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Sample records for high yield oligonucleotide

  1. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    Science.gov (United States)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  2. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

    DEFF Research Database (Denmark)

    Chen, Fuqiang; Pruett-Miller, Shondra M; Huang, Yuping

    2011-01-01

    Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point...

  3. Gene Assembly from Chip-Synthesized Oligonucleotides

    Science.gov (United States)

    Eroshenko, Nikolai; Kosuri, Sriram; Marblestone, Adam H; Conway, Nicholas; Church, George M.

    2012-01-01

    De novo synthesis of long double-stranded DNA constructs has a myriad of applications in biology and biological engineering. However, its widespread adoption has been hindered by high costs. Cost can be significantly reduced by using oligonucleotides synthesized on high-density DNA chips. However, most methods for using off-chip DNA for gene synthesis have failed to scale due to the high error rates, low yields, and high chemical complexity of the chip-synthesized oligonucleotides. We have recently demonstrated that some commercial DNA chip manufacturers have improved error rates, and that the issues of chemical complexity and low yields can be solved by using barcoded primers to accurately and efficiently amplify subpools of oligonucleotides. This article includes protocols for computationally designing the DNA chip, amplifying the oligonucleotide subpools, and assembling 500-800 basepair (bp) constructs. PMID:25077042

  4. Specific yield, High Plains aquifer

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This raster data set represents specific-yield ranges in the High Plains aquifer of the United States. The High Plains aquifer underlies 112.6 million acres (176,000...

  5. High Yielding Microbubble Production Method

    Directory of Open Access Journals (Sweden)

    Joe Fiabane

    2016-01-01

    Full Text Available Microfluidic approaches to microbubble production are generally disadvantaged by low yield and high susceptibility to (microchannel blockages. This paper presents an alternative method of producing microbubbles of 2.6 μm mean diameter at concentrations in excess of 30 × 106 mL−1. In this method, the nitrogen gas flowing inside the liquid jet is disintegrated into spray of microbubble when air surrounding this coflowing nitrogen gas-liquid jet passes through a 100 μm orifice at high velocity. Resulting microbubble foam has the polydispersity index of 16%. Moreover, a ratio of mean microbubble diameter to channel width ratio was found to be less than 0.025, which substantially alleviates the occurrence of blockages during production.

  6. Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection

    Directory of Open Access Journals (Sweden)

    Lewis A. Fraser

    2015-12-01

    Full Text Available The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR and Fluorescence Activated Cell Sorting (FACS to high-throughput selection techniques. Within these systems, monoclonal aptamer microbeads can be individually generated and assayed to assess aptamer candidate fitness thereby helping eliminate stochastic effects which are common to classical SELEX techniques. Such techniques have given rise to aptamers with 1000 times greater binding affinities when compared to traditional SELEX. Another emerging technique is Fluorescence Activated Droplet Sorting (FADS whereby selection does not rely on binding capture allowing evolution of a greater diversity of aptamer properties such as fluorescence or enzymatic activity. Within this review we explore examples and applications of oligonucleotide functionalised microbeads in aptamer selection and reflect upon new opportunities arising for aptamer science.

  7. Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection.

    Science.gov (United States)

    Fraser, Lewis A; Kinghorn, Andrew B; Tang, Marco S L; Cheung, Yee-Wai; Lim, Bryce; Liang, Shaolin; Dirkzwager, Roderick M; Tanner, Julian A

    2015-12-01

    The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR) and Fluorescence Activated Cell Sorting (FACS) to high-throughput selection techniques. Within these systems, monoclonal aptamer microbeads can be individually generated and assayed to assess aptamer candidate fitness thereby helping eliminate stochastic effects which are common to classical SELEX techniques. Such techniques have given rise to aptamers with 1000 times greater binding affinities when compared to traditional SELEX. Another emerging technique is Fluorescence Activated Droplet Sorting (FADS) whereby selection does not rely on binding capture allowing evolution of a greater diversity of aptamer properties such as fluorescence or enzymatic activity. Within this review we explore examples and applications of oligonucleotide functionalised microbeads in aptamer selection and reflect upon new opportunities arising for aptamer science.

  8. Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects

    National Research Council Canada - National Science Library

    Radelof, U; Hennig, S; Seranski, P; Steinfath, M; Ramser, J; Reinhardt, R; Poustka, A; Francis, F; Lehrach, H

    1998-01-01

    .... To reduce the overall effort and cost of those projects and to accelerate the sequencing throughput, we have developed an efficient, high throughput oligonucleotide fingerprinting protocol to select...

  9. Oligonucleotide Antiviral Therapeutics: Antisense and RNA Interference for Highly Pathogenic RNA Viruses

    National Research Council Canada - National Science Library

    Spurgers, Kevin B; Sharkey, C. M; Warfield, Kelly L; Bavari, Sina

    2008-01-01

    .... Important advances in the field include the characterization of RNA interference in mammalian cells and chemical modifications that can dramatically increase the in vivo stability of therapeutic oligonucleotides...

  10. Identification of GalNAc-Conjugated Antisense Oligonucleotide Metabolites Using an Untargeted and Generic Approach Based on High Resolution Mass Spectrometry.

    Science.gov (United States)

    Husser, Christophe; Brink, Andreas; Zell, Manfred; Müller, Martina B; Koller, Erich; Schadt, Simone

    2017-06-20

    Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl galactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells. A highly sensitive method was developed to identify metabolites of oligonucleotides using capillary flow liquid chromatography with column switching coupled to a high resolution Orbitrap Fusion mass spectrometer. Detection of GalNAc-conjugated oligonucleotides and their metabolites was achieved by combining full scan MS with two parallel MS2 experiments, one data-dependent scan and an untargeted MS2 experiment (all ion fragmentation) applying high collision energy. In the all ion fragmentation scan, a diagnostic fragment originating from the phosphorothioate backbone (O2PS-: m/z 94.936) was formed efficiently upon collisional activation. Based on this fragment an accurate determination of metabolites of oligonucleotides was achieved, independent of their sequence or conjugation in an untargeted but highly selective manner. The method was effectively applied to investigate uptake and metabolism of GalNAc-conjugated oligonucleotides in incubations of primary rat hepatocytes; the elucidation of expected and unexpected degradation products was achieved in subnanomolar range.

  11. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

    Directory of Open Access Journals (Sweden)

    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  12. Oligonucleotides containing a piperazino-modified 2'-amino-LNA monomer exhibit very high duplex stability and remarkable nuclease resistance

    DEFF Research Database (Denmark)

    Lou, Chenguang; Vester, Birte; Wengel, Jesper

    2015-01-01

    Incorporation of a piperazino-modified 2'-amino-LNA monomer (PipLNA-T) into oligonucleotides conferred very high affinity and base-pairing selectivity towards complementary DNA and RNA strands. Furthermore, one PipLNA-T modification provided a robust nuclease resistance that safeguarded three...

  13. MerMade: an oligodeoxyribonucleotide synthesizer for high throughput oligonucleotide production in dual 96-well plates.

    Science.gov (United States)

    Rayner, S; Brignac, S; Bumeister, R; Belosludtsev, Y; Ward, T; Grant, O; O'Brien, K; Evans, G A; Garner, H R

    1998-07-01

    We have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. The machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. The run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nM. The reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. The two plates are placed in separate vacuum chucks and mounted on an xy table. Each well in turn is positioned under the appropriate reagent injection line and the reagent is injected by switching a dedicated valve. All aspects of machine operation are controlled by a Macintosh computer, which also guides the user through the startup and shutdown procedures, provides a continuous update on the status of the run, and facilitates a number of service procedures that need to be carried out periodically. Over 25,000 oligos have been synthesized for use in dye terminator sequencing reactions, polymerase chain reactions (PCRs), hybridization, and RT-PCR. Oligos up to 100 bases in length have been made with a coupling efficiency in excess of 99%. These machines, working in conjunction with our oligo prediction code are particularly well suited to application in automated high throughput genomic sequencing.

  14. Assembly of Designed Oligonucleotides: a useful tool in synthetic biology for creating high-quality combinatorial DNA libraries.

    Science.gov (United States)

    Acevedo-Rocha, Carlos G; Reetz, Manfred T

    2014-01-01

    The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3.

  15. Factors influencing the separation of oligonucleotides using reversed-phase/ion-exchange mixed-mode high performance liquid chromatography columns.

    Science.gov (United States)

    Biba, Mirlinda; Jiang, Eileen; Mao, Bing; Zewge, Daniel; Foley, Joe P; Welch, Christopher J

    2013-08-23

    New mixed-mode columns consisting of reversed-phase and ion-exchange separation modes were evaluated for the analysis of short RNA oligonucleotides (∼20mers). Conventional analysis for these samples typically involves using two complementary methods: strong anion-exchange liquid chromatography (SAX-LC) for separation based on charge, and ion-pair reversed-phase liquid chromatography (IP-RPLC) for separation based on hydrophobicity. Recently introduced mixed-mode high performance liquid chromatography (HPLC) columns combine both reversed-phase and ion-exchange modes, potentially offering a simpler analysis by combining the benefits of both separation modes into a single method. Analysis of a variety of RNA oligonucleotide samples using three different mixed-mode stationary phases showed some distinct benefits for oligonucleotide separation and analysis. When using these mixed-mode columns with typical IP-RPLC mobile phase conditions, such as ammonium acetate or triethylammonium acetate as the primary ion-pair reagent, the separation was mainly based on the IP-RPLC mode. However, when changing the mobile phase conditions to those more typical for SAX-LC, such as salt gradients with NaCl or NaBr, very different separation patterns were observed due to mixed-mode interactions. In addition, the Scherzo SW-C18 and SM-C18 columns with sodium chloride or sodium bromide salt gradients also showed significant improvements in peak shape. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. High yield fabrication of fluorescent nanodiamonds

    Science.gov (United States)

    Boudou, Jean-Paul; Curmi, Patrick; Jelezko, Fedor; Wrachtrup, Joerg; Aubert, Pascal; Sennour, Mohamed; Balasubramanian, Gopalakrischnan; Reuter, Rolf; Thorel, Alain; Gaffet, Eric

    2009-01-01

    A new fabrication method to produce homogeneously fluorescent nanodiamonds with high yields is described. The powder obtained by high energy ball milling of fluorescent high pressure, high temperature diamond microcrystals was converted in a pure concentrated aqueous colloidal dispersion of highly crystalline ultrasmall nanoparticles with a mean size less than or equal to 10 nm. The whole fabrication yield of colloidal quasi-spherical nanodiamonds was several orders of magnitude higher than those previously reported starting from microdiamonds. The results open up avenues for the industrial cost-effective production of fluorescent nanodiamonds with well-controlled properties. PMID:19451687

  17. Studies on oligonucleotides and analogues: from drug candidates to components for high-ordered supramolecular structures

    OpenAIRE

    Nici, Fabrizia

    2016-01-01

    Last century advances in molecular biology and biotechnologies enabled us to understand the exceptionally broad repertoire of nucleic acids functions. For a long time DNA was regarded as a rigid molecule with the sole purpose to store and transmit genetic information. However, this idea has been completely overtaken with the discovery of the catalytic activity of specific RNA molecules. In effect, the early 1970s and the embryonic works on antisense oligonucleotides paved the way for our c...

  18. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.

    Science.gov (United States)

    Urban, Alexander Eckehart; Korbel, Jan O; Selzer, Rebecca; Richmond, Todd; Hacker, April; Popescu, George V; Cubells, Joseph F; Green, Roland; Emanuel, Beverly S; Gerstein, Mark B; Weissman, Sherman M; Snyder, Michael

    2006-03-21

    Deletions and amplifications of the human genomic sequence (copy number polymorphisms) are the cause of numerous diseases and a potential cause of phenotypic variation in the normal population. Comparative genomic hybridization (CGH) has been developed as a useful tool for detecting alterations in DNA copy number that involve blocks of DNA several kilobases or larger in size. We have developed high-resolution CGH (HR-CGH) to detect accurately and with relatively little bias the presence and extent of chromosomal aberrations in human DNA. Maskless array synthesis was used to construct arrays containing 385,000 oligonucleotides with isothermal probes of 45-85 bp in length; arrays tiling the beta-globin locus and chromosome 22q were prepared. Arrays with a 9-bp tiling path were used to map a 622-bp heterozygous deletion in the beta-globin locus. Arrays with an 85-bp tiling path were used to analyze DNA from patients with copy number changes in the pericentromeric region of chromosome 22q. Heterozygous deletions and duplications as well as partial triploidies and partial tetraploidies of portions of chromosome 22q were mapped with high resolution (typically up to 200 bp) in each patient, and the precise breakpoints of two deletions were confirmed by DNA sequencing. Additional peaks potentially corresponding to known and novel additional CNPs were also observed. Our results demonstrate that HR-CGH allows the detection of copy number changes in the human genome at an unprecedented level of resolution.

  19. High quantum yield III-V photoanodes

    Energy Technology Data Exchange (ETDEWEB)

    Erne, B.H.

    1995-09-01

    The morphological and electrochemical aspects of the (photo)anodic etching of the n-type 3-5 semiconductors GaP, GaAs, and InP are examined. The etched surfaces are characterized experimentally by electrochemical and other methods. Particular attention is paid to the anodic photocurrent quantum yield. The processes investigated lead to a large enhancement of the quantum yield or give a quantum yield in excess of unity, hence the title of the thesis. The quantum yield of a photoanode is determined by processes both in the bulk and at the surface of the semiconductor. The competition between charge separation and recombination in the bulk of the semiconductor determines the fraction of the photogenerated holes which reaches the surface, and surface processes determine the fraction of those holes which contributes to current in the external circuit. Chapter 2 examines the increased effective absorption due to surface roughness and the increase in the diffusion length of holes associated with photocurrent flow, two effects which can cause charge separation to compete more effectively with bulk recombination. Chapter 3 considers the influence of the wavelength of the light used for photoanodic etching on the morphology. Chapter 4 demonstrates that porous etching may lead to an enormous enhancement of the photoresponse. The influence of surface (electro)chemistry on the quantum yield is investigated for n-type InP electrodes by means of optoelectrical impedance spectroscopy. Even in indifferent electrolyte, InP photoanodes have remarkably high quantum yields in excess of unity, due to electron injection by dissolution intermediates (Chapter 5). Interaction with a chemical etchant can increase the quantum yield even further (Chapter 6). The main conclusions of the thesis are summarized in Chapter 7. 52 figs., 180 refs., 1 appendix

  20. Methods for high yield production of terpenes

    Energy Technology Data Exchange (ETDEWEB)

    Kutchan, Toni; Higashi, Yasuhiro; Feng, Xiaohong

    2017-01-03

    Provided are enhanced high yield production systems for producing terpenes in plants via the expression of fusion proteins comprising various combinations of geranyl diphosphate synthase large and small subunits and limonene synthases. Also provided are engineered oilseed plants that accumulate monoterpene and sesquiterpene hydrocarbons in their seeds, as well as methods for producing such plants, providing a system for rapidly engineering oilseed crop production platforms for terpene-based biofuels.

  1. Peptide-LNA oligonucleotide conjugates

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Hansen, Lykke Haastrup; Vester, Birte

    2013-01-01

    Although peptide-oligonucleotide conjugates (POCs) are well-known for nucleic acids delivery and therapy, reports on internal attachment of peptides to oligonucleotides are limited in number. To develop a convenient route for preparation of internally labeled POCs with improved biomedical...... properties, peptides were introduced into oligonucleotides via a 2'-alkyne-2'-amino-LNA scaffold. Derivatives of methionine- and leucine-enkephalins were chosen as model peptides of mixed amino acid content, which were singly and doubly incorporated into LNA/DNA strands using highly efficient copper......(i)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry. DNA/RNA target binding affinity and selectivity of the resulting POCs were improved in comparison to LNA/DNA mixmers and unmodified DNA controls. This clearly demonstrates that internal attachment of peptides to oligonucleotides can significantly...

  2. Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm

    Directory of Open Access Journals (Sweden)

    Malyj Wasyl

    2005-08-01

    Full Text Available Abstract Background Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear 1. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray data sets. Results Isomap discovered low-dimensional structures embedded in the Affymetrix microarray data sets. These structures correspond to and help to interpret biological phenomena present in the data. This analysis provides examples of temporal, spatial, and functional processes revealed by the Isomap algorithm. In a spinal cord injury data set, Isomap discovers the three main modalities of the experiment – location and severity of the injury and the time elapsed after the injury. In a multiple tissue data set, Isomap discovers a low-dimensional structure that corresponds to anatomical locations of the source tissues. This model is capable of describing low- and high-resolution differences in the same model, such as kidney-vs.-brain and differences between the nuclei of the amygdala, respectively. In a high-throughput drug screening data set, Isomap discovers the monocytic and granulocytic differentiation of myeloid cells and maps several chemical compounds on the two-dimensional model. Conclusion Visualization of Isomap models provides useful tools for exploratory analysis of microarray data sets. In most instances, Isomap models explain more of the variance present in the microarray data than PCA or MDS. Finally, Isomap is a promising new algorithm for class discovery and class prediction in high-density oligonucleotide data sets.

  3. Correlation test to assess low-level processing of high-density oligonucleotide microarray data

    Directory of Open Access Journals (Sweden)

    Bergh Jonas

    2005-03-01

    Full Text Available Abstract Background There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data. Results We analyzed coregulation between genes in order to detect insufficient normalization between arrays, where coregulation is measured in terms of statistical correlation. In a large collection of genes, a random pair of genes should have on average zero correlation, hence allowing a correlation test. For all data sets that we evaluated, and the three most commonly used low-level processing procedures including MAS5, RMA and MBEI, the housekeeping-gene normalization failed the test. For a real clinical data set, RMA and MBEI showed significant correlation for absent genes. We also found that a second round of normalization on the probe set level improved normalization significantly throughout. Conclusion Previous evaluation of low-level processing in the literature has been limited to artificial spike-in and mixture data sets. In the absence of a known gold-standard, the correlation criterion allows us to assess the appropriateness of low-level processing of a specific data set and the success of normalization for subsets of genes.

  4. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

    Science.gov (United States)

    Barrera, Leah; Benner, Chris; Tao, Yong-Chuan; Winzeler, Elizabeth; Zhou, Yingyao

    2004-04-20

    To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of probe-level expression data for each probe set and compare replicates of these values across conditions using a form of the t-test or rank sum test. Here we propose the use of a statistical method that takes advantage of the built-in redundancy architecture of high-density oligonucleotide arrays. We employ parametric and nonparametric variants of two-way analysis of variance (ANOVA) on probe-level data to account for probe-level variation, and use the false-discovery rate (FDR) to account for simultaneous testing on thousands of genes (multiple testing problem). Using publicly available data sets, we systematically compared the performance of parametric two-way ANOVA and the nonparametric Mack-Skillings test to the t-test and Wilcoxon rank-sum test for detecting differentially expressed genes at varying levels of fold change, concentration, and sample size. Using receiver operating characteristic (ROC) curve comparisons, we observed that two-way methods with FDR control on sample sizes with 2-3 replicates exhibits the same high sensitivity and specificity as a t-test with FDR control on sample sizes with 6-9 replicates in detecting at least two-fold change. Our results suggest that the two-way ANOVA methods using probe-level data are substantially more powerful tests for detecting differential gene expression than corresponding methods for probe-set level data.

  5. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Tao Yong-Chuan

    2004-04-01

    Full Text Available Abstract Background To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of probe-level expression data for each probe set and compare replicates of these values across conditions using a form of the t-test or rank sum test. Here we propose the use of a statistical method that takes advantage of the built-in redundancy architecture of high-density oligonucleotide arrays. Results We employ parametric and nonparametric variants of two-way analysis of variance (ANOVA on probe-level data to account for probe-level variation, and use the false-discovery rate (FDR to account for simultaneous testing on thousands of genes (multiple testing problem. Using publicly available data sets, we systematically compared the performance of parametric two-way ANOVA and the nonparametric Mack-Skillings test to the t-test and Wilcoxon rank-sum test for detecting differentially expressed genes at varying levels of fold change, concentration, and sample size. Using receiver operating characteristic (ROC curve comparisons, we observed that two-way methods with FDR control on sample sizes with 2–3 replicates exhibits the same high sensitivity and specificity as a t-test with FDR control on sample sizes with 6–9 replicates in detecting at least two-fold change. Conclusions Our results suggest that the two-way ANOVA methods using probe-level data are substantially more powerful tests for detecting differential gene expression than corresponding methods for probe-set level data.

  6. Radioisotopic, Culture-Based, and Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir†

    Science.gov (United States)

    Bonch-Osmolovskaya, Elizaveta A.; Miroshnichenko, Margarita L.; Lebedinsky, Alexander V.; Chernyh, Nikolai A.; Nazina, Tamara N.; Ivoilov, Valery S.; Belyaev, Sergey S.; Boulygina, Eugenia S.; Lysov, Yury P.; Perov, Alexander N.; Mirzabekov , Andrei D.; Hippe, Hans; Stackebrandt, Erko; L'Haridon, Stéphane; Jeanthon, Christian

    2003-01-01

    Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H2S liter−1 day−1 occurred at 60 and 80°C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH4 liter−1 day−1. Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected. PMID:14532074

  7. High-Yield Functional Molecular Electronic Devices.

    Science.gov (United States)

    Jeong, Hyunhak; Kim, Dongku; Xiang, Dong; Lee, Takhee

    2017-07-25

    An ultimate goal of molecular electronics, which seeks to incorporate molecular components into electronic circuit units, is to generate functional molecular electronic devices using individual or ensemble molecules to fulfill the increasing technical demands of the miniaturization of traditional silicon-based electronics. This review article presents a summary of recent efforts to pursue this ultimate aim, covering the development of reliable device platforms for high-yield ensemble molecular junctions and their utilization in functional molecular electronic devices, in which distinctive electronic functionalities are observed due to the functional molecules. In addition, other aspects pertaining to the practical application of molecular devices such as manufacturing compatibility with existing complementary metal-oxide-semiconductor technology, their integration, and flexible device applications are also discussed. These advances may contribute to a deeper understanding of charge transport characteristics through functional molecular junctions and provide a desirable roadmap for future practical molecular electronics applications.

  8. The tetramethylammonium chloride method for screening of cDNA libraries using highly degenerate oligonucleotides obtained by backtranslation of amino-acid sequences

    DEFF Research Database (Denmark)

    Honoré, B; Madsen, Peder; Leffers, H

    1993-01-01

    We describe a method for screening of cDNA libraries with highly degenerate oligonucleotides using tetramethylammonium chloride (TMAC). This method is a convenient alternative to using probes generated by the polymerase chain reaction (PCR), especially when these cannot easily be made. Nylon...

  9. Combining high biodiversity with high yields in tropical agroforests

    Science.gov (United States)

    Clough, Yann; Barkmann, Jan; Juhrbandt, Jana; Kessler, Michael; Wanger, Thomas Cherico; Anshary, Alam; Buchori, Damayanti; Cicuzza, Daniele; Darras, Kevin; Putra, Dadang Dwi; Erasmi, Stefan; Pitopang, Ramadhanil; Schmidt, Carsten; Schulze, Christian H.; Seidel, Dominik; Steffan-Dewenter, Ingolf; Stenchly, Kathrin; Vidal, Stefan; Weist, Maria; Wielgoss, Arno Christian; Tscharntke, Teja

    2011-01-01

    Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substantial opportunities for wildlife-friendly management. Species richness of trees, fungi, invertebrates, and vertebrates did not decrease with yield. Moderate shade, adequate labor, and input level can be combined with a complex habitat structure to provide high biodiversity as well as high yields. Although livelihood impacts are held up as a major obstacle for wildlife-friendly farming in the tropics, our results suggest that in some situations, agroforests can be designed to optimize both biodiversity and crop production benefits without adding pressure to convert natural habitat to farmland. PMID:21536873

  10. The high stability of the triple helices formed between short purine oligonucleotides and SIV/HIV-2 vpx genes is determined by the targeted DNA structure.

    Science.gov (United States)

    Svinarchuk, F; Monnot, M; Merle, A; Malvy, C; Fermandjian, S

    1995-10-11

    In our previous works we have shown that the oligonucleotides 5'-GGGGAGGGGGAGG-3' and 5'-GGAGGGGGAGGGG-3' give very stable and specific triplexes with their target double stranded DNAs [Svinarchuk, F., Bertrand, J.-R. and Malvy, C. (1994) Nucleic Acids Res., 22, 3742-3747; Svinarchuk, F., Paoletti, J. and Malvy, C. (1995) J. Biol. Chem., 270, 14 068-14,071]. The target for the invariable part of these oligonucleotides, 5'-GGAGGGGGAGG-3', is found in a highly conserved 20 bp long purine/pyrimidine tract of the vpx gene of the SIV and HIV-2 viruses and could be a target for oligonucleotide directed antivirus therapy. Here were report on the ability of four purine oligonucleotides with different lengths (11-, 14-, 17- and 20-mer) to form triplexes with the purine/pyrimidine stretch of the vpx gene. Triplex formation was tested by joint dimethyl sulfate (DMS) footprint, gel-retardation assay, circular dichroism (CD) and UV-melting studies. Dimethyl sulfate footprint studies revealed the antiparallel orientation of the third strand to the purine strand of the Watson-Crick duplex. However, the protection of the guanines at the ends of the target sequence decreased as the length of the third strand oligonucleotide increased. Melting temperature studies provided profiles with only one transition for all of the triplexes. The melting temperatures of the triplexes were found to be the same as for the targeted duplex in the case of the 11- and 14-mer third strands while for the 17- and 20-mer third strands the melting temperature of the triplexes were correspondingly 4 and 8 degrees C higher than for the duplex. Heating and cooling melting curves were reversible for all of the tested triplexes except one with the 20-mer third strand oligonucleotide. Circular dichroism spectra showed the ability of the target DNA to adopt an A-like DNA conformation. Upon triplex formation the A-DNA form becomes even more pronounced. This effect depends on the length of the third strand

  11. Triple X syndrome in a patient with partial lipodystrophy discovered using a high-density oligonucleotide microarray: a case report

    Directory of Open Access Journals (Sweden)

    Lanktree Matthew B

    2009-08-01

    Full Text Available Abstract Introduction Patients with lipodystrophy experience selective or generalized atrophy of adipose tissue. The disruption of lipid metabolism results in an increased risk for development of metabolic syndrome and coronary artery disease. Currently, the mutations responsible for approximately half of lipodystrophy patients are known, but new techniques and examination of different types of genetic variation may identify new disease-causing mechanisms. Case presentation A 53-year-old woman of African descent was referred to a tertiary care endocrinology clinic for treatment of severe insulin resistance, treatment-resistant hypertension and dyslipidemia. After all known lipodystrophy-causing mutations were excluded by DNA sequencing, the patient was found to have triple X syndrome after an initial investigation into copy number variation using a high-density oligonucleotide microarray. The patient also had a previously unobserved duplication of 415 kilobases of chromosome 5q33.2. This is the first case report of a patient with lipodystrophy who also had triple X syndrome. Conclusion While we cannot make a direct link between the presence of triple X syndrome and partial lipodystrophy, if unrelated, this is an extremely rare convergence of syndromes. This patient poses an interesting possibility regarding the influence triple X syndrome may have on an individual with other underlying lipodystrophy susceptibility. Finally, impending large-scale case-control and cohort copy number variation investigations will, as a by-product, further document the prevalence of triple X syndrome in various patient groups.

  12. MerMade: An Oligodeoxyribonucleotide Synthesizer for High Throughput Oligonucleotide Production in Dual 96-Well Plates

    Science.gov (United States)

    Rayner, Simon; Brignac, Stafford; Bumeister, Ron; Belosludtsev, Yuri; Ward, Travis; Grant, O’dell; O’Brien, Kevin; Evans, Glen A.; Garner, Harold R.

    1998-01-01

    We have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. The machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. The run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nm. The reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. The two plates are placed in separate vacuum chucks and mounted on an xy table. Each well in turn is positioned under the appropriate reagent injection line and the reagent is injected by switching a dedicated valve. All aspects of machine operation are controlled by a Macintosh computer, which also guides the user through the startup and shutdown procedures, provides a continuous update on the status of the run, and facilitates a number of service procedures that need to be carried out periodically. Over 25,000 oligos have been synthesized for use in dye terminator sequencing reactions, polymerase chain reactions (PCRs), hybridization, and RT–PCR. Oligos up to 100 bases in length have been made with a coupling efficiency in excess of 99%. These machines, working in conjunction with our oligo prediction code are particularly well suited to application in automated high throughput genomic sequencing. PMID:9685322

  13. Combining high biodiversity with high yields in tropical agroforests

    OpenAIRE

    Clough, Y; Barkmann, J.; Juhrbandt, J.; Kessler, M.; Wanger, T.C.; Anshary, A.; Buchori, D.; Cicuzza, D.; Darras, K; Putra, D. D.; S. Erasmi; Pitopang, R.; Schmidt, C; Schulze, C H; Seidel, D

    2011-01-01

    Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substan...

  14. Willow yield is highly dependent on clone and site

    DEFF Research Database (Denmark)

    Ugilt Larsen, Søren; Jørgensen, Uffe; Lærke, Poul Erik

    2014-01-01

    , differing considerably in soil type, climatic conditions and management. Compared to the best clone, the yield was up to 36 % lower for other clones across sites and up to 51 % lower within sites. Tordis was superior to other clones with dry matter yields between 5.2 and 10.2 Mg ha−1 year−1 during the first...... to the best site, yield level was up to 51 % lower on other sites across all clones, probably due to combined effects of differences in soil type, climate and management. Thus, willow yield depends both on the use of high-yielding clones and on the combined site effects of soil, climate, and management.......Use of high-yielding genotypes is one of the means to achieve high yield and profitability in willow (Salix spp.) short rotation coppice. This study investigated the performance of eight willow clones (Inger, Klara, Linnea, Resolution, Stina, Terra Nova, Tora, Tordis) on five Danish sites...

  15. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis.

    Science.gov (United States)

    Boyle, Shelagh; Rodesch, Matthew J; Halvensleben, Heather A; Jeddeloh, Jeffrey A; Bickmore, Wendy A

    2011-10-01

    The ability to visualize specific DNA sequences, on chromosomes and in nuclei, by fluorescence in situ hybridization (FISH) is fundamental to many aspects of genetics, genomics and cell biology. Probe selection is currently limited by the availability of DNA clones or the appropriate pool of DNA sequences for PCR amplification. Here, we show that liquid-phase probe pools from sequence capture technology can be adapted to generate fluorescently labelled pools of oligonucleotides that are very effective as repeat-free FISH probes in mammalian cells. As well as detection of small (15 kb) and larger (100 kb) specific loci in both cultured cells and tissue sections, we show that complex oligonucleotide pools can be used as probes to visualize features of nuclear organization. Using this approach, we dramatically reveal the disposition of exons around the outside of a chromosome territory core and away from the nuclear periphery.

  16. Hybridization with synthetic oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Szostak, J.W.; Stiles, J.I.; Tye, B.K.; Sherman, F.; Wu, R.

    1978-01-01

    Procedures are described for the use of synthetic oligonucleotides for Southern blot experiments and gene bank screening, and the effect of various mismatches on the efficiency of hybridization is demonstrated. The following topics are discussed: sensitivity vs. specificity, hybridization of a 12-mer to the lambda endolysin gene; hybridization of oligonucleotide probes to the E. coli lac operator; hybridization of synthetic probes to the CYC1 gene of yeast; and cloning eucaryotic genes. (HLW)

  17. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Madsen, Charlotte Stahl; Jensen, Knud Jørgen

    2015-01-01

    Functionalized synthetic oligonucleotides are finding growing applications in research, clinical studies, and therapy. However, it is not easy to prepare them in a biocompatible and highly efficient manner. We report a new strategy to synthesize oligonucleotides with promising nucleic acid...... conditions with fluorophore, peptide, and carbohydrate azide derivatives. In thermal denaturation studies, the modified probes showed specific binding to complementary DNA and RNA targets. Finally, we demonstrated the pH sensitivity of the new rhodamine-based fluorescent probes in vitro and rationalize our...... results by electronic structure calculations. Functionalized oligonucleotides were prepared in good yields by protein-mediated CuAAC click reactions for the first time with a human copper-binding chaperon. The carbohydrate, peptide, and fluorescent derivatives display high binding affinity and selectivity...

  18. High yield DNA fragmentation using cyclical hydrodynamic shearing

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Spang, Peter; Roeser, Tina; Nieto, Benjamin; Guasch, Francesc; Corbera, Antoni Homs; van den Berg, Albert; Carlen, Edwin

    2013-01-01

    We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and

  19. Electron detachment dissociation (EDD) pathways in oligonucleotides

    Science.gov (United States)

    Kinet, Catherine; Gabelica, Valérie; Balbeur, Dorothée; de Pauw, Edwin

    2009-06-01

    Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are two novel fragmentation methods yielding radicals from negatively charged ions. With the goal of comparing EDD, EPD and the more traditional collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) fragmentation processes in oligonucleotides, we studied here the EDD fragmentation pathways of oligonucleotides of varying length. We chose polythymine oligonucleotides because these are the least prone to secondary structure formation, and found complete sequence coverage by EDD for up to dT20. We also found that the fragmentation pathways change with oligonucleotide length: electron detachment is a mandatory step in the fragmentation of larger sequences, while shorter oligonucleotides can also fragment via direct electronic or vibrational excitation by the electrons. This is supported by (1) the fact that continuous ejection of the charge-reduced species does not totally prevent fragmentation of short oligonucleotides dT5 and dT6, (2) the fact that CID and EDD fragments are more similar for small oligonucleotides (although double resonance experiments show that they are not all issued from the same mechanisms), and (3) the fact that electron-induced dissociation (EID) of singly charged dT3 and dT4 gives similar fragments as EDD of doubly charged dT5 and dT6. Finally, the detachment efficiency as a function of the nature of the nucleobase was studied. The effect of base on electron detachment in EDD (G > T > A > C) is different than in EPD (G > A > C > T), indicating different electron loss mechanisms.

  20. [Study on High-yield Cultivation Measures for Arctii Fructus].

    Science.gov (United States)

    Liu, Shi-yong; Jiang, Xiao-bo; Wang, Tao; Sun, Ji-ye; Hu, Shang-qin; Zhang, Li

    2015-02-01

    To find out the high yield cultivation measures for Arctii Fructus. Completely randomized block experiment design method was used in the field planting, to analyze the effect of different cultivation way on agronomic characters, phenological phase,quality and quantity of Arctii Fructus. Arctium lappa planted on August 28 had the best results of plant height, thousand seeds weight and yield. The highest yield of Arctii Fructus was got at the density of 1,482 plants/667 m2. Arctiin content was in an increase trend with the planting time delay and planting density increasing. The plant height, thousand seeds weight, yield and arctiin content by split application of fertilizer were significantly higher than that by one-time fertilization. Compared with open field Arctium lappa, plant height, yield, arctiin content and relative water content of plastic film mulching Arctium lappa was higher by 7.74%, 10.87%, 6.38% and 24.20%, respectively. In the topping Arctium lappa, the yield was increased by 11.09%, with 39. 89% less branching number. Early planting time and topping shortened the growth cycle of Arctium lappa plant. The high-yield cultivation measures of Arctii Fructus are: around August 28 to sowing, planting density of 1 482 plants/667 m2, split application of fertilizer for four times, covering film on surface of the soil and topping in bolting.

  1. Ultrasensitive detection of Hg{sup 2+} using oligonucleotide-functionalized AlGaN/GaN high electron mobility transistor

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Junjie [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031 (China); Division of Nanobiomedicine, Key Laboratory for Nano-Bio Interface Research, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123 (China); Li, Jiadong; Miao, Bin; Wu, Dongmin, E-mail: dmwu2008@sinano.ac.cn [i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125 (China); Key Laboratory of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123 (China); Wang, Jine; Pei, Renjun, E-mail: rjpei2011@sinano.ac.cn [Division of Nanobiomedicine, Key Laboratory for Nano-Bio Interface Research, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123 (China); Wu, Zhengyan, E-mail: zywu@ipp.ac.cn [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031 (China)

    2014-08-25

    An oligonucleotide-functionalized ion sensitive AlGaN/GaN high electron mobility transistor (HEMT) was fabricated to detect trace amounts of Hg{sup 2+}. The advantages of ion sensitive AlGaN/GaN HEMT and highly specific binding interaction between Hg{sup 2+} and thymines were combined. The current response of this Hg{sup 2+} ultrasensitive transistor was characterized. The current increased due to the accumulation of Hg{sup 2+} ions on the surface by the highly specific thymine-Hg{sup 2+}-thymine recognition. The dynamic linear range for Hg{sup 2+} detection has been determined in the concentrations from 10{sup −14} to 10{sup −8} M and a detection limit below 10{sup −14} M level was estimated, which is the best result of AlGaN/GaN HEMT biosensors for Hg{sup 2+} detection till now.

  2. High yielding synthesis of N-ethyl dehydroamino acids.

    Science.gov (United States)

    Monteiro, Luís S; Suárez, Ana S

    2012-10-01

    Recently we reported the use of a sequence of alkylation and dehydration methodologies to obtain N-ethyl-α, β-dehydroamino acid derivatives. The application of this N-alkylation procedure to several methyl esters of β,β-dibromo and β-bromo, β-substituted dehydroamino acids protected with standard amine protecting groups was subsequently reported. The corresponding N-ethyl, β-bromo dehydroamino acid derivatives were obtained in fair to high yields and some were used as substrates in Suzuki cross-coupling reactions to give N-ethyl, β,β-disubstituted dehydroalanine derivatives. Herein, we further explore N-ethylation of β-halo dehydroamino acid derivatives using triethyloxonium tetrafluoroborate as alkylating agent, but substituting N,N-diisopropylethylamine for potassium tert-butoxide as auxiliary base. In these conditions, for all β-halo dehydroamino acid derivatives, reactions were complete and the N-ethylated derivative could be isolated in high yield. This method was also applied for N-ethylation of non-halogenated dehydroamino acids. Again, with all compounds the reactions were complete and the N-ethyl dehydroamino acid derivatives could be isolated in high yields. Some of these N-ethyl dehydroamino acid methyl ester derivatives were converted in high yields to their corresponding acids and coupled to an amino acid methyl ester to give N-ethyl dehydrodipeptide derivatives in good yields. Thus, this method constitutes a general procedure for high yielding synthesis of N-ethylated dehydroamino acids, which can be further applied in peptide synthesis.

  3. Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides.

    Science.gov (United States)

    Eeltink, Sebastiaan; Wouters, Sam; Dores-Sousa, José Luís; Svec, Frantisek

    2017-05-19

    This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Executive Summary High-Yield Scenario Workshop Series Report

    Energy Technology Data Exchange (ETDEWEB)

    Leslie Park Ovard; Thomas H. Ulrich; David J. Muth Jr.; J. Richard Hess; Steven Thomas; Bryce Stokes

    2009-12-01

    To get a collective sense of the impact of research and development (R&D) on biomass resource availability, and to determine the feasibility that yields higher than baseline assumptions used for past assessments could be achieved to support U.S. energy independence, an alternate “High-Yield Scenario” (HYS) concept was presented to industry experts at a series of workshops held in December 2009. The workshops explored future production of corn/agricultural crop residues, herbaceous energy crops (HECs), and woody energy crops (WECs). This executive summary reports the findings of that workshop.

  5. Development of high-yield influenza A virus vaccine viruses.

    Science.gov (United States)

    Ping, Jihui; Lopes, Tiago J S; Nidom, Chairul A; Ghedin, Elodie; Macken, Catherine A; Fitch, Adam; Imai, Masaki; Maher, Eileen A; Neumann, Gabriele; Kawaoka, Yoshihiro

    2015-09-02

    Vaccination is one of the most cost-effective ways to prevent infection. Influenza vaccines propagated in cultured cells are approved for use in humans, but their yields are often suboptimal. Here, we screened A/Puerto Rico/8/34 (PR8) virus mutant libraries to develop vaccine backbones (defined here as the six viral RNA segments not encoding haemagglutinin and neuraminidase) that support high yield in cell culture. We also tested mutations in the coding and regulatory regions of the virus, and chimeric haemagglutinin and neuraminidase genes. A combination of high-yield mutations from these screens led to a PR8 backbone that improved the titres of H1N1, H3N2, H5N1 and H7N9 vaccine viruses in African green monkey kidney and Madin-Darby canine kidney cells. This PR8 backbone also improves titres in embryonated chicken eggs, a common propagation system for influenza viruses. This PR8 vaccine backbone thus represents an advance in seasonal and pandemic influenza vaccine development.

  6. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  7. FLUORESCENT OLIGONUCLEOTIDES CONTAINING A NOVEL PERYLENE 2 '-AMINO-alpha-L-LNA MONOMER: SYNTHESIS AND ANALYTICAL POTENTIAL

    DEFF Research Database (Denmark)

    Astakhova, I. V.; Kumar, T. S.; Wengel, J.

    2011-01-01

    efficiency of the resulting perylene-2'-amino-alpha-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomer T* showed high binding affinity towards...... incorporations of monomers T* was quenched (quantum yield Phi(F) = 0.21) relative to duplexes of this probe with complementary DNA and RNA (Phi(F) = 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues...... sequences containing monomers T* at 5'- and 3'-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose...

  8. A comparative analysis of existing oligonucleotides selection ...

    African Journals Online (AJOL)

    SERVER

    2007-07-04

    Jul 4, 2007 ... rence of poly-morphisms in genomic DNA (Schena,. 1996). Two DNA chips format currently in wide use are, the cDNA array format and high density synthetic oligo- nucleotide array format (oligos). The oligonucleotide app- roach has some advantages because it allows the user to design oligos for each ...

  9. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

    Directory of Open Access Journals (Sweden)

    Townsend Henrik J

    2005-11-01

    Full Text Available Abstract High-density oligonucleotide (oligo arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L. Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal

  10. Multiplex pairwise assembly of array-derived DNA oligonucleotides.

    Science.gov (United States)

    Klein, Jason C; Lajoie, Marc J; Schwartz, Jerrod J; Strauch, Eva-Maria; Nelson, Jorgen; Baker, David; Shendure, Jay

    2016-03-18

    While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192-252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131-250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput 'Dial-Out PCR' protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Development of high-yield influenza B virus vaccine viruses.

    Science.gov (United States)

    Ping, Jihui; Lopes, Tiago J S; Neumann, Gabriele; Kawaoka, Yoshihiro

    2016-12-20

    The burden of human infections with influenza A and B viruses is substantial, and the impact of influenza B virus infections can exceed that of influenza A virus infections in some seasons. Over the past few decades, viruses of two influenza B virus lineages (Victoria and Yamagata) have circulated in humans, and both lineages are now represented in influenza vaccines, as recommended by the World Health Organization. Influenza B virus vaccines for humans have been available for more than half a century, yet no systematic efforts have been undertaken to develop high-yield candidates. Therefore, we screened virus libraries possessing random mutations in the six "internal" influenza B viral RNA segments [i.e., those not encoding the major viral antigens, hemagglutinin (HA) and neuraminidase NA)] for mutants that confer efficient replication. Candidate viruses that supported high yield in cell culture were tested with the HA and NA genes of eight different viruses of the Victoria and Yamagata lineages. We identified combinations of mutations that increased the titers of candidate vaccine viruses in mammalian cells used for human influenza vaccine virus propagation and in embryonated chicken eggs, the most common propagation system for influenza viruses. These influenza B virus vaccine backbones can be used for improved vaccine virus production.

  12. High-yield secretion of multiple client proteins in Aspergillus.

    Science.gov (United States)

    Segato, Fernando; Damásio, André R L; Gonçalves, Thiago A; de Lucas, Rosymar C; Squina, Fabio M; Decker, Stephen R; Prade, Rolf A

    2012-07-15

    Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degrading enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. High-Yield Secretion of Multiple Client Proteins in Aspergillus

    Energy Technology Data Exchange (ETDEWEB)

    Segato, F.; Damasio, A. R. L.; Goncalves, T. A.; de Lucas, R. C.; Squina, F. M.; Decker, S. R.; Prade, R. A.

    2012-07-15

    Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degrading enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished.

  14. High yield production of extracellular recombinant levansucrase by Bacillus megaterium.

    Science.gov (United States)

    Korneli, Claudia; Biedendieck, Rebekka; David, Florian; Jahn, Dieter; Wittmann, Christoph

    2013-04-01

    In this study, a high yield production bioprocess with recombinant Bacillus megaterium for the production of the extracellular enzyme levansucrase (SacB) was developed. For basic optimization of culture parameters and nutrients, a recombinant B. megaterium reporter strain that produced green fluorescent protein under control of a vector-based xylose-inducible promoter was used. It enabled efficient microtiter plate-based screening via fluorescence analysis. A pH value of pH 6, 20 % of dissolved oxygen, 37 °C, and elevated levels of biotin (100 μg L(-1)) were found optimal with regard to high protein yield and reduced overflow metabolism. Among the different compounds tested, fructose and glycerol were identified as the preferred source of carbon. Subsequently, the settings were transferred to a B. megaterium strain recombinantly producing levansucrase SacB based on the plasmid-located xylose-inducible expression system. In shake flask culture under the optimized conditions, the novel strain already secreted the target enzyme in high amounts (14 U mL(-1) on fructose and 17.2 U mL(-1) on glycerol). This was further increased in high cell density fed-batch processes up to 55 U mL(-1), reflecting a levansucrase concentration of 0.52 g L(-1). This is 100-fold more than previous efforts for this enzyme in B. megaterium and more than 10-fold higher than reported values of other extracellular protein produced in this microorganism so far. The recombinant strain could also handle raw glycerol from biodiesel industry which provided the same amount and quality of the recombinant protein and suggests future implementation into existing biorefinery concepts.

  15. 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.

  16. 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.

  17. The use of urinary and kidney SILAM proteomics to monitor kidney response to high dose morpholino oligonucleotides in the mdx mouse

    Directory of Open Access Journals (Sweden)

    Aiping Zhang

    2015-01-01

    Full Text Available Phosphorodiamidate morpholino oligonucleotides (PMO are used as a promising exon-skipping gene therapy for Duchenne muscular dystrophy (DMD. One potential complication of high dose PMO therapy is its transient accumulation in the kidneys. Therefore new urinary biomarkers are needed to monitor this treatment. Here, we carried out a pilot proteomic profiling study using stable isotope labeling in mammals (SILAM strategy to identify new biomarkers to monitor the effect of PMO on the kidneys of the dystrophin deficient mouse model for DMD (mdx-23. We first assessed the baseline renal status of the mdx-23 mouse compared to the wild type (C57BL10 mouse, and then followed the renal outcome of mdx-23 mouse treated with a single high dose intravenous PMO injection (800 mg/kg. Surprisingly, untreated mdx-23 mice showed evidence of renal injury at baseline, which was manifested by albuminuria, increased urine output, and changes in established urinary biomarker of acute kidney injury (AKI. The PMO treatment induced further transient renal injury, which peaked at 7 days, and returned to almost the baseline status at 30 days post-treatment. In the kidney, the SILAM approach followed by western blot validation identified changes in Meprin A subunit alpha at day 2, then returned to normal levels at days 7 and 30 after PMO injection. In the urine, SILAM approach identified an increase in Clusterin and γ-glutamyl transpeptidase 1 as potential candidates to monitor the transient renal accumulation of PMO. These results, which were confirmed by Western blots or ELISA, demonstrate the value of the SILAM approach to identify new candidate biomarkers of renal injury in mdx-23 mice treated with high dose PMO.

  18. Film quantum yields of EUV& ultra-high PAG photoresists

    Energy Technology Data Exchange (ETDEWEB)

    Hassanein, Elsayed; Higgins, Craig; Naulleau, Patrick; Matyi, Richard; Gallatin, Greg; Denbeaux, Gregory; Antohe, Alin; Thackery, Jim; Spear, Kathleen; Szmanda, Charles; Anderson, Christopher N.; Niakoula, Dimitra; Malloy, Matthew; Khurshid, Anwar; Montgomery, Cecilia; Piscani, Emil C.; Rudack, Andrew; Byers, Jeff; Ma, Andy; Dean, Kim; Brainard, Robert

    2008-01-10

    Base titration methods are used to determine C-parameters for three industrial EUV photoresist platforms (EUV-2D, MET-2D, XP5496) and twenty academic EUV photoresist platforms. X-ray reflectometry is used to measure the density of these resists, and leads to the determination of absorbance and film quantum yields (FQY). Ultrahigh levels ofPAG show divergent mechanisms for production of photo acids beyond PAG concentrations of 0.35 moles/liter. The FQY of sulfonium PAGs level off, whereas resists prepared with iodonium PAG show FQY s that increase beyond PAG concentrations of 0.35 moles/liter, reaching record highs of 8-13 acids generatedlEUV photons absorbed.

  19. Maximize rhamnolipid production with low foaming and high yield.

    Science.gov (United States)

    Sodagari, Maysam; Invally, Krutika; Ju, Lu-Kwang

    2018-03-01

    Rhamnolipids are well-known microbial surfactants with many potential applications. Their production cost, however, remains high due to the severe foaming tendency in aerobic fermentation and the relatively low productivity and yield. In this study, we assessed the boundaries set by these constraints after optimization of basic parameters such as dissolved oxygen concentration (DO), pH and carbon sources. DO 10% and pH 5.5-5.7 were found optimal; cell growth and/or rhamnolipid production were slower at lower DO (5%) or pH (5.0) while foaming became hard to control at higher DO (30%) or pH (6.0 and 6.5). Although the Pseudomonas aeruginosa strain used was selected for its high rhamnolipid production from glycerol as substrate, soybean oil was still found to be a better substrate that increased specific rhamnolipid productivity to 25.8mg/g cells-h from the glycerol-supported maximum of 8.9mg/g cells-h. In addition, the foam volume was approximately halved by using soybean oil instead of glycerol as substrate. Analysis by liquid chromatography coupled with mass spectrometry revealed that rhamnolipid compositions from the two carbon sources were also very different, with primarily (82%) monorhamnolipids from soybean oil and more (64%) dirhamnolipids from glycerol. The optimized fermentation produced 42g/l rhamnolipids at a yield of approximately 47% and a volumetric productivity of 220mg/l-h. These values are among the highest reported. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Highly sensitive electrochemical sensor for mercury(II) ions by using a mercury-specific oligonucleotide probe and gold nanoparticle-based amplification.

    Science.gov (United States)

    Zhu, Zhiqiang; Su, Yuanyuan; Li, Jiang; Li, Di; Zhang, Jiong; Song, Shiping; Zhao, Yun; Li, Genxi; Fan, Chunhai

    2009-09-15

    We report a highly sensitive electrochemical sensor for the detection of Hg(2+) ions in aqueous solution by using a thymine (T)-rich, mercury-specific oligonucleotide (MSO) probe and gold nanoparticles (Au NPs)-based signal amplification. The MSO probe contains seven thymine bases at both ends and a "mute" spacer in the middle, which, in the presence of Hg(2+), forms a hairpin structure via the Hg(2+)-mediated coordination of T-Hg(2+)-T base pairs. The thiolated MSO probe is immobilized on Au electrodes to capture free Hg(2+) in aqueous media, and the MSO-bound Hg(2+) can be electrochemically reduced to Hg(+), which provides a readout signal for quantitative detection of Hg(2+). This direct immobilization strategy leads to a detection limit of 1 microM. In order to improve the sensitivity, MSO probe-modified Au NPs are employed to amplify the electrochemical signals. Au NPs are comodified with the MSO probe and a linking probe that is complementary to a capture DNA probe immobilized on gold electrodes. We demonstrated that this Au NPs-based sensing strategy brings about an amplification factor of more than 3 orders of magnitude, leading to a limit of detection of 0.5 nM (100 ppt), which satisfactorily meets the sensitivity requirement of U.S. Environmental Protection Agency (EPA). This Au NPs-based Hg(2+) sensor also exhibits excellent selectivity over a spectrum of interference metal ions. Considering the high sensitivity and selectivity of this sensor, as well as the cost-effective and portable features of electrochemical techniques, we expect this Au NPs amplified electrochemical sensor will be a promising candidate for field detection of environmentally toxic mercury.

  1. Production of cis-syn thymine-thymine cyclobutane dimer oligonucleotide in the presence of acetone photosensitizer.

    Science.gov (United States)

    Mu, Wanmeng; Han, Qingkai; Luo, Zhaofeng; Wang, Yuzhen

    2006-06-01

    cis-syn Cyclobutane pyrimidine dimer (CPD) oligonucleotide was produced by UV irradiation in the presence of acetone photosensitizer. Acetone could enhance the productivity but evidently induced the photocleavage of oligonucleotide under a long time irradiation. A statistical approach of orthogonal design was applied to optimize the preparation condition for the production of the modified oligonucleotide. Optimal conditions for maximal cis-syn CPD oligonucleotide productivity were determined based on three factors: acetone concentration, initial oligonucleotide concentration, and irradiation time at several different levels. The optimal modified oligonucleotide that this optimization could produce was 32.7%. Through analysis of 20% polyacrylamide gel electrophoresis, it was found that modified oligonucleotide migrated slightly more slowly than the parent oligonucleotide. The photoreactivation of cis-syn thymine-thymine dimer oligonucleotide displayed the selectivity of the substrate specificity of DNA photolyase with high-performance liquid chromatography (HPLC) analysis.

  2. CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Ishikawa Shumpei

    2006-02-01

    Full Text Available Abstract Background DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell. Results We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods. Conclusion Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.

  3. Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.

    Science.gov (United States)

    Kamalakaran, Sitharthan; Kendall, Jude; Zhao, Xiaoyue; Tang, Chunlao; Khan, Sohail; Ravi, Kandasamy; Auletta, Theresa; Riggs, Michael; Wang, Yun; Helland, Aslaug; Naume, Bjørn; Dimitrova, Nevenka; Børresen-Dale, Anne-Lise; Hicks, Jim; Lucito, Robert

    2009-07-01

    Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species.

  4. Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

    Directory of Open Access Journals (Sweden)

    Cam Margaret C

    2007-03-01

    Full Text Available Abstract Background Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis. Results Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. Conclusion We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.

  5. Diagnostics of Shiva Nova produced high yield thermonuclear events

    Energy Technology Data Exchange (ETDEWEB)

    Ahlstrom, H.G.; Banner, D.L.; Boyle, M.J.; Campbell, E.M.; Coleman, L.W.; Koppel, L.N.; Kornblum, H.N. Jr.; Rienecker, F.; Severyn, J.R.; Slivinsky, V.W.

    1978-01-01

    Experiments with the Shiva Nova laser facility which produce yield levels of scientific breakeven and above will result in neutron, x-ray and particle fluxes which will require specific attention to the survivability of diagnostic instrumentation. These yield levels will also allow the utilization of new diagnotics techniques which can provide detailed information on the state of the imploded fuel and pusher shells.

  6. Ovarian cysts in high-yielding dairy cows.

    Science.gov (United States)

    Braw-Tal, R; Pen, S; Roth, Z

    2009-09-15

    We examined the hormonal and morphologic changes associated with ovarian cyst formation in high-yielding dairy cows. Follicle fluid was aspirated from 90 cysts and 15 preovulatory and 18 subordinate follicles and used for hormonal determination. Pieces of cystic wall were subjected to morphologic and immunohistochemical evaluation. Cysts were characterized by low concentrations of insulin, insulin-like growth factor-I (IGF-I), and glucose and high activity of IGF binding proteins (IGFBPs). Insulin and IGF-I levels were (mean+/-SEM) 205+/-22 pg/mL and 146+/-42 ng/mL in preovulatory follicles and 3+/-1 pg/mL and 61+/-6 ng/mL in cysts, respectively (Pcysts than in preovulatory follicles. Cysts were classified into three types according to their estradiol-to-progesterone (E/P) ratio. Type 1 cysts (n=23) exhibited the highest E/P ratio (10.8+/-2.3), partial loss of granulosa cells, and severe morphologic changes in the theca interna. Expression of P(450) side-chain cleavage and P(450) 17 alpha-hydroxylase was noted in theca cells and expression of inhibin-alpha in granulosa cells. Type 2 cysts (n=35) had a low E/P ratio (0.07+/-0.02), and patches of luteal-like tissue in the cystic wall. Type 3 cysts (n=32) had an E/P ratio of 0.91+/-0.17, and no recognizable granulosa or theca cells. In summary, intrafollicular steroid levels as expressed by E/P ratio, together with IGF-I and insulin levels and morphologic changes in the follicular wall, may serve as accurate cyst-classification parameters. Because IGF-I and/or insulin play an essential role in the final stage of follicle development, it can be speculated that abnormal levels of these metabolic hormones might lead to follicle dysfunction, resulting in follicular regression or cyst formation.

  7. Nutritional status of high yielding crossbred cow around parturition

    Directory of Open Access Journals (Sweden)

    Mohammad Yousuf

    2016-03-01

    Materials and methods: Nutritional status of cows around the peri-parturient period was investigated for six months in dairy farm. Seven to eight months' pregnant cows were selected for this study. Blood samples from 24 randomly selected cows were collected at stage-1, -2 and -3. The serum was stored at -20C until analyzing glucose, total protein (TP, albumin (Alb, triglycerides (Tg, cholesterol, high density lipoprotein (HDL, low density lipoprotein (LDL, calcium (Ca, magnesium (Mg and phosphorus (P. Results: An increasing trend of glucose level was evidenced (P=0.07 during stage-1. Instead, higher levels of TP were found during stage-3 as compared to the stage-1 and -2. The Alb levels differed significantly (P<0.01 among different stages. A significantly increased (P<0.01 cholesterol, Tg, and HDL were found after parturition (stage-2 and -3 than before parturition (stage-1. LDL was significantly (P=0.02 increased during stage-2 and -3. A significantly higher level of Ca (P<0.01, Mg (P<0.01 and P (P=0.03 were present during stage-1. Glucose, TP, cholesterol and Tg were significantly higher (P<0.01 in cows two months after parturition, while Alb was found to be the highest (P<0.01 in cows immediately after parturition. An increasing trend of LDL (P=0.07 and HDL (P=0.07 were found in the cows two months after parturition. However, Ca levels were significantly (P=0.04 higher in cows two months after parturition. Conclusion: The results indicate that there is alteration of biochemical levels among the study population at three different stages, and these data may be helpful in using the necessary nutrients to the the high yielding cows around their parturition. [J Adv Vet Anim Res 2016; 3(1.000: 68-74

  8. The Radioactive Waste Management course: 14 High-yield editions

    Energy Technology Data Exchange (ETDEWEB)

    Alonso, A.; Gallego, E.; Marco, M. L.; Falcon, S.

    2003-07-01

    The doctorate course on Radioactive Waste Management was initiated in February 1988, by initiative of the Chair of Nuclear Technology, under the sponsoring of the national radioactive waste management company (ENRESA), in a fruitful collaboration between the Institute Artigas of the Technical School of Industrial Engineering and the Institute of Formation on Energy of the research centre CIEMAT. The course is also offered as a post-graduate through both institutes. After completion of fourteen consecutive editions in 2002, the course constituted a landmark in the field of nuclear education in Spain. The last edition offered, along 35 lessons published in two books, the general aspects of generation, treatment and conditioning of radioactive wastes, the basic Safety and Radiological Protection criteria, the detailed technical questions of the management of both low-intermediate.activity and the high-activity level, together with the wastes generated during decommissioning and dismantling of installations, as well as the general and institutional aspects. Experts in each field, belonging either to ENRESA, CIEMAT, the Nuclear Safety Council, the UPM and the industry, present such wide programme. A technical visit to the low and intermediate radioactive waste repository of El Cabril was also offered to the participants as part of the course, as in previous years the visit to the dismantling workers of Vandellos I NPP. More than 500 engineers and graduates in different science branches have participated in the course along 14 years, with both students and professionals belonging to ENRESA, the Nuclear Safety Council, CIEMAT and other research centers, hospitals, civil protection at different levels, service and engineering companies related with the radioactive waste management. Altogether, it is possible to say, as the title is expressed, that the course has given in these 14 years a high-production yield. (Author)

  9. Nanocrystalline silicon-based oligonucleotide chips.

    Science.gov (United States)

    Zhu, Z Q; Zhu, B; Zhang, J; Zhu, J Z; Fan, C H

    2007-04-15

    A novel oligonucleotide array sensor has been developed with nanocrystalline Si (ncSi) substrates. The ncSi was prepared by electrochemical etching technique. Our study indicated that both the binding capacity and the hybridization efficiency are dependent upon the particle size of ncSi. In contrary, the chips developed with Si substrates exhibit the lower binding capacity and hybridization efficiency. The improved performances of the sensor chips are attributed to the large specific surface area of ncSi compared to the existing conventional techniques. The sensor chips with the ncSi substrate of 13 nm-sized particle can be regenerated and reused for at least 12 times. The oligonucleotide array sensor also shows high stability, which can bear relatively the stringent conditions (e.g. 80 degrees C, 75% of relative humidity and 3.6 klx of irradiation).

  10. Lichen Symbiosis: Nature's High Yielding Machines for Induced Hydrogen Production

    Science.gov (United States)

    Papazi, Aikaterini; Kastanaki, Elizabeth; Pirintsos, Stergios; Kotzabasis, Kiriakos

    2015-01-01

    Hydrogen is a promising future energy source. Although the ability of green algae to produce hydrogen has long been recognized (since 1939) and several biotechnological applications have been attempted, the greatest obstacle, being the O2-sensitivity of the hydrogenase enzyme, has not yet been overcome. In the present contribution, 75 years after the first report on algal hydrogen production, taking advantage of a natural mechanism of oxygen balance, we demonstrate high hydrogen yields by lichens. Lichens have been selected as the ideal organisms in nature for hydrogen production, since they consist of a mycobiont and a photobiont in symbiosis. It has been hypothesized that the mycobiont’s and photobiont’s consumption of oxygen (increase of COX and AOX proteins of mitochondrial respiratory pathways and PTOX protein of chrolorespiration) establishes the required anoxic conditions for the activation of the phycobiont’s hydrogenase in a closed system. Our results clearly supported the above hypothesis, showing that lichens have the ability to activate appropriate bioenergetic pathways depending on the specific incubation conditions. Under light conditions, they successfully use the PSII-dependent and the PSII-independent pathways (decrease of D1 protein and parallel increase of PSaA protein) to transfer electrons to hydrogenase, while under dark conditions, lichens use the PFOR enzyme and the dark fermentative pathway to supply electrons to hydrogenase. These advantages of lichen symbiosis in combination with their ability to survive in extreme environments (while in a dry state) constitute them as unique and valuable hydrogen producing natural factories and pave the way for future biotechnological applications. PMID:25826211

  11. Lichen symbiosis: nature's high yielding machines for induced hydrogen production.

    Directory of Open Access Journals (Sweden)

    Aikaterini Papazi

    Full Text Available Hydrogen is a promising future energy source. Although the ability of green algae to produce hydrogen has long been recognized (since 1939 and several biotechnological applications have been attempted, the greatest obstacle, being the O2-sensitivity of the hydrogenase enzyme, has not yet been overcome. In the present contribution, 75 years after the first report on algal hydrogen production, taking advantage of a natural mechanism of oxygen balance, we demonstrate high hydrogen yields by lichens. Lichens have been selected as the ideal organisms in nature for hydrogen production, since they consist of a mycobiont and a photobiont in symbiosis. It has been hypothesized that the mycobiont's and photobiont's consumption of oxygen (increase of COX and AOX proteins of mitochondrial respiratory pathways and PTOX protein of chrolorespiration establishes the required anoxic conditions for the activation of the phycobiont's hydrogenase in a closed system. Our results clearly supported the above hypothesis, showing that lichens have the ability to activate appropriate bioenergetic pathways depending on the specific incubation conditions. Under light conditions, they successfully use the PSII-dependent and the PSII-independent pathways (decrease of D1 protein and parallel increase of PSaA protein to transfer electrons to hydrogenase, while under dark conditions, lichens use the PFOR enzyme and the dark fermentative pathway to supply electrons to hydrogenase. These advantages of lichen symbiosis in combination with their ability to survive in extreme environments (while in a dry state constitute them as unique and valuable hydrogen producing natural factories and pave the way for future biotechnological applications.

  12. Selection of common bean lines with high grain yield and high grain calcium and iron concentrations

    Directory of Open Access Journals (Sweden)

    Nerinéia Dalfollo Ribeiro

    2014-02-01

    Full Text Available Genetic improvement of common bean nutritional quality has advantages in marketing and can contribute to society as a food source. The objective of this study was to evaluate the genetic variability for grain yield, calcium and iron concentrations in grains of inbred common bean lines obtained by different breeding methods. For this, 136 F7 inbred lines were obtained using the Pedigree method and 136 F7 inbred lines were obtained using the Single-Seed Descent (SSD method. The lines showed genetic variability for grain yield, and concentrations of calcium and iron independently of the method of advancing segregating populations. The Pedigree method allows obtaining a greater number of lines with high grain yield. Selection using the SSD method allows the identification of a larger number of lines with high concentrations of calcium and iron in grains. Weak negative correlations were found between grain yield and calcium concentration (r = -0.0994 and grain yield and iron concentration (r = -0.3926. Several lines show genetic superiority for grain yield and concentrations of calcium and iron in grains and their selection can result in new common bean cultivars with high nutritional quality.

  13. CG FARRAPO: a sudangrass cultivar with high biomass and grain yields

    Directory of Open Access Journals (Sweden)

    Emilio Ghisleni Arenhardt

    2016-07-01

    Full Text Available The new sudangrass cultivar [Sorghum sudanense (Piper Stapf.] was developed by the method of selection of individual plants with progeny testing. The most important traits are high biomass yield with high grain yield.

  14. Exploring options to combine high yields with high nitrogen use efficiencies in irrigated rice in China

    NARCIS (Netherlands)

    Jing, Q.; Bouman, B.A.M.; Hengsdijk, H.; Keulen, van H.; Cao, W.

    2007-01-01

    In Jiangsu province, Southeast China, high irrigated rice yields (6-8000 kg ha(-1)) are supported by high nitrogen (N) fertilizer inputs (260-300 kg N ha(-1)) and low fertilizer N use efficiencies (recoveries of 30-35%). Improvement of fertilizer N use efficiency can increase farmers' profitability

  15. Approaches to achieve high grain yield and high resource use efficiency in rice

    Directory of Open Access Journals (Sweden)

    Jianchang YANG

    2015-06-01

    Full Text Available This article discusses approaches to simultaneously increase grain yield and resource use efficiency in rice. Breeding nitrogen efficient cultivars without sacrificing rice yield potential, improving grain fill in later-flowering inferior spikelets and enhancing harvest index are three important approaches to achieving the dual goal of high grain yield and high resource use efficiency. Deeper root distribution and higher leaf photosynthetic N use efficiency at lower N rates could be used as selection criteria to develop N-efficient cultivars. Enhancing sink activity through increasing sugar-spikelet ratio at the heading time and enhancing the conversion efficiency from sucrose to starch though increasing the ratio of abscisic acid to ethylene in grains during grain fill could effectively improve grain fill in inferior spikelets. Several practices, such as post-anthesis controlled soil drying, an alternate wetting and moderate soil drying regime during the whole growing season, and non-flooded straw mulching cultivation, could substantially increase grain yield and water use efficiency, mainly via enhanced remobilization of stored carbon from vegetative tissues to grains and improved harvest index. Further research is needed to understand synergistic interaction between water and N on crop and soil and the mechanism underlying high resource use efficiency in high-yielding rice.

  16. Engineered polymer-supported synthesis of 3'-carboxyalkyl-modified oligonucleotides and their applications in the construction of biochips for diagnosis of the diseases.

    Science.gov (United States)

    Patnaik, Satyakam; Dash, Sandip K; Sethi, Dalip; Kumar, Ashok; Gupta, K C; Kumar, Pradeep

    2012-03-21

    An engineered polymer support 5 has been prepared for the solid-phase assembly of 3'-carboxyalkyl-modified oligonucleotides using commonly available reagents. A two-step deprotection procedure resulted in the quantitative cleavage of oligonucleotides from the support and removal of the protecting groups from phosphodiesters and exocyclic amino groups of the nucleic bases. The fully deprotected oligomers, obtained in high yield, were desalted and analyzed on RP-HPLC. After characterization by MALDI-TOF, these carboxyalkylated oligonucleotides were immobilized onto the epoxy-functionalized glass microslides to prepare biochips. The performance of these biochips was evaluated under different sets of conditions and then successfully validated by the detection of base mismatches and human infectious disease, bacterial meningitis, caused by N. meningitidis.

  17. Evaluation of high yielding mutants of Hordeumvulgare cultivar Izgrev

    Directory of Open Access Journals (Sweden)

    B. Dyulgerova

    2017-06-01

    Full Text Available Abstract. Seeds of Hordeum vulgare L. cultivar Izgrev were treated with different concentrations of sodium azide to induce genetic variability for the selection of genotypes with improved traits. After passing through different stages of selection, 18 promising mutants were selected for further studies. Eighteen mutants and their parent and national standard cultivar Veslets were evaluated in Complete Block Design with four replications. The research was conducted in 2013 – 2014 and 2014 – 2015 growing seasons in the experimental field of the Institute of Agriculture Karnobat, Southeastern Bulgaria. The characters studied included days to heading, plant height, lodging, peduncle length, spike length, awn length, spikelet number per spike, grain number per spike, grain weight per spike, 1000 grains weight and grain yield. Wide variation among mutant lines was observed for different traits. Mutant lines M4/16 and M 3/14 produced significantly greater grain yield than the parent and standard cultivar. Positive changes in lodging tolerance, grain number per spike, grain weight per spike, 1000 grains weightwere also observed. This study showed positive effects in the use of mutation in inducing improvement for grain yield and some yield related traits.

  18. combining high seed number and weight to improve seed yield ...

    African Journals Online (AJOL)

    ACSS

    ABSTRACT. Increasing seed size and seed weight is an important trait for trade, yield component and adaptation of chickpea. (Cicer arietinum). ..... between photosynthesis and seed number at phloem isolated nodes in soybean. Crop. Science39: 1769-1775. Carlson, J.B. 1973. Morphology. pp. 17-95. In: Wilcox, J.R. (Ed.).

  19. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    Energy Technology Data Exchange (ETDEWEB)

    Katebi, Samira; Esmaeili, Abolghasem, E-mail: aesmaeili@sci.ui.ac.ir; Ghaedi, Kamran

    2016-03-15

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (P<0.001) when spermatozoa were incubated in exogenous oligonucleotide solution and MNPs. However, by applying static magnetic field during magnetofection method, a significant decrease in exogenous oligonucleotide uptake was observed (P<0.05). Findings of this study showed that MNPs were effective to increase exogenous oligonucleotide uptake by rooster spermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer. - Highlights: • Core/shell type Iron oxide nanoparticles were used as a novel and efficient method. • This method increases exogenous DNA uptake by rooster spermatozoa. • Static magnetic field decreased DNA uptake by rooster spermatozoa.

  20. Oligonucleotide conjugates for therapeutic applications.

    Science.gov (United States)

    Winkler, Johannes

    2013-07-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake mechanisms and pharmacokinetic properties.

  1. Differences in rumen fermentation characteristics between low-yield and high-yield dairy cows in early lactation.

    Science.gov (United States)

    Sofyan, Ahmad; Mitsumori, Makoto; Ohmori, Hideyuki; Uyeno, Yutaka; Hasunuma, Toshiya; Akiyama, Kiyoshi; Yamamoto, Hiroshi; Yokokawa, Hiroaki; Yamaguchi, Tsuneko; Shinkai, Takumi; Hirako, Makoto; Kushibiki, Shiro

    2017-07-01

    Relationship between rumen fermentation parameters, blood biochemical profiles and milk production traits in different yielding dairy cows during early lactation was investigated. Twelve dairy cows were divided into two groups based on their milk yield, that is low-yield (LY) and high-yield (HY) groups. Rumen fluid and blood were collected at 3 weeks prepartum and 4, 8 and 12 weeks postpartum. Results showed that proportions of acetate, propionate to total short chain fatty acids and acetate : propionate ratio were changed (P cholesterol, beta-hydroxybutyric acid (BHBA) and glutamic oxaloacetic transaminase in the HY group were higher (P milk yield and milk compositions were differently clustered between groups. These parameters showed similar direction with dry matter intake in the HY group and adverse direction in the LY group. Linear regression analysis indicated that butyrate was positively correlated with BHBA (P cows in the HY group seem to accommodate appropriately to negative energy balance in early lactation through rumen fermentation. © 2016 Japanese Society of Animal Science.

  2. Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought.

    Science.gov (United States)

    Shamsudin, Noraziyah Abd Aziz; Swamy, B P Mallikarjuna; Ratnam, Wickneswari; Sta Cruz, Ma Teressa; Sandhu, Nitika; Raman, Anitha K; Kumar, Arvind

    2016-12-01

    With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI. The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background. Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.

  3. 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.

  4. Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting.

    Science.gov (United States)

    Poustka, A J; Herwig, R; Krause, A; Hennig, S; Meier-Ewert, S; Lehrach, H

    1999-07-15

    We describe the use of oligonucleotide fingerprinting for the generation of a normalized cDNA library from unfertilized sea urchin eggs and report the preliminary analysis of this library, which resulted in the establishment of a partial gene catalogue of the sea urchin egg. In an analysis of 21,925 cDNA clones by hybridization with 217 oligonucleotide probes, we were able to identify 6291 clusters corresponding to different transcripts, ranging in size from 1 to 265 clones. This corresponds to an average 3.5-fold normalization of the starting library. The normalized library represents about one-third of all genes expressed in the sea urchin egg. To generate sequence information for the transcripts represented by the clusters, representative clones selected from 711 clusters were sequenced. The construction and preliminary analysis of the normalized library are the first steps in the assembly of an increasingly complete collection of maternal genes expressed in the sea urchin egg, which will provide a number of insights into the early development of this well-characterized model organism. Copyright 1999 Academic Press.

  5. Oligonucleotide fingerprinting to individualize ungulates.

    Science.gov (United States)

    Schwaiger, F W; Gomolka, M; Geldermann, H; Zischler, H; Buitkamp, J; Epplen, J T; Ammer, H

    1992-01-01

    The optimal combination of restriction enzyme and oligonucleotide probe has been determined for the individualization of hoofed animal species (cattle, pig, goat, sheep, horse and camel). Four different restriction endonucleases were used as well as five synthetic oligonucleotide probes hybridizing to different simple tandem repeats for fingerprint analyses in unrelated cattle (Swiss and German Simmental of unknown relationship and three families): 4 x 10(15) cows and oxes would reveal different banding patterns after HinfI digestion using the probe (CAC)5/(GTG)5. The other species were investigated using HinfI (and HaeIII) and five different oligonucleotide probes specific for simple tandem repeats. Using (CAC)5/(GTG)5 the discrimination potential in sheep was about one order of magnitude lower than in cattle while in goats 6 x 10(10) specimen are easily differentiated with (CA)8/(GT)8. From an evolutionary standpoint it may be of interest that also in all other ungulate species tested, (CAC)5/(GTG)5 and (CA)8/(GT)8 exhibited the highest potential for individualization. Advantages of oligonucleotide fingerprinting are discussed.

  6. Frequency of cardiac arrhythmias in high and low- yielding dairy cows

    Directory of Open Access Journals (Sweden)

    Afshin Jafari Dehkordi

    2014-06-01

    Full Text Available Electrocardiography (ECG may be used to recognize cardiac disorders. Levels of milk production may change the serum electrolytes which its imbalance has a role in cardiac arrhythmia. Fifty high yielding and fifty low yielding Holstein dairy cows were used in this study. Electrocardiography was recorded by base-apex lead and blood samples were collected from jugular vein for measurement of serum elements such as sodium, potassium, calcium, phosphorous, iron and magnesium. Cardiac dysrhythmias were detected more frequent in low yielding Holstein cows (62.00% compared to high yielding Holstein cows (46.00%. The cardiac dysrhythmias that were observed in low yielding Holstein cows included sinus arrhythmia (34.70%, wandering pacemaker (22.45 %, bradycardia (18.37%, tachycardia (10.20%, atrial premature beat (2.04%, sinoatrial block (2.04%, atrial fibrillation (8.16% and atrial tachycardia (2.04%. The cardiac dysrhythmias were observed in high yielding Holstein cows including, sinus arrhythmia (86.95% and wandering pacemaker (13.05%. Also, notched P wave was observed to be 30% and 14% in high- and low- yielding Holstein cows respectively. The serum calcium concentration of low yielding Holstein cows was significantly lower than that of high yielding Holstein cows. There was not any detectable significant difference in other serum elements between high- and low- yielding Holstein cows. Based on the result of present study, could be concluded that low serum concentration of calcium results to more frequent dysrhythmias in low yielding Holstein cows.

  7. Enhancement of Blood–Brain Barrier Permeability and Delivery of Antisense Oligonucleotides or Plasmid DNA to the Brain by the Combination of Bubble Liposomes and High-Intensity Focused Ultrasound

    Directory of Open Access Journals (Sweden)

    Yoichi Negishi

    2015-09-01

    Full Text Available The blood–brain barrier (BBB is a major obstacle that prevents therapeutic drugs or genes from being delivered to the central nervous system. Therefore, it is important to develop methods to enhance the permeability of the BBB. We have developed echo-contrast gas (C3F8 entrapping liposomes (Bubble liposomes, BLs that can work as a gene delivery tool in combination with ultrasound (US exposure. Here, we studied whether the permeability of the BBB can be enhanced by the combination of BLs and high-intensity focused ultrasound (HIFU. Mice were intravenously injected with Evans blue (EB. BLs were subsequently injected, and the right hemispheres were exposed to HIFU. As a result, the accumulation of EB in the HIFU-exposed brain hemispheres was increased over that observed in the non-HIFU-exposed hemispheres, depending on the intensity and the duration of the HIFU. Similarly, the combination of BLs and HIFU allowed fluorescent-labeled antisense oligonucleotides to be delivered into the HIFU-exposed left hemispheres of the treated mice. Furthermore, a firefly luciferase-expressing plasmid DNA was delivered to the brain by the combination method of BLs and HIFU, which resulted in the increased gene expression in the brain at the focused-US exposure site. These results suggest that the method of combining BLs and HIFU together serves as a useful means for accelerating the permeability of BBB and thereby enabling antisense oligonucleotides or genes to be delivered to the focused brain site.

  8. A new enzymatic route for production of long 5'-phosphorylated oligonucleotides using suicide cassettes and rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-08-01

    Full Text Available Abstract Background The quality of chemically synthesized oligonucleotides falls with the length of the oligonucleotide, not least due to depurinations and premature termination during production. This limits the use of long oligonucleotides in assays where long high-quality oligonucleotides are needed (e.g. padlock probes. Another problem with chemically synthesized oligonucleotides is that secondary structures contained within an oligonucleotide reduce the efficiency of HPLC and/or PAGE purification. Additionally, ligation of chemically synthesized oligonucleotides is less efficient than the ligation of enzymatically produced DNA molecules. Results Chemically synthesized oligonucleotides with hairpin structures were acquired from our standard supplier. The stem of the hairpin contained recognition sequences for the Nt. Alw I nicking enzyme and the Mly I restriction enzyme. These double stranded regions were positioned in a way to allow self-templated circularization of the oligonucleotide. Following ligation, tandem repeats of the complementary sequence of the circular oligonucleotide could be produced through rolling circle DNA synthesis. By running successive rounds of ligation, rolling circle DNA synthesis, and nicking, the original oligonucleotide could be amplified as either the (+-strand or the (--strand. Alternatively, the hairpin structure could be removed by cleavage with the Mly I restriction enzyme, thereby releasing the oligonucleotide sequence contained within the hairpin structure from the hairpin. Conclusion We present here a method for the enzymatic production through DNA amplification of oligonucleotides with freely designable 5'-ends and 3'-ends, using hairpin-containing self-templating oligonucleotides. The hairpin comprises recognition sequences for a nicking enzyme and a restriction enzyme. The oligonucleotides are amplified by successive rounds of ligation, rolling circle DNA synthesis and nicking. Furthermore, the

  9. Improved completion practices yield high productivity wells. [Louisiana Gulf Coast

    Energy Technology Data Exchange (ETDEWEB)

    Olivier, D.A.

    1981-04-01

    In the mid-1960's, a special in-house task force was assembled in response to a number of sand ups and casing failures in Shell's production complex at the mouth of the Mississippi River. This task force developed concepts and techniques for better completions. The techniques have been modified and adjusted to specific situations, but the concepts remain the fundamental backbone of Shell's high success ratio and excellent response from completions in the shallow unconsolidated sands in the Louisiana Gulf Coast. Five major steps leading to high performance producers are identified as the following: clean fluids, adequate perforation, effective perforation cleanup, efficient gravel pack, and proper initiation of production.

  10. High school student physics research experience yields positive results

    Science.gov (United States)

    Podolak, K. R.; Walters, M. J.

    2016-03-01

    All high school students that wish to continue onto college are seeking opportunities to be competitive in the college market. They participate in extra-curricular activities which are seen to foster creativity and the skills necessary to do well in the college environment. In the case of students with an interest in physics, participating in a small scale research project while in high school gives them the hands on experience and ultimately prepares them more for the college experience. SUNY Plattsburgh’s Physics department started a five-week summer program for high school students in 2012. This program has proved not only beneficial for students while in the program, but also as they continue on in their development as scientists/engineers. Independent research, such as that offered by SUNY Plattsburgh’s five-week summer program, offers students a feel and taste of the culture of doing research, and life as a scientist. It is a short-term, risk free way to investigate whether a career in research or a particular scientific field is a good fit.

  11. Clickstream data yields high-resolution maps of science

    Energy Technology Data Exchange (ETDEWEB)

    Bollen, Johan [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory; Hagberg, Aric [Los Alamos National Laboratory; Bettencourt, Luis [Los Alamos National Laboratory; Chute, Ryan [Los Alamos National Laboratory; Rodriguez, Marko A [Los Alamos National Laboratory; Balakireva, Lyudmila [Los Alamos National Laboratory

    2009-01-01

    Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantagees of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science.

  12. High confinement, high yield Si3N4 waveguides for nonlinear optical application

    CERN Document Server

    Epping, Jörn P; Mateman, Richard; Leinse, Arne; Heideman, René G; van Rees, Albert; van der Slot, Peter J M; Lee, Chris J; Boller, Klaus-J

    2014-01-01

    In this paper we present a novel fabrication technique for silicon nitride (Si3N4) waveguides with a thickness of up to 900 nm, which are suitable for nonlinear optical applications. The fabrication method is based on etching trenches in thermally oxidized silicon and filling the trenches with Si3N4. Using this technique no stress-induced cracks in the Si3N4 layer were observed resulting in a high yield of devices on the wafer. The propagation losses of the obtained waveguides were measured to be as low as 0.4 dB/cm at a wavelength of around 1550 nm.

  13. High yield polyol synthesis of round- and sharp-end silver nanowires with high aspect ratio

    Energy Technology Data Exchange (ETDEWEB)

    Nekahi, A.; Marashi, S.P.H., E-mail: pmarashi@aut.ac.ir; Fatmesari, D. Haghshenas

    2016-12-01

    Long silver nanowires (average length of 28 μm, average aspect ratio of 130) with uniform diameter along their length were produced by polyol synthesis of AgNO{sub 3} in ethylene glycol in the presence of PVP as preferential growth agent. Nanowires were produced with no addition of chloride salts such as NaCl or CuCl{sub 2} (or other additives such as Na{sub 2}S) which are usually used for lowering reduction rate of Ag ions by additional etchant of O{sub 2}/Cl{sup −}. Lower reduction rate was obtained by increasing the injection time of PVP and AgNO{sub 3} solutions, which was the significant factor in the formation of nanowires. Therefore, there was enough time for reduced Ag atoms to be deposited preferentially in the direction of PVP chains, resulting in high yield (the fraction of nanowires in the products) of nanowires (more than 95%) with high aspect ratio. The produced nanowires had both round- and sharp-ends with pentagonal cross section. Higher energy level of Ag atoms in borders of MTPs, which increases the dissolution rate of precipitated atoms, in addition to partial melting of MTPs at high synthesis temperatures, leads to the curving of the surfaces of exposed (111) crystalline planes in some MTPs and the formation of round-end silver nanowires. - Highlights: • Long silver nanowires with high aspect ratio of 130 were produced. • More than 95% nanowires were produced in products. • The produced nanowires had round- and sharp-ends with pentagonal cross section. • Additives were needed neither for high yield synthesis nor for round-end nanowires. • Melting and etching of MTPs in high energy borders resulted to round-end nanowires.

  14. Mass yield in high-energy proton-uranium collisions from a complete, microcanonical statistical decay

    Energy Technology Data Exchange (ETDEWEB)

    Abul-Magd, A.Y.; Gross, D.H.E.; Xu Shuyan; Zheng Yuming

    1986-11-01

    The mass-yield of fragments produced in the statistical decay of /sup 238/U/sup */ is compared to the yield from high energy p-U collisions. The distributions of the initial excitation energy are calculated using a Glauber approximation. The mass yield shows good agreement with the data. Intermediate-mass fragment production, the fission peak, and the 'Au-finger' show up in the calculation. No separate mechanisms producing these different features have to be invoked.

  15. Phosphorothioate oligonucleotides induction into experimental choroidal neovascularization by HVJ-liposome system.

    Science.gov (United States)

    Ogata, N; Otsuji, T; Matsushima, M; Kimoto, T; Yamanaka, R; Takahashi, K; Wada, M; Uyama, M; Kaneda, Y

    1999-04-01

    The purpose of this study was to determine whether the inactivated hemagglutinating virus of Japan (HVJ)-liposome method can induce phosphorothioate oligonucleotides effectively into an experimentally-induced choroidal neovascularization of rats. We also examined whether antisense phosphorothioate oligonucleotides against VEGF could be induced into choroidal neovascularization as a therapeutic agent by the HVJ-liposome method. The experiments were conducted on a rat model of choroidal neovascularization. FITC-labeled phosphorothioate oligonucleotides were coencapsulated in liposomes. The liposomes were coated with the envelope of inactivated HVJ and injected into the vitreous cavity following photocoagulation of pigmented rat eyes. The eyes were removed following injection, fixed, frozen and cut into thin sections. Induction of oligonucleotides was observed under a laser confocal scanning microscope for fluorescence and the development of choroidal neovascularization was evaluated histopathologically. Phosphorothioate oligonucleotides were effectively induced into ganglion cells and into the cells of the choroidal neovascularization induced by laser photocoagulation. Highly effective induction of oligos was observed 3 to 14 days after intravitreal injection of HVJ-liposomes after which the level decreased. Antisense oligonucleotides against VEGF were induced specifically into cells in the choroidal neovascularization, however neovascularization was still observed. Phosphorothioate oligonucleotides can be effectively induced into ganglion cells, and specifically into cells in choroidal neovascularization. Although antisense oligonucleotides against VEGF failed to prevent choroidal neovascularization, the HVJ-liposome method provided a highly effective means of inducing antisense oligos for in vivo antisense therapy.

  16. Oligonucleotide Therapy for Obstructive and Restrictive Respiratory Diseases

    Directory of Open Access Journals (Sweden)

    Wupeng Liao

    2017-01-01

    Full Text Available Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF. The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO, small interfering RNA (siRNA, and microRNA (miRNA are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

  17. Water use and grain yield in drought-tolerant corn in the Texas High Plains

    Science.gov (United States)

    Drought is an important factor limiting corn (Zea mays L.) yields in the Texas High Plains, and adoption of drought-tolerant (DT) hybrids could be a management tool under water shortage. We conducted a 3-yr field study to investigate grain yield, evapotranspiration (ET), and water use efficiency (WU...

  18. 31 CFR 356.21 - How are awards at the high yield or discount rate calculated?

    Science.gov (United States)

    2010-07-01

    ... discount rate calculated? 356.21 Section 356.21 Money and Finance: Treasury Regulations Relating to Money... high yield or discount rate calculated? (a) Awards to submitters. We generally prorate bids at the highest accepted yield or discount rate under § 356.20(a)(2) of this part. For example, if 80.15% is the...

  19. Response of high yielding rice varieties to NaCl salinity in ...

    African Journals Online (AJOL)

    Salinity is one the biggest constraint to obtain crop potential yield throughout paddy fields in some part of the coastal line of rice cultivated area in Iran. In order to find resistant varieties and study the reaction of some newly released high yielding varieties to different levels of salinity of irrigation water an experiment was ...

  20. Linear model for fast background subtraction in oligonucleotide microarrays

    NARCIS (Netherlands)

    Kroll, K.M.; Barkema, G.T.; Carlon, E.

    2009-01-01

    Background One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. Results We propose here an

  1. SELECTION RESPONSE FOR INCREASED GRAIN YIELD IN TWO HIGH OIL MAIZE SYNTHETICS

    Directory of Open Access Journals (Sweden)

    Made J. Mejaya

    2016-10-01

    Full Text Available Selection for increased oil level in maize showed the increase was associated with decrease in starch concentration, kernel weight, and grain yield. The study was conducted with the objectives: (1 to evaluate response to six cycles for increased grain yield in the high oil maize Alexho Elite (AE: 60-90 g kg-1 oil concentration and Ultra High Oil (UHO: 100-140 g kg-1 oil concentration using inbred tester B73; (2 to measure responses to selection for increased grain yield with changes in yield components; and (3 to determine a suitable tester. Previously the two synthetics had been selected for oil concentration. After six cycles, the six genotypes i.e. AE C0, AE C3, AE C6, UHO C0, UHO C3, and UHO C6 were testcrossed to B73, LH185, and LH202 inbreds (40 g kg-1 oil concentration to a total of 18 testcrosses. Two field experiments were used to evaluate selection in AE and UHO testcrosses. The study showed selection using inbred tester B73 in AE and UHO was effective in increasing grain yield of AE testcrosses without changing (i.e. decreasing oil and protein concentrations. AE testcrosses produced higher grain yield and greater selection response for grain yield than UHO testcrosses. LH185 was best for grain yield in AE and UHO testcrosses. Increase in grain yield in most of the testcrosses was associated with increases in starch concentration, kernel weight, kernel number, and grain weight.

  2. Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Fisker, Niels; Hedtjärn, Maj

    2010-01-01

    -high-density lipoprotein (non-HDL) cholesterol without increasing serum liver toxicity markers. The data presented here show that oligonucleotide length as a parameter needs to be considered in the design of antisense oligonucleotide and that potent short oligonucleotides with sufficient target affinity can be generated...... using the LNA chemistry. Conclusively, we present a 13-mer LNA oligonucleotide with therapeutic potential that produce beneficial cholesterol lowering effect in non-human primates....

  3. Selection Criteria for Combining High Yield and Striga Resistance in Sorghum

    Directory of Open Access Journals (Sweden)

    Showemimo, FA.

    2003-01-01

    Full Text Available Ten genetically diverse but homozygote sorghum cultivars that are adapted to northern Guinea savanna zone of Nigeria were grown in Striga sick-field for two years. Agronomic traits of maturity, Striga resistance traits and actual grain yield were quantitatively heritable. Correlation coefficients computed among these traits revealed that grain yield was positively correlated with plant vigour, stem girth, root weight, shoot weight and plant height, while Striga count was negative and highly significantly correlated (r= -0.86 with grain yield. Correlated response indicated that selecting for bigger stem girth, high root, good plant vigour and shoot weight, and taller plants under Striga infestation will lead to a corresponding increase of 1.1%, 1.4%, 2.7%, 7.8% and 14.9% respectively on grain yield, while a 52.4% reduction in grain yield is observed by selecting Striga encouraging traits.

  4. High field MRI in the diagnosis of multiple sclerosis: high field-high yield?

    Energy Technology Data Exchange (ETDEWEB)

    Wattjes, Mike P.; Barkhof, Frederik [VU University Medical Center, MS Center Amsterdam, Department of Radiology, Amsterdam (Netherlands)

    2009-05-15

    Following the approval of the U.S. Food and Drug Administration (FDA), high field magnetic resonance imaging (MRI) has been increasingly incorporated into the clinical setting. Especially in the field of neuroimaging, the number of high field MRI applications has been increased dramatically. Taking advantage on increased signal-to-noise ratio (SNR) and chemical shift, higher magnetic field strengths offer new perspectives particularly in brain imaging and also challenges in terms of several technical and physical consequences. Over the past few years, many applications of high field MRI in patients with suspected and definite multiple sclerosis (MS) have been reported including conventional and quantitative MRI methods. Conventional pulse sequences at 3 T offers higher lesion detection rates when compared to 1.5 T, particularly in anatomic regions which are important for the diagnosis of patients with MS. MR spectroscopy at 3 T is characterized by an improved spectral resolution due to increased chemical shift allowing a better quantification of metabolites. It detects significant axonal damage already in patients presenting with clinically isolated syndromes and can quantify metabolites of special interest such as glutamate which is technically difficult to quantify at lower field strengths. Furthermore, the higher susceptibility and SNR offer advantages in the field of functional MRI and diffusion tensor imaging. The recently introduced new generation of ultra-high field systems beyond 3 T allows scanning in submillimeter resolution and gives new insights into in vivo MS pathology on MRI. The objectives of this article are to review the current knowledge and level of evidence concerning the application of high field MRI in MS and to give some ideas of research perspectives in the future. (orig.)

  5. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches.

    Science.gov (United States)

    Kumar, Arvind; Dixit, Shalabh; Ram, T; Yadaw, R B; Mishra, K K; Mandal, N P

    2014-11-01

    The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1 , qDTY 2.2 , qDTY 3.1 , qDTY 3.2 , qDTY 6.1 , and qDTY 12.1 ) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  6. Optimal yield-related attributes of irrigated rice for high yield potential based on path analysis and stability analysis

    Directory of Open Access Journals (Sweden)

    Ganghua Li

    2014-08-01

    Full Text Available Improvement of yield in rice (Oryza sativa L. is vital for ensuring food security in China. Both rice breeders and growers need an improved understanding of the relationship between yield and yield-related traits. New indica cultivars (53 in 2007 and 48 in 2008 were grown in Taoyuan, Yunnan province, to identify important components contributing to yield. Additionally, two standard indica rice cultivars with similar yield potentials, II You 107 (a large-panicle type and Xieyou 107 (a heavy-panicle type, were planted in Taoyuan, Yunnan province and Nanjing, Jiangsu province, from 2006 to 2008 to evaluate the stability of yield and yield-related attributes. Growth duration (GD, leaf area index (LAI, panicles per m2 (PN, and spikelets per m2 (SM were significantly and positively correlated with grain yield (GY over all years. Sequential path analysis identified PN and panicle weight (PW as important first-order traits that influenced grain yield. All direct effects were significant, as indicated by bootstrap analysis. Yield potential varied greatly across locations but not across years. Plant height (PH, days from heading to maturity (HM, and grain weight (GW were stable traits that showed little variation across sites or years, whereas GD (mainly the pre-heading period, PHP and PN varied significantly across locations. To achieve a yield of 15 t ha− 1, a cultivar should have a PH of 110–125 cm, a long GD with HM of approximately 40 days, a PN of 300–400 m− 2, and a GW of 29–31 mg.

  7. Exploiting protected maleimides to modify oligonucleotides, peptides and peptide nucleic acids.

    Science.gov (United States)

    Paris, Clément; Brun, Omar; Pedroso, Enrique; Grandas, Anna

    2015-04-10

    This manuscript reviews the possibilities offered by 2,5-dimethylfuran-protected maleimides. Suitably derivatized building blocks incorporating the exo Diels-Alder cycloadduct can be introduced at any position of oligonucleotides, peptide nucleic acids, peptides and peptoids, making use of standard solid-phase procedures. Maleimide deprotection takes place upon heating, which can be followed by either Michael-type or Diels-Alder click conjugation reactions. However, the one-pot procedure in which maleimide deprotection and conjugation are simultaneously carried out provides the target conjugate more quickly and, more importantly, in better yield. This procedure is compatible with conjugates involving oligonucleotides, peptides and peptide nucleic acids. A variety of cyclic peptides and oligonucleotides can be obtained from peptide and oligonucleotide precursors incorporating protected maleimides and thiols.

  8. Exploiting Protected Maleimides to Modify Oligonucleotides, Peptides and Peptide Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Clément Paris

    2015-04-01

    Full Text Available This manuscript reviews the possibilities offered by 2,5-dimethylfuran-protected maleimides. Suitably derivatized building blocks incorporating the exo Diels-Alder cycloadduct can be introduced at any position of oligonucleotides, peptide nucleic acids, peptides and peptoids, making use of standard solid-phase procedures. Maleimide deprotection takes place upon heating, which can be followed by either Michael-type or Diels-Alder click conjugation reactions. However, the one-pot procedure in which maleimide deprotection and conjugation are simultaneously carried out provides the target conjugate more quickly and, more importantly, in better yield. This procedure is compatible with conjugates involving oligonucleotides, peptides and peptide nucleic acids. A variety of cyclic peptides and oligonucleotides can be obtained from peptide and oligonucleotide precursors incorporating protected maleimides and thiols.

  9. Potentialities of high yield and managerial techniques of annual-working bamboo groves of Phyllostachys pubescens

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Y.L.

    1983-01-01

    Studies over 20 years have demonstrated that bamboo groves that are worked annually have nearly twice the yield of those worked every other year. Such groves have a higher stand density and a high leaf area index. 5 references.

  10. Mid-Season High-Resolution Satellite Imagery for Forecasting Site-Specific Corn Yield

    Directory of Open Access Journals (Sweden)

    Nahuel R. Peralta

    2016-10-01

    Full Text Available A timely and accurate crop yield forecast is crucial to make better decisions on crop management, marketing, and storage by assessing ahead and implementing based on expected crop performance. The objective of this study was to investigate the potential of high-resolution satellite imagery data collected at mid-growing season for identification of within-field variability and to forecast corn yield at different sites within a field. A test was conducted on yield monitor data and RapidEye satellite imagery obtained for 22 cornfields located in five different counties (Clay, Dickinson, Rice, Saline, and Washington of Kansas (total of 457 ha. Three basic tests were conducted on the data: (1 spatial dependence on each of the yield and vegetation indices (VIs using Moran’s I test; (2 model selection for the relationship between imagery data and actual yield using ordinary least square regression (OLS and spatial econometric (SPL models; and (3 model validation for yield forecasting purposes. Spatial autocorrelation analysis (Moran’s I test for both yield and VIs (red edge NDVI = NDVIre, normalized difference vegetation index = NDVIr, SRre = red-edge simple ratio, near infrared = NIR and green-NDVI = NDVIG was tested positive and statistically significant for most of the fields (p < 0.05, except for one. Inclusion of spatial adjustment to model improved the model fit on most fields as compared to OLS models, with the spatial adjustment coefficient significant for half of the fields studied. When selected models were used for prediction to validate dataset, a striking similarity (RMSE = 0.02 was obtained between predicted and observed yield within a field. Yield maps could assist implementing more effective site-specific management tools and could be utilized as a proxy of yield monitor data. In summary, high-resolution satellite imagery data can be reasonably used to forecast yield via utilization of models that include spatial adjustment to

  11. Microbial Carbon Substrate Utilization Differences among High- and Average-Yield Soybean Areas

    Directory of Open Access Journals (Sweden)

    Taylor C. Adams

    2017-05-01

    Full Text Available Since soybean (Glycine max L. (Merr. yields greater than 6719 kg ha−1 have only recently and infrequently been achieved, little is known about the soil microbiological environment related to high-yield soybean production. Soil microbiological properties are often overlooked when assessing agronomic practices for optimal production. Therefore, a greater understanding is needed regarding how soil biological properties may differ between high- and average-yielding areas within fields. The objectives of this study were to (i evaluate the effects of region on soil microbial carbon substrate utilization differences between high- (HY and average-yield (AY areas and (ii assess the effect of yield area on selected microbiological property differences. Replicate soil samples were collected from the 0–10 cm depth from yield-contest-entered fields in close proximity that had both a HY and an AY area. Samples were collected immediately prior to or just after soybean harvest in 2014 and 2015 from each of seven geographic regions within Arkansas. Averaged across yield area, community-level carbon substrate utilization and Shannon’s and Simpson’s functional diversity and evenness were greater (p < 0.05 in Region 7 than all other regions. Averaged across regions, Shannon’s functional diversity and evenness were greater (p < 0.05 in HY than in AY areas. Principal component analysis demonstrated that a greater variety of carbon substrates were used in HY than AY areas. These results may help producers understand the soil microbiological environment in their own fields that contribute to or hinder achieving high-yielding soybeans; however, additional parameters may need to be assessed for a more comprehensive understanding of the soil environment that is associated with high-yielding soybean.

  12. LNA-modified isothermal oligonucleotide microarray for ...

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of .... Sequences and calculated melting temperatures of DNA oligonucleotide probes and LNA-modified oligonucleotide probes for. Bacillus .... quick chilling on ice for 5 min. 13.5 μL of ...

  13. Fed-Batch Enzymatic Saccharification of High Solids Pretreated Lignocellulose for Obtaining High Titers and High Yields of Glucose.

    Science.gov (United States)

    Jung, Young Hoon; Park, Hyun Min; Kim, Dong Hyun; Yang, Jungwoo; Kim, Kyoung Heon

    2017-07-01

    To reduce the distillation costs of cellulosic ethanol, it is necessary to produce high sugar titers in the enzymatic saccharification step. To obtain high sugar titers, high biomass loadings of lignocellulose are necessary. In this study, to overcome the low saccharification yields and the low operability of high biomass loadings, a fed-batch saccharification process was developed using an enzyme reactor that was designed and built in-house. After optimizing the cellulase and biomass feeding profiles and the agitation speed, 132.6 g/L glucose and 76.0% theoretical maximum glucose were obtained from the 60 h saccharification of maleic acid-pretreated rice straw at a 30% (w/v) solids loading with 15 filter paper units (FPU) of Cellic CTec2/g glucan. This study demonstrated that through the proper optimization of fed-batch saccharification, both high sugar titers and high saccharification yields are possible, even with using the high solids loading (i.e., ≥30%) with the moderate enzyme loading (i.e., high solids saccharification process in cellulosic fuel and chemical production.

  14. Enhanced electron yield from a laser-plasma accelerator using high-Z gas jet targets

    CERN Document Server

    Mirzaie, Mohammad; Li, Song; Sokollik, Thomas; He, Fei; Cheng, Ya; Sheng, Zhengming; Zhang, Jie

    2014-01-01

    An investigation of the multi-hundred MeV electron beam yield (charge) form helium, nitrogen, neon and argon gas jet plasmas in a laser-plasma wakefield acceleration experiment was carried out. The charge measurement has been made via imaging the electron beam intensity profile on a fluorescent screen into a 14-bit charge coupled device (CCD) which was cross-calibrated with nondestructive electronics-based method. Within given laser and plasma parameters, we found that laser-driven low Z- gas jet targets generate high-quality and well-collimated electron beams with reasonable yields at the level of 10-100 pC. On the other hand, filamentary electron beams which were observed from high-Z gas jets at higher densities reached much higher yield. Evidences for cluster formation were clearly observed in high-Z gases, especially in the argon gas jet target where we received the highest yield of ~ 3 nC

  15. Neglecting rice milling yield and quality underestimates economic losses from high-temperature stress.

    Directory of Open Access Journals (Sweden)

    Nathaniel B Lyman

    Full Text Available Future increases in global surface temperature threaten those worldwide who depend on rice production for their livelihoods and food security. Past analyses of high-temperature stress on rice production have focused on paddy yield and have failed to account for the detrimental impact of high temperatures on milling quality outcomes, which ultimately determine edible (marketable rice yield and market value. Using genotype specific rice yield and milling quality data on six common rice varieties from Arkansas, USA, combined with on-site, half-hourly and daily temperature observations, we show a nonlinear effect of high-temperature stress exposure on yield and milling quality. A 1 °C increase in average growing season temperature reduces paddy yield by 6.2%, total milled rice yield by 7.1% to 8.0%, head rice yield by 9.0% to 13.8%, and total milling revenue by 8.1% to 11.0%, across genotypes. Our results indicate that failure to account for changes in milling quality leads to understatement of the impacts of high temperatures on rice production outcomes. These dramatic losses result from reduced paddy yield and increased percentages of chalky and broken kernels, which together decrease the quantity and market value of milled rice. Recently published estimates show paddy yield reductions of up to 10% across the major rice-producing regions of South and Southeast Asia due to rising temperatures. The results of our study suggest that the often-cited 10% figure underestimates the economic implications of climate change for rice producers, thus potentially threatening future food security for global rice producers and consumers.

  16. Antisense oligonucleotide therapeutics for inherited neurodegenerative diseases.

    Science.gov (United States)

    Southwell, Amber L; Skotte, Niels H; Bennett, C Frank; Hayden, Michael R

    2012-11-01

    The rising median age of our population and the age-dependent risk of neurodegeneration translate to exponentially increasing numbers of afflicted individuals in the coming years. Although symptomatic treatments are available for some neurodegenerative diseases, most are only moderately efficacious and are often associated with significant side effects. The development of small molecule, disease-modifying drugs has been hindered by complex pathogenesis and a failure to clearly define the rate-limiting steps in disease progression. An alternative approach is to directly target the mutant gene product or a defined causative protein. Antisense oligonucleotides (ASOs) - with their diverse functionality, high target specificity, and relative ease of central nervous system (CNS) delivery - are uniquely positioned as potential therapies for neurological diseases. Here we review the development of ASOs for the treatment of inherited neurodegenerative diseases. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. High-biomass C4 grasses-Filling the yield gap.

    Science.gov (United States)

    Mullet, John E

    2017-08-01

    A significant increase in agricultural productivity will be required by 2050 to meet the needs of an expanding and rapidly developing world population, without allocating more land and water resources to agriculture, and despite slowing rates of grain yield improvement. This review examines the proposition that high-biomass C4 grasses could help fill the yield gap. High-biomass C4 grasses exhibit high yield due to C4 photosynthesis, long growth duration, and efficient capture and utilization of light, water, and nutrients. These C4 grasses exhibit high levels of drought tolerance during their long vegetative growth phase ideal for crops grown in water-limited regions of agricultural production. The stems of some high-biomass C4 grasses can accumulate high levels of non-structural carbohydrates that could be engineered to enhance biomass yield and utility as feedstocks for animals and biofuels production. The regulatory pathway that delays flowering of high-biomass C4 grasses in long days has been elucidated enabling production and deployment of hybrids. Crop and landscape-scale modeling predict that utilization of high-biomass C4 grass crops on land and in regions where water resources limit grain crop yield could increase agricultural productivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Effect of high oleic acid soybean on seed oil, protein concentration, and yield

    Science.gov (United States)

    Soybeans with high oleic acid content are desired by oil processors because of their improved oxidative stability for broader use in food, fuel and other products. However, non-GMO high-oleic soybeans have tended to have low seed yield. The objective of this study was to test non-GMO, high-oleic s...

  19. Identification of potentially high yielding irradiated cassava ‘Gajah’ genotype with different geographic coordinates

    Science.gov (United States)

    Subekti, I.; Khumaida, N.; Ardie, SW

    2017-01-01

    Cassava is one of the main and important carbohydrate producing crops in Indonesia. Thus cassava production and its tuber quality need to be improved. ‘Gajah’ genotype is a local genotypes cassava from East Kalimantan, has high potential yield (> 60 ton Ha-1). However, the harvest time of this genotype is quite long (>= 12 months). The objective of this research was to identify the high yielding cassava mutants from the gamma rays irradiated ‘Gajah’ genotype at M1V3 population and potential yield at different location. Several putative cassava mutants (12 mutants) were planted in Cikabayan Experimental Field, IPB from March 2015 to March 2016 and the yields compared with the same genotype grown at different location by seeing its coordinates to observe the potential yield. Our result showed that the fresh tuber weight per plant of some putative mutants could reach more than 8 kg (yield potential of 64 ton Ha-1). The harvested tubers also had sweet flavor, although the tubers of some putative mutants were bitter. Based on previous research study, the different geographic coordinate has resulted variability on fresh tuber yield. It seems that it needs to observe the stability of ‘Gajah’- irradiated mutants in several location in Java Island.

  20. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

    Science.gov (United States)

    Takeuchi, Koh; Arthanari, Haribabu; Shimada, Ichio; Wagner, Gerhard

    2015-12-01

    Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.

  1. Mutation breeding of Bacillus subtilis YTB4 with high yield of ...

    African Journals Online (AJOL)

    Helium-neon (He-Ne) laser irradiation is a highly efficient mutation breeding technology and is widely applied to various fields of biological science. Using Bacillus subtilis YTB4 with high yield of multienzyme complex as original strain, mutation breeding was carried out by He-Ne laser irradiation in this study. Based on the ...

  2. Metabolic characterization of high- and low-yielding strains of Penicillium chrysogenum

    DEFF Research Database (Denmark)

    Christensen, Bjarke; Thykær, Jette; Nielsen, Jens

    2000-01-01

    A recently developed method for analyzing metabolic networks using C-13-labels was employed for investigating the metabolism of a high- and a low-yielding strain of Penicillium chrysogenum. Under penicillin-producing conditions, the flux through the pentose phosphate (PP) pathway in the high...

  3. 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

  4. Highly Luminescent Carbon-​Nanoparticle-​Based Materials: Factors Influencing Photoluminescence Quantum Yield

    NARCIS (Netherlands)

    Qu, S.; Shen, D.; Liu, X.; Jing, P.; Zhang, L.; Ji, W.; Zhao, H.; Fan, X.; Zhang, H.

    2014-01-01

    Unravelling the factors influencing photoluminescence (PL) quantum yield of the carbon nanoparticles (CNPs) is the prerequisite for prepg. highly luminescent CNP-​based materials. In this work, an easy and effective method is reported for prepg. highly luminescent CNP-​based materials. Water-​sol.

  5. Fragment-based solid-phase assembly of oligonucleotide conjugates with peptide and polyethylene glycol ligands.

    Science.gov (United States)

    Dirin, Mehrdad; Urban, Ernst; Noe, Christian R; Winkler, Johannes

    2016-10-04

    Ligand conjugation to oligonucleotides is an attractive strategy for enhancing the therapeutic potential of antisense and siRNA agents by inferring properties such as improved cellular uptake or better pharmacokinetic properties. Disulfide linkages enable dissociation of ligands and oligonucleotides in reducing environments found in endosomal compartments after cellular uptake. Solution-phase fragment coupling procedures for producing oligonucleotide conjugates are often tedious, produce moderate yields and reaction byproducts are frequently difficult to remove. We have developed an improved method for solid-phase coupling of ligands to oligonucleotides via disulfides directly after solid-phase synthesis. A 2'-thiol introduced using a modified nucleotide building block was orthogonally deprotected on the controlled pore glass solid support with N-butylphosphine. Oligolysine peptides and a short monodisperse ethylene glycol chain were successfully coupled to the deprotected thiol. Cleavage from the resin and full removal of oligonucleotide protection groups were achieved using methanolic ammonia. After standard desalting, and without further purification, homogenous conjugates were obtained as demonstrated by HPLC, gel electrophoresis, and mass spectrometry. The attachment of both amphiphilic and cationic ligands proves the versatility of the conjugation procedure. An antisense oligonucleotide conjugate with hexalysine showed pronounced gene silencing in a cell culture tumor model in the absence of a transfection reagent and the corresponding ethylene glycol conjugate resulted in down regulation of the target gene to nearly 50% after naked application. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  6. Creating high yield water soluble luminescent graphene quantum dots via exfoliating and disintegrating carbon nanotubes and graphite flakes.

    Science.gov (United States)

    Lin, Liangxu; Zhang, Shaowei

    2012-10-21

    We have developed an effective method to exfoliate and disintegrate multi-walled carbon nanotubes and graphite flakes. With this technique, high yield production of luminescent graphene quantum dots with high quantum yield and low oxidization can be achieved.

  7. Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice.

    Science.gov (United States)

    Tanger, Paul; Klassen, Stephen; Mojica, Julius P; Lovell, John T; Moyers, Brook T; Baraoidan, Marietta; Naredo, Maria Elizabeth B; McNally, Kenneth L; Poland, Jesse; Bush, Daniel R; Leung, Hei; Leach, Jan E; McKay, John K

    2017-02-21

    To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution.

  8. Extracting DNA from 'jaws': High yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Morgan, J. A T; Maher, S. L.

    2017-01-01

    archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae...... of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples...... of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were...

  9. Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

    Directory of Open Access Journals (Sweden)

    Preiser Peter

    2007-09-01

    Full Text Available Abstract Background The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonucleotide element that represents each genetic locus/gene in the genome and is unique, devoid of internal structures and repetitive sequences and its Tm is uniform with all other elements on the microarray. Currently, all of the publicly available programs for DNA long oligonucleotide microarray selection utilize various combinations of cutoffs in which each parameter (uniqueness, Tm, and secondary structure is evaluated and filtered individually. The use of the cutoffs can, however, lead to information loss and to selection of suboptimal oligonucleotides, especially for genomes with extreme distribution of the GC content, a large proportion of repetitive sequences or the presence of large gene families with highly homologous members. Results Here we present the program OligoRankPick which is using a weighted rank-based strategy to select microarray oligonucleotide elements via an integer weighted linear function. This approach optimizes the selection criteria (weight score for each gene individually, accommodating variable properties of the DNA sequence along the genome. The designed algorithm was tested using three microbial genomes Escherichia coli, Saccharomyces cerevisiae and the human malaria parasite species Plasmodium falciparum. In comparison to other published algorithms OligoRankPick provides significant improvements in oligonucleotide design for all three genomes with the most significant improvements observed in the microarray design for P. falciparum whose genome is characterized by large fluctuations of GC content, and abundant gene duplications. Conclusion OligoRankPick is an efficient tool for the design of long oligonucleotide DNA microarrays which does not rely on direct oligonucleotide exclusion by

  10. Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

  11. Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach.

    Science.gov (United States)

    McCarthy, S D; Waters, S M; Kenny, D A; Diskin, M G; Fitzpatrick, R; Patton, J; Wathes, D C; Morris, D G

    2010-11-15

    In high-yielding dairy cows the liver undergoes extensive physiological and biochemical changes during the early postpartum period in an effort to re-establish metabolic homeostasis and to counteract the adverse effects of negative energy balance (NEB). These adaptations are likely to be mediated by significant alterations in hepatic gene expression. To gain new insights into these events an energy balance model was created using differential feeding and milking regimes to produce two groups of cows with either a mild (MNEB) or severe NEB (SNEB) status. Cows were slaughtered and liver tissues collected on days 6-7 of the first follicular wave postpartum. Using an Affymetrix 23k oligonucleotide bovine array to determine global gene expression in hepatic tissue of these cows, we found a total of 416 genes (189 up- and 227 downregulated) to be altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with widespread changes in gene expression classified into 36 gene networks including those associated with lipid metabolism, connective tissue development and function, cell signaling, cell cycle, and metabolic diseases, the three most significant of which are discussed in detail. SNEB cows displayed reduced expression of transcription activators and signal transducers that regulate the expression of genes and gene networks associated with cell signaling and tissue repair. These alterations are linked with increased expression of abnormal cell cycle and cellular proliferation associated pathways. This study provides new information and insights on the effect of SNEB on gene expression in high-yielding Holstein Friesian dairy cows in the early postpartum period.

  12. Genetic Linkage Map of a High Yielding FELDA Deli×Yangambi Oil Palm Cross

    Science.gov (United States)

    Seng, Tzer-Ying; Mohamed Saad, Siti Hawa; Chin, Cheuk-Weng; Ting, Ngoot-Chin; Harminder Singh, Rajinder Singh; Qamaruz Zaman, Faridah; Tan, Soon-Guan; Syed Alwee, Sharifah Shahrul Rabiah

    2011-01-01

    Enroute to mapping QTLs for yield components in oil palm, we constructed the linkage map of a FELDA high yielding oil palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi origin. The cross out-yielded the average by 8–21% in four trials all of which yielded comparably to the best current commercial planting materials. The higher yield derived from a higher fruit oil content. SSR markers in the public domain - from CIRAD and MPOB, as well as some developed in FELDA - were used for the mapping, augmented by locally-designed AFLP markers. The female parent linkage map comprised 317 marker loci and the male parent map 331 loci, both in 16 linkage groups each. The number of markers per group ranged from 8–47 in the former and 12–40 in the latter. The integrated map was 2,247.5 cM long and included 479 markers and 168 anchor points. The number of markers per linkage group was 15–57, the average being 29, and the average map density 4.7 cM. The linkage groups ranged in length from 77.5 cM to 223.7 cM, with an average of 137 cM. The map is currently being validated against a closely related population and also being expanded to include yield related QTLs. PMID:22069457

  13. Electronic Structures of LNA Phosphorothioate Oligonucleotides

    DEFF Research Database (Denmark)

    Bohr, Henrik G.; Shim, Irene; Stein, Cy

    2017-01-01

    Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces...... or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical...

  14. 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 ...

  15. Typing of enteroviruses by use of microwell oligonucleotide arrays.

    Science.gov (United States)

    Susi, P; Hattara, L; Waris, M; Luoma-Aho, T; Siitari, H; Hyypiä, T; Saviranta, P

    2009-06-01

    We have developed a straightforward assay for the rapid typing of enteroviruses using oligonucleotide arrays in microtiter wells. The viral nucleic acids are concomitantly amplified and labeled during reverse transcription-PCR, and unpurified PCR products are used for hybridization. DNA strands are separated by alkaline denaturation, and hybridization is started by neutralization. The microarray hybridization reactions and the subsequent washes are performed in standard 96-well microtiter plates, which makes the method easily adaptable to high-throughput analysis. We describe here the assay principle and its potential in clinical laboratory use by correctly identifying 10 different enterovirus reference strains. Furthermore, we explore the detection of unknown sequence variants using serotype consensus oligonucleotide probes. With just two consensus probes for the coxsackievirus A9 (CVA9) serotype, we detected 23 out of 25 highly diverse CVA9 isolates. Overall, the assay involves several features aiming at ease of performance, robustness, and applicability to large-scale studies.

  16. Typing of Enteroviruses by Use of Microwell Oligonucleotide Arrays▿ †

    Science.gov (United States)

    Susi, P.; Hattara, L.; Waris, M.; Luoma-aho, T.; Siitari, H.; Hyypiä, T.; Saviranta, P.

    2009-01-01

    We have developed a straightforward assay for the rapid typing of enteroviruses using oligonucleotide arrays in microtiter wells. The viral nucleic acids are concomitantly amplified and labeled during reverse transcription-PCR, and unpurified PCR products are used for hybridization. DNA strands are separated by alkaline denaturation, and hybridization is started by neutralization. The microarray hybridization reactions and the subsequent washes are performed in standard 96-well microtiter plates, which makes the method easily adaptable to high-throughput analysis. We describe here the assay principle and its potential in clinical laboratory use by correctly identifying 10 different enterovirus reference strains. Furthermore, we explore the detection of unknown sequence variants using serotype consensus oligonucleotide probes. With just two consensus probes for the coxsackievirus A9 (CVA9) serotype, we detected 23 out of 25 highly diverse CVA9 isolates. Overall, the assay involves several features aiming at ease of performance, robustness, and applicability to large-scale studies. PMID:19357207

  17. Extractive Fermentation of Sugarcane Juice to Produce High Yield and Productivity of Bioethanol

    Science.gov (United States)

    Rofiqah, U.; Widjaja, T.; Altway, A.; Bramantyo, A.

    2017-04-01

    Ethanol production by batch fermentation requires a simple process and it is widely used. Batch fermentation produces ethanol with low yield and productivity due to the accumulation of ethanol in which poisons microorganisms in the fermenter. Extractive fermentation technique is applied to solve the microorganism inhibition problem by ethanol. Extractive fermentation technique can produce ethanol with high yield and productivity. In this process raffinate still, contains much sugar because conversion in the fermentation process is not perfect. Thus, to enhance ethanol yield and productivity, recycle system is applied by returning the raffinate from the extraction process to the fermentation process. This raffinate also contains ethanol which would inhibit the performance of microorganisms in producing ethanol during the fermentation process. Therefore, this study aims to find the optimum condition for the amount of solvent to broth ratio (S: B) and recycle to fresh feed ratio (R: F) which enter the fermenter to produce high yield and productivity. This research was carried out by experiment. In the experiment, sugarcane juice was fermented using Zymomonasmobilis mutant. The fermentation broth was extracted using amyl alcohol. The process was integrated with the recycle system by varying the recycle ratio. The highest yield and productivity is 22.3901% and 103.115 g / L.h respectively, obtained in a process that uses recycle to fresh feed ratio (R: F) of 50:50 and solvents to both ratio of 1.

  18. Yield-determining factors in high-solids enzymatic hydrolysis of lignocellulose

    Directory of Open Access Journals (Sweden)

    Felby Claus

    2009-06-01

    Full Text Available Abstract Background Working at high solids (substrate concentrations is advantageous in enzymatic conversion of lignocellulosic biomass as it increases product concentrations and plant productivity while lowering energy and water input. However, for a number of lignocellulosic substrates it has been shown that at increasing substrate concentration, the corresponding yield decreases in a fashion which can not be explained by current models and knowledge of enzyme-substrate interactions. This decrease in yield is undesirable as it offsets the advantages of working at high solids levels. The cause of the 'solids effect' has so far remained unknown. Results The decreasing conversion at increasing solids concentrations was found to be a generic or intrinsic effect, describing a linear correlation from 5 to 30% initial total solids content (w/w. Insufficient mixing has previously been shown not to be involved in the effect. Hydrolysis experiments with filter paper showed that neither lignin content nor hemicellulose-derived inhibitors appear to be responsible for the decrease in yields. Product inhibition by glucose and in particular cellobiose (and ethanol in simultaneous saccharification and fermentation at the increased concentrations at high solids loading plays a role but could not completely account for the decreasing conversion. Adsorption of cellulases was found to decrease at increasing solids concentrations. There was a strong correlation between the decreasing adsorption and conversion, indicating that the inhibition of cellulase adsorption to cellulose is causing the decrease in yield. Conclusion Inhibition of enzyme adsorption by hydrolysis products appear to be the main cause of the decreasing yields at increasing substrate concentrations in the enzymatic decomposition of cellulosic biomass. In order to facilitate high conversions at high solids concentrations, understanding of the mechanisms involved in high-solids product inhibition

  19. Yield-determining factors in high-solids enzymatic hydrolysis of lignocellulose

    Science.gov (United States)

    Kristensen, Jan B; Felby, Claus; Jørgensen, Henning

    2009-01-01

    Background Working at high solids (substrate) concentrations is advantageous in enzymatic conversion of lignocellulosic biomass as it increases product concentrations and plant productivity while lowering energy and water input. However, for a number of lignocellulosic substrates it has been shown that at increasing substrate concentration, the corresponding yield decreases in a fashion which can not be explained by current models and knowledge of enzyme-substrate interactions. This decrease in yield is undesirable as it offsets the advantages of working at high solids levels. The cause of the 'solids effect' has so far remained unknown. Results The decreasing conversion at increasing solids concentrations was found to be a generic or intrinsic effect, describing a linear correlation from 5 to 30% initial total solids content (w/w). Insufficient mixing has previously been shown not to be involved in the effect. Hydrolysis experiments with filter paper showed that neither lignin content nor hemicellulose-derived inhibitors appear to be responsible for the decrease in yields. Product inhibition by glucose and in particular cellobiose (and ethanol in simultaneous saccharification and fermentation) at the increased concentrations at high solids loading plays a role but could not completely account for the decreasing conversion. Adsorption of cellulases was found to decrease at increasing solids concentrations. There was a strong correlation between the decreasing adsorption and conversion, indicating that the inhibition of cellulase adsorption to cellulose is causing the decrease in yield. Conclusion Inhibition of enzyme adsorption by hydrolysis products appear to be the main cause of the decreasing yields at increasing substrate concentrations in the enzymatic decomposition of cellulosic biomass. In order to facilitate high conversions at high solids concentrations, understanding of the mechanisms involved in high-solids product inhibition and adsorption inhibition

  20. Improved forage strategies for high-yielding dairy cows in Vietnam : report of a workshop

    NARCIS (Netherlands)

    Wouters, A.P.; Lee, van der J.

    2013-01-01

    This report presents results of the workshop "Improved forage strategies for high-yielding dairy cows in Vietnam" which was held with Vietnamese stakeholders on January 17-18, 2013 in Ho Chi Minh City as part of the project "Forage and Grass Production for Dairy Development in Vietnam" funded by the

  1. CULTIVAR RELEASE - FAEM Carlasul: new white oat cultivar with high grain yield

    Directory of Open Access Journals (Sweden)

    Antônio Costa de Oliveira

    2012-01-01

    Full Text Available The white oat cultivar FAEM Carlasul was developed at the Plant Genomics and Breeding Center, Faculty of Agronomy Eliseu Maciel, Federal University of Pelotas, as a result of the cross between UFRGS 10 and 90SAT-28 (Coronado2/Cortez3/Pendek/ME 1563. It is characterized by high yield and grain quality.

  2. Barbarasul: a high-yielding and lodging-resistant white oat cultivar

    Directory of Open Access Journals (Sweden)

    Fernando Irajá Félix de Carvalho

    2009-01-01

    Full Text Available The white-oat cultivar Barbarasul was developed by the Universidade Federal de Pelotas. It resulted from across between UPF18 and CTC5. It is adapted to the southern region of Brazil, with excellent grain yield potential, shortstature and high lodging tolerance.

  3. Assessment of growth and yield of some high-and low- cyanide ...

    African Journals Online (AJOL)

    ENGR C.J

    2014-01-29

    Jan 29, 2014 ... 2Department of Crop Production Technology, Federal College of Agriculture, P. M. B. 7008, Ishiagu, Ebonyi State, .... Growth and yield characters of twenty five high-cyanide cassava genotypes in 2004 and 2005 cropping seasons. ..... International Center for Tropical Agriculture (CIAT), Cali Colombia,.

  4. Microbial Electrolysis Cells for High Yield Hydrogen Gas Production from Organic Matter

    NARCIS (Netherlands)

    Logan, B.E.; Call, D.; Cheng, S.; Hamelers, H.V.M.; Sleutels, T.H.J.A.; Jeremiasse, A.W.; Rozendal, R.A.

    2008-01-01

    The use of electrochemically active bacteria to break down organic matter, combined with the addition of a small voltage (>0.2 V in practice) in specially designed microbial electrolysis cells (MECs), can result in a high yield of hydrogen gas. While microbial electrolysis was invented only a few

  5. Mutation breeding of Bacillus subtilis YTB4 with high yield of ...

    African Journals Online (AJOL)

    DR TONUKARI NYEROVWO

    2012-07-17

    Jul 17, 2012 ... activity, bacteria of Bacillus are generally of poor cellulase and amylase activities. Furthermore, there are few reports about the strain of Bacillus of multienzyme complex. In this study, using Bacillus subtilis YTB4 with high yield of multienzyme complex as original strain, we reported our recent attempt to ...

  6. CRSM-38, a new high yielding coupled with CLCuV tolerance cotton ...

    African Journals Online (AJOL)

    Yomi

    2012-03-06

    Mar 6, 2012 ... CRSM-38 is a high yielding and leaf curl virus tolerant cotton variety, developed in Pakistan. Hybridization and subsequent pedigree method's selection work was carried out under natural field conditions at Cotton Research Station, Multan during the year 2001 and 2002 by using a virus tolerant.

  7. Surrogate models for identifying robust, high yield regions of parameter space for ICF implosion simulations

    Science.gov (United States)

    Humbird, Kelli; Peterson, J. Luc; Brandon, Scott; Field, John; Nora, Ryan; Spears, Brian

    2016-10-01

    Next-generation supercomputer architecture and in-transit data analysis have been used to create a large collection of 2-D ICF capsule implosion simulations. The database includes metrics for approximately 60,000 implosions, with x-ray images and detailed physics parameters available for over 20,000 simulations. To map and explore this large database, surrogate models for numerous quantities of interest are built using supervised machine learning algorithms. Response surfaces constructed using the predictive capabilities of the surrogates allow for continuous exploration of parameter space without requiring additional simulations. High performing regions of the input space are identified to guide the design of future experiments. In particular, a model for the yield built using a random forest regression algorithm has a cross validation score of 94.3% and is consistently conservative for high yield predictions. The model is used to search for robust volumes of parameter space where high yields are expected, even given variations in other input parameters. Surrogates for additional quantities of interest relevant to ignition are used to further characterize the high yield regions. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, Lawrence Livermore National Security, LLC. LLNL-ABS-697277.

  8. Thermoplastic polymers surfaces for Dip-Pen Nanolithography of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Suriano, Raffaella [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Biella, Serena, E-mail: serena.biella@polimi.it [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Cesura, Federico; Levi, Marinella; Turri, Stefano [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-05-15

    Different thermoplastic polymers were spin-coated to prepare smooth surfaces for the direct deposition of end-group modified oligonucleotides by Dip-Pen Nanolithography. A study of the diffusion process was done in order to investigate the dependence of calibration coefficient and quality of deposited features on environmental parameters (temperature, relative humidity) and ink's molecular weight and functionality. The optimization of the process parameters led to the realization of high quality and density nanoarrays on plastics.

  9. Observation of yielding and strain hardening in a titanium alloy having high oxygen content

    Energy Technology Data Exchange (ETDEWEB)

    Geng, F., E-mail: iamgengfang@gmail.com [Institute for Materials Research, Tohoku University, Sendai 850-8577 (Japan); Niinomi, M.; Nakai, M. [Institute for Materials Research, Tohoku University, Sendai 850-8577 (Japan)

    2011-06-25

    Highlights: {yields} TNTZ with high oxygen content indicates special mechanical properties. {yields} The phenomenon was explained by the interaction between oxygen atoms and dislocations. {yields} The deformation behavior changes with the addition of oxygen in TNTZ. {yields} There is a specific compositional area of oxygen in TNTZ exhibits good property. - Abstract: Plastic deformation behavior and its relation to tensile properties were investigated in an attractive {beta}-type titanium alloy (Ti-29Nb-13Ta-4.6Zr) with the oxygen content of 0.1-0.7 mass% subjected to hot rolling and solution treatment after hot rolling. Hereafter, Ti-29Nb-13Ta-4.6Zr is abbreviated to TNTZ. With the increase of oxygen content, the tensile strength and 0.2% proof stress of all the samples increase, however, their elongation indicates special change, which is contradictory to that reported conventionally. The elongation firstly decreases and then increases with the increase in the oxygen content. Therefore, TNTZ with high strength and high ductility due to the addition of high oxygen content (0.7 mass%) is obtained. Remarkable yielding phenomenon and strain hardening are observed in TNTZ, which can be explained by the interaction between oxygen atoms and a lot of screw and edge dislocations leading to the easy activation of the multiple slip systems. The deformation behavior changes with the addition of oxygen in TNTZ. The plastic deformation mode changes from the deformation-induced martensite transformation to slip mechanism. It is realized that there is a specific compositional area of oxygen in which the TNTZ exhibits strain hardening and high strength, and appropriate Young's modulus value.

  10. Complexes of carbon nanotubes with oligonucleotides in thin Langmuir-Blodgett films to detect electrochemically hybridization

    Science.gov (United States)

    Egorov, A. S.; Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Orekhovskaya, T. I.; Veligura, A. A.; Govorov, M. I.; Shulitsky, B. G.

    2014-10-01

    Self-assembled complexes consisting of thin multi-walled carbon nanotubes (MWCNTs) and DNA-oligonucleotides which are able to a cooperative binding to complementary oligonucleotides have been investigated. It was establised a high-performance charge transport in nanostructured Langmuir-Blodgett complexes thin MWCNTs/DNA. A method to electrochemically detect DNA hybridization on the self-organized structures has been proposed.

  11. Biogas production from high-yielding energy crops in boreal conditions

    Energy Technology Data Exchange (ETDEWEB)

    Seppala, M.

    2013-11-01

    In this thesis, the methane production potential of traditional and novel energy crops was evaluated in boreal conditions. The highest methane yield per hectare was achieved with maize (4 000-9 200 m{sup 3}CH{sub 4} ha{sup -1} a{sup -1}) and the second highest with brown knapweed (2 700-6 100 m{sup 3}CH{sub 4} ha{sup -1} a{sup -1}). Recently, the most feasible energy crop, grass, produced 1 200-3 600 m{sup 3}CH{sub 4} ha{sup -1} a{sup -1}. The specific methane yields of traditional and novel energy crops varied from 170-500 l kg{sup -1} volatile solid (VS). The highest specific methane yields were obtained with maize, while the novel energy crops were at a lower range. The specific methane yields decreased in the later harvest time with maize and brown knapweed, and the specific methane yield of the grasses decreased from the 1st to 2nd harvests. Maize and brown knapweed produced the highest total solid (TS) yields per hectare 13-23 tTS ha{sup -1}, which were high when compared with the TS yields of grasses (6-13 tTS ha{sup -1}). The feasibility of maize and brown knapweed in co-digestion with liquid cow manure, in continuously stirred tank reactors (CSTR), was evaluated. According to the CSTR runs, maize and brown knapweed are suitable feeds and have stable processes, producing the highest methane yields (organic loading rate 2 kgVS m{sup -3}d{sup -1}), with maize at 259 l kgVS{sup -1} and brown knapweed at 254 l kgVS{sup -1}. The energy balance (input/output) of the cultivation of the grasses, maize and brown knapweed was calculated in boreal conditions, and it was better when the digestate was used as a fertilizer (1.8-4.8 %) than using chemical fertilizers (3.7-16.2 %), whose production is the most energy demanding process in cultivation. In conclusion, the methane production of maize, grasses and novel energy crops can produce high methane yields and are suitable feeds for anaerobic digestion. The cultivation managements of maize and novel energy crops for

  12. Site-directed selection of oligonucleotide antagonists by competitive elution.

    Science.gov (United States)

    Bridonneau, P; Chang, Y F; Buvoli, A V; O'Connell, D; Parma, D

    1999-02-01

    Oligonucleotide ligands that bind a protein or a small molecule of interest are readily isolated by in vitro selection and amplification of rare sequences from combinatorial libraries of sequence-randomized oligonucleotides (Gold et al., 1995). Classic systematic evolution of ligands by exponential enrichment (SELEX) protocols are affinity based (Tuerk and Gold, 1990), but because many problems and applications require antagonists, protocols for selecting inhibitors are both desirable and valuable. A widely applicable approach for isolating inhibitors is competitive elution with a molecule that binds the targeted molecule's active or binding site. We have used this approach to isolate antagonists of wheat germ agglutinin (WGA) from a library of 2'NH2-pyrimidine, 2'OH-purine oligonucleotides by elution with N N' N"-triacetylchitotriose, (GlcNAc)3. The highest affinity aptamers have equilibrium dissociation constants of 1 nM-20 nM for WGA, a 10(3)-10(4)-fold improvement relative to (GlcNAc)3, and unlike the carbohydrate, are highly specific. In addition to competing for binding with (GlcNAc)3, aptamers inhibit WGA-mediated agglutination of sheep erythrocytes, demonstrating that they are able to compete with natural ligands presented on the surfaces of cells. These results illustrate the feasibility of isolating high-affinity, high-specificity antagonists by competitive elution with low molecular weight, relatively low-affinity, and low-specificity small molecules.

  13. Pd0-Catalyzed Methyl Transfer on Nucleosides and Oligonucleotides, Envisaged as a PET Tracer

    Directory of Open Access Journals (Sweden)

    Eric Fouquet

    2013-11-01

    Full Text Available The methyl transfer reaction from activated monomethyltin, via a modified Stille coupling reaction, was studied under “ligandless” conditions on fully deprotected 5'-modified nucleosides and one dinucleotide. The reaction was optimized to proceed in a few minutes and quantitative yield, even under dilute conditions, thus affording a rapid and efficient new method for oligonucleotide labelling with carbon-11.

  14. LNA for Optimization of Fluorescent Oligonucleotide Probes: Improved Spectral Properties and Target Binding

    DEFF Research Database (Denmark)

    Astakhova, Irina V; Ustinov, Alexey V; Korshun, Vladimir A

    2011-01-01

    Mixmer LNA/DNA fluorescent probes containing the 1-(phenylethynyl)pyrene fluorophore attached to 2'-arabino-uridine were synthesized and studied. The conjugates displayed significantly higher hybridization affinity to target DNA, increased fluorescence quantum yields of single-stranded oligonucle......-stranded oligonucleotides and their duplexes, and improved ability to form an interstrand excimer compared to analogous non-LNA probes....

  15. Secondary electron emission yield from high aspect ratio carbon velvet surfaces

    Science.gov (United States)

    Jin, Chenggang; Ottaviano, Angelica; Raitses, Yevgeny

    2017-11-01

    The plasma electrons bombarding a plasma-facing wall surface can induce secondary electron emission (SEE) from the wall. A strong SEE can enhance the power losses by reducing the wall sheath potential and thereby increasing the electron flux from the plasma to the wall. The use of the materials with surface roughness and the engineered materials with surface architecture is known to reduce the effective SEE by trapping the secondary electrons. In this work, we demonstrate a 65% reduction of SEE yield using a velvet material consisting of high aspect ratio carbon fibers. The measurements of SEE yield for different velvet samples using the electron beam in vacuum demonstrate the dependence of the SEE yield on the fiber length and the packing density, which is strongly affected by the alignment of long velvet fibers with respect to the electron beam impinging on the velvet sample. The results of SEE measurements support the previous observations of the reduced SEE measured in Hall thrusters.

  16. Differential Metabolite Profiles during Fruit Development in High-Yielding Oil Palm Mesocarp

    Science.gov (United States)

    Teh, Huey Fang; Neoh, Bee Keat; Hong, May Ping Li; Low, Jaime Yoke Sum; Ng, Theresa Lee Mei; Ithnin, Nalisha; Thang, Yin Mee; Mohamed, Mohaimi; Chew, Fook Tim; Yusof, Hirzun Mohd.; Kulaveerasingam, Harikrishna; Appleton, David R.

    2013-01-01

    To better understand lipid biosynthesis in oil palm mesocarp, in particular the differences in gene regulation leading to and including de novo fatty acid biosynthesis, a multi-platform metabolomics technology was used to profile mesocarp metabolites during six critical stages of fruit development in comparatively high- and low-yielding oil palm populations. Significantly higher amino acid levels preceding lipid biosynthesis and nucleosides during lipid biosynthesis were observed in a higher yielding commercial palm population. Levels of metabolites involved in glycolysis revealed interesting divergence of flux towards glycerol-3-phosphate, while carbon utilization differences in the TCA cycle were proven by an increase in malic acid/citric acid ratio. Apart from insights into the regulation of enhanced lipid production in oil palm, these results provide potentially useful metabolite yield markers and genes of interest for use in breeding programmes. PMID:23593468

  17. Microbial Electrolysis Cells for High Yield Hydrogen Gas Production from Organic Matter

    KAUST Repository

    Logan, Bruce E.

    2008-12-01

    The use of electrochemically active bacteria to break down organic matter, combined with the addition of a small voltage (>0.2 V in practice) in specially designed microbial electrolysis cells (MECs), can result in a high yield of hydrogen gas. While microbial electrolysis was invented only a few years ago, rapid developments have led to hydrogen yields approaching 100%, energy yields based on electrical energy input many times greater than that possible by water electrolysis, and increased gas production rates. MECs used to make hydrogen gas are similar in design to microbial fuel cells (MFCs) that produce electricity, but there are important differences in architecture and analytical methods used to evaluate performance. We review here the materials, architectures, performance, and energy efficiencies of these MEC systems that show promise as a method for renewable and sustainable energy production, and wastewater treatment. © 2008 American Chemical Society.

  18. Differential metabolite profiles during fruit development in high-yielding oil palm mesocarp.

    Directory of Open Access Journals (Sweden)

    Huey Fang Teh

    Full Text Available To better understand lipid biosynthesis in oil palm mesocarp, in particular the differences in gene regulation leading to and including de novo fatty acid biosynthesis, a multi-platform metabolomics technology was used to profile mesocarp metabolites during six critical stages of fruit development in comparatively high- and low-yielding oil palm populations. Significantly higher amino acid levels preceding lipid biosynthesis and nucleosides during lipid biosynthesis were observed in a higher yielding commercial palm population. Levels of metabolites involved in glycolysis revealed interesting divergence of flux towards glycerol-3-phosphate, while carbon utilization differences in the TCA cycle were proven by an increase in malic acid/citric acid ratio. Apart from insights into the regulation of enhanced lipid production in oil palm, these results provide potentially useful metabolite yield markers and genes of interest for use in breeding programmes.

  19. Microbial electrolysis cells for high yield hydrogen gas production from organic matter.

    Science.gov (United States)

    Logan, Bruce E; Call, Douglas; Cheng, Shaoan; Hamelers, Hubertus V M; Sleutels, Tom H J A; Jeremiasse, Adriaan W; Rozendal, René A

    2008-12-01

    The use of electrochemically active bacteria to break down organic matter, combined with the addition of a small voltage (> 0.2 V in practice) in specially designed microbial electrolysis cells (MECs), can result in a high yield of hydrogen gas. While microbial electrolysis was invented only a few years ago, rapid developments have led to hydrogen yields approaching 100%, energy yields based on electrical energy input many times greater than that possible by water electrolysis, and increased gas production rates. MECs used to make hydrogen gas are similar in design to microbial fuel cells (MFCs) that produce electricity, but there are important differences in architecture and analytical methods used to evaluate performance. We review here the materials, architectures, performance, and energy efficiencies of these MEC systems that show promise as a method for renewable and sustainable energy production, and wastewater treatment.

  20. High-Yield Production of Levulinic Acid from Pretreated Cow Dung in Dilute Acid Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Jialei Su

    2017-02-01

    Full Text Available Agricultural waste cow dung was used as feedstock for the production of a high value–added chemical levulinic acid (LA in dilute acid aqueous solutions. A high LA yield of 338.9 g/kg was obtained from the pretreated cow dung, which was much higher than that obtained from the crude cow dung (135 g/kg, mainly attributed to the breakage of the lignin fraction in the lignocellulose structure of the cow dung by potassium hydroxide (KOH pretreatment, and thus enhanced the accessibility of cow dung to the acid sites in the catalytic reaction. Meanwhile, another value-added chemical formic acid could be obtained with a yield of ca. 160 g/kg in the process, implying a total production of ca. 500 g/kg yield for LA and formic acid from the pretreated cow dung with the proposed process. The developed process was shown to be tolerant to high initial substrate loading with a satisfied LA yield. This work provides a promising strategy for the value-increment utilization of liglocellulosic agricultural residues.

  1. Selected wild strains of Agaricus bisporus produce high yields of mushrooms at 25°C.

    Science.gov (United States)

    Navarro, Pilar; Savoie, Jean-Michel

    2015-01-01

    To cultivate the button mushroom Agaricus bisporus in warm countries or during summer in temperate countries, while saving energy, is a challenge that could be addressed by using the biological diversity of the species. The objective was to evaluate the yield potential of eight wild strains previously selected in small scale experiments for their ability to produce mature fruiting bodies at 25°C and above. Culture units of 8 kg of compost were used. The yield expressed as weight or number per surface unit and earliness of fruiting were recorded during cultivation in climatic rooms at 17, 25 or 30°C. Only strains of A. bisporus var. burnettii were able to fruit at 30°C. At 25°C they produced the highest yields (27 kg m(-2)) and had best earliness. The yields at 25°C for the strains of A. bisporus var. bisporus ranged from 12 to 16 kg m(-2). The yield ratios 25°C/17°C ranged from 0.8 to 1.2. The variety burnettii originated in the Sonoran Desert in California showed adaptation for quickly producing fruiting bodies at high temperature when humidity conditions were favorable. Strains of the variety bisporus showed interesting potentials for their ability to produce mature fruiting bodies at higher temperature than present cultivars and might be used in breeding programs. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  2. Synthesis and characterization of poly (dihydroxybiphenyl borate) with high char yield for high-performance thermosetting resins

    Science.gov (United States)

    Wang, Shujuan; Xing, Xiaolong; Li, Jian; Jing, Xinli

    2018-01-01

    The objective of the current work is to synthesize novel boron-containing polymers with excellent thermal resistance, and reveal the structure and the reason for the high char yield. Thus, poly (dihydroxybiphenyl borate) (PDDB) with a more rigid molecular chain, was successfully synthesized using 4,4‧-dihydroxybiphenyl and boric acid. Structural characterizations of the prepared PDDB were performed via NMR, FTIR, XPS, and XRD analyses. The results reveal that PDDB consists of aromatic, Phsbnd Osbnd B and Bsbnd Osbnd B structures as well as a small number of boron hydroxyl and phenolic hydroxyl groups. PDDB shows good solubility in strong polar solvents, which is of great importance for the modification of thermosetting resins. TGA combined with DSC were employed to evaluate the thermal properties of PDDB, and increases in the glass transition temperature (Tg) and char yield were observed with increased boron content. Tg and char yield of PDDB (800 °C, nitrogen atmosphere) reached up to 219 °C and 66.5%, respectively. PDDB was extensively characterized during pyrolysis to reveal the high char yield of PDDB. As briefly discussed, the boron oxide and boron carbide that formed during pyrolysis play a crucial role in the high char yield of PDDB, which reduces the release of volatile carbon dioxide and carbon. This research suggests that PDDB has great potential as a novel modified agent for the improvement of the comprehensive performance of thermosetting resins to broaden their applicability in the field of advanced composites.

  3. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection.

    Science.gov (United States)

    Jung, Il Young; Lee, Eun Hee; Suh, Ah Young; Lee, Seung Jin; Lee, Hyukjin

    2016-04-01

    Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

  4. Antiproliferative effects of antisense oligonucleotides directed to the RNA of c-myc oncogene.

    Science.gov (United States)

    Degols, G; Leonetti, J P; Mechti, N; Lebleu, B

    1991-01-01

    Several groups have reported the use of antisense oligonucleotides to inhibit c-myc gene expression and study its biological role. However high concentrations of free oligonucleotides were generally needed. To lower their concentration and stabilize the antisense effect against c-myc, oligonucleotides were covalently linked to poly(L-lysine) and administered in ternary complexes formed with heparin (100 micrograms/ml). A sequence specific growth inhibition was observed at concentrations lower than 1 microM, while oligonucleotide-poly(L-lysine) conjugates alone were inefficient. Similar results occurred with other polyanionic compounds. Inhibition of proliferation was correlated to a reduction of c-myc protein and to a transient decrease in c-myc mRNA level. However, implication of RNase H in this process could not be demonstrated. Images PMID:1708128

  5. Flow “Fine” Synthesis: High Yielding and Selective Organic Synthesis by Flow Methods

    Science.gov (United States)

    2015-01-01

    Abstract The concept of flow “fine” synthesis, that is, high yielding and selective organic synthesis by flow methods, is described. Some examples of flow “fine” synthesis of natural products and APIs are discussed. Flow methods have several advantages over batch methods in terms of environmental compatibility, efficiency, and safety. However, synthesis by flow methods is more difficult than synthesis by batch methods. Indeed, it has been considered that synthesis by flow methods can be applicable for the production of simple gasses but that it is difficult to apply to the synthesis of complex molecules such as natural products and APIs. Therefore, organic synthesis of such complex molecules has been conducted by batch methods. On the other hand, syntheses and reactions that attain high yields and high selectivities by flow methods are increasingly reported. Flow methods are leading candidates for the next generation of manufacturing methods that can mitigate environmental concerns toward sustainable society. PMID:26337828

  6. Surface studies and implanted helium measurements following NOVA high-yield DT experiments

    Energy Technology Data Exchange (ETDEWEB)

    Stoyer, M.A.; Hudson, G.B.

    1997-02-18

    This paper presents the results of three March 6, 1996 direct-drive high-yield DT NOVA experiments and provides `proof-of-principal` results for the quantitative measurement of energetic He ions. Semiconductor quality Si wafers and an amorphous carbon wafer were exposed to NOVA high-yield implosions. Surface damage was sub-micron in general, although the surface ablation was slightly greater for the carbon wafer than for the Si wafers. Melting of a thin ({approx} 0.1{mu}) layer of Si was evident from microscopic investigation. Electron microscopy indicated melted blobs of many different metals (e.g. Al, Au, Ta, Fe alloys, Cu and even Cd) on the surfaces. The yield measured by determining the numbers of atoms of implanted {sup 4}He and {sup 3}He indicate the number of DT fusions to be 9.1({plus_minus}2.3) X 10{sup 12} and DD fusions to be 4.8({plus_minus}1.0) x 10{sup 10}, respectively. The helium DT fusion yield is slightly lower than that of the Cu activation measurement, which was 1.3({plus_minus}0.l) x 10{sup 13} DT fusions.

  7. Adaptability and stability of corn hybrids grown for high grain yield

    Directory of Open Access Journals (Sweden)

    Paulo Roberto da Silva

    2014-04-01

    Full Text Available The objective of the present study was to evaluate the adaptability and stability of corn hybrids for grain yield in environments with high crop management standards. Ten corn hybrids were evaluated for grain yield in 48 environments, consisting of 12 locations over a period of four years inSouth Brazil. A complete experimental, random block design with two repetitions was used. Adaptability and stability were analyzed according to the bi-segmented discontinuous model with measurement errors in the variables. The behavior of hybrids was studied as a function of the average yield in the inferior and/or superior environments, the estimates of the parameters of the equation, and the quality of the fit. The 30F36 hybrid behaved better in the superior environments and it is indicated for farmers who adopt the highest technological standards for crop management, whereas the 30F53 hybrid was classified as close to ideal; that is, it is indicated for cultivation under various environmental conditions. The 30R50 and 32R48 hybrids are appropriate only for average environments. There is a very good phenotypic stability in simple hybrids associated with high potential yield.

  8. Development of bioprocess for high density cultivation yield of the probiotic Bacillus coagulans and its spores

    Directory of Open Access Journals (Sweden)

    Kavita R. Pandey

    2016-09-01

    Full Text Available Bacillus coagulans is a spore forming lactic acid bacterium. Spore forming bacteria, have been extensively studied and commercialized as probiotics. Probiotics are produced by fermentation technology. There is a limitation to biomass produced by conventional modes of fermentation. With the great demand generated by range of probiotic products, biomass is becoming very valuable for several pharmaceutical, dairy and probiotic companies. Thus, there is a need to develop high cell density cultivation processes for enhanced biomass accumulation. The bioprocess development was carried out in 6.6 L bench top lab scale fermentor. Four different cultivation strategies were employed to develop a bioprocess for higher growth and sporulation efficiencies of probiotic B. coagulans. Batch fermentation of B. coagulans yielded 18 g L-1 biomass (as against 8.0 g L-1 productivity in shake flask with 60% spore efficiency. Fed-batch cultivation was carried out for glucose, which yielded 25 g L-1 of biomass. C/N ratio was very crucial in achieving higher spore titres. Maximum biomass yield recorded was 30 g L-1, corresponding to 3.8 × 1011 cells mL-1 with 81% of cells in sporulated stage. The yield represents increment of 85 times the productivity and 158 times the spore titres relative to the highest reported values for high density cultivation of B. coagulans.

  9. Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction.

    Science.gov (United States)

    Malone, Marie L; Cavett, Valerie J; Paegel, Brian M

    2017-01-09

    Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼106 primers/2.8-μm-diameter bead) via either azide-alkyne click chemistry or Michael addition. The primers are viable polymerase substrates (4-7% bead-immobilized enzymatic extension product yield from one thermal cycle). Carbodiimide-activated carboxylic acid beads only react with oligonucleotides under conditions that promote nonspecific interactions (low salt, low pH, no detergent), comparably immobilizing primers on beads, but yielding no detectable enzymatic extension product. Click-functionalized beads perform satisfactorily in emPCR of a site-saturation mutagenesis library, generating monoclonal templated beads (104-105 copies/bead, 1.4-kb amplicons). This simpler, chemical approach to primer immobilization may spur more economical library preparation for high-throughput sequencing and enable more complex surface elaboration for in vitro evolution.

  10. Designing a high-yielding maize ideotype for a changing climate in Lombardy plain (northern Italy).

    Science.gov (United States)

    Perego, Alessia; Sanna, Mattia; Giussani, Andrea; Chiodini, Marcello Ermido; Fumagalli, Mattia; Pilu, Salvatore Roberto; Bindi, Marco; Moriondo, Marco; Acutis, Marco

    2014-11-15

    The expected climate change will affect the maize yields in view of air temperature increase and scarce water availability. The application of biophysical models offers the chance to design a drought-resistant ideotype and to assist plant breeders and agronomists in the assessment of its suitability in future scenarios. The aim of the present work was to perform a model-based estimation of the yields of two hybrids, current vs ideotype, under future climate scenarios (2030-2060 and 2070-2100) in Lombardy (northern Italy), testing two options of irrigation (small amount at fixed dates vs optimal water supply), nitrogen (N) fertilization (300 vs 400 kg N ha(-1)), and crop cycle durations (current vs extended). For the designing of the ideotype we set several parameters of the ARMOSA process-based crop model: the root elongation rate and maximum depth, stomatal resistance, four stage-specific crop coefficients for the actual transpiration estimation, and drought tolerance factor. The work findings indicated that the current hybrid ensures good production only with high irrigation amount (245-565 mm y(-1)). With respect to the current hybrid, the ideotype will require less irrigation water (-13%, p<0.01) and it resulted in significantly higher yield under water stress condition (+15%, p<0.01) and optimal water supply (+2%, p<0.05). The elongated cycle has a positive effect on yield under any combination of options. Moreover, higher yields projected for the ideotype implicate more crop residues to be incorporated into the soil, which are positively correlated with the SOC sequestration and negatively with N leaching. The crop N uptake is expected to be adequate in view of higher rate of soil mineralization; the N fertilization rate of 400 kg N ha(-1) will involve significant increasing of grain yield, and it is expected to involve a higher rate of SOC sequestration. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Metabolic engineering of biomass for high energy density: oilseed-like triacylglycerol yields from plant leaves.

    Science.gov (United States)

    Vanhercke, Thomas; El Tahchy, Anna; Liu, Qing; Zhou, Xue-Rong; Shrestha, Pushkar; Divi, Uday K; Ral, Jean-Philippe; Mansour, Maged P; Nichols, Peter D; James, Christopher N; Horn, Patrick J; Chapman, Kent D; Beaudoin, Frederic; Ruiz-López, Noemi; Larkin, Philip J; de Feyter, Robert C; Singh, Surinder P; Petrie, James R

    2014-02-01

    High biomass crops have recently attracted significant attention as an alternative platform for the renewable production of high energy storage lipids such as triacylglycerol (TAG). While TAG typically accumulates in seeds as storage compounds fuelling subsequent germination, levels in vegetative tissues are generally low. Here, we report the accumulation of more than 15% TAG (17.7% total lipids) by dry weight in Nicotiana tabacum (tobacco) leaves by the co-expression of three genes involved in different aspects of TAG production without severely impacting plant development. These yields far exceed the levels found in wild-type leaf tissue as well as previously reported engineered TAG yields in vegetative tissues of Arabidopsis thaliana and N. tabacum. When translated to a high biomass crop, the current levels would translate to an oil yield per hectare that exceeds those of most cultivated oilseed crops. Confocal fluorescence microscopy and mass spectrometry imaging confirmed the accumulation of TAG within leaf mesophyll cells. In addition, we explored the applicability of several existing oil-processing methods using fresh leaf tissue. Our results demonstrate the technical feasibility of a vegetative plant oil production platform and provide for a step change in the bioenergy landscape, opening new prospects for sustainable food, high energy forage, biofuel and biomaterial applications. © 2013 CSIRO. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  12. High Precision and High Yield Fabrication of Dense Nanoparticle Arrays onto DNA Origami at Statistically Independent Binding Sites †

    Science.gov (United States)

    Takabayashi, Sadao; Klein, William P.; Onodera, Craig; Rapp, Blake; Flores-Estrada, Juan; Lindau, Elias; Snowball, Lejmarc; Sam, Joseph Tyler; Padilla, Jennifer E.; Lee, Jeunghoon; Knowlton, William B.; Graugnard, Elton; Yurke, Bernard; Kuang, Wan; Hughes, William L.

    2015-01-01

    High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities. PMID:25311051

  13. Recent developments in reversible photoregulation of oligonucleotide structure and function.

    Science.gov (United States)

    Lubbe, Anouk S; Szymanski, Wiktor; Feringa, Ben L

    2017-02-20

    There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.

  14. Development of High Yield Feedstocks and Biomass Conversion Technology for Renewable Energy

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, Andrew G. [Univ. of Hawaii, Honolulu, HI (United States); Crow, Susan [Univ. of Hawaii, Honolulu, HI (United States); DeBeryshe, Barbara [Univ. of Hawaii, Honolulu, HI (United States); Ha, Richard [Hamakua Springs County Farms, Hilo, HI (United States); Jakeway, Lee [Hawaiian Commercial and Sugar Company, Puunene, HI (United States); Khanal, Samir [Univ. of Hawaii, Honolulu, HI (United States); Nakahata, Mae [Hawaiian Commercial and Sugar Company, Puunene, HI (United States); Ogoshi, Richard [Univ. of Hawaii, Honolulu, HI (United States); Shimizu, Erik [Univ. of Hawaii, Honolulu, HI (United States); Stern, Ivette [Univ. of Hawaii, Honolulu, HI (United States); Turano, Brian [Univ. of Hawaii, Honolulu, HI (United States); Turn, Scott [Univ. of Hawaii, Honolulu, HI (United States); Yanagida, John [Univ. of Hawaii, Honolulu, HI (United States)

    2015-04-09

    This project had two main goals. The first goal was to evaluate several high yielding tropical perennial grasses as feedstock for biofuel production, and to characterize the feedstock for compatible biofuel production systems. The second goal was to assess the integration of renewable energy systems for Hawaii. The project focused on high-yield grasses (napiergrass, energycane, sweet sorghum, and sugarcane). Field plots were established to evaluate the effects of elevation (30, 300 and 900 meters above sea level) and irrigation (50%, 75% and 100% of sugarcane plantation practice) on energy crop yields and input. The test plots were extensive monitored including: hydrologic studies to measure crop water use and losses through seepage and evapotranspiration; changes in soil carbon stock; greenhouse gas flux (CO2, CH4, and N2O) from the soil surface; and root morphology, biomass, and turnover. Results showed significant effects of environment on crop yields. In general, crop yields decrease as the elevation increased, being more pronounced for sweet sorghum and energycane than napiergrass. Also energy crop yields were higher with increased irrigation levels, being most pronounced with energycane and less so with sweet sorghum. Daylight length greatly affected sweet sorghum growth and yields. One of the energy crops (napiergrass) was harvested at different ages (2, 4, 6, and 8 months) to assess the changes in feedstock characteristics with age and potential to generate co-products. Although there was greater potential for co-products from younger feedstock, the increased production was not sufficient to offset the additional cost of harvesting multiple times per year. The feedstocks were also characterized to assess their compatibility with biochemical and thermochemical conversion processes. The project objectives are being continued through additional support from the Office of Naval Research, and the Biomass Research and Development

  15. Fluoro-Julia Olefination as a Mild, High-Yielding Route to α-Fluoro Acrylonitriles†

    Science.gov (United States)

    del Solar, Maria; Ghosh, Arun K.; Zajc, Barbara

    2009-01-01

    Synthesis of a novel, stable reagent (1,3-benzothiazol-2-ylsulfonyl)fluoroacetonitrile from readily available ethyl α-(1,3-benzothiazol-2-ylsulfanyl)- α-fluoroacetate is reported. Aldehydes undergo condensations with (1,3-benzothiazol-2-ylsulfonyl)fluoroacetonitrile in the presence of DBU leading to α-fluoro acrylonitriles in high yields and with good Z-stereoselectivity. Lowering of reaction temperature increases the Z selectivity. PMID:18841918

  16. Fluoro-Julia olefination as a mild, high-yielding route to alpha-fluoro acrylonitriles.

    Science.gov (United States)

    del Solar, Maria; Ghosh, Arun K; Zajc, Barbara

    2008-11-07

    Synthesis of a novel, stable reagent (1,3-benzothiazol-2-ylsulfonyl)fluoroacetonitrile from readily synthesized ethyl alpha-(1,3-benzothiazol-2-ylsulfanyl)-alpha-fluoroacetate is reported. Aldehydes undergo condensations with (1,3-benzothiazol-2-ylsulfonyl)fluoroacetonitrile in the presence of DBU leading to alpha-fluoro acrylonitriles in high yields and with good Z-stereoselectivity. Lowering of reaction temperature increases the Z selectivity.

  17. Construction high-yield candidate influenza vaccine viruses in Vero cells by reassortment.

    Science.gov (United States)

    Yu, Wei; Yang, Fan; Yang, Jinghui; Ma, Lei; Cun, Yina; Song, Shaohui; Liao, Guoyang

    2016-11-01

    Usage of influenza vaccine is the best choice measure for preventing and conclusion of influenza virus infection. Although it has been used of chicken embryo to produce influenza vaccine, following with WHO recommended vaccine strain, there were uncontrollable factors and its deficiencies, specially, during an influenza pandemic in the world. The Vero cells are used for vaccine production of a few strains including influenza virus, because of its homology with human, recommended by WHO. However, as known most of the influenza viruses strains could not culture by Vero cells. It was used two high-yield influenza viruses adapted in Vero cells as donor viruses, such as A/Yunnan/1/2005Va (H3N2) and B/Yunnan/2/2005Va (B), to construct high-yield wild influenza virus in Vero cells under antibody selection pressure. After reassortment and passages, it obtained the new Vaccine strains with A/Tianjin/15/2009Va (H1N1), A/Fujian/196/2009Va (H3N2) and B/Chongqing/1384/2010Va (B), which was not only completely keeping their original antigenic (HA and NA), but also grown well in Vero cells with high-yield. All results of gene analysis and HA, HI shown that this reassortment method could be used to find new direction to product the influenza vaccine. J. Med. Virol. 88:1914-1921, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  18. Synthesis of Luminescent Graphene Quantum Dots with High Quantum Yield and Their Toxicity Study.

    Directory of Open Access Journals (Sweden)

    Dan Jiang

    Full Text Available High fluorescence quantum yield graphene quantum dots (GQDs have showed up as a new generation for bioimaging. In this work, luminescent GQDs were prepared by an ameliorative photo-Fenton reaction and a subsequent hydrothermal process using graphene oxide sheets as the precursor. The as-prepared GQDs were nanomaterials with size ranging from 2.3 to 6.4 nm and emitted intense green luminescence in water. The fluorescence quantum yield was as high as 24.6% (excited at 340 nm and the fluorescence was strongest at pH 7. Moreover, the influences of low-concentration (12.5, 25 μg/mL GQDs on the morphology, viability, membrane integrity, internal cellular reactive oxygen species level and mortality of HeLa cells were relatively weak, and the in vitro imaging demonstrated GQDs were mainly in the cytoplasm region. More strikingly, zebrafish embryos were co-cultured with GQDs for in vivo imaging, and the results of heart rate test showed the intake of small amounts of GQDs brought little harm to the cardiovascular of zebrafish. GQDs with high quantum yield and strong photoluminescence show good biocompatibility, thus they show good promising for cell imaging, biolabeling and other biomedical applications.

  19. Synthesis of Luminescent Graphene Quantum Dots with High Quantum Yield and Their Toxicity Study

    Science.gov (United States)

    Jiang, Dan; Chen, Yunping; Li, Na; Li, Wen; Wang, Zhenguo; Zhu, Jingli; Zhang, Hong; Liu, Bin; Xu, Shan

    2015-01-01

    High fluorescence quantum yield graphene quantum dots (GQDs) have showed up as a new generation for bioimaging. In this work, luminescent GQDs were prepared by an ameliorative photo-Fenton reaction and a subsequent hydrothermal process using graphene oxide sheets as the precursor. The as-prepared GQDs were nanomaterials with size ranging from 2.3 to 6.4 nm and emitted intense green luminescence in water. The fluorescence quantum yield was as high as 24.6% (excited at 340 nm) and the fluorescence was strongest at pH 7. Moreover, the influences of low-concentration (12.5, 25 μg/mL) GQDs on the morphology, viability, membrane integrity, internal cellular reactive oxygen species level and mortality of HeLa cells were relatively weak, and the in vitro imaging demonstrated GQDs were mainly in the cytoplasm region. More strikingly, zebrafish embryos were co-cultured with GQDs for in vivo imaging, and the results of heart rate test showed the intake of small amounts of GQDs brought little harm to the cardiovascular of zebrafish. GQDs with high quantum yield and strong photoluminescence show good biocompatibility, thus they show good promising for cell imaging, biolabeling and other biomedical applications. PMID:26709828

  20. Clinical utilization of high-resolution single nucleotide polymorphism based oligonucleotide arrays in diagnostic studies of pediatric patients with solid tumors.

    Science.gov (United States)

    Dougherty, Margaret J; Tooke, Laura S; Sullivan, Lisa M; Hakonarson, Hakon; Wainwright, Luanne M; Biegel, Jaclyn A

    2012-01-01

    High-resolution single nucleotide polymorphism (SNP) arrays have been effectively implemented as a first tier test in clinical cytogenetics laboratories for the detection of constitutional chromosomal abnormalities in patients with suspected genomic disorders. We recently published our experience utilizing SNP array analysis of bone marrow aspirates as a clinical test for patients with suspected leukemia or lymphoma in the Clinical Cancer Cytogenetics Laboratory at The Children's Hospital of Philadelphia. In the present report we summarize our clinical experience using the Illumina HumanHap610 BeadChip array (Illumina, San Diego, CA) for whole genome analysis of pediatric solid tumors. A total of 168 DNA samples isolated from a variety of solid tumors, including brain tumors, sarcomas, neuroblastomas, and Wilms tumors, as well as benign neoplasms and reactive processes, were analyzed over a 2 1/2 year period. One hundred thirty-seven of 168 (82%) specimens had at least one copy number alteration or region of loss of heterozygosity detected by the SNP array. Thirty-three of 168 (20%) of cases had a normal karyotype or targeted fluorescence in situ hybridization (FISH) study, but had an abnormal finding by the array analysis. Sixty-three of 168 (37%) samples for which cytogenetic studies were unsuccessful or not performed demonstrated an abnormal array result. In 44 of 168 cases (26%) the array and karyotype or FISH were abnormal, but each demonstrated alterations not detected by the other methodology. Based on our experience in the last 2 1/2 years, we suggest that SNP array analysis can be used as a first tier clinical test for the majority of pediatric solid tumors. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Economics of fertility in high-yielding dairy cows on confined TMR systems.

    Science.gov (United States)

    Cabrera, V E

    2014-05-01

    The objective of this review paper was to summarise the latest findings in dairy cattle reproductive economics with an emphasis on high yielding, confined total mixed ration systems. The economic gain increases as the reproductive efficiency improves. These increments follow the law of diminishing returns, but are still positive even at high reproductive performance. Reproductive improvement results in higher milk productivity and, therefore, higher milk income over feed cost, more calf sales and lower culling and breeding expenses. Most high-yielding herds in the United States use a combination of timed artificial insemination (TAI) and oestrous detection (OD) reproductive programme. The ratio of achievable pregnancies between OD and TAI determines the economic value difference between both and their combinations. Nonetheless, complex interactions between reproductive programme, herd relative milk yield, and type of reproductive programme are reported. For example, higher herd relative milk yield would favour programme relying more on TAI. In addition, improved reproductive efficiency produces extra replacements. The availability of additional replacements could allow more aggressive culling policies (e.g. less services for non-pregnant cows) to balance on-farm supply and demand of replacements. Balancing heifer replacement availability in an efficient reproductive programme brings additional economic benefits. New technologies such as the use of earlier chemical tests for pregnancy diagnosis could be economically effective depending on the goals and characteristics of the farm. Opportunities for individual cow reproductive management within defined reproductive programme exist. These decisions would be based on economic metrics derived from the value of a cow such as the value of a new pregnancy, the cost of a pregnancy loss, or the cost of an extra day open.

  2. High yield polycarbosilane precursors to stoichiometric SiC. Synthesis, pyrolysis and application

    Energy Technology Data Exchange (ETDEWEB)

    Interrante, L.V.; Wu, H.J. [Rensselaer Polytechnic Inst., Troy, NY (United States). Dept. of Chemistry; Whitmarsh, C.W.; Sherwood, W. [Starfire Systems, Inc., Glenville, NY (United States); Lewis, R.; Maciel, G. [Colorado State Univ., Fort Collins, CO (United States). Dept. of Chemistry

    1994-12-31

    The synthesis and properties of two polycarbosilanes that have essentially a ``SiH{sub 2}CH{sub 2}`` composition is described. One of these polymers is a highly branched hydridopolycarbosilane (HPCS) derived from Grignard coupling of Cl{sub 3}SiCH{sub 2}Cl followed by LiAlH{sub 4} reduction. This synthesis is amenable to large scale production and the authors are exploring applications of HPCS as a source of SiC coatings and its allyl-derivative, AHPCS, as a matrix source for SiC and C-fiber reinforced composites. These polymers thermoset on heating at 200--400 C (or at 100 C with a catalyst) and give near stoichiometric SiC with low O content in ca. 80% yield on pyrolysis to 1,000 C. The second method involves ring-opening polymerization of 1,1,3,3-tetrachlorodisilacyclobutane and yields a high molecular weight, linear polymer that can be reduced to [SiH{sub 2}CH{sub 2}]{sub n} (PSE), the monosilicon analog of polyethylene. In contrast to high density polyethylene which melts at 135 C, PSE is a liquid at room temperature which crystallizes at ca. 5 C. On pyrolysis to 1,000 C, PSE gives stoichiometric, nanocrystalline, SiC in virtually quantitative yield. The polymer-to-ceramic conversion was examined for PSE by using TGA, mass spec., solid state NMR, and IR methods yielding information regarding the cross-linking and structural evolution processes. The results of these studies of the polymer-to-ceramic conversion process and their efforts to employ the AHPCS polymer as a source of SiC matrices are described.

  3. High Titer and Yields Achieved with Novel, Low-Severity Pretreatment Strategy

    Energy Technology Data Exchange (ETDEWEB)

    2016-03-01

    NREL researchers obtained high concentration sugar syrups in enzymatic hydrolysis that are fermentable to ethanol and other advanced biofuels and intermediate products at high yields. The novel DMR process is simpler and bypasses all severe pretreatment methods, thus reducing the environmental impact. The results are unprecedented. Researchers achieved a high concentration of sugars (230g/L of monomeric sugar and 270 g/L total sugar) and this low toxicity, highly fermentable syrup yielded 86 g/L ethanol (> 90 percent conversion). In addition, the lignin streams from this process can readily be converted to jet or renewable diesel blendstocks through a hydrodeoxygenation step. The NREL-developed, low severity DMR process may potentially replace higher severity chemical pretreatments and associated expensive reactors constructed of exotic alloys with a simpler process, using commercial-scale equipment commonly associated with the pulp and paper industry, to produce high concentration, low toxicity sugar streams and highly reactive lignin streams from non-food renewable biomass for biological and catalytic upgrading to advanced biofuels and chemicals. The simpler DMR process with black liquor recycling could reduce environmental and life-cycle impacts, and repurpose shuttered pulp and paper mills to help revitalize rural economies.

  4. Once-daily milking effects in high-yielding Alpine dairy goats.

    Science.gov (United States)

    Komara, M; Boutinaud, M; Ben Chedly, H; Guinard-Flament, J; Marnet, P G

    2009-11-01

    Two experiments were conducted to determine the milk loss of high-yielding Alpine goats resulting from once-daily milking (ODM) and its relationship to udder cisternal size. We investigated the effects of application of this management strategy on milk yield, composition, and technological parameters: lipolysis, fat globule size, and cheese yield. In a second experiment, we investigated the effect of repeated periods of ODM management during lactation. Goats at the beginning of both experiments were at 25 d in milk on average and were previously milked twice daily (twice-daily milking; TDM). In experiment 1, which was conducted for 2 periods (P) of 9 wk (P1, P2), 48 goats were grouped (1, 2, 3, and 4) according to milk yield, parity, and somatic cell count (SCC). Over the 2 periods, goats from group 1 were managed with TDM and those from group 2 were managed with ODM. In group 3, goats were assigned to TDM during P1 and ODM during P2, conversely, those in group 4 were assigned to ODM in P1 and TDM in P2. During P1, the 12 goats from group 3 underwent 2 distinct morning machine milkings to measure milk repartition (cisternal and alveolar) in the udder based on the "atosiban method." On P1 plus the P2 period of 18 wk, milk loss caused by ODM (compared with TDM) was 16%. In our condition of 24-h milk accumulation, there was no correlation between milk loss and udder cisternal size. Milk fat content, fat globule size, or apparent laboratory cheese yield was not modified by ODM, but milk protein content (+2.7 g/kg), casein (+1.8 g/kg), milk soluble protein concentration (+1.0 g/kg), and SCC increased, whereas lipolysis decreased (-0.3 mEq/100 g of oleic acid). In experiment 2, which was conducted for 4 periods (P1, P2, P3, P4) of 5 wk each, 8 goats, blocked into 2 homogenous groups (5 and 6), were used to study the effects of a double inversion of milking frequency (TDM or ODM) for 20 wk of lactation. Milk loss was 17% and ODM did not modify milk fat or protein contents

  5. HIGH YIELD AND RAPID SYNTHESES METHODS FOR PRODUCING METALLO-ORGANIC SALTS

    DEFF Research Database (Denmark)

    2005-01-01

    A new method for preparing salts of metal cations and organic acids, especially divalent salts of alkaline earth metal ions from group II of the periodic system and carboxylic acids. The method comprising the use of a high temperature (about 90° or more) and, optionally. high pressure, in order...... to obtain a higher yield, purity and faster reaction speed than obtained with known synthesis methods. In particular, the present invention relates to the production of strontium salts of carboxylic acids. Novel strontium salts are also provided by the present method....

  6. High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway

    Science.gov (United States)

    Zhang, Y.-H. Percival; Evans, Barbara R.; Mielenz, Jonathan R.; Hopkins, Robert C.; Adams, Michael W.W.

    2007-01-01

    Background The future hydrogen economy offers a compelling energy vision, but there are four main obstacles: hydrogen production, storage, and distribution, as well as fuel cells. Hydrogen production from inexpensive abundant renewable biomass can produce cheaper hydrogen, decrease reliance on fossil fuels, and achieve zero net greenhouse gas emissions, but current chemical and biological means suffer from low hydrogen yields and/or severe reaction conditions. Methodology/Principal Findings Here we demonstrate a synthetic enzymatic pathway consisting of 13 enzymes for producing hydrogen from starch and water. The stoichiometric reaction is C6H10O5 (l)+7 H2O (l)→12 H2 (g)+6 CO2 (g). The overall process is spontaneous and unidirectional because of a negative Gibbs free energy and separation of the gaseous products with the aqueous reactants. Conclusions Enzymatic hydrogen production from starch and water mediated by 13 enzymes occurred at 30°C as expected, and the hydrogen yields were much higher than the theoretical limit (4 H2/glucose) of anaerobic fermentations. Significance The unique features, such as mild reaction conditions (30°C and atmospheric pressure), high hydrogen yields, likely low production costs ($∼2/kg H2), and a high energy-density carrier starch (14.8 H2-based mass%), provide great potential for mobile applications. With technology improvements and integration with fuel cells, this technology also solves the challenges associated with hydrogen storage, distribution, and infrastructure in the hydrogen economy. PMID:17520015

  7. High-yield hydrogen production from starch and water by a synthetic enzymatic pathway.

    Directory of Open Access Journals (Sweden)

    Y-H Percival Zhang

    Full Text Available BACKGROUND: The future hydrogen economy offers a compelling energy vision, but there are four main obstacles: hydrogen production, storage, and distribution, as well as fuel cells. Hydrogen production from inexpensive abundant renewable biomass can produce cheaper hydrogen, decrease reliance on fossil fuels, and achieve zero net greenhouse gas emissions, but current chemical and biological means suffer from low hydrogen yields and/or severe reaction conditions. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate a synthetic enzymatic pathway consisting of 13 enzymes for producing hydrogen from starch and water. The stoichiometric reaction is C(6H(10O(5 (l+7 H(2O (l-->12 H(2 (g+6 CO(2 (g. The overall process is spontaneous and unidirectional because of a negative Gibbs free energy and separation of the gaseous products with the aqueous reactants. CONCLUSIONS: Enzymatic hydrogen production from starch and water mediated by 13 enzymes occurred at 30 degrees C as expected, and the hydrogen yields were much higher than the theoretical limit (4 H(2/glucose of anaerobic fermentations. SIGNIFICANCE: The unique features, such as mild reaction conditions (30 degrees C and atmospheric pressure, high hydrogen yields, likely low production costs ($ approximately 2/kg H(2, and a high energy-density carrier starch (14.8 H(2-based mass%, provide great potential for mobile applications. With technology improvements and integration with fuel cells, this technology also solves the challenges associated with hydrogen storage, distribution, and infrastructure in the hydrogen economy.

  8. Research Advances in High-Yielding Cultivation and Physiology of Super Rice

    Directory of Open Access Journals (Sweden)

    Jing FU

    2012-09-01

    Full Text Available In 1996, China launched a program to breed super rice or super hybrid rice by combining intersubspecific heterosis with ideal plant types. Today, approximately 80 super rice varieties have been released and some of them show high grain yields of 12–21 t/hm2 in field experiments. The main reasons for the high yields of super rice varieties, compared with those of conventional varieties, can be summarized as follows: more spikelets per panicle and larger sink size (number of spikelets per square meter; larger leaf area index, longer duration of green leaf, greater photosynthetic rate, higher lodging resistance, greater dry matter accumulation before the heading stage, greater remobilization of pre-stored carbohydrates from stems and leaves to grains during the grain-filling period; and larger root system and greater root activity. However, there are two main problems in super rice production: poor grain-filling of the later-flowering inferior spikelets (in contrast to earlier-flowering superior spikelets, and low and unstable seed-setting rate. Here, we review recent research advances in the crop physiology of super rice, focusing on biological features, formation of yield components, and population quality. Finally, we suggest further research on crop physiology of super rice.

  9. Coupling Strategies for the Synthesis of Peptide-Oligonucleotide Conjugates for Patterned Synthetic Biomineralization

    Directory of Open Access Journals (Sweden)

    Joshua D. Carter

    2011-01-01

    Full Text Available This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl carbodiimide hydrochloride and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl-4-methyl-morpholinium chloride, and two in dimethylformamide (DMF, PyBOP ((Benzotriazol-1-yloxy tripyrrolidinophosphonium hexafluorophosphate and HBTU (O-benzotriazole-N,N,N′,N′-tetramethyluronium hexafluorophosphate, while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5′ amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95% and solid-phase strategies (24%, while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability.

  10. Responses of Yield Characteristics to High Temperature During Flowering Stage in Hybrid Rice Guodao 6

    Directory of Open Access Journals (Sweden)

    Guan-fu FU

    2008-09-01

    Full Text Available By sowing at different dates during 2005 and 2006 both in paddy fields and greenhouse, a super hybrid rice combination Guodao 6 and a conventional hybrid rice combination Xieyou 46 (as control were used to analyze the differences in heat injury index, seed setting rate, grain yield and its components. Guodao 6 showed more stable yield and spikelet fertility, and lower heat injury index than Xieyou 46. Further studies indicated that the spikelet sterility is positively correlated with the average daily temperature and the maximum daily temperature, with the coefficients of 0.8604 and 0.9850 (P<0.05 respectively in Guodao 6. The effect of high temperature injury on seed setting caused by maximum daily temperature was lower than that by average daily temperature during the grain filling stage.

  11. Variation in Yield Responses to Elevated CO₂ and a Brief High Temperature Treatment in Quinoa.

    Science.gov (United States)

    Bunce, James A

    2017-07-05

    Intraspecific variation in crop responses to global climate change conditions would provide opportunities to adapt crops to future climates. These experiments explored intraspecific variation in response to elevated CO₂ and to high temperature during anthesis in Chenopodium quinoa Wild. Three cultivars of quinoa were grown to maturity at 400 ("ambient") and 600 ("elevated") μmol·mol(-1) CO₂ concentrations at 20/14 °C day/night ("control") temperatures, with or without exposure to day/night temperatures of 35/29 °C ("high" temperatures) for seven days during anthesis. At control temperatures, the elevated CO₂ concentration increased the total aboveground dry mass at maturity similarly in all cultivars, but by only about 10%. A large down-regulation of photosynthesis at elevated CO₂ occurred during grain filling. In contrast to shoot mass, the increase in seed dry mass at elevated CO₂ ranged from 12% to 44% among cultivars at the control temperature. At ambient CO₂, the week-long high temperature treatment greatly decreased (0.30 × control) or increased (1.70 × control) seed yield, depending on the cultivar. At elevated CO₂, the high temperature treatment increased seed yield moderately in all cultivars. These quinoa cultivars had a wide range of responses to both elevated CO₂ and to high temperatures during anthesis, and much more variation in harvest index responses to elevated CO₂ than other crops that have been examined.

  12. Optimization of Escherichia coli cultivation methods for high yield neuropeptide Y receptor type 2 production.

    Science.gov (United States)

    Berger, Christian; Montag, Cindy; Berndt, Sandra; Huster, Daniel

    2011-03-01

    The recombinant expression of human G protein-coupled receptors usually yields low production levels using commonly available cultivation protocols. Here, we describe the development of a high yield production protocol for the human neuropeptide Y receptor type 2 (Y2R), which provides the determination of expression levels in a time, media composition, and process parameter dependent manner. Protein was produced by Escherichia coli in a defined medium composition suitable for isotopic labeling required for investigations by nuclear magnetic resonance spectroscopy. The Y2 receptor was fused to a C-terminal 8x histidine tag by means of the pET vector system for easy one-step purification via affinity chromatography, yielding a purity of 95-99% for every condition tested, which was determined by SDS-PAGE and Western blot analysis. The Y2 receptor was expressed as inclusion body aggregates in complex media and minimal media, using different carbon sources. We investigated the influences of media composition, temperature, pH, and set specific growth rate on cell behavior, biomass wet weight specific and culture volume specific amounts of the target protein, which had been identified by inclusion body preparation, solubilization, followed by purification and spectrometric determination of the protein concentration. The developed process control strategy led to very high reproducibility of cell growth and protein concentrations with a maximum yield of 800 μg purified Y2 receptor per gram wet biomass when glycerol was used as carbon source in the mineral salt medium composition (at 38 °C, pH 7.0, and a set specific growth rate of 0.14 g/(gh)). The maximum biomass specific amount of purified Y2 receptor enabled the production of 35 mg Y2R per liter culture medium at an optical density (600 nm) of 25. Copyright © 2010 Elsevier Inc. All rights reserved.

  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. Wafer scale fabrication of carbon nanotube thin film transistors with high yield

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Boyuan; Liang, Xuelei, E-mail: liangxl@pku.edu.cn, E-mail: ssxie@iphy.ac.cn; Yan, Qiuping; Zhang, Han; Xia, Jiye; Dong, Guodong; Peng, Lianmao [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China); Xie, Sishen, E-mail: liangxl@pku.edu.cn, E-mail: ssxie@iphy.ac.cn [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China); Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2016-07-21

    Carbon nanotube thin film transistors (CNT-TFTs) are promising candidates for future high performance and low cost macro-electronics. However, most of the reported CNT-TFTs are fabricated in small quantities on a relatively small size substrate. The yield of large scale fabrication and the performance uniformity of devices on large size substrates should be improved before the CNT-TFTs reach real products. In this paper, 25 200 devices, with various geometries (channel width and channel length), were fabricated on 4-in. size ridged and flexible substrates. Almost 100% device yield were obtained on a rigid substrate with high out-put current (>8 μA/μm), high on/off current ratio (>10{sup 5}), and high mobility (>30 cm{sup 2}/V·s). More importantly, uniform performance in 4-in. area was achieved, and the fabrication process can be scaled up. The results give us more confidence for the real application of the CNT-TFT technology in the near future.

  15. High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders.

    Science.gov (United States)

    Yavarna, Tarunashree; Al-Dewik, Nader; Al-Mureikhi, Mariam; Ali, Rehab; Al-Mesaifri, Fatma; Mahmoud, Laila; Shahbeck, Noora; Lakhani, Shenela; AlMulla, Mariam; Nawaz, Zafar; Vitazka, Patrik; Alkuraya, Fowzan S; Ben-Omran, Tawfeg

    2015-09-01

    Clinical exome sequencing (CES) has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. Utility of CES in consanguineous populations has not yet been determined on a large scale. A clinical cohort of 149 probands from Qatar with suspected Mendelian, mainly neurocognitive phenotypes, underwent CES from July 2012 to June 2014. Intellectual disability and global developmental delay were the most common clinical presentations but our cohort displayed other phenotypes, such as epilepsy, dysmorphism, microcephaly and other structural brain anomalies and autism. A pathogenic or likely pathogenic mutation, including pathogenic CNVs, was identified in 89 probands for a diagnostic yield of 60%. Consanguinity and positive family history predicted a higher diagnostic yield. In 5% (7/149) of cases, CES implicated novel candidate disease genes (MANF, GJA9, GLG1, COL15A1, SLC35F5, MAGE4, NEUROG1). CES uncovered two coexisting genetic disorders in 4% (6/149) and actionable incidental findings in 2% (3/149) of cases. Average time to diagnosis was reduced from 27 to 5 months. CES, which already has the highest diagnostic yield among all available diagnostic tools in the setting of Mendelian disorders, appears to be particularly helpful diagnostically in the highly consanguineous Middle Eastern population.

  16. Photosynthesis of the flag leaf blade and its sheath in high-yielding hybrid rice 'Liangyoupeijiu'.

    Science.gov (United States)

    Guo, Zhao-Wu; Li, He-Song; Wang, Ruo-Zhong; Xiao, Lang-Tao

    2007-12-01

    Using high-yielding hybrid rice 'Liangyoupeijiu' (LYP9) and hybrid rice 'Shanyou 63' (SY63) as the experimental materials and using (14)C radio-autography, the photosynthetic capacities and distribution of photosynthates in flag leaf blades and sheaths of LYP9 were studied. The results showed that net photosynthetic rates (Pn) of the flag leaf blades and sheaths of LYP9 were much higher than those of SY63; the light transmissivity rates (LT) measured at the medium height of the flag leaf sheaths and the penultimate leaf sheaths were also significantly higher than those of SY63. The incipient activities, total activities and activation percentages of Rubisco in the flag leaf blade and sheath of LYP9 were all higher than those of SY63. The photosynthate transport rate in the sheaths of LYP9, and the quantity of photosynthate transported to the spikes and transformed to economic yield of LYP9 were all higher than those of SY63. The photosynthates produced by the sheaths were mainly transported to spike to make a certain contribution (about 15%) to yield.

  17. Cacao Cultivation under Diverse Shade Tree Cover Allows High Carbon Storage and Sequestration without Yield Losses.

    Science.gov (United States)

    Abou Rajab, Yasmin; Leuschner, Christoph; Barus, Henry; Tjoa, Aiyen; Hertel, Dietrich

    2016-01-01

    One of the main drivers of tropical forest loss is their conversion to oil palm, soy or cacao plantations with low biodiversity and greatly reduced carbon storage. Southeast Asian cacao plantations are often established under shade tree cover, but are later converted to non-shaded monocultures to avoid resource competition. We compared three co-occurring cacao cultivation systems (3 replicate stands each) with different shade intensity (non-shaded monoculture, cacao with the legume Gliricidia sepium shade trees, and cacao with several shade tree species) in Sulawesi (Indonesia) with respect to above- and belowground biomass and productivity, and cacao bean yield. Total biomass C stocks (above- and belowground) increased fivefold from the monoculture to the multi-shade tree system (from 11 to 57 Mg ha-1), total net primary production rose twofold (from 9 to 18 Mg C ha-1 yr-1). This increase was associated with a 6fold increase in aboveground biomass, but only a 3.5fold increase in root biomass, indicating a clear shift in C allocation to aboveground tree organs with increasing shade for both cacao and shade trees. Despite a canopy cover increase from 50 to 93%, cacao bean yield remained invariant across the systems (variation: 1.1-1.2 Mg C ha-1 yr-1). The monocultures had a twice as rapid leaf turnover suggesting that shading reduces the exposure of cacao to atmospheric drought, probably resulting in greater leaf longevity. Thus, contrary to general belief, cacao bean yield does not necessarily decrease under shading which seems to reduce physical stress. If planned properly, cacao plantations under a shade tree cover allow combining high yield with benefits for carbon sequestration and storage, production system stability under stress, and higher levels of animal and plant diversity.

  18. High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Jon M Kuchenreuther

    Full Text Available BACKGROUND: The realization of hydrogenase-based technologies for renewable H(2 production is presently limited by the need for scalable and high-yielding methods to supply active hydrogenases and their required maturases. PRINCIPAL FINDINGS: In this report, we describe an improved Escherichia coli-based expression system capable of producing 8-30 mg of purified, active [FeFe] hydrogenase per liter of culture, volumetric yields at least 10-fold greater than previously reported. Specifically, we overcame two problems associated with other in vivo production methods: low protein yields and ineffective hydrogenase maturation. The addition of glucose to the growth medium enhances anaerobic metabolism and growth during hydrogenase expression, which substantially increases total yields. Also, we combine iron and cysteine supplementation with the use of an E. coli strain upregulated for iron-sulfur cluster protein accumulation. These measures dramatically improve in vivo hydrogenase activation. Two hydrogenases, HydA1 from Chlamydomonas reinhardtii and HydA (CpI from Clostridium pasteurianum, were produced with this improved system and subsequently purified. Biophysical characterization and FTIR spectroscopic analysis of these enzymes indicate that they harbor the H-cluster and catalyze H(2 evolution with rates comparable to those of enzymes isolated from their respective native organisms. SIGNIFICANCE: The production system we describe will facilitate basic hydrogenase investigations as well as the development of new technologies that utilize these prolific H(2-producing enzymes. These methods can also be extended for producing and studying a variety of oxygen-sensitive iron-sulfur proteins as well as other proteins requiring anoxic environments.

  19. Study of optimal extraction conditions for achieving high yield and antioxidant activity of tomato seed oil.

    Science.gov (United States)

    Shao, Dongyan; Atungulu, Griffiths G; Pan, Zhongli; Yue, Tianli; Zhang, Ang; Li, Xuan

    2012-08-01

    Value of tomato seed has not been fully recognized. The objectives of this research were to establish suitable processing conditions for extracting oil from tomato seed by using solvent, determine the impact of processing conditions on yield and antioxidant activity of extracted oil, and elucidate kinetics of the oil extraction process. Four processing parameters, including time, temperature, solvent-to-solid ratio and particle size were studied. A second order model was established to describe the oil extraction process. Based on the results, increasing temperature, solvent-to-solid ratio, and extraction time increased oil yield. In contrast, larger particle size reduced the oil yield. The recommended oil extraction conditions were 8 min of extraction time at temperature of 25 °C, solvent-to-solids ratio of 5/1 (v/w) and particle size of 0.38 mm, which gave oil yield of 20.32% with recovery rate of 78.56%. The DPPH scavenging activity of extracted oil was not significantly affected by the extraction parameters. The inhibitory concentration (IC(50) ) of tomato seed oil was 8.67 mg/mL which was notably low compared to most vegetable oils. A 2nd order model successfully described the kinetics of tomato oil extraction process and parameters of extraction kinetics including initial extraction rate (h), equilibrium concentration of oil (C(s) ), and the extraction rate constant (k) could be precisely predicted with R(2) of at least 0.957. The study revealed that tomato seed which is typically treated as a low value byproduct of tomato processing has great potential in producing oil with high antioxidant capability. The impact of processing conditions including time, temperature, solvent-to-solid ratio and particle size on yield, and antioxidant activity of extracted tomato seed oil are reported. Optimal conditions and models which describe the extraction process are recommended. The information is vital for determining the extraction processing conditions for industrial

  20. Synthetic oligonucleotides : Useful molecules? A review

    NARCIS (Netherlands)

    Calogero, A; Hospers, GAP; Mulder, NH

    1997-01-01

    Specific inhibition of mammalian genes is possible through the use of antisense oligonucleotides (AS ODNs) or ribozymes. These strategies have led to a better understanding of several cellular and molecular mechanisms, among which cancer development. Recently, these strategies have been applied also

  1. Associating Oligonucleotides with Positively Charged Liposomes

    Czech Academy of Sciences Publication Activity Database

    Jurkiewicz, P.; Okruszek, A.; Hof, Martin; Langner, M.

    2003-01-01

    Roč. 8, č. 1 (2003), s. 77-84 ISSN 1425-8153 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : oligonucleotides * fluorescence correlation spectroscopy * DOTAP Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.455, year: 2003

  2. High night temperatures during grain number determination reduce wheat and barley grain yield: a field study.

    Science.gov (United States)

    García, Guillermo A; Dreccer, M Fernanda; Miralles, Daniel J; Serrago, Román A

    2015-11-01

    Warm nights are a widespread predicted feature of climate change. This study investigated the impact of high night temperatures during the critical period for grain yield determination in wheat and barley crops under field conditions, assessing the effects on development, growth and partitioning crop-level processes driving grain number per unit area (GN). Experiments combined: (i) two contrasting radiation and temperature environments: late sowing in 2011 and early sowing in 2013, (ii) two well-adapted crops with similar phenology: bread wheat and two-row malting barley and (iii) two temperature regimes: ambient and high night temperatures. The night temperature increase (ca. 3.9 °C in both crops and growing seasons) was achieved using purpose-built heating chambers placed on the crop at 19:000 hours and removed at 7:00 hours every day from the third detectable stem node to 10 days post-flowering. Across growing seasons and crops, the average minimum temperature during the critical period ranged from 11.2 to 17.2 °C. Wheat and barley grain yield were similarly reduced under warm nights (ca. 7% °C(-1) ), due to GN reductions (ca. 6% °C(-1) ) linked to a lower number of spikes per m(2) . An accelerated development under high night temperatures led to a shorter critical period duration, reducing solar radiation capture with negative consequences for biomass production, GN and therefore, grain yield. The information generated could be used as a starting point to design management and/or breeding strategies to improve crop adaptation facing climate change. © 2015 John Wiley & Sons Ltd.

  3. Selection of molecular structure and delivery of RNA oligonucleotides to activate TLR7 versus TLR8 and to induce high amounts of IL-12p70 in primary human monocytes.

    Science.gov (United States)

    Ablasser, Andrea; Poeck, Hendrik; Anz, David; Berger, Michael; Schlee, Martin; Kim, Sarah; Bourquin, Carole; Goutagny, Nadege; Jiang, Zhaozhao; Fitzgerald, Katherine A; Rothenfusser, Simon; Endres, Stefan; Hartmann, Gunther; Hornung, Veit

    2009-06-01

    Detection of non-self RNA by TLRs within endosomes and by retinoic acid-inducible gene I (RIG-I)-like helicases in the cytosol is central to mammalian antiviral immunity. In this study, we used pathway-specific agonists and targeted delivery to address RNA immunorecognition in primary human immune cells. Within PBMC, plasmacytoid dendritic cells (pDC) and monocytes were found to be responsible for IFN-alpha production upon immunorecognition of RNA. The mechanisms of RNA recognition in pDC and monocytes were distinct. In pDC, recognition of ssRNA and dsRNA oligonucleotides was TLR7-dependent, whereas a 5' triphosphate moiety (RIG-I ligand activity) had no major contribution to IFN-alpha production. In monocytes, the response to RNA oligonucleotides was mediated by either TLR8 or RIG-I. TLR8 was responsible for IL-12 induction upon endosomal delivery of ssRNA oligonucleotides and RIG-I was responsible for IFN-alpha production upon delivery of 5' triphosphate RNA into the cytosol. In conclusion, the dissection of these pathways by selecting the appropriate structure and delivery of RNA reveals pDC as major producer of IFN-alpha upon TLR-mediated stimulation and monocytes as major producer of IFN-alpha upon RIG-I-mediated stimulation. Furthermore, our results uncover the potential of monocytes to function as major producers of IL-12p70, a key Th1 cytokine classically ascribed to myeloid dendritic cells that cannot be induced by CpG oligonucleotides in the human system.

  4. Registration of a High Yielding Malt Barley Variety HB1454 for the ...

    African Journals Online (AJOL)

    else

    Registration of a High Yielding Malt Barley Variety. HB1454 for the Potential Highlands of Ethiopia. Berhane Lakew and Wondimu Fekadu. EIAR, Holetta Research Center, P O Box- 2003, Addis Ababa. አህፅርኦት. ኤች ቢ1454 የተባሇው ባሇሁሇት መስመር የብቅል ገብስ ዝርያ የተመዘገበበት ስም EH 1847/F4.2P.5.2). ሲሆን በሆሇታ ...

  5. Engineering of High Yield Production of L-serine in Escherichia coli

    DEFF Research Database (Denmark)

    Mundhada, Hemanshu; Schneider, Konstantin; Christensen, Hanne Bjerre

    2016-01-01

    L-serine is a widely used amino acid that has been proposed as a potential building block biochemical. The high theoretical yield from glucose makes a fermentation based production attractive. In order to achieve this goal, serine degradation to pyruvate and glycine in E. coli MG1655 was prevented.......3 g/L. The production strain was therefore evolved by random mutagenesis to achieve increased tolerance towards serine. Additionally, overexpression of eamA, a cysteine/homoserine transporter was demonstrated to increase serine tolerance from 1.6 g/L to 25 g/L. During fed batch fermentation...

  6. RNA isolation from loquat and other recalcitrant woody plants with high quality and yield.

    Science.gov (United States)

    Morante-Carriel, Jaime; Sellés-Marchart, Susana; Martínez-Márquez, Ascensión; Martínez-Esteso, María José; Luque, Ignacio; Bru-Martínez, Roque

    2014-05-01

    RNA isolation is difficult in plants that contain large amounts of polysaccharides and polyphenol compounds. To date, no commercial kit has been developed for the isolation of high-quality RNA from tissues with these characteristics, especially for fruit. The common protocols for RNA isolation are tedious and usually result in poor yields when applied to recalcitrant plant tissues. Here an efficient RNA isolation protocol based on cetyltrimethylammonium bromide (CTAB) and two successive precipitations with 10 M lithium chloride (LiCl) was developed specifically for loquat fruits, but it was proved to work efficiently in other tissues of loquat and woody plants. The RNA isolated by this improved protocol was not only of high purity and integrity (A260/A280 ratios ranged from 1.90 to 2.04 and A260/A230 ratios were>2.0) but also of high yield (up to 720 μg on average [coefficient of variation=21%] total RNA per gram fresh tissue). The protocol was tested on loquat fruit (different stages of development, postharvest, ripening, and bruising), leaf, root, flower, stem, and bud; quince fruit and root; grapevine cells in liquid culture; and rose petals. The RNA obtained with this method is amenable to enzymatic treatments and can be efficiently applied for research on gene characterization, expression, and function. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. High-scale yield of nano hydroxyapatite through combination of mechanical activation and chemical dispersion.

    Science.gov (United States)

    Gao, Xueling; Dai, Chunchu; Liu, Weiwei; Liu, Yumei; Shen, Ru; Zheng, Xiaotong; Duan, Ke; Weng, Jie; Qu, Shuxin

    2017-06-01

    The aim of this study is to develop a simple, convenient and effective approach to synthesize nano-sized hydroxyapatite (nano-HA) at high-scale yield. Nano-HA was wet synthesized in the presence or absence of alendronate sodium (ALN), one of bisphosphonates for anti-osteoporotic. Then aged and washed nano-HA precipitate was directly treated by mechanical activation combined with the chemical dispersion of ALN to prevent the agglomeration of nano-HA. ALN acted not only as a chemical dispersant but also as an orthopedic drug. In vitro release showed that ALN was released slowly from nano-HA. Transmission electron microscopy (TEM) revealed that nano-HA with size less than 100 nm appeared as single particle after being treated by mechanical activation combined with the dispersion of ALN (AMA-HA and MA-HA). High resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) confirmed that as-prepared nanoparticles were HA with low crystallinity and crystallite size. Fourier transform infrared spectroscopy (FTIR) indicated that the phosphonate groups in ALN were introduced to bond with the Ca2+ of HA to impede the growth of HA crystal. Zeta potential illustrated that the absolute value of surface negative charge of nano-HA increased significantly with the addition of ALN, which inhibited the agglomeration of nano-HA. The present approach makes it feasible to produce nano-HA at high-scale yield, which provide the possibility to construct bone graft.

  8. Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation.

    Science.gov (United States)

    Krivos, Kady L; Limbach, Patrick A

    2010-08-01

    Mass spectrometry analysis of protein-nucleic acid cross-links is challenging due to the dramatically different chemical properties of the two components. Identifying specific sites of attachment between proteins and nucleic acids requires methods that enable sequencing of both the peptide and oligonucleotide component of the heteroconjugate cross-link. While collision-induced dissociation (CID) has previously been used for sequencing such heteroconjugates, CID generates fragmentation along the phosphodiester backbone of the oligonucleotide preferentially. The result is a reduction in peptide fragmentation within the heteroconjugate. In this work, we have examined the effectiveness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) for sequencing heteroconjugates. Both methods were found to yield preferential fragmentation of the peptide component of a peptide:oligonucleotide heteroconjugate, with minimal differences in sequence coverage between these two electron-induced dissociation methods. Sequence coverage was found to increase with increasing charge state of the heteroconjugate, but decreases with increasing size of the oligonucleotide component. To overcome potential intermolecular interactions between the two components of the heteroconjugate, supplemental activation with ETD was explored. The addition of a supplemental activation step was found to increase peptide sequence coverage over ETD alone, suggesting that electrostatic interactions between the peptide and oligonucleotide components are one limiting factor in sequence coverage by these two approaches. These results show that ECD/ETD methods can be used for the tandem mass spectrometry sequencing of peptide:oligonucleotide heteroconjugates, and these methods are complementary to existing CID methods already used for sequencing of protein-nucleic acid cross-links. Copyright 2010. Published by Elsevier Inc.

  9. The effect of dha omega-3 feeding in the high yielding holstein herd

    Directory of Open Access Journals (Sweden)

    Juraj Karcol

    2017-01-01

    Full Text Available The aim of this study was to analyse the effect of supplementary feeding of DHA (Docosahexaenoic Acid rich algae product (Algae STM Alltech Inc. on production of milk, fat and protein as well as on reproduction of high yielding Holstein dairy herd. Field trial was set up on Top 10 dairy farm in western part of Slovakia, under commercial conditions. The data of high yielding dairy cows, separated in two groups of 30 (control and 29 (trial animals, were recorded for period of 3 subsequent months from October to December 2015. Animals were fed once a day Total Mixed Ration based diet with different feed mixture composition in trial group (+100 g Algae STM Alltech Inc. per cow and day. Performance data were collected in accordance with official milk recording system of Breeding Services of Slovak Republic s. e. and milk samples were collected once per month according to the A4 standard methodology. The control group showed higher level of milk production compared to trial. Our study indicated that the feeding of algae caused milk fat depression and generally lower protein content in milk. Significant impact of algae feeding was found also for the level of urea in milk. In addition, the supplementary feeding of DHA may represent effective strategy to increase the percentage of pregnancies per inseminations in lactating dairy cows.

  10. Yield gains of coffee plants from phosphorus fertilization may not be generalized for high density planting

    Directory of Open Access Journals (Sweden)

    Samuel Vasconcelos Valadares

    2014-06-01

    Full Text Available Inconclusive responses of the adult coffee plant to phosphorus fertilization have been reported in the literature, especially when dealing with application of this nutrient in high density planting systems. Thus, this study was carried out for the purpose of assessing the response of adult coffee plants at high planting density in full production (in regard to yield and their biennial cycle/stability to the addition of different sources and application rates of P in the Zona da Mata region of Minas Gerais, Brazil. The experiment with coffee plants of the Catucaí Amarelo 6/30 variety was carried out over four growing seasons. Treatments were arranged in a full factorial design [(4 × 3 + 1] consisting of four P sources (monoammonium phosphate, simple superphosphate, natural reactive rock phosphate from Algeria (Djebel-Onk, and FH 550®, three P rates (100, 200, and 400 kg ha-1 year-1 of P2O5, and an additional treatment without application of the nutrient (0 kg ha-¹ year-¹. A randomized block experimental design was used with three replicates. The four seasons were evaluated as subplots in a split plot experiment. The P contents in soil and leaves increased with increased rates of P application. However, there was no effect from P application on the yield and its biennial cycle/stability regardless of the source used over the four seasons assessed.

  11. OPERATIONAL CHALLENGES IN MIXING AND TRANSFER OF HIGH YIELD STRESS SLUDGE WASTE

    Energy Technology Data Exchange (ETDEWEB)

    Caldwell, T.; Bhatt, P.

    2009-12-07

    The ability to mobilize and transport non-Newtonian waste is essential to advance the closure of highly radioactive storage tanks. Recent waste removal operations from Tank 12H at the Savannah River Site (SRS) encountered sludge mixtures with a yield stress too high to pump. The waste removal equipment for Tank 12H was designed to mobilize and transport a diluted slurry mixture through an underground 550m long (1800 ft) 0.075m diameter (3 inch) pipeline. The transfer pump was positioned in a well casing submerged in the sludge slurry. The design allowed for mobilized sludge to enter the pump suction while keeping out larger tank debris. Data from a similar tank with known rheological properties were used to size the equipment. However, after installation and startup, field data from Tank 12H confirmed the yield stress of the slurry to exceed 40 Pa, whereas the system is designed for 10 Pa. A revision to the removal strategy was required, which involved metered dilution, blending, and mixing to ensure effective and safe transfer performance. The strategy resulted in the removal of over 255,000 kgs of insoluble solids with four discrete transfer evolutions for a total transfer volume of 2400 m{sup 3} (634,000 gallons) of sludge slurry.

  12. High yielding biomass genotypes of willow (Salix spp.) show differences in below ground biomass allocation.

    Science.gov (United States)

    Cunniff, Jennifer; Purdy, Sarah J; Barraclough, Tim J P; Castle, March; Maddison, Anne L; Jones, Laurence E; Shield, Ian F; Gregory, Andrew S; Karp, Angela

    2015-09-01

    Willows (Salix spp.) grown as short rotation coppice (SRC) are viewed as a sustainable source of biomass with a positive greenhouse gas (GHG) balance due to their potential to fix and accumulate carbon (C) below ground. However, exploiting this potential has been limited by the paucity of data available on below ground biomass allocation and the extent to which it varies between genotypes. Furthermore, it is likely that allocation can be altered considerably by environment. To investigate the role of genotype and environment on allocation, four willow genotypes were grown at two replicated field sites in southeast England and west Wales, UK. Above and below ground biomass was intensively measured over two two-year rotations. Significant genotypic differences in biomass allocation were identified, with below ground allocation differing by up to 10% between genotypes. Importantly, the genotype with the highest below ground biomass also had the highest above ground yield. Furthermore, leaf area was found to be a good predictor of below ground biomass. Growth environment significantly impacted allocation; the willow genotypes grown in west Wales had up to 94% more biomass below ground by the end of the second rotation. A single investigation into fine roots showed the same pattern with double the volume of fine roots present. This greater below ground allocation may be attributed primarily to higher wind speeds, plus differences in humidity and soil characteristics. These results demonstrate that the capacity exists to breed plants with both high yields and high potential for C accumulation.

  13. High-Yield Synthesis of Helical Carbon Nanofibers Using Iron Oxide Fine Powder as a Catalyst

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Suda

    2015-01-01

    Full Text Available Carbon nanocoil (CNC, which is synthesized by a catalytic chemical vapor deposition (CCVD method, has a coil diameter of 300–900 nm and a length of several tens of μm. Although it is very small, CNC is predicted to have a high mechanical strength and hence is expected to have a use in nanodevices such as electromagnetic wave absorbers and field emitters. For nanodevice applications, it is necessary to synthesize CNC in high yield and purity. In this study, we improved the conditions of catalytic layer formation and CCVD. Using optimized CVD conditions, a CNC layer with a thickness of >40 μm was grown from a SnO2/Fe2O3/SnO2 catalyst on a substrate, and its purity increased to 81% ± 2%.

  14. Catalytic oxidative conversion of cellulosic biomass to formic acid and acetic acid with exceptionally high yields

    KAUST Repository

    Zhang, Jizhe

    2014-09-01

    Direct conversion of raw biomass materials to fine chemicals is of great significance from both economic and ecological perspectives. In this paper, we report that a Keggin-type vanadium-substituted phosphomolybdic acid catalyst, namely H4PVMo11O40, is capable of converting various biomass-derived substrates to formic acid and acetic acid with high selectivity in a water medium and oxygen atmosphere. Under optimized reaction conditions, H4PVMo11O40 gave an exceptionally high yield of formic acid (67.8%) from cellulose, far exceeding the values achieved in previous catalytic systems. Our study demonstrates that heteropoly acids are generally effective catalysts for biomass conversion due to their strong acidities, whereas the composition of metal addenda atoms in the catalysts has crucial influence on the reaction pathway and the product selectivity. © 2013 Elsevier B.V.

  15. Radiation Hard and High Light Yield Scintillator Search for CMS Phase II Upgrade

    CERN Document Server

    Tiras, Emrah

    2015-01-01

    The CMS detector at the LHC requires a major upgrade to cope with the higher instantaneous luminosity and the elevated radiation levels. The active media of the forward backing hadron calorimeters is projected to be radiation-hard, high light yield scintillation materials or similar alternatives. In this context, we have studied various radiation-hard scintillating materials such as Polyethylene Terephthalate (PET), Polyethylene Naphthalate (PEN), High Efficiency Mirror (HEM) and quartz plates with various coatings. The quartz plates are pure Cerenkov radiators and their radiation hardness has been confirmed. In order to increase the light output, we considered organic and inorganic coating materials such as p-Terphenyl (pTp), Anthracene and Gallium-doped Zinc Oxide (ZnO Ga) that are applied as thin layers on the surface of the quartz plates. Here, we present the results of the related test beam activities, laboratory measurements and recent developments.

  16. Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields

    Directory of Open Access Journals (Sweden)

    Kristina M. Ilieva

    2017-09-01

    Full Text Available Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1 antibody cloning, using polymerase incomplete primer extension (PIPE polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ, and high (S239D/I332E, DE FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells.

  17. Variation in Yield Responses to Elevated CO2 and a Brief High Temperature Treatment in Quinoa

    Science.gov (United States)

    Bunce, James A.

    2017-01-01

    Intraspecific variation in crop responses to global climate change conditions would provide opportunities to adapt crops to future climates. These experiments explored intraspecific variation in response to elevated CO2 and to high temperature during anthesis in Chenopodium quinoa Wild. Three cultivars of quinoa were grown to maturity at 400 (“ambient”) and 600 (“elevated”) μmol·mol−1 CO2 concentrations at 20/14 °C day/night (“control”) temperatures, with or without exposure to day/night temperatures of 35/29 °C (“high” temperatures) for seven days during anthesis. At control temperatures, the elevated CO2 concentration increased the total aboveground dry mass at maturity similarly in all cultivars, but by only about 10%. A large down-regulation of photosynthesis at elevated CO2 occurred during grain filling. In contrast to shoot mass, the increase in seed dry mass at elevated CO2 ranged from 12% to 44% among cultivars at the control temperature. At ambient CO2, the week-long high temperature treatment greatly decreased (0.30 × control) or increased (1.70 × control) seed yield, depending on the cultivar. At elevated CO2, the high temperature treatment increased seed yield moderately in all cultivars. These quinoa cultivars had a wide range of responses to both elevated CO2 and to high temperatures during anthesis, and much more variation in harvest index responses to elevated CO2 than other crops that have been examined. PMID:28678208

  18. Variation in Yield Responses to Elevated CO2 and a Brief High Temperature Treatment in Quinoa

    Directory of Open Access Journals (Sweden)

    James A. Bunce

    2017-07-01

    Full Text Available Intraspecific variation in crop responses to global climate change conditions would provide opportunities to adapt crops to future climates. These experiments explored intraspecific variation in response to elevated CO2 and to high temperature during anthesis in Chenopodium quinoa Wild. Three cultivars of quinoa were grown to maturity at 400 (“ambient” and 600 (“elevated” μmol·mol−1 CO2 concentrations at 20/14 °C day/night (“control” temperatures, with or without exposure to day/night temperatures of 35/29 °C (“high” temperatures for seven days during anthesis. At control temperatures, the elevated CO2 concentration increased the total aboveground dry mass at maturity similarly in all cultivars, but by only about 10%. A large down-regulation of photosynthesis at elevated CO2 occurred during grain filling. In contrast to shoot mass, the increase in seed dry mass at elevated CO2 ranged from 12% to 44% among cultivars at the control temperature. At ambient CO2, the week-long high temperature treatment greatly decreased (0.30 × control or increased (1.70 × control seed yield, depending on the cultivar. At elevated CO2, the high temperature treatment increased seed yield moderately in all cultivars. These quinoa cultivars had a wide range of responses to both elevated CO2 and to high temperatures during anthesis, and much more variation in harvest index responses to elevated CO2 than other crops that have been examined.

  19. Harnessing the respiration machinery for high-yield production of chemicals in metabolically engineered Lactococcus lactis.

    Science.gov (United States)

    Liu, Jianming; Wang, Zhihao; Kandasamy, Vijayalakshmi; Lee, Sang Yup; Solem, Christian; Jensen, Peter Ruhdal

    2017-11-01

    When modifying the metabolism of living organisms with the aim of achieving biosynthesis of useful compounds, it is essential to ensure that it is possible to achieve overall redox balance. We propose a generalized strategy for this, based on fine-tuning of respiration. The strategy was applied on metabolically engineered Lactococcus lactis strains to optimize the production of acetoin and (R,R)-2,3-butanediol (R-BDO). In the absence of an external electron acceptor, a surplus of two NADH per acetoin molecule is produced. We found that a fully activated respiration was able to efficiently regenerate NAD+, and a high titer of 371mM (32g/L) of acetoin was obtained with a yield of 82% of the theoretical maximum. Subsequently, we extended the metabolic pathway from acetoin to R-BDO by introducing the butanediol dehydrogenase gene from Bacillus subtilis. Since one mole of NADH is consumed when acetoin is converted into R-BDO per mole, only the excess of NADH needs to be oxidized via respiration. Either by fine-tuning the respiration capacity or by using a dual-phase fermentation approach involving a switch from fully respiratory to non-respiratory conditions, we obtained 361mM (32g/L) R-BDO with a yield of 81% or 365mM (33g/L) with a yield of 82%, respectively. These results demonstrate the great potential in using finely-tuned respiration machineries for bio-production. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  20. High-yield extraction of Escherichia coli RNA from human whole blood.

    Science.gov (United States)

    Brennecke, Johannes; Kraut, Simone; Zwadlo, Klara; Gandi, Senthil Kumar; Pritchard, David; Templeton, Kate; Bachmann, Till

    2017-03-01

    Studies of bacterial transcriptomics during bloodstream infections are limited to-date because unbiased extraction of bacterial mRNA from whole blood in sufficient quantity and quality has proved challenging. Problems include the high excess of human cells, the presence of PCR inhibitors and the short intrinsic half-life of bacterial mRNA. This study aims to provide a framework for the choice of the most suitable sample preparation method. Escherichia coli cells were spiked into human whole blood and the bacterial gene expression was stabilized with RNAprotect either immediately or after lysis of the red blood cells with Triton X-100, saponin, ammonium chloride or the commercial MolYsis buffer CM. RNA yield, purity and integrity were assessed by absorbance measurements at 260 and 280 nm, real-time PCR and capillary electrophoresis. For low cell numbers, the best mRNA yields were obtained by adding the commercial RNAprotect reagent directly to the sample without prior lyses of the human blood cells. Using this protocol, significant amounts of human RNA were co-purified, however, this had a beneficial impact on the yields of bacterial mRNA. Among the tested lysis agents, Triton X-100 was the most effective and reduced the human RNA background by three to four orders of magnitude. For most applications, lysis of the human blood cells is not required. However, co-purified human RNA may interfere with some downstream processes such as RNA sequencing. In this case, blood cell lysis with Triton X-100 is desirable.

  1. Future consequences of decreasing marginal production efficiency in the high-yielding dairy cow.

    Science.gov (United States)

    Moallem, U

    2016-04-01

    The objectives were to examine the gross and marginal production efficiencies in high-yielding dairy cows and the future consequences on dairy industry profitability. Data from 2 experiments were used in across-treatments analysis (n=82 mid-lactation multiparous Israeli-Holstein dairy cows). Milk yields, body weights (BW), and dry matter intakes (DMI) were recorded daily. In both experiments, cows were fed a diet containing 16.5 to 16.6% crude protein and net energy for lactation (NEL) at 1.61 Mcal/kg of dry matter (DM). The means of milk yield, BW, DMI, NEL intake, and energy required for maintenance were calculated individually over the whole study, and used to calculate gross and marginal efficiencies. Data were analyzed in 2 ways: (1) simple correlation between variables; and (2) cows were divided into 3 subgroups, designated low, moderate, and high DMI (LDMI, MDMI, and HDMI), according to actual DMI per day: ≤ 26 kg (n=27); >26 through 28.2 kg (n=28); and >28.2 kg (n=27). The phenotypic Pearson correlations among variables were analyzed, and the GLM procedure was used to test differences between subgroups. The relationships between milk and fat-corrected milk yields and the corresponding gross efficiencies were positive, whereas BW and gross production efficiency were negatively correlated. The marginal production efficiency from DM and energy consumed decreased with increasing DMI. The difference between BW gain as predicted by the National Research Council model (2001) and the present measurements increased with increasing DMI (r=0.68). The average calculated energy balances were 1.38, 2.28, and 4.20 Mcal/d (standard error of the mean=0.64) in the LDMI, MDMI, and HDMI groups, respectively. The marginal efficiency for milk yields from DMI or energy consumed was highest in LDMI, intermediate in MDMI, and lowest in HDMI. The predicted BW gains for the whole study period were 22.9, 37.9, and 75.8 kg for the LDMI, MDMI, and HDMI groups, respectively. The

  2. The Dynamics of Compound, Transcript, and Protein Effects After Treatment With 2OMePS Antisense Oligonucleotides in mdx Mice

    Directory of Open Access Journals (Sweden)

    Ingrid E C Verhaart

    2014-01-01

    Full Text Available Antisense-mediated exon skipping is currently in clinical development for Duchenne muscular dystrophy (DMD to amend the consequences of the underlying genetic defect and restore dystrophin expression. Due to turnover of compound, transcript, and protein, chronic treatment with effector molecules (antisense oligonucleotides will be required. To investigate the dynamics and persistence of antisense 2′-O-methyl phosphorothioate oligonucleotides, exon skipping, and dystrophin expression after dosing was concluded, mdx mice were treated subcutaneously for 8 weeks with 100 mg/kg oligonucleotides twice weekly. Thereafter, mice were sacrificed at different time points after the final injection (36 hours–24 weeks. Oligonucleotide half-life was longer in heart (~65 days compared with that in skeletal muscle, liver, and kidney (~35 days. Exon skipping half-lives varied between 33 and 53 days, whereas dystrophin protein showed a long half-life (>100 days. Oligonucleotide and exon-skipping levels peaked in the first week and declined thereafter. By contrast, dystrophin expression peaked after 3–8 weeks and then slowly declined, remaining detectable after 24 weeks. Concordance between levels of oligonucleotides, exon skipping, and proteins was observed, except in heart, wherein high oligonucleotide levels but low exon skipping and dystrophin expression were seen. Overall, these results enhance our understanding of the pharmacokinetics and pharmacodynamics of 2′-O-methyl phosphorothioate oligos used for the treatment of DMD.

  3. Enhancing biomass energy yield from pilot-scale high rate algal ponds with recycling.

    Science.gov (United States)

    Park, J B K; Craggs, R J; Shilton, A N

    2013-09-01

    This paper investigates the effect of recycling on biomass energy yield in High Rate Algal Ponds (HRAPs). Two 8 m(3) pilot-scale HRAPs treating primary settled sewage were operated in parallel and monitored over a 2-year period. Volatile suspended solids were measured from both HRAPs and their gravity settlers to determine biomass productivity and harvest efficiency. The energy content of the biomass was also measured. Multiplying biomass productivity and harvest efficiency gives the 'harvestable biomass productivity' and multiplying this by the energy content defines the actual 'biomass energy yield'. In Year 1, algal recycling was implemented in one of the ponds (HRAPr) and improved harvestable biomass productivity by 58% compared with the control (HRAPc) without recycling (HRAPr: 9.2 g/m(2)/d; HRAPc: 5.8 g/m(2)/d). The energy content of the biomass grown in HRAPr, which was dominated by Pediastrun boryanum, was 25% higher than the control HRAPc which contained a mixed culture of 4-5 different algae (HRAPr: 21.5 kJ/g; HRAPc: 18.6 kJ/g). In Year 2, HRAPc was then seeded with the biomass harvested from the P. boryanum dominated HRAPr. This had the effect of shifting algal dominance from 89% Dictyosphaerium sp. (which is poorly-settleable) to over 90% P. boryanum in 5 months. Operation of this pond was then switched to recycling its own harvested biomass, which maintained P. boryanum dominance for the rest of Year 2. This result confirms, for the first time in the literature, that species control is possible for similarly sized co-occurring algal colonies in outdoor HRAP by algal recycling. With regard to the overall improvement in biomass energy yield, which is a critical parameter in the context of algal cultivation for biofuels, the combined improvements that recycling triggered in biomass productivity, harvest efficiency and energy content enhanced the harvested biomass energy yield by 66% (HRAPr: 195 kJ/m(2)/day; HRAPc: 118 kJ/m(2)/day). Copyright © 2013

  4. Mixed models for selection of Jatropha progenies with high adaptability and yield stability in Brazilian regions.

    Science.gov (United States)

    Teodoro, P E; Bhering, L L; Costa, R D; Rocha, R B; Laviola, B G

    2016-08-19

    The aim of this study was to estimate genetic parameters via mixed models and simultaneously to select Jatropha progenies grown in three regions of Brazil that meet high adaptability and stability. From a previous phenotypic selection, three progeny tests were installed in 2008 in the municipalities of Planaltina-DF (Midwest), Nova Porteirinha-MG (Southeast), and Pelotas-RS (South). We evaluated 18 families of half-sib in a randomized block design with three replications. Genetic parameters were estimated using restricted maximum likelihood/best linear unbiased prediction. Selection was based on the harmonic mean of the relative performance of genetic values method in three strategies considering: 1) performance in each environment (with interaction effect); 2) performance in each environment (with interaction effect); and 3) simultaneous selection for grain yield, stability and adaptability. Accuracy obtained (91%) reveals excellent experimental quality and consequently safety and credibility in the selection of superior progenies for grain yield. The gain with the selection of the best five progenies was more than 20%, regardless of the selection strategy. Thus, based on the three selection strategies used in this study, the progenies 4, 11, and 3 (selected in all environments and the mean environment and by adaptability and phenotypic stability methods) are the most suitable for growing in the three regions evaluated.

  5. Accelerated high-yield generation of limb-innervating motor neurons from human stem cells

    Science.gov (United States)

    Amoroso, Mackenzie W.; Croft, Gist F.; Williams, Damian J.; O’Keeffe, Sean; Carrasco, Monica A.; Davis, Anne R.; Roybon, Laurent; Oakley, Derek H.; Maniatis, Tom; Henderson, Christopher E.; Wichterle, Hynek

    2013-01-01

    Human pluripotent stem cells are a promising source of differentiated cells for developmental studies, cell transplantation, disease modeling, and drug testing. However, their widespread use even for intensely studied cell types like spinal motor neurons is hindered by the long duration and low yields of existing protocols for in vitro differentiation and by the molecular heterogeneity of the populations generated. We report a combination of small molecules that within 3 weeks induce motor neurons at up to 50% abundance and with defined subtype identities of relevance to neurodegenerative disease. Despite their accelerated differentiation, motor neurons expressed combinations of HB9, ISL1 and column-specific markers that mirror those observed in vivo in human fetal spinal cord. They also exhibited spontaneous and induced activity, and projected axons towards muscles when grafted into developing chick spinal cord. Strikingly, this novel protocol preferentially generates motor neurons expressing markers of limb-innervating lateral motor column motor neurons (FOXP1+/LHX3−). Access to high-yield cultures of human limb-innervating motor neuron subtypes will facilitate in-depth study of motor neuron subtype-specific properties, disease modeling, and development of large-scale cell-based screening assays. PMID:23303937

  6. Rapid, high-yield production in plants of individualized idiotype vaccines for non-Hodgkin's lymphoma.

    Science.gov (United States)

    Bendandi, M; Marillonnet, S; Kandzia, R; Thieme, F; Nickstadt, A; Herz, S; Fröde, R; Inogés, S; Lòpez-Dìaz de Cerio, A; Soria, E; Villanueva, H; Vancanneyt, G; McCormick, A; Tusé, D; Lenz, J; Butler-Ransohoff, J-E; Klimyuk, V; Gleba, Y

    2010-12-01

    Animal and clinical studies with plant-produced single-chain variable fragment lymphoma vaccines have demonstrated specific immunogenicity and safety. However, the expression levels of such fragments were highly variable and required complex engineering of the linkers. Moreover, the downstream processing could not be built around standard methods like protein A affinity capture. We report a novel vaccine manufacturing process, magnifection, devoid of the above-mentioned shortcomings and allowing consistent and efficient expression in plants of whole immunoglobulins (Igs). Full idiotype (Id)-containing IgG molecules of 20 lymphoma patients and 2 mouse lymphoma models were expressed at levels between 0.5 and 4.8 g/kg of leaf biomass. Protein A affinity capture purification yielded antigens of pharmaceutical purity. Several patient Igs produced in plants showed specific cross-reactivity with sera derived from the same patients immunized with hybridoma-produced Id vaccine. Mice vaccinated with plant- or hybridoma-produced Igs showed comparable protection levels in tumor challenge studies. This manufacturing process is reliable and robust, the manufacturing time from biopsy to vaccine is antibodies in plants, providing 50- to 1000-fold higher yields than alternative plant expression methods.

  7. The yield of high-detail radiographic skeletal surveys in suspected infant abuse.

    Science.gov (United States)

    Barber, Ignasi; Perez-Rossello, Jeannette M; Wilson, Celeste R; Kleinman, Paul K

    2015-01-01

    Skeletal surveys are routinely performed in cases of suspected child abuse, but there are limited data regarding the yield of high-detail skeletal surveys in infants. To determine the diagnostic yield of high-detail radiographic skeletal surveys in suspected infant abuse. We reviewed the high-detail American College of Radiology standardized skeletal surveys performed for suspected abuse in 567 infants (median: 4.4 months, SD 3.47; range: 4 days-12 months) at a large urban children's hospital between 2005 and 2013. Skeletal survey images, radiology reports and medical records were reviewed. A skeletal survey was considered positive when it showed at least one unsuspected fracture. In 313 of 567 infants (55%), 1,029 definite fractures were found. Twenty-one percent (119/567) of the patients had a positive skeletal survey with a total of 789 (77%) unsuspected fractures. Long-bone fractures were the most common injuries, present in 145 children (26%). The skull was the site of fracture in 138 infants (24%); rib cage in 77 (14%), clavicle in 24 (4.2%) and uncommon fractures (including spine, scapula, hands and feet and pelvis) were noted in 26 infants (4.6%). Of the 425 infants with neuroimaging, 154 (36%) had intracranial injury. No significant correlation between positive skeletal survey and associated intracranial injury was found. Scapular fractures and complex skull fractures showed a statistically significant correlation with intracranial injury (P = 0.029, P = 0.007, respectively). Previously unsuspected fractures are noted on skeletal surveys in 20% of cases of suspected infant abuse. These data may be helpful in the design and optimization of global skeletal imaging in this vulnerable population.

  8. The yield of high-detail radiographic skeletal surveys in suspected infant abuse

    Energy Technology Data Exchange (ETDEWEB)

    Barber, Ignasi [Hospital Vall d' Hebron, Universitat Autonoma de Barcelona, Pediatric Radiology Department, Barcelona (Spain); Perez-Rossello, Jeannette M.; Kleinman, Paul K. [Boston Children' s Hospital, Radiology Department, Boston, MA (United States); Wilson, Celeste R. [Boston Children' s Hospital, Division of General Pediatrics, Boston, MA (United States)

    2014-07-06

    Skeletal surveys are routinely performed in cases of suspected child abuse, but there are limited data regarding the yield of high-detail skeletal surveys in infants. To determine the diagnostic yield of high-detail radiographic skeletal surveys in suspected infant abuse. We reviewed the high-detail American College of Radiology standardized skeletal surveys performed for suspected abuse in 567 infants (median: 4.4 months, SD 3.47; range: 4 days-12 months) at a large urban children's hospital between 2005 and 2013. Skeletal survey images, radiology reports and medical records were reviewed. A skeletal survey was considered positive when it showed at least one unsuspected fracture. In 313 of 567 infants (55%), 1,029 definite fractures were found. Twenty-one percent (119/567) of the patients had a positive skeletal survey with a total of 789 (77%) unsuspected fractures. Long-bone fractures were the most common injuries, present in 145 children (26%). The skull was the site of fracture in 138 infants (24%); rib cage in 77 (14%), clavicle in 24 (4.2%) and uncommon fractures (including spine, scapula, hands and feet and pelvis) were noted in 26 infants (4.6%). Of the 425 infants with neuroimaging, 154 (36%) had intracranial injury. No significant correlation between positive skeletal survey and associated intracranial injury was found. Scapular fractures and complex skull fractures showed a statistically significant correlation with intracranial injury (P = 0.029, P = 0.007, respectively). Previously unsuspected fractures are noted on skeletal surveys in 20% of cases of suspected infant abuse. These data may be helpful in the design and optimization of global skeletal imaging in this vulnerable population. (orig.)

  9. High-Yield Synthesis of Silver Nanoparticles by Precipitation in a High-Aqueous Phase Content Reverse Microemulsion

    Directory of Open Access Journals (Sweden)

    Y. D. Sosa

    2010-01-01

    Full Text Available Silver nanoparticles were precipitated at 70°C in a reverse microemulsion containing a high concentration of 0.5 M silver nitrate aqueous solution, toluene as organic phase, and a mixture of surfactants sodium bis (2-ethylhexyl sulfosuccinate/sodium dodecyl sulfate (2/1, w/w. Nanoparticles were characterized by X-ray diffraction, atomic absorption spectroscopy, and high-resolution transmission electron microscopy. In spite of the high-water/surfactant molar ratio and concentration of silver nitrate solution used in this study, characterizations demonstrated that nanoparticles were silver crystals (purity >99% with 8.6–8.8 nm in average diameter and 2.9–4.7 nm in standard deviation. It is proposed that slow dosing rate of aqueous solution of precipitating agent and the small molecular volume of toluene attenuated both particle aggregation and polydispersity widening. Experimental yield of silver nanoparticles obtained in this study was much higher than theoretical yields calculated from available data in the literature on preparation of silver nanoparticles in reverse microemulsions.

  10. BRS 369RF and BRS 370RF: Glyphosate tolerant, high-yielding upland cotton cultivars for central Brazilian savanna

    Directory of Open Access Journals (Sweden)

    Camilo de Lelis Morello

    2015-12-01

    Full Text Available BRS 369RF and BRS 370RF were developed by the EMBRAPA as a part of efforts to create high-yielding germplasm with combinations of transgenic traits. BRS 369RF and BRS 370RF are midseason cultivars and have yield stability, adaptation to the central Brazilian savanna, good fiber quality and tolerance to glyphosate herbicide.

  11. BRS FC402: high-yielding common bean cultivar with carioca grain, resistance to anthracnose and fusarium wilt

    Directory of Open Access Journals (Sweden)

    Leonardo Cunha Melo

    2016-12-01

    Full Text Available BRS FC402 is a common bean cultivar of the carioca-grain group with commercial grain quality, suitable for cultivation in 21 Brazilian states. Cultivar has a normal cycle (85-94 days, high yield potential (4479 kg ha-1, 10.1% higher mean yield than the controls (2462 kg ha-1 and resistance to fusarium wilt and anthracnose.

  12. Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm.

    Science.gov (United States)

    Wong, Yick Ching; Teh, Huey Fang; Mebus, Katharina; Ooi, Tony Eng Keong; Kwong, Qi Bin; Koo, Ka Loo; Ong, Chuang Kee; Mayes, Sean; Chew, Fook Tim; Appleton, David R; Kulaveerasingam, Harikrishna

    2017-06-21

    The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations. A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms. Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to

  13. A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Chen Feng

    2010-10-01

    Full Text Available Abstract Background Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Results Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals and Plasmodium falciparum (a related parasite responsible for severe human malaria, we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at

  14. Molecular signature of high yield (growth influenza a virus reassortants prepared as candidate vaccine seeds.

    Directory of Open Access Journals (Sweden)

    Manojkumar Ramanunninair

    Full Text Available BACKGROUND: Human influenza virus isolates generally grow poorly in embryonated chicken eggs. Hence, gene reassortment of influenza A wild type (wt viruses is performed with a highly egg adapted donor virus, A/Puerto Rico/8/1934 (PR8, to provide the high yield reassortant (HYR viral 'seeds' for vaccine production. HYR must contain the hemagglutinin (HA and neuraminidase (NA genes of wt virus and one to six 'internal' genes from PR8. Most studies of influenza wt and HYRs have focused on the HA gene. The main objective of this study is the identification of the molecular signature in all eight gene segments of influenza A HYR candidate vaccine seeds associated with high growth in ovo. METHODOLOGY: The genomes of 14 wt parental viruses, 23 HYRs (5 H1N1; 2, 1976 H1N1-SOIV; 2, 2009 H1N1pdm; 2 H2N2 and 12 H3N2 and PR8 were sequenced using the high-throughput sequencing pipeline with big dye terminator chemistry. RESULTS: Silent and coding mutations were found in all internal genes derived from PR8 with the exception of the M gene. The M gene derived from PR8 was invariant in all 23 HYRs underlining the critical role of PR8 M in high yield phenotype. None of the wt virus derived internal genes had any silent change(s except the PB1 gene in X-157. The highest number of recurrent silent and coding mutations was found in NS. With respect to the surface antigens, the majority of HYRs had coding mutations in HA; only 2 HYRs had coding mutations in NA. SIGNIFICANCE: In the era of application of reverse genetics to alter influenza A virus genomes, the mutations identified in the HYR gene segments associated with high growth in ovo may be of great practical benefit to modify PR8 and/or wt virus gene sequences for improved growth of vaccine 'seed' viruses.

  15. High-yield electrosynthesis of hydrogen peroxide from oxygen reduction by hierarchically porous carbon.

    Science.gov (United States)

    Liu, Yanming; Quan, Xie; Fan, Xinfei; Wang, Hua; Chen, Shuo

    2015-06-01

    H2O2 production by electroreduction of O2 is an attractive alternative to the current anthraquinone process, which is highly desirable for chemical industries and environmental remediation. However, it remains a great challenge to develop cost-effective electrocatalysts for H2O2 synthesis. Here, hierarchically porous carbon (HPC) was proposed for the electrosynthesis of H2O2 from O2 reduction. It exhibited high activity for O2 reduction and good H2O2 selectivity (95.0-70.2%, most of them >90.0% at pH 1-4 and >80.0% at pH 7). High-yield H2O2 generation has been achieved on HPC with H2O2 concentrations of 222.6-62.0 mmol L(-1) (2.5 h) and corresponding H2O2 production rates of 395.7-110.2 mmol h(-1)  g(-1) at pH 1-7 and -0.5 V. Moreover, HPC was energy-efficient for H2O2 production with current efficiency of 81.8-70.8%. The exceptional performance of HPC for electrosynthesis of H2O2 could be attributed to its high content of sp(3)-C and defects, large surface area and fast mass transfer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. A Scalable and High-Yield Strategy for the Synthesis of Sequence-Defined Macromolecules.

    Science.gov (United States)

    Solleder, Susanne C; Zengel, Deniz; Wetzel, Katharina S; Meier, Michael A R

    2016-01-18

    The efficient synthesis of a sequence-defined decamer, its characterization, and its straightforward dimerization through self-metathesis are described. For this purpose, a monoprotected AB monomer was designed and used to synthesize a decamer bearing ten different and selectable side chains by iterative Passerini three-component reaction (P-3CR) and subsequent deprotection. The highly efficient procedure provided excellent yields and allows for the multigram-scale synthesis of such perfectly defined macromolecules. An olefin was introduced at the end of the synthesis, allowing the self-metathesis reaction of the resulting decamer to provide a sequence-defined 20-mer with a molecular weight of 7046.40 g mol(-1). The obtained oligomers were carefully characterized by NMR and IR spectroscopy, GPC and GPC coupled to ESI-MS, and mass spectrometry (FAB and orbitrap ESI-MS). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. High-yield self-limiting single-nanowire assembly with dielectrophoresis.

    Science.gov (United States)

    Freer, Erik M; Grachev, Oleg; Duan, Xiangfeng; Martin, Samuel; Stumbo, David P

    2010-07-01

    Single-crystal nanowire transistors and other nanowire-based devices could have applications in large-area and flexible electronics if conventional top-down fabrication techniques can be integrated with high-precision bottom-up nanowire assembly. Here, we extend dielectrophoretic nanowire assembly to achieve a 98.5% yield of single nanowires assembled over 16,000 patterned electrode sites with submicrometre alignment precision. The balancing of surface, hydrodynamic and dielectrophoretic forces makes the self-assembly process controllable, and a hydrodynamic force component makes it self-limiting. Our approach represents a methodology to quantify nanowire assembly, and makes single nanowire assembly possible over an area limited only by the ability to reproduce process conditions uniformly.

  18. Novel fully-BODIPY functionalized cyclotetraphosphazene photosensitizers having high singlet oxygen quantum yields

    Science.gov (United States)

    Şenkuytu, Elif; Eçik, Esra Tanrıverdi

    2017-07-01

    Novel fully-BODIPY functionalized dendrimeric cyclotetraphosphazenes (FBCP 1 and 2) have been synthesized and characterized by 1H, 13C and 31P NMR spectroscopies. The photophysical and photochemical properties of FBCP 1 and 2 are investigated in dichloromethane solution. The effectiveness of singlet oxygen generation was measured for FBCP 1 and 2 by UV-Vis spectra monitoring of the solution of 1,3-diphenylisobenzofuran (DPBF), which is a well-known trapping molecule used in detection of singlet oxygen. FBCP 1 and 2 show high molar extinction coefficients in the NIR region, good singlet oxygen quantum yields and appropriate photo degradation. The data presented in the work indicate that the dendrimeric cyclotetraphosphazenes are effective singlet oxygen photosensitizers that might be used for various areas of applications such as photodynamic therapy and photocatalysis.

  19. Improvement of production of high-yield poplar varieties seedlings by mycorrhiza application

    Directory of Open Access Journals (Sweden)

    Galić Zoran A.

    2007-01-01

    Full Text Available Research related to the effects of treatment by mycorrhiza preparations Ectovit, Rhodovit (preparations Symbio-m Ltd., Czech Rep. and their combination on growth of four high-yield poplar clones of Populus deltoides and one variety of Populus x euramericana are presented in this paper. In order to make more accurate assessment of mycorrhiza effect, soil characteristics such as morphology, texture and chemical composition were determined. The study results indicate that mycorrhized cuttings had the same or the better survival in all the study clones compared to the control. The application of the preparation Ectovit and Rhodovit resulted averagely in the first class planting stock of all the study clones. The combination of the preparations Ectovit and Rhodovit produced averagely the first class planting stock only of the clone Populus x euramericana.

  20. Novel Efficient Cell-Penetrating, Peptide-Mediated Strategy for Enhancing Telomerase Inhibitor Oligonucleotides.

    Science.gov (United States)

    Muñoz-Alarcón, Andrés; Eriksson, Jonas; Langel, Ülo

    2015-12-01

    At present, there are several therapeutic approaches for targeting telomerase in tumors. One in particular, currently undergoing clinical trials, is based on synthetic lipid-modified oligonucleotide antagonists aimed at inhibiting the ribonucleoprotein subunit of human telomerase. However, while enabling efficient uptake, the lipid modifications reduce the potency of the therapeutic oligonucleotides compared to nonmodified oligonucleotides. Moreover, lipid modification may increase oligonucleotide accumulation in the liver causing undesirable hepatotoxicity. Noncovalent complexation strategies for cell-penetrating peptide (CPP)-mediated delivery present an option to circumvent the need for potency-reducing modifications, while allowing for a highly efficient uptake, and could significantly improve the efficiency of telomerase-targeting cancer therapeutics. Delivery of a nonlipidated locked nucleic acid/2'-O-methyl mixmer significantly inhibits the telomerase activity in treated HeLa cells. The inhibitory effect was further improved through addition of a CPP. Furthermore, calculated IC50-values for the oligonucleotide delivered by CPPs into HeLa cells are more than 20 times lower than telomerase inhibitor Imetelstat, currently undergoing clinical trials. These results emphasize the potential of CPP-mediated delivery of future pharmaceuticals and provide means by which to enhance an already promising therapeutic strategy for cancer treatment.

  1. High-yield Synthesis of Multiwalled Carbon Nanotube by Mechanothermal Method

    Directory of Open Access Journals (Sweden)

    Manafi SA

    2009-01-01

    Full Text Available Abstract This study reports on the mechanothermal synthesis of multiwalled carbon nanotube (MWCNTs from elemental graphite powder. Initially, high ultra-active graphite powder can be obtained by mechanical milling under argon atmosphere. Finally, the mechanical activation product is heat-treated at 1350°C for 2–4 h under argon gas flow. After heat-treatment, active graphite powders were successfully changed into MWCNTs with high purity. The XRD analyses showed that in the duration 150 h of milling, all the raw materials were changed to the desired materials. From the broadening of the diffraction lines in the XRD patterns, it was concluded that the graphite crystallites were nanosized, and raising the milling duration resulted in the fineness of the particles and the increase of the strain. The structure and morphology of MWCNTs were investigated using scanning electron microscopy (SEM and high-resolution transmission electron microscopy (HRTEM. The yield of MWCNTs was estimated through SEM and TEM observations of the as-prepared samples was to be about 90%. Indeed, mechanothermal method is of interest for fundamental understanding and improvement of commercial synthesis of carbon nanotubes (CNTs. As a matter of fact, the method of mechanothermal guarantees the production of MWCNTs suitable for different applications.

  2. High-yield Synthesis of Multiwalled Carbon Nanotube by Mechanothermal Method

    Science.gov (United States)

    Manafi, S. A.; Amin, M. H.; Rahimipour, M. R.; Salahi, E.; Kazemzadeh, A.

    2009-04-01

    This study reports on the mechanothermal synthesis of multiwalled carbon nanotube (MWCNTs) from elemental graphite powder. Initially, high ultra-active graphite powder can be obtained by mechanical milling under argon atmosphere. Finally, the mechanical activation product is heat-treated at 1350°C for 2-4 h under argon gas flow. After heat-treatment, active graphite powders were successfully changed into MWCNTs with high purity. The XRD analyses showed that in the duration 150 h of milling, all the raw materials were changed to the desired materials. From the broadening of the diffraction lines in the XRD patterns, it was concluded that the graphite crystallites were nanosized, and raising the milling duration resulted in the fineness of the particles and the increase of the strain. The structure and morphology of MWCNTs were investigated using scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). The yield of MWCNTs was estimated through SEM and TEM observations of the as-prepared samples was to be about 90%. Indeed, mechanothermal method is of interest for fundamental understanding and improvement of commercial synthesis of carbon nanotubes (CNTs). As a matter of fact, the method of mechanothermal guarantees the production of MWCNTs suitable for different applications.

  3. A High Yield and Cost-efficient Expression System of Human Granzymes in Mammalian Cells.

    Science.gov (United States)

    Dotiwala, Farokh; Fellay, Isabelle; Filgueira, Luis; Martinvalet, Denis; Lieberman, Judy; Walch, Michael

    2015-06-10

    When cytotoxic T lymphocytes (CTL) or natural killer (NK) cells recognize tumor cells or cells infected with intracellular pathogens, they release their cytotoxic granule content to eliminate the target cells and the intracellular pathogen. Death of the host cells and intracellular pathogens is triggered by the granule serine proteases, granzymes (Gzms), delivered into the host cell cytosol by the pore forming protein perforin (PFN) and into bacterial pathogens by the prokaryotic membrane disrupting protein granulysin (GNLY). To investigate the molecular mechanisms of target cell death mediated by the Gzms in experimental in-vitro settings, protein expression and purification systems that produce high amounts of active enzymes are necessary. Mammalian secreted protein expression systems imply the potential to produce correctly folded, fully functional protein that bears posttranslational modification, such as glycosylation. Therefore, we used a cost-efficient calcium precipitation method for transient transfection of HEK293T cells with human Gzms cloned into the expression plasmid pHLsec. Gzm purification from the culture supernatant was achieved by immobilized nickel affinity chromatography using the C-terminal polyhistidine tag provided by the vector. The insertion of an enterokinase site at the N-terminus of the protein allowed the generation of active protease that was finally purified by cation exchange chromatography. The system was tested by producing high levels of cytotoxic human Gzm A, B and M and should be capable to produce virtually every enzyme in the human body in high yields.

  4. Does high yield spread dampen economic growth? : the case of US-Japan

    Directory of Open Access Journals (Sweden)

    Yutaka Kurihara

    2014-04-01

    Full Text Available This article focuses on the relationship between the United States' and Japan's yield spread of interest rates and economic growth in Japan. The yield spread is defined in this article as the difference between the Japanese government bond yield minus the US government bond yield. Some studies have tackled this issue and found a negative relationship between the yield spread and economic growth; however, recent studies have shown no or a weak relationship. This problem has not yet consensus in spite of its importance. As the Japanese interest rate has been quite low since the adoption of the zero interest rate policy at the end of 1990s, the situation may change the results. The empirical results show that reliability of yield spread as a leading indicator of output growth exists in Japan; however, term structure of interest rate is not related to economic growth.

  5. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

    Directory of Open Access Journals (Sweden)

    Roberta D'Agata

    2017-01-01

    Full Text Available Gold nanoparticles (AuNPs exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays.

  6. Single-step, high yield synthesis of gold nanoworms and their surface enhanced Raman scattering properties

    Science.gov (United States)

    Ahmed, Waqqar; van Ruitenbeek, Jan M.

    Rod-shaped gold nanoparticles have attracted enormous attention owing to their interesting optical properties arising from the surface plasmon resonances. Slight deviation from the rod morphology can markedly change the optical properties. For-example, worm-shaped gold nanoparticles can have more than two plasmon peaks. Furthermore, they show much higher local field enhancements as compared to their rod-shaped counterparts. We have devised a simple seedless, high-yield protocol for the synthesis of gold nanoworms (NWs). NWs were grown simply by reducing HAuCl4 with ascorbic acid in a high pH reaction medium, and in the presence of growth directional agents, cetyltrimethylammonium bromide and AgNO3. In contrast to the seed-mediated growth of gold nanorods where a seed grows into a rod, NWs grow by oriental attachment of nanoparticles. By varying different reaction parameters we were able to control the length of NWs from a few nanometers to micrometers. Furthermore, the aspect ratio can also be tuned over a wide range. Gold NWs show excellent surface enhanced Raman scattering (SERS) properties. Ultra-low concentrations of various target molecules were detected using NWs based SERS substrates.

  7. Breeding of a high yielding chamomile variety (Matricaria recutita L. with improved traits for machine harvesting

    Directory of Open Access Journals (Sweden)

    Albrecht, Sebastian

    2016-07-01

    Full Text Available A more productive variety of chamomile (Matricaria recutita L., which is more efficient in machine processing with consistent quality traits, will benefit the viability of german products in the global market. Breeding of an enhanced chamomile variety is part of a german multi-network project called KAMEL whose research aims on Matricaria recutita L., Valeriana officinalis L. and Melissa officinalis L. The agronomic and qualitative improvement of these speciality crops are the basis for further economic prosperity of medicinal and aromatic plant cultivation in Germany. The main breeding goals of a new variety of chamomile are the increase of blossom product yield (Matricariae flos to 6 dt/ha in up to three harvest stages through a homogenous flower horizon (pick height, an even flowering time, large flower heads and a high regeneration rate after each harvest stage. The upgrade of the content of essential oil content to a minimum of 0.8 % with its compostion according to Ph. Eur. and a chamazulene content of min. 25 % are further objectives of the breeding process. In addition to these quality traits, high tolerances against common fungal diseases are of particular interest. Development of an innovative chamomile variety is realized over nine years in three stages (2010 - 2019.

  8. Highly Efficient Red-Emitting Carbon Dots with Gram-Scale Yield for Bioimaging.

    Science.gov (United States)

    Ding, Hui; Wei, Ji-Shi; Zhong, Ning; Gao, Qing-Yu; Xiong, Huan-Ming

    2017-11-07

    Carbon dots (CDs) are a new class of photoluminescent (PL), biocompatible, environment-friendly, and low-cost carbon nanomaterials. Synthesis of highly efficient red-emitting carbon dots (R-CDs) on a gram scale is a great challenge at present, which heavily restricts the wide applications of CDs in the bioimaging field. Herein, R-CDs with a high quantum yield (QY) of 53% are produced on a gram scale by heating a formamide solution of citric acid and ethylenediamine. The as-prepared R-CDs have an average size of 4.1 nm and a nitrogen content of about 30%, with an excitation-independent emission at 627 nm. After detailed characterizations, such strong red fluorescence is ascribed to the contribution from the nitrogen- and oxygen-related surface states and the nitrogen-derived structures in the R-CD cores. Our R-CDs show good photostability and low cytotoxicity, and thus they are excellent red fluorescence probes for bioimaging both in vitro and in vivo.

  9. Fast co-pyrolysis of waste newspaper with high-density polyethylene for high yields of alcohols and hydrocarbons.

    Science.gov (United States)

    Chen, Weimin; Shi, Shukai; Chen, Minzhi; Zhou, Xiaoyan

    2017-09-01

    Waste newspaper (WP) was first co-pyrolyzed with high-density polyethylene (HDPE) using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) to enhance the yields of alcohols and hydrocarbons. The effects of WP: HDPE feed ratio (100:0, 75:25, 50:50, 25:75, 0:100) and temperature (500-800°C) on products distribution were investigated and the interaction mechanism during co-pyrolysis was also proposed. Maximum yields of alcohols and hydrocarbons reached 85.88% (feed ratio 50:50wt.%, 600°C). Hydrogen supplements and deoxidation by HDPE and subsequently fragments recombination result in the conversion of aldehydes and ketones into branched hydrocarbons. Radicals from WP degradation favor the secondary crack for HDPE products resulting in the formation of linear hydrocarbons with low carbon number. Hydrocarbons with activated radical site from HDPE degradation were interacted with hydroxyl from WP degradation promoting the formation of linear long chain alcohols. Moreover, co-pyrolysis significantly enhanced condensable oil qualities, which were close to commercial diesel No. 0. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Induction of embryogenic callus and plantlet regeneration from young leaves of high yielding mature oil palm

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    Yeedum, I.

    2004-09-01

    Full Text Available Callus induction and plantlet regeneration from young leaves of high-yielding mature oil palm were carried out using 10-year and 20-year-old trees from Thepa Research Station, Faculty of Natural Resources,Prince of Songkla University, Hat Yai, and Trang Agricultural College, respectively. Culture media used in this experiment were Murashige and Skoog (1962 and Oil Palm supplemented with various concentrations of α-naphthaleneacetic acid (NAA or 2,4- dichlorophenoxy acetic acid (2,4-D or dicamba (Di and antioxidants.Young leaves from 6th to 11st frond were excised, sterilized, cut into 5x5 mm pieces and cultured in the dark at 26±4ºC or 28±0.5ºC for 3 months. The results revealed that MS medium with 200 mg/l ascorbic acid (As and 1 mg/l Di (MS-AsDi gave the highest callus induction percentage (7.93 after culture for 3 months at 28±0.5ºC. Leaf segments from 6th - 8th frond yielded callus forming percentage at 10% (averaged from 1, 2.5 and 5 mg/l Di containing MS medium. Ascorbic acid as an antioxidant at concentration of 200 mg/l supplemented in MS medium in the presence of 2.5 mg/l Di produced the highest callus induction percentage (11.2 and number of nodules (7.06. A high percentage of embryogenic callus formation (66.67 was obtained when the calli were transferred to the same medium component supplemented with 0.5 mg/l Di and 1,000 mg/l casein hydrolysate (CH (MS-AsDiCH. Haustorial-staged embryos were observed to be isolated as an individual embryo and germinated on MS medium without plant growth regulator (MS-free. Development of root could be classified into two distinct types, fibrous and tap root.

  11. Semi-dwarf tef lines for high seed yield and lodging tolerance in ...

    African Journals Online (AJOL)

    The grain of tef is not only nutritious but also gluten-free, the cause for celiac disease, which affects humans world wide. The objective of this study was to evaluate the morpho-agronomic performance of newly developed semi-dwarf tef genotypes for grain yield and yield related agronomic traits under diverse environmental ...

  12. semi-dwarf tef lines for high seed yield and lodging tolerance in ...

    African Journals Online (AJOL)

    ACSS

    The grain of tef is not only nutritious but also gluten-free, the cause for celiac disease, which affects humans world wide. The objective of this study was to evaluate the morpho-agronomic performance of newly developed semi-dwarf tef genotypes for grain yield and yield related agronomic traits under diverse environmental ...

  13. Sense oligonucleotide competition for gene promoter binding and activation.

    Science.gov (United States)

    Cutroneo, Kenneth R; Chiu, Jen-Fu

    2003-01-01

    Considerable evidence has ensued on the importance of growth factors during regeneration both for cell replication and for stimulation of reparative cells to synthesize and secrete extracellular matrix components. During the healing process if the growth factor concentration is too high because of over-expression, abnormal wound healing and tissue fibrosis will occur. The growth factor concentration at the wound site may be controlled by gene therapy and the titration of gene dosage. However, if there is a narrow window between the beneficial effects and adverse effects of gene therapy, oligonucleotide approaches may be used concurrently with gene therapy to control growth factor concentration(s) at the wound site. Antisense oligos offer a method to control the concentration of growth factors at the level of translation. A novel method using sense oligos to the proalpha1 (I) collagen gene to inhibit gene transcription and collagen synthesis has recently been reported. The exogenous modified oligodeoxynucleotide competes with the cis-element (i.e. the transforming growth factor-beta (TGF-beta) element) in the distal 5'-flanking region of the proalpha1 (I) collagen gene for the trans-acting factor (i.e. the TGF-beta activator protein complex), thereby down regulating promoter activity of the proalpha1 (I) collagen gene and inhibiting type I collagen synthesis. The oligonucleotide approaches, both antisense and sense therapies, may be used to regulate over-expression of growth factors and thereby either eliminate or lessen the potential adverse effects of gene therapy.

  14. Non-food/feed seeds as biofactories for the high-yield production of recombinant pharmaceuticals.

    Science.gov (United States)

    Morandini, Francesca; Avesani, Linda; Bortesi, Luisa; Van Droogenbroeck, Bart; De Wilde, Kirsten; Arcalis, Elsa; Bazzoni, Flavia; Santi, Luca; Brozzetti, Annalisa; Falorni, Alberto; Stoger, Eva; Depicker, Ann; Pezzotti, Mario

    2011-10-01

    We describe an attractive cloning system for the seed-specific expression of recombinant proteins using three non-food/feed crops. A vector designed for direct subcloning by Gateway® recombination was developed and tested in Arabidopsis, tobacco and petunia plants for the production of a chimeric form (GAD67/65) of the 65 kDa isoform of glutamic acid decarboxylase (GAD65). GAD65 is one of the major human autoantigens involved in type 1 diabetes (T1D). The murine anti-inflammatory cytokine interleukin-10 (IL-10) was expressed with the described system in Arabidopsis and tobacco, whereas proinsulin, another T1D major autoantigen, was expressed in Arabidopsis. The cost-effective production of these proteins in plants could allow the development of T1D prevention strategies based on the induction of immunological tolerance. The best yields were achieved in Arabidopsis seeds, where GAD67/65 reached 7.7% of total soluble protein (TSP), the highest levels ever reported for this protein in plants. IL-10 and proinsulin reached 0.70% and 0.007% of TSP, respectively, consistent with levels previously reported in other plants or tissues. This versatile cloning vector could be suitable for the high-throughput evaluation of expression levels and stability of many valuable and difficult to produce proteins. © 2011 The Authors. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  15. High Quantum Yield Blue Emission from Lead-Free Inorganic Antimony Halide Perovskite Colloidal Quantum Dots.

    Science.gov (United States)

    Zhang, Jian; Yang, Ying; Deng, Hui; Farooq, Umar; Yang, Xiaokun; Khan, Jahangeer; Tang, Jiang; Song, Haisheng

    2017-09-26

    Colloidal quantum dots (QDs) of lead halide perovskite have recently received great attention owing to their remarkable performances in optoelectronic applications. However, their wide applications are hindered from toxic lead element, which is not environment- and consumer-friendly. Herein, we utilized heterovalent substitution of divalent lead (Pb(2+)) with trivalent antimony (Sb(3+)) to synthesize stable and brightly luminescent Cs3Sb2Br9 QDs. The lead-free, full-inorganic QDs were fabricated by a modified ligand-assisted reprecipitation strategy. A photoluminescence quantum yield (PLQY) was determined to be 46% at 410 nm, which was superior to that of other reported halide perovskite QDs. The PL enhancement mechanism was unraveled by surface composition derived quantum-well band structure and their large exciton binding energy. The Br-rich surface and the observed 530 meV exciton binding energy were proposed to guarantee the efficient radiative recombination. In addition, we can also tune the inorganic perovskite QD (Cs3Sb2X9) emission wavelength from 370 to 560 nm via anion exchange reactions. The developed full-inorganic lead-free Sb-perovskite QDs with high PLQY and stable emission promise great potential for efficient emission candidates.

  16. High Yield of Adult Oligodendrocyte Lineage Cells Obtained from Meningeal Biopsy

    Directory of Open Access Journals (Sweden)

    Sissi Dolci

    2017-10-01

    Full Text Available Oligodendrocyte loss can lead to cognitive and motor deficits. Current remyelinating therapeutic strategies imply either modulation of endogenous oligodendrocyte precursors or transplantation of in vitro expanded oligodendrocytes. Cell therapy, however, still lacks identification of an adequate source of oligodendrocyte present in adulthood and able to efficiently produce transplantable cells. Recently, a neural stem cell-like population has been identified in meninges. We developed a protocol to obtain high yield of oligodendrocyte lineage cells from one single biopsy of adult rat meningeal tissue. From 1 cm2 of adult rat spinal cord meninges, we efficiently expanded a homogenous culture of 10 millions of meningeal-derived oligodendrocyte lineage cells in a short period of time (approximately 4 weeks. Meningeal-derived oligodendrocyte lineage cells show typical mature oligodendrocyte morphology and express specific oligodendrocyte markers, such as galactosylceramidase and myelin basic protein. Moreover, when transplanted in a chemically demyelinated spinal cord model, meningeal-derived oligodendrocyte lineage cells display in vivo-remyelinating potential. This oligodendrocyte lineage cell population derives from an accessible and adult source, being therefore a promising candidate for autologous cell therapy of demyelinating diseases. In addition, the described method to differentiate meningeal-derived neural stem cells into oligodendrocyte lineage cells may represent a valid in vitro model to dissect oligodendrocyte differentiation and to screen for drugs capable to promote oligodendrocyte regeneration.

  17. EXTREME METEOROLOGICAL CONDITIONS AND METABOLIC PROFILE IN HIGH YIELDING HOLSTEINFRIESIAN DAIRY COWS

    Directory of Open Access Journals (Sweden)

    Z. GERGÁCZ

    2008-10-01

    Full Text Available The impact of two years (2002 and 2003 with different summer temperature extremes on variation in metabolic profile was analyzed in blood and urine samples taken from healthy, primiparous (n = 371 and multiparous (n = 795 high yielding Holstein-Friesian dairy cows. In this study main focus was lead on three most critical physiological phases, thus cows were assigned into three groups as follows: (1 dry cows for 10 days prior to calving; (2 cows 1-30 days after delivery, and (3 cows with more than 31 days post partum. Findings reveal clear response of the cows to heat in selected blood (hemoglobin, plasma aceto-acetic-acid, FFA, AST, glucose, urea and urine (pH, NABE and urea parameters. In the majority of cows, glucose and hemoglobin level, one of the most significant blood parameters, indicated symptoms of insufficient energy supply. Further metabolic indicators differed more or less from reference values depending on actual condition. Due to heat load dry matter intake has been decreased even by 10-15 per cent in primiparous cows. They were expected to increase body weight and size and simultaneously produce attain at large milk yields. In doing so that cows would have require large amount of nutrients. Out of parameters such as hemoglobin, glucose, FFA, AST and blood-urea differed from the reference values in most cases; however, this phenomenon seemed to be present in almost every case for hemoglobin and glucose. The lack of energy caused by heat stress can be contributed to the decrease of dry matter intake which has been indicated by the urea levels and pH both in blood and urine prevailing unfavorable and insufficient feeding practice. The results reconfirm the need to reconsider both the actual feeding practice (e.g. to increase of nutrient content in rations, reduce the intake of soluble proteins in rumen, pay attention of crude fiber in Total Mixed Rations (TMR, NDF and ADF, avoid overfeeding of inorganic buffers, to control moisture

  18. Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield.

    Science.gov (United States)

    Anazi, S; Maddirevula, S; Faqeih, E; Alsedairy, H; Alzahrani, F; Shamseldin, H E; Patel, N; Hashem, M; Ibrahim, N; Abdulwahab, F; Ewida, N; Alsaif, H S; Al Sharif, H; Alamoudi, W; Kentab, A; Bashiri, F A; Alnaser, M; AlWadei, A H; Alfadhel, M; Eyaid, W; Hashem, A; Al Asmari, A; Saleh, M M; AlSaman, A; Alhasan, K A; Alsughayir, M; Al Shammari, M; Mahmoud, A; Al-Hassnan, Z N; Al-Husain, M; Osama Khalil, R; Abd El Meguid, N; Masri, A; Ali, R; Ben-Omran, T; El Fishway, P; Hashish, A; Ercan Sencicek, A; State, M; Alazami, A M; Salih, M A; Altassan, N; Arold, S T; Abouelhoda, M; Wakil, S M; Monies, D; Shaheen, R; Alkuraya, F S

    2017-04-01

    Intellectual disability (ID) is a measurable phenotypic consequence of genetic and environmental factors. In this study, we prospectively assessed the diagnostic yield of genomic tools (molecular karyotyping, multi-gene panel and exome sequencing) in a cohort of 337 ID subjects as a first-tier test and compared it with a standard clinical evaluation performed in parallel. Standard clinical evaluation suggested a diagnosis in 16% of cases (54/337) but only 70% of these (38/54) were subsequently confirmed. On the other hand, the genomic approach revealed a likely diagnosis in 58% (n=196). These included copy number variants in 14% (n=54, 15% are novel), and point mutations revealed by multi-gene panel and exome sequencing in the remaining 43% (1% were found to have Fragile-X). The identified point mutations were mostly recessive (n=117, 81%), consistent with the high consanguinity of the study cohort, but also X-linked (n=8, 6%) and de novo dominant (n=19, 13%). When applied directly on all cases with negative molecular karyotyping, the diagnostic yield of exome sequencing was 60% (77/129). Exome sequencing also identified likely pathogenic variants in three novel candidate genes (DENND5A, NEMF and DNHD1) each of which harbored independent homozygous mutations in patients with overlapping phenotypes. In addition, exome sequencing revealed de novo and recessive variants in 32 genes (MAMDC2, TUBAL3, CPNE6, KLHL24, USP2, PIP5K1A, UBE4A, TP53TG5, ATOH1, C16ORF90, SLC39A14, TRERF1, RGL1, CDH11, SYDE2, HIRA, FEZF2, PROCA1, PIANP, PLK2, QRFPR, AP3B2, NUDT2, UFC1, BTN3A2, TADA1, ARFGEF3, FAM160B1, ZMYM5, SLC45A1, ARHGAP33 and CAPS2), which we highlight as potential candidates on the basis of several lines of evidence, and one of these genes (SLC39A14) was biallelically inactivated in a potentially treatable form of hypermanganesemia and neurodegeneration. Finally, likely causal variants in previously published candidate genes were identified (ASTN1, HELZ, THOC6, WDR45B, ADRA

  19. Comparative analysis of measles virus RNA by oligonucleotide fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Stephenson, J.R.; Meulen, V. ter (Wuerzburg Univ. (Germany, F.R.))

    1982-01-01

    Isolates from two cases of acute measles, one case of acute measles encephalitis and three patients with subacute sclerosing panencephalitis were compared. This comparison was based upon the electrophoretic analysis of T/sub 1/ oligonucleotides from single-stranded, full-length RNA isolated from cytoplasmic nucleocapsids. Although all viruses have oligonucleotides in common, each isolate generated a unique pattern of oligonucleotides. However, no group of oligonucleotides was observed which would allow differentiation between viruses isolated from acute infections and those isolated from CNS diseases; indicating that probably all measles viruses differ in their nucleotide sequence, regardless of origin.

  20. High-yield synthesis of few-layer graphene flakes through electrochemical expansion of graphite in propylene carbonate electrolyte.

    Science.gov (United States)

    Wang, Junzhong; Manga, Kiran Kumar; Bao, Qiaoliang; Loh, Kian Ping

    2011-06-15

    High-yield production of few-layer graphene flakes from graphite is important for the scalable synthesis and industrial application of graphene. However, high-yield exfoliation of graphite to form graphene sheets without using any oxidation process or super-strong acid is challenging. Here we demonstrate a solution route inspired by the lithium rechargeable battery for the high-yield (>70%) exfoliation of graphite into highly conductive few-layer graphene flakes (average thickness graphene sheets with the aid of sonication. The dispersible graphene can be ink-brushed to form highly conformal coatings of conductive films (15 ohm/square at a graphene loading of <1 mg/cm(2)) on commercial paper. © 2011 American Chemical Society

  1. Unravelling the mechanisms behind mixed catalysts for the high yield production of single-walled carbon nanotubes.

    Science.gov (United States)

    Tetali, Sailaja; Zaka, Mujtaba; Schönfelder, Ronny; Bachmatiuk, Alicja; Börrnert, Felix; Ibrahim, Imad; Lin, Jarrn H; Cuniberti, Gianaurelio; Warner, Jamie H; Büchner, Bernd; Rümmeli, Mark H

    2009-12-22

    The use of mixed catalysts for the high-yield production of single-walled carbon nanotubes is well-known. The mechanisms behind the improved yield are poorly understood. In this study, we systematically explore different catalyst combinations from Ni, Co, and Mo for the synthesis of carbon nanotubes via laser evaporation. Our findings reveal that the mixing of catalysts alters the catalyst cluster size distribution, maximizing the clusters' potential to form a hemispherical cap at nucleation and, hence, form a single-walled carbon nanotube. This process significantly improves the single-walled carbon nanotube yields.

  2. Oligonucleotide and Parylene Surface Coating of Polystyrene and ePTFE for Improved Endothelial Cell Attachment and Hemocompatibility

    Directory of Open Access Journals (Sweden)

    Martina Schleicher

    2012-01-01

    Full Text Available In vivo self-endothelialization by endothelial cell adhesion on cardiovascular implants is highly desirable. DNA-oligonucleotides are an intriguing coating material with nonimmunogenic characteristics and the feasibility of easy and rapid chemical fabrication. The objective of this study was the creation of cell adhesive DNA-oligonucleotide coatings on vascular implant surfaces. DNA-oligonucleotides immobilized by adsorption on parylene (poly(monoaminomethyl-para-xylene coated polystyrene and ePTFE were resistant to high shear stress (9.5 N/m2 and human blood serum for up to 96 h. Adhesion of murine endothelial progenitor cells, HUVECs and endothelial cells from human adult saphenous veins as well as viability over a period of 14 days of HUVECs on oligonucleotide coated samples under dynamic culture conditions was significantly enhanced (P<0.05. Oligonucleotide-coated surfaces revealed low thrombogenicity and excellent hemocompatibility after incubation with human blood. These properties suggest the suitability of immobilization of DNA-oligonucleotides for biofunctionalization of blood vessel substitutes for improved in vivo endothelialization.

  3. Air-insufflated high-definition dacryoendoscopy yields significantly better image quality than conventional dacryoendoscopy.

    Science.gov (United States)

    Sasaki, Tsugihisa; Sounou, Tsutomu; Tsuji, Hideki; Sugiyama, Kazuhisa

    2017-01-01

    To facilitate the analysis of lacrimal conditions, we utilized high-definition dacryoendoscopy (HDD) and undertook observations with a pressure-controlled air-insufflation system. We report the safety and performance of HDD. In this retrospective, non-randomized clinical trial, 46 patients (14 males and 32 females; age range 39-91 years; mean age ± SD 70.3±12.0 years) who had lacrimal disorders were examined with HDD and conventional dacryoendoscopy (CD). The high-definition dacryoendoscope had 15,000 picture element image fibers and an advanced objective lens. Its outer diameter was 0.9-1.2 mm. Air insufflation was controlled at 0-20 kPa with a digital manometer-based pressure-controlled air-insufflation system to evaluate the quality of the image. The HDD had an air/saline irrigation channel between the outer sheath (outer diameter =1.2 mm) and the metal inner sheath of the endoscope. We used it and the CD in air, saline, and diluted milk saline with and without manual irrigation to quantitatively evaluate the effect of air pressure and saline irrigation on image quality. In vivo, the most significant improvement in image quality was demonstrated with air-insufflated (5-15 kPa) HDD, as compared with saline-irrigated HDD and saline-irrigated CD. No emphysema or damage was noted under observation with HDD. In vitro, no significant difference was demonstrated between air-insufflated HDD and saline-irrigated HDD. In vitro, the image quality of air-insufflated HDD was significantly improved as compared with that of saline-irrigated CD. Pressure-controlled (5-15 kPa) air-insufflated HDD is safe, and yields significantly better image quality than CD and saline-irrigated HDD.

  4. High Photoluminescence Quantum Yields in Organic Semiconductor-Perovskite Composite Thin Films.

    Science.gov (United States)

    Longo, Giulia; La-Placa, Maria-Grazia; Sessolo, Michele; Bolink, Henk J

    2017-10-09

    One of the obstacles towards efficient radiative recombination in hybrid perovskites is a low exciton binding energy, typically in the orders of tens of meV. It has been shown that the use of electron-donor additives can lead to a substantial reduction of the non-radiative recombination in perovskite films. Herein, the approach using small molecules with semiconducting properties, which are candidates to be implemented in future optoelectronic devices, is presented. In particular, highly luminescent perovskite-organic semiconductor composite thin films have been developed, which can be processed from solution in a simple coating step. By tuning the relative concentration of methylammonium lead bromide (MAPbBr3 ) and 9,9spirobifluoren-2-yl-diphenyl-phosphine oxide (SPPO1), it is possible to achieve photoluminescent quantum yields (PLQYs) as high as 85 %. This is attributed to the dual functions of SPPO1 that limit the grain growth while passivating the perovskite surface. The electroluminescence of these materials was investigated by fabricating multilayer LEDs, where charge injection and transport was found to be severely hindered for the perovskite/SPPO1 material. This was alleviated by partially substituting SPPO1 with a hole-transporting material, 1,3-bis(N-carbazolyl)benzene (mCP), leading to bright electroluminescence. The potential of combining perovskite and organic semiconductors to prepare materials with improved properties opens new avenues for the preparation of simple lightemitting devices using perovskites as the emitter. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. A Low-cost, High-yield Process for the Direct Productin of High Energy Density Liquid Fuel from Biomass

    Energy Technology Data Exchange (ETDEWEB)

    Agrawal, Rakesh

    2014-02-21

    The primary objective and outcome of this project was the development and validation of a novel, low-cost, high-pressure fast-hydropyrolysis/hydrodeoxygenation (HDO) process (H{sub 2}Bioil) using supplementary hydrogen (H{sub 2}) to produce liquid hydrocarbons from biomass. The research efforts under the various tasks of the project have culminated in the first experimental demonstration of the H2Bioil process, producing 100% deoxygenated >C4+ hydrocarbons containing 36-40% of the carbon in the feed of pyrolysis products from biomass. The demonstrated H{sub 2}Bioil process technology (i.e. reactor, catalyst, and downstream product recovery) is scalable to a commercial level and is estimated to be economically competitive for the cases when supplementary H{sub 2} is sourced from coal, natural gas, or nuclear. Additionally, energy systems modeling has revealed several process integration options based on the H{sub 2}Bioil process for energy and carbon efficient liquid fuel production. All project tasks and milestones were completed or exceeded. Novel, commercially-scalable, high-pressure reactors for both fast-hydropyrolysis and hydrodeoxygenation were constructed, completing Task A. These reactors were capable of operation under a wide-range of conditions; enabling process studies that lead to identification of optimum process conditions. Model compounds representing biomass pyrolysis products were studied, completing Task B. These studies were critical in identifying and developing HDO catalysts to target specific oxygen functional groups. These process and model compound catalyst studies enabled identification of catalysts that achieved 100% deoxygenation of the real biomass feedstock, sorghum, to form hydrocarbons in high yields as part of Task C. The work completed during this grant has identified and validated the novel and commercially scalable H2Bioil process for production of hydrocarbon fuels from biomass. Studies on model compounds as well as real biomass

  6. A high-yielding, generic fed-batch process for recombinant antibody production of GS-engineered cell lines

    DEFF Research Database (Denmark)

    Fan, Li; Zhao, Liang; Sun, Yating

    2009-01-01

    . Compared to batch cultures, the fed-batch technology generated the magnitude of the increase in cell yields (5 fold) and final antibody concentrations (4-8 fold). The majority of the increase in final antibody concentration was functions of the increased cell density and the prolonged culture time....... This generic and high-yielding fed-batch process would shorten development time, and ensure process stability, thereby facilitating the manufacture of therapeutic antibodies by GS-engineered cell lines....

  7. [Use of a synthetic oligonucleotide (CAC)5 in the genomic "dactyloscopy" method].

    Science.gov (United States)

    Korokhov, N P; Popovskiĭ, A V; Sharonova, D A; Novoselov, V P

    1993-01-01

    Potentialities of a chemically synthetized oligonucleotide of a certain structure in the genomic "dactyloscopy" method were under study. A random sample analysis has demonstrated a high resolving power of this variant of the method. Arguments in favor of introducing this approach in practical forensic medical direct identification of biologic material are presented.

  8. 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...

  9. Enhancement of Biogas Yield of Poplar Leaf by High-Solid Codigestion with Swine Manure.

    Science.gov (United States)

    Wangliang, Li; Zhikai, Zhang; Guangwen, Xu

    2016-05-01

    The aim of this work was to examine the improvement of anaerobic biodegradability of organic fractions of poplar leaf from codigestion with swine manure (SM), thus biogas yield and energy recovery. When poplar leaf was used as a sole substrate, the cumulative biogas yield was low, about 163 mL (g volatile solid (VS))(-1) after 45 days of digestion with a substrate/inoculum ratio of 2.5 and a total solid (TS) of 22 %. Under the same condition, the cumulative biogas yield of poplar leaf reached 321 mL (g VS)(-1) when SM/poplar leaf ratio was 2:5 (based on VS). The SM/poplar leaf ratio can determine C/N ratio of the cosubstrate and thus has significant influence on biogas yield. When the SM/poplar leaf ratio was 2:5, C/N ratio was calculated to be 27.02, and the biogas yield in 45 days of digestion was the highest. The semi-continuous digestion of poplar leaf was carried out with the organic loading rate of 1.25 and 1.88 g VS day(-1). The average daily biogas yield was 230.2 mL (g VS)(-1) and 208.4 mL (g VS)(-1). The composition analysis revealed that cellulose and hemicellulose contributed to the biogas production.

  10. High-yield synthesis and electrochemical and photovoltaic properties of indene-C{sub 70} bisadduct

    Energy Technology Data Exchange (ETDEWEB)

    He, Youjun; Zhao, Guangjin; Peng, Bo; Li, Yongfang [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China)

    2010-10-08

    [6, 6]-Phenyl-C{sub 61}-butyric acid methyl ester (PC{sub 60}BM) is the widely used acceptor material in polymer solar cells (PSCs). Nevertheless, the low LUMO energy level and weak absorption in visible region are its two weak points. For enhancing the solar light harvest, the soluble C{sub 70} derivative PC{sub 70}BM has been used as acceptor instead of PC{sub 60}BM in high efficiency PSCs in recent years. But, the LUMO level of PC{sub 70}BM is the same as that of PC{sub 60}BM, which is too low for the PSCs based on the polymer donors with higher HOMO level, such as poly (3-hexylthiophene) (P3HT). Here, a new soluble C{sub 70} derivative, indene-C{sub 70} bisadduct (IC{sub 70}BA), is synthesized with high yield of 58% by a one-pot reaction of indene and C{sub 70} at 180 C for 72 h. The electrochemical properties and electronic energy levels of the fullerene derivatives are measured by cyclic voltammetry. The LUMO energy level of IC{sub 70}BA is 0.19 eV higher than that of PC{sub 70}BM. The PSC based on P3HT with IC{sub 70}BA as acceptor shows a higher V{sub oc} of 0.84 V and higher power conversion efficiency (PCE) of 5.64%, while the PSC based on P3HT/PC{sub 60}BM and P3HT/PC{sub 70}BM displays V{sub oc} of 0.59 V and 0.58 V, and PCE of 3.55% and 3.96%, respectively, under the illumination of AM1.5G, 100 mW cm{sup -2}. The results indicate that IC{sub 70}BA is an excellent acceptor for the P3HT-based PSCs and could be a promising new acceptor instead of PC{sub 70}BM for the high performance PSCs based on narrow bandgap conjugated polymer donor. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  11. High-Yield Fabrication of Entangled Photon Emitters for Hybrid Quantum Networking Using High-Temperature Droplet Epitaxy.

    Science.gov (United States)

    Basso Basset, Francesco; Bietti, Sergio; Reindl, Marcus; Esposito, Luca; Fedorov, Alexey; Huber, Daniel; Rastelli, Armando; Bonera, Emiliano; Trotta, Rinaldo; Sanguinetti, Stefano

    2018-01-10

    Several semiconductor quantum dot techniques have been investigated for the generation of entangled photon pairs. Among the other techniques, droplet epitaxy enables the control of the shape, size, density, and emission wavelength of the quantum emitters. However, the fraction of the entanglement-ready quantum dots that can be fabricated with this method is still limited to around 5%, and matching the energy of the entangled photons to atomic transitions (a promising route toward quantum networking) remains an outstanding challenge. Here, we overcome these obstacles by introducing a modified approach to droplet epitaxy on a high symmetry (111)A substrate, where the fundamental crystallization step is performed at a significantly higher temperature as compared with previous reports. Our method drastically improves the yield of entanglement-ready photon sources near the emission wavelength of interest, which can be as high as 95% due to the low values of fine structure splitting and radiative lifetime, together with the reduced exciton dephasing offered by the choice of GaAs/AlGaAs materials. The quantum dots are designed to emit in the operating spectral region of Rb-based slow-light media, providing a viable technology for quantum repeater stations.

  12. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

    Science.gov (United States)

    Hijri, Mohamed

    2016-04-01

    An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

  13. A multi-region assessment of population rates of cardiac catheterization and yield of high-risk coronary artery disease

    Directory of Open Access Journals (Sweden)

    Clement Fiona M

    2011-11-01

    Full Text Available Abstract Background There is variation in cardiac catheterization utilization across jurisdictions. Previous work from Alberta, Canada, showed no evidence of a plateau in the yield of high-risk disease at cardiac catheterization rates as high as 600 per 100,000 population suggesting that the optimal rate is higher. This work aims 1 To determine if a previously demonstrated linear relationship between the yield of high-risk coronary disease and cardiac catheterization rates persists with contemporary data and 2 to explore whether the linear relationship exists in other jurisdictions. Methods Detailed clinical information on all patients undergoing cardiac catheterization in 3 Canadian provinces was available through the Alberta Provincial Project for Outcomes Assessment in Coronary Heart (APPROACH disease and partner initiatives in British Columbia and Nova Scotia. Population rates of catheterization and high-risk coronary disease detection for each health region in these three provinces, and age-adjusted rates produced using direct standardization. A mixed effects regression analysis was performed to assess the relationship between catheterization rate and high-risk coronary disease detection. Results In the contemporary Alberta data, we found a linear relationship between the population catheterization rate and the high-risk yield. Although the yield was slightly less in time period 2 (2002-2006 than in time period 1(1995-2001, there was no statistical evidence of a plateau. The linear relationship between catheterization rate and high-risk yield was similarly demonstrated in British Columbia and Nova Scotia and appears to extend, without a plateau in yield, to rates over 800 procedures per 100,000 population. Conclusions Our study demonstrates a consistent finding, over time and across jurisdictions, of linearly increasing detection of high-risk CAD as population rates of cardiac catheterization increase. This internationally-relevant finding

  14. High-yield growth of vertically aligned carbon nanotubes on a continuously moving substrate

    Energy Technology Data Exchange (ETDEWEB)

    Guzman de Villoria, R; Hart, A J; Steiner, S A III; Wardle, B L [Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Figueredo, S L; Slocum, A H, E-mail: rguzman@mit.ed [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2009-10-07

    Vertically aligned carbon nanotube (CNT) arrays are grown on a moving substrate, demonstrating continuous growth of nanoscale materials with long-range order. A cold-wall chamber with an oscillating moving platform is used to locally heat a silicon growth substrate coated with an Fe/Al{sub 2}O{sub 3} catalyst film for CNT growth via chemical vapor deposition. The reactant gases are introduced over the substrate through a directed nozzle to attain high-yield CNT growth. Aligned multi-wall carbon nanotube arrays (or 'forests') with heights of {approx}1 mm are achieved at substrate speeds up to 2.4 mm s{sup -1}. Arrays grown on moving substrates at different velocities are studied in order to identify potential physical limitations of repeatable and fast growth on a continuous basis. No significant differences are noted between static and moving growth as characterized by scanning electron microscopy and Raman spectroscopy, although overall growth height is marginally reduced at the highest substrate velocity. CNT arrays produced on moving substrates are also found to be comparable to those produced through well-characterized batch processes consistent with a base-growth mechanism. Growth parameters required for the moving furnace are found to differ only slightly from those used in a comparable batch process; thermal uniformity appears to be the critical parameter for achieving large-area uniform array growth. If the continuous-growth technology is combined with a reaction zone isolation scheme common in other types of processing (e.g., in the manufacture of carbon fibers), large-scale dense and aligned CNT arrays may be efficiently grown and harvested for numerous applications including providing interlayers for advanced composite reinforcement and improved electrical and thermal transport.

  15. A New Strategy for Production of 5-Aminolevulinic Acid in Recombinant Corynebacterium glutamicum with High Yield

    Science.gov (United States)

    Yang, Peng; Liu, Wenjing; Cheng, Xuelian; Wang, Jing; Qi, Qingsheng

    2016-01-01

    ABSTRACT 5-Aminolevulinic acid (ALA), a nonprotein amino acid involved in tetrapyrrole synthesis, has been widely applied in agriculture, medicine, and food production. Many engineered metabolic pathways have been constructed; however, the production yields are still low. In this study, several 5-aminolevulinic acid synthases (ALASs) from different sources were evaluated and compared with respect to their ALA production capacities in an engineered Corynebacterium glutamicum CgS1 strain that can accumulate succinyl-coenzyme A (CoA). A codon-optimized ALAS from Rhodobacter capsulatus SB1003 displayed the best potential. Recombinant strain CgS1/pEC-SB produced 7.6 g/liter ALA using a mineral salt medium in a fed-batch fermentation mode. Employing two-stage fermentation, 12.46 g/liter ALA was produced within 17 h, with a productivity of 0.73 g/liter/h, in recombinant C. glutamicum. Through overexpression of the heterologous nonspecific ALA exporter RhtA from Escherichia coli, the titer was further increased to 14.7 g/liter. This indicated that strain CgS1/pEC-SB-rhtA holds attractive industrial application potential for the future. IMPORTANCE In this study, a two-stage fermentation strategy was used for production of the value-added nonprotein amino acid 5-aminolevulinic acid from glucose and glycine in a generally recognized as safe (GRAS) host, Corynebacterium glutamicum. The ALA titer represented the highest in the literature, to our knowledge. This high production capacity, combined with the potential easy downstream processes, made the recombinant strain an attractive candidate for industrial use in the future. PMID:26921424

  16. High diagnostic yield of syndromic intellectual disability by targeted next-generation sequencing.

    Science.gov (United States)

    Martínez, Francisco; Caro-Llopis, Alfonso; Roselló, Mónica; Oltra, Silvestre; Mayo, Sonia; Monfort, Sandra; Orellana, Carmen

    2017-02-01

    Intellectual disability is a very complex condition where more than 600 genes have been reported. Due to this extraordinary heterogeneity, a large proportion of patients remain without a specific diagnosis and genetic counselling. The need for new methodological strategies in order to detect a greater number of mutations in multiple genes is therefore crucial. In this work, we screened a large panel of 1256 genes (646 pathogenic, 610 candidate) by next-generation sequencing to determine the molecular aetiology of syndromic intellectual disability. A total of 92 patients, negative for previous genetic analyses, were studied together with their parents. Clinically relevant variants were validated by conventional sequencing. A definitive diagnosis was achieved in 29 families by testing the 646 known pathogenic genes. Mutations were found in 25 different genes, where only the genes KMT2D, KMT2A and MED13L were found mutated in more than one patient. A preponderance of de novo mutations was noted even among the X linked conditions. Additionally, seven de novo probably pathogenic mutations were found in the candidate genes AGO1, JARID2, SIN3B, FBXO11, MAP3K7, HDAC2 and SMARCC2. Altogether, this means a diagnostic yield of 39% of the cases (95% CI 30% to 49%). The developed panel proved to be efficient and suitable for the genetic diagnosis of syndromic intellectual disability in a clinical setting. Next-generation sequencing has the potential for high-throughput identification of genetic variations, although the challenges of an adequate clinical interpretation of these variants and the knowledge on further unknown genes causing intellectual disability remain to be solved. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  17. Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer.

    Science.gov (United States)

    Bates, Paula J; Laber, Damian A; Miller, Donald M; Thomas, Shelia D; Trent, John O

    2009-06-01

    Certain guanine-rich (G-rich) DNA and RNA molecules can associate intermolecularly or intramolecularly to form four stranded or "quadruplex" structures, which have unusual biophysical and biological properties. Several synthetic G-rich quadruplex-forming oligodeoxynucleotides have recently been investigated as therapeutic agents for various human diseases. We refer to these biologically active G-rich oligonucleotides as aptamers because their activities arise from binding to protein targets via shape-specific recognition (analogous to antibody-antigen binding). As therapeutic agents, the G-rich aptamers may have some advantages over monoclonal antibodies and other oligonucleotide-based approaches. For example, quadruplex oligonucleotides are non-immunogenic, heat stable and they have increased resistance to serum nucleases and enhanced cellular uptake compared to unstructured sequences. In this review, we describe the characteristics and activities of G-rich oligonucleotides. We also give a personal perspective on the discovery and development of AS1411, an antiproliferative G-rich phosphodiester oligonucleotide that is currently being tested as an anticancer agent in Phase II clinical trials. This molecule functions as an aptamer to nucleolin, a multifunctional protein that is highly expressed by cancer cells, both intracellularly and on the cell surface. Thus, the serendipitous discovery of the G-rich oligonucleotides also led to the identification of nucleolin as a new molecular target for cancer therapy.

  18. High yield purification of full-length functional hERG K+ channels produced in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Molbaek, Karen; Scharff-Poulsen, Peter; Hélix-Nielsen, Claus

    2015-01-01

    knowledge this is the first reported high-yield production and purification of full length, tetrameric and functional hERG. This significant breakthrough will be paramount in obtaining hERG crystal structures, and in establishment of new high-throughput hERG drug safety screening assays....

  19. Oligonucleotide probes for DNA fingerprinting in dogs.

    Science.gov (United States)

    Jung, M; Wilke, K; Geldermann, H

    1994-01-12

    Ten different oligonucleotide probes were evaluated for DNA fingerprinting in dogs. Seven probes are able to detect polymorphic bands. Probes (GT)(8) , (GTG)(5) and (GGAT)(4) are most informative for individual identification. The probabilities that two individuals from different breeds have the same DNA fingerprint pattern are 1.7 × 10(-7) , 5.5 × 10(-8) and 4.5 × 10(-6) , respectively. Using a combination of the three probes, paternity tests were performed with exclusion probabilities between 0.006% and 3%. ZUSAMMENFASSUNG: Oligonucleotid Sonden für DNA fingerprinting bei Hunden Zur Darstellung von DNA-Fingerprints beim Hund wurden zehn verschiedene Oligonukleotid-Sonden verglichen. Mit sieben Sonden konnten polymorphe Banden nachgewiesen werden. Die Sonden (GT)(8) , (GTG)(5) und (GGAT)(4) besaßen die größte Informativität für den Indentitätsnachweis. Die Wahrscheinlichkeit, daß zwei Individuen dieselben Fingerprint-Muster aufweisen, liegt bei 1,7 × 10(-7) , 5,5 × 10(-8) bzw. 4,5 × 10(-6) . Bei Verwendung einer Kombination der drei Sonden wurden Vaterschaftskontrollen mit Ausschlußwahrscheinlichkeiten zwischen 0,006% und 3 % erreicht. 1994 Blackwell Verlag GmbH.

  20. High-yield production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate.

    Science.gov (United States)

    Zhang, Min; Gu, Lei; Cheng, Chao; Zhu, Junru; Wu, Hao; Ma, Jiangfeng; Dong, Weiliang; Kong, Xiangping; Jiang, Min; Ouyang, Pingkai

    2017-08-01

    Chicory is an agricultural plant with considerable potential as a carbohydrate substrate for low-cost production of biochemicals. In this work, the production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate was investigated. The bioconversion process initially suffered from the leakage of fructose to the phosphoketolase pathway, resulting in a low mannitol yield. When inulin hydrolysate was supplemented with glucose as a substrate for mannitol production in combination with aeration induction and nicotinic acid induced redox modulation strategies, the mannitol yield greatly improved. Under these conditions, significant improvement in the glucose consumption rate, intracellular NADH levels and mannitol dehydrogenase specific activity were observed, with mannitol production increasing from 64.6 to 88.1 g/L and overall yield increase from 0.69 to 0.94 g/g. This work demonstrated an efficient method for the production of mannitol from inulin hydrolysate with a high overall yield.

  1. Biosolar cells: global artificial photosynthesis needs responsive matrices with quantum coherent kinetic control for high yield.

    Science.gov (United States)

    Purchase, R L; de Groot, H J M

    2015-06-06

    propose that synergy gains by such processes form a basis for further progress towards high efficiency and yield for a global project on artificial photosynthesis. Finally, we look at artificial photosynthesis research in The Netherlands and use this as an example of how an interdisciplinary approach is beneficial to artificial photosynthesis research. We conclude with some of the potential societal consequences of a large-scale roll out of artificial photosynthesis.

  2. Biosolar cells: global artificial photosynthesis needs responsive matrices with quantum coherent kinetic control for high yield

    Science.gov (United States)

    Purchase, R. L.; de Groot, H. J. M.

    2015-01-01

    . We propose that synergy gains by such processes form a basis for further progress towards high efficiency and yield for a global project on artificial photosynthesis. Finally, we look at artificial photosynthesis research in The Netherlands and use this as an example of how an interdisciplinary approach is beneficial to artificial photosynthesis research. We conclude with some of the potential societal consequences of a large-scale roll out of artificial photosynthesis. PMID:26052428

  3. High-yield secretion of recombinant proteins from the microalga Chlamydomonas reinhardtii

    DEFF Research Database (Denmark)

    Ramos Martinez, Erick Miguel; Fimognari, Lorenzo; Sakuragi, Yumiko

    2017-01-01

    reinhardtii, a widely used green microalga as a model organism and a potential industrial biotechnology platform. We demonstrated that the putative signal sequence from C. reinhardtii gametolysin can assist the secretion of the yellow fluorescent protein Venus into the culture media. To increase the secretion...... yields, Venus was C-terminally fused with synthetic glycomodules comprised of tandem serine (Ser) and proline (Pro) repeats of 10 and 20 units [hereafter (SP)n , wherein n = 10 or 20]. The yields of the (SP)n -fused Venus were higher than Venus without the glycomodule by up to 12-fold, with the maximum...... yield of 15 mg/L. Moreover, the presence of the glycomodules conferred an enhanced proteolytic protein stability. The Venus-(SP)n proteins were shown to be glycosylated, and a treatment of the cells with brefeldin A led to a suggestion that glycosylation of the (SP)n glycomodules starts...

  4. Cesium hafnium chloride: A high light yield, non-hygroscopic cubic crystal scintillator for gamma spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Burger, Arnold, E-mail: aburger@fisk.edu [Department of Life and Physical Sciences, Fisk University, Nashville, Tennessee 37208 (United States); Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37235 (United States); Rowe, Emmanuel; Groza, Michael; Morales Figueroa, Kristle [Department of Life and Physical Sciences, Fisk University, Nashville, Tennessee 37208 (United States); Cherepy, Nerine J.; Beck, Patrick R.; Hunter, Steven; Payne, Stephen A. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2015-10-05

    We report on the scintillation properties of Cs{sub 2}HfCl{sub 6} (cesium hafnium chloride or CHC) as an example of a little-known class of non-hygroscopic compounds having the generic cubic crystal structure of K{sub 2}PtCl{sub 6}. The crystals are easily growable from the melt using the Bridgman method with minimal precursor treatments or purification. CHC scintillation is centered at 400 nm, with a principal decay time of 4.37 μs and a light yield of up to 54 000 photons/MeV when measured using a silicon CCD photodetector. The light yield is the highest ever reported for an undoped crystal, and CHC also exhibits excellent light yield nonproportionality. These desirable properties allowed us to build and test CHC gamma-ray spectrometers providing energy resolution of 3.3% at 662 keV.

  5. Whole lactation production responses in high-yielding dairy cows using high-quality grass/clover silage.

    Science.gov (United States)

    Patel, Mikaela; Wredle, Ewa; Spörndly, Eva; Bertilsson, Jan

    2017-07-01

    Limiting the use of purchased concentrate for livestock and replacing it with home-grown forage without compromising milk production can offer benefits in both organic and conventional dairy systems. A full lactation trial was conducted with 92 cows over two years comparing three diets, each differing in the mean forage proportion over the lactation, 500 (500F), 600 (600F) and 700 (700F) g kg-1 dry matter (DM) respectively. The diets were designed to represent common conventional feeding, current regulations for organic production and more extreme high-forage-based production respectively. The aims were to determine the effects of forage proportion in the diet on milk production and feed utilisation. Compared with 500F, daily milk yield did not differ in 600F but was lower in 700F (31.3, 31.1 and 29.2 kg energy-corrected milk respectively). Daily dry matter intake (DMI) was similar between treatments (20.3, 20.4 and 19.9 kg in 500F, 600F and 700F respectively). Increasing the forage proportion from 500 to 600 g kg-1 DM did not have any adverse effects on milk production or DMI. Thus it is possible to produce the same quantity of milk with less concentrate and reduce the use of potential human feeds in dairy production. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  6. Innovations in papermaking: an LCA of printing and writing paper from conventional and high yield pulp.

    Science.gov (United States)

    Manda, B M Krishna; Blok, Kornelis; Patel, Martin K

    2012-11-15

    Pulp and paper industry is facing challenges such as resource scarcity and greenhouse gas (GHG) emissions. The objective of this research is to investigate whether the use of new coatings (micro or nano TiO(2)) and different pulp types could bring savings in wood, energy, GHG emissions and other environmental impacts in comparison with conventional printing and writing paper. We studied three types of pulp, namely i) unbleached virgin kraft pulp, ii) recovered fiber, and iii) high yield virgin chemithermo-mechanical pulp (CTMP). A life cycle assessment (LCA) was conducted from cradle to grave. Applying attributional modeling, we found that wood savings amount to 60% for the nanoparticle coated recovered fiber paper and 35% for the micro TiO(2) coated CTMP paper. According to the ReCiPe single score impact assessment method, the new product configurations allow the reduction of the environmental impacts by 10-35% compared to conventional kraft paper. Applying consequential modeling, we found larger energy and GHG emission savings compared to attributional modeling because the saved wood is used for producing energy, thereby replacing fossil fuels. The nanoparticle coated recovered fiber paper offered savings of non-renewable energy use (NREU) by 100% (13GJ/ton paper) and GHG emission reduction by 75% (0.6 tonCO(2)eq./ton paper). Micro TiO(2) coated CTMP paper offered NREU savings by 25% (3GJ/ton paper) and savings of GHG emissions by 10% (0.1 tonCO(2)eq./ton paper). The taking into account of all environmental impacts with the ReCiPe single score method leads to comparable results as that of attributional modeling. We conclude that the nanoparticle coated recovered fiber paper offered the highest savings and lowest environmental impacts. However, human toxicity and ecotoxicity impacts of the nanoparticles were not included in this analysis and need further research. If this leads to the conclusion that the toxicity impacts of the nanoparticles are serious, then the

  7. Investigations of oligonucleotide usage variance within and between prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J.; Skjerve, E.; Ussery, David

    2008-01-01

    Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di-to tetranucleotides). We wanted to assess the statistical information potential...... of different DNA 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found...... was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i. e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than...

  8. semi-dwarf tef lines for high seed yield and lodging tolerance in ...

    African Journals Online (AJOL)

    ACSS

    genetic advance (20.2 cm) and heritability estimates (86.7%) were obtained for plant height indicating that selection for this trait can be made easily. Grain yield showed significant and positive genotypic association with plant height, whole culm and second culm internode length, second culm internode diameter, number of ...

  9. Highly productive forage legume stands show no positive biodiversity effect on yield and N2-fixation

    DEFF Research Database (Denmark)

    Dhamala, Nawa Raj; Eriksen, Jørgen; Carlsson, Georg

    2017-01-01

    . Methodology N fixation, dry matter (DM) and nitrogen (N) yields were quantified in a field experiment for red clover (Trifolium pratense L.), white clover (Trifolium repens L.) and lucerne (Medicago sativa L.) pure stands and mixtures using the isotope dilution method. Results All three forage legume species...

  10. Nuclear Engineering of Microalgae for High Yield Secretion of Recombinant Proteins

    DEFF Research Database (Denmark)

    Ramos Martinez, Erick Miguel

    to the glycomodules, accumulation of a fusion protein was dramatically increased by up to 12 folds, with the maximum yield of 15 mg L-1. Characterization of the secreted Venus showed the presence of glycosylations and increased resistance to proteolytic degradation. The results from this thesis demonstrate...

  11. High-yield preparation of polystyrene/silica clusters of controlled morphology

    OpenAIRE

    Désert, Anthony; Chaduc, Isabelle; Fouilloux, Sarah; Taveau, Jean-Christophe; Lambert, Olivier; Lansalot, Muriel; Bourgeat-Lami, Elodie; Thill, Antoine; Spalla, Olivier; Ravaine, Serge; Duguet, Etienne

    2012-01-01

    3 pages; International audience; Large amounts of regular tetrapods and hexapods made of a central silica core and four or six polystyrene satellite nodules were prepared with yields over 80% from 55 nm and 85 nm silica seeds, respectively. The robustness of the process is supported by extensive statistical analyses and large-field transmission electron microscopy images.

  12. Predicting yields of high priced trimmed beef cuts by means of ...

    African Journals Online (AJOL)

    The total and individual trimmed meat yield of six hind quarter cuts and one fore quarter cut were estimated for 200 carcasses from animals of mixed origin with regard to breed, sex and feeding regimen. The linear models included carcass weight and visual assessment of fatness and conformation by means of seven fat and ...

  13. High-yield production of Streptavidin with native C-terminal in ...

    African Journals Online (AJOL)

    To increase the production yield of functional recombinant streptavidin in Escherichia coli, the effects of host strains and culture conditions on expression of streptavidin with native C terminal (CNSA, amino acid residues 13 to 159) were investigated. Results show that the CNSA, encoded by the CNSA gene, was produced ...

  14. High Diagnostic Yield of Dedicated Pulmonary Screening before Hematopoietic Cell Transplantation in Children

    NARCIS (Netherlands)

    Versluijs, Anne Birgitta; van der Ent, Korstiaan; Boelens, Jaap J.; Wolfs, Tom; de Jong, Pim; Bierings, Marc B.

    2015-01-01

    Pulmonary complications are an important cause for treatment-related morbidity and mortality in hematopoietic cell transplantation (HCT) in children. The aim of this study was to investigate the yield of our pre-HCT pulmonary screening program. We also describe our management guidelines based on

  15. Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells

    Directory of Open Access Journals (Sweden)

    Muyrers Joep PP

    2003-01-01

    Full Text Available Abstract Background The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. Results Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα but only requires a phage annealing protein (RecT or Redβ. Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. Conclusion Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ.

  16. High-yield exfoliation of tungsten disulphide nanosheets by rational mixing of low-boiling-point solvents

    Science.gov (United States)

    Sajedi-Moghaddam, Ali; Saievar-Iranizad, Esmaiel

    2018-01-01

    Developing high-throughput, reliable, and facile approaches for producing atomically thin sheets of transition metal dichalcogenides is of great importance to pave the way for their use in real applications. Here, we report a highly promising route for exfoliating two-dimensional tungsten disulphide sheets by using binary combination of low-boiling-point solvents. Experimental results show significant dependence of exfoliation yield on the type of solvents as well as relative volume fraction of each solvent. The highest yield was found for appropriate combination of isopropanol/water (20 vol% isopropanol and 80 vol% water) which is approximately 7 times higher than that in pure isopropanol and 4 times higher than that in pure water. The dramatic increase in exfoliation yield can be attributed to perfect match between the surface tension of tungsten disulphide and binary solvent system. Furthermore, solvent molecular size also has a profound impact on the exfoliation efficiency, due to the steric repulsion.

  17. Short communication: Estimating lactation curves for highly inhomogeneous milk yield data of an F2 population (Charolais × German Holstein).

    Science.gov (United States)

    Melzer, N; Trißl, S; Nürnberg, G

    2017-11-01

    Fitting of lactation curves is a common tool to obtain the entire milk yield as well as to estimate the main curve characteristic (such as day of peak milk yield) for a lactation. These models are primarily designed for dairy cattle, but have been applied to nondairy cattle breeds and also for other species. In this study we considered milk yield data of 197 F2 crossbred cows of Charolais and German Holstein (founder breeds) for the first and the beginning of the second lactation. The F2 cows showed a high variability regarding the length of lactation, which varied between 7 and 406 d in milk for the first lactation. Thus, the data also show high variation regarding the daily and overall milk yield. To obtain complete lactation curves, we evaluated the lactation models of Ali-Schaeffer and Wilmink. To compare the 2 lactation models, we evaluated the goodness of fit using 6 evaluation criteria. The results show that the model of Ali-Schaeffer performs better on these highly inhomogeneous data, in contrast to the model of Wilmink. We discuss our findings from a statistical point of view and present possible biological reasons for the high variability regarding milk yield within the F2 population. Hence our findings may be helpful when milk yield data of crosses between dairy and beef cows (dual purpose) are investigated, whose lactation curves may not show the typical characteristics of dairy cattle. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

  18. A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide.

    Science.gov (United States)

    Roh, Changhyun

    2012-01-01

    Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS), and the rate of global death from SARS has remarkably increased. Hence, the development of efficient drug treatments for the biological effects of SARS is highly needed. We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. In this study, we found that a designed biochip could analyze inhibitors of the SARS-CoV N protein using nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, (-)-catechin gallate and (-)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. (-)-catechin gallate and (-)-gallocatechin gallate attenuated the binding affinity in a concentrated manner as evidenced by QDs-conjugated RNA oligonucleotide on a designed biochip. At a concentration of 0.05 μg mL(-1), (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a nanoparticle-based RNA oligonucleotide biochip system.

  19. Precise construction of oligonucleotide-Fab fragment conjugate for homogeneous immunoassay using HaloTag technology.

    Science.gov (United States)

    Päkkilä, Henna; Peltomaa, Riikka; Lamminmäki, Urpo; Soukka, Tero

    2015-03-01

    The use of oligonucleotide-protein conjugates enables the development of novel types of bioanalytical assays. However, convenient methods for producing covalent and stoichiometric oligonucleotide-protein conjugates are still rare. Here we demonstrate, for the first time, covalent conjugation of DNA oligonucleotide to Fab fragments with a 1:1 ratio using HaloTag self-labeling technology. The oligonucleotide coupling was carried out while the Fab was attached to protein G matrix, thereby enabling straightforward production of covalent conjugates. Furthermore, it allowed convenient purification of the product because the unreacted components were easily removed before the elution of the high-purity conjugate. The prepared conjugate was employed in a homogeneous immunoassay where prostate-specific antigen was used as a model analyte. Switchable lanthanide luminescence was used for detection, and the obtained limit of detection was 0.27 ng/ml. In the future, the developed method for covalent conjugation and successive purification in protein G column could also be applied for introducing other kinds of modifications to Fab fragments in a simple and site-specific manner. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries.

    Science.gov (United States)

    Murgha, Yusuf E; Rouillard, Jean-Marie; Gulari, Erdogan

    2014-01-01

    Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification.

  1. DNA fingerprinting in cattle using oligonucleotide probes.

    Science.gov (United States)

    Buitkamp, J; Zischler, H; Epplen, J T; Geldermann, H

    1991-01-01

    Oligonucleotide probes specific for simple tandem repeat sequences produce individual specific DNA fingerprints in man and all animal species tested so far. Here 11 different synthetic probes were hybridized to bovine genomic DNAs which had been digested with the restriction endonucleases HinfI, AluI and HaeIII. Two of these probes gave DNA fingerprint patterns which were analysed for three German breeds. Different parameters were calculated, such as the average number of bands per individual or the probability of finding identical fingerprints in two unrelated individuals. The number of polymorphic bands varies from 11 to 23 in the different breeds and the probability of finding the same banding pattern in two unrelated individuals ranges from 1.5 x 10(-7) to 2.4 x 10(-7). Hence this DNA fingerprinting procedure allows precise identification of individuals. It is also a useful additional method for paternity testing in cattle.

  2. Anisotropic yielding of rocks at high temperatures and pressures; Annual Progress Report, 1988-1989

    Energy Technology Data Exchange (ETDEWEB)

    Kronenberg, A.K.; Russell, J.E.; Carter, N.L.

    1989-11-30

    The experimental results we have obtained on Four-Mile gneiss have demonstrated that the yield behavior of quartzo-feldspathic rocks containing only a small percentage (10%) of mica can be markedly anisotropic, provided the mica minerals exhibit a strong crystallographic preferred orientation. Samples of gneiss oriented such that resolved shear stresses on the foliation plane are large are considerably weaker than granites of similar grain size and composition, and this weakness is attributed to enhanced nucleation of microcracks in quartz and feldspar adjacent to mica grains that are suitably oriented for slip. We expect the yield behavior of rocks containing a higher proportion of phyllosilicates to be influenced by the strongly anisotropic nature of these minerals as well, although the strengths, temperature and pressure dependencies, and flow-controlling mechanisms in such rocks may be significantly different.

  3. Gallium loading of gold seed for high yield of patterned GaAs nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Boulanger, J. P.; Chia, A. C. E.; LaPierre, R. R., E-mail: lapierr@mcmaster.ca [Department of Engineering Physics, McMaster University, Hamilton, Ontario L8S 4L7 (Canada)

    2014-08-25

    A method is presented for maximizing the yield and crystal phase purity of vertically aligned Au-assisted GaAs nanowires grown with an SiO{sub x} selective area epitaxy mask on GaAs (111)B substrates. The nanowires were grown by the vapor-liquid-solid (VLS) method in a gas source molecular beam epitaxy system. During annealing, Au VLS seeds will alloy with the underlying GaAs substrate and collect beneath the SiO{sub x} mask layer. This behavior is detrimental to obtaining vertically aligned, epitaxial nanowire growth. To circumvent this issue, Au droplets were pre-filled with Ga assuring vertical yields in excess of 99%.

  4. High yield direct 76Br-bromination of monoclonal antibodies using chloramine-T.

    Science.gov (United States)

    Sundin, J; Tolmachev, V; Koziorowski, J; Carlsson, J; Lundqvist, H; Welt, S; Larson, S; Sundin, A

    1999-11-01

    Monoclonal antibody (MAb) A33 was labeled with the positron emitter 76Br (T(1/2) = 16.2 h). Direct labeling was done using the conventional chloramine-T method. After optimization of the labeling conditions, a maximum yield (mean +/- max error) of 77 +/- 2% was obtained at pH 6.8. In vitro binding of 76Br-A33 to SW1222 colonic cancer cells showed that the immunoreactivity was retained. Also, the MAbs 38S1 and 3S193 and the peptide hEGF were 76Br-labeled, resulting in labeling yields (mean +/- max error) of 75 +/- 3%, 63 +/- 4%, and 73 +/- 0.1%, respectively. We conclude that antibodies and peptides can be labeled conveniently with 76Br for the purpose of whole-body tumour imaging by positron emission tomography.

  5. Multitrait, random regression, or simple repeatability model in high-throughput phenotyping data improve genomic prediction for wheat grain yield

    Science.gov (United States)

    High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat (Triticum aestivum L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect s...

  6. The effect of high-sugar grass on predicted nitrogen excretion and milk yield simulated using a dynamic model

    NARCIS (Netherlands)

    Ellis, J.L.; Dijkstra, J.; Bannink, A.; Parsons, A.J.; Rasmussen, S.; Edwards, G.R.; Kebreab, E.; France, J.

    2011-01-01

    High-sugar grass varieties have received considerable attention for their potential to reduce nitrogen (N) excretion and increase milk yield in cattle. However, considerable variation exists in the magnitude of response in published results. The purpose of this study is to explain the variation in

  7. Ultrafiltration with size-exclusion liquid chromatography for high yield isolation of extracellular vesicles preserving intact biophysical and functional properties

    NARCIS (Netherlands)

    Nordin, Joel Z.; Lee, Yi; Vader, Pieter; Mäger, Imre; Johansson, Henrik J.; Heusermann, Wolf; Wiklander, Oscar P B; Hällbrink, Mattias; Seow, Yiqi; Bultema, Jarred J.; Gilthorpe, Jonathan; Davies, Tim; Fairchild, Paul J.; Gbrielsson, Susanne; Meisner-Kober, Nicole C.; Lehtiö, Janne; Smith, C. I Edvard; Wood, Matthew J A; Andaloussi, Samir E L

    2015-01-01

    Extracellular vesicles (EVs) are natural nanoparticles that mediate intercellular transfer of RNA and proteins and are of great medical interest; serving as novel biomarkers and potential therapeutic agents. However, there is little consensus on the most appropriate method to isolate high-yield and

  8. Yields in high density, short rotation intensive culture (SRIC)—plantations of Eucalyptus and Other Hardwood Species

    Science.gov (United States)

    R.M. Sachs; C.B. Low

    1983-01-01

    Initial high density (17,200 trees ha-1, 6961 trees a-1) plantations of Eucalyptus grandis yielded up to 22 oven dry tons (ODT) ha-l yr-I (10 ta-1 yr-1) on an approximate 6 month rotation. Border effects could not be eliminated from the small sized plots used...

  9. REGIONAL ANALYSIS OF INORGANIC NITROGEN YIELD AND RETENTION IN HIGH-ELEVATION ECOSYSTEMS OF THE SIERRA NEVADA AND ROCKY MOUNTAINS

    Science.gov (United States)

    Yields and retention of inorganic nitrogen (DIN) and nitrate concentrations in surface runoff are summarized for 28 high elevation watersheds in the Sierra Nevada, California and Rocky Mountains of Wyoming and Colorado. Catchments ranged in elevation from 2475 to 3603 m and from...

  10. Effects of Biomass Feedstock on the Yield and Reactivity of Soot from Fast Pyrolysis at High Temperatures

    DEFF Research Database (Denmark)

    Trubetskaya, Anna; Jensen, Peter A.; Glarborg, Peter

    This study investigated the effect of feedstock on the yield, nanostructure and reactivity of soot. Woody and herbaceous biomass were pyrolyzed at high heating rates and temperatures of 1250 and 1400°C in a drop tube furnace. The collected solid residues were structurally characterized by electron...

  11. High-yielding Wheat Varieties Harbour Superior Plant Growth Promoting-Bacterial Endophytes

    Directory of Open Access Journals (Sweden)

    Mehwish Yousaf

    2017-06-01

    Full Text Available Background and Objective: The purpose of this study was to compare the endophytic microbial flora of different wheat varieties to check whether a better yielding variety also harbours superior plant growth promoting bacteria. Such bacteria are helpful in food biotechnology as their application can enhance the yield of the crop.Material and Methods: Three wheat varieties (Seher, Faisalabad and Lasani were selected, Seher being the most superior variety. endophytic bacteria were isolated from the histosphere of the leaves and roots at different growth phases of the plants. The isolates were analyzed for plant growth promoting activities. Isolates giving best results were identified through 16S rRNA gene sequencing. Statistical analysis was done using Microsoft Excel 2013. All the experiments were conducted in triplicates.Results and Conclusion: The endophytes of Seher variety showed maximum plant growth promoting abilities. Among the shoot endophytes, the highest auxin production was shown by Seher isolate SHHP1-3 up to 51.9μg ml-1, whereas in the case of root endophytes, the highest auxin was produced by SHHR1-5 up to 36 μg ml-1. The bacteria showing significant plant growth promoting abilities were identified by 16S rRNA sequencing. Bacillus, Proteobacteria and Actinobacteria species were the dominant bacteria showing all the traits of plant growth promotion. It can be concluded that Seher variety harbours superior plant growth promoting endophytes that must be one of the reasons for its better growth and yield as compared to the other two varieties. The investigated results support possible utilization of the selected isolates in wheat growth promotion with respect to increase in agro-productivity. The application of such bacteria could be useful to enhance wheat yield and can help in food biotechnology.Conflict of interest: The authors declare no conflict of interest.

  12. High-yield secretion of recombinant proteins from the microalga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Ramos-Martinez, Erick Miguel; Fimognari, Lorenzo; Sakuragi, Yumiko

    2017-09-01

    Microalga-based biomanufacturing of recombinant proteins is attracting growing attention due to its advantages in safety, metabolic diversity, scalability and sustainability. Secretion of recombinant proteins can accelerate the use of microalgal platforms by allowing post-translational modifications and easy recovery of products from the culture media. However, currently, the yields of secreted recombinant proteins are low, which hampers the commercial application of this strategy. This study aimed at expanding the genetic tools for enhancing secretion of recombinant proteins in Chlamydomonas reinhardtii, a widely used green microalga as a model organism and a potential industrial biotechnology platform. We demonstrated that the putative signal sequence from C. reinhardtii gametolysin can assist the secretion of the yellow fluorescent protein Venus into the culture media. To increase the secretion yields, Venus was C-terminally fused with synthetic glycomodules comprised of tandem serine (Ser) and proline (Pro) repeats of 10 and 20 units [hereafter (SP)n , wherein n = 10 or 20]. The yields of the (SP)n -fused Venus were higher than Venus without the glycomodule by up to 12-fold, with the maximum yield of 15 mg/L. Moreover, the presence of the glycomodules conferred an enhanced proteolytic protein stability. The Venus-(SP)n proteins were shown to be glycosylated, and a treatment of the cells with brefeldin A led to a suggestion that glycosylation of the (SP)n glycomodules starts in the endoplasmic reticulum (ER). Taken together, the results demonstrate the utility of the gametolysin signal sequence and (SP)n glycomodule to promote a more efficient biomanufacturing of microalgae-based recombinant proteins. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  13. Temperature-dependent yield criterion for high strength steel sheets under warm-forming conditions

    Directory of Open Access Journals (Sweden)

    Cai Zhengyang

    2015-01-01

    Full Text Available In this paper, uniaxial and biaxial tensile tests with cruciform specimens were conducted to investigate the deformation behaviour of dual phase steel sheet with a tensile strength of 590 MPa (DP590 under evaluated warm-forming temperatures (20–190 ∘C. Detailed analyses were then carried out to obtain the corresponding experimental yield loci. For the purpose of describing the temperature-dependent yield behaviour of DP590 appropriately, the Yld2000–2d yield function with temperature-dependent exponent was proposed. The identification procedures of the introduced parameters were then proposed based on Levenberg-Marquardt optimization algorithm. Afterwards, the proposed model was implemented into ABAQUS as user subroutine VUMAT with NICE (Next Increment Corrects Error explicit integration scheme. The numerical simulations of biaxial tensile tests were then conducted to confirm the validity of the proposed model. It could be concluded that the flexibility and accuracy of the proposed model guarantee the applicability in warm-forming applications.

  14. High-precision location and yield of North Korea's 2013 nuclear test

    Science.gov (United States)

    Zhang, Miao; Wen, Lianxing

    2013-06-01

    Using North Korea's 2009 nuclear test as reference and satellite imagery, we show that the location and yield of North Korea's 2013 nuclear test can be quickly and accurately determined based on seismic data. North Korea's 2013 nuclear test site is pinpointed by deriving relative location of North Korea's 2009 and 2013 nuclear tests and using the previously determined location of the 2009 nuclear test, while its yield is estimated based on the relative amplitude ratios of the Lg waves recorded for both events, the previously determined Lg-magnitude of 2009 nuclear test and burial depth inferred from satellite imagery. North Korea's 2013 test site is determined to be located at (41°17'26.88″N, 129°4'34.68″E), about 345 m south and 453 m west of its 2009 nuclear test site, with a geographic precision of 94 m. Its yield is estimated to be 12.2 ± 3.8 kt.

  15. High quantum yield ZnO quantum dots synthesizing via an ultrasonication microreactor method.

    Science.gov (United States)

    Yang, Weimin; Yang, Huafang; Ding, Wenhao; Zhang, Bing; Zhang, Le; Wang, Lixi; Yu, Mingxun; Zhang, Qitu

    2016-11-01

    Green emission ZnO quantum dots were synthesized by an ultrasonic microreactor. Ultrasonic radiation brought bubbles through ultrasonic cavitation. These bubbles built microreactor inside the microreactor. The photoluminescence properties of ZnO quantum dots synthesized with different flow rate, ultrasonic power and temperature were discussed. Flow rate, ultrasonic power and temperature would influence the type and quantity of defects in ZnO quantum dots. The sizes of ZnO quantum dots would be controlled by those conditions as well. Flow rate affected the reaction time. With the increasing of flow rate, the sizes of ZnO quantum dots decreased and the quantum yields first increased then decreased. Ultrasonic power changed the ultrasonic cavitation intensity, which affected the reaction energy and the separation of the solution. With the increasing of ultrasonic power, sizes of ZnO quantum dots first decreased then increased, while the quantum yields kept increasing. The effect of ultrasonic temperature on the photoluminescence properties of ZnO quantum dots was influenced by the flow rate. Different flow rate related to opposite changing trend. Moreover, the quantum yields of ZnO QDs synthesized by ultrasonic microreactor could reach 64.7%, which is higher than those synthesized only under ultrasonic radiation or only by microreactor. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Targeted oligonucleotide-mediated microsatellite identification (TOMMI from large-insert library clones

    Directory of Open Access Journals (Sweden)

    Ren Jun

    2005-11-01

    integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions. Conclusion The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.

  17. Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones.

    Science.gov (United States)

    Chen, Kefei; Knorr, Christoph; Bornemann-Kolatzki, Kirsten; Ren, Jun; Huang, Lusheng; Rohrer, Gary A; Brenig, Bertram

    2005-11-15

    broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions. The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.

  18. Exploiting the synergy between fluid catalytic cracking and visbreaking to increase the high-value product yields

    Energy Technology Data Exchange (ETDEWEB)

    Stratiev, D.; Stratiev, G. [Lukoil Neftochim Bourgas AD, Bourgas (Bulgaria); Minkov, D. [Univ. Assen Zlatorov, Bourgas (Bulgaria)

    2003-09-01

    An investigation was carried out to test the feasibility of processing a 360-510 C visbreaker fraction in the fluid catalytic cracking unit, in order to maximize high-value product yields. It was found that in a commercial visbreaker unit with a soaker, the viscosity of visbreaker residue (>200 C) and the conversion of the visbreaker feedstock - vacuum residue (>482 C) - correlated directly with vacuum residue viscosity. Depending on the conversion in the visbreaker, the yield of 360-510 C cut varied in the range 16-24% on feed. Characterization of this fraction showed no difference in quality with conversion and a high level of gasoline precursors - 68%. Cracking experiments with a heavy vacuum gas oil, distilled from Russian Export Blend crude oil (73% gasoline precursors) and with an 80% Russian Export Blend heavy vacuum gas oil / 20% visbreaker 360-510 C cut blend using a commercial equilibrium catalyst in a laboratory MAT unit exhibited almost the same yield patterns. Therefore, addition of 25% of the visbreaker 360-510 C cut to the FCC feed does not negatively affect the FCC yield pattern. Deriving the 360-510 C fraction from the visbreaker and processing it in the FCC unit could increase the crude oil conversion by 2.8%. The yield of high value LPG and gasoline could increase by 0.8% and 2.6% of the crude oil respectively whilst reducing yields of fuel oil and FCC LCO by 3.7% and 0.6% respectively. Characterization of the 200-360 C visbreaker cut showed that this material is more suitable as a component for transportation diesel than FCC LCO because of the lower aromatics content, 41% versus 72% of FCC LCO and higher cetane index - 42 versus 21 of FCC LCO. (orig.)

  19. Exogenously Applied Plant Growth Regulators Enhance the Morpho-Physiological Growth and Yield of Rice under High Temperature.

    Science.gov (United States)

    Fahad, Shah; Hussain, Saddam; Saud, Shah; Hassan, Shah; Ihsan, Zahid; Shah, Adnan N; Wu, Chao; Yousaf, Muhammad; Nasim, Wajid; Alharby, Hesham; Alghabari, Fahad; Huang, Jianliang

    2016-01-01

    A 2-year experiment was conducted to ascertain the effects of exogenously applied plant growth regulators (PGR) on rice growth and yield attributes under high day (HDT) and high night temperature (HNT). Two rice cultivars (IR-64 and Huanghuazhan) were subjected to temperature treatments in controlled growth chambers and four different combinations of ascorbic acid (Vc), alpha-tocopherol (Ve), brassinosteroids (Br), methyl jasmonates (MeJA), and triazoles (Tr) were applied. High temperature severely affected rice morphology, and also reduced leaf area, above-, and below-ground biomass, photosynthesis, and water use efficiency, while increased the leaf water potential of both rice cultivars. Grain yield and its related attributes except number of panicles, were reduced under high temperature. The HDT posed more negative effects on rice physiological attributes, while HNT was more detrimental for grain formation and yield. The Huanghuazhan performed better than IR-64 under high temperature stress with better growth and higher grain yield. Exogenous application of PGRs was helpful in alleviating the adverse effects of high temperature. Among PGR combinations, the Vc+Ve+MejA+Br was the most effective treatment for both cultivars under high temperature stress. The highest grain production by Vc+Ve+MejA+Br treated plants was due to enhanced photosynthesis, spikelet fertility and grain filling, which compensated the adversities of high temperature stress. Taken together, these results will be of worth for further understanding the adaptation and survival mechanisms of rice to high temperature and will assist in developing heat-resistant rice germplasm in future.

  20. Exploiting the Rotational Dynamics of Asymmetric Top Molecules to make Angle Resolved, Molecular Frame Ion Yield and High Harmonic Measurements

    Science.gov (United States)

    Makhija, Varun; Ren, Xiaoming; Tross, Jan; Mondal, Sudipta; Le, Anh-Thu; Trallero, Carlos; Kumarappan, Vinod; JRM HHG-Alignment Collaboration

    2013-05-01

    We extract the angle-dependent ionization rate of ethylene in an intense femtosecond laser pulse from the rotational revivals of the yield of the singly-charged molecular ion. By fitting the measured delay-dependent ion yield to the molecular axis distribution calculated using a rigid rotor code for asymmetric top molecules, we show that the dependence of the ionization rate on two Euler angles can be on obtained. Additionally we explore the possibility of extracting molecular frame information from similar pump-probe measurements of high harmonic generation. Office of Basic Energy Sciences, U.S. Department of Energy.

  1. Productivity, Profitability and Resource Use Efficiency: A Comparative Analysis between Conventional and High Yielding Rice in Rajbari District, Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Yahia Bapari

    2016-10-01

    Full Text Available The study was analyzed the determinants, costs and benefits and resources allocation of both conventional and high yielding rice cultivation over the Rajbari district of Bangladesh. Data were accumulated from 300 regular rice growers of conventional and high yielding varieties and random sampling technique was applied for selecting the respondents from the study area from which information was collected through pre-tested questionnaire. Cobb – Douglas production function and gross margin were mainly used to determine the productivities and profits of both rice and the marginal value of the product was highly recommended to derive the optimal use of the resources. Results obtained by applying ordinary least square method showed that the most important factors of production in the study area were irrigation, labor, fertilizer and insecticide costs whose elasticities were 0.904, 0.048, 0.045 and 0.044 respectively and insignificant factors were seed and ploughing costs whose elasticities were – 0.009 and 0.030 respectively for high yielding rice. On the other hand, irrigation, insecticide, seed and ploughing costs of elasticities 0.880, 0.589, 0.116 and – 0.127 respectively were the important factors and minor role playing factors were labor and fertilizer costs whose elasticities were 0.098 and 0.077 respectively for conventional yielding rice. The core message from productivity analysis was that the irrigation was key variable which played a positive and vital role in producing rice of both varieties. All variables (resources were economically misallocated in the production activities of both varieties along the study area but high yielding rice was more profitable than conventional one. Results also showed that the farmers of the study area produced rice of both varieties in the inefficient range of production. Continuous supply of electricity, flexible credit and improving the existing resources were the prime policy recommendations of

  2. Effects of Lignocellulosic Compounds on the Yield, Nanostructure and Reactivity of Soot from Fast Pyrolysis at High Temperatures

    DEFF Research Database (Denmark)

    Trubetskaya, Anna; Broström, Markus; Kling, Jens

    Gasification offers the utilization of biomass to a wide variety of applications such as heat, electricity, chemicals and transport fuels in an efficient and sustainable manner. High soot yields in the high-temperature entrained flow gasification lead to intensive gas cleaning and can cause...... reactor. The specific objectives of this study were to: (1) obtain knowledge about lignocellulosic compounds and monolignols influence on the yield, nanostructure, composition, and reactivity of soot during high-temperature gasification, (2) understand the influence of Soxhlet extraction on the soot...... reactivity and characteristics, and (3) determine the reaction conditions and fuel composition which minimize soot formation leading to the efficient operation of high-temperature gasification process....

  3. Ferrocene-oligonucleotide conjugates for electrochemical probing of DNA.

    Science.gov (United States)

    Ihara, T; Maruo, Y; Takenaka, S; Takagi, M

    1996-01-01

    Toward the development of a universal, sensitive and convenient method of DNA (or RNA) detection, electrochemically active oligonucleotides were prepared by covalent linkage of a ferrocenyl group to the 5'-aminohexyl-terminated synthetic oligonucleotides. Using these electrochemically active probes, we have been able to demonstrate the detection of DNA and RNA at femtomole levels by HPLC equipped with an ordinary electrochemical detector (ECD) [Takenaka,S., Uto,Y., Kondo,H., Ihara,T. and Takagi,M. (1994) Anal. Biochem., 218, 436-443]. Thermodynamic and electrochemical studies of the interaction between the probes and the targets are presented here. The thermodynamics obtained revealed that the conjugation stabilizes the triple-helix complexes by 2-3 kcal mol-1 (1-2 orders increment in binding constant) at 298 K, which corresponds to the effect of elongation of additional several base triplets. The main cause of this thermodynamic stabilization by the conjugation is likely to be the overall conformational change of whole structure of the conjugate rather than the additional local interaction. The redox potential of the probe was independent of the target structure, which is either single- or double stranded. However, the potential is slightly dependent (with a 10-30 mV negative shift on complexation) on the extra sequence in the target, probably because the individual sequence is capable of contacting or interacting with the ferrocenyl group in a slightly different way from each other. This small potential shift itself, however, does not cause any inconvenience on practical applications in detecting the probes by using ECD. These results lead to the conclusion that the redox-active probes are very useful for the microanalysis of nucleic acids due to the stability of the complexes, high detection sensitivity and wide applicability to the target structures (DNA and RNA; single- and double strands) and the sequences. PMID:8932383

  4. Direct microcontact printing of oligonucleotides for biochip applications

    Directory of Open Access Journals (Sweden)

    Trévisiol E

    2005-07-01

    Full Text Available Abstract Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting

  5. Selective Covalent Conjugation of Phosphorothioate DNA Oligonucleotides with Streptavidin

    Directory of Open Access Journals (Sweden)

    Christof M. Niemeyer

    2011-08-01

    Full Text Available Protein-DNA conjugates have found numerous applications in the field of diagnostics and nanobiotechnology, however, their intrinsic susceptibility to DNA degradation by nucleases represents a major obstacle for many applications. We here report the selective covalent conjugation of the protein streptavidin (STV with phosphorothioate oligonucleotides (psDNA containing a terminal alkylthiolgroup as the chemically addressable linking unit, using a heterobifunctional NHS-/maleimide crosslinker. The psDNA-STV conjugates were synthesized in about 10% isolated yields. We demonstrate that the terminal alkylthiol group selectively reacts with the maleimide while the backbone sulfur atoms are not engaged in chemical conjugation. The novel psDNA-STV conjugates retain their binding capabilities for both biotinylated macromolecules and the complementary nucleic acid. Moreover, the psDNA-STV conjugate retained its binding capacity for complementary oligomers even after a nuclease digestion step, which effectively degrades deoxyribonucleotide oligomers and thus the binding capability of regular DNA-STV conjugates. The psDNA-STV therefore hold particular promise for applications e.g. in proteome research and novel biosensing devices, where interfering endogenous nucleic acids need to be removed from analytes by nuclease digestion.

  6. High-yield production of biologically active recombinant protein in shake flask culture by combination of enzyme-based glucose delivery and increased oxygen transfer

    National Research Council Canada - National Science Library

    Ukkonen, Kaisa; Vasala, Antti; Ojamo, Heikki; Neubauer, Peter

    2011-01-01

    ...®) and high-aeration shake flask (Ultra Yield Flask™). The benefit of this combination is demonstrated by over 100-fold improvement in the active yield of recombinant alcohol dehydrogenase expressed in E. coli...

  7. Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield.

    Science.gov (United States)

    Sun, Jin; Rutkoski, Jessica E; Poland, Jesse A; Crossa, José; Jannink, Jean-Luc; Sorrells, Mark E

    2017-07-01

    High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment. Copyright © 2017 Crop Science Society of America.

  8. Vineyard Yield Estimation Based on the Analysis of High Resolution Images Obtained with Artificial Illumination at Night

    Directory of Open Access Journals (Sweden)

    Davinia Font

    2015-04-01

    Full Text Available This paper presents a method for vineyard yield estimation based on the analysis of high-resolution images obtained with artificial illumination at night. First, this paper assesses different pixel-based segmentation methods in order to detect reddish grapes: threshold based, Mahalanobis distance, Bayesian classifier, linear color model segmentation and histogram segmentation, in order to obtain the best estimation of the area of the clusters of grapes in this illumination conditions. The color spaces tested were the original RGB and the Hue-Saturation-Value (HSV. The best segmentation method in the case of a non-occluded reddish table-grape variety was the threshold segmentation applied to the H layer, with an estimation error in the area of 13.55%, improved up to 10.01% by morphological filtering. Secondly, after segmentation, two procedures for yield estimation based on a previous calibration procedure have been proposed: (1 the number of pixels corresponding to a cluster of grapes is computed and converted directly into a yield estimate; and (2 the area of a cluster of grapes is converted into a volume by means of a solid of revolution, and this volume is converted into a yield estimate; the yield errors obtained were 16% and −17%, respectively.

  9. Antisense Oligonucleotide-Based Therapy for Neuromuscular Disease

    Directory of Open Access Journals (Sweden)

    Valentina Sardone

    2017-04-01

    Full Text Available Neuromuscular disorders such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy are neurodegenerative genetic diseases characterized primarily by muscle weakness and wasting. Until recently there were no effective therapies for these conditions, but antisense oligonucleotides, a new class of synthetic single stranded molecules of nucleic acids, have demonstrated promising experimental results and are at different stages of regulatory approval. The antisense oligonucleotides can modulate the protein expression via targeting hnRNAs or mRNAs and inducing interference with splicing, mRNA degradation, or arrest of translation, finally, resulting in rescue or reduction of the target protein expression. Different classes of antisense oligonucleotides are being tested in several clinical trials, and limitations of their clinical efficacy and toxicity have been reported for some of these compounds, while more encouraging results have supported the development of others. New generation antisense oligonucleotides are also being tested in preclinical models together with specific delivery systems that could allow some of the limitations of current antisense oligonucleotides to be overcome, to improve the cell penetration, to achieve more robust target engagement, and hopefully also be associated with acceptable toxicity. This review article describes the chemical properties and molecular mechanisms of action of the antisense oligonucleotides and the therapeutic implications these compounds have in neuromuscular diseases. Current strategies and carrier systems available for the oligonucleotides delivery will be also described to provide an overview on the past, present and future of these appealing molecules.

  10. Effect of sowing date on yield and quality of high moisture ear and grain production for maize

    Directory of Open Access Journals (Sweden)

    Zlatko Svečnjak

    2007-12-01

    Full Text Available High moisture ear and grain production of maize (Zea mays L. hasadvantages in comparison with dry grain production because longer maturity hybrids might be grown and there are no grain drying costs. A two year study was carried out at the Faculty of Agriculture experimental field Maksimir to evaluate the effect of delayed sowing dates on yield and quality of high moisture ear and grain production when compared to optimum sowing date. Maize hybrids belonging to the maturity groups FAO 200 (PR39K38 and 300 (PR38P05 were sown at optimum (early May and two delayed sowing dates (middle May and early June and grown under intensive cropping system.When compared to optimum sowing date, grain and ear yield significantly decreased with delayed sowing dates despite the fact that grown hybrids reached physiological maturity before the first autumn frosts. These yield reductions at delayed sowing dates were mainly associated with fewer grains per ear, and partly due to lighter 1000-grain weights. Both hybrids resulted in similar ear yield; however, a longer maturity hybrid (PR38P05 had larger grain yields than a shorter-maturity hybrid (PR39K38 because the latter hadsignificantly smaller shelling index (82,1 % than the former one (87,0 %. Sowing date and growing conditions showed no significant effect on grain protein and oil contents. Hybrids also had similar grain protein content, whereas PR38P05 had absolutely small, but significantly higher grain oil content than PR39K38. Thus, delayed sowing of the maize hybrids of FAO 200 - 300 maturity groups might occur into early June with no effect on grain quality, but with significant yield losses when compared to optimum sowing date.

  11. A novel bioreactor and culture method drives high yields of platelets from stem cells.

    Science.gov (United States)

    Avanzi, Mauro P; Oluwadara, Oluwasijibomi E; Cushing, Melissa M; Mitchell, Maxwell L; Fischer, Stephen; Mitchell, W Beau

    2016-01-01

    Platelet (PLT) transfusion is the primary treatment for thrombocytopenia. PLTs are obtained exclusively from volunteer donors, and the PLT product has only a 5-day shelf life, which can limit supply and result in PLT shortages. PLTs derived from stem cells could help to fill this clinical need. However, current culture methods yield far too few PLTs for clinical application. To address this need, a defined, serum-free culture method was designed using a novel bioreactor to increase the yield of PLTs from stem cell-derived megakaryocytes. CD34 cells isolated from umbilical cord blood were expanded with a variety of reagents and on a nanofiber membrane using serum-free medium. These cells were then differentiated into megakaryocytic lineage by culturing with thrombopoietin and stem cell factor in serum-free conditions. Polyploidy was induced by addition of Rho kinase inhibitor or actin polymerization inhibitor to the CD41 cells. A novel bioreactor was developed that recapitulated aspects of the marrow vascular niche. Polyploid megakaryocytes that were subjected to flow in the bioreactor extended proPLTs and shed PLTs, as confirmed by light microscopy, fluorescence imaging, and flow cytometry. CD34 cells were expanded 100-fold. CD41 cells were expanded 100-fold. Up to 100 PLTs per input megakaryocyte were produced from the bioreactor, for an overall yield of 10(6) PLTs per input CD34 cell. The PLTs externalized P-selectin after activation. Functional PLTs can be produced ex vivo on a clinically relevant scale using serum-free culture conditions with a novel stepwise approach and an innovative bioreactor. © 2015 AABB.

  12. Towards the development of systems for high-yield production of microbial lipases.

    Science.gov (United States)

    Turki, Saoussen

    2013-10-01

    Microbial lipases are a versatile and attractive class of biocatalysts for a wide variety of applications. Lipases can be produced by bacteria, yeasts or filamentous fungi. Nevertheless, they are often not optimal for direct use in industrial conditions due to low yields, low specific activities and a limited spectrum of activities. Improvements in the productivity of lipases have been made by genetic manipulation of the cell factory production hosts and by optimizing production media and conditions. Advances in protein engineering technology, ranging from directed evolution to rational design, have also been able to tailor lipases to particular applications. This review describes various approaches used to improve lipase production and applications.

  13. High-Yield Method for Dispersing Simian Kidneys for Cell Cultures

    Science.gov (United States)

    de Oca, H. Montes; Probst, P.; Grubbs, R.

    1971-01-01

    A technique for dispersion of animal tissue cells is described. The proposed technique is based on the concomitant use of trypsin and disodium ethylenediamine tetraacetate (EDTA). The use of the two dispersing agents (trypsin and disodium EDTA) markedly enhances cell yield as compared with the standard cell dispersion methods. Moreover, significant reduction in the amount of time required for complete tissue dispersal, presence of a very low number of nonviable cells, less cell clumping, and more uniform monolayer formation upon cultivation compare favorably with the results usually obtained with the standard trypsinization technique. Images PMID:4993235

  14. High-yield production and transfer of graphene flakes obtained by anodic bonding

    OpenAIRE

    Moldt, Thomas; Eckmann, Axel; Klar, Philipp; Morozov, Sergey V.; Zhukov, Alexander A.; Novoselov, Kostya S.; CASIRAGHI, cinzia

    2011-01-01

    We report large-yield production of graphene flakes on glass by anodic bonding. Under optimum conditions, we counted several tens of flakes with lateral size around 20-30 {\\mu}m and few tens of flakes with larger size. 60-70% of the flakes have negligible D peak. We show that it is possible to easily transfer the flakes by wedging technique. The transfer on silicon does not damage graphene and lowers the doping. The charge mobility of the transferred flakes on silicon is of the order of 6000 ...

  15. Antisense oligonucleotide induction of progerin in human myogenic cells.

    Directory of Open Access Journals (Sweden)

    Yue-Bei Luo

    Full Text Available We sought to use splice-switching antisense oligonucleotides to produce a model of accelerated ageing by enhancing expression of progerin, translated from a mis-spliced lamin A gene (LMNA transcript in human myogenic cells. The progerin transcript (LMNA Δ150 lacks the last 150 bases of exon 11, and is translated into a truncated protein associated with the severe premature ageing disease, Hutchinson-Gilford progeria syndrome (HGPS. HGPS arises from de novo mutations that activate a cryptic splice site in exon 11 of LMNA and result in progerin accumulation in tissues of mesodermal origin. Progerin has also been proposed to play a role in the 'natural' ageing process in tissues. We sought to test this hypothesis by producing a model of accelerated muscle ageing in human myogenic cells. A panel of splice-switching antisense oligonucleotides were designed to anneal across exon 11 of the LMNA pre-mRNA, and these compounds were transfected into primary human myogenic cells. RT-PCR showed that the majority of oligonucleotides were able to modify LMNA transcript processing. Oligonucleotides that annealed within the 150 base region of exon 11 that is missing in the progerin transcript, as well as those that targeted the normal exon 11 donor site induced the LMNA Δ150 transcript, but most oligonucleotides also generated variable levels of LMNA transcript missing the entire exon 11. Upon evaluation of different oligomer chemistries, the morpholino phosphorodiamidate oligonucleotides were found to be more efficient than the equivalent sequences prepared as oligonucleotides with 2'-O-methyl modified bases on a phosphorothioate backbone. The morpholino oligonucleotides induced nuclear localised progerin, demonstrated by immunostaining, and morphological nuclear changes typical of HGPS cells. We show that it is possible to induce progerin expression in myogenic cells using splice-switching oligonucleotides to redirect splicing of LMNA. This may offer a model

  16. A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging

    Science.gov (United States)

    Antaris, Alexander L.; Chen, Hao; Diao, Shuo; Ma, Zhuoran; Zhang, Zhe; Zhu, Shoujun; Wang, Joy; Lozano, Alexander X.; Fan, Quli; Chew, Leila; Zhu, Mark; Cheng, Kai; Hong, Xuechuan; Dai, Hongjie; Cheng, Zhen

    2017-05-01

    Fluorescence imaging in the second near-infrared window (NIR-II) allows visualization of deep anatomical features with an unprecedented degree of clarity. NIR-II fluorophores draw from a broad spectrum of materials spanning semiconducting nanomaterials to organic molecular dyes, yet unfortunately all water-soluble organic molecules with >1,000 nm emission suffer from low quantum yields that have limited temporal resolution and penetration depth. Here, we report tailoring the supramolecular assemblies of protein complexes with a sulfonated NIR-II organic dye (CH-4T) to produce a brilliant 110-fold increase in fluorescence, resulting in the highest quantum yield molecular fluorophore thus far. The bright molecular complex allowed for the fastest video-rate imaging in the second NIR window with ~50-fold reduced exposure times at a fast 50 frames-per-second (FPS) capable of resolving mouse cardiac cycles. In addition, we demonstrate that the NIR-II molecular complexes are superior to clinically approved ICG for lymph node imaging deep within the mouse body.

  17. High yield lipase-catalyzed synthesis of Engkabang fat esters for the cosmetic industry.

    Science.gov (United States)

    Abd Rahman, Nur Fariza; Basri, Mahiran; Rahman, Mohd Basyaruddin Abdul; Rahman, Raja Noor Zaliha Raja Abdul; Salleh, Abu Bakar

    2011-02-01

    Engkabang fat esters were produced via alcoholysis reaction between Engkabang fat and oleyl alcohol, catalyzed by Lipozyme RM IM. The reaction was carried out in a 500 ml Stirred tank reactor using heptane and hexane as solvents. Response surface methodology (RSM) based on a four-factor-five-level Central composite design (CCD) was applied to evaluate the effects of synthesis parameters, namely temperature, substrate molar ratio (oleyl alcohol: Engkabang fat), enzyme amount and impeller speed. The optimum yields of 96.2% and 91.4% were obtained for heptane and hexane at the optimum temperature of 53.9°C, impeller speeds of 309.5 and 309.0 rpm, enzyme amounts of 4.82 and 5.65 g and substrate molar ratios of 2.94 and 3.39:1, respectively. The actual yields obtained compared well with the predicted values of 100.0% and 91.5%, respectively. Meanwhile, the properties of the esters show that they are suitable to be used as ingredient for cosmetic applications. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. High-yield Escherichia coli-based cell-free expression of human proteins

    Energy Technology Data Exchange (ETDEWEB)

    Michel, Erich; Wuethrich, Kurt, E-mail: wuthrich@mol.biol.ethz.ch [ETH Zurich, Institute of Molecular Biology and Biophysics (Switzerland)

    2012-05-15

    Production of sufficient amounts of human proteins is a frequent bottleneck in structural biology. Here we describe an Escherichia coli-based cell-free system which yields mg-quantities of human proteins in N-terminal fusion constructs with the GB1 domain, which show significantly increased translation efficiency. A newly generated E. coli BL21 (DE3) RIPL-Star strain was used, which contains a variant RNase E with reduced activity and an excess of rare-codon tRNAs, and is devoid of lon and ompT protease activity. In the implementation of the expression system we used freshly in-house prepared cell extract. Batch-mode cell-free expression with this setup was up to twofold more economical than continuous-exchange expression, with yields of 0.2-0.9 mg of purified protein per mL of reaction mixture. Native folding of the proteins thus obtained is documented with 2D [{sup 15}N,{sup 1}H]-HSQC NMR.

  19. Physiological characteristics of high yield under cluster planting: photosynthesis and canopy microclimate of cotton

    Directory of Open Access Journals (Sweden)

    Ting-ting Xie

    2016-01-01

    Full Text Available Cotton produces more biomass and economic yield when cluster planting pattern (three plants per hole than in a traditional planting pattern (one plant per hole, even at similar plant densities, indicating that individual plant growth is promoted by cluster planting. The causal factors for this improved growth induced by cluster planting pattern, the light interception, canopy microclimate and photosynthetic rate of cotton were investigated in an arid region of China. The results indicated that the leaf area index and light interception were higher in cluster planting, and significantly different from those in traditional planting during the middle and late growth stages. Cotton canopy humidity at different growth stages was increased but canopy temperatures were reduced by cluster planting. In the later growth stage of cluster planting, the leaf chlorophyll content was higher and the leaf net photosynthetic rate and canopy photosynthetic rate were significantly increased in comparing with traditional planting pattern. We concluded that differences in canopy light interception and photosynthetic rate were the primary factors responsible for increased biomass production and economic yield in cluster planting compared with the traditional planting of cotton.

  20. Native promoter strategy for high-yielding synthesis and engineering of fungal secondary metabolites.

    Science.gov (United States)

    Kakule, Thomas B; Jadulco, Raquel C; Koch, Michael; Janso, Jeffrey E; Barrows, Louis R; Schmidt, Eric W

    2015-05-15

    Strategies are needed for the robust production of cryptic, silenced, or engineered secondary metabolites in fungi. The filamentous fungus Fusarium heterosporum natively synthesizes the polyketide equisetin at >2 g L(-1) in a controllable manner. We hypothesized that this production level was achieved by regulatory elements in the equisetin pathway, leading to the prediction that the same regulatory elements would be useful in producing other secondary metabolites. This was tested by using the native eqxS promoter and eqxR regulator in F. heterosporum, synthesizing heterologous natural products in yields of ∼1 g L(-1). As proof of concept for the practical application, we resurrected an extinct pathway from an endophytic fungus with an initial yield of >800 mg L(-1), leading to the practical synthesis of a selective antituberculosis agent. Finally, the method enabled new insights into the function of polyketide synthases in filamentous fungi. These results demonstrate a strategy for optimally employing native regulators for the robust synthesis of secondary metabolites.

  1. Oligonucleotides Containing Aminated 2′-Amino-LNA Nucleotides

    DEFF Research Database (Denmark)

    Lou, Chenguang; Samuelsen, Simone V.; Christensen, Niels Johan

    2017-01-01

    Mono- and diaminated 2′-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that stru...... that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2′-amino-LNA monomers and the host oligonucleotide backbone.......Mono- and diaminated 2′-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested...

  2. Modern methods for the synthesis of peptide-oligonucleotide conjugates

    Science.gov (United States)

    Zubin, Evgenii M.; Romanova, Elena A.; Oretskaya, Tat'yana S.

    2002-03-01

    The published data on the methods of chemical solution and solid-phase synthesis of peptide-oligonucleotide conjugates are reviewed. The known methods are systematised and their advantages and disadvantages are considered. The approaches to the solution synthesis of peptide-oligonucleotide conjugates are systematised according to the type of chemical bonds between the fragments, whereas those to the solid-phase synthesis are classified according to the procedure used for the preparation of conjugates, viz., stepwise elongation of oligonucleotide and peptide chains on the same polymeric support or solid-phase condensation of two presynthesised fragments. The bibliography includes 141 references.

  3. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  4. Selection of strawberry cultivars with tolerance to Tetranychus urticae (Acari: Tetranychidae) and high yield under different managements.

    Science.gov (United States)

    Costa, A F; Teodoro, P E; Bhering, L L; Fornazier, M J; Andrade, J S; Martins, D S; Zanuncio Junior, J S

    2017-04-28

    Tetranychus urticae Koch (Acari: Tetranychidae) is considered the main pest of strawberry. Several factors can favor its development, among them the genotype susceptibility and cropping system. The aims of this study were to evaluate the agronomic performance of strawberry cultivars under different managements and to identify strawberry cultivars that meet tolerance to T. urticae and high fruit yield. Thirteen cultivars of strawberry ('Albion', 'Aleluia', 'Aromas', 'Camarosa', 'Camino Real', 'Campinas', 'Diamante', 'Dover', 'Festival', 'Seascape', 'Toyonoka', 'Tudla', and 'Ventana') under three managements (open field, low tunnel, and high tunnel) were evaluated. The T. urticae attack to different cultivars was influenced by managements, being low tunnel the one that provided higher infestations in the most evaluated cultivars. 'Camarosa' was the cultivar with the lower incidence of pest and 'Dover' had the higher infestation. The genotype most suitable for growing under different managements is the 'Festival' genotype, since it meets tolerance to T. urticae, high fruit yield, and phenotypic stability.

  5. Transcriptome analysis suggests that starch synthesis may proceed via multiple metabolic routes in high yielding potato cultivars.

    Directory of Open Access Journals (Sweden)

    Kacper Piotr Kaminski

    Full Text Available BACKGROUND: Glucose-6-phosphate is imported into the amyloplast of potato tubers and thought to constitute the precursor for starch synthesis in potato tubers. However, recently it was shown that glucose-1-phosphate can also be imported into the amyloplast and incorporated into starch via an ATP independent mechanism under special conditions. Nonetheless, glucose-6-phosphate is believed to be the quantitatively important precursor for starch synthesis in potato. PRINCIPAL FINDING: Potato tubers of the high yielding cv Kuras had low gene expression of plastidial phophoglucomutase (PGM and normal levels of transcripts for other enzymes involved in starch metabolism in comparison with medium and low yielding cultivars as determined by DeepSAGE transcriptome profiling. The decrease in PGM activity in Kuras was confirmed by measuring the enzyme activity from potato tuber extracts. Contrary to expectations, this combination lead to a higher level of intracellular glucose-1-phosphate (G1P in Kuras suggesting that G1P is directly imported into plastids and can be quantitatively important for starch synthesis under normal conditions in high yielding cultivars. SIGNIFICANCE: This could open entirely new possibilities for metabolic engineering of the starch metabolism in potato via the so far uncharacterized G1P transporter. The perspectives are to increase yield and space efficiency of this important crop. In the light of the increasing demands imposed on agriculture to support a growing global population this presents an exciting new possibility.

  6. High liquid fuel yielding biofuel processes and a roadmap for the future transportation

    Science.gov (United States)

    Singh, Navneet R.

    In a fossil-fuel deprived world when crude oil will be scarce and transportation need cannot be met with electricity and transportation liquid fuel must be produced, biomass derived liquid fuels can be a natural replacement. However, the carbon efficiency of the currently known biomass to liquid fuel conversion processes ranges from 35-40%, yielding 90 ethanol gallon equivalents (ege) per ton of biomass. This coupled with the fact that the efficiency at which solar energy is captured by biomass (fast-hydropyrolysis/hydrodeoxygenation is proposed which can achieve liquid fuel yield of 215 ege/ton consuming 0.11 kg hydrogen per liter of oil. Due to the lower hydrogen consumption of the H2Bioil process, synergistically integrated transition pathways are feasible where hot syngas derived from coal gasification (H2Bioil-C) or a natural gas reformer (H 2Bioil-NG) is used to supply the hydrogen and process heat for the biomass fast-hydropyrolysis/hydrodeoxygenation. Another off-shoot of the H2Bioil process is the H2Bioil-B process, where hydrogen required for the hydropyrolysis is obtained from gasification of a fraction of the biomass. H2Bioil-B achieves the highest liquid fuel yield (126-146 ege/ton of biomass) reported in the literature for any self-contained conversion of biomass to biofuel. Finally, an integration of the H2Bioil process with the H2CAR process is suggested which can achieve 100% carbon efficiency (330 ege/ton of biomass) at the expense of 0.24 kg hydrogen/liter of oil. A sun-to-fuel efficiency analysis shows that extracting CO2 from air and converting it to liquid fuel is at least two times more efficient than growing dedicated fuel crops and converting them to liquid fuel even for the highest biomass growth rates feasible by algae. This implies that liquid fuel should preferably be produced from sustainably available waste (SAW) biomass first and if the SAW biomass is unable to meet the demand for liquid fuel, then, CO2 should be extracted from air

  7. Engineering high yields of secondary metabolites in Rubia cell cultures through transformation with rol genes.

    Science.gov (United States)

    Bulgakov, Victor P; Shkryl, Yuri N; Veremeichik, Galina N

    2010-01-01

    Among the different methods currently used to improve yields of secondary metabolites in cultured plant cells, the method involving transformation by rol genes represents an example of relatively new technology. These genes, isolated from plasmids of the plant pathogen Agrobacterium rhizogenes, are potential activators of secondary metabolism in transformed cells from the Solanaceae, Araliaceae, Rubiaceae, Vitaceae, and Rosaceae families. In some cases, the activator effect of individual rol genes was sufficient to overcome the inability of cultured plant cells to produce large amounts of secondary metabolites. Stimulation of production characteristics of cultured plant cells mediated by the rol genes was shown to be remarkably stable over long-term cultivation. In this chapter, we describe transformation of Rubia cordifolia L. cells with the rol genes as an example of metabolic engineering of secondary metabolites.

  8. Use of Niobium High Strength Steels with 450 MPA Yield Strength for Construction

    Science.gov (United States)

    Silvestre, Leonardo; Langenberg, Peter; Amaral, Thiago; Carboni, Marcelo; Meira, Marcos; Jordão, Alexandre

    This paper presents an actual case of a new industrial building at CBMM's plant in Araxá, Brazil as an example of lean design using microalloyed steels. The structure consists mostly of microalloyed ASTM A572 steel grades 65 and 50 instead of the conventional carbon manganese ASTM A36 steel. The application of grade 65 with more than 450 MPa of yield strength is an innovative solution for this type of construction in South America. A complete welding evaluation performed on the low carbon, niobium microalloyed grade 65 steel showed the welding properties and benefits. Niobium's effect of increasing strength and toughness simultaneously resulted in relevant savings in total steel consumption for the project. The paper also quantifies the expected savings in costs, energy and carbon dioxide emissions.

  9. Tailoring Wet Explosion Process Parameters for the Pretreatment of Cocksfoot Grass for High Sugar Yields

    DEFF Research Database (Denmark)

    Njoku, Stephen Ikechukwu; Ahring, Birgitte Kiær; Uellendahl, Hinrich

    2013-01-01

    glucose release with low formation of by-products. Under these conditions, the cellulose and hemicellulose sugar recovery was 94 % and 70 %, respectively. The efficiency of the enzymatic hydrolysis of cellulose under these conditions was 91 %. On the other hand, the release of pentose sugars was higher......The pretreatment of lignocellulosic biomass is crucial for efficient subsequent enzymatic hydrolysis and ethanol fermentation. In this study, wet explosion (WEx) pretreatment was applied to cocksfoot grass and pretreatment conditions were tailored for maximizing the sugar yields using response...... when applying less severe pretreatment conditions C (160 °C, 5 min, 0.2 % dilute sulfuric acid). Therefore, the choice of the most suitable pretreatment conditions is depending on the main target product, i.e., hexose or pentose sugars....

  10. High-yield production and transfer of graphene flakes obtained by anodic bonding.

    Science.gov (United States)

    Moldt, Thomas; Eckmann, Axel; Klar, Philipp; Morozov, Sergey V; Zhukov, Alexander A; Novoselov, Kostya S; Casiraghi, Cinzia

    2011-10-25

    We report large-yield production of graphene flakes on glass by anodic bonding. Under optimum conditions, we counted several tens of flakes with lateral size around 20-30 μm and a few tens of flakes with larger size. About 60-70% of the flakes have a negligible D peak. We show that it is possible to easily transfer the flakes by the wedging technique. The transfer on silicon does not damage graphene and lowers the doping. The charge mobility of the transferred flakes on silicon is on the order of 6000 cm(2)/V s (at a carrier concentration of 10(12) cm(-2)), which is typical for devices prepared on this substrate with exfoliated graphene.

  11. Use of Nonspecific, Glutamic Acid-Free, Media and High Glycerol or High Amylase as Inducing Parameters for Screening Bacillus Isolates Having High Yield of Polyglutamic Acid.

    Science.gov (United States)

    Baxi, Nandita N

    2014-01-01

    Out of fifty-five Bacillus isolates obtained from ten different regional locations and sources, seven showed the ability to consistently produce specific extracellular polymeric substance (EPS) on rich as well as synthetic but nonspecific media which did not contain glutamic acid. The isolates were identified as either Bacillus licheniformis or Bacillus subtilis. The EPS from all isolates was resistant to alpha protease, proteinase K, and was thus of high molecular weight. Further it was detected after SDS-PAGE by methylene blue but not by coomassie blue R staining as in case of proteins with high proportion of acidic amino acids. Cell-free EPS, after acid hydrolysis, showed absence of carbohydrates and presence of only glutamic acid. Thus the native the EPS from all seven isolates was confirmed to be gamma polyglutamic acid (PGA) and not exopolysaccharide. The Bacillus isolate T which produced maximum polymer on all media tested had higher amylase: protease activity as compared to other strains. If inoculum was developed in rich medium as compared to synthetic medium, the PGA produced increased by twofold in the subsequent synthetic production medium. Similarly, use of inoculum consisting of young and vegetative cells also increased the PGA production by twofold though amount of inoculum did not affect yield of PGA. Though PGA was produced in even in the absence of glutamic acid supplementation in the production medium by all isolates, the yield of PGA increased by fourfold in the presence glutamic acid and the maximum yield was 30 g/l for isolate K. The supplementation of glutamine instead of glutamic acid into the medium caused an increase in the viscosity of the non-Newtonian solution of PGA.

  12. Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors

    Science.gov (United States)

    Yang, Kyung-Ae; Barbu, Mihaela; Halim, Marlin; Pallavi, Payal; Kim, Benjamin; Kolpashchikov, Dmitry M.; Pecic, Stevan; Taylor, Steven; Worgall, Tilla S.; Stojanovic, Milan N.

    2014-11-01

    Oligonucleotide-based receptors or aptamers can interact with small molecules, but the ability to achieve high-affinity and specificity of these interactions depends strongly on functional groups or epitopes displayed by the binding targets. Some classes of targets are particularly challenging: for example, monosaccharides have scarce functionalities and no aptamers have been reported to recognize, let alone distinguish from each other, glucose and other hexoses. Here we report aptamers that differentiate low-epitope targets such as glucose, fructose or galactose by forming ternary complexes with high-epitope organic receptors for monosaccharides. In a follow-up example, we expand this method to isolate high-affinity oligonucleotides against aromatic amino acids complexed in situ with a nonspecific organometallic receptor. The method is general and enables broad clinical use of aptamers for the detection of small molecules in mix-and-measure assays, as demonstrated by monitoring postprandial waves of phenylalanine in human subjects.

  13. High-yield production of a stable Vero cell-based vaccine candidate against the highly pathogenic avian influenza virus H5N1

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Fangye; Zhou, Jian; Ma, Lei; Song, Shaohui; Zhang, Xinwen; Li, Weidong; Jiang, Shude [No. 5, Department of Bioproducts, Institute of Medical Biology, Chinese Academy of Medical Science and Pecking Union Medical College, Jiaoling Avenue 935, Kunming, Yunnan Province 650102, People' s Republic of China (China); Wang, Yue, E-mail: euy-tokyo@umin.ac.jp [National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Yingxin Lane 100, Xicheng District, Beijing 100052, People' s Republic of China (China); Liao, Guoyang, E-mail: liaogy@21cn.com [No. 5, Department of Bioproducts, Institute of Medical Biology, Chinese Academy of Medical Science and Pecking Union Medical College, Jiaoling Avenue 935, Kunming, Yunnan Province 650102, People' s Republic of China (China)

    2012-05-18

    Highlights: Black-Right-Pointing-Pointer Vero cell-based HPAI H5N1 vaccine with stable high yield. Black-Right-Pointing-Pointer Stable high yield derived from the YNVa H3N2 backbone. Black-Right-Pointing-Pointer H5N1/YNVa has a similar safety and immunogenicity to H5N1delta. -- Abstract: Highly pathogenic avian influenza (HPAI) viruses pose a global pandemic threat, for which rapid large-scale vaccine production technology is critical for prevention and control. Because chickens are highly susceptible to HPAI viruses, the supply of chicken embryos for vaccine production might be depleted during a virus outbreak. Therefore, developing HPAI virus vaccines using other technologies is critical. Meeting vaccine demand using the Vero cell-based fermentation process has been hindered by low stability and yield. In this study, a Vero cell-based HPAI H5N1 vaccine candidate (H5N1/YNVa) with stable high yield was achieved by reassortment of the Vero-adapted (Va) high growth A/Yunnan/1/2005(H3N2) (YNVa) virus with the A/Anhui/1/2005(H5N1) attenuated influenza vaccine strain (H5N1delta) using the 6/2 method. The reassorted H5N1/YNVa vaccine maintained a high hemagglutination (HA) titer of 1024. Furthermore, H5N1/YNVa displayed low pathogenicity and uniform immunogenicity compared to that of the parent virus.

  14. Patch clamping on plane glass-fabrication of hourglass aperture and high-yield ion channel recording.

    Science.gov (United States)

    Chen, Chang-Yu; Tu, Ting-Yuan; Chen, Chang-Hung; Jong, De-Shien; Wo, Andrew M

    2009-08-21

    Planar patch-clamp has revolutionized ion-channel measurement by eliminating laborious manipulation from the traditional micropipette approach and enabling high throughput. However, low yield in gigaseal formation and/or relatively high cost due to microfabricated processes are two main drawbacks. This paper presents patch clamping on glass substrate-an economical solution without sacrificing gigaseal yield rate. Two-stage CO(2) laser drilling methodology was used to generate an hourglass, funnel-like aperture of a specified diameter with smooth and debris-free surfaces on 150 microm borosilicate cover glass. For 1-3 microm apertures as patch-clamp chips, seal resistance was tested on human embryonic kidney, Chinese hamster ovary, and Jurkat T lymphoma cells with a gigaseal success rate of 62.5%, 43.6% and 66.7% respectively. Results also demonstrated both whole-cell and single channel recording on endogenously expressed ion channels to confirm the capability of different patch configurations.

  15. Sequence-dependent theory of oligonucleotide hybridization kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-05-07

    A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions.

  16. Oligonucleotide-based theranostic nanoparticles in cancer therapy.

    Science.gov (United States)

    Shahbazi, Reza; Ozpolat, Bulent; Ulubayram, Kezban

    2016-05-01

    Theranostic approaches, combining the functionality of both therapy and imaging, have shown potential in cancer nanomedicine. Oligonucleotides such as small interfering RNA and microRNA, which are powerful therapeutic agents, have been effectively employed in theranostic systems against various cancers. Nanoparticles are used to deliver oligonucleotides into tumors by passive or active targeting while protecting the oligonucleotides from nucleases in the extracellular environment. The use of quantum dots, iron oxide nanoparticles and gold nanoparticles and tagging with contrast agents, like fluorescent dyes, optical or magnetic agents and various radioisotopes, has facilitated early detection of tumors and evaluation of therapeutic efficacy. In this article, we review the advantages of theranostic applications in cancer therapy and imaging, with special attention to oligonucleotide-based therapeutics.

  17. Sequence-dependent theory of oligonucleotide hybridization kinetics.

    Science.gov (United States)

    Marimuthu, Karthikeyan; Chakrabarti, Raj

    2014-05-07

    A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions.

  18. Rapid Transient Production in Plants by Replicating and Non-Replicating Vectors Yields High Quality Functional Anti-HIV Antibody

    OpenAIRE

    Frank Sainsbury; Markus Sack; Johannes Stadlmann; Heribert Quendler; Rainer Fischer; Lomonossoff, George P.

    2010-01-01

    Background The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product. Meth...

  19. A cDNA Clone-Launched Platform for High-Yield Production of Inactivated Zika Vaccine

    Directory of Open Access Journals (Sweden)

    Yujiao Yang

    2017-03-01

    Full Text Available A purified inactivated vaccine (PIV using the Zika virus (ZIKV Puerto Rico strain PRVABC59 showed efficacy in monkeys, and is currently in a phase I clinical trial. High-yield manufacture of this PIV is essential for its development and vaccine access. Here we report an infectious cDNA clone-launched platform to maximize its yield. A single NS1 protein substitution (K265E was identified to increase ZIKV replication on Vero cells (a cell line approved for vaccine production for both Cambodian FSS13025 and Puerto Rico PRVABC59 strains. The NS1 mutation did not affect viral RNA synthesis, but significantly increased virion assembly through an increased interaction between NS1 and NS2A (a known regulator of flavivirus assembly. The NS1 mutant virus retained wild-type virulence in the A129 mouse model, but decreased its competence to infect Aedes aegypti mosquitoes. To further increase virus yield, we constructed an infectious cDNA clone of the clinical trial PIV strain PRVABC59 containing three viral replication-enhancing mutations (NS1 K265E, prM H83R, and NS3 S356F. The mutant cDNA clone produced >25-fold more ZIKV than the wild-type parent on Vero cells. This cDNA clone-launched manufacture platform has the advantages of higher virus yield, shortened manufacture time, and minimized chance of contamination.

  20. A cDNA Clone-Launched Platform for High-Yield Production of Inactivated Zika Vaccine.

    Science.gov (United States)

    Yang, Yujiao; Shan, Chao; Zou, Jing; Muruato, Antonio E; Bruno, Diniz Nunes; de Almeida Medeiros Daniele, Barbosa; Vasconcelos, Pedro F C; Rossi, Shannan L; Weaver, Scott C; Xie, Xuping; Shi, Pei-Yong

    2017-03-01

    A purified inactivated vaccine (PIV) using the Zika virus (ZIKV) Puerto Rico strain PRVABC59 showed efficacy in monkeys, and is currently in a phase I clinical trial. High-yield manufacture of this PIV is essential for its development and vaccine access. Here we report an infectious cDNA clone-launched platform to maximize its yield. A single NS1 protein substitution (K265E) was identified to increase ZIKV replication on Vero cells (a cell line approved for vaccine production) for both Cambodian FSS13025 and Puerto Rico PRVABC59 strains. The NS1 mutation did not affect viral RNA synthesis, but significantly increased virion assembly through an increased interaction between NS1 and NS2A (a known regulator of flavivirus assembly). The NS1 mutant virus retained wild-type virulence in the A129 mouse model, but decreased its competence to infect Aedes aegypti mosquitoes. To further increase virus yield, we constructed an infectious cDNA clone of the clinical trial PIV strain PRVABC59 containing three viral replication-enhancing mutations (NS1 K265E, prM H83R, and NS3 S356F). The mutant cDNA clone produced >25-fold more ZIKV than the wild-type parent on Vero cells. This cDNA clone-launched manufacture platform has the advantages of higher virus yield, shortened manufacture time, and minimized chance of contamination. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  1. Assessing the Interplay between the Physicochemical Parameters of Ion-Pairing Reagents and the Analyte Sequence on the Electrospray Desorption Process for Oligonucleotides

    Science.gov (United States)

    Basiri, Babak; Murph, Mandi M.; Bartlett, Michael G.

    2017-08-01

    Alkylamines are widely used as ion-pairing agents during LC-MS of oligonucleotides. In addition to a better chromatographic separation, they also assist with the desorption of oligonucleotide ions into the gas phase, cause charge state reduction, and decrease cation adduction. However, the choice of such ion-pairing agents has considerable influence on the MS signal intensity of oligonucleotides as they can also cause significant ion suppression. Interestingly, optimal ion-pairing agents should be selected on a case by case basis as their choice is strongly influenced by the sequence of the oligonucleotide under investigation. Despite imposing major practical difficulties to analytical method development, such a highly variable system that responds very strongly to the nuances of the electrospray composition provides an excellent opportunity for a fundamental study of the electrospray ionization process. Our investigations using this system quantitatively revealed the major factors that influenced the ESI ionization efficiency of oligonucleotides. Parameters such as boiling point, proton affinity, partition coefficient, water solubility, and Henry's law constants for the ion-pairing reagents and the hydrophobic thymine content of the oligonucleotides were found to be the most significant contributors. Identification of these parameters also allowed for the development of a statistical predictive algorithm that can assist with the choice of an optimum IP agent for each particular oligonucleotide sequence. We believe that research in the field of oligonucleotide bioanalysis will significantly benefit from this algorithm (included in Supplementary Material) as it advocates for the use of lesser-known but more suitable ion-pair alternatives to TEA for many oligonucleotide sequences.

  2. Oligonucleotide probes for DNA fingerprinting in horses.

    Science.gov (United States)

    Wilke, K; Weimann, M; Jung, M; Geldermann, H

    1993-01-12

    10 different oligonucleotide probes were evaluated for DNA fingerprinting in horses. Five probes were able to detect polymorphic bands. The probes (GT)(8) , (GTG)(5) and (GGAT)(4) are most informative for individual identification and were used to analyze a population of Hannoveranian horses. The probability that two individuals have the same DNA fingerprint pattern is 1.2 × 10(-8) , 5.2 × 10(-10) and 1.5 × 10(-7) respectively. Using a combination of the three probes, paternity tests were performed with exclusion probabilities between 0.08% and 4%. ZUSAMMENFASSUNG: Oligonukleotide-Sonden für DNS-Fingerprints von Pferden Zur Darstellung von DNA-Fingerprints beim Pferd wurden zehn verschiedene Oligonukleotid-Sonden verglichen. Mit fünf Sonden konnten polymorphe Banden nachgewiesen werden. Die Sonden (GT)(8) , (GTG)(5) und (GGAT)(4) besaßen die größte Informativität für den Identitätsnachweis und wurden für die Analyse einer Population von Hannoverschen Pferden benutzt. Die Wahrscheinlichkeit, daß zwei Individuen dieselben Fingerprint-Muster aufweisen, liegt bei 1,2 × 10(-8) , 5,2 × 10(-10) bzw. 1,5 × 10(-7) . Bei Verwendung einer Kombination der drei Sonden wurden Vaterschaftskontrollen mit Ausschlußwahrscheinlichkeiten zwischen 0,08% und 4% erreicht. 1993 Blackwell Verlag GmbH.

  3. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  4. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Directory of Open Access Journals (Sweden)

    Eric B Alsop

    Full Text Available Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  5. Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch.

    Science.gov (United States)

    Hasegawa, Yusuke; Takada, Tadao; Nakamura, Mitsunobu; Yamana, Kazushige

    2017-08-01

    We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Understanding scaling of ignition metrics for high-yield implosions on the NIF

    Science.gov (United States)

    Springer, Paul; Hurricane, Omar; Hammer, J. H.; Callahan, D. A.; Casey, D. T.; Cerjan, C. J.; Edwards, M. J.; Field, J. E.; Gaffney, J.; Grim, G. P.; Kritcher, A. L.; Ma, T.; Macphee, A. G.; Munro, D. H.; Nora, R. C.; Patel, P. K.; Peterson, L.; Spears, B.

    2016-10-01

    The self-heating condition for an imploding hotspot requires understanding the balance between mechanical work, heating via fusion reactions, and the radiative and conduction losses. A 3D cognizant Lawson ignition threshold metric is derived based on net fusion hotspot heating achieved when hotspot rho-r and ion temperature exceed critical values that depend on the temperature-dependent loss mechanisms. Key to understanding and scaling such analysis is an accurate determination of hotspot density and pressure, which are generally inferred using the yield, the thermal temperature, and other experimental data. 3D flow and its effect on neutron spectra can lead to overestimation of the temperature, and underestimation of hotspot rho-r, energy, and ignition margin. In this work, we analyze these effects in NIF data, and propose new methods to avoid them. These simple, analytical methods are tested using the largest 2D ICF simulation dataset ever produced. Work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA273.

  7. Harnessing the respiration machinery for high-yield production of chemicals in metabolically engineered Lactococcus lactis

    DEFF Research Database (Denmark)

    Liu, Jianming; Wang, Zhihao; Kandasamy, Vijayalakshmi

    2017-01-01

    When modifying the metabolism of living organisms with the aim of achieving biosynthesis of useful compounds, it is essential to ensure that it is possible to achieve overall redox balance. We propose a generalized strategy for this, based on fine-tuning of respiration. The strategy was applied...... on metabolically engineered Lactococcus lactis strains to optimize the production of acetoin and (R,R)−2,3-butanediol (R-BDO). In the absence of an external electron acceptor, a surplus of two NADH per acetoin molecule is produced. We found that a fully activated respiration was able to efficiently regenerate NAD...... is converted into R-BDO per mole, only the excess of NADH needs to be oxidized via respiration. Either by fine-tuning the respiration capacity or by using a dual-phase fermentation approach involving a switch from fully respiratory to non-respiratory conditions, we obtained 361 mM (32 g/L) R-BDO with a yield...

  8. Synthesis of Biotin Linkers with the Activated Triple Bond Donor [p-(N-propynoylaminotoluic Acid] (PATA for Efficient Biotinylation of Peptides and Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Martina Jezowska

    2012-11-01

    Full Text Available Biotin is an important molecule for modern biological studies including, e.g., cellular transport. Its exclusive affinity to fluorescent streptavidin/avidin proteins allows ready and specific detection. As a consequence methods for the attachment of biotin to various biological targets are of high importance, especially when they are very selective and can also proceed in water. One useful method is Hüisgen dipolar [3+2]-cycloaddition, commonly referred to as “click chemistry”. As we reported recently, the activated triple bond donor p-(N-propynoylaminotoluic acid (PATA gives excellent results when used for conjugations at submicromolar concentrations. Thus, we have designed and synthesized two biotin linkers, with different lengths equipped with this activated triple bond donor and we proceeded with biotinylation of oligonucleotides and C-myc peptide both in solution and on solid support with excellent yields of conversion.

  9. Spotted cotton oligonucleotide microarrays for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Nettleton Dan

    2007-03-01

    Full Text Available Abstract Background Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Results Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. Conclusion The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.

  10. Effects of field high temperature on grain yield and quality of a subtropical type japonica rice—Pon-Lai rice

    Directory of Open Access Journals (Sweden)

    Yi-Chien Wu

    2016-01-01

    Full Text Available Typical japonica type rice is sensitive to high temperature. Pon-Lai rice is a special japonica type with adaptation to the subtropical climate in Taiwan. Facing climate change, rising temperatures would damage the yield and quality of rice production. This research was conducted using Pon-Lai rice in the field of a subtropical climate. We conducted 2 experiments, including a year-round experiment and collection of samples from different districts for building different temperature conditions. We analyzed the correlation between rising temperature and rice yield or quality. In our results, the critical period of temperature effect is 0–15 days after heading (H15. The threshold of high temperature damage in yield and appearance quality was 25–27 °C. Grain weight decreased about 2–6%, while the temperature of H15 was raised 1 °C above the thresholds. Perfect grain ratio and chalky grain ratio decreased and increased, respectively, while the temperature of H15 was raised above the thresholds. However, the high temperature in H15 affected the physicochemical characteristics. In addition, we found positive correlation between grain length to width ratio and perfect grain ratio. Grain length to width ratio could be an index of temperature effects for grain quality. In our study, when the temperature was below 30 °C, a rising temperature of H15 could damage rice yield and appearance quality, and change grain shape. Our results could provide reference for dealing with the warming future in other temperate rice-cultivated countries.

  11. Freezing point of milk in a herd of high yielding dairy cows

    Directory of Open Access Journals (Sweden)

    Slavica Golc Teger

    2005-04-01

    Full Text Available Factors affecting the freezing point of milk in a herd of 200 Black and White cows with the average milk yield of 8 386 kg in the lactation and 8 328 kg in the standard lactation were examinated. Over the period of one year (2002 and based upon 1 773 individual monthly collected milk samples with the average contents of 3.91% fat, 3.26% protein, 4.54% lactose, 33.4 mg/100 ml urea and 331000 somatic cells per ml in milk were determined. The average freezing point of milk (n = 1 680 was estimated to be –0.527 ºC, with a range from -0.562 ºC to -0.423 ºC. In 210 (12.5% samples was higher than -0.515 ºC. The lowest freezing point (-0.532 ºC was found in the samples collected in the first month after calving and highest (-0.522 ºC in the samples of 12th month of lactation. The differences between the freezing point of milk after the first and the second calving (-0.530 ºC; P < 0.05 and those after the fifth calving (-0.523 ºC; P < 0.05 were also significant. The samples collected in month from January to April (-0.538 ºC to -0.532 ºC were significantly lower in comparison to samples collected in May and June (-0.517 ºC and -0.519 ºC. The following statistically significant correlation coefficients between cows' properties, milk composition and the freezing point of milk were found: month of lactation r = 0.233 (P < 0.001; lactation number r = 0.196 (P < 0.001; age of cows (years r = 0.231 (P < 0.001; month of the year r = 0.0253 (P < 0.001; milk yield per milking day r = -0.106 (P < 0.001; fat corrected milk content (FCM per milking day r = -0.234 (P < 0.001; lactose % r = -0.530 (P < 0.001; fat % r = -0.351 (P < 0.001; protein % r = 0.058 (P < 0.05; urea mg/100 mL r = 0.091 (P < 0.001 and somatic cell count r = 0.154 (P < 0.001. The sum of effects (month of the year, lactation lenght and fat, protein and lactose content of milk was found to account for about 70% variability of the total depression of milk freezing point (R2 = 0.698.

  12. Embedded pitch adapters: A high-yield interconnection solution for strip sensors

    Energy Technology Data Exchange (ETDEWEB)

    Ullán, M., E-mail: miguel.ullan@imb-cnm.csic.es [Centro Nacional de Microelectronica (IMB-CNM, CSIC), Campus UAB-Bellaterra, 08193 Barcelona (Spain); Allport, P.P.; Baca, M.; Broughton, J.; Chisholm, A.; Nikolopoulos, K.; Pyatt, S.; Thomas, J.P.; Wilson, J.A. [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Kierstead, J.; Kuczewski, P.; Lynn, D. [Brookhaven National Laboratory, Physics Department and Instrumentation Division, Upton, NY 11973-5000 (United States); Hommels, L.B.A. [Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Fleta, C.; Fernandez-Tejero, J.; Quirion, D. [Centro Nacional de Microelectronica (IMB-CNM, CSIC), Campus UAB-Bellaterra, 08193 Barcelona (Spain); Bloch, I.; Díez, S.; Gregor, I.M.; Lohwasser, K. [DESY, Notkestrasse 85, 22607 Hamburg (Germany); and others

    2016-09-21

    A proposal to fabricate large area strip sensors with integrated, or embedded, pitch adapters is presented for the End-cap part of the Inner Tracker in the ATLAS experiment. To implement the embedded pitch adapters, a second metal layer is used in the sensor fabrication, for signal routing to the ASICs. Sensors with different embedded pitch adapters have been fabricated in order to optimize the design and technology. Inter-strip capacitance, noise, pick-up, cross-talk, signal efficiency, and fabrication yield have been taken into account in their design and fabrication. Inter-strip capacitance tests taking into account all channel neighbors reveal the important differences between the various designs considered. These tests have been correlated with noise figures obtained in full assembled modules, showing that the tests performed on the bare sensors are a valid tool to estimate the final noise in the full module. The full modules have been subjected to test beam experiments in order to evaluate the incidence of cross-talk, pick-up, and signal loss. The detailed analysis shows no indication of cross-talk or pick-up as no additional hits can be observed in any channel not being hit by the beam above 170 mV threshold, and the signal in those channels is always below 1% of the signal recorded in the channel being hit, above 100 mV threshold. First results on irradiated mini-sensors with embedded pitch adapters do not show any change in the interstrip capacitance measurements with only the first neighbors connected.

  13. Ultrahigh Yield Strength Rhenium for High-Performance Combustion Chambers Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The state-of-the-art material system for high-performance radiation-cooled liquid rocket engines is iridium/rhenium manufactured by chemical vapor deposition (CVD)....

  14. Effect of Admixtures on the Yield Stresses of Cement Pastes under High Hydrostatic Pressures

    Directory of Open Access Journals (Sweden)

    Hong Jae Yim

    2016-03-01

    Full Text Available When cement-based materials are transported at a construction site, they undergo high pressures during the pumping process. The rheological properties of the materials under such high pressures are unknown, and estimating the workability of the materials after pumping is a complex problem. Among various influential factors on the rheology of concrete, this study investigated the effect of mineral and chemical admixtures on the high-pressure rheology. A rheometer was fabricated that could measure the rheological properties while maintaining a high pressure to simulate the pumping process. The effects of superplasticizer, silica fume, nanoclay, fly ash, or ground granulated blast furnace slag were investigated when mixed with two control cement pastes. The water-to-cement ratios were 0.35 and 0.50.

  15. Effects of Fluctuating Environments on the Selection of High Yielding Microalgae

    Energy Technology Data Exchange (ETDEWEB)

    Benemann, J. R.; Tillett, D. M.

    1987-02-27

    Microalgae have the potential of producing biomass with a high content of lipids at high productivities using seawater or saline ground water resources. Microalgal lipids are similar to vegetable oils and suitable for processing to liquid fuels. Engineering cost analysis studies have concluded that, at a favorable site, microalgae cultivation for fuel production could be economically viable. The major uncertainties involve the microalgae themselves: biomass and lipid productivity and culture stability.

  16. Taurus Littrow Pyroclastic Deposit: High-Yield Feedstock for Lunar Oxygen

    Science.gov (United States)

    Allen, Carlton C.

    2015-01-01

    Future human habitation of the Moon will likely require the use of locally derived materials because of the high cost of transportation from Earth. Oxygen, extracted from oxides and silicates, is a potentially abundant lunar resource vital for life support and spacecraft propulsion. The anticipated costs of supplying all oxygen needs for a lunar base from Earth are high enough to warrant serious study of oxygen production from local resources.

  17. Reassortment of high-yield influenza viruses in vero cells and safety assessment as candidate vaccine strains.

    Science.gov (United States)

    Zhou, Jian; Yang, Fan; Yang, Jinghui; Ma, Lei; Cun, Yina; Song, Shaohui; Liao, Guoyang

    2017-01-02

    Vaccination is the practiced and accessible measure for preventing influenza infection. Because chicken embryos used for vaccine production have various insufficiencies, more efficient methods are needed. African green monkey kidney (Vero) cells are recommended by the World Health Organization (WHO) as a safe substitute for influenza vaccine production for humans. However, the influenza virus usually had low-yield in Vero cells, which limits the usage of Vero cellular vaccines. This study used 2 high-yield influenza viruses in Vero cells: A/Yunnan/1/2005Va (H3N2) and B/Yunnan/2/2005Va (B) as donor viruses. It used 3 wild strain viruses to reassort new adaptation viruses, including: A/Tianjin/15/2009(H1N1), A/Fujian/196/2009(H3N2), and B/Chongqing/1384/2010(B). These three new viruses could maintain the characteristic of high-yield in Vero cells. Furthermore, they could keep the immunogenic characteristics of the original wild influenza viruses. Importantly, these viruses were shown as safe in chicken embryo and guinea pigs assessment systems. These results provide an alternative method to produce influenza vaccine based on Vero cells.

  18. High-yield production of a chimeric glycoprotein based on permuted E1 and E2 HCV envelope ectodomains.

    Science.gov (United States)

    Tello, Daniel; Rodríguez-Rodríguez, Mar; Yélamos, Belén; Gómez-Gutiérrez, Julián; Peterson, Darrell L; Gavilanes, Francisco

    2015-03-01

    In this report it is described for the first time the expression and purification of large quantities of a soluble and correctly folded chimeric recombinant protein, E2661E1340, containing the permuted Hepatitis C virus (HCV) glycoprotein ectodomains E1 (amino acids 192-340) and E2 (amino acids 384-661). Using the baculovirus/insect cell expression system, 8mg of secreted protein were purified from 1L of culture media, a yield 4 times higher than the described for its counterpart E1341E2661. This permuted chimeric protein is glycosylated and possesses a high tendency to self-associate. The fluorescence emission spectrum indicates that Trp residues occupy a relatively low hydrophobic environment. The secondary structure was determined by deconvolution of the far-UV circular dichroism spectrum yielding 13% α-helix structure, 49% extended structure and 38% non-ordered structure. E2661E1340 binds to antibodies present in human sera from HCV-positive patients, a binding that is blocked at different levels by a rabbit anti-E2661 antibody. All these structural and antigenic features of E2661E1340 are very similar to those described for E1340E2661, Thus, this high-yield isolated chimeric protein may be a valuable tool to study the first steps of the HCV infection. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Waveform optimization for enhancing high-harmonic yield by synthesizing two or three-color laser fields.

    Science.gov (United States)

    Jin, Cheng; Wang, Guoli; Wei, Hui; Le, Anh-Thu; Lin, C. D.

    2014-05-01

    High-order harmonics (HH) extending to the X-ray region generated in a gas medium by intense lasers offer the potential for providing tabletop broadband light sources but so far are limited by their low conversion efficiency. We show that HH yield can be enhanced by one to two orders of magnitude if the laser's waveform is optimized by synthesizing two- or three-color fields compared to a sinusoidal wave without an increase in the total laser power. The optimization procedure carried out by genetic algorithm is designed to take into account of macroscopic propagation effects. The HH thus generated are also favorably phase-matched so that radiation is efficiently built up in the gas medium. In addition, we demonstrate the generation of a single-attosecond pulse by synthesizing three incommensurate lasers while the harmonic yield is optimized as well. Our results, combined with the emerging intense high-repetition MHz lasers, promise to increase harmonic yields by several orders to make HH feasible in the near future as general bright tabletop light sources. Supported by U.S. DOE.

  20. Homogeneity analysis of high yield manufacturing process of mems-based pzt thick film vibrational energy harvesters

    DEFF Research Database (Denmark)

    Lei, Anders; Xu, Ruichao; Pedersen, C.M.

    2011-01-01

    This work presents a high yield wafer scale fabrication of MEMS-based unimorph silicon/PZT thick film vibrational energy harvesters aimed towards vibration sources with peak frequencies in the range of a few hundred Hz. By combining KOH etching with mechanical front side protection, SOI wafer...... to accurately define the thickness of the silicon part of the harvester and a silicon compatible PZT thick film screen-printing technique, we are able to fabricate energy harvesters on wafer scale with a yield higher than 90%. The characterization of the fabricated harvesters is focused towards the full wafer....../mass-production aspect; hence the analysis of uniformity in harvested power and resonant frequency....

  1. Transcriptome Analysis Suggests That Starch Synthesis May Proceed via Multiple Metabolic Routes in High Yielding Potato Cultivars

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Høgh Petersen, Annabeth; Sønderkær, Mads

    2012-01-01

    new possibilities for metabolic engineering of the starch metabolism in potato via the so far uncharacterized G1P transporter. The perspectives are to increase yield and space efficiency of this important crop. In the light of the increasing demands imposed on agriculture to support a growing global......Background: Glucose-6-phosphate is imported into the amyloplast of potato tubers and thought to constitute the precursor for starch synthesis in potato tubers. However, recently it was shown that glucose-1-phosphate can also be imported into the amyloplast and incorporated into starch via an ATP...... independent mechanism under special conditions. Nonetheless, glucose 6-phosphate is believed to be the quantitatively important precursor for starch synthesis in potato. Principal Finding: Potato tubers of the high yielding cv Kuras had low gene expression of plastidial phophoglucomutase (PGM) and normal...

  2. Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China

    Directory of Open Access Journals (Sweden)

    Lilian Wu

    2016-07-01

    Full Text Available Selecting rice varieties with a high nitrogen (N use efficiency (NUE is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of thirteen and fourteen candidate varieties with two controls were determined at a N rate of 100 kg ha-1 in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha-1, except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha-1. HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM ranged from 144 to 210 kg ha-1, while the nitrogen use efficiency for grain production (NUEg ranged from 35.2 to 62.0 kg kg-1. Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPM and NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N

  3. Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine

    DEFF Research Database (Denmark)

    Lou, Chenguang; Xiao, Qiang; Brennan, Lavinia

    2010-01-01

    2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability with their ta...... with their target duplexes as measured by ultraviolet/fluorescence melting and DNase I footprinting. The incorporation of MEPU into TFOs renders them resistant to degradation by serum nucleases....

  4. Development of an FPW Biosensor with Low Insertion Loss and High Fabrication Yield for Detection of Carcinoembryonic Antigen

    Science.gov (United States)

    Lan, Je-Wei; Huang, I-Yu; Lin, Yu-Cheng; Lin, Chang-Yu; Chen, Jian-Lin; Hsieh, Chia-Hsu

    2016-01-01

    In the last two decades, various flexural plate-wave (FPW)-based biosensors with low phase velocity, low operation frequency, high sensitivity, and short response time, have been developed. However, conventional FPW transducers have low fabrication yield because controlling the thickness of silicon/isolation/metal/piezoelectric multilayer floating thin-plate is difficult. Additionally, conventional FPW devices usually have high insertion loss because of wave energy dissipation to the silicon substrate or outside area of the output interdigital transducers (IDTs). These two disadvantages hinder the application of FPW devices. To reduce the high insertion loss of FPW devices, we designed two focus-type IDTs (fan-shaped and circular, respectively) that can effectively confine the launched wave energy, and adopted a focus-type silicon-grooved reflective grating structure (RGS) that can reduce the wave propagation loss. To accurately control the thickness of the silicon thin-plate and substantially improve the fabrication yield of FPW transducers, a 60 °C/27 °C two-step anisotropic wet etching process was developed. Compared with conventional FPW devices (with parallel-type IDTs and without RGS), the proposed FPW devices have lower insertion loss (36.04 dB) and higher fabrication yield (63.88%). Furthermore, by using cystamine-based self-assembled monolayer (SAM) nanotechnology, we used the improved FPW device to develop a novel FPW-based carcinoembryonic antigen (CEA) biosensor for detection of colorectal cancer, and this FPW-CEA biosensor has a low detection limit (5 ng/mL), short response time (<10 min), high sensitivity (60.16–70.06 cm2/g), and high sensing linearity (R-square = 0.859–0.980). PMID:27834798

  5. Influence of a High-Pressure Comminution Technology on Concentrate Yields in Copper Ore Flotation Processes

    Directory of Open Access Journals (Sweden)

    Saramak D.

    2014-10-01

    Full Text Available The article concerns the issues of flotation process effectiveness in relationship to the operating conditions of a high-pressure comminution process course. Experimental programme covering a flotation laboratory batch tests was a verification technique of a high-pressure crushing operations course. The most favorable values of flotation concentrate weight recoveries were obtained for the pressing force 6 kN and 4% of the feed moisture. It was also determined the model of the concentrate weight recovery as a function of pressing force in the press and feed moisture content. This model was the basis for the optimization of effects of copper ore flotation processes preceded in high-pressure crushing operation in roller presses.

  6. Electropolymerized Star-Shaped Benzotrithiophenes Yield π-Conjugated Hierarchical Networks with High Areal Capacitance

    KAUST Repository

    Ringk, Andreas

    2016-03-30

    High-surface-area π-conjugated polymeric networks have the potential to lend outstanding capacitance to supercapacitors because of the pronounced faradaic processes that take place across the dense intimate interface between active material and electrolytes. In this report, we describe how benzo[1,2-b:3,4-b’:5,6-b’’]trithiophene (BTT) and tris-EDOT-benzo[1,2-b:3,4-b’:5,6-b’’]trithiophene (TEBTT) can serve as 2D (trivalent) building blocks in the development of electropolymerized hierarchical π-conjugated frameworks with particularly high areal capacitance. In comparing electropolymerized networks of BTT, TEBTT, and their copolymers with EDOT, we show that P(TEBTT/EDOT)-based frameworks can achieve higher areal capacitance (e.g., as high as 443.8 mF cm-2 at 1 mA cm-2) than those achieved by their respective homopolymers (PTEBTT and PEDOT) in the same experimental conditions of electrodeposition (PTEBTT: 271.1 mF cm-2 (at 1 mA cm-2) and PEDOT: 12.1 mF cm-2 (at 1 mA cm-2)). For example, P(TEBTT/EDOT)-based frameworks synthesized in a 1:1 monomer-to-comonomer ratio show a ca. 35x capacitance improvement over PEDOT. The high areal capacitance measured for P(TEBTT/EDOT) copolymers can be explained by the open, highly porous hierarchical morphologies formed during the electropolymerization step. With >70% capacitance retention over 1,000 cycles (up to 89% achieved), both PTEBTT- and P(TEBTT/EDOT)-based frameworks are resilient to repeated electrochemical cycling and can be considered promising systems for high life cycle capacitive electrode applications.

  7. A Mutagenesis Assay for Reporter Gene Screening Using Partially Degenerate Oligonucleotides of the Tandems NNT and NNC

    Directory of Open Access Journals (Sweden)

    Huifen Xu

    2015-01-01

    Full Text Available Not all proteins are tolerable to mutations. Whether a specific protein can be a mutable target is of importance in the biotechnology and pharmaceutical industry. This study reported a novel mutagenesis assay using tandem NNT and NNC oligonucleotides to test the mutability of a candidate gene. These two tandem oligonucleotides avoid the risk of forming nonsense mutations and render flexibility of truncating or expanding the insertion size. As a reporter gene, ZeoR (zeocin resistance gene was confirmed to have a high tolerance for mutagenesis by this new assay.

  8. Critical parameters in cost-effective alkaline extraction for high protein yield from leaves

    NARCIS (Netherlands)

    Zhang, C.; Sanders, J.P.M.; Bruins, M.E.

    2014-01-01

    Leaves are potential resources for feed or food, but their applications are limited due to a high proportion of insoluble protein and inefficient processing. To overcome these problems, parameters of alkaline extraction were evaluated using green tea residue (GTR). Protein extraction could be

  9. Response of high yielding rice varieties to NaCl salinity in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-11-05

    Nov 5, 2008 ... in the experiment include: Dasht, Khazar, Kadous, Nemat, Neda,. Fajr, Shafagh and Sahel. To obtain the accurate result and exclude any unwanted and interfering variable in the environment and to minimize their effects, the experiment was conducted in a highly controlled greenhouse. The greenhouse ...

  10. High yield synthesis of high specific activity R-(-)-[[sup 11]C]epinephrine for routine PET studies in humans

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, P.K.; Gildersleeve, D.L.; Jewett, D.M.; Toorongian, S.A.; Kilbourn, M.R.; Schwaiger, M.; Wieland, D.M. (Michigan Univ., Ann Arbor, MI (United States). Div. of Nuclear Medicine)

    1993-11-01

    R-(-)-[[sup 11]C]Epinephrine ([[sup 11]C]EPI) has been synthesized from R-(-)-norepinephrine by direct methylation with [[sup 11]C]methyl iodide or [[sup 11]C]methyl triflate. The total synthesis time including HPLC purification was 35-40 min. The radiochemical yields (EOB) were 5-10% for [[sup 11]C]methyl iodide and 15-25% for [[sup 11]C]methyl triflate. Radiochemical purity was >98%; optical purity determined by radio-chiral HPLC was > 97%. The [[sup 11]C]methyl triflate technique produces R-(-)-[[sup 11]C]epinephrine in quantities (80-170 mCi) sufficient for multiple positron emission tomography studies in humans. The two synthetic methods are generally applicable to the production of other N-[[sup 11]C]methyl phenolamines and N-[[sup 11]C]methyl catecholamines. (Author).

  11. Enhancement of yield point at high pressure high temperature wells by using polymer nanocomposites based on ZnO & CaCO3 nanoparticles

    Directory of Open Access Journals (Sweden)

    A.Z. Noah

    2017-03-01

    Full Text Available Zinc oxide nanoparticles (ZnO-NPs and modified calcium carbonate (nano-CaCO3 nanoparticles were successfully prepared and added to polystyrene-butadiene rubber copolymer (PSBR matrix to prepare PSBR nanocomposites. The prepared nanomaterials (ZnO-NPs & nano-CaCO3 were characterized using scanning electron microscope (SEM, transmission electron microscope (TEM and X-ray diffraction (XRD. Furthermore, the prepared polymer nanocomposites and oil base mud were used for drilling in high pressure high temperature (HPHT wells. The consequence of using polymer nanocomposites based on different loading of ZnO-NPs and nano-CaCO3 on the rheological properties of oil base mud was evaluated and enhanced the yield point at high pressure high temperature wells (HPHT. The using of the polymer with different percentage from (0.5 in all percent the obtained results is very promising; this means that the increase of polymer is reasonable for the increase of apparent viscosity, plastic viscosity and yield point at high temperature. Correspondingly, polymer nanocomposites displayed rise of apparent viscosity, plastic viscosity, and yield point, decreased in fluid loss and increased in electrical stability at high pressure high temperature wells.

  12. Ultrahigh molecular recognition specificity of competing DNA oligonucleotide strands in thermal equilibrium

    CERN Document Server

    Schenkelberger, Marc; Mai, Timo; Ott, Albrecht

    2016-01-01

    The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize their binding partner with astonishing accuracy. In thermal equilibrium it is usually admitted that the affinity of recognizer pairs only depends on the nature of the two binding molecules. Accordingly, Boltzmann factors of binding energy differences relate the molecular affinities among different target molecules that compete for the same probe. Here, we consider the molecular recognition of short DNA oligonucleotide single strands. We show that a better matching oligonucleotide strand can prevail against a disproportionally more concentrated competitor that exhibits reduced affinity due to a mismatch. The magnitude of deviation from the simple picture above may reach several orders of magnitude. In our experiments the effective molecular affinity of a given strand remains...

  13. LNA-modified oligonucleotides mediate specific inhibition of microRNA function

    DEFF Research Database (Denmark)

    Ørom, Ulf Andersson; Kauppinen, Sakari; Lund, Anders H

    2006-01-01

    observed in many human cancers. Here we present a method for specific inhibition of miRNA function through interaction with LNA-modified antisense oligonucleotides and report the specificity of this application. We show that LNA-modified oligonucleotides can inhibit exogenously introduced miRNAs with high......microRNAs are short, endogenous non-coding RNAs that act as post-transcriptional modulators of gene expression. Important functions for microRNAs have been found in the regulation of development, cellular proliferation and differentiation, while perturbed miRNA expression patterns have been...... specificity using a heterologous reporter assay, and furthermore demonstrate their ability to inhibit an endogenous miRNA in Drosophila melanogaster cells, leading to up-regulation of the cognate target protein. The method shows stoichiometric and reliable inhibition of the targeted miRNA and can thus...

  14. Growth and Yield Responses of Green Pepper (Capsicum annum L. to Manure Rates under Field and High Tunnel Conditions

    Directory of Open Access Journals (Sweden)

    Ima-obong I. DOMINIC

    2017-03-01

    Full Text Available The present study was conducted to determine growth and yield responses of green pepper to varying manure rates under field and high tunnel conditions. Experiment 1 was a pot experiment to evaluate three rates (0.5 and 10 t/ha of poultry manure (PM on green pepper production under high tunnel and open field conditions. Experiment 2 was to determine the performance of green pepper as influenced by different manure rates (0, 5 and 10 t/ha of PM, 300 kg/ha of NPK, 5 t/ha of PM + 200 kg of NPK and 10 t/ha of PM + 100 kg of NPK on the field. High tunnel produced about 3.1 fruits/plant that weighted 102.8 g, which was significantly higher than open field experiment in which 1.7 fruits/plant, with a medium weight of 32.3 g were noted. High tunnel enhanced successful production of green pepper during rainy season, whereas the open field production during the same season was near failure. Application of 10 t/ha of PM produced significantly larger fruits in the pot experiment. Good fertilizer effects on growth and yield components were recorded for the field study. Plant height, number of leaves and branches, number and weight of harvested fruit followed similar trend in 5 and 10 t/ha of PM which gave statistically similar results, and provided the best performance during the experiment. Application of 5 t/ha of PM produced the highest total fruits yield.

  15. Genomics approaches to unlock the high yield potential of cassava, a tropical model plant

    Directory of Open Access Journals (Sweden)

    Shengkui ZHANG,Ping'an MA,Haiyan WANG,Cheng LU,Xin CHEN,Zhiqiang XIA,Meiling ZOU,Xinchen ZHOU,Wenquan WANG

    2014-12-01

    Full Text Available Cassava, a tropical food, feed and biofuel crop, has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition, which makes it highly suitable as a model plant for tropical crops. However, the understanding of the metabolism and genomics of this important crop is limited. The recent breakthroughs in the genomics of cassava, including whole-genome sequencing and transcriptome analysis, as well as advances in the biology of photosynthesis, starch biosynthesis, adaptation to drought and high temperature, and resistance to virus and bacterial diseases, are reviewed here. Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars. Finally, the current challenges and future potential of cassava as a model plant are discussed.

  16. Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity

    Science.gov (United States)

    Salvat, Regina S.; Parker, Andrew S.; Kirsch, Jack R.; Brooks, Seth A.

    2017-01-01

    Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide–MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 109 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening. PMID:28607051

  17. Fabrication of high yield horizontally aligned single wall carbon nanotubes for molecular electronics

    OpenAIRE

    Ibrahim, Imad

    2014-01-01

    The extraordinary properties of the single wall carbon nanotubes (SWCNTs) have stimulated an enormous amount of research towards the realization of SWCNT-based products for different applications ranging form nanocomposites to nanoelectronics. Their high charge mobility, exceedingly good current-carrying capacities and ability to be either semiconducting or metallic render them ideal building blocks for nanoelectronics. For nanoelectronic applications, either individual or parallel aligned SW...

  18. Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity.

    Science.gov (United States)

    Salvat, Regina S; Verma, Deeptak; Parker, Andrew S; Kirsch, Jack R; Brooks, Seth A; Bailey-Kellogg, Chris; Griswold, Karl E

    2017-06-27

    Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide-MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 10 9 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening.

  19. Registration of a high yielding malt barley variety HB1454 for the ...

    African Journals Online (AJOL)

    HB1454 (Reg. No. EH 1847/F4.2P.5.2) is a two - rowed, hulled, malting barley developed at Holetta Research Center (HRC). HB 1454 was tested in a multi location variety trial as EH 1847/F4.2P.5.2 from 2005- 2007 along with twelve genotypes advanced from the local crossing program. It was released in 2011 for its high ...

  20. Investigation of Ozone Yield of Air Fed Ozonizer by High Pressure Homogeneous Dielectric Barrier Discharge

    Science.gov (United States)

    2013-07-01

    around 2 ms and 12 ms in this figure, and during the discharge period, the current was continuous without any pulse . Once a discharge generated in...electron avalanches [10]. Fig. 1. High pressure ozone generator. (a) Top view (b) Side view Fig. 2. Barrier discharge device. Table 1... discharge N. Osawa P1 P, UY. Yoshioka UP2 P, R. Hanaoka P1 P 1 Center for Electric, Optic and Energy applications, Department of Electric and

  1. High Yields of Hydrogen Production Induced by Meta-Substituted Dichlorophenols Biodegradation from the Green Alga Scenedesmus obliquus

    Science.gov (United States)

    Papazi, Aikaterini; Andronis, Efthimios; Ioannidis, Nikolaos E.; Chaniotakis, Nikolaos; Kotzabasis, Kiriakos

    2012-01-01

    Hydrogen is a highly promising energy source with important social and economic implications. The ability of green algae to produce photosynthetic hydrogen under anaerobic conditions has been known for years. However, until today the yield of production has been very low, limiting an industrial scale use. In the present paper, 73 years after the first report on H2-production from green algae, we present a combinational biological system where the biodegradation procedure of one meta-substituted dichlorophenol (m-dcp) is the key element for maintaining continuous and high rate H2-production (>100 times higher than previously reported) in chloroplasts and mitochondria of the green alga Scenedesmus obliquus. In particular, we report that reduced m-dcps (biodegradation intermediates) mimic endogenous electron and proton carriers in chloroplasts and mitochondria, inhibit Photosystem II (PSII) activity (and therefore O2 production) and enhance Photosystem I (PSI) and hydrogenase activity. In addition, we show that there are some indications for hydrogen production from sources other than chloroplasts in Scenedesmus obliquus. The regulation of these multistage and highly evolved redox pathways leads to high yields of hydrogen production and paves the way for an efficient application to industrial scale use, utilizing simple energy sources and one meta-substituted dichlorophenol as regulating elements. PMID:23145057

  2. Tuning of ZIF-Derived Carbon with High Activity, Nitrogen Functionality, and Yield - A Case for Superior CO2 Capture.

    Science.gov (United States)

    Gadipelli, Srinivas; Guo, Zheng Xiao

    2015-06-22

    A highly effective and facile synthesis route is developed to create and tailor metal-decorated and nitrogen-functionalized active microporous carbon materials from ZIF-8. Clear metal- and pyrrolic-N-induced enhancements of the cyclic CO2 uptake capacities and binding energies are achieved, particularly at a much lower carbonization temperature of 700 °C than those often reported (1000 °C). The high-temperature carbonization can enhance the porosity but only at the expense of considerable losses of sample yield and metal and N functional sites. The findings are comparatively discussed with carbons derived from metal-organic frameworks (MOFs) reported previously. Furthermore, the porosity of the MOF-derived carbon is critically dependent on the structure of the precursor MOF and the crystal growth. The current strategy offers a new and effective route for the creation and tuning of highly active and functionalized carbon structures in high yields and with low energy consumption. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  3. A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

    Science.gov (United States)

    Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

    2013-01-01

    Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993

  4. Biocontrol potential of Halotolerant bacterial chitinase from high yielding novel Bacillus Pumilus MCB-7 autochthonous to mangrove ecosystem.

    Science.gov (United States)

    Rishad, K S; Rebello, Sharrel; Shabanamol, P S; Jisha, M S

    2017-04-01

    The multifaceted role of chitinase in medicine, agriculture, environmental remediation and various other industries greatly demands the isolation of high yielding chitinase producing microorganisms with improved properties. The current study aimed to investigate the isolation, characterization and biocontrol prospective of chitinase producing bacterial strains autochthonous to the extreme conditions of mangrove ecosystems. Among the 51 bacterial isolates screened, Bacillus pumilus MCB-7 with highest chitinase production potential was identified and confirmed by 16S rDNA typing. Chitinase enzyme of MCB-7 was purified; the chitin degradation was evaluated by SEM and LC-MS. Unlike previously reported B.pumilus isolates, MCB-7 exhibited highest chitinase activity of 3.36U/mL, active even at high salt concentrations and temperature up to 60°C. The crude as well as purified enzyme showed significant antimycotic activity against agricultural pathogens such as Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus, Ceratorhiza hydrophila and Fusarium oxysporum. The enzyme also exhibited biopesticidal role against larvae of Scirpophaga incertulas (Walker). [Lep.: Pyralidae], a serious agricultural pest of rice. The high chitinolytic and antimycotic potential of MCB-7 increases the prospects of the isolate as an excellent biocontrol agent. To the best of our knowledge, this is the first report of high chitinase yielding Bacillus pumilus strain from mangrove ecosystem with a biocontrol role against phytopathogenic fungi and insect larval pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. High-yield recombinant expression of the chicken antimicrobial peptide fowlicidin-2 in Escherichia coli.

    Science.gov (United States)

    Feng, Xingjun; Xu, Wenshan; Qu, Pei; Li, Xiaochong; Xing, Liwei; Liu, Di; Jiao, Jian; Wang, Jue; Li, Zhongqiu; Liu, Chunlong

    2015-01-01

    The antimicrobial peptide fowlicidin-2 identified in chicken is a member of the cathelicidins family. The mature fowlicidin-2 possesses high antibacterial efficacy and lipopolysaccharide (LPS) neutralizing activity, and also represents an excellent candidate as an antimicrobial agent. In the present study, the recombinant fowlicidin-2 was successfully produced by Escherichia coli (E. coli) recombinant expression system. The gene encoding fowlicidin-2 with the codon preference of E. coli was designed through codon optimization and synthesized in vitro. The gene was then ligated into the plasmid pET-32a(+), which features fusion protein thioredoxin at the N-terminal. The recombinant plasmid was transformed into E. coli BL21(DE3) and cultured in Luria-Bertani (LB) medium. After isopropyl-β-D-thiogalactopyranoside (IPTG) induction, the fowlicidin-2 fusion protein was successfully expressed as inclusion bodies. The inclusion bodies were dissolved and successfully released the peptide in 70% formic acid solution containing cyanogen bromide (CNBr) in a single step. After purification by reverse-phase high-performance liquid chromatography (RP-HPLC), ∼6.0 mg of fowlicidin-2 with purity more than 97% was obtained from 1 litre of bacteria culture. The recombinant peptide exhibited high antibacterial activity against the Gram-positive and Gram-negative bacteria, and even drug-resistant strains. This system could be used to rapidly and efficiently produce milligram quantities of a battery of recombinant antimicrobial peptides as well as for large-scale production. © 2015 American Institute of Chemical Engineers.

  6. High yield hydrogen production in a single-chamber membrane-less microbial electrolysis cell.

    Science.gov (United States)

    Ye, Yejie; Wang, Liyong; Chen, Yingwen; Zhu, Shemin; Shen, Shubao

    2010-01-01

    The single-chamber membrane-less MEC exerted much better hydrogen production performance while given higher applied voltages than it did at lower. High applied voltages that could shorten the reaction time and the exposure of anode to air for at least 30 min between cycles can significantly suppress methanogen and increase hydrogen production. At an applied voltage of 1.0 V, a hydrogen production rate of 1.02 m(3)/m(3)/day with a current density of 5.7 A/m(2) was achieved. Cathodic hydrogen recovery and coulombic efficiency were 63.4% and 69.3% respectively. The hydrogen concentration of mixture gas produced of 98.4% was obtained at 1.0 V, which was the best result of reports. The reasons that such a high hydrogen concentration can be achieved were probably the high electrochemical activity and hydrogen production capability of the active microorganisms. Increase in substrate concentrations could not improve MEC's performance, but increased the reaction times. Further, reactor configuration and operation factors optimisation should be considered to increase current density, hydrogen production rate and hydrogen recovery.

  7. Assessment of the Full Compatibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition and Oxime Click Reactions for bis-Labelling of Oligonucleotides.

    Science.gov (United States)

    Estalayo-Adriàn, Sandra; Lartia, Rémy; Meyer, Albert; Vasseur, Jean-Jacques; Morvan, François; Defrancq, Eric

    2015-04-01

    The conjugation of oligonucleotides with reporters is of great interest for improving their intrinsic properties or endowing new ones. In this context, we report herein a new procedure for the bis-labelling of oligonucleotides through oxime ligation (Click-O) and copper(I)-catalyzed alkyne-azide cycloaddition (Click-H). 5'-Azido and 3'-aldehyde precursors were incorporated into oligonucleotides, and subsequent coupling reactions through Click-O and Click-H (or vice versa) were successfully achieved. In particular, we exhaustively investigated the full compatibility of each required step for both tethering strategies. The results demonstrate that click Huisgen and click oxime reactions are fully compatible. However, whilst both approaches can deliver the targeted doubly conjugated oligonucleotide, the route involving click oxime ligation prior to click Huisgen is significantly more successful. Thus the reactions investigated here can be considered to be key elements of the chemical toolbox for the synthesis of highly sophisticated bioconjugates.

  8. Stable oligonucleotide-functionalized gold nanosensors for environmental biocontaminant monitoring.

    Science.gov (United States)

    Riquelme, Maria V; Leng, Weinan; Carzolio, Marcos; Pruden, Amy; Vikesland, Peter

    2017-12-01

    The global propagation of environmental biocontaminants such as antibiotic resistant pathogens and their antibiotic resistance genes (ARGs) is a public health concern that highlights the need for improved monitoring strategies. Here, we demonstrate the environmental stability and applicability of an oligonucleotide-functionalized gold nanosensor. The mecA ARG was targeted as model biocontaminant due to its presence in clinically-relevant pathogens and to its emergence as an environmental contaminant. mecA-specific nanosensors were tested for antibiotic resistance gene (ARG) detection in ARG-spiked effluent from four wastewater treatment plants (WWTPs). The mecA-specific nanosensors showed stability in environmental conditions and in high ionic strength ([MgCl2]<50mM), and high selectivity against mismatched targets. Spectrophotometric detection was reproducible with an LOD of 70pM (≈4×107genes/μL), even in the presence of interferences associated with non-target genomic DNA and complex WWTP effluent. This contribution supports the environmental applicability of a new line of cost-effective, field-deployable tools needed for wide-scale biocontaminant monitoring. Copyright © 2017. Published by Elsevier B.V.

  9. Specificity tests of an oligonucleotide probe against food-outbreak salmonella for biosensor detection

    Science.gov (United States)

    Chen, I.-H.; Horikawa, S.; Xi, J.; Wikle, H. C.; Barbaree, J. M.; Chin, B. A.

    2017-05-01

    Phage based magneto-elastic (ME) biosensors have been shown to be able to rapidly detect Salmonella in various food systems to serve food pathogen monitoring purposes. In this ME biosensor platform, the free-standing strip-shaped magneto-elastic sensor is the transducer and the phage probe that recognizes Salmonella in food serves as the bio-recognition element. According to Sorokulova et al. at 2005, a developed oligonucleotide probe E2 was reported to have high specificity to Salmonella enterica Typhimurium. In the report, the specificity tests were focused in most of Enterobacterace groups outside of Salmonella family. Here, to understand the specificity of phage E2 to different Salmonella enterica serotypes within Salmonella Family, we further tested the specificity of the phage probe to thirty-two Salmonella serotypes that were present in the major foodborne outbreaks during the past ten years (according to Centers for Disease Control and Prevention). The tests were conducted through an Enzyme linked Immunosorbent Assay (ELISA) format. This assay can mimic probe immobilized conditions on the magnetoelastic biosensor platform and also enable to study the binding specificity of oligonucleotide probes toward different Salmonella while avoiding phage/ sensor lot variations. Test results confirmed that this oligonucleotide probe E2 was high specific to Salmonella Typhimurium cells but showed cross reactivity to Salmonella Tennessee and four other serotypes among the thirty-two tested Salmonella serotypes.

  10. Long-range order of organized oligonucleotide monolayers on Au(111) electrodes

    DEFF Research Database (Denmark)

    Wackerbarth, Hainer; Grubb, Mikala; Zhang, Jingdong

    2004-01-01

    , with electrochemical potential control of both the sample electrode and the tip. All the data are based on single-crystal, atomically planar Au(111)-electrode surfaces. The high sensitivity of such surfaces provides accurate HS-10A and HS-10AT electrode coverages on the basis of the reductive desorption of the Au......Oligonucleotides modified by a hexamethylene linker group adsorb on gold electrodes via Au-S bond formation. We have obtained novel data for adsorption of thiol-modified (HS) single-strand HS-10A and double-stranded HS-10AT oligonucleotides and for analogous thiol-free 10A (A = adenine) and 10T (T......-S bond. The coverage is high and in keeping with dense monolayers of adsorbed HS-10A and HS-10AT in an upright or tilted orientation, with the oligonucleotide backbone repelled from the strongly negatively charged electrode surface. Adsorbed thiol-free 10A only gives aAu(111)-reconstruction peak, while...

  11. Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

    Science.gov (United States)

    Yokota, Toshifumi; Wood, Matthew J. A.

    2013-01-01

    Duchenne muscular dystrophy (DMD) is an incurable, X-linked progressive muscle degenerative disorder that results from the absence of dystrophin protein and leads to premature death in affected individuals due to respiratory and/or cardiac failure typically by age of 30. Very recently the exciting prospect of an effective oligonucleotide therapy has emerged which restores dystrophin protein expression to affected tissues in DMD patients with highly promising data from a series of clinical trials. This therapeutic approach is highly mutation specific and thus is personalised. Therefore DMD has emerged as a model genetic disorder for understanding and overcoming of the challenges of developing personalised genetic medicines. One of the greatest weaknesses of the current oligonucleotide approach is that it is a mutation-specific therapy. To address this limitation, we have recently demonstrated that exons 45–55 skipping therapy has the potential to treat clusters of mutations that cause DMD, which could significantly reduce the number of compounds that would need to be developed in order to successfully treat all DMD patients. Here we discuss and review the latest preclinical work in this area as well as a variety of accompanying issues, including efficacy and potential toxicity of antisense oligonucleotides, prior to human clinical trials. PMID:23984357

  12. Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Yoshitsugu Aoki

    2013-01-01

    Full Text Available Duchenne muscular dystrophy (DMD is an incurable, X-linked progressive muscle degenerative disorder that results from the absence of dystrophin protein and leads to premature death in affected individuals due to respiratory and/or cardiac failure typically by age of 30. Very recently the exciting prospect of an effective oligonucleotide therapy has emerged which restores dystrophin protein expression to affected tissues in DMD patients with highly promising data from a series of clinical trials. This therapeutic approach is highly mutation specific and thus is personalised. Therefore DMD has emerged as a model genetic disorder for understanding and overcoming of the challenges of developing personalised genetic medicines. One of the greatest weaknesses of the current oligonucleotide approach is that it is a mutation-specific therapy. To address this limitation, we have recently demonstrated that exons 45–55 skipping therapy has the potential to treat clusters of mutations that cause DMD, which could significantly reduce the number of compounds that would need to be developed in order to successfully treat all DMD patients. Here we discuss and review the latest preclinical work in this area as well as a variety of accompanying issues, including efficacy and potential toxicity of antisense oligonucleotides, prior to human clinical trials.

  13. High yield combustion synthesis of nanomagnesia and its application for fluoride removal.

    Science.gov (United States)

    Maliyekkal, Shihabudheen M; Anshup; Antony, K R; Pradeep, T

    2010-04-15

    We describe a novel combustion synthesis for the preparation of Nanomagnesia (NM) and its application in water purification. The synthesis is based on the self-propagated combustion of the magnesium nitrate trapped in cellulose fibers. Various characterization studies confirmed that NM formed is crystalline with high phase purity, and the particle size varied in the range of 3-7nm. The fluoride scavenging potential of this material was tested as a function of pH, contact time and adsorbent dose. The result showed that fluoride adsorption by NM is highly favorable and the capacity does not vary in the pH range usually encountered in groundwater. The effects of various co-existing ions usually found in drinking water, on fluoride removal were also investigated. Phosphate was the greatest competitor for fluoride followed by bicarbonate. The presence of other ions studied did not affect the fluoride adsorption capacity of NM significantly. The adsorption kinetics followed pseudo-second-order equation and the equilibrium data are well predicted by Frendlich equation. Our experimental evidence shows that fluoride removal happened through isomorphic substitution of fluoride in brucite. A batch household defluoridation unit was developed using precipitation-sedimentation-filtration techniques, addressing the problems of high fluoride concentration as well as the problem of alkaline pH of the magnesia treated water. The method of synthesis reported here is advantageous from the perspectives of small size of the nanoparticle, cost-effective recovery of the material and improvement in the fluoride adsorption capacity. Copyright 2010 Elsevier B.V. All rights reserved.

  14. High yield of synchronous lesions in referred patients with large lateral spreading colorectal tumors.

    Science.gov (United States)

    Bick, Benjamin L; Ponugoti, Prasanna L; Rex, Douglas K

    2017-01-01

    There are few data on the prevalence of synchronous colorectal lesions in patients who have large lateral spreading tumors (LLSTs). We sought to describe the rate of synchronous lesions found in patients who underwent endoscopic resection of large sessile adenomas and serrated lesions. This is a retrospective assessment of a prospectively created database of 728 consecutive patients with resected LLSTs who underwent complete clearing of the colon during 2 colonoscopies by a single expert endoscopist. The 728 patients with resected LLSTs and complete clearing had 4578 synchronous lesions, including 584 patients (80.2%) with at least 1 synchronous conventional adenoma, 132 (18.1%) with at least 1 synchronous conventional adenoma ≥ 20 mm in size, 294 (40.4%) with at least 1 synchronous advanced conventional adenoma, and 6 patients with a synchronous lesion with cancer. Patients with an index large sessile conventional adenoma compared with those with an index large serrated lesion had on average more synchronous conventional adenomas (4.8 vs 2.9, P = .001) and fewer synchronous serrated lesions (1.4 vs 4.5, P < .001). Of the 97 patients with a serrated class index lesion, 28 (28.9%) met criteria for serrated polyposis. There is a very high prevalence of synchronous lesions, including other large and advanced synchronous lesions, in patients with flat or sessile conventional adenomas and serrated colorectal polyps. Patients with LLSTs in the colon need detailed clearing of the rest of the colon. Patients referred for endoscopic resection of serrated lesions ≥ 20 mm have a very high prevalence of serrated polyposis. This study has potential implications for further stratification of high-risk patient groups in postpolypectomy surveillance guidelines. Copyright © 2017. Published by Elsevier Inc.

  15. High-yield synthesis of brookite TiO.sub.2 nanoparticles

    Science.gov (United States)

    Huber, Dale L [Albuquerque, NM; Monson, Todd C [Albuquerque, NM

    2011-05-17

    A method for forming non-agglomerated brookite TiO.sub.2 nanoparticles without the use of expensive organic surfactants or high temperature processing. Embodiments of this invention use titanium isopropoxide as the titanium precursor and isopropanol as both the solvent and ligand for ligand-stabilized brookite-phase titania. Isopropanol molecules serve as the ligands interacting with the titania surfaces that stabilize the titania nanoparticles. The isopropanol ligands can be exchanged with other alcohols and other ligands during or after the nanoparticle formation reaction.

  16. Extracting DNA from 'jaws': High yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Morgan, J. A T; Maher, S. L.

    2017-01-01

    Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant...... archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae...

  17. Nuclear Engineering of Microalgae for High Yield Secretion of Recombinant Proteins

    DEFF Research Database (Denmark)

    Ramos Martinez, Erick Miguel

    Photosynthetic microorganism like microalgae and cyanobacteria are considered as emerging biotechnology platforms for production of recombinant proteins and other high-value biomolecules with a wide range of applications. Moreover, microalgae offer significant advantages compared with other...... the potential of microalgae as a cell factory for secretion of recombinant proteins. The second research project presented in this thesis aimed to establish a new robust method to allow in vivo measurements of metabolic enzyme activities in cyanobacteria, with a hope that the method would facilitate further...

  18. High-yield isolation of extracellular vesicles using aqueous two-phase system

    Science.gov (United States)

    Shin, Hyunwoo; Han, Chungmin; Labuz, Joseph M.; Kim, Jiyoon; Kim, Jongmin; Cho, Siwoo; Gho, Yong Song; Takayama, Shuichi; Park, Jaesung

    2015-01-01

    Extracellular vesicles (EVs) such as exosomes and microvesicles released from cells are potential biomarkers for blood-based diagnostic applications. To exploit EVs as diagnostic biomarkers, an effective pre-analytical process is necessary. However, recent studies performed with blood-borne EVs have been hindered by the lack of effective purification strategies. In this study, an efficient EV isolation method was developed by using polyethylene glycol/dextran aqueous two phase system (ATPS). This method provides high EV recovery efficiency (~70%) in a short time (~15 min). Consequently, it can significantly increase the diagnostic applicability of EVs. PMID:26271727

  19. High Photoluminescence Quantum Yield in Band Gap Tunable Bromide Containing Mixed Halide Perovskites

    OpenAIRE

    Carolin M. Sutter-Fella Yanbo Li Matin Amani Joel W. Ager III Francesca M. Toma; Eli Yablonovitch Ian D. Sharp and Ali Javey

    2016-01-01

    Hybrid organic–inorganic halide perovskite based semiconductor materials are attractive for use in a wide range of optoelectronic devices because they combine the advantages of suitable optoelectronic attributes and simultaneously low cost solution processability. Here we present a two step low pressure vapor assisted solution process to grow high quality homogeneous CH3NH3PbI3–xBrx perovskite films over the full band gap range of 1.6–2.3 eV. Photoluminescence light in versus light out charac...

  20. High yields of hydrogen production from methanol steam reforming with a cross-U type reactor.

    Science.gov (United States)

    Zhang, Shubin; Zhang, Yufeng; Chen, Junyu; Zhang, Xuelin; Liu, Xiaowei

    2017-01-01

    This paper presents a numerical and experimental study on the performance of a methanol steam reformer integrated with a hydrogen/air combustion reactor for hydrogen production. A CFD-based 3D model with mass and momentum transport and temperature characteristics is established. The simulation results show that better performance is achieved in the cross-U type reactor compared to either a tubular reactor or a parallel-U type reactor because of more effective heat transfer characteristics. Furthermore, Cu-based micro reformers of both cross-U and parallel-U type reactors are designed, fabricated and tested for experimental validation. Under the same condition for reforming and combustion, the results demonstrate that higher methanol conversion is achievable in cross-U type reactor. However, it is also found in cross-U type reactor that methanol reforming selectivity is the lowest due to the decreased water gas shift reaction under high temperature, thereby carbon monoxide concentration is increased. Furthermore, the reformed gas generated from the reactors is fed into a high temperature proton exchange membrane fuel cell (PEMFC). In the test of discharging for 4 h, the fuel cell fed by cross-U type reactor exhibits the most stable performance.

  1. High yields of hydrogen production from methanol steam reforming with a cross-U type reactor.

    Directory of Open Access Journals (Sweden)

    Shubin Zhang

    Full Text Available This paper presents a numerical and experimental study on the performance of a methanol steam reformer integrated with a hydrogen/air combustion reactor for hydrogen production. A CFD-based 3D model with mass and momentum transport and temperature characteristics is established. The simulation results show that better performance is achieved in the cross-U type reactor compared to either a tubular reactor or a parallel-U type reactor because of more effective heat transfer characteristics. Furthermore, Cu-based micro reformers of both cross-U and parallel-U type reactors are designed, fabricated and tested for experimental validation. Under the same condition for reforming and combustion, the results demonstrate that higher methanol conversion is achievable in cross-U type reactor. However, it is also found in cross-U type reactor that methanol reforming selectivity is the lowest due to the decreased water gas shift reaction under high temperature, thereby carbon monoxide concentration is increased. Furthermore, the reformed gas generated from the reactors is fed into a high temperature proton exchange membrane fuel cell (PEMFC. In the test of discharging for 4 h, the fuel cell fed by cross-U type reactor exhibits the most stable performance.

  2. High yields of hydrogen production from methanol steam reforming with a cross-U type reactor

    Science.gov (United States)

    Zhang, Shubin; Chen, Junyu; Zhang, Xuelin; Liu, Xiaowei

    2017-01-01

    This paper presents a numerical and experimental study on the performance of a methanol steam reformer integrated with a hydrogen/air combustion reactor for hydrogen production. A CFD-based 3D model with mass and momentum transport and temperature characteristics is established. The simulation results show that better performance is achieved in the cross-U type reactor compared to either a tubular reactor or a parallel-U type reactor because of more effective heat transfer characteristics. Furthermore, Cu-based micro reformers of both cross-U and parallel-U type reactors are designed, fabricated and tested for experimental validation. Under the same condition for reforming and combustion, the results demonstrate that higher methanol conversion is achievable in cross-U type reactor. However, it is also found in cross-U type reactor that methanol reforming selectivity is the lowest due to the decreased water gas shift reaction under high temperature, thereby carbon monoxide concentration is increased. Furthermore, the reformed gas generated from the reactors is fed into a high temperature proton exchange membrane fuel cell (PEMFC). In the test of discharging for 4 h, the fuel cell fed by cross-U type reactor exhibits the most stable performance. PMID:29121067

  3. Simple room-temperature preparation of high-yield large-area graphene oxide.

    Science.gov (United States)

    Huang, N M; Lim, H N; Chia, C H; Yarmo, M A; Muhamad, M R

    2011-01-01

    Graphene has attracted much attention from researchers due to its interesting mechanical, electrochemical, and electronic properties. It has many potential applications such as polymer filler, sensor, energy conversion, and energy storage devices. Graphene-based nanocomposites are under an intense spotlight amongst researchers. A large amount of graphene is required for preparation of such samples. Lately, graphene-based materials have been the target for fundamental life science investigations. Despite graphene being a much sought-after raw material, the drawbacks in the preparation of graphene are that it is a challenge amongst researchers to produce this material in a scalable quantity and that there is a concern about its safety. Thus, a simple and efficient method for the preparation of graphene oxide (GO) is greatly desired to address these problems. In this work, one-pot chemical oxidation of graphite was carried out at room temperature for the preparation of large-area GO with ~100% conversion. This high-conversion preparation of large-area GO was achieved using a simplified Hummer's method from large graphite flakes (an average flake size of 500 μm). It was found that a high degree of oxidation of graphite could be realized by stirring graphite in a mixture of acids and potassium permanganate, resulting in GO with large lateral dimension and area, which could reach up to 120 μm and ~8000 μm(2), respectively. The simplified Hummer's method provides a facile approach for the preparation of large-area GO.

  4. High biohydrogen yielding Clostridium sp. DMHC-10 isolated from sludge of distillery waste treatment plant

    Energy Technology Data Exchange (ETDEWEB)

    Kamalaskar, Leena B.; Dhakephalkar, P.K.; Meher, K.K.; Ranade, D.R. [Microbial Sciences Division, Agharkar Research Institute, G.G. Agarkar Road, Pune 411004 (India)

    2010-10-15

    A mesophilic high hydrogen producing strain DMHC-10 was isolated from a lab scale anaerobic reactor being operated on distillery wastewater for hydrogen production. DMHC-10 was identified as Clostridium sp. on the basis of 16S rRNA gene sequencing. Various medium components (carbon and nitrogen sources) and environmental factors (initial pH, temperature of incubation) were optimized for hydrogen production by Clostridium sp. DMHC-10. The strain, in late exponential growth phase, showed maximum hydrogen production (3.35 mol-H{sub 2} mol{sup -1} glucose utilized) at 37 C, pH 5.0 in a medium supplemented with organic nitrogen source. Butyric acid to acetic acid ratio was ca. 2.3. Hydrogen production declined when organic nitrogen was replaced with inorganic nitrogen. (author)

  5. Simple room-temperature preparation of high-yield large-area graphene oxide

    Science.gov (United States)

    Huang, NM; Lim, HN; Chia, CH; Yarmo, MA; Muhamad, MR

    2011-01-01

    Graphene has attracted much attention from researchers due to its interesting mechanical, electrochemical, and electronic properties. It has many potential applications such as polymer filler, sensor, energy conversion, and energy storage devices. Graphene-based nanocomposites are under an intense spotlight amongst researchers. A large amount of graphene is required for preparation of such samples. Lately, graphene-based materials have been the target for fundamental life science investigations. Despite graphene being a much sought-after raw material, the drawbacks in the preparation of graphene are that it is a challenge amongst researchers to produce this material in a scalable quantity and that there is a concern about its safety. Thus, a simple and efficient method for the preparation of graphene oxide (GO) is greatly desired to address these problems. In this work, one-pot chemical oxidation of graphite was carried out at room temperature for the preparation of large-area GO with ~100% conversion. This high-conversion preparation of large-area GO was achieved using a simplified Hummer’s method from large graphite flakes (an average flake size of 500 μm). It was found that a high degree of oxidation of graphite could be realized by stirring graphite in a mixture of acids and potassium permanganate, resulting in GO with large lateral dimension and area, which could reach up to 120 μm and ~8000 μm2, respectively. The simplified Hummer’s method provides a facile approach for the preparation of large-area GO. PMID:22267928

  6. In silico screening based on predictive algorithms as a design tool for exon skipping oligonucleotides in Duchenne muscular dystrophy.

    Science.gov (United States)

    Echigoya, Yusuke; Mouly, Vincent; Garcia, Luis; Yokota, Toshifumi; Duddy, William

    2015-01-01

    The use of antisense 'splice-switching' oligonucleotides to induce exon skipping represents a potential therapeutic approach to various human genetic diseases. It has achieved greatest maturity in exon skipping of the dystrophin transcript in Duchenne muscular dystrophy (DMD), for which several clinical trials are completed or ongoing, and a large body of data exists describing tested oligonucleotides and their efficacy. The rational design of an exon skipping oligonucleotide involves the choice of an antisense sequence, usually between 15 and 32 nucleotides, targeting the exon that is to be skipped. Although parameters describing the target site can be computationally estimated and several have been identified to correlate with efficacy, methods to predict efficacy are limited. Here, an in silico pre-screening approach is proposed, based on predictive statistical modelling. Previous DMD data were compiled together and, for each oligonucleotide, some 60 descriptors were considered. Statistical modelling approaches were applied to derive algorithms that predict exon skipping for a given target site. We confirmed (1) the binding energetics of the oligonucleotide to the RNA, and (2) the distance in bases of the target site from the splice acceptor site, as the two most predictive parameters, and we included these and several other parameters (while discounting many) into an in silico screening process, based on their capacity to predict high or low efficacy in either phosphorodiamidate morpholino oligomers (89% correctly predicted) and/or 2'O Methyl RNA oligonucleotides (76% correctly predicted). Predictions correlated strongly with in vitro testing for sixteen de novo PMO sequences targeting various positions on DMD exons 44 (R² 0.89) and 53 (R² 0.89), one of which represents a potential novel candidate for clinical trials. We provide these algorithms together with a computational tool that facilitates screening to predict exon skipping efficacy at each position of

  7. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies

    Science.gov (United States)

    Van Blarcom, Thomas; Melton, Zea; Cheung, Wai Ling; Wagstrom, Chris; McDonough, Dan; Valle Oseguera, Cendy; Ding, Sheng; Rossi, Andrea; Potluri, Shobha; Sundar, Purnima; Sirota, Marina; Yan, Yu; Jones, Jeffrey; Roe-Zurz, Zygy; Srivatsa Srinivasan, Surabhi; Zhai, Wenwu; Pons, Jaume; Rajpal, Arvind; Chaparro-Riggers, Javier

    2018-01-01

    ABSTRACT The commercial success of bispecific antibodies generally has been hindered by the complexities associated with generating appropriate molecules for both research scale and large scale manufacturing purposes. Bispecific IgG (BsIgG) based on two antibodies that use an identical common light chain can be combined with a minimal set of Fc mutations to drive heavy chain heterodimerization in order to address these challenges. However, the facile generation of common light chain antibodies with properties similar to traditional monoclonal antibodies has not been demonstrated and they have only been used sparingly. Here, we describe the design of a synthetic human antibody library based on common light chains to generate antibodies with biochemical and biophysical properties that are indistinguishable to traditional therapeutic monoclonal antibodies. We used this library to generate diverse panels of well-behaved, high affinity antibodies toward a variety of epitopes across multiple antigens, including mouse 4-1BB, a therapeutically important T cell costimulatory receptor. Over 200 BsIgG toward 4-1BB were generated using an automated purification method we developed that enables milligram-scale production of BsIgG. This approach allowed us to identify antibodies with a wide range of agonistic activity that are being used to further investigate the therapeutic potential of antibodies targeting one or more epitopes of 4-1BB. PMID:29227213

  8. Evaluation of low-cost cathode catalysts for high yield biohydrogen production in microbial electrolysis cell.

    Science.gov (United States)

    Wang, L; Chen, Y; Ye, Y; Lu, B; Zhu, S; Shen, S

    2011-01-01

    As an ideal fuel due to the advantages of no pollution, high combustion heat and abundant sources, hydrogen gas can be produced from organic matter through the electrohydrogenesis process in microbial electrolysis cells. But in many MECs, platinum is often used as catalyst, which limits the practical applications of MECs. To reduce the cost of the MECs, Ni-based alloy cathodes were developed by electrodepositing. In this paper hydrogen production using Ni-W-P cathode was studied for the first time in a single-chamber membrane-free MEC. At an applied voltage of 0.9 V, MECs with Ni-W-P cathodes obtained a hydrogen production rate of 1.09 m3/m3/day with an cathodic hydrogen recovery of 74%, a Coulombic efficiency of 56% and an electrical energy efficiency relative to electrical input of 139%, which was the best result of reports in this study. The Ni-W-P cathode demonstrated a better electrocatalytic activity than the Ni-Ce-P cathode and achieved a comparable performance to the Pt cathode in terms of hydrogen production rate, Coulombic efficiency, cathodic hydrogen recovery and electrical energy efficiency at 0.9 V.

  9. Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

    Energy Technology Data Exchange (ETDEWEB)

    Su, J.; Hu, C.; Yan, X.; Jin, Y.; Chen, Z.; Guan, Q.; Wang, Y.; Zhong, D.; Jansson, Georg C.; Wang, F.; Schnrer, Anna; Sun, Chuanxin

    2015-07-22

    Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7–17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25–100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades4. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement5. Despite proposed strategies to increase rice productivity and reduce methane emissions4,6, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2, conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane

  10. Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice.

    Science.gov (United States)

    Su, J; Hu, C; Yan, X; Jin, Y; Chen, Z; Guan, Q; Wang, Y; Zhong, D; Jansson, C; Wang, F; Schnürer, A; Sun, C

    2015-07-30

    Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7-17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25-100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement. Despite proposed strategies to increase rice productivity and reduce methane emissions, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased

  11. The effect of high-sugar grass on predicted nitrogen excretion and milk yield simulated using a dynamic model.

    Science.gov (United States)

    Ellis, J L; Dijkstra, J; Bannink, A; Parsons, A J; Rasmussen, S; Edwards, G R; Kebreab, E; France, J

    2011-06-01

    High-sugar grass varieties have received considerable attention for their potential to reduce nitrogen (N) excretion and increase milk yield in cattle. However, considerable variation exists in the magnitude of response in published results. The purpose of this study is to explain the variation in response using a dynamic mechanistic model to predict observed N and milk yield results from the literature, and from simulated data. Examined effects were (1) water-soluble carbohydrate [WSC; g/kg of dry matter (DM)] increase; (2) change in crude protein (CP) and neutral detergent fiber (NDF) content of the plant with WSC increase; and (3) the level of N fertilization. The database for evaluation of model N and milk yield predictions consisted of 4 published studies with 28 treatment means for which high-sugar grasses were being evaluated. Water-soluble carbohydrate content of the diets ranged from 95 to 248 g/kg of DM, CP content ranged from 115 to 263 g/kg of DM, and the NDF content ranged from 400 to 568 g/kg of DM. Urine N, milk N, and total N excretion were predicted well by the model and followed the directional pattern of observed values within each study. Simulation results showed that the N utilization ratio increased as the WSC content of the diet increased, but to varying degrees depending on the grass scenario examined. The greatest benefit in terms of N utilization ratio and urine N levels were seen when the WSC content of grass increased at the expense of CP, followed by a 50:50 CP and NDF mix, followed by a trade for NDF. Simulated milk yield decreased slightly when WSC increased at the expense of CP, increased slightly when it increased at the expense of a CP and NDF mix, and increased most when WSC increased at the expense of NDF. Results were amplified slightly under conditions of low-N fertilization and in the absence of grain feeding. Overall, modeling is useful as an explanatory tool. The variation from results in the literature with high-WSC grass

  12. Linear model for fast background subtraction in oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Barkema Gerard T

    2009-11-01

    Full Text Available Abstract Background One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. Results We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1 Correlated intensities between neighboring features in the chip and 2 sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. Conclusion The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.

  13. Chimeric Antisense Oligonucleotide Conjugated to α-Tocopherol

    Directory of Open Access Journals (Sweden)

    Tomoko Nishina

    2015-01-01

    Full Text Available We developed an efficient system for delivering short interfering RNA (siRNA to the liver by using α-tocopherol conjugation. The α-tocopherol–conjugated siRNA was effective and safe for RNA interference–mediated gene silencing in vivo. In contrast, when the 13-mer LNA (locked nucleic acid-DNA gapmer antisense oligonucleotide (ASO was directly conjugated with α-tocopherol it showed markedly reduced silencing activity in mouse liver. Here, therefore, we tried to extend the 5′-end of the ASO sequence by using 5′-α-tocopherol–conjugated 4- to 7-mers of unlocked nucleic acid (UNA as a “second wing.” Intravenous injection of mice with this α-tocopherol–conjugated chimeric ASO achieved more potent silencing than ASO alone in the liver, suggesting increased delivery of the ASO to the liver. Within the cells, the UNA wing was cleaved or degraded and α-tocopherol was released from the 13-mer gapmer ASO, resulting in activation of the gapmer. The α-tocopherol–conjugated chimeric ASO showed high efficacy, with hepatic tropism, and was effective and safe for gene silencing in vivo. We have thus identified a new, effective LNA-DNA gapmer structure in which drug delivery system (DDS molecules are bound to ASO with UNA sequences.

  14. Global warming potential and greenhouse gas intensity in rice agriculture driven by high yields and nitrogen use efficiency

    Science.gov (United States)

    Zhang, Xiaoxu; Xu, Xin; Liu, Yinglie; Wang, Jinyang; Xiong, Zhengqin

    2016-05-01

    Our understanding of how global warming potential (GWP) and greenhouse gas intensity (GHGI) is affected by management practices aimed at food security with respect to rice agriculture remains limited. In the present study, a field experiment was conducted in China to evaluate the effects of integrated soil-crop system management (ISSM) on GWP and GHGI after accounting for carbon dioxide (CO2) equivalent emissions from all sources, including methane (CH4) and nitrous oxide (N2O) emissions, agrochemical inputs and farm operations and sinks (i.e., soil organic carbon sequestration). The ISSM mainly consisted of different nitrogen (N) fertilization rates and split, manure, Zn and Na2SiO3 fertilization and planting density for the improvement of rice yield and agronomic nitrogen use efficiency (NUE). Four ISSM scenarios consisting of different chemical N rates relative to the local farmers' practice (FP) rate were carried out, namely, ISSM-N1 (25 % reduction), ISSM-N2 (10 % reduction), ISSM-N3 (FP rate) and ISSM-N4 (25 % increase). The results showed that compared with the FP, the four ISSM scenarios significantly increased the rice yields by 10, 16, 28 and 41 % and the agronomic NUE by 75, 67, 35 and 40 %, respectively. In addition, compared with the FP, the ISSM-N1 and ISSM-N2 scenarios significantly reduced the GHGI by 14 and 18 %, respectively, despite similar GWPs. The ISSM-N3 and ISSM-N4 scenarios remarkably increased the GWP and GHGI by an average of 69 and 39 %, respectively. In conclusion, the ISSM strategies are promising for both food security and environmental protection, and the ISSM scenario of ISSM-N2 is the optimal strategy to realize high yields and high NUE together with low environmental impacts for this agricultural rice field.

  15. Optimal barn characteristics for high-yielding Holstein cows as derived by a new heat-stress model.

    Science.gov (United States)

    Shoshani, E; Hetzroni, A

    2013-01-01

    Meticulous planning is required to minimize heat-stress conditions in barns. The objective of this study was to determine optimum barn characteristics for high-yielding dairy cows under Israeli (Mediterranean) summer ambient conditions, by using a new stress model that takes ambient temperature, relative humidity and wind velocity into account. During the summers of 2004 and 2005, three meteorological stations were alternately installed in 39 barns: two stations inside the barn at the prevailing downwind direction, and a third station outside the upwind end of the barn. Ambient temperature, relative humidity, wind speed and direction were measured and recorded every 10 min for 3 to 5 consecutive days at each barn in turn. The data were collected at different geographical and climatic conditions. Therefore, the data collected by an outside station were used as covariates. A heat-stress model was used to determine the threshold temperature (THRT) at which a cow begins to increase its respiratory rate; THRT was the response variable in the statistical model. The THRT model takes in account assumed values of a cow's physiological characteristics: daily milk yield of 45 kg, containing 3.5% fat, and 3 mm fur depth. The independent variables were: orientation, barn type, roof slope, roof ridge, marginal height, roof type (fixed or sliding) and barn width. Results showed that the optimal barn for high-yielding cows is the loose-housing type, oriented with its long axis perpendicular to the prevailing wind direction. Advantageous to the design would be an open ridge or pagoda with marginal height of over 4.7 m for north-south orientation and over 5 m for east-west orientation, roof slope over 11%, and barn width between 43 and 51 m for north-south orientation but lower than 42 m for east-west orientation. A sliding roof was also found to be an excellent solution when outside yards are banned by environmental regulations.

  16. Effect of dietary probiotic and high stocking density on the performance, carcass yield, gut microflora, and stress indicators of broilers.

    Science.gov (United States)

    Cengiz, Özcan; Köksal, Bekir H; Tatlı, Onur; Sevim, Ömer; Ahsan, Umair; Üner, Aykut G; Ulutaş, Pınar A; Beyaz, Devrim; Büyükyörük, Sadık; Yakan, Akın; Önol, Ahmet G

    2015-10-01

    A study was carried out to evaluate the effect of dietary probiotic supplementation and stocking density on the performance, relative carcass yield, gut microflora, and stress markers of broilers. One-day-old Ross 308 male broiler chickens (n = 480) were allocated to 4 experimental groups for 42 d. Each treatment had 8 replicates of 15 chicks each. Two groups were subjected to a high stocking density (HSD) of 20 birds/m² and the other 2 groups were kept at low stocking density (LSD) of 10 birds/m². A basal diet supplemented with probiotic 1 and 0.5 g/kg of diet (in starter and finisher diets, respectively) was fed to 2 treatments, one with HSD and the other with LSD, thereby making a 2 × 2 factorial arrangement. There was no interaction between stocking density (LSD and HSD) and dietary probiotic (supplemented and unsupplemented) for all the variables. Feed intake and weight gain were significantly low and feed conversion ratio was poor in broilers at HSD. Dietary probiotic significantly enhanced the feed intake and weight gain in starter phase only. Dietary probiotic supplementation had no effect (P > 0.05) on total aerobs, Salmonella sp., and Lactobacilli populations in the intestines of broilers. However, HSD reduced the Lactobacilli population only (P < 0.05). Relative breast yields were significantly higher in broilers reared at LSD than HSD. Thigh meat yield was higher in broilers in HSD group compared to LSD. Dietary probiotic did not affect the relative carcass yield and weight of lymphoid organs. Serum malondialdehyde, corticosterone, nitric oxide, and plasma heterophil:lymphocyte ratio were not affected either by stocking density or dietary probiotic supplementation. In conclusion, HSD negatively affected the performance and intestinal Lactobacilli population of broilers only, whereas probiotic supplementation enhanced the performance of broilers during the starter phase only. Total aerobes, Salmonella, Lactobacilli carcass yield, and stress indicators

  17. High yield derivation of enriched glutamatergic neurons from suspension-cultured mouse ESCs for neurotoxicology research

    Directory of Open Access Journals (Sweden)

    Hubbard Kyle S

    2012-10-01

    . Conclusions These findings demonstrate a cost-effective, scalable and flexible method to produce a highly enriched glutamatergic neuron population. The functional characterization of pathophysiological responses to neurotropic toxins and the compatibility with multi-well plating formats were used to demonstrate the suitability of ESNs as a discovery platform for molecular mechanisms of action, moderate-throughput analytical approaches and diagnostic screening. Furthermore, for the first time we demonstrate a cell-based model that is sensitive to all seven BoNT serotypes with EC50 values comparable to those reported in primary neuron populations. These data providing compelling evidence that ESNs offer a neuromimetic platform suitable for the evaluation of molecular mechanisms of neurotoxicity.

  18. Metallo-Phthalocyanine Near-IR Fluorophores: Oligonucleotide Conjugates and Their Applications in PCR Assays

    Science.gov (United States)

    Nesterova, Irina V.; Verdree, Vera T.; Pakhomov, Serhii; Strickler, Karen L.; Allen, Michael W.; Hammer, Robert P.; Soper, Steven A.

    2011-01-01

    Water soluble, metallo-pthalocyanine (MPc) near-IR fluorophores were designed, synthesized, and evaluated as highly stable and sensitive reporters for fluorescence assays. Their conjugation to oligonucleotides was achieved via succinimidyl ester-amino coupling chemistry with the conditions for conjugation extensively examined and optimized. In addition, various conjugate purification and isolation techniques were evaluated as well. Results showed that under proper conditions and following purification using reverse-phase ion-pair chromatography, labeling efficiencies near 80% could be achieved using ZnPc (Zn phthalocyanine) as the labeling fluorophore. Absorption and fluorescence spectra accumulated for the conjugates indicated that the intrinsic fluorescence properties of the MPc’s were not significantly altered by covalent attachment to oligonucleotides. As an example of the utility of MPc reporters, we used the MPc–oligonucleotide conjugates as primers for PCR (polymerase chain reaction) amplifications with the products sorted via electrophoresis and detected using near-IR fluorescence (λex = 680 nm). The MPc dyes were found to be more chemically stable under typical thermal cycling conditions used for PCR compared to the carbocyanine-based near-IR reporter systems typically used and produced single and narrow bands in the electrophoretic traces, indicative of producing a single PCR product during amplification. PMID:18030995

  19. Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides.

    Science.gov (United States)

    Tran, Tuan; Childs-Disney, Jessica L; Liu, Biao; Guan, Lirui; Rzuczek, Suzanne; Disney, Matthew D

    2014-04-18

    We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)(exp)) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)(exp) toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)(exp) in vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)(exp)'s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2'-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide.

  20. Site-Selective Artificial Ribonucleases: Oligonucleotide Conjugates Containing Multiple Imidazole Residues in the Catalytic Domain

    Directory of Open Access Journals (Sweden)

    Natalia G. Beloglazova

    2011-01-01

    Full Text Available Design of site-selective artificial ribonucleases (aRNases is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond.

  1. Probe selection algorithm for oligonucleotide array-based medium-resolution genotyping.

    Science.gov (United States)

    Zhou, Y; Peng, S; Gao, H; Cheng, J

    2004-11-01

    Medium-resolution genotyping has the goal of distinguishing different subgroups instead of each element in a group. An oligonucleotide array provides an inexpensive, high-throughput method to identify differences in DNA sequence among individuals, which is fundamental for genotyping. As the cost and difficulty of designing and fabricating the oligonucleotide array dramatically increase with the number of probes used, it is therefore important to have a design with a minimum number of probes meeting the requirement of medium-resolution genotyping. The first algorithm for designing and selecting probes for oligonucleotide array-based medium-resolution typing is reported. The goal in deriving the algorithm was to select a minimum number of probes from a large probe set on the premise of minimum loss of resolution. The algorithm, which was based on entropy, conditional entropy and mutual information theory, was used to select the minimum number of probes from a large probe set. The algorithm was tested on a human leukocyte antigen (HLA) sequence data set Thirty probes were selected from 390 probes for HLA-A, and 60 probes were selected from 767 probes for HLA-B. Although the number of probes was reduced by almost ten times, the distinguishability was reduced only a little, by 0.45% (from 99.90% to 99.45%) for HLA-A and 0.27% (from 99.84% to 99.57%) for HLA-B, respectively. This is a satisfactory and practical result.

  2. The estimation of quantitative parameters of oligonucleotides immobilization on mica surface

    Science.gov (United States)

    Sharipov, T. I.; Bakhtizin, R. Z.

    2017-05-01

    Immobilization of nucleic acids on the surface of various materials is increasingly being used in research and some practical applications. Currently, the DNA chip technology is rapidly developing. The basis of the immobilization process can be both physical adsorption and chemisorption. A useful way to control the immobilization of nucleic acids on a surface is to use atomic force microscopy. It allows you to investigate the topography of the surface by its direct imaging with high resolution. Usually, to fix the DNA on the surface of mica are used cations which mediate the interaction between the mica surface and the DNA molecules. In our work we have developed a method for estimation of quantitative parameter of immobilization of oligonucleotides is their degree of aggregation depending on the fixation conditions on the surface of mica. The results on study of aggregation of oligonucleotides immobilized on mica surface will be presented. The single oligonucleotides molecules have been imaged clearly, whereas their surface areas have been calculated and calibration curve has been plotted.

  3. Structure/nuclease activity relationships of DNA cleavers based on cationic metalloporphyrin-oligonucleotide conjugates.

    Science.gov (United States)

    Mestre, B; Jakobs, A; Pratviel, G; Meunier, B

    1996-07-16

    The covalent attachment of a managanese-tris(methylpyridiniumyl)porphyrin entity to an antisense oligonucleotide allowed sequence-selective oxidative cleavage of DNA when the metalloporphyrin was activated by potassium monopersulfate (KHSO5). We prepared several structurally modified metallo-porphyrin-oligonucleotide conjugates in order to find out the most efficient compound for in vitro DNA cleavage. The nature and the length of the tether were modulated, the metalloporphyrin entity was modified (metal, ligand), and different ways of activation of the metalloporphyrin were assayed. We noticed that the location of the peptidic bond within the linker could greatly affect the cleavage efficiency of the different conjugates. We showed that the most efficient conjugate for oxidative DNA cleavage was a manganese tetracationic porphyrin-oligonucleotide compound. When the metalloporphyrin moiety was activated by a reducing agent in the presence of molecular oxygen, DNA cleavage was efficient at suitable concentrations of the reducing agent, in order to avoid the reduction of the activated DNA cleaver, a putative high-valent metal-oxo species, by the excess of reducing agent.

  4. Efficient surface patterning of oligonucleotides inside a glass capillary through oxime bond formation.

    Science.gov (United States)

    Dendane, Nabil; Hoang, Antoine; Guillard, Ludovic; Defrancq, Eric; Vinet, Françoise; Dumy, Pascal

    2007-01-01

    The efficient surface patterning of oligonucleotides was accomplished onto the inner wall of fused-silica capillary tubes as well as on the surface of glass slides through oxime bond formation. The robustness of the method was demonstrated by achieving the surface immobilization of up to three different oligonucleotide sequences inside the same capillary tube. The method involves the preparation of surfaces grafted with reactive aminooxy functionalities masked with the photocleavable protecting group, 2-(2-nitrophenyl) propyloxycarbonyl group (NPPOC). Briefly, NPPOC-aminooxy silane 1 was prepared and used to silanize the glass surfaces. The NPPOC group was cleaved under brief irradiation to unmask the reactive aminooxy group on surfaces. These reactive aminooxy groups were allowed to react with aldehyde-containing oligonucleotides to achieve an efficient surface immobilization. The advantage associated with the present approach is that it combines the high-coupling efficiency of oxime bond formation with the convenience associated with the use of photolabile groups. The present strategy thus offers an alternative approach for the immobilization of biomolecules in the microchannels of "labs on a chip" devices.

  5. A High-Yield Synthesis of Chalcopyrite CuInS2 Nanoparticles with Exceptional Size Control

    Directory of Open Access Journals (Sweden)

    Chivin Sun

    2009-01-01

    Full Text Available We report high-yield and efficient size-controlled syntheses of Chalcopyrite CuInS2 nanoparticles by decomposing molecular single source precursors (SSPs via microwave irradiation in the presence of 1,2-ethanedithiol at reaction temperatures as low as 100°C and times as short as 30 minutes. The nanoparticles sizes were 1.8 nm to 10.8 nm as reaction temperatures were varied from 100°C to 200°C with the bandgaