-sulfoximine (BSO), a substance that depletes the levels of the antioxidant glutathione (GSH) and the amino acid cysteine, two elements that switch melanogenesis from eumelanin to pheomelanin. Final bib size is negatively related to pheomelanin levels in the bib feathers. BSO reduced cysteine and GSH levels in all birds, but improved phenotypes (bibs larger than controls) were only expressed by high-quality birds (BSO birds with largest bibs initially). Negative associations between final bib size and cysteine levels in erythrocytes, and between pheomelanin and cysteine levels, were observed in high-quality birds only. These findings suggest that a mechanism uncoupling pheomelanin and cysteine levels may have evolved in low-quality birds to avoid producing bibs of size not corresponding to their quality and greater relative costs. Indeed, greater oxidative stress in cells was not observed in low-quality birds. This may represent the first mechanism maintaining signal honesty without producing greater relative costs on low-quality signalers. PMID:25330349

  16. Low-quality birds do not display high-quality signals: The cysteine-pheomelanin mechanism of honesty.

    Science.gov (United States)

    Galván, Ismael; Wakamatsu, Kazumasa; Camarero, Pablo R; Mateo, Rafael; Alonso-Alvarez, Carlos

    2015-01-01

    The mechanisms that make that the costs of producing high-quality signals are unaffordable to low-quality signalers are a current issue in animal communication. The size of the melanin-based bib of male house sparrows Passer domesticus honestly signals quality. We induced the development of new bibs while treating males with buthionine-sulfoximine (BSO), a substance that depletes the levels of the antioxidant glutathione (GSH) and the amino acid cysteine, two elements that switch melanogenesis from eumelanin to pheomelanin. Final bib size is negatively related to pheomelanin levels in the bib feathers. BSO reduced cysteine and GSH levels in all birds, but improved phenotypes (bibs larger than controls) were only expressed by high-quality birds (BSO birds with largest bibs initially). Negative associations between final bib size and cysteine levels in erythrocytes, and between pheomelanin and cysteine levels, were observed in high-quality birds only. These findings suggest that a mechanism uncoupling pheomelanin and cysteine levels may have evolved in low-quality birds to avoid producing bibs of size not corresponding to their quality and greater relative costs. Indeed, greater oxidative stress in cells was not observed in low-quality birds. This may represent the first mechanism maintaining signal honesty without producing greater relative costs on low-quality signalers. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  17. Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

    Science.gov (United States)

    Zou, Jiaqi; Li, Na

    2013-09-01

    Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Quality Factor for the Hadronic Calorimeter in High Luminosity Conditions

    CERN Document Server

    Seixas, Jose; The ATLAS collaboration; Manhaes de Andrade Filho, Luciano; Sotto-Maior-Peralva, Bernardo

    2015-01-01

    The Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of ATLAS experiment and has about 10,000 eletronic channels. An Optimal Filter (OF) has been used to estimate the energy sampled by the calorimeter and applies a Quality Factor (QF) for signal acceptance. An approach using Matched Filter (MF) has also been pursued. In order to cope with the luminosity rising foreseen for LHC operation upgrade, different algorithms have been developed. Currently, the OF measure for signal acceptance is implemented through a chi-square test. At a low luminosity scenario, such QF measure has been used as a way to describe how the acquired signal is compatible to the pulse shape pattern. However, at high-luminosity conditions, due to pile up, this QF acceptance is no longer possible when OF is employed, and the QF becomes a measure to indicate whether the reconstructed signal suffers or not from pile up. Methods are being developed in order to recover the superposed information, and the QF may be us...

  19. High-quality weather data for grid integration studies

    Science.gov (United States)

    Draxl, C.

    2016-12-01

    As variable renewable power penetration levels increase in power systems worldwide, renewable integration studies are crucial to ensure continued economic and reliable operation of the power grid. In this talk we will shed light on requirements for grid integration studies as far as wind and solar energy are concerned. Because wind and solar plants are strongly impacted by weather, high-resolution and high-quality weather data are required to drive power system simulations. Future data sets will have to push limits of numerical weather prediction to yield these high-resolution data sets, and wind data will have to be time-synchronized with solar data. Current wind and solar integration data sets will be presented. The Wind Integration National Dataset (WIND) Toolkit is the largest and most complete grid integration data set publicly available to date. A meteorological data set, wind power production time series, and simulated forecasts created using the Weather Research and Forecasting Model run on a 2-km grid over the continental United States at a 5-min resolution is now publicly available for more than 126,000 land-based and offshore wind power production sites. The Solar Integration National Dataset (SIND) is available as time synchronized with the WIND Toolkit, and will allow for combined wind-solar grid integration studies. The National Solar Radiation Database (NSRDB) is a similar high temporal- and spatial resolution database of 18 years of solar resource data for North America and India. Grid integration studies are also carried out in various countries, which aim at increasing their wind and solar penetration through combined wind and solar integration data sets. We will present a multi-year effort to directly support India's 24x7 energy access goal through a suite of activities aimed at enabling large-scale deployment of clean energy and energy efficiency. Another current effort is the North-American-Renewable-Integration-Study, with the aim of providing

  20. Novel Signal-Enhancing Approaches for Optical Detection of Nucleic Acids—Going beyond Target Amplification

    Directory of Open Access Journals (Sweden)

    Laura Miotke

    2015-09-01

    Full Text Available Detection of low-abundance nucleic acids is a challenging task, which over the last two decades has been solved using enzymatic target amplification. Enzymatic synthesis enhances the signal so that diverse, scientifically and clinically relevant molecules can be identified and studied, including cancer DNA, viral nucleic acids, and regulatory RNAs. However, using enzymes increases the detection time and cost, not to mention the high risk of mistakes with amplification and data alignment. These limitations have stimulated a growing interest in enzyme-free methods within researchers and industry. In this review we discuss recent advances in signal-enhancing approaches aimed at nucleic acid diagnostics that do not require target amplification. Regardless of enzyme usage, signal enhancement is crucial for the reliable detection of nucleic acids at low concentrations. We pay special attention to novel nanomaterials, fluorescence microscopy, and technical advances in detectors for optical assessment. We summarize sensitivity parameters of the currently available assays and devices which makes this review relevant to the broad spectrum of researchers working in fields from biophysics, to engineering, to synthetic biology and bioorganic chemistry.

  1. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Olga A. Krasheninina

    2017-11-01

    Full Text Available In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield, ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs, aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

  2. Quality Assurance Roadmap for High Performance Residential Buildings

    Energy Technology Data Exchange (ETDEWEB)

    None

    2008-10-05

    This report outlines the approach to quality assurance in the construction process for new residential construction, including seven process steps from the assessment of current construction practice, through design and documentation changes, to training and quality control for on-site personnel.

  3. Design of peptide-targeted liposomes containing nucleic acids.

    Science.gov (United States)

    Santos, Adriana O; da Silva, Lígia C Gomes; Bimbo, Luís M; de Lima, Maria C Pedroso; Simões, Sérgio; Moreira, João N

    2010-03-01

    Anticancer systemic gene silencing therapy has been so far limited by the inexistence of adequate carrier systems that ultimately provide an efficient intracellular delivery into target tumor cells. In this respect, one promising strategy involves the covalent attachment of internalizing-targeting ligands at the extremity of PEG chains grafted onto liposomes. Therefore, the present work aims at designing targeted liposomes containing nucleic acids, with small size, high encapsulation efficiency and able to be actively internalized by SCLC cells, using a hexapeptide (antagonist G) as a targeting ligand. For this purpose, the effect of the liposomal preparation method, loading material (ODN versus siRNA) and peptide-coupling procedure (direct coupling versus post-insertion) on each of the above-mentioned parameters was assessed. Post-insertion of DSPE-PEG-antagonist G conjugates into preformed liposomes herein named as stabilized lipid particles, resulted in targeted vesicles with a mean size of about 130 nm, encapsulation efficiency close to 100%, and a loading capacity of approximately 5 nmol siRNA/mumol of total lipid. In addition, the developed targeted vesicles showed increased internalization in SCLC cells, as well as in other tumor cells and HMEC-1 microvascular endothelial cells. The improved cellular association, however, did not correlate with enhanced downregulation of the target protein (Bcl-2) in SCLC cells. These results indicate that additional improvements need to be performed in the future, namely by ameliorating the access of the nucleic acids to the cytoplasm of the tumor cells following receptor-mediated endocytosis. Copyright 2009 Elsevier B.V. All rights reserved.

  4. Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization.

    Science.gov (United States)

    Anahtar, Melis N; Bowman, Brittany A; Kwon, Douglas S

    2016-04-14

    There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing technologies have allowed for the rapid and efficient characterization of bacterial communities using 16S rRNA gene sequencing from a variety of sources. Although readily available tools for 16S rRNA sequence analysis have standardized computational workflows, sample processing for DNA extraction remains a continued source of variability across studies. Here we describe an efficient, robust, and cost effective method for extracting nucleic acid from swabs. We also delineate downstream methods for 16S rRNA gene sequencing, including generation of sequencing libraries, data quality control, and sequence analysis. The workflow can accommodate multiple samples types, including stool and swabs collected from a variety of anatomical locations and host species. Additionally, recovered DNA and RNA can be separated and used for other applications, including whole genome sequencing or RNA-seq. The method described allows for a common processing approach for multiple sample types and accommodates downstream analysis of genomic, metagenomic and transcriptional information.

  5. 75 FR 41693 - Export Inspection and Weighing Waiver for High Quality Specialty Grains Transported in Containers

    Science.gov (United States)

    2010-07-19

    ... and Weighing Waiver for High Quality Specialty Grains Transported in Containers AGENCY: Grain... quality grain exported in containers ] from the mandatory inspection and weighing requirements of the... for high quality specialty grains exported in containers that was established by a final rule on...

  6. New developments in high quality grey cast irons

    Directory of Open Access Journals (Sweden)

    Iulian Riposan

    2014-07-01

    Full Text Available The paper reviews original data obtained by the present authors, revealed in recent separate publications, describing specific procedures for high quality grey irons, and reflecting the forecast needs of the worldwide iron foundry industry. High power, medium frequency coreless induction furnaces are commonly used in electric melting grey iron foundries. This has resulted in low sulphur (1,500 °C, contributing to unfavourable conditions for graphite nucleation. Thin wall castings are increasingly produced by these electric melt shops with a risk of greater eutectic undercooling during solidification. The paper focused on two groups of grey cast irons and their specific problems: carbides and graphite morphology control in lower carbon equivalent high strength irons (CE=3.4%-3.8%, and austenite dendrite promotion in eutectic and slightly hypereutectic irons (CE=4.1%-4.5%, in order to increase their strength characteristics. There are 3 stages and 3 steps involving graphite formation, iron chemistry and iron processing that appear to be important. The concept in the present paper sustains a threestage model for nucleating flake graphite [(Mn,XS type nuclei]. There are three important groups of elements (deoxidizer, Mn/S, and inoculant and three technological stages in electric melting of iron (superheat, pre-conditioning of base iron, final inoculation. Attention is drawn to a control factor (%Mn x (%S ensuring it equals to 0.03 – 0.06, accompanied by 0.005wt.%–0.010wt.% Al and/or Zr content in inoculated irons. It was found that iron powder addition promotes austenite dendrite formation in eutectic and slightly eutectic, acting as reinforcement for the eutectic cells. But, there is an accompanying possible negative influence on the characteristics of the (Mn,XS type graphite nuclei (change the morphology of nuclei from polygonal compact to irregular polygonal, and therefore promote chill tendency in treated irons. A double addition (iron

  7. Measuring quality of omnidirectional high dynamic range content

    Science.gov (United States)

    Perrin, Anne-Flore; Bist, Cambodge; Cozot, Rémi; Ebrahimi, Touradj

    2017-09-01

    Although HDR content processing, coding and quality assessment have been largely addressed in the last few years, little to no work has been concentrating on how to assess quality in HDR for 360° or omnidirectional content. This paper is an attempt to answer to various questions in this direction. As a minimum, a new data set for 360° HDR content is proposed and a new methodology is designed to assess subjective quality of HDR 360° content when it is displayed on SDR HMD after applying various tone mapping operators. The results are then analyzed and conclusions are drawn.

  8. Nucleic acid-binding polymers as anti-inflammatory agents

    Science.gov (United States)

    Lee, Jaewoo; Sohn, Jang Wook; Zhang, Ying; Leong, Kam W.; Pisetsky, David; Sullenger, Bruce A.

    2011-01-01

    Dead and dying cells release nucleic acids. These extracellular RNAs and DNAs can be taken up by inflammatory cells and activate multiple nucleic acid-sensing toll-like receptors (TLR3, 7, 8, and 9). The inappropriate activation of these TLRs can engender a variety of inflammatory and autoimmune diseases. The redundancy of the TLR family encouraged us to seek materials that can neutralize the proinflammatory effects of any nucleic acid regardless of its sequence, structure or chemistry. Herein we demonstrate that certain nucleic acid-binding polymers can inhibit activation of all nucleic acid-sensing TLRs irrespective of whether they recognize ssRNA, dsRNA or hypomethylated DNA. Furthermore, systemic administration of such polymers can prevent fatal liver injury engendered by proinflammatory nucleic acids in an acute toxic shock model in mice. Therefore these polymers represent a novel class of anti-inflammatory agent that can act as molecular scavengers to neutralize the proinflammatory effects of various nucleic acids. PMID:21844380

  9. Improving the quality of pork and pork products for the consumer : development of innovative, integrated, and sustainable food production chains of high quality pork products matching consumer demands

    NARCIS (Netherlands)

    Heimann, B.; Christensen, M.; Rosendal Rasmussen, S.; Bonneau, M.; Grunert, K.G.; Arnau, J.; Trienekens, J.H.; Oksbjerg, N.; Greef, de K.H.; Petersen, B.

    2012-01-01

    Improving the quality of pork and pork products for the consumer: development of innovative, integrated, and sustainable food production chains of high quality pork products matching consumer demands.

  10. Long-run benefits from universal high-quality preschooling

    DEFF Research Database (Denmark)

    Bauchmüller, Robert; Gørtz, Mette; Rasmussen, Astrid Würtz

    2014-01-01

    a formal preschool institution in 1998 are used in the analyses. OLS analyses show that three out of five quality indicators, a higher staff-per-child ratio, a higher share of male staff, and a higher share of staff with formal preschool teacher training are associated with significant improvements...... in children's test results in Danish. Boys benefit more from preschool quality than girls. Ethnic minority children benefit from higher staff stability....

  11. Lateral flow biosensors for the detection of nucleic acid.

    Science.gov (United States)

    Zeng, Lingwen; Lie, Puchang; Fang, Zhiyuan; Xiao, Zhuo

    2013-01-01

    The detection of nucleic acid is of central importance for the diagnosis of genetic diseases, infectious agents, and biowarfare agents. Traditional strategies and technologies for nucleic acid detection are time-consuming and labor-intensive. Recently, isothermal strand-displacement reaction-based lateral flow biosensors have attracted a great deal of research interest because they are sensitive, simple, fast, and easy to use. Here, we describe a lateral flow biosensor based on isothermal strand-displacement polymerase reaction and gold nanoparticles for the visual detection of nucleic acid.

  12. Recent developments in nucleic acid based techniques for use in rumen manipulation

    Directory of Open Access Journals (Sweden)

    Christopher McSweeney

    2009-07-01

    Full Text Available Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial

  13. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    Science.gov (United States)

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  14. Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes.

    Science.gov (United States)

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2015-04-05

    The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model. © 2015 Wiley Periodicals, Inc.

  15. Continuously Tunable Nucleic Acid Hybridization Probes

    Science.gov (United States)

    Wu, Lucia R.; Wang, J. Sherry; Fang, John Z.; Reiser, Emily; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J.; Beechem, Joseph; Zhang, David Yu

    2015-01-01

    In silico designed nucleic acid probes and primers often fail to achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. Here, we present a novel, on-the-fly method of tuning probe affinity and selectivity via the stoichiometry of auxiliary species, allowing independent and decoupled adjustment of hybridization yield for different probes in multiplexed assays. Using this method, we achieve near-continuous tuning of probe effective free energy (0.03 kcal·mol−1 granularity). As applications, we enforced uniform capture efficiency of 31 DNA molecules (GC content 0% – 100%), maximized signal difference for 11 pairs of single nucleotide variants, and performed tunable hybrid-capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples (FFPE). PMID:26480474

  16. NAPP: the Nucleic Acid Phylogenetic Profile Database.

    Science.gov (United States)

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2012-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.

  17. Latest Technologies and Equipment to Obtain High Quality Drinking Water

    Directory of Open Access Journals (Sweden)

    Goncharuk, V.V.

    2015-01-01

    Full Text Available A principally new concept of providing the Ukrainian population with quality drinking water have been proposed. It is based on a system of autonomous complexes for water purification in places of direct consumption. Water treatment autonomous complexes for collective and individual use with biotesting and analytical quality control of drinking water have been developed. The choice of the cleaning methods of tap and other waters up to the quality of genetic safe is performed in accordance with its composition and is based on a block concept that provides the possibility of varying the number of units depending on the composition of the source water. The proposed technology and equipment at cost and complex problems to be solved have no analogues in the world. Over thousand of modular installations «Vega» and disinfecting vehicles «Promin» are implemented in many settlement in all regions of Ukraine.

  18. Safe and High Quality Food Production using Low Quality Waters and Improved Irrigation Systems and Management, EU Project

    DEFF Research Database (Denmark)

    Plauborg, Finn; Jensen, Christian Richardt; Dalsgaard, Anders

    2009-01-01

    a multi-disciplinary team, with food safety and quality experts, engineers, agronomists and economists from17 research institutes and private companies in Europe, Israel and China working together. The project assesses potential risks to farmers. Coupled with farm management and economic models, a new......: the safety and quality of food products, and the increasing competition for clean freshwater. SAFIR is funded for the period 2005-2009 under the Food Quality and Safety thematic area of the EU 6th Framework Research Programme. The challenge for the next years will be to produce safe and high quality foods...... while at the same time reducing the use of natural resources and the impact on aquatic ecosystems that are frequently already polluted. These problems are linked, since most of our vegetables are produced using irrigation water from the same ecosystems. To ensure food safety and quality, the innovative...

  19. Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids

    DEFF Research Database (Denmark)

    Pedersen, Erik Bjerregaard; Nielsen, Jakob Toudahl; Nielsen, Claus

    2011-01-01

    Two G-quadruplex forming sequences, 50-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4......-(1-pyrenylethynyl)phenylmethyl]glycerol (twisted intercalating nucleic acid, TINA). Incorporation of LNA or INA/TINA monomers provide as much as 8-fold improvement of anti-HIV-1 activity. We demonstrate for the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming...

  20. Consumers' expected quality and intention to purchase high quality pork meat.

    Science.gov (United States)

    Papanagiotou, P; Tzimitra-Kalogianni, I; Melfou, K

    2013-03-01

    Expected quality is believed to be one of the most important factors that influence consumers' intention to purchase food. The present study seeks to explore the concept of pork meat expected quality and compare it with self-stated consumer intention to purchase pork meat. The aim is attempted by means of a field research conducted in Greece, following a conjoint analytic procedure. Results show that quality expectations comply with intention to buy pork, in many aspects. However, several differences have been identified. More specifically, country of origin and marbling appear to be more important for respondents' purchase decisions than they are for their quality evaluations, while the opposite appears to be true for price. Finally, socio-demographic factors such as gender, level of education, place of purchase and consumption habits seem to influence perceptions. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Safe and high quality food production using low quality waters and improved irrigation systems and management

    DEFF Research Database (Denmark)

    Plauborg, Finn; Andersen, Mathias Neumann; Liu, Fulai

    2010-01-01

    The present paper presents the SAFIR project (www.safir4eu.org), which addresses two fundamental problems that over the past decade increasingly have become concerns of the general public: the one problem being the jeopardizing of safety and quality of our food products, while the other being...... the increasing competition for clean freshwater. The SAFIR project has a multi-disciplinary approach, which integrates the European as well as the global dimension of the EU-policy on food quality and safety. The main driving force behind the project idea is new research results that demonstrated that scheduled...... uneven irrigation patterns can increase the water use efficiency as well as the quality of vegetable crops. Furthermore, recent innovations in the water treatment and irrigation industry have shown potential for the use of low quality water resources, such as reclaimed water or surface water in peri...

  2. Symmetry in nucleic acid structure and its role in protein--nucleic acid interactions

    Energy Technology Data Exchange (ETDEWEB)

    Sobell, H.M.

    1976-01-01

    It is clear that symmetry concepts will play an increasingly important role in understanding the structural aspects of many protein--nucleic acid interactions. This review summarizes current data and concepts along these lines. Exact crystallographic symmetries are rarely expected to occur in biological systems, and the departures from symmetry that occur may eventually prove to play important roles in modulating physiological function. In this respect, x-ray crystallography can make important additions to our understanding of the atomic nature of these associations, and it is hoped that the next review in this area will describe these.

  3. Nanopore biosensors for detection of proteins and nucleic acids

    NARCIS (Netherlands)

    Maglia, Giovanni; Soskine, Mikhael

    2014-01-01

    Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromoiecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

  4. NPIDB: Nucleic acid-Protein Interaction DataBase

    National Research Council Canada - National Science Library

    Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

    2013-01-01

    The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank...

  5. Quality assessment and potential utilization of high amylolytic ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-03

    Dec 3, 2008 ... This study was carried out to compare the qualities of two acclaimed Nigerian amylolytic maize cultivars; SPMAT and TZEE*TZEE-W*DEMARSCUS*TZEE-W with barley, red and white sorghum. Results obtained (P ≤ 0.05) showed marked differences in the properties of the two maize cultivars compared to ...

  6. Twin pregnancy possibly associated with high semen quality

    DEFF Research Database (Denmark)

    Asklund, Camilla; Jensen, Tina Kold; Jørgensen, Niels

    2007-01-01

    BACKGROUND: Recent studies found an association between a long waiting time to pregnancy (TTP) and reduced probability of twinning and a reduced dizygotic (DZ) twinning rate in subfertile men. However, it remains unsolved whether semen quality is associated with twin offspring. We therefore studied...

  7. Sustainable Inclusion of Smallholders in the Emerging High Quality ...

    African Journals Online (AJOL)

    ... assisting smallholders to produce value-added products competitively, working with a range of partners at different stages in the value chain to take pilot studies to scale, ensuring and maintaining quality, selecting appropriate technologies for different circumstances, anticipating negative effects of the market environment ...

  8. Innovation in Business Education: Developing a High Quality Online MBA

    Science.gov (United States)

    Roe, C. William; Toma, Alfred G.; Yallapragada, RamMohan R.

    2015-01-01

    Online degree programs were probably pioneered by for-profit universities such as University of Phoenix. Many online degree programs were initially considered low quality academic programs compared to traditional programs. Therefore, many public and private universities were slow to adopt the online programs. However, gradually more and more…

  9. Creating High-Quality Paths for Motion Planning

    NARCIS (Netherlands)

    Geraerts, R.J.; Overmars, M.H.

    2007-01-01

    Many algorithms have been proposed that create a path for a robot in an environment with obstacles. Most methods are aimed at finding a solution. However, for many applications, the path must be of a good quality as well. That is, a path should be short and should keep some amount of minimum

  10. Analyzing and Building Nucleic Acid Structures with 3DNA

    OpenAIRE

    Colasanti, Andrew V.; Lu, Xiang-Jun; Olson, Wilma K.

    2013-01-01

    The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic...

  11. Biological activity and biotechnological aspects of locked nucleic acids

    DEFF Research Database (Denmark)

    Lundin, Karin E; Højland, Torben; Hansen, Bo

    2013-01-01

    Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). ...... and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers....

  12. Peptide Nucleic Acids Having 2,6-Diaminopurine Nucleobases

    DEFF Research Database (Denmark)

    2003-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. The peptide nucleic acids of the invention comprise ligands selected from a group cons...... consisting of naturally-occurring nucleobases and non-naturally-occurring nucleobases attached to a polyamide backbone. Some PNAs of the invention also contain C1-C8 alkylamine side chains....

  13. Peptide Nucleic Acids Having Amino Acid Side Chains

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than the corresponding DNA or RNA strands, and exhibit increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting of nat...... of naturally-occurring nucleobases and non-naturally-occurring nucleobases attached to a polyamide backbone, and contain alkylamine side chains....

  14. The Politics of Quality Teacher Discourses: Implications for Pre-Service Teachers in High Poverty Schools

    Science.gov (United States)

    Scholes, Laura; Lampert, Jo; Burnett, Bruce; Comber, Barbara M.; Hoff, Lutz; Ferguson, Angela

    2017-01-01

    Improving the quality of education for young people growing up in high poverty and culturally diverse communities is an escalating problem in affluent nations with increasing gaps between the wealthy and the poor. Improving the quality of teachers and improving the quality of teaching are amongst the prominent solutions offered to redress the…

  15. Building High-Performing and Improving Education Systems: Quality Assurance and Accountability. Review

    Science.gov (United States)

    Slater, Liz

    2013-01-01

    Monitoring, evaluation, and quality assurance in their various forms are seen as being one of the foundation stones of high-quality education systems. De Grauwe, writing about "school supervision" in four African countries in 2001, linked the decline in the quality of basic education to the cut in resources for supervision and support.…

  16. Modeling the Subjective Quality of Highly Contrasted Videos Displayed on LCD With Local Backlight Dimming

    DEFF Research Database (Denmark)

    Mantel, Claire; Bech, Søren; Korhonen, Jari

    2015-01-01

    signal can then be used as input to objective quality metrics. The focus of this paper is on determining which characteristics of locally backlit displays influence quality assessment. A subjective experiment assessing the quality of highly contrasted videos displayed with various local backlight...

  17. The Cost of Inequality: The Importance of Investing in High Quality Early Childhood Education Programs

    Science.gov (United States)

    Keith, Rebecca S.

    2017-01-01

    The focus of this dissertation was to explore the importance of high quality early education in later secondary education development, quantifying quality in early childhood education programs, and examining how teacher education contributes to quality of early childhood education programs. For phase I, early childhood education positively…

  18. Most clinical laboratory testing in Kampala occurs in high-volume, high-quality laboratories or low-volume, low-quality laboratories. A tale of two cities.

    Science.gov (United States)

    Amukele, Timothy K; Schroeder, Lee F; Jackson, J Brooks; Elbireer, Ali

    2015-01-01

    To describe key characteristics (laboratory quality, test volumes, and complexity) of clinical laboratories in Kampala, Uganda (population ~1.7 million). Cross-sectional survey using a standard questionnaire to document laboratory type and quality, as well as test menus and volumes. Quality was based on the World Health Organization-Africa Region checklist. Of the 954 laboratories identified (a density of one laboratory per 1,781 persons), 779 (82%) performed only simple kit tests or light microscope examinations. The 95% (907/954) of laboratories for whom volumes were obtained performed an average aggregate of 13,189 tests daily, for a test utilization rate of around 2 tests per individual per year. Laboratories could be segregated into eight groups based on quality, test volume, and complexity. However, 90% of the testing was performed by just two groups: (1) low-volume (≤100 tests daily), low-quality laboratories performing simple tests or (2) high-volume (>100 tests daily), high-quality laboratories. Each of these two groups did 45% of the daily testing volume (90% combined). Clinical laboratory density in Kampala (1/1,781 persons) is high, approaching that in the United States (1/1,347 persons). Low-volume/low-quality and high-volume/high-quality laboratories do 90% of the daily aggregate testing. Quality improvement (QI) schemes for Africa must be appropriate to low-volume laboratories as well as to the large laboratories that have been the focus of previous QI efforts. Copyright© by the American Society for Clinical Pathology.

  19. High fidelity system modeling for high quality image reconstruction in clinical CT.

    Directory of Open Access Journals (Sweden)

    Synho Do

    Full Text Available Today, while many researchers focus on the improvement of the regularization term in IR algorithms, they pay less concern to the improvement of the fidelity term. In this paper, we hypothesize that improving the fidelity term will further improve IR image quality in low-dose scanning, which typically causes more noise. The purpose of this paper is to systematically test and examine the role of high-fidelity system models using raw data in the performance of iterative image reconstruction approach minimizing energy functional. We first isolated the fidelity term and analyzed the importance of using focal spot area modeling, flying focal spot location modeling, and active detector area modeling as opposed to just flying focal spot motion. We then compared images using different permutations of all three factors. Next, we tested the ability of the fidelity terms to retain signals upon application of the regularization term with all three factors. We then compared the differences between images generated by the proposed method and Filtered-Back-Projection. Lastly, we compared images of low-dose in vivo data using Filtered-Back-Projection, Iterative Reconstruction in Image Space, and the proposed method using raw data. The initial comparison of difference maps of images constructed showed that the focal spot area model and the active detector area model also have significant impacts on the quality of images produced. Upon application of the regularization term, images generated using all three factors were able to substantially decrease model mismatch error, artifacts, and noise. When the images generated by the proposed method were tested, conspicuity greatly increased, noise standard deviation decreased by 90% in homogeneous regions, and resolution also greatly improved. In conclusion, the improvement of the fidelity term to model clinical scanners is essential to generating higher quality images in low-dose imaging.

  20. Manufacturing High-Quality Carbon Nanotubes at Lower Cost

    Science.gov (United States)

    Benavides, Jeanette M.; Lidecker, Henning

    2004-01-01

    A modified electric-arc welding process has been developed for manufacturing high-quality batches of carbon nanotubes at relatively low cost. Unlike in some other processes for making carbon nanotubes, metal catalysts are not used and, consequently, it is not necessary to perform extensive cleaning and purification. Also, unlike some other processes, this process is carried out at atmospheric pressure under a hood instead of in a closed, pressurized chamber; as a result, the present process can be implemented more easily. Although the present welding-based process includes an electric arc, it differs from a prior electric-arc nanotube-production process. The welding equipment used in this process includes an AC/DC welding power source with an integral helium-gas delivery system and circulating water for cooling an assembly that holds one of the welding electrodes (in this case, the anode). The cathode is a hollow carbon (optionally, graphite) rod having an outside diameter of 2 in. (approximately equal to 5.1 cm) and an inside diameter of 5/8 in. (approximately equal to 1.6 cm). The cathode is partly immersed in a water bath, such that it protrudes about 2 in. (about 5.1 cm) above the surface of the water. The bottom end of the cathode is held underwater by a clamp, to which is connected the grounding cable of the welding power source. The anode is a carbon rod 1/8 in. (approximately equal to 0.3 cm) in diameter. The assembly that holds the anode includes a thumbknob- driven mechanism for controlling the height of the anode. A small hood is placed over the anode to direct a flow of helium downward from the anode to the cathode during the welding process. A bell-shaped exhaust hood collects the helium and other gases from the process. During the process, as the anode is consumed, the height of the anode is adjusted to maintain an anode-to-cathode gap of 1 mm. The arc-welding process is continued until the upper end of the anode has been lowered to a specified height

  1. Homogenous 96-plex PEA immunoassay exhibiting high sensitivity, specificity, and excellent scalability

    DEFF Research Database (Denmark)

    Assarsson, Erika; Lundberg, Martin; Holmquist, Göran

    2014-01-01

    Medical research is developing an ever greater need for comprehensive high-quality data generation to realize the promises of personalized health care based on molecular biomarkers. The nucleic acid proximity-based methods proximity ligation and proximity extension assays have, with their dual...

  2. DNA nanotechnology for nucleic acid analysis: DX motif-based sensor.

    Science.gov (United States)

    Kolpashchikov, Dmitry M; Gerasimova, Yulia V; Khan, Mohammad S

    2011-11-25

    A light on the tiles: A sensor that fluoresces in the presence of specific nucleic acids was designed and characterized. The sensor uses a molecular beacon probe and three adaptor strands to form a five-stranded assembly, a DX-tile, with a specific analyte. This sensor is a highly selective and affordable tool for the real-time analysis of DNA and RNA. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Develop high quality nursing service and normalize management of neonatal ward

    Directory of Open Access Journals (Sweden)

    Hua YANG

    2014-08-01

    Full Text Available Objective: To tamp basic neonatal care, provide high quality nursing service, improve the quality of neonatal care, guarantee the safety of nursing care, achieve satisfactory project. Methods:Adjust the staff of the neonatal ward , optimize schedule; strengthen the training and knowledge; strengthen the supervision and ensure the basic nursing; the nursing quality management group work out the rate of incidence of high quality nursing service, the incidence rate of hospital infection of the newborn as well as the satisfaction of their families. Results: The different data between the control group and observation group was statistically significant ( P < 0.05 . Conclusion: Develop the neonatal ward of high quality nursing service, ensure the basic nursing implement, significantly improve the quality of nursing, reduce nursing adverse events and neonatal hospital infection incidence to" zero defects and zero tolerance", and that ensures nursing safety, and achieve the goal of " quality care demonstration project" --- patient satisfaction, social satisfaction, and government satisfaction.

  4. What makes a high quality clinical research paper?

    Science.gov (United States)

    Groves, T

    2010-05-01

    The quality of a research paper depends primarily on the quality of the research study it reports. However, there is also much that authors can do to maximise the clarity and usefulness of their papers. Journals' instructions for authors often focus on the format, style, and length of articles but do not always emphasise the need to clearly explain the work's science and ethics: so this review reminds researchers that transparency is important too. The research question should be stated clearly, along with an explanation of where it came from and why it is important. The study methods must be reported fully and, where appropriate, in line with an evidence based reporting guideline such as the CONSORT statement for randomised controlled trials. If the study was a trial the paper should state where and when the study was registered and state its registration identifier. Finally, any relevant conflicts of interest should be declared.

  5. High quality factor photonic resonators for nitride quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Guillet, T. [Universite Montpellier 2, Laboratoire Charles Coulomb UMR 5221, 34095 Montpellier (France); Mexis, M.; Rennesson, S.; Brimont, C.; Bretagnon, T.; Gil, B. [Universite Montpellier 2, Laboratoire Charles Coulomb UMR 5221, 34095 Montpellier (France); CNRS, Laboratoire Charles Coulomb UMR 5221, 34095 Montpellier (France); Sergent, S. [CRHEA-CNRS, Valbonne 06560 (France); Universite de Nice Sophia Antipolis, Parc Valrose, Nice 06102 Cedex 2 (France); Neel, D.; David, S.; Checoury, X.; Boucaud, P. [Institut d' Electronique Fondamentale, CNRS - Universite Paris Sud 11, 91405 Orsay (France); Sam-Giao, D.; Gayral, B. [CEA-INAC, 17 rue des Martyrs, 38054 Grenoble (France); Semond, F.; Leroux, M. [CRHEA-CNRS, Valbonne 06560 (France)

    2012-03-15

    We report the realization and the optical study of nitride photonic resonators dedicated to the blue and UV spectral range. Microdisks and photonic crystal (PC) cavities are investigated containing GaN/AlN quantum dots (QDs) embedded in an AlN waveguide. The PC cavities are fabricated through the conformal growth of nitrides on a patterned Si substrate, and present delocalized and confined cavity modes in their microphotoluminescence spectra, that are compared to simulations. A large quality factor of 1800 is reached for a modified L3 cavity. In the case of microdisks, which are fabricated through a classical top-down approach, the series of whispering gallery modes (WGMs) with large quality factors (up to 7300) are observed and analysed. Scanning electron micrograph and microphotoluminescence spectrum of a 2 {mu}m AlN microdisk embedding GaN QDs; the WGMs appear as sharp peaks, with quality factors up to 5000. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Downregulation of p21(WAF1/CIP1) and estrogen receptor alpha in MCF-7 cells by antisense oligonucleotides containing locked nucleic acid (LNA)

    DEFF Research Database (Denmark)

    Jepsen, Jan Stenvang; Pfundheller, Henrik M; Lykkesfeldt, Anne E

    2004-01-01

    Locked nucleic acid (LNA) is a nucleic acid analog with very high affinity to complementary RNA and a promising compound in the field of antisense research. The intracellular localization and quantitative uptake of oligonucleotides containing LNA were found to be equivalent to those of phosphorot......Locked nucleic acid (LNA) is a nucleic acid analog with very high affinity to complementary RNA and a promising compound in the field of antisense research. The intracellular localization and quantitative uptake of oligonucleotides containing LNA were found to be equivalent to those......) and the estrogen receptor alpha (ERalpha). For downregulation of both target proteins, the most efficient design was achieved with oligonucleotides containing LNA monomers in the extremities and a central gap of PS-linked DNA monomers, so called LNA gapmers. Such LNA gapmers caused more potent downregulation...

  7. Real-World Solutions for Developing High-Quality PHP Frameworks and Applications

    CERN Document Server

    Bergmann, Sebastian

    2011-01-01

    Learn to develop high-quality applications and frameworks in PHP Packed with in-depth information and step-by-step guidance, this book escorts you through the process of creating, maintaining and extending sustainable software of high quality with PHP. World-renowned PHP experts present real-world case studies for developing high-quality applications and frameworks in PHP that can easily be adapted to changing business requirements. . They offer different approaches to solving  typical development and quality assurance problems that every developer needs to know and master.Details the process

  8. A Survey of Advancements in Nucleic Acid-based Logic Gates and Computing for Applications in Biotechnology and biomedicine

    Science.gov (United States)

    Wu, Cuichen; Wan, Shuo; Hou, Weijia; Zhang, Liqin; Xu, Jiehua; Cui, Cheng; Wang, Yanyue; Hu, Jun

    2015-01-01

    Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gating and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications. PMID:25597946

  9. Health-Related Quality of Life in Children with High-Functioning Autism

    Science.gov (United States)

    Potvin, Marie-Christine; Snider, Laurie; Prelock, Patricia A.; Wood-Dauphinee, Sharon; Kehayia, Eva

    2015-01-01

    The health-related quality of life of school-aged children with high-functioning autism is poorly understood. The objectives of this study were to compare the health-related quality of life of children with high-functioning autism to that of typically developing peers and to compare child-self and parent-proxy reports of health-related quality of…

  10. Evaluation of problematic use of mobile phones and quality of sleep among high school students

    OpenAIRE

    Fatih Öz; Didem Arslantaş; Necati Buğrul; Tuğçe Koyuncu; Alaettin Ünsal

    2015-01-01

    It was aimed to evaluate the problematic use of mobile phones and quality of sleep among high school students. This is a cross-sectional study carried out on 1,131 high school students studying at Sivrihisar, a district of Eskisehir, in December 2012. The questionnaire form include the sociodemographic characteristics, problematic use of mobile phones and quality of sleep. Bianchi-Phillips problematic use of mobile phones (PUMP) scale and Pittsburgh Sleep Quality Index (PSQI) was used. Median...

  11. Rehosting of Bacterial Chaperones for High-Quality Protein Production▿

    Science.gov (United States)

    Martínez-Alonso, Mónica; Toledo-Rubio, Verónica; Noad, Rob; Unzueta, Ugutz; Ferrer-Miralles, Neus; Roy, Polly; Villaverde, Antonio

    2009-01-01

    Coproduction of DnaK/DnaJ in Escherichia coli enhances solubility but promotes proteolytic degradation of their substrates, minimizing the yield of unstable polypeptides. Higher eukaryotes have orthologs of DnaK/DnaJ but lack the linked bacterial proteolytic system. By coexpression of DnaK and DnaJ in insect cells with inherently misfolding-prone recombinant proteins, we demonstrate simultaneous improvement of soluble protein yield and quality and proteolytic stability. Thus, undesired side effects of bacterial folding modulators can be avoided by appropriate rehosting in heterologous cell expression systems. PMID:19820142

  12. Nucleic Acid Sensing Machinery: Targeting Innate Immune System for Cancer Therapy.

    Science.gov (United States)

    Iurescia, Sandra; Fioretti, Daniela; Rinaldi, Monica

    2017-10-30

    targeting compounds is reported. • Conclusion It is highly relevant to deepen the study of the nucleic acid-sensing mechanisms to develop new pharmacological approaches to engage these pathways within the tumour microenvironment. Indeed, further clarification will be functional to develop advanced anticancer strategies or to design new vaccines formulation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. Publishing high-quality climate data on the semantic web

    Science.gov (United States)

    Woolf, Andrew; Haller, Armin; Lefort, Laurent; Taylor, Kerry

    2013-04-01

    The effort over more than a decade to establish the semantic web [Berners-Lee et. al., 2001] has received a major boost in recent years through the Open Government movement. Governments around the world are seeking technical solutions to enable more open and transparent access to Public Sector Information (PSI) they hold. Existing technical protocols and data standards tend to be domain specific, and so limit the ability to publish and integrate data across domains (health, environment, statistics, education, etc.). The web provides a domain-neutral platform for information publishing, and has proven itself beyond expectations for publishing and linking human-readable electronic documents. Extending the web pattern to data (often called Web 3.0) offers enormous potential. The semantic web applies the basic web principles to data [Berners-Lee, 2006]: using URIs as identifiers (for data objects and real-world 'things', instead of documents) making the URIs actionable by providing useful information via HTTP using a common exchange standard (serialised RDF for data instead of HTML for documents) establishing typed links between information objects to enable linking and integration Leading examples of 'linked data' for publishing PSI may be found in both the UK (http://data.gov.uk/linked-data) and US (http://www.data.gov/page/semantic-web). The Bureau of Meteorology (BoM) is Australia's national meteorological agency, and has a new mandate to establish a national environmental information infrastructure (under the National Plan for Environmental Information, NPEI [BoM, 2012a]). While the initial approach is based on the existing best practice Spatial Data Infrastructure (SDI) architecture, linked-data is being explored as a technological alternative that shows great promise for the future. We report here the first trial of government linked-data in Australia under data.gov.au. In this initial pilot study, we have taken BoM's new high-quality reference surface

  14. Rapid Bedside Inactivation of Ebola Virus for Safe Nucleic Acid Tests

    DEFF Research Database (Denmark)

    Rosenstierne, Maiken Worsøe; Karlberg, Helen; Bragstad, Karoline

    2016-01-01

    for nucleic acid extraction inactivates Ebola virus. A rapid bedside inactivation method for nucleic acid tests is obtained by simply adding Magna Pure lysis/binding buffer directly into vacuum blood collection EDTA tubes using a thin needle and syringe prior to sampling. The ready-to-use inactivation vacuum......Rapid bedside inactivation of Ebola virus would be a solution for the safety of medical and technical staff, risk containment, sample transport, and high-throughput or rapid diagnostic testing during an outbreak. We show that the commercially available Magna Pure lysis/binding buffer used...... tubes are stable for more than 4 months, and Ebola virus RNA is preserved in the Magna Pure lysis/binding buffer for at least 5 weeks independent of the storage temperature. We also show that Ebola virus RNA can be manually extracted from Magna Pure lysis/binding buffer-inactivated samples using...

  15. Single-molecule pull-down for investigating protein-nucleic acid interactions.

    Science.gov (United States)

    Fareh, Mohamed; Loeff, Luuk; Szczepaniak, Malwina; Haagsma, Anna C; Yeom, Kyu-Hyeon; Joo, Chirlmin

    2016-08-01

    The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein complexes, it remains challenging to study the interactions between macromolecular protein complexes and nucleic acids. Here, we combined single-molecule fluorescence with various protein complex pull-down techniques to determine the function and stoichiometry of ribonucleoprotein complexes. Through the use of three examples of protein complexes from eukaryotic cells (Drosha, Dicer, and TUT4 protein complexes), we provide step-by-step guidance for using novel single-molecule techniques. Our single-molecule methods provide sub-second and nanometer resolution and can be applied to other nucleoprotein complexes that are essential for cellular processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Magnetic bead-based nucleic acid purification kit: Clinical application and performance evaluation in stool specimens.

    Science.gov (United States)

    Yoon, Jihoon G; Kang, Jin Seok; Hwang, Seung Yong; Song, Jaewoo; Jeong, Seok Hoon

    2016-05-01

    Two different methods - the semi-automated magnetic bead-based kit (SK, Stool DNA/RNA Purification kit®) and the manual membrane column-based kit (QS, QIAamp® DNA Stool Mini kit) - for purifying nucleic acids from clinical stool samples were compared and evaluated. The SK kit was more user-friendly than QS due to the reduced manual processing, partial automation, and short turnaround time with half cost. Furthermore, SK produced high yields in both DNA and RNA extractions but poor purity in RNA extraction. In the assessment of rotavirus and Clostridium difficile infection, both kits had equivalent or more sensitive performance compared with the standard method. Although SK showed some interference and inhibition in nucleic acid extraction, the performance, including the repeatability, linearity, analytical sensitivity, and matrix effect, was sufficient for routine clinical use. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Preliminary Classification of Viruses Based on Quantitative Comparisons of Viral Nucleic Acids

    Science.gov (United States)

    Bellett, A. J. D.

    1967-01-01

    It is proposed that classifications used in science are of two main types; those which are designed to solve practical problems and which are based on conventions, and those which are designed to solve theoretical problems, based on theories, and in which the classes are tested by experiment. An attempt has been made to construct a preliminary classification of viruses which is of the second type. It is based on the theories of molecular biology, with the use of computer-based comparisons of the molecular weights and base ratios of viral nucleic acids to assign the viruses to clusters which show a high degree of correlation with groupings based on nucleic acid hybridization, serological cross-reactions, and phenotypic properties. Images PMID:5623961

  18. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

    Science.gov (United States)

    Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

    2015-01-01

    Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

  19. Transient cavitation in high-quality-factor resonators at high static pressures.

    Science.gov (United States)

    Gaitan, D Felipe; Tessien, Ross A; Hiller, Robert A; Gutierrez, Joel; Scott, Corey; Tardif, Henry; Callahan, Brant; Matula, Thomas J; Crum, Lawrence A; Holt, R Glynn; Church, Charles C; Raymond, Jason L

    2010-06-01

    It is well known that cavitation collapse can generate intense concentrations of mechanical energy, sufficient to erode even the hardest metals and to generate light emissions visible to the naked eye [sonoluminescence (SL)]. Considerable attention has been devoted to the phenomenon of "single bubble sonoluminescence" (SBSL) in which a single stable cavitation bubble radiates light flashes each and every acoustic cycle. Most of these studies involve acoustic resonators in which the ambient pressure is near 0.1 MPa (1 bar), and with acoustic driving pressures on the order of 0.1 MPa. This study describes a high-quality factor, spherical resonator capable of achieving acoustic cavitation at ambient pressures in excess of 30 MPa (300 bars). This system generates bursts of violent inertial cavitation events lasting only a few milliseconds (hundreds of acoustic cycles), in contrast with the repetitive cavitation events (lasting several minutes) observed in SBSL; accordingly, these events are described as "inertial transient cavitation." Cavitation observed in this high pressure resonator is characterized by flashes of light with intensities up to 1000 times brighter than SBSL flashes, as well as spherical shock waves with amplitudes exceeding 30 MPa at the resonator wall. Both SL and shock amplitudes increase with static pressure.

  20. [Development of A synthetic positive control for the nucleic acid detection of mumps virus].

    Science.gov (United States)

    Cui, Ai-li; Jin, Li; Xu, Wen-bo

    2013-09-01

    To rapidly identify the cross-contamination problems caused by the positive control in the process of mumps virus nucleic acid detection, a new mumps virus RNA positive control was developed in this study. Using the same primers and reaction conditions, the cross-contamination problems caused by the positive control could be readily identified by comparing the fragments lengths of the PCR products between the positive control and the samples. This new RNA positive control of mumps virus can be widely used in the diagnosis and genotyping of mumps virus as a better laboratory quality control.

  1. Sustainable Inclusion of Smallholders in the Emerging High Quality ...

    African Journals Online (AJOL)

    BRIAN

    security and the general livelihood conditions of any population. Agriculture, being one of the most weather-dependent of all human activities is highly vulnerable to climate change. African countries are particularly vulnerable to climate change because of their dependence on rain fed agriculture, high levels of poverty, low.

  2. A high-quality annotated transcriptome of swine peripheral blood

    Science.gov (United States)

    Background: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes an...

  3. Anomalous Behavior of High Quality Factor Planar Superconducting Resonators

    Science.gov (United States)

    Megrant, Anthony; Chen, Zijun; Chiaro, Ben; Dunsworth, Andrew; Quintana, Chris; Campbell, Brooks; Kelly, Julian; Barends, Rami; Chen, Yu; Jeffrey, Evan; Mutus, Josh; Neill, Charles; O'Malley, Peter; Sank, Daniel; Vainsencher, Amit; Wenner, Jim; White, Ted; Bochmann, Jorg; Hoi, Iochun; Palmstrom, Christopher; Martinis, John; Cleland, Andrew

    2014-03-01

    Superconducting coplanar waveguide resonators have proven to be invaluable tools in studying some of the decoherence mechanisms found in superconducting qubits. Surface two-level states tend to dominate decoherence at temperatures below Tc/10 and at very low microwave powers, assuming loss through other channels (e.g. quasiparticles, vortices, and radiation loss) has been mitigated through proper shielding and design. I will present recent measurements of resonators whose behavior diverges significantly from the standard two-level state model at low temperatures and low excitation energies, resulting in startling behavior of the internal quality factor. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office grant W911NF-09-1-0375.

  4. Academic coordination at university: Strategies for high quality education

    Directory of Open Access Journals (Sweden)

    Maria del Mar Durán Bellonch

    2009-08-01

    Full Text Available Most lecturers and professors involved in teaching School Management and Education Management courses have been engaged in developing some innovative actions to improve the training quality that we offer to students in the Pedagogy degree at the Autonomous University of Barcelona. These actions are aimed at increasing co-ordination among the teaching staff when designing and implementing the course curricula. Co-ordination meetings, exchanges of teaching experiences, discussions about what, how and when to teach the different contents, in which courses and at what level, methodological issues pointed out through technical description cards or the elaboration of study cases to be solved have become the basis of relevant actions during the last academic years. This paper explains each one of them, and provides useful information about the theoretical background, the process carried out, some of the results obtained, the output and the tools created.

  5. Possibilities of obtaining and controlling high-quality pressure castings

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2011-07-01

    Full Text Available The paper presents the influence of the type of furnace charging melting, refining and modification silumins 226 and 231 on the porosity and microstructure of castings. It was shown that in order to reduce or eliminate the porosity of the castings is necessary to the refining ECOSAL-AL113 of liquid silumin both in the melting furnace, and in the ladle and an additional nitrogen, in the heat furnace modified and refining with nitrogen. To control the effects of refining and modifying the TDA method was used. It was found that based on crystal- lization curve can be qualitatively assess the gas porosity of the castings. In order to control and quality control silumins author developed a computer program using the method of TDA, which sets out: Rm, A5, HB and casting porosity P and the concentration of hydrogen in them. The program also informs the technological procedures to be performed for liquid silumin improper preparation.

  6. Monitoring Gene Expression In Vivo with Nucleic Acid Molecular Switches

    Energy Technology Data Exchange (ETDEWEB)

    David C. Ward; Patricia Bray-Ward

    2005-01-26

    The overall objectives of this project were (1) to develop allosteric ribozymes capable of acting as molecular switches for monitoring the levels of both wild-type and mutant mRNA species in living cells and whole animals and (2) to develop highly efficient reagents to deliver nucleic acid molecular switches into living cells, tissues and animals with the ultimate goal of expression profiling specific mRNAs of diagnostic or prognostic value within tumors in animals. During the past year, we have moved our laboratory to Nevada and in the moving process we have lost electronic and paper copies of prior progress reports concerning the construction and biological properties of the molecular switches. Since there was minimal progress during the last year on molecular switches, we are relying on past project reports to provide a summary of our data on this facet of the grant. Here we are summarizing the work done on the delivery reagents and their application to inducing mutations in living cells, which will include work done during the no cost extension.

  7. High-quality lossy compression: current and future trends

    Science.gov (United States)

    McLaughlin, Steven W.

    1995-01-01

    This paper is concerned with current and future trends in the lossy compression of real sources such as imagery, video, speech and music. We put all lossy compression schemes into common framework where each can be characterized in terms of three well-defined advantages: cell shape, region shape and memory advantages. We concentrate on image compression and discuss how new entropy constrained trellis-based compressors achieve cell- shape, region-shape and memory gain resulting in high fidelity and high compression.

  8. Extraction of viral nucleic acids: comparison of five automated nucleic acid extraction platforms.

    Science.gov (United States)

    Verheyen, Jens; Kaiser, Rolf; Bozic, Michael; Timmen-Wego, Monika; Maier, Barbara K; Kessler, Harald H

    2012-07-01

    Nucleic acid extraction has a major impact on the reliability of results in routine molecular diagnostics. Optimal isolation of nucleic acids and removal of inhibitors are essential. This study compares five different automated extraction platforms for the extraction of norovirus RNA from stool and cytomegalovirus (CMV) DNA from plasma samples. Norovirus positive stool samples and CMV positive plasma samples were aliquoted and analyzed using five different automated platforms (easyMAG, bioMerieux; m2000sp, Abbott; MagNA Pure LC 2.0, Roche; QiaSymphony, Qiagen; sample preparation module of the VERSANT kPCR Molecular System, Siemens). Similar sample input and output volumes, the identical real-time PCR cycler, and the identical assays for amplification and detection for norovirus RNA and CMV DNA, respectively, were chosen. Of 39 stool samples, 36 tested positive for norovirus RNA with all extraction platforms. The three discrepant samples showed inhibition after extraction with at least one platform. Only with the VERSANT platform all samples tested positive for both the target RNA and the internal controls. Of 42 plasma samples, 27 gave quantifiable results for CMV DNA with all extraction platforms. There was significant variance between viral concentrations when different extraction platforms were compared. The majority of the 15 discrepant samples showed low viral concentrations. The internal control of the CMV assay gave positive results for all samples tested below the limit of quantification. The five automated extraction platforms yielded comparable results. However, the extraction performance was found to be impaired by inhibitory substances in stool samples. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.

    Science.gov (United States)

    Cheatham, T E; Young, M A

    In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic acids. This increase has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions, the availability of faster parallel computers, and the development of well-validated empirical molecular mechanical force fields. With these technologies, it has been demonstrated that simulation is not only capable of consistently reproducing experimental observations of sequence specific fine structure of DNA, but also can give detailed insight into prevalent problems in nucleic acid structure, ion association and specific hydration of nucleic acids, polyadenine tract bending, and the subtle environmental dependence of the A-DNA-B-DNA duplex equilibrium. Despite the advances, there are still issues with the methods that need to be resolved through rigorous controlled testing. In general, these relate to deficiencies of the underlying molecular mechanical potentials or applied methods (such as the imposition of true periodicity in Ewald simulations and the need for energy conservation), and significant limits in effective conformational sampling. In this perspective, we provide an overview of our experiences, provide some cautionary notes, and provide recommendations for further study in molecular dynamics simulation of nucleic acids. Copyright 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 232-256, 2001

  10. Differences in Use of High-quality and Low-quality Hospitals Among Working-age Individuals by Insurance Type.

    Science.gov (United States)

    Popescu, Ioana; Heslin, Kevin C; Coffey, Rosanna M; Washington, Raynard E; Barrett, Marguerite L; Karnell, Lucy H; Escarce, José J

    2017-02-01

    Research suggests that individuals with Medicaid or no insurance receive fewer evidence-based treatments and have worse outcomes than those with private insurance for a broad range of conditions. These differences may be due to patients' receiving care in hospitals of different quality. We used the Healthcare Cost and Utilization Project State Inpatient Databases 2009-2010 data to identify patients aged 18-64 years with private insurance, Medicaid, or no insurance who were hospitalized with acute myocardial infarction, heart failure, pneumonia, stroke, or gastrointestinal hemorrhage. Multinomial logit regressions estimated the probability of admissions to hospitals classified as high, medium, or low quality on the basis of risk-adjusted, in-hospital mortality. Compared with patients who have private insurance, those with Medicaid or no insurance were more likely to be minorities and to reside in areas with low-socioeconomic status. The probability of admission to high-quality hospitals was similar for patients with Medicaid (23.3%) and private insurance (23.0%) but was significantly lower for patients without insurance (19.8%, Pinsurance groups. Accounting for demographic, socioeconomic, and clinical characteristics did not influence the results. Previously noted disparities in hospital quality of care for Medicaid recipients are not explained by differences in the quality of hospitals they use. Patients without insurance have lower use of high-quality hospitals, a finding that needs exploration with data after 2013 in light of the Affordable Care Act, which is designed to improve access to medical care for patients without insurance.

  11. Molecular Recognition and Structural Influences on Function in Bio-nanosystems of Nucleic Acids and Proteins

    Science.gov (United States)

    Sethaphong, Latsavongsakda

    This work examines smart material properties of rational self-assembly and molecular recognition found in nano-biosystems. Exploiting the sequence and structural information encoded within nucleic acids and proteins will permit programmed synthesis of nanomaterials and help create molecular machines that may carry out new roles involving chemical catalysis and bioenergy. Responsive to different ionic environments thru self-reorgnization, nucleic acids (NA) are nature's signature smart material; organisms such as viruses and bacteria use features of NAs to react to their environment and orchestrate their lifecycle. Furthermore, nucleic acid systems (both RNA and DNA) are currently exploited as scaffolds; recent applications have been showcased to build bioelectronics and biotemplated nanostructures via directed assembly of multidimensional nanoelectronic devices 1. Since the most stable and rudimentary structure of nucleic acids is the helical duplex, these were modeled in order to examine the influence of the microenvironment, sequence, and cation-dependent perturbations of their canonical forms. Due to their negatively charged phosphate backbone, NA's rely on counterions to overcome the inherent repulsive forces that arise from the assembly of two complementary strands. As a realistic model system, we chose the HIV-TAR helix (PDB ID: 397D) to study specific sequence motifs on cation sequestration. At physiologically relevant concentrations of sodium and potassium ions, we observed sequence based effects where purine stretches were adept in retaining high residency cations. The transitional space between adenine and guanosine nucleotides (ApG step) in a sequence proved the most favorable. This work was the first to directly show these subtle interactions of sequence based cationic sequestration and may be useful for controlling metallization of nucleic acids in conductive nanowires. Extending the study further, we explored the degree to which the structure of NA

  12. Screening for Trichomonas vaginalis in high-risk adolescent females with a new transcription-mediated nucleic acid amplification test (NAAT): associations with ethnicity, symptoms, and prior and current STIs.

    Science.gov (United States)

    Hollman, Dominic; Coupey, Susan M; Fox, Amy S; Herold, Betsy C

    2010-10-01

    The importance of diagnosing trichomoniasis is highlighted by its strong association with HIV acquisition and viral shedding. The low sensitivity of wet preparation and often asymptomatic nature of trichomoniasis results in failure to recognize and treat this sexually transmitted infection. The purpose of this study was to evaluate the feasibility of screening high-risk adolescent females using a new highly sensitive and specific NAAT assay. We enrolled a consecutive, clinical sample of 144 sexually active females, aged 13 through 21. Subjects completed a questionnaire on sexual history and current vaginal symptoms, and provided two self- or physician-collected vaginal swabs and urine. A wet preparation test was performed with one swab and the APTIMA Trichomonas vaginalis (ATV) assay (Gen-Probe, Inc.) was performed with the other and with urine. Mean age was 18 +/- 1.6 years; 55% Hispanic and 35% black. A three-fold higher prevalence of trichomoniasis (6.3%) was detected by ATV than by wet preparation (2.1%) with 100% concordance between vaginal swab and urine. Prevalence of chlamydia by APTIMA was 11%; no gonorrhea was detected. Subjects with trichomoniasis were more likely than those without to be black (P trichomoniasis. Three times as many cases of trichomoniasis were identified with ATV compared to wet preparation and identical results were obtained with vaginal swabs and urine. No symptoms were associated with trichomoniasis. These findings highlight the imperative and feasibility of screening and treating at-risk populations. Copyright 2010 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

  13. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corrored steel

    NARCIS (Netherlands)

    Marty, F.; Ghiglione, J.-F.; Païsse, S.; Gueuné, H.; Quillet, L.; van Loosdrecht, M.C.M.; Muyzer, G.

    2012-01-01

    Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high

  14. Plasmodium Detection and Differentiation by Direct-on-Blood PCR Nucleic Acid Lateral Flow Immunoassay Development, Validation, and Evaluation

    NARCIS (Netherlands)

    Roth, Johanna M.; de Bes, Laura; Sawa, Patrick; Omweri, George; Osoti, Victor; Oberheitmann, Boris; Schallig, Henk D. F. H.; Mens, Pètra F.

    2018-01-01

    Decreasing malaria transmission warrants the search for highly sensitive point-of-care diagnostics, especially in resource-limited settings. The direct-on-blood PCR nucleic add lateral flow immunoassay (db-PCR-NALFIA) is a simplified PCR-based technique with a lateral flow readout that does not

  15. Health care in small prisons: incorporating high-quality standards.

    Science.gov (United States)

    Rieder, Jean-Pierre; Casillas, Alejandra; Mary, Gérard; Secretan, Anne-Dominique; Gaspoz, Jean-Michel; Wolff, Hans

    2013-01-01

    In the past, health management in Geneva's six post-trial prisons had been variable and inconsistent. In 2008, the unit of penitentiary medicine of the Geneva University Hospitals was mandated to re-organize and provide health care at all six prison facilities. The specific aim of this paper is to outline the example as a practical solution to some of the common challenges in unifying the structure and process of health services across multiple small facilities, while meeting European prison health and local quality standards. Geneva's post-trial prisons are small and close to one another in geographical proximity - ideal conditions for the construction of a health mobile team (HMT). This multidisciplinary mobile team operated like a community ambulatory care model; it was progressively launched in all prison facilities in Geneva. The authors incorporated an implementation strategy where health providers partnered with prison and community stakeholders in the health delivery model's development and adaption process. The model's strategic initiatives are described along the following areas, in light of other international prison health activity and prior care models: access to a health care professional, equivalence of care, patient consent, confidentiality, humanitarian interventions, and professional competence and independence. From the perspective of the HMT members, the authors provide the "lessons learned" through this experience, especially to providers who are working on prison health services reform and coordination improvement. The paper particularly stresses the importance of partnering with community health stakeholders and prison staff, a key component to the approach.

  16. Experimental Warming Decreases the Average Size and Nucleic Acid Content of Marine Bacterial Communities

    KAUST Repository

    Huete-Stauffer, Tamara M.

    2016-05-23

    Organism size reduction with increasing temperature has been suggested as a universal response to global warming. Since genome size is usually correlated to cell size, reduction of genome size in unicells could be a parallel outcome of warming at ecological and evolutionary time scales. In this study, the short-term response of cell size and nucleic acid content of coastal marine prokaryotic communities to temperature was studied over a full annual cycle at a NE Atlantic temperate site. We used flow cytometry and experimental warming incubations, spanning a 6°C range, to analyze the hypothesized reduction with temperature in the size of the widespread flow cytometric bacterial groups of high and low nucleic acid content (HNA and LNA bacteria, respectively). Our results showed decreases in size in response to experimental warming, which were more marked in 0.8 μm pre-filtered treatment rather than in the whole community treatment, thus excluding the role of protistan grazers in our findings. Interestingly, a significant effect of temperature on reducing the average nucleic acid content (NAC) of prokaryotic cells in the communities was also observed. Cell size and nucleic acid decrease with temperature were correlated, showing a common mean decrease of 0.4% per °C. The usually larger HNA bacteria consistently showed a greater reduction in cell and NAC compared with their LNA counterparts, especially during the spring phytoplankton bloom period associated to maximum bacterial growth rates in response to nutrient availability. Our results show that the already smallest planktonic microbes, yet with key roles in global biogeochemical cycling, are likely undergoing important structural shrinkage in response to rising temperatures.

  17. Enzyme-Free Nucleic Acid Amplification Assay Using a Cellphone-Based Well Plate Fluorescence Reader.

    Science.gov (United States)

    Kim, Donghyuk; Wei, Qingshan; Kim, Dong Hyeok; Tseng, Derek; Zhang, Jingzi; Pan, Eric; Garner, Omai; Ozcan, Aydogan; Di Carlo, Dino

    2018-01-02

    Nucleic acids, DNA and RNA, provide important fingerprint information for various pathogens and have significant diagnostic value; however, improved approaches are urgently needed to enable rapid detection of nucleic acids in simple point-of-care formats with high sensitivity and specificity. Here, we present a system that utilizes a series of toehold-triggered hybridization/displacement reactions that are designed to convert a given amount of RNA molecules (i.e., the analyte) into an amplified amount of signaling molecules without any washing steps or thermocycling. Fluorescent probes for signal generation were designed to consume products of the catalytic reaction in order to push the equilibrium and enhance the assay fold amplification for improved sensitivity and reaction speed. The system of toehold-assisted reactions is also modeled to better understand its performance and capabilities, and we empirically demonstrate the success of this approach with two analytes of diagnostic importance, i.e., influenza viral RNA and a micro RNA (miR-31). We also show that the amplified signal permits using a compact and cost-effective smartphone-based fluorescence reader, an important requirement toward a nucleic-acid-based point-of-care diagnostic system.

  18. Nucleic-Acid-Binding Chromophores as Efficient Indicators of Aptamer-Target Interactions

    Directory of Open Access Journals (Sweden)

    Kwabena Sarpong

    2012-01-01

    Full Text Available The binding affinity and specificity of nucleic acid aptamers have made them valuable candidates for use as sensors in diagnostic applications. In particular, chromophore-functionalized aptamers offer a relatively simple format for detection and quantification of target molecules. We describe the use of nucleic-acid-staining reagents as an effective tool for detecting and signaling aptamer-target interactions. Aptamers varying in size and structure and targeting a range of molecules have been used in conjunction with commercially available chromophores to indicate and quantify the presence of cognate targets with high sensitivity and selectivity. Our assay precludes the covalent modification of nucleic acids and relies on the differential fluorescence signal of chromophores when complexed with aptamers with or without their cognate target. We also evaluate factors that are critical for the stability of the complex between the aptamer and chromophore in presence or absence of target molecules. Our results indicate the possibility of controlling those factors to enhance the sensitivity of target detection by the aptamers used in such assays.

  19. Rapid amplification/detection of nucleic acid targets utilizing a HDA/thin film biosensor.

    Science.gov (United States)

    Jenison, Robert; Jaeckel, Heidi; Klonoski, Joshua; Latorra, David; Wiens, Jacinta

    2014-08-07

    Thin film biosensors exploit a flat, optically coated silicon-based surface whereupon formation of nucleic acid hybrids are enzymatically transduced in a molecular thin film that can be detected by the unaided human eye under white light. While the limit of sensitivity for detection of nucleic acid targets is at sub-attomole levels (60 000 copies) many clinical specimens containing bacterial pathogens have much lower levels of analyte present. Herein, we describe a platform, termed HDA/thin film biosensor, which performs helicase-dependant nucleic acid amplification on a thin film biosensor surface to improve the limit of sensitivity to 10 copies of the mecA gene present in methicillin-resistant strains of Staphylococcus. As double-stranded DNA is unwound by helicase it was either bound by solution-phase DNA primers to be copied by DNA polymerase or hybridized to surface immobilized probe on the thin film biosensor surface to be detected. Herein, we show that amplification reactions on the thin film biosensor are equivalent to in standard thin wall tubes, with detection at the limit of sensitivity of the assay occurring after 30 minutes of incubation time. Further we validate the approach by detecting the presence of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) from positive blood culture aliquots with high specificity (signal/noise ratio of 105).

  20. Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking.

    Science.gov (United States)

    Fecko, Christopher J; Munson, Katherine M; Saunders, Abbie; Sun, Guangxing; Begley, Tadhg P; Lis, John T; Webb, Watt W

    2007-01-01

    Crosslinking proteins to the nucleic acids they bind affords stable access to otherwise transient regulatory interactions. Photochemical crosslinking provides an attractive alternative to formaldehyde-based protocols, but irradiation with conventional UV sources typically yields inadequate product amounts. Crosslinking with pulsed UV lasers has been heralded as a revolutionary technique to increase photochemical yield, but this method had only been tested on a few protein-nucleic acid complexes. To test the generality of the yield enhancement, we have investigated the benefits of using approximately 150 fs UV pulses to crosslink TATA-binding protein, glucocorticoid receptor and heat shock factor to oligonucleotides in vitro. For these proteins, we find that the quantum yields (and saturating yields) for forming crosslinks using the high-peak intensity femtosecond laser do not improve on those obtained with low-intensity continuous wave (CW) UV sources. The photodamage to the oligonucleotides and proteins also has comparable quantum yields. Measurements of the photochemical reaction yields of several small molecules selected to model the crosslinking reactions also exhibit nearly linear dependences on UV intensity instead of the previously predicted quadratic dependence. Unfortunately, these results disprove earlier assertions that femtosecond pulsed laser sources provide significant advantages over CW radiation for protein-nucleic acid crosslinking.

  1. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

    Science.gov (United States)

    Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

    2015-01-01

    The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  2. The influence of knowledge management implementation toward the quality of high schools

    Directory of Open Access Journals (Sweden)

    Hilda Ainissyifa

    2012-09-01

    Full Text Available The purpose of this study is to analyze the influence of knowledge management implementation toward the quality of high schools. This study was conducted among five high schools under an education foundation. The analysis models used in the study were correlation analysis and t-test. The respondents were used as the profession references are 86 teachers. The result of the study shows that knowledge management implementation has a positive and significant influence toward the quality of high schools.

  3. Estimating the number of available high quality recruits at a county level

    OpenAIRE

    Duening, Timothy J

    1997-01-01

    Approved for public release; distribution is unlimited Whether or not a person is available to be recruited is essentially determined by two factors. First, the person has to be desirable to the military in terms of meeting the entry screens. Desirable, as defined by the military, is a person of high quality. The high quality market is defined as high school graduates scoring above the Both percentile on the Armed Forces Qualification Test (AFQT). The second factor is determined by the ind...

  4. Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.

    Science.gov (United States)

    Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

    2015-02-01

    We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Bust economics: foragers choose high quality habitats in lean times

    Directory of Open Access Journals (Sweden)

    Sonny S. Bleicher

    2016-01-01

    Full Text Available In environments where food resources are spatially variable and temporarily impoverished, consumers that encounter habitat patches with different food density should focus their foraging initially where food density is highest before they move to patches where food density is lower. Increasing missed opportunity costs should drive individuals progressively to patches with lower food density as resources in the initially high food density patches deplete. To test these expectations, we assessed the foraging decisions of two species of dasyurid marsupials (dunnarts: Sminthopsis hirtipes and S. youngsoni during a deep drought, or bust period, in the Simpson Desert of central Australia. Dunnarts were allowed access to three patches containing different food densities using an interview chamber experiment. Both species exhibited clear preference for the high density over the lower food density patches as measured in total harvested resources. Similarly, when measuring the proportion of resources harvested within the patches, we observed a marginal preference for patches with initially high densities. Models analyzing behavioral choices at the population level found no differences in behavior between the two species, but models analyzing choices at the individual level uncovered some variation. We conclude that dunnarts can distinguish between habitat patches with different densities of food and preferentially exploit the most valuable. As our observations were made during bust conditions, experiments should be repeated during boom times to assess the foraging economics of dunnarts when environmental resources are high.

  6. Nonparametric control charts for bivariate high-quality processes

    NARCIS (Netherlands)

    Albers, Willem/Wim

    For attribute data with (very) low rates of defectives, attractive control charts can be based on the maximum of subsequent groups of r failure times, for some suitable r≥1, like r=5. Such charts combine good performance with often highly needed robustness, as they allow a nonparametric adaptation

  7. Sustainable Inclusion of Smallholders in the Emerging High Quality ...

    African Journals Online (AJOL)

    BRIAN

    2010). The vulnerability of the developing countries like Nigeria is worsened by ... unpredictable yields, thereby making farmers more vulnerable, particularly in Africa ..... or build resilience .488 .400 .009 -.041 .212 -.296 .337. High cost of improved varieties .175 .124 .862 .082 .086 .053 -.045. Non-availability of farm labour.

  8. Whole high-quality light environment for humans and plants

    Science.gov (United States)

    Sharakshane, Anton

    2017-11-01

    Plants sharing a single light environment on a spaceship with a human being and bearing a decorative function should look as natural and attractive as possible. And consequently they can be illuminated only with white light with a high color rendering index. Can lighting optimized for a human eye be effective and appropriate for plants? Spectrum-based effects have been compared under artificial lighting of plants by high-pressure sodium lamps and general-purpose white LEDs. It has been shown that for the survey sample phytochrome photo-equilibria does not depend significantly on the parameters of white LED light, while the share of phytoactive blue light grows significantly as the color temperature increases. It has been revealed that yield photon flux is proportional to luminous efficacy and increases as the color temperature decreases, general color rendering index Ra and the special color rendering index R14 (green leaf) increase. General-purpose white LED lamps with a color temperature of 2700 K, Ra > 90 and luminous efficacy of 100 lm/W are as efficient as the best high-pressure sodium lamps, and at a higher luminous efficacy their yield photon flux per joule is even bigger in proportion. Here we show that demand for high color rendering white LED light is not contradictory to the agro-technical objectives.

  9. Spin Transport in High-Quality Suspended Graphene Devices

    NARCIS (Netherlands)

    Guimaraes, Marcos H. D.; Veligura, A.; Zomer, P. J.; Maassen, T.; Vera-Marun, I. J.; Tombros, N.; van Arees, B. J.; Wees, B.J. van

    We measure spin transport in high mobility suspended graphene (mu approximate to 10(5)cm(2)/(V s)), obtaining a (spin) diffusion coefficient of 0.1 m(2)/s and giving a lower bound on the spin relaxation time (tau(s) approximate to 150 ps) and spin relaxation length (lambda(s) = 4.7 mu m) for

  10. Whole high-quality light environment for humans and plants.

    Science.gov (United States)

    Sharakshane, Anton

    2017-11-01

    Plants sharing a single light environment on a spaceship with a human being and bearing a decorative function should look as natural and attractive as possible. And consequently they can be illuminated only with white light with a high color rendering index. Can lighting optimized for a human eye be effective and appropriate for plants? Spectrum-based effects have been compared under artificial lighting of plants by high-pressure sodium lamps and general-purpose white LEDs. It has been shown that for the survey sample phytochrome photo-equilibria does not depend significantly on the parameters of white LED light, while the share of phytoactive blue light grows significantly as the color temperature increases. It has been revealed that yield photon flux is proportional to luminous efficacy and increases as the color temperature decreases, general color rendering index Ra and the special color rendering index R14 (green leaf) increase. General-purpose white LED lamps with a color temperature of 2700 K, Ra > 90 and luminous efficacy of 100 lm/W are as efficient as the best high-pressure sodium lamps, and at a higher luminous efficacy their yield photon flux per joule is even bigger in proportion. Here we show that demand for high color rendering white LED light is not contradictory to the agro-technical objectives. Copyright © 2017. Published by Elsevier Ltd.

  11. Design and Evaluation of Peptide Nucleic Acid Probes for Specific Identification of Candida albicans

    Science.gov (United States)

    Kim, Hyun-Joong

    2014-01-01

    Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM. PMID:25428160

  12. Design and evaluation of peptide nucleic acid probes for specific identification of Candida albicans.

    Science.gov (United States)

    Kim, Hyun-Joong; Brehm-Stecher, Byron F

    2015-02-01

    Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  13. Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology.

    Science.gov (United States)

    Michelotti, Nicole; Johnson-Buck, Alexander; Manzo, Anthony J; Walter, Nils G

    2012-01-01

    Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA 'staples'. This revolutionary approach has led to the creation of a multitude of two-dimensional and three-dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. Copyright © 2011 Wiley Periodicals, Inc.

  14. Soni-removal of nucleic acids from inclusion bodies.

    Science.gov (United States)

    Neerathilingam, Muniasamy; Mysore, Sumukh; Gandham, Sai Hari A

    2014-05-23

    Inclusion bodies (IBs) are commonly formed in Escherichia coli due to over expression of recombinant proteins in non-native state. Isolation, denaturation and refolding of these IBs is generally performed to obtain functional protein. However, during this process IBs tend to form non-specific interactions with sheared nucleic acids from the genome, thus getting carried over into downstream processes. This may hinder the refolding of IBs into their native state. To circumvent this, we demonstrate a methodology termed soni-removal which involves disruption of nucleic acid-inclusion body interaction using sonication; followed by solvent based separation. As opposed to conventional techniques that use enzymes and column-based separations, soni-removal is a cost effective alternative for complete elimination of buried and/or strongly bound short nucleic acid contaminants from IBs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  15. High cortisol levels are associated with low quality food choice in type 2 diabetes.

    Science.gov (United States)

    Duong, Michelle; Cohen, Jessica I; Convit, Antonio

    2012-02-01

    Hypothalamic-pituitary-adrenal (HPA) axis control may be impaired in type 2 diabetes (T2DM). Glucocorticoids increase consumption of low quality foods high in calories, sugar, and fat. We explored the relationship between cortisol levels, poor blood glucose control, and food quality choice in T2DM. Twenty-seven healthy controls were age-, gender- and education-matched to 27 T2DM participants. Standard clinical blood tests and cortisol values were measured from fasting blood samples. Participants recorded all consumed food and drink items in a consecutive 3-day food diary. Diaries were analyzed for "high quality" and "low quality" foods using a standardized method with high reliability (0.97 and 0.86, respectively). Controlling for education, body mass index (BMI) and hemoglobin A1C (HbA1C), log-transformed cortisol (LogC) predicted the percent of low quality foods (R (2) = 0.092, β = 0.360, P quality foods chosen. Controlling for education, BMI, and LogC, HbA1C significantly predicted both the percent of low quality foods (ΔR (2) = 0.079, β = 0.348, P = 0.024) and high quality foods chosen (ΔR (2) = 0.085, β = -0.362, P = 0.022). The relationship between HbA1C and low quality food choice may be mediated by cortisol, controlling for BMI and education (P quality food choice (P quality food choice may be partially mediated by cortisol. Poor blood glucose control may cause HPA axis disruption, increased consumption of low quality foods.

  16. Toward Complete Sequence Flexibility of Nucleic Acid Base Analogue FRET.

    Science.gov (United States)

    Wranne, Moa S; Füchtbauer, Anders Foller; Dumat, Blaise; Bood, Mattias; El-Sagheer, Afaf H; Brown, Tom; Gradén, Henrik; Grøtli, Morten; Wilhelmsson, L Marcus

    2017-07-12

    Förster resonance energy transfer (FRET) using fluorescent base analogues is a powerful means of obtaining high-resolution nucleic acid structure and dynamics information that favorably complements techniques such as NMR and X-ray crystallography. Here, we expand the base-base FRET repertoire with an adenine analogue FRET-pair. Phosphoramidite-protected quadracyclic 2'-deoxyadenosine analogues qAN1 (donor) and qAnitro (acceptor) were synthesized and incorporated into DNA by a generic, reliable, and high-yielding route, and both constitute excellent adenine analogues. The donor, qAN1, has quantum yields reaching 21% and 11% in single- and double-strands, respectively. To the best of our knowledge, this results in the highest average brightness of an adenine analogue inside DNA. Its potent emissive features overlap well with the absorption of qAnitro and thus enable accurate FRET-measurements over more than one turn of B-DNA. As we have shown previously for our cytosine analogue FRET-pair, FRET between qAN1 and qAnitro positioned at different base separations inside DNA results in efficiencies that are highly dependent on both distance and orientation. This facilitates significantly enhanced resolution in FRET structure determinations, demonstrated here in a study of conformational changes of DNA upon binding of the minor groove binder netropsin. Finally, we note that the donor and acceptor of our cytosine FRET-pair, tC(O) and tCnitro, can be conveniently combined with the acceptor and donor of our current adenine pair, respectively. Consequently, our base analogues can now measure base-base FRET between 3 of the 10 possible base combinations and, through base-complementarity, between all sequence positions in a duplex.

  17. A high-quality catalog of the Drosophila melanogaster proteome

    DEFF Research Database (Denmark)

    Brunner, Erich; Ahrens, Christian H.; Mohanty, Sonaly

    2007-01-01

    % of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis...... matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism....

  18. Methods of introducing nucleic acids into cellular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lajoie, Marc J.; Gregg, Christopher J.; Mosberg, Joshua A.; Church, George M.

    2017-06-27

    A method of introducing a nucleic acid sequence into a cell is provided where the cell has impaired or inhibited or disrupted DnaG primase activity or impaired or inhibited or disrupted DnaB helicase activity, or larger or increased gaps or distance between Okazaki fragments or lowered or reduced frequency of Okazaki fragment initiation, or the cell has increased single stranded DNA (ssDNA) on the lagging strand of the replication fork including transforming the cell through recombination with a nucleic acid oligomer.

  19. Self-regulation and quality of life in high-functioning young adults with autism

    NARCIS (Netherlands)

    Dijkhuis, R.R.; Ziermans, T.B.; Rijn, S. Van; Staal, W.G.; Swaab, H.

    2017-01-01

    BACKGROUND: Autism is generally associated with poor functional outcome but little is known about predictors of quality of life, especially during early adulthood. This study was conducted to assess subjective quality of life during early adulthood in high-functioning autism spectrum disorder and

  20. Representations of a High-Quality System of Undergraduate Education in English Higher Education Policy Documents

    Science.gov (United States)

    Ashwin, Paul; Abbas, Andrea; McLean, Monica

    2015-01-01

    This article examines the ways in which a high-quality system of undergraduate education is represented in recent policy documents from a range of actors interested in higher education. Drawing on Basil Bernstein's ideas, the authors conceptualise the policy documents as reflecting a struggle over competing views of quality that are expressed…

  1. Hospital-wide education committees and high-quality residency training : A qualitative study

    NARCIS (Netherlands)

    Silkens, Milou E. W. M.; Slootweg, Irene A.; Scherpbier, Albert J. J. A.; Heineman, Maas Jan; Lombarts, Kiki M. J. M. H.

    2017-01-01

    High-quality residency training is of utmost importance for residents to become competent medical specialists. Hospital-wide education committees have been adopted by several healthcare systems to govern postgraduate medical education and to support continuous quality improvement of residency

  2. Self-Regulation and Quality of Life in High-Functioning Young Adults with Autism

    Science.gov (United States)

    Dijkhuis, Renee R.; Ziermans, Tim B.; Van Rijn, Sophie; Staal, Wouter G.; Swaab, Hanna

    2017-01-01

    Background: Autism is generally associated with poor functional outcome but little is known about predictors of quality of life, especially during early adulthood. This study was conducted to assess subjective quality of life during early adulthood in high-functioning autism spectrum disorder and its relation with self-regulating abilities.…

  3. The Relationship between Quality of Life and Eating Attitudes in Turkish High School Students

    Science.gov (United States)

    Kumcagiz, Hatice

    2017-01-01

    The aim of this study is to examine the relationship between quality of life and eating attitudes of adolescents. This study was designed as a correlational study. Participants were 640 voluntarily participating 15-18 years old students studying at public high schools in Samsun, Turkey. Data was collected with the Quality of Life Scale for…

  4. High pulse energy, high beam quality microsecond-pulse Ti:sapphire laser at 819.7 nm

    Science.gov (United States)

    Xu, Chang; Guo, Chuan; Yu, Hai-Bo; Wang, Zhi-Min; Zuo, Jun-Wei; Xia, Yuan-Qin; Bian, Qi; Bo, Yong; Gao, Hong-Wei; Guo, Ya-Ding; Zhang, Sheng; Cui, Da-Fu; Peng, Qin-Jun; Xu, Zu-Yan

    2017-03-01

    In this letter, a high pulse energy and high beam quality 819.7 nm Ti:sapphire laser pumped by a frequency-doubled Nd:YAG laser is demonstrated. At incident pump energy of 774 mJ, the maximum output energy of 89 mJ at 819.7 nm with a pulse width of 100 μs is achieved at a repetition rate of 5 Hz. To the best of our knowledge, this is the highest pulse energy at 819.7 nm with pulse width of hundred microseconds for a Ti:sapphire laser. The beam quality factor M 2 is measured to be 1.18. This specific wavelength with the high pulse energy and high beam quality at 819.7 nm is a promising light source to create a polychromatic laser guide star together with a home-made 589 nm laser via exciting the sodium atoms in the mesospheric atmosphere.

  5. On-Chip, Amplification-Free Quantification of Nucleic Acid for Point-of-Care Diagnosis

    Science.gov (United States)

    Yen, Tony Minghung

    This dissertation demonstrates three physical device concepts to overcome limitations in point-of-care quantification of nucleic acids. Enabling sensitive, high throughput nucleic acid quantification on a chip, outside of hospital and centralized laboratory setting, is crucial for improving pathogen detection and cancer diagnosis and prognosis. Among existing platforms, microarray have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, this dissertation presents theoretical and experimental progress to develop a platform nucleic acid quantification technology that is drastically more sensitive than current microarrays while compatible with microarray architecture. The first device concept explores on-chip nucleic acid enrichment by natural evaporation of nucleic acid solution droplet. Using a micro-patterned super-hydrophobic black silicon array device, evaporative enrichment is coupled with nano-liter droplet self-assembly workflow to produce a 50 aM concentration sensitivity, 6 orders of dynamic range, and rapid hybridization time at under 5 minutes. The second device concept focuses on improving target copy number sensitivity, instead of concentration sensitivity. A comprehensive microarray physical model taking into account of molecular transport, electrostatic intermolecular interactions, and reaction kinetics is considered to guide device optimization. Device pattern size and target copy number are optimized based on model prediction to achieve maximal hybridization efficiency. At a 100-mum pattern size, a quantum leap in detection limit of 570 copies is achieved using black silicon array device with self-assembled pico-liter droplet workflow. Despite its merits, evaporative enrichment on black silicon device suffers from coffee-ring effect at 100-mum pattern size, and thus not compatible with clinical patient samples. The

  6. Bio-Orthogonal Mediated Nucleic Acid Transfection of Cells via Cell Surface Engineering

    Science.gov (United States)

    2017-01-01

    The efficient delivery of foreign nucleic acids (transfection) into cells is a critical tool for fundamental biomedical research and a pillar of several biotechnology industries. There are currently three main strategies for transfection including reagent, instrument, and viral based methods. Each technology has significantly advanced cell transfection; however, reagent based methods have captured the majority of the transfection market due to their relatively low cost and ease of use. This general method relies on the efficient packaging of a reagent with nucleic acids to form a stable complex that is subsequently associated and delivered to cells via nonspecific electrostatic targeting. Reagent transfection methods generally use various polyamine cationic type molecules to condense with negatively charged nucleic acids into a highly positively charged complex, which is subsequently delivered to negatively charged cells in culture for association, internalization, release, and expression. Although this appears to be a straightforward procedure, there are several major issues including toxicity, low efficiency, sorting of viable transfected from nontransfected cells, and limited scope of transfectable cell types. Herein, we report a new strategy (SnapFect) for nucleic acid transfection to cells that does not rely on electrostatic interactions but instead uses an integrated approach combining bio-orthogonal liposome fusion, click chemistry, and cell surface engineering. We show that a target cell population is rapidly and efficiently engineered to present a bio-orthogonal functional group on its cell surface through nanoparticle liposome delivery and fusion. A complementary bio-orthogonal nucleic acid complex is then formed and delivered to which chemoselective click chemistry induced transfection occurs to the primed cell. This new strategy requires minimal time, steps, and reagents and leads to superior transfection results for a broad range of cell types

  7. High oleic sunflower biodiesel: quality control and different purification methods

    Directory of Open Access Journals (Sweden)

    Pighinelli, Anna L.M.T.

    2011-06-01

    Full Text Available The objective of the present work is to evaluate the production of biodiesel using ethanol and sunflower oil. The extraction of the sunflower oil was evaluated first. An experimental design was used to estimate the influence of the independent variables grain temperature (25º to 110ºC and expeller rotation (85 to 119rpm on the crude oil. The best result obtained was 68.38%, achieved with a rotation from 100 to 115rpm, grain temperature ranging from 25º to 30ºC and moisture content of around 7%. The next study consisted of transesterification, evaluating the influence of the ethanol, oil molar ratio and the catalyst concentration (sodium methylate on the ester-rich phase yield. The highest yield was 98.39% obtained with a molar ratio of 9:1 and 3% catalyst. An experiment was then carried out on a small reactor and the biodiesel produced was purified by three different methods: acidified water, silica and distillation. The quality aspects of the purified biodiesel samples were evaluated according to the Brazilian specifications for biodiesel, and distillation was shown to be the best method of purification.

    El objetivo del presente trabajo es evaluar la producción de biodiesel usando etanol y aceite de girasol. La extracción del aceite de girasol fue evaluada primero. Un diseño experimental fue usado para estimar la influencia de las variables independientes: temperatura del grano (25º a 110ºC y rotación del expeller (85 a 119 rpm en la obtención del aceite crudo. El mejor resultado obtenido fue un 68,38%, conseguido con una rotación de 100 a 115 rpm, una temperatura del grano de 25º a 30ºC y un contenido de humedad de alrededor del 7%. El siguiente estudio mediante transesterificación, evaluó la influencia de la relación molar etanol: aceite y concentración de catalizador (metilato sódico en el rendimiento de la fase rica en esteres. El rendimiento más alto fue 98,39% obtenido con una relación molar de 9.1 y 3% de

  8. Nucleic acid-binding glycoproteins which solubilize nucleic acids in dilute acid: re-examination of the Ustilago maydis glycoproteins

    Energy Technology Data Exchange (ETDEWEB)

    Unrau, P.; Champ, D.R.; Young, J.L.; Grant, C.E.

    1980-01-01

    Holloman reported the isolation from Ustilago maydis of a glycoprotein which prevented the precipitation of nucleic acids in cold 5% trichloroacetic acid. Two glycoprotein fractions from U. maydis with this nucleic acid-solubilizing activity were isolated in our laboratory using improved purification procedures. The activity was not due to nuclease contamination. The glycoproteins are distinguished by: their ability to bind to concanavalin A-Sepharose; their differential binding to double- and single-stranded deoxyribonucleic acid, and to ribonucleic acid; their molecular weights (46,000 and 69,000); and the relative amounts present in growing versus nongrowing cells. Both fractions required sulfhydryl-reducing conditions for optimal yields, specific activity, and stability. Nucleic acid binding was cooperative, the minimum number of glycoproteins required to make a native T7 DNA molecule soluble in dilute acid being estimated at 2 and 15, respectively.

  9. Dual-Readout Calorimetry for High-Quality Energy

    CERN Multimedia

    During the past seven years, the DREAM collaboration has systematically investigated all factors that determine and limit the precision with which the properties of hadrons and jets can be measured in calorimeters. Using simultaneous detection of the deposited energy and the Cerenkov light produced in hadronic shower development ${(dual}$ ${readout}$), the fluctuations in the electromagnetic shower fraction could be measured event by event their effects on signal linearity, response function and energy resolution eliminated. Detailed measurement of the time structure of the signals made it possible to measure the contirbutions of nuclear evaporation neutrons to the signals and thus reduce the effects of fluctuations in "invisible energy". We are now embarking on the construction of a full-scale calorimeter which incorporates all these elements and which should make it possible to measure the four-vectors of both electrons, hadrons and jets with very high precision, in an instrument that can be simply calibrat...

  10. Dual-Readout Calorimetry for High-Quality Energy Measurements

    CERN Document Server

    Wigmans, R

    2010-01-01

    During the past seven years, the DREAM Collaboration has systematically investigated all factors that determine and limit the precision with which the properties of hadrons and jets can be measured in calorimeters. Using simultaneous detection of the deposited energy and the Cerenkov light produced in hadronic shower development (dual readout), the fluctuations in the electromagnetic shower fraction could be measured event by event and their effects on signal linearity, response function and energy resolution eliminated. Detailed measurement of the time structure of the signals made it possible to measure the contributions of nuclear evaporation to the signals and thus reduce the effects of fluctuations in “invisible energy”. We are now embarking on the construction of a full-scale calorimeter which incorporates all these elements and which should make it possible to measure the four-vectors of both electrons, hadrons and jets with very high precision, in an instrument that can be simply calibrated with e...

  11. A Comprehensive, High-Quality Orthopedic Intern Surgical Skills Program.

    Science.gov (United States)

    Ford, Samuel E; Patt, Joshua C; Scannell, Brian P

    2016-01-01

    To design and implement a month-long, low-cost, comprehensive surgical skills curriculum built to address the needs of orthopedic surgery interns with high satisfaction among both interns and faculty. The study design was retrospective and descriptive. The study was conducted at tertiary care referral center with a medium sized orthopedic residency surgery program (5 residents/year). Totally 5 orthopedic surgery residents and 16 orthopedic surgery faculty participated. A general mission was established-to orient the resident to the postgraduate year 1 and prepare them for success in residency. The basic tenets of the American Board of Orthopaedic Surgeons surgical skills program framework were built. Curricular additions included anatomic study, surgical approaches, joint-specific physical examination, radiographic interpretation, preoperative planning, reduction techniques, basic emergency and operating room procedures, cadaveric procedure practice, and introduction to arthroplasty. The program was held in August during protected time for intern participants. In total, 16 orthopedic surgeons instructed 85% of the educational sessions. One faculty member did most of the preparation and organization to facilitate the program. The program ran for a cumulative 89 hours, including 14.5 hours working with cadaveric specimens. The program cost a total of $8100. The average module received a 4.15 rating on a 5-point scale, with 4 representing "good" and 5 representing "excellent." The program was appropriately timed and addressed topics relevant to the intern without sacrificing clinical experience or burdening inpatient services with interns' absence. The program received high satisfaction ratings from both the interns as well as the faculty. Additionally, the program fostered early relationships between interns and faculty-an unforeseen benefit. In the future, our program plans to better integrate validated learning metrics and improve instruction pertaining to both

  12. New lighting for the design of high quality biomedical devices

    Science.gov (United States)

    Jaffe, Claudia B.; Jaffe, Steven M.; Conner, Arlie R.

    2009-02-01

    Among the trends redefining 21st century biomedical diagnostics and therapeutics are the advent of low-cost portable analyzers. Because light is a powerful tool in many of today's most widely used life science instruments, high intensity, low cost light engines are essential to the design and proliferation of the newest bioanalytical instruments, medical devices and miniaturized analyzers. The development of new light technology represents a critical technical hurdle in the realization of point-of-care analysis. Lumencor has developed an inexpensive lighting solution, uniquely well suited to the production of safe, effective and commercially viable life science tools and biomedical devices. Lumencor's proprietary, solid-state light engine provides powerful, pure, stable, inexpensive light across the UV-Vis- NIR. Light engines are designed to directly replace the entire configuration of light management components with a single, simple unit. Power, spectral breadth and purity, stability and reliability data will demonstrate the advantages of these light engines for today's bioanalytical needs. Performance and cost analyses will be compared to traditional optical subsystems based on lamps, lasers and LEDs with respect to their suitability as sources for biomedical applications, implementation for development/evaluation of novel measurement tools and overall superior reliability. Next generation products based on such sources will be described to fulfill the demand for portable, hand-held analyzers and affordable devices with highly integrated light sources. A four color violet/cyan/green/red product will be demonstrated. A variety of multicolor prototypes, their spectral outputs and facile modulation will be discussed and their performance capabilities disclosed.

  13. EXPERT-ANALITICAL MONITORING OF LEARNING PROCESS QUALITY IN HIGH SCHOOL

    Directory of Open Access Journals (Sweden)

    T. M. Korotun

    2010-10-01

    Full Text Available The technological model is proposed for monitoring process of learning process quality in high school compliant with current European and home standards. The mathematical methods are elaborated for diverse activities as to learning process objects quality determination unified support. They self-consistently combine: automatic expert evaluation with Bayesian net and Value tree models; Delphi technique enhancement; best practices for education quality assessment. Quality estimates’ consistency index is introduced for their choice and acceptability analysis. Its permanent increasing over monitoring stages is guaranteed. The tools for these stages’ automatic support are described.

  14. Human capital, percieved domestic institutional quality and entrepreneurship among highly skilled Chinese returnees

    DEFF Research Database (Denmark)

    Bao, Yue; Miao, Qi; Liu, Ying

    2016-01-01

    aimed at assisting returnee entrepreneurs. Based on a survey of Chinese returnees and returnee entrepreneurship from 2011 to 2012, this paper examines how human capital and perceptions of domestic institutional quality affect entrepreneurial activity among highly skilled returnees. We find...

  15. The Institute of Medicine report on high-quality cancer care: implications for oncology nursing.

    Science.gov (United States)

    Ferrell, Betty; McCabe, Mary S; Levit, Laura

    2013-11-01

    To present key recommendations from a recently released Institute of Medicine (IOM) report on high-quality cancer care. The recommendations were derived from the IOM report Delivering High-Quality Cancer Care: Charting a New Course for a System in Crisis. The authors reviewed each of the recommendations to identify implications for oncology nurses. Nurses will play a vital role in the future design and delivery of high-quality cancer care. Oncology nurses should use the IOM recommendations in their settings to prepare for the delivery of oncology care amidst health system challenges, including an aging society. The IOM recommendations identify key areas of concern to nurses. Key aspects of nursing practice, including involvement in advanced care planning, patient-centered care, and evidence-based practice, are essential for high-quality care. Oncology nurses will be centrally involved in healthcare innovations, such as rapid learning systems, and as key members of a well-trained workforce.

  16. High-quality real-time temporal segmentation tool for video editing software

    OpenAIRE

    Cuevas Rodríguez, Carlos; García Santos, Narciso

    2012-01-01

    The increasing use of video editing software has resulted in a necessity for faster and more efficient editing tools. Here, we propose a lightweight high-quality video indexing tool that is suitable for video editing software.

  17. Diode pumped 1kHz high power Nd:YAG laser with excellent beam quality

    NARCIS (Netherlands)

    Godfried, Herman; Godfried, H.P; Offerhaus, Herman L.

    1997-01-01

    The design and operation of a one kilohertz diode pumped all solid-state Nd:YAG master oscillator power amplifier system with a phase conjugate mirror is presented. The setup allows high power scaling without reduction in beam quality.

  18. Egg Quality Traits and their Repeatability Estimates in High and Low ...

    African Journals Online (AJOL)

    Egg Quality Traits and their Repeatability Estimates in High and Low Body Weight Lines of Crossbred normal Feather, Naked Neck and Frizzle Chicken. ... Shell thickness was not significantly different in both body weight lines, while yolk index ...

  19. Recycle food wastes into high quality fish feeds for safe and quality fish production.

    Science.gov (United States)

    Wong, Ming-Hung; Mo, Wing-Yin; Choi, Wai-Ming; Cheng, Zhang; Man, Yu-Bon

    2016-12-01

    The amount of food waste generated from modern societies is increasing, which has imposed a tremendous pressure on its treatment and disposal. Food waste should be treated as a valuable resource rather than waste, and turning it into fish feeds would be a viable alternative. This paper attempts to review the feasibility of using food waste to formulate feed pellets to culture a few freshwater fish species, such as grass carp, grey mullet, and tilapia, under polyculture mode (growing different species in the same pond). These species occupy different ecological niches, with different feeding modes (i.e., herbivorous, filter feeding, etc.), and therefore all the nutrients derived from the food waste could be efficiently recycled within the ecosystem. The problems facing environmental pollution and fish contamination; the past and present situation of inland fish culture (focusing on South China); upgrade of food waste based feed pellets by adding enzymes, vitamin-mineral premix, probiotics (yeast), prebiotics, and Chinese medicinal herbs into feeds; and potential health risks of fish cultivated by food waste based pellets are discussed, citing some local examples. It can be concluded that appropriate portions of different types of food waste could satisfy basic nutritional requirements of lower trophic level fish species such as grass carp and tilapia. Upgrading the fish pellets by adding different supplements mentioned above could further elevated the quality of feeds, leading to higher growth rates, and enhanced immunity of fish. Health risk assessments based on the major environmental contaminants (mercury, PAHs and DDTs) in fish flesh showed that fish fed food waste based pellets are safer for consumption, when compared with those fed commercial feed pellets. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. High-quality thorium TRISO fuel performance in HTGRs

    Energy Technology Data Exchange (ETDEWEB)

    Verfondern, Karl [Forschungszentrum Juelich GmbH (Germany); Allelein, Hans-Josef [Forschungszentrum Juelich GmbH (Germany); Technische Hochschule Aachen (Germany); Nabielek, Heinz; Kania, Michael J.

    2013-11-01

    Thorium as a nuclear fuel has received renewed interest, because of its widespread availability and the good irradiation performance of Th and mixed (Th,U) oxide compounds as fuels in nuclear power systems. Early HTGR development employed thorium together with high-enriched uranium (HEU). After 1980, HTGR fuel systems switched to low-enriched uranium (LEU). After completing fuel development for the AVR and the THTR with BISO coated particles, the German program expanded its efforts utilizing thorium and HEU TRISO coated particles in advanced HTGR concepts for process heat applications (PNP) and direct-cycle electricity production (HHT). The combination of a low-temperature isotropic (LTI) inner and outer pyrocarbon layers surrounding a strong, stable SiC layer greatly improved manufacturing conditions and the subsequent contamination and defective particle fractions in production fuel elements. In addition, this combination provided improved mechanical strength and a higher degree of solid fission product retention, not known previously with high-temperature isotropic (HTI) BISO coatings. The improved performance of the HEU (Th, U)O{sub 2} TRISO fuel system was successfully demonstrated in three primary areas of development: manufacturing, irradiation testing under normal operating conditions, and accident simulation testing. In terms of demonstrating performance for advanced HTGR applications, the experimental failure statistic from manufacture and irradiation testing are significantly below the coated particle requirements specified for PNP and HHT designs at the time. Covering a range to 1300 C in normal operations and 1600 C in accidents, with burnups to 13% FIMA and fast fluences to 8 x 10{sup 25} n/m{sup 2} (E> 16 fJ), the performance results exceed the design limits on manufacturing and operational requirements for the German HTR-Modul concept, which are 6.5 x 10{sup -5} for manufacturing, 2 x 10{sup -4} for normal operating conditions, and 5 x 10{sup -4

  1. Bacteriophage-insensitive mutants for high quality Crescenza manufacture

    Directory of Open Access Journals (Sweden)

    Donatella eChirico

    2014-05-01

    Full Text Available Streptococcus thermophilus is a thermophilic lactic acid bacterium used as starter culture for the manufacture of fermented dairy products. For the production of Crescenza and other soft cheeses, Sacco has developed and provides dairies with 3 different defined blends of S. thermophilus strains. Each blend contains 2 different S. thermophilus strains. The strains were selected based on their unique technological properties as well as different phage profiles. Analysis of 133 whey samples collected in 2009-2010 from Italian dairies showed a high prevalence (about 50% of bacteriophage attacks on the blend ST020. More specifically, the strain S. thermophilus ST1A was found to be the preferred target of the bacteriophages. A bacteriophage insensitive mutant (BIM5 of the phage-sensitive strain ST1A was successfully developed and used to substitute strain ST1A in the Crescenza starter culture ST020. The strain BIM5 showed identical technological and industrial traits as those of the phage-sensitive strain ST1A. The improved resistance of the modified Crescenza starter culture ST020R was confirmed at Italian dairies, and its effectiveness monitored on 122 whey samples collected in 2011-2012. Compared to the previous values (2009-2010, the use of the phage-hardened blend ST020R allowed reducing of frequency of phage attacks from about 50 to less than 5% of the whey samples investigated.

  2. Bacteriophage-insensitive mutants for high quality Crescenza manufacture.

    Science.gov (United States)

    Chirico, Donatella; Gorla, Arianna; Verga, Viola; Pedersen, Per D; Polgatti, Eliseo; Cava, Antonio; Dal Bello, Fabio

    2014-01-01

    Streptococcus thermophilus is a thermophilic lactic acid bacterium used as starter culture for the manufacture of fermented dairy products. For the production of Crescenza and other soft cheeses, Sacco has developed and provides dairies with three different defined blends of S. thermophilus strains. Each blend contains two different S. thermophilus strains. The strains were selected based on their unique technological properties as well as different phage profiles. Analysis of 133 whey samples collected in 2009-2010 from Italian dairies showed a high prevalence (about 50%) of bacteriophage attacks on the blend ST020. More specifically, the strain S. thermophilus ST1A was found to be the preferred target of the bacteriophages. A bacteriophage insensitive mutant (BIM5) of the phage-sensitive strain ST1A was successfully developed and used to substitute strain ST1A in the Crescenza starter culture ST020. The strain BIM5 showed identical technological and industrial traits as those of the phage-sensitive strain ST1A. The improved resistance of the modified Crescenza starter culture ST020R was confirmed at Italian dairies, and its effectiveness monitored on 122 whey samples collected in 2011-2012. Compared to the previous values (2009-2010), the use of the phage-hardened blend ST020R allowed reducing of frequency of phage attacks from about 50 to less than 5% of the whey samples investigated.

  3. Modeling the subjective quality of highly contrasted videos displayed on LCD with local backlight dimming.

    Science.gov (United States)

    Mantel, Claire; Bech, Søren; Korhonen, Jari; Forchhammer, Søren; Pedersen, Jesper Melgaard

    2015-02-01

    Local backlight dimming is a technology aiming at both saving energy and improving visual quality on television sets. As the rendition of the image is specified locally, the numerical signal corresponding to the displayed image needs to be computed through a model of the display. This simulated signal can then be used as input to objective quality metrics. The focus of this paper is on determining which characteristics of locally backlit displays influence quality assessment. A subjective experiment assessing the quality of highly contrasted videos displayed with various local backlight-dimming algorithms is set up. Subjective results are then compared with both objective measures and objective quality metrics using different display models. The first analysis indicates that the most significant objective features are temporal variations, power consumption (probably representing leakage), and a contrast measure. The second analysis shows that modeling of leakage is necessary for objective quality assessment of sequences displayed with local backlight dimming.

  4. Effects of parent-child affective quality during high school years on subsequent substance use.

    OpenAIRE

    Ralston, Ekaterina S.; Trudeau, Linda S.; Richard Spoth

    2012-01-01

    The literature indicates that the quality of affective relationships between youth and parents is associated with lower levels of a range of problem behaviors during childhood, early and late adolescence. While the protective effect of parental monitoring on substance use in the high school and post high school years has been demonstrated, there is a knowledge gap concerning effects of parent-child affective quality (PCAQ) during the same periods. We tested a conceptual theoretical model to e...

  5. A DNA origami nanorobot controlled by nucleic acid hybridization

    KAUST Repository

    Torelli, Emanuela

    2014-03-20

    A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Karyotype and nucleic acid content in Zantedeschia aethiopica Spr ...

    African Journals Online (AJOL)

    Analysis of karyotype, nucleic deoxyribonucleic acid (DNA) content and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were performed in Zantedeschia aethiopica and Zantedeschia elliottiana. Mitotic metaphase in both species showed 2n=32. The chromosomes of both species were quite similar ...

  7. Cell cycle nucleic acids, polypeptides and uses thereof

    Science.gov (United States)

    Gordon-Kamm, William J.; Lowe, Keith S.; Larkins, Brian A.; Dilkes, Brian R.; Sun, Yuejin

    2007-08-14

    The invention provides isolated nucleic acids and their encoded proteins that are involved in cell cycle regulation. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions. The present invention provides methods and compositions relating to altering cell cycle protein content, cell cycle progression, cell number and/or composition of plants.

  8. Karyotype and nucleic acid content in Zantedeschia aethiopica Spr ...

    African Journals Online (AJOL)

    DR. NJ TONUKARI

    2012-07-03

    Jul 3, 2012 ... Analysis of karyotype, nucleic deoxyribonucleic acid (DNA) content and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were performed in Zantedeschia aethiopica and. Zantedeschia elliottiana. Mitotic metaphase in both species showed 2n=32. The chromosomes of both species ...

  9. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    Science.gov (United States)

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  10. Peptide nucleic acids and their potential applications in biotechnology

    DEFF Research Database (Denmark)

    Buchardt, O.; Egholm, M.; Berg, R.H.

    1993-01-01

    Peptide nucleic acids (PNAs) are novel DNA mimics in which the sugar-phosphate backbone has been replaced with a backbone based on amino acids1-3. PNAs exhibit sequence-specific binding to DNA and RNA with higher affinities and specificities than unmodified DNA. They,are resistant to nuclease...

  11. Modulating gene function with peptide nucleic acids (PNA)

    DEFF Research Database (Denmark)

    Nielsen, Peter E.; Crooke, Stanley T.

    2008-01-01

    A review on peptide nucleic acid (PNA) oligomers as modulators of gene expression ranging from gene silencing at the mRNAor the dsDNA (antigene) level, and redirection of mRNA splicing to gene activation through transcription bubble mimicking. PNA chem., anti-infective agents, cellular delivery, ......, and in vivo bioavailability of PNA are briefly discussed. [on SciFinder (R)]...

  12. A simple and rapid nucleic acid preparation method for reverse ...

    African Journals Online (AJOL)

    USER

    2010-03-29

    Mar 29, 2010 ... Key words: Nucleic acid preparation, reverse transcription polymerase chain reaction, dormant tubers, potato leafroll virus, potato virus S. INTRODUCTION. The vegetative propagation of potato (Solano tuberous. L.) presents ample opportunity for .... were amplified in 35 cycles. Annealing temperature was ...

  13. Non-enzymatic Polymerization of Nucleic Acids from Monomers

    DEFF Research Database (Denmark)

    Dörr, Mark; Löffler, Philipp M. G.; Monnard, Pierre-Alain

    2012-01-01

    This review deals with the state-of-the-art techniques in non-enzymatic nucleic acid condensation from monomers. In particular, the procedures called \\emph{monomer self-condensation} and \\emph{template-directed monomer condensation} are described, which have been developed to achieve efficient...

  14. Circulating nucleic acids as a diagnostic and prognostic marker in ...

    African Journals Online (AJOL)

    Elevated levels of circulating nucleic acids have been found in a variety of benign and malignant pathological conditions. The ability to detect and quantitate specific DNA, RNA and micro-RNA sequences in serum/ plasma has opened up the possibilities of non-invasive diagnosis and monitoring of diseases. Circulating ...

  15. PYRENE INTERCALATING NUCLEIC ACIDS WITH A CARBON LINKER

    DEFF Research Database (Denmark)

    Østergaard, Michael E.; Wamberg, Michael Chr.; Pedersen, Erik Bjerregaard

    2011-01-01

    geminally attached. Fluorescence studies of this intercalating nucleic acid with the pyrene moieties inserted as a bulge showed formation of an excimer band. When a mismatch was introduced at the site of the intercalator, an excimer band was formed for the destabilized duplexes whereas an exciplex band...

  16. Nucleic acid therapy for lifespan prolongation: Present and future

    Indian Academy of Sciences (India)

    Lifespan prolongation is a common desire of the human race. With advances in biotechnology, the mechanism of aging has been gradually unraveled, laying the theoretical basis of nucleic acid therapy for lifespan prolongation. Regretfully, clinically applicable interventions do not exist without the efforts of converting theory ...

  17. Prediction of molecular alignment of nucleic acids in aligned media

    NARCIS (Netherlands)

    Wu, B.; Petersen, M.; Girard, F.C.; Tessari, M.; Wijmenga, S.S.

    2006-01-01

    We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor

  18. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2017-09-05

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  19. Surface plasmon resonance sensing of nucleic acids: A review

    Czech Academy of Sciences Publication Activity Database

    Šípová, Hana; Homola, Jiří

    -, č. 773 (2013), s. 9-23 ISSN 0003-2670 R&D Projects: GA MŠk(CZ) LH11102 Institutional support: RVO:67985882 Keywords : Surface plasmon resonance * Nucleic acid * Biosensor Subject RIV: JB - Sensors, Measurment, Regulation Impact factor: 4.517, year: 2013

  20. Nucleic acid detection with surface plasmon resonance using cationic latex

    NARCIS (Netherlands)

    de Vries, E.F.A.; Schasfoort, Richardus B.M.; van der Plas, J.; Greve, Jan

    1994-01-01

    An affinity sensor based on Surface Plasmon Resonance (SPR) was used to detect nucleic acids. SPR is an optical technique that is able to detect small changes in the refractive index of the immediate vicinity of a metal surface. After a specific amplification of DNA, achieved using the polymerase

  1. nucleic acid amplification as used in the diagnosis and management ...

    African Journals Online (AJOL)

    DR. AMINU

    2014-06-01

    Jun 1, 2014 ... thus, amplification based methods offer superior performance ... self-sustaining sequence replication), Amplification of nucleic acid probe (e.g., ligase chain reaction and Q-beta replicase) and Signal amplification (e.g., branched-probe DNA assay). PCR ... advantages, limitations and clinical utility (Fredricks.

  2. DNA-like double helix formed by peptide nucleic acid

    DEFF Research Database (Denmark)

    Wittung, P; Nielsen, Peter E.; Buchardt, O

    1994-01-01

    Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...

  3. Watson-Crick hydrogen bonding of unlocked nucleic acids

    DEFF Research Database (Denmark)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-01-01

    We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmo...... unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like....

  4. A nucleic acid dependent chemical photocatalysis in live human cells

    DEFF Research Database (Denmark)

    Arian, Dumitru; Cló, Emiliano; Gothelf, Kurt V

    2010-01-01

    Only two nucleic acid directed chemical reactions that are compatible with live cells have been reported to date. Neither of these processes generate toxic species from nontoxic starting materials. Reactions of the latter type could be applied as gene-specific drugs, for example, in the treatment...

  5. Isolation of high quality DNA and RNA from cambium of the East ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-06

    Jul 6, 2009 ... Key words: Nucleic acid extraction, polyphenols, polysaccharides, medicinal plants. INTRODUCTION. Traditional medicine .... dium bromide and visualized under UV light. DNA PCR analysis. Polymerase ... SDS and then exposed to Kodak X-ray film, stored at -80°C for 3 days and subsequently developed.

  6. Modeling nucleic acid structure in the presence of single-stranded binding proteins

    Science.gov (United States)

    Forties, Robert; Bundschuh, Ralf

    2009-03-01

    There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV, the RecA DNA repair protein in bacteria, and all proteins involved in mRNA splicing and translation. We extend the Vienna Package for quantitatively modeling the secondary structure of nucleic acids to include proteins which bind to unpaired portions of the nucleic acid. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously measured. This leaves the footprint and sequence dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid, and FRET distributions for fluorophores attached to the nucleic acid.

  7. Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

    Science.gov (United States)

    Nasarabadi, Shanavaz [Livermore, CA

    2011-01-11

    A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

  8. High quality factor multi-layer symmetric hybrid plasmonic microresonator for sensing applications

    Science.gov (United States)

    Zhang, Meng; Wu, Genzhu

    2017-11-01

    A multi-layer symmetric hybrid plasmonic microresonator with two high-index dielectric microrings symmetrically near the metallic structure is proposed. Benefiting from introducing two dielectric rings near the metal, the multi-layer hybrid plasmonic microresonator has a high quality factor about 10,000, while still capable of retaining a small mode volume around 1 . 27 μm3. As a potential application, the symmetric hybrid microresonator with air-filled gap regions could be used for sensing with a sensitivity high of 210 nm per refraction index unit, a large figure of merit of 1319 due to the high quality factor.

  9. A modern mode of activation for nucleic acid enzymes.

    Directory of Open Access Journals (Sweden)

    Dominique Lévesque

    2007-07-01

    Full Text Available Through evolution, enzymes have developed subtle modes of activation in order to ensure the sufficiently high substrate specificity required by modern cellular metabolism. One of these modes is the use of a target-dependent module (i.e. a docking domain such as those found in signalling kinases. Upon the binding of the target to a docking domain, the substrate is positioned within the catalytic site. The prodomain acts as a target-dependent module switching the kinase from an off state to an on state. As compared to the allosteric mode of activation, there is no need for the presence of a third partner. None of the ribozymes discovered to date have such a mode of activation, nor does any other known RNA. Starting from a specific on/off adaptor for the hepatitis delta virus ribozyme, that differs but has a mechanism reminiscent of this signalling kinase, we have adapted this mode of activation, using the techniques of molecular engineering, to both catalytic RNAs and DNAs exhibiting various activities. Specifically, we adapted three cleaving ribozymes (hepatitis delta virus, hammerhead and hairpin ribozymes, a cleaving 10-23 deoxyribozyme, a ligating hairpin ribozyme and an artificially selected capping ribozyme. In each case, there was a significant gain in terms of substrate specificity. Even if this mode of control is unreported for natural catalytic nucleic acids, its use needs not be limited to proteinous enzymes. We suggest that the complexity of the modern cellular metabolism might have been an important selective pressure in this evolutionary process.

  10. Polarizable model potential function for nucleic acid bases.

    Science.gov (United States)

    Nakagawa, Setsuko

    2007-07-15

    A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms. Copyright (c) 2007 Wiley Periodicals, Inc.

  11. The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen.

    Science.gov (United States)

    Liu, Keyuan; Hao, Xiaoyan; Li, Yang; Luo, Guobin; Zhang, Yonggen; Xin, Hangshu

    2017-11-01

    This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs) and microbial nucleic acid bases in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. To develop the regression equations, data on the rumen contents of individual cows were obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C). The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same stage of pregnancy. For each lactation stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and lactation stages of dairy cows (pacids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (pacid bases established by ruminal OBCFAs contents showed a good predictive capacity, as indicated by reasonably low standard errors and high R-squared values. This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

  12. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  13. High Quality RNA Isolation from Leaf, Shell, Root Tissues and Callus of Hazelnut (Corylus avellana L.

    Directory of Open Access Journals (Sweden)

    Hossein Khosravi

    2017-12-01

    Full Text Available Extraction of high quality RNA is a critical step in molecular genetics studies. Hazelnut is one of the most important nuts plants in the world. The presence of the taxol and other taxanes in hazelnut plant necessitates explaining their biosynthesis pathway and identifying the candidate genes. Therefore, an easy and practical method is necessary for RNA extraction from hazelnuts. Hazelnut has high levels of phenolic compounds. High amounts of polyphenolic and polysaccharide compounds in plants could be causing problems in RNA extraction procedures.  To avoid these problems, a simple and efficient method can be used based on cetyltrimethylammonium bromide (CTAB extraction buffer and lithium chloride for extraction of high quality RNA from different parts of hazelnut plant. Using this method, a high-quality RNA sample (light absorbed in the A260/A280 was 2.04

  14. Quality metrics for high order meshes: analysis of the mechanical simulation of the heart beat.

    Science.gov (United States)

    Lamata, Pablo; Roy, Ishani; Blazevic, Bojan; Crozier, Andrew; Land, Sander; Niederer, Steven A; Hose, D Rod; Smith, Nicolas P

    2013-01-01

    The quality of a computational mesh is an important characteristic for stable and accurate simulations. Quality depends on the regularity of the initial mesh, and in mechanical simulations it evolves in time, with deformations causing changes in volume and distortion of mesh elements. Mesh quality metrics are therefore relevant for both mesh personalization and the monitoring of the simulation process. This work evaluates the significance, in meshes with high order interpolation, of four quality metrics described in the literature, applying them to analyse the stability of the simulation of the heart beat. It also investigates how image registration and mesh warping parameters affect the quality and stability of meshes. Jacobian-based metrics outperformed or matched the results of coarse geometrical metrics of aspect ratio or orthogonality, although they are more expensive computationally. The stability of simulations of a complete heart cycle was best predicted with a specificity of 61%, sensitivity of 85%, and only nominal differences were found changing the intra-element and per-element combination of quality values. A compromise between fitting accuracy and mesh stability and quality was found. Generic geometrical quality metrics have a limited success predicting stability, and an analysis of the simulation problem may be required for an optimal definition of quality.

  15. Temporal vairations in water quality of the Ogallala Aquifer on the Texas High Plains

    Science.gov (United States)

    Goebel, T.; Lascano, R. J.; Stout, J. E.

    2016-12-01

    The Ogallala Aquifer, under eight States of the Great Plains of US, from Texas to South Dakota, is among the largest aquifers in the world. In some regions, extraction of water for urban and agricultural uses far exceeds recharge resulting in a decline of the water table. In the southern region of the Texas High Plains (THP) this decline prompted restrictions set by a local water conservation agency in 2009 stating that in 50 years about 50% of the saturated thickness of the Ogallala Aquifer should be preserved. However, this restriction only addressed quantity and not the quality of the remaining water. In general, the quality of water being mined from an aquifer tends to change over time, leading us to measure changes in water quality over the length of a crop's growing season in the THP. We measured water quality including: EC, pH, and ion analysis, at several locations covering 5 counties in the THP. Preliminary results show that when wells are actively pumped water quality can change in complex and unpredictable ways. In some cases, water quality declines and in others water quality improves. This result encouraged us to expand and continue to measure changes in ground water quality and develop a model to quantify changes in water quality.

  16. Bullying as a risk for poor sleep quality among high school students in China.

    Science.gov (United States)

    Zhou, Ying; Guo, Lan; Lu, Ci-yong; Deng, Jian-xiong; He, Yuan; Huang, Jing-hui; Huang, Guo-liang; Deng, Xue-qing; Gao, Xue

    2015-01-01

    To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China. A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI) and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality. Among the 23,877 students, 6,127 (25.66%) reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91%) were pure victims of bullying, 401 (1.68%) were bullies and 784 (3.28%) were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others) was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32), bullied others (OR=2.30, 95%CI=1.85-2.86) or both (OR=2.58, 95%CI=2.20-3.03) were at a higher risk for poor sleep quality. Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents.

  17. Bullying as a Risk for Poor Sleep Quality among High School Students in China

    Science.gov (United States)

    Lu, Ci-yong; Deng, Jian-xiong; Huang, Jing-hui; Huang, Guo-liang; Deng, Xue-qing; Gao, Xue

    2015-01-01

    Objective To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China. Methods A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI) and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality. Results Among the 23,877 students, 6,127 (25.66%) reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91%) were pure victims of bullying, 401 (1.68%) were bullies and 784 (3.28%) were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others) was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32), bullied others (OR=2.30, 95%CI=1.85-2.86) or both (OR=2.58, 95%CI=2.20-3.03) were at a higher risk for poor sleep quality. Conclusions Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents. PMID:25811479

  18. 78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

    Science.gov (United States)

    2013-06-19

    ... Nucleic Acid-Based Systems for Mycobacterium tuberculosis Complex in Respiratory Specimens AGENCY: Food...) is proposing to reclassify nucleic acid-based in vitro diagnostic devices for the detection of... Controls Guideline: Nucleic Acid-Based In Vitro Diagnostic Devices for the Detection of Mycobacterium...

  19. High yield and high quality DNA from vegetative and sexual tissues ...

    African Journals Online (AJOL)

    Pines are considered to be difficult for DNA extraction. However, from one species to the other there is variation in phenolic profiles and seed size that might affect final DNA yields and quality. Two DNA extraction protocols (CTAB and SDS based) were compared for their ability to produce DNA on leaves, gametophyte and ...

  20. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    El-Yazbi, Amira F.; Loppnow, Glen R., E-mail: glen.loppnow@ualberta.ca

    2013-07-05

    Graphical abstract: -- Highlights: •Simple, inexpensive, mix-and-read assay for positive detection of DNA damage. •Recognition of undamaged DNA via hybridization to a hairpin probe. •Terbium(III) fluorescence reports the amount of damage by binding to ssDNA. •Tb/hairpin is a highly selective and sensitive fluorescent probe for DNA damage. -- Abstract: Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb{sup 3+}). Single-stranded oligonucleotides greatly enhance the Tb{sup 3+} emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb{sup 3+}/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb{sup 3+}, producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb{sup 3+}/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb{sup 3+}/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36 ± 1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

  1. Certifying leaders? high-quality management practices and healthy organisations: an ISO-9000 based standardisation approach.

    Science.gov (United States)

    Montano, Diego

    2016-08-05

    The present study proposes a set of quality requirements to management practices by taking into account the empirical evidence on their potential effects on health, the systemic nature of social organisations, and the current conceptualisations of management functions within the framework of comprehensive quality management systems. Systematic reviews and meta-analyses focusing on the associations between leadership and/or supervision and health in occupational settings are evaluated, and the core elements of an ISO 9001 standardisation approach are presented. Six major occupational health requirements to high-quality management practices are identified pertaining to communication processes, organisational justice, role clarity, decision making, social influence processes and management support. It is concluded that the quality of management practices may be improved by developing a quality management system of management practices that ensures not only conformity to product but also to occupational safety and health requirements. Further research may evaluate the practicability of the proposed approach.

  2. Towards a High Quality High School Workforce: A Longitudinal, Demographic Analysis of U.S. Public School Physics Teachers

    Science.gov (United States)

    Rushton, Gregory T.; Rosengrant, David; Dewar, Andrew; Shah, Lisa; Ray, Herman E.; Sheppard, Keith; Watanabe, Lynn

    2017-01-01

    Efforts to improve the number and quality of the high school physics teaching workforce have taken several forms, including those sponsored by professional organizations. Using a series of large-scale teacher demographic data sets from the National Center for Education Statistics (NCES), this study sought to investigate trends in teacher quality…

  3. Combined microfluidization and ultrasonication: a synergistic protocol for high-efficient processing of SWCNT dispersions with high quality

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Sida, E-mail: s.luo@buaa.edu.cn [Beihang University, School of Mechanical Engineering and Automation (China); Liu, Tao, E-mail: tliu@fsu.edu [Florida State University, High-Performance Materials Institute (United States); Wang, Yong; Li, Liuhe [Beihang University, School of Mechanical Engineering and Automation (China); Wang, Guantao; Luo, Yun [China University of Geosciences, Center of Safety Research, School of Engineering and Technology (China)

    2016-08-15

    High-efficient and large-scale production of high-quality CNT dispersions is necessary for meeting the future needs to develop various CNT-based electronic devices. Herein, we have designed novel processing protocols by combining conventional ultrasonication process with a new microfluidization technique to produce high-quality SWCNT dispersions with improved processing efficiency. To judge the quality of SWCNT dispersions, one critical factor is the degree of exfoliation, which could be quantified by both geometrical dimension of the exfoliated nanotubes and percentage of individual tubes in a given dispersion. In this paper, the synergistic effect of the combined protocols was systematically investigated through evaluating SWCNT dispersions with newly developed characterization techniques, namely preparative ultracentrifuge method (PUM) and simultaneous Raman scattering and photoluminescence spectroscopy (SRSPL). The results of both techniques draw similar conclusions that as compared with either of the processes operated separately, a low-pass microfluidization followed by a reasonable duration of ultrasonication could substantially improve the processing efficiency to produce high-quality SWCNT dispersions with averaged particle length and diameter as small as ~600 and ~2 nm, respectively.Graphical abstract.

  4. The effect of the amiodarone-warfarin interaction on anticoagulation quality in a single, high-quality anticoagulation center.

    Science.gov (United States)

    White, Ryan D; Riggs, Kyle W; Ege, Ed J; Petroski, Gregory F; Koerber, Scott M; Flaker, Greg

    2016-03-01

    Clinical trials have reported a low time in therapeutic range (TTR) in patients with atrial fibrillation treated with both warfarin andamiodarone. These trials included centers and countries with both high and low TTRs. What is the impact of amiodarone on the TTR in a single, high-quality anticoagulation clinic? TTR was assessed in amiodarone and nonamiodarone-treated patients from a University anticoagulation clinic. Baseline characteristics between patients ever-taking or never-taking amiodarone were similar, except more amiodarone patients were smokers (19.5 vs. 6.1%, P = 0.0031). The TTR calculated from 8901international normalized ratios (INRs) in 249 nonamiodarone patients with a mean follow-up of 34 ± 20 months (mean INR 36 ± 18) was 66 ± 16.6% compared with 61.3 ± 16.2% (P = 0.111) from 1455 INRs in 41 amiodarone-treated patients with a mean follow-up of 28 ± 20 months (mean INR 35 ± 22). Factors associated with a low TTR were male sex (P = 0.0013), smoker (P = 0.0048), and amiodarone use (P = 0.0374). A second on-treatment analysis, in which the TTR was calculated only during amiodarone therapy, resulted in similar findings; however, amiodarone did not emerge as a predictor of a low TTR. In 11 patients, the TTR prior to amiodarone (54.5 ± 22.2%) was not significantly different in the first 3 months (54.6 ± 33.4%) or after 3 months (67.2 ± 33.7%) of amiodarone. In a single high-quality anticoagulation center, anticoagulation quality, as measured by the TTR, can be comparable in amiodarone and nonamiodarone-treated patients.

  5. Brisk walking to improve quality of life of high technology industrial ...

    African Journals Online (AJOL)

    The purpose of this study was to examine the effects of short periods of brisk walking on the quality of life (QOL) of workers in high technology industries. 86 workers were recruited from a high technology company in northern Taiwan who had not participated in regular physical activity within the last three months. They were ...

  6. The role of young, recently disturbed upland hardwood forest as high quality food patches

    Science.gov (United States)

    Cathryn H. Greenberg; Roger W. Perry; Craig A. Harper; Douglas J. Levey; John M. McCord

    2011-01-01

    Young (1-10 year post-disturbance) upland hardwood forests function as high-quality food patches by providing abundant fruit, and nutritious foliage and flowers that attract pollinating and foliar arthropods and support high populations of small mammals that, in turn, are prey for numerous vertebrate predators. Reductions in basal area increase light penetration to the...

  7. Grain yield and quality responses of tropical hybrid rice to high night-time temperature

    NARCIS (Netherlands)

    Shi, W.; Yin, X.; Struik, P.C.; Xie, F.; Schmidt, R.C.; Jagadish, K.S.V.

    2016-01-01

    High temperature has a pronounced effect on grain yield and quality in rice. Climate change has increased night temperature more than day temperature in many parts of the world. How rice responds to high night-time temperature (HNT) is largely unknown. This study presents the first effort to assess

  8. Effects of High School Students' Perceptions of School Life Quality on Their Academic Motivation Levels

    Science.gov (United States)

    Akin Kösterelioglu, Meltem; Kösterelioglu, Ilker

    2015-01-01

    This study aims to identify the effects of high school students' perceptions of school life quality on their academic motivation levels. The study was conducted on a sample of high school students (n = 2371) in Amasya Province in the fall semester of 2013-2014 academic year. Study sample was selected with the help of cluster sampling method. Data…

  9. Sequence-specific inhibition of duck hepatitis B virus reverse transcription by peptide nucleic acids (PNA)

    DEFF Research Database (Denmark)

    Robaczewska, Magdalena; Narayan, Ramamurthy; Seigneres, Beatrice

    2005-01-01

    BACKGROUND/AIMS: Peptide nucleic acids (PNAs) appear as promising new antisense agents, that have not yet been examined as hepatitis B virus (HBV) inhibitors. Our aim was to study the ability of PNAs targeting the duck HBV (DHBV) encapsidation signal epsilon to inhibit reverse transcription (RT...... inhibitor than the PNA targeting only the bulge. Importantly, the inhibition was highly sequence-specific since double-mismatched PNA had no effect on the RT reaction. Moreover, in PDH the PNA coupled to Arg(7) cationic delivery peptide decreased DHBV replication. CONCLUSIONS: We provide the first evidence...

  10. The use of atomic force microscopy for 3D analysis of nucleic acid hybridization on microarrays

    OpenAIRE

    Dubrovin, E.; Presnova, G.; Rubtsova, M.; Egorov, A.; Grigorenko, V.; Yaminsky, I.

    2015-01-01

    Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, ...

  11. A novel highly differentially expressed gene in wheat endosperm associated with bread quality

    Science.gov (United States)

    Furtado, A.; Bundock, P. C.; Banks, P. M.; Fox, G.; Yin, X.; Henry, R. J.

    2015-01-01

    Analysis of gene expression in developing wheat seeds was used to identify a gene, wheat bread making (wbm), with highly differential expression (~1000 fold) in the starchy endosperm of genotypes varying in bread making quality. Several alleles differing in the 5’-upstream region (promoter) of this gene were identified, with one present only in genotypes with high levels of wbm expression. RNA-Seq analysis revealed low or no wbm expression in most genotypes but high expression (0.2-0.4% of total gene expression) in genotypes that had good bread loaf volume. The wbm gene is predicted to encode a mature protein of 48 amino acids (including four cysteine residues) not previously identified in association with wheat quality, possibly because of its small size and low frequency in the wheat gene pool. Genotypes with high wbm expression all had good bread making quality but not always good physical dough qualities. The predicted protein was sulphur rich suggesting the possibility of a contribution to bread loaf volume by supporting the crossing linking of proteins in gluten. Improved understanding of the molecular basis of differences in bread making quality may allow more rapid development of high performing genotypes with acceptable end-use properties and facilitate increased wheat production. PMID:26011437

  12. Ethnic/racial discrimination moderates the effect of sleep quality on school engagement across high school.

    Science.gov (United States)

    Dunbar, Margaret; Mirpuri, Sheena; Yip, Tiffany

    2017-10-01

    Previous research has indicated that school engagement tends to decline across high school. At the same time, sleep problems and exposure to social stressors such as ethnic/racial discrimination increase. The current study uses a biopsychosocial perspective to examine the interactive and prospective effects of sleep and discrimination on trajectories of academic performance. Growth curve models were used to explore changes in 6 waves of academic outcomes in a sample of 310 ethnically and racially diverse adolescents (mean age = 14.47 years, SD = .78, and 64.1% female). Ethnic/racial discrimination was assessed at Time 1 in a single survey. Sleep quality and duration were also assessed at Time 1 with daily diary surveys. School engagement and grades were reported every 6 months for 3 years. Higher self-reported sleep quality in the ninth grade was associated with higher levels of academic engagement at the start of high school. Ethnic/racial discrimination moderated the relationship between sleep quality and engagement such that adolescents reporting low levels of discrimination reported a steeper increase in engagement over time, whereas their peers reporting poor sleep quality and high levels of discrimination reported the worse engagement in the ninth grade and throughout high school. The combination of poor sleep quality and high levels of discrimination in ninth grade has downstream consequences for adolescent academic outcomes. This study applies the biopsychosocial model to understand the development and daily experiences of diverse adolescents. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  13. High-resolution remote sensing of water quality in the San Francisco Bay-Delta Estuary

    Science.gov (United States)

    Fichot, Cédric G.; Downing, Bryan D.; Bergamaschi, Brian; Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark C.; Thompson, David R.; Gierach, Michelle M.

    2015-01-01

    The San Francisco Bay–Delta Estuary watershed is a major source of freshwater for California and a profoundly human-impacted environment. The water quality monitoring that is critical to the management of this important water resource and ecosystem relies primarily on a system of fixed water-quality monitoring stations, but the limited spatial coverage often hinders understanding. Here, we show how the latest technology in visible/near-infrared imaging spectroscopy can facilitate water quality monitoring in this highly dynamic and heterogeneous system by enabling simultaneous depictions of several water quality indicators at very high spatial resolution. The airborne portable remote imaging spectrometer (PRISM) was used to derive high-spatial-resolution (2.6 × 2.6 m) distributions of turbidity, and dissolved organic carbon (DOC) and chlorophyll-a concentrations in a wetland-influenced region of this estuary. A filter-passing methylmercury vs DOC relationship was also developed using in situ samples and enabled the high-spatial-resolution depiction of surface methylmercury concentrations in this area. The results illustrate how high-resolution imaging spectroscopy can inform management and policy development in important inland and estuarine water bodies by facilitating the detection of point- and nonpoint-source pollution, and by providing data to help assess the complex impacts of wetland restoration and climate change on water quality and ecosystem productivity.

  14. High-Resolution Remote Sensing of Water Quality in the San Francisco Bay-Delta Estuary.

    Science.gov (United States)

    Fichot, Cédric G; Downing, Bryan D; Bergamaschi, Brian A; Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark; Thompson, David R; Gierach, Michelle M

    2016-01-19

    The San Francisco Bay-Delta Estuary watershed is a major source of freshwater for California and a profoundly human-impacted environment. The water quality monitoring that is critical to the management of this important water resource and ecosystem relies primarily on a system of fixed water-quality monitoring stations, but the limited spatial coverage often hinders understanding. Here, we show how the latest technology in visible/near-infrared imaging spectroscopy can facilitate water quality monitoring in this highly dynamic and heterogeneous system by enabling simultaneous depictions of several water quality indicators at very high spatial resolution. The airborne portable remote imaging spectrometer (PRISM) was used to derive high-spatial-resolution (2.6 × 2.6 m) distributions of turbidity, and dissolved organic carbon (DOC) and chlorophyll-a concentrations in a wetland-influenced region of this estuary. A filter-passing methylmercury vs DOC relationship was also developed using in situ samples and enabled the high-spatial-resolution depiction of surface methylmercury concentrations in this area. The results illustrate how high-resolution imaging spectroscopy can inform management and policy development in important inland and estuarine water bodies by facilitating the detection of point- and nonpoint-source pollution, and by providing data to help assess the complex impacts of wetland restoration and climate change on water quality and ecosystem productivity.

  15. The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen

    Directory of Open Access Journals (Sweden)

    Keyuan Liu

    2017-11-01

    Full Text Available Objective This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs and microbial nucleic acid bases in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. Methods To develop the regression equations, data on the rumen contents of individual cows were obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C. The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same stage of pregnancy. For each lactation stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. Results The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and lactation stages of dairy cows (p<0.05. The concentrations of OBCFAs, especially odd-chain fatty acids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (p<0.05. The equations of ruminal microbial nucleic acid bases established by ruminal OBCFAs contents showed a good predictive capacity, as indicated by reasonably low standard errors and high R-squared values. Conclusion This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

  16. Experimental approaches to the interaction of the prion protein with nucleic acids and glycosaminoglycans: Modulators of the pathogenic conversion.

    Science.gov (United States)

    Silva, Jerson L; Vieira, Tuane C R G; Gomes, Mariana P B; Rangel, Luciana P; Scapin, Sandra M N; Cordeiro, Yraima

    2011-03-01

    The concept that transmissible spongiform encephalopathies (TSEs) are caused only by proteins has changed the traditional paradigm that disease transmission is due solely to an agent that carries genetic information. The central hypothesis for prion diseases proposes that the conversion of a cellular prion protein (PrP(C)) into a misfolded, β-sheet-rich isoform (PrP(Sc)) accounts for the development of (TSE). There is substantial evidence that the infectious material consists chiefly of a protein, PrP(Sc), with no genomic coding material, unlike a virus particle, which has both. However, prions seem to have other partners that chaperone their activities in converting the PrP(C) into the disease-causing isoform. Nucleic acids (NAs) and glycosaminoglycans (GAGs) are the most probable accomplices of prion conversion. Here, we review the recent experimental approaches that have been employed to characterize the interaction of prion proteins with nucleic acids and glycosaminoglycans. A PrP recognizes many nucleic acids and GAGs with high affinities, and this seems to be related to a pathophysiological role for this interaction. A PrP binds nucleic acids and GAGs with structural selectivity, and some PrP:NA complexes can become proteinase K-resistant, undergoing amyloid oligomerization and conversion to a β-sheet-rich structure. These results are consistent with the hypothesis that endogenous polyanions (such as NAs and GAGs) may accelerate the rate of prion disease progression by acting as scaffolds or lattices that mediate the interaction between PrP(C) and PrP(Sc) molecules. In addition to a still-possible hypothesis that nucleic acids and GAGs, especially those from the host, may modulate the conversion, the recent structural characterization of the complexes has raised the possibility of developing new diagnostic and therapeutic strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    Directory of Open Access Journals (Sweden)

    Fördös Gergely

    2005-07-01

    Full Text Available Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s c. defines a distance from these atoms (3–15 Å. The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s; provides a DotPlot-like visualization (Residues Contact Map, and calculates the frequency of every possible residue pairs (Residue Contact Table in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA. Results obtained on protein structures showed highly significant correlations with results obtained from literature (p Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements http://janbiro.com/Downloads.html SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] http://www.sun.com and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. Additional File 1 SeqX_1.041_05601.jar. see this article Click here for file

  18. Nanoparticle strategies for cancer therapeutics: Nucleic acids, polyamines, bovine serum amine oxidase and iron oxide nanoparticles (Review).

    Science.gov (United States)

    Agostinelli, Enzo; Vianello, Fabio; Magliulo, Giuseppe; Thomas, Thresia; Thomas, T J

    2015-01-01

    Nanotechnology for cancer gene therapy is an emerging field. Nucleic acids, polyamine analogues and cytotoxic products of polyamine oxidation, generated in situ by an enzyme-catalyzed reaction, can be developed for nanotechnology-based cancer therapeutics with reduced systemic toxicity and improved therapeutic efficacy. Nucleic acid-based gene therapy approaches depend on the compaction of DNA/RNA to nanoparticles and polyamine analogues are excellent agents for the condensation of nucleic acids to nanoparticles. Polyamines and amine oxidases are found in higher levels in tumours compared to that of normal tissues. Therefore, the metabolism of polyamines spermidine and spermine, and their diamine precursor, putrescine, can be targets for antineoplastic therapy since these naturally occurring alkylamines are essential for normal mammalian cell growth. Intracellular polyamine concentrations are maintained at a cell type-specific set point through the coordinated and highly regulated interplay between biosynthesis, transport, and catabolism. In particular, polyamine catabolism involves copper-containing amine oxidases. Several studies showed an important role of these enzymes in developmental and disease-related processes in animals through the control of polyamine homeostasis in response to normal cellular signals, drug treatment, and environmental and/or cellular stress. The production of toxic aldehydes and reactive oxygen species (ROS), H2O2 in particular, by these oxidases suggests a mechanism by which amine oxidases can be exploited as antineoplastic drug targets. The combination of bovine serum amine oxidase (BSAO) and polyamines prevents tumour growth, particularly well if the enzyme has been conjugated with a biocompatible hydrogel polymer. The findings described herein suggest that enzymatically formed cytotoxic agents activate stress signal transduction pathways, leading to apoptotic cell death. Consequently, superparamagnetic nanoparticles or other

  19. Disordered eating partly mediates the relationship between poor sleep quality and high body mass index.

    Science.gov (United States)

    Yeh, Shin-Shyuan Sally; Brown, Rhonda Frances

    2014-04-01

    We evaluated the relationship between poor sleep quality and high body mass index (BMI) in a community-derived sample. In addition, we explored the premise that disordered eating (i.e. eating late at night and/or binge eating, which can occur at night) may partly explain the relationship. An online survey asked 330 participants about their height and weight, recent sleep quality, and recent experiences of binge-eating and night-time eating. Using multiple regression analyses, high BMI was shown to be related to shorter sleep duration, increased sleep latency, use of sleeping medications and worse binge-eating, whereas worse sleep quality was related to worse night-eating, after controlling for depression and demographics. Using mediational analyses, binge-eating was shown to partly mediate the relationship between worse sleep quality to higher BMI, whereas night-eating mediated the reverse association of high BMI to worse sleep quality. The results suggest that night- and/or binge-eating may partly explain the observed relationship between worse sleep quality and overweight/obesity. Thus, the relationship may simply reflect that overweight people are more likely to binge-eat while they wait for sleep to come, and this may contribute to weight gain over time. In addition, the results may indicate that eating rather than weight gain or obesity may be responsible for causing the sleep deficits in overweight people. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Isolation of high-quality total RNA from leaves of Myrciaria dubia "CAMU CAMU".

    Science.gov (United States)

    Gómez, Juan Carlos Castro; Reátegui, Alina Del Carmen Egoavil; Flores, Julián Torres; Saavedra, Roberson Ramírez; Ruiz, Marianela Cobos; Correa, Sixto Alfredo Imán

    2013-01-01

    Myrciaria dubia is a main source of vitamin C for people in the Amazon region. Molecular studies of M. dubia require high-quality total RNA from different tissues. So far, no protocols have been reported for total RNA isolation from leaves of this species. The objective of this research was to develop protocols for extracting high-quality total RNA from leaves of M. dubia. Total RNA was purified following two modified protocols developed for leaves of other species (by Zeng and Yang, and by Reid et al.) and one modified protocol developed for fruits of the studied species (by Silva). Quantity and quality of purified total RNA were assessed by spectrophotometric and electrophoretic analysis. Additionally, quality of total RNA was evaluated with reverse-transcription polymerase chain reaction (RT-PCR). With these three modified protocols we were able to isolate high-quality RNA (A260nm/A280nm >1.9 and A260nm/A230nm >2.0). Highest yield was produced with the Zeng and Yang modified protocol (384±46µg ARN/g fresh weight). Furthermore, electrophoretic analysis showed the integrity of isolated RNA and the absence of DNA. Another proof of the high quality of our purified RNA was the successful cDNA synthesis and amplification of a segment of the M. dubia actin 1 gene. We report three modified protocols for isolation total RNA from leaves of M. dubia. The modified protocols are easy, rapid, low in cost, and effective for high-quality and quantity total RNA isolation suitable for cDNA synthesis and polymerase chain reaction.

  1. Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

    Directory of Open Access Journals (Sweden)

    Leclerc Mario

    2005-04-01

    Full Text Available Abstract Background Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization. Results Using surface-bound peptide nucleic acids (PNA probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray. Conclusion This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes.

  2. Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

    Science.gov (United States)

    Raymond, Frédéric R; Ho, Hoang-Anh; Peytavi, Régis; Bissonnette, Luc; Boissinot, Maurice; Picard, François J; Leclerc, Mario; Bergeron, Michel G

    2005-01-01

    Background Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization. Results Using surface-bound peptide nucleic acids (PNA) probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray. Conclusion This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes. PMID:15850478

  3. Present status of protein and nucleic acid database activities in the world

    Science.gov (United States)

    Tsugita, Akira

    The first protein database was founded in 1965, followed by the establishment of nucleic acid databases from 1971. Presently there are six major sequence databases, located in Japan, USA and the FRG-three for protein data and three for nucleic acid data. International cooperation between the protein databases and between the nucleic acid databases have greatly facilitated compilation and dissemination of data. Coordination between these protein and nucleic acid databases have progressed with the support of the CODATA Task Group and the International Advisory Board for Nucleic Acid Databases. In the protein field, several additional database activities are initiated to contribute to protein engineering and structure-activity relationships.

  4. Assessment Sleep Quality and its Relationship with Test Anxiety among High School Students in Qom- Iran

    Directory of Open Access Journals (Sweden)

    Saman barmeh ziyar

    2016-10-01

    Full Text Available Background Test anxiety is a special case of a general anxiety which is of particular importance in students, because students will be the future of the country and the society activists. On the other hand, sleep quality and sleep disorders, have correlation with ailments, poor performance, decreased quality of life and increase of associated costs; This study aimed to determine the quality of sleep and its relationship with test anxiety among students in Qom city, Iran. Materials and Methods This study was a cross-sectional study, which was performed among 250 students who were going to pass the exam preparation classes. In order to collect data Pittsburgh Sleep Quality Index (PSQI questionnaires and Test Anxiety Inventory (TAI questionnaire were used. Data were analyzed using SPSS-16 with descriptive statistics and statistical methods, independent t-test, ANOVA and Pearson correlation coefficient. Results In this study, 50% of participants were boys (n=125 and 50 percent were girls (n=125. 81.4% of subjects had poor sleep quality and 69.6% had average to high score for test anxiety. Based on the results of anxiety test and sleep quality index there was a significant correlation between anxiety and sleep quality with gender (P=0.003, r=0.447. Conclusion School children had poor sleep quality and high test anxiety, and due to their direct and significant correlation, attention to this category of students, especially for girls, is important. Therefore, anxiety and promoting sleep quality control programs are recommended in this group.

  5. Growth of high quality InGaAsN heterostructures and their laser application

    Science.gov (United States)

    Egorov, A. Yu.; Bernklau, D.; Borchert, B.; Illek, S.; Livshits, D.; Rucki, A.; Schuster, M.; Kaschner, A.; Hoffmann, A.; Dumitras, Gh.; Amann, M. C.; Riechert, H.

    2001-07-01

    Focus of this work is the optimization of growth to achieve high quality laser material for emission at 1.3 μm and beyond. GaAs/GaAsN/InGaAsN heterostructures were grown by solid source molecular beam epitaxy. To achieve optimum crystal quality of InGaAsN heterostructures, growth was followed by a high temperature treatment at about 700°C. The high optical quality of our annealed material is attested by large exciton recombination lifetimes (more than 2 ns). Consequently, a decrease of single quantum well transparency current density down to 100 A/cm 2 is found and SWQ lasers with threshold current densities as low as 350 A/cm 2 have been made. This represents clearly the lowest laser thresholds reported so far for emission around 1.3 μm from the InGaAsN material system.

  6. Combined angiography for high-quality near-infrared autofluorescence images.

    Science.gov (United States)

    Querques, Giuseppe; Souied, Eric H

    2014-01-01

    To describe an innovative imaging technique to obtain high-quality near-infrared autofluorescence (NIA) images. Simultaneous fluorescein angiography + indocyanine green angiography (FA + ICGA) acquisition mode (without dye injection) of Spectralis HRA + OCT (Heidelberg Retina Angiograph; Heidelberg Engineering, Heidelberg, Germany), setting maximum level of illuminance, and Automatic Real-time (ART) Module (Heidelberg Engineering) to increase signal-to-noise ratio. The combined confocal scanning laser ophthalmoscope technique allows the Spectralis HRA + OCT device to create high-quality NIA ART images. This innovative imaging technique, consisting of simultaneous FA + ICGA acquisition mode, setting maximum level of illuminance, and ART, allows the Spectralis HRA + OCT device to create high-quality NIA ART images, without requiring the need for the HRA2 (Heidelberg Retina Angiograph; Heidelberg Engineering) device.

  7. NPIDB: Nucleic acid-Protein Interaction DataBase.

    Science.gov (United States)

    Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

    2013-01-01

    The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

  8. Devices, systems, and methods for detecting nucleic acids using sedimentation

    Energy Technology Data Exchange (ETDEWEB)

    Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory J.

    2017-10-24

    Embodiments of the present invention are directed toward devices, systems, and method for conducting nucleic acid purification and quantification using sedimentation. In one example, a method includes generating complexes which bind to a plurality of beads in a fluid sample, individual ones of the complexes comprising a nucleic acid molecule such as DNA or RNA and a labeling agent. The plurality of beads including the complexes may be transported through a density media, wherein the density media has a density lower than a density of the beads and higher than a density of the fluid sample, and wherein the transporting occurs, at least in part, by sedimentation. Signal may be detected from the labeling agents of the complexes.

  9. Nucleic Acid Engineering: RNA Following the Trail of DNA.

    Science.gov (United States)

    Kim, Hyejin; Park, Yongkuk; Kim, Jieun; Jeong, Jaepil; Han, Sangwoo; Lee, Jae Sung; Lee, Jong Bum

    2016-02-08

    The self-assembly feature of the naturally occurring biopolymer, DNA, has fascinated researchers in the fields of materials science and bioengineering. With the improved understanding of the chemical and structural nature of DNA, DNA-based constructs have been designed and fabricated from two-dimensional arbitrary shapes to reconfigurable three-dimensional nanodevices. Although DNA has been used successfully as a building block in a finely organized and controlled manner, its applications need to be explored. Hence, with the myriad of biological functions, RNA has recently attracted considerable attention to further the application of nucleic acid-based structures. This Review categorizes different approaches of engineering nucleic acid-based structures and introduces the concepts, principles, and applications of each technique, focusing on how DNA engineering is applied as a guide to RNA engineering.

  10. Surface plasmon resonance sensing of nucleic acids: A review

    Energy Technology Data Exchange (ETDEWEB)

    Šípová, Hana [Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague (Czech Republic); Homola, Jiří, E-mail: homola@ufe.cz [Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague (Czech Republic)

    2013-04-22

    Highlights: ► Advances of nucleic acid (NA) surface plasmon resonance (SPR) sensors are presented. ► Bioanalytical applications of NA SPR biosensors are reviewed. ► Applications for study of molecular interactions involving NAs are also discussed. -- Abstract: Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA–NA, NA–protein, NA–small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

  11. An extended IUPAC nomenclature code for polymorphic nucleic acids.

    Science.gov (United States)

    Johnson, Andrew D

    2010-05-15

    The International Union of Pure and Applied Chemistry (IUPAC) code specified nearly 25 years ago provides a nomenclature for incompletely specified nucleic acids. However, no system currently exists that allows for the informatics representation of the relative abundance at polymorphic nucleic acids (e.g. single nucleotide polymorphisms) in a single specified character, or a string of characters. Here, I propose such an information code as a natural extension to the IUPAC nomenclature code, and present some potential uses and limitations to such a code. The primary anticipated use of this extended nomenclature code is to assist in the representation of the rapidly growing space of information in human genetic variation. johnsonad2@nhlbi.nih.gov Supplementary data are available at Bioinformatics online.

  12. Universal nucleic acids sample preparation method for cells, spores and their mixture

    Science.gov (United States)

    Bavykin, Sergei [Darien, IL

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  13. Cellular Interactions and Immune Response of Spherical Nucleic Acid (SNA) Nanoconjugates

    Science.gov (United States)

    Massich, Matthew David

    Spherical nucleic acid (SNA) nanoconjugates consist of a densely packed monolayer shell of highly-oriented oligonucleotides covalently bound to a gold nanoparticle core. The nanoconjugates exhibit several important qualities, which make them useful for various biological applications, such as antisense gene regulation strategies and the intracellular detection of biomolecules. The focus of this thesis was to characterize the nanoconjugates interaction with cultured cells and specifically the immune response to their intracellular presence. The immune response of macrophage cells to internalized nanoconjugates was studied, and due to the dense functionalization of oligonucleotides on the surface of the nanoparticle and the resulting high localized salt concentration the innate immune response to the nanoconjugates is ˜25-fold less when compared to a lipoplex carrying the same sequence. Additionally, genome-wide expression profiling was used to study the biological response of cultured cells to the nanoconjugates. The biological response of HeLa cells to gold nanoparticles stabilized by weakly bound ligands was significant, yet when these same nanoparticles were stably functionalized with covalently attached oligonucleotides the cells showed no measurable response. In human keratinocytes, the oligonucleotide sequences caused 427 genes to be differentially expressed when complexed with Dharmafect, but when the oligonucleotides were conjugated to nanoparticles only 7 genes were differentially expressed. Beyond characterizing the cellular interactions and immune response of the nanoconjugates, the optimal length of siRNA (from 19--34 base pairs) that induces the most gene knockdown while maintaining limited immune activation was determined to be 24 base pairs. Further, the SNAs were shown to be useful as a potential antiviral gene therapy by demonstrating approximately 50% knockdown of the Ebola VP35 gene. Lastly, a scanning probe-enabled method was used to rapidly

  14. Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit.

    Science.gov (United States)

    Jaakola, L; Pirttilä, A M; Halonen, M; Hohtola, A

    2001-10-01

    A simple and efficient method is described for isolating high quality RNA from bilberry fruit. The procedure is based on the use of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and beta-mercaptoethanol in an extraction buffer in order to eliminate the polysaccharides and prevent the oxidation of phenolic compounds. This method is a modification of the one described for pine trees, and yields high-quality RNA suitable for cDNA based methodologies. This method is applicable for a variety of plant tissues.

  15. Development of Sorbents for Extraction and Stabilization of Nucleic Acids

    Science.gov (United States)

    2016-09-13

    biomolecules, espe - cially DNA and RNA. The goal was to provide stabilization methods for reagents and targets in order to allow for a wider range of...within the scaffolds, and optimal methodologies for using the systems to capture, stabilize, and recover nucleic acids. Sorbent design...currently in use. In addition, stabilizing technologies can provide new sampling methodologies that can enhance the capacity for obtaining environmental

  16. Watson-Crick hydrogen bonding of unlocked nucleic acids.

    Science.gov (United States)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-11-15

    We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Los Alamos sequence analysis package for nucleic acids and proteins.

    OpenAIRE

    Kanehisa, M I

    1982-01-01

    An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a large-scale database can be used for comparative studies on sequence and structural homologies in order to find unnoted information stored i...

  18. Different Polar Metabolites and Protein Profiles between High- and Low-Quality Japanese Ginjo Sake.

    Directory of Open Access Journals (Sweden)

    Kei Takahashi

    Full Text Available Japanese ginjo sake is a premium refined sake characterized by a pleasant fruity apple-like flavor and a sophisticated taste. Because of technical difficulties inherent in brewing ginjo sake, off-flavors sometimes occur. However, the metabolites responsible for off-flavors as well as those present or absent in higher quality ginjo sake remain uncertain. Here, the relationship between 202 polar chemical compounds in sake identified using capillary electrophoresis coupled with time-of-flight mass spectrometry and its organoleptic properties, such as quality and off-flavor, was examined. First, we found that some off-flavored sakes contained higher total amounts of metabolites than other sake samples. The results also identified that levels of 2-oxoglutaric acid and fumaric acid, metabolites in the tricarboxylic acid cycle, were highly but oppositely correlated with ginjo sake quality. Similarly, pyridoxine and pyridoxamine, co-enzymes for amino transferase, were also highly but oppositely correlated with ginjo sake quality. Additionally, pyruvic acid levels were associated with good quality as well. Compounds involved in the methionine salvage cycle, oxidative glutathione derivatives, and amino acid catabolites were correlated with low quality. Among off-flavors, an inharmonious bitter taste appeared attributable to polyamines. Furthermore, protein analysis displayed that a diversity of protein components and yeast protein (triosephosphate isomerase, TPI leakage was linked to the overall metabolite intensity in ginjo sake. This research provides insight into the relationship between sake components and organoleptic properties.

  19. Quality metrics in high-dimensional data visualization: an overview and systematization.

    Science.gov (United States)

    Bertini, Enrico; Tatu, Andrada; Keim, Daniel

    2011-12-01

    In this paper, we present a systematization of techniques that use quality metrics to help in the visual exploration of meaningful patterns in high-dimensional data. In a number of recent papers, different quality metrics are proposed to automate the demanding search through large spaces of alternative visualizations (e.g., alternative projections or ordering), allowing the user to concentrate on the most promising visualizations suggested by the quality metrics. Over the last decade, this approach has witnessed a remarkable development but few reflections exist on how these methods are related to each other and how the approach can be developed further. For this purpose, we provide an overview of approaches that use quality metrics in high-dimensional data visualization and propose a systematization based on a thorough literature review. We carefully analyze the papers and derive a set of factors for discriminating the quality metrics, visualization techniques, and the process itself. The process is described through a reworked version of the well-known information visualization pipeline. We demonstrate the usefulness of our model by applying it to several existing approaches that use quality metrics, and we provide reflections on implications of our model for future research. © 2010 IEEE

  20. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  1. PARENTS AS TUTORS FIRST AND PRINCIPAL TO CREATE HIGH-QUALITY HUMAN RESOURCES

    Directory of Open Access Journals (Sweden)

    Agus Ria Kumara

    2015-10-01

    Full Text Available AbstractThe change of new era means that each individual always evolves.Developments marked with the demands of improving the quality of human resources in its different aspects.Nation character very much dependent on the quality of human resources are.The character of quality need to fostered since an early age.There are two factors that influence character, which is innate from within yourselves sons of and views the children of the world it does possess, such as knowledge, experience, moral principles accepted, guidance, parent-child interaction and briefing.A positive environment will form the positive character also on child.The process begins with the conditions develop the character of the private tua as an influential figure to be a bust children. Keywords: character, parent, high-quality human resources

  2. Electromigration behavior of nucleic acids in capillary electrophoresis under pulsed-field conditions.

    Science.gov (United States)

    Li, Zhenqing; Liu, Chenchen; Dou, Xiaoming; Ni, Yi; Wang, Jiaxuan; Yamaguchi, Yoshinori

    2014-02-28

    We have presented a study focused on the migration pattern of double-stranded DNA (dsDNA) and RNA under pulsed field conditions. By calculating the dependence of nucleic acid mobility on its molecular size in a double logarithm plot, we found that (I) dsDNA molecules proceeded by a sigmoidal migration regime which was probably related to Ogston sieving, transition regime, and reptation model. Furthermore, the transition regime disappeared if DNA was resolved in a higher molecular mass HEC. (II) The migration pattern of RNA was relevant to the denaturant used for separation. When RNA was denatured by acetic acid, its mobility parabolically declined with its molecular size. The mobility was linearly decreased with the molecular size if urea was employed as denaturant. (III) RNA may migrate by Ogston, reptation without orientation mechanism when denatured by urea, whereas these two models were not suitable for RNA if denatured by acetic acid. Even though the electrophoretic conditions of PFCE were varied, the sigmoidal, linear, parabolic migration patterns could still be observed. (IV) Under certain modulation depth, the migration time (Tm) of acetic acid decreased with the increase of average separation voltage (Va), and when RNA denatured in 4.0M urea, Tm showed a linear correlation with Va. (V) The mobility of nucleic acids increased with the growth of artificial temperature in the capillary volume due to the decrease in the viscosity of the polymer. This is the first systematic and comparative research of high molecular mass nucleic acids in PFCE, which provides us deep insight into RNA and DNA migration behavior under pulsed electric field conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Effect of high hydrostatic pressure on overall quality parameters of watermelon juice.

    Science.gov (United States)

    Liu, Y; Zhao, X Y; Zou, L; Hu, X S

    2013-06-01

    High hydrostatic pressure as a kind of non-thermal processing might maintain the quality of thermo-sensitive watermelon juice. So, the effect of high hydrostatic pressure treatment on enzymes and quality of watermelon juice was investigated. After high hydrostatic pressure treatment, the activities of polyphenol oxidase, peroxidase, and pectin methylesterase of juice decreased significantly with the pressure (P  0.05). No significant difference was observed in lycopene and total phenolics after high hydrostatic pressure treatment when compared to the control (P > 0.05). Cloudiness and viscosity increased with pressure (P  0.05). a*- and b*-value both unchanged after high hydrostatic pressure treatment (P > 0.05) while L*-value increased but the values had no significant difference among treated juices. Browning degree after high hydrostatic pressure treatment decreased with increase in pressure and treatment time (P high hydrostatic pressure had little effect on color of juice. The results of this study demonstrated the efficacy of high hydrostatic pressure in inactivating enzymes and maintaining the quality of watermelon juice.

  4. Exome sequencing generates high quality data in non-target regions

    Directory of Open Access Journals (Sweden)

    Guo Yan

    2012-05-01

    Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

  5. Providing high-quality care in primary care settings: how to make trade-offs.

    Science.gov (United States)

    Beaulieu, Marie-Dominique; Geneau, Robert; Del Grande, Claudio; Denis, Jean-Louis; Hudon, Eveline; Haggerty, Jeannie L; Bonin, Lucie; Duplain, Réjean; Goudreau, Johanne; Hogg, William

    2014-05-01

    To gain a deeper understanding of how primary care (PC) practices belonging to different models manage resources to provide high-quality care. Multiple-case study embedded in a cross-sectional study of a random sample of 37 practices. Three regions of Quebec. Health care professionals and staff of 5 PC practices. Five cases showing above-average results on quality-of-care indicators were purposefully selected to contrast on region, practice size, and PC model. Data were collected using an organizational questionnaire; the Team Climate Inventory, which was completed by health care professionals and staff; and 33 individual interviews. Detailed case histories were written and thematic analysis was performed. The core common feature of these practices was their ongoing effort to make trade-offs to deliver services that met their vision of high-quality care. These compromises involved the same 3 areas, but to varying degrees depending on clinic characteristics: developing a shared vision of high-quality care; aligning resource use with that vision; and balancing professional aspirations and population needs. The leadership of the physician lead was crucial. The external environment was perceived as a source of pressure and dilemmas rather than as a source of support in these matters. Irrespective of their models, PC practices' pursuit of high-quality care is based on a vision in which accessibility is a key component, balanced by appropriate management of available resources and of external environment expectations. Current PC reforms often create tensions rather than support PC practices in their pursuit of high-quality care. Copyright© the College of Family Physicians of Canada.

  6. MEASURING THE QUALITY OF THE HIGH EDUCATION IN THE REPUBLIC OF MACEDONIA

    Directory of Open Access Journals (Sweden)

    Elizabeta Mitreva

    2016-01-01

    Full Text Available The question of quality of private and public high educational institutions in the Republic of Macedonia is being asked every academic year and results in numerous public debates which very often lead to stereotyping of individual institutions. This paper provides a comparative overview of the situation in the private and public high education system in the country through the analysis of subjective and objective indicators based on which a comparison is made between two types of high education institutions. The instruments used in the comparative analysis of subjective and objective indicators are statistical data, application of the SWOT method for comparative analysis between the units, as well as usage of various methods and techniques to improve the quality of high education. This comparative analysis raises questions and offers recommendations for the potential improvement of the quality of work of these institutions. The intent is to encourage continuous comparative evaluation and proposing practices for continuous development and growth of quality in the high education in the country.

  7. The effect of water stress on super-high- density 'Koroneiki' olive oil quality.

    Science.gov (United States)

    Dag, Arnon; Naor, Amos; Ben-Gal, Alon; Harlev, Guy; Zipori, Isaac; Schneider, Doron; Birger, Reuven; Peres, Moti; Gal, Yoni; Kerem, Zohar

    2015-08-15

    Over the last two decades, the area of cultivated super-high-density olive orchards has increased rapidly. Water stress is an important tool in super-high-density orchards to reduce tree growth and promote suitability for overhead mechanical harvesters. Little is known regarding the effect of water stress in super-high-density orchards on oil quality parameters. In this study the effect of irrigation rate on oil quality parameters was evaluated in a six-year-old super-high-density 'Koreneiki' olive orchard for five consecutive seasons. Five water status levels, determined by irrigating in order to maintain various midday stem water potential threshold values (-1.5, -2, -2.5, -3 and -4 MPa), were applied during the oil accumulation stage. The MUFA/PUFA ratio and free fatty acid content generally decreased as a function of increasing tree water stress. In most seasons a reduction in polyphenols was found with decreasing irrigation level. Peroxide value was not affected by the water stress level. The present study demonstrates that limiting irrigation and exposure of olive trees to water stress in a super-high-density orchard lowers free fatty acid content and therefore benefits oil quality. However, the decreased MUFA/PUFA ratio and the reduction in polyphenol content that were also found under increased water stress negatively influence oil quality. © 2014 Society of Chemical Industry.

  8. Air Quality Standards for Particulate Matter (PM) at high altitude cities.

    Science.gov (United States)

    Bravo Alvarez, H; Sosa Echeverria, R; Sanchez Alvarez, P; Krupa, S

    2013-02-01

    The Air Quality Standards for Particulate Matter (PM) at high altitude urban areas in different countries, must consider the pressure and temperature due to the effect that these parameters have on the breath volume. This paper shows the importance to correct Air Quality Standards for PM considering pressure and temperature at different altitudes. Specific factors were suggested to convert the information concerning PM, from local to standard conditions, and adjust the Air Quality Standards for different high altitudes cities. The correction factors ranged from: 1.03 for Santiago de Chile to 1.47 for El Alto Bolivia. Other cities in this study include: Mexico City, México; La Paz, Bolivia; Bogota, Cali and Medellin, Colombia; Quito, Ecuador and Cuzco, Peru. If these corrections are not considered, the atmospheric concentrations will be underestimated. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Quality and performance of laser cutting with a high power SM fiber laser

    DEFF Research Database (Denmark)

    Kristiansen, Morten; Selchau, Jacob; Olsen, F. O.

    2013-01-01

    The introduction of high power single mode fiber lasers allows for a beam of high power and a good beam quality factor (M2 ” 1.2), compared to the multimode fiber lasers often utilised in macro laser metal cutting. This paper describes fundamental studies of macro laser metal cutting with a single...... mode fiber laser to study the performance of such lasers in terms of cut quality and process performance. Linear cut experiments have been performed applying a 3kW single mode fiber laser and varying the following parameters: laser power, cutting speed, focal length, focus position, cutting gas...... influence the cut quality and the maximum cutting speed in the investigated parameter space. Furthermore the achieved cutting performance is benchmarked to laser cutting with other types of lasers, CO2-lasers, disc-lasers as well as multimode fiber lasers....

  10. Three-dimensional dictionary-based deblocking for high-quality stereoscopic view generation

    Science.gov (United States)

    Jung, Cheolkon; Qi, Hongtao; Sun, Zengzeng; Jiao, Licheng

    2013-10-01

    Image quality and depth perception rates in three-dimensional television (3-D TV) are undesirably decreased by coding due to the loss of high-frequency components caused by a block-based discrete cosine transform transform. Representative coding artifacts are blocking artifacts that seriously degrade the picture quality and depth perception rates. We propose a new blocking artifact reduction method in 3-D TV using an overcomplete 3-D dictionary. We first generate the overcomplete 3-D dictionary from natural and depth images using the k-singular value decomposition algorithm. Then, we perform deblocking using the 3-D dictionary after estimating an error threshold of the objective function by the third-order polynomial fitting. Experimental results demonstrate that the proposed method can effectively reduce annoying blocking artifacts in compressed 3-D images, i.e., video-plus-depth, and generate high-quality 3-D stereoscopic views.

  11. A formalin-free method for stabilizing cells for nucleic acid amplification, hybridization and next-generation sequencing.

    Science.gov (United States)

    Qin, Jianbing; Sanmann, Jennifer N; Kittrell, Jeff S; Althof, Pamela A; Kaspar, Erin E; Hunsley, Bradford A

    2015-12-09

    Formalin has been widely used by pathology laboratories. Its carcinogenicity has led researchers to explore formalin substitutes. Streck Cell Preservative (SCP) is a formalin-free preservative that can preserve cellular antigens. This study was undertaken to investigate the effects of cell preservation using SCP on nucleic acid amplification, hybridization, and next-generation sequencing (NGS) as compared to control frozen cells and cells fixed in the traditional cell and tissue fixative, 10 % neutral buffered formalin (NBF). The breast cancer cell line, SKBR-3, was used as a model system. Prior to nucleic acid extraction and fluorescence in situ hybridization (FISH), cells were fixed in SCP or NBF overnight at room temperature with frozen cells in parallel. Analysis showed that similar DNA extraction yields and amplification profiles determined by PCR in SCP preserved cells and control frozen cells, whereas NBF preserved cells had decreased DNA yield and impaired PCR amplification. Molecular cytogenetic studies by FISH technique indicated that the ratios of ERBB2 (HER-2/neu) signals to the chromosome 17 centromere (CEP17) were comparable for frozen cells and SCP preserved cells. The fluorescence images of both SCP fixed and control frozen cells were also clear and comparable. On the contrary, the same analysis was unsuccessful with NBF preserved cells due to poor hybridization quality. Our data also demonstrated that SCP had negligible effect on NGS testing. We conclude that SCP can be used as an alternative to NBF as a preservative for maintaining the integrity of nucleic acids for nucleic acid amplification, sequencing and FISH analysis.

  12. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

    Science.gov (United States)

    Hu, Ruifeng; Sun, Xiaobo

    2016-08-01

    Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

  13. msmsEval: tandem mass spectral quality assignment for high-throughput proteomics

    Directory of Open Access Journals (Sweden)

    Cartwright Hugh M

    2007-02-01

    Full Text Available Abstract Background In proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for these programs have become prohibitive, particularly in searches for modified proteins. Recently, methods to limit the number of spectra to be searched based on spectral quality have been proposed by different research groups, but rankings of spectral quality have thus far been based on arbitrary cut-off values. In this work, we develop a more readily interpretable spectral quality statistic by providing probability values for the likelihood that spectra will be identifiable. Results We describe an application, msmsEval, that builds on previous work by statistically modeling the spectral quality discriminant function using a Gaussian mixture model. This allows a researcher to filter spectra based on the probability that a spectrum will ultimately be identified by database searching. We show that spectra that are predicted by msmsEval to be of high quality, yet remain unidentified in standard database searches, are candidates for more intensive search strategies. Using a well studied public dataset we also show that a high proportion (83.9% of the spectra predicted by msmsEval to be of high quality but that elude standard search strategies, are in fact interpretable. Conclusion msmsEval will be useful for high-throughput proteomics projects and is freely available for download from http://proteomics.ucd.ie/msmseval. Supports Windows, Mac OS X and Linux/Unix operating systems.

  14. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity.

    Science.gov (United States)

    Martin, Sandra L; Bushman, Diane; Wang, Fei; Li, Patrick Wai-Lun; Walker, Ann; Cummiskey, Jessica; Branciforte, Dan; Williams, Mark C

    2008-10-01

    L1 is a ubiquitous interspersed repeated sequence in mammals that achieved its high copy number by autonomous retrotransposition. Individual L1 elements within a genome differ in sequence and retrotransposition activity. Retrotransposition requires two L1-encoded proteins, ORF1p and ORF2p. Chimeric elements were used to map a 15-fold difference in retrotransposition efficiency between two L1 variants from the mouse genome, T(FC) and T(Fspa), to a single amino acid substitution in ORF1p, D159H. The steady-state levels of L1 RNA and protein do not differ significantly between these two elements, yet new insertions are detected earlier and at higher frequency in T(FC), indicating that it converts expressed L1 intermediates more effectively into new insertions. The two ORF1 proteins were purified and their nucleic acid binding and chaperone activities were examined in vitro. Although the RNA and DNA oligonucleotide binding affinities of these two ORF1 proteins were largely indistinguishable, D159 was significantly more effective as a nucleic acid chaperone than H159. These findings support a requirement for ORF1p nucleic acid chaperone activity at a late step during L1 retrotransposition, extend the region of ORF1p that is known to be critical for its functional interactions with nucleic acids, and enhance understanding of nucleic acid chaperone activity.

  15. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes.

    Science.gov (United States)

    Largy, Eric; Hamon, Florian; Teulade-Fichou, Marie-Paule

    2012-05-01

    Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Porous Silicon and Polymer Nanocomposites for Delivery of Peptide Nucleic Acids as anti-microRNA Therapies

    OpenAIRE

    Beavers, Kelsey R.; Werfel, Thomas A.; Shen, Tianwei; Kavanaugh, Taylor E.; Kilchrist, Kameron V.; Mares, Jeremy W.; Fain, Joshua S.; Wiese, Carrie B.; Kasey C. Vickers; Weiss, Sharon M.; Duvall, Craig L.

    2016-01-01

    Self-assembled polymer/porous silicon nanocomposites overcome intracellular and systemic barriers for in vivo application of peptide nucleic acid (PNA) anti-microRNA therapeutics. Porous silicon (PSi) is leveraged as a biodegradable scaffold with high drug cargo loading capacity. Functionalization with a diblock polymer improves PSi nanoparticle colloidal stability, in vivo pharmacokinetics, and intracellular bioavailability through endosomal escape, enabling PNA to inhibit miR-122 in vivo.

  17. Recent developments in high-quality drying of vegetables, fruits, and aquatic products.

    Science.gov (United States)

    Zhang, Min; Chen, Huizhi; Mujumdar, Arun S; Tang, Juming; Miao, Song; Wang, Yuchuan

    2017-04-13

    Fresh foods like vegetables, fruits, and aquatic products have high water activity and they are highly heat-sensitive and easily degradable. Dehydration is one of the most common methods used to improve food shelf-life. However, drying methods used for food dehydration must not only be efficient and economic but also yield high-quality products based on flavor, nutrients, color, rehydration, uniformity, appearance, and texture. This paper reviews some new drying technologies developed for dehydration of vegetables, fruits, and aquatic products. These include: infrared drying, microwave drying, radio frequency drying, electrohydrodynamic drying, etc., as well as hybrid drying methods combining two or more different drying techniques. A comprehensive review of recent developments in high-quality drying of vegetables, fruits and aquatic products is presented and recommendations are made for future research.

  18. High-Density, High-Resolution, Low-Cost Air Quality Sensor Networks for Urban Air Monitoring

    Science.gov (United States)

    Mead, M. I.; Popoola, O. A.; Stewart, G.; Bright, V.; Kaye, P.; Saffell, J.

    2012-12-01

    Monitoring air quality in highly granular environments such as urban areas which are spatially heterogeneous with variable emission sources, measurements need to be made at appropriate spatial and temporal scales. Current routine air quality monitoring networks generally are either composed of sparse expensive installations (incorporating e.g. chemiluminescence instruments) or higher density low time resolution systems (e.g. NO2 diffusion tubes). Either approach may not accurately capture important effects such as pollutant "hot spots" or adequately capture spatial (or temporal) variability. As a result, analysis based on data from traditional low spatial resolution networks, such as personal exposure, may be inaccurate. In this paper we present details of a sophisticated, low-cost, multi species (gas phase, speciated PM, meteorology) air quality measurement network methodology incorporating GPS and GPRS which has been developed for high resolution air quality measurements in urban areas. Sensor networks developed in the Centre for Atmospheric Science (University of Cambridge) incorporated electrochemical gas sensors configured for use in urban air quality studies operating at parts-per-billion (ppb) levels. It has been demonstrated that these sensors can be used to measure key air quality gases such as CO, NO and NO2 at the low ppb mixing ratios present in the urban environment (estimated detection limits CO and NO and NO2. Mead et al (submitted Aug., 2012)). Based on this work, a state of the art multi species instrument package for deployment in scalable sensor networks has been developed which has general applicability. This is currently being employed as part of a major 3 year UK program at London Heathrow airport (the Sensor Networks for Air Quality (SNAQ) Heathrow project). The main project outcome is the creation of a calibrated, high spatial and temporal resolution data set for O3, NO, NO2, SO2, CO, CO2, VOCstotal, size-speciated PM, temperature, relative

  19. High performance catalytic distillation using CNTs-based holistic catalyst for production of high quality biodiesel

    Science.gov (United States)

    Zhang, Dongdong; Wei, Dali; Li, Qi; Ge, Xin; Guo, Xuefeng; Xie, Zaiku; Ding, Weiping

    2014-01-01

    For production of biodiesel from bio oils by heterogeneous catalysis, high performance catalysts of transesterification and the further utilization of glycerol have been the two points of research. The process seemed easy, however, has never been well established. Here we report a novel design of catalytic distillation using hierachically integrated CNTs-based holistic catalyst to figure out the two points in one process, which shows high performance both for the conversion of bio oils to biodiesel and, unexpectedly, for the conversion of glycerol to more valuable chemicals at the same time. The method, with integration of nano, meso to macro reactor, has overwhelming advantages over common technologies using liquid acids or bases to catalyze the reactions, which suffer from the high cost of separation and unsolved utilization of glycerol. PMID:24503897

  20. High performance catalytic distillation using CNTs-based holistic catalyst for production of high quality biodiesel.

    Science.gov (United States)

    Zhang, Dongdong; Wei, Dali; Li, Qi; Ge, Xin; Guo, Xuefeng; Xie, Zaiku; Ding, Weiping

    2014-02-07

    For production of biodiesel from bio oils by heterogeneous catalysis, high performance catalysts of transesterification and the further utilization of glycerol have been the two points of research. The process seemed easy, however, has never been well established. Here we report a novel design of catalytic distillation using hierachically integrated CNTs-based holistic catalyst to figure out the two points in one process, which shows high performance both for the conversion of bio oils to biodiesel and, unexpectedly, for the conversion of glycerol to more valuable chemicals at the same time. The method, with integration of nano, meso to macro reactor, has overwhelming advantages over common technologies using liquid acids or bases to catalyze the reactions, which suffer from the high cost of separation and unsolved utilization of glycerol.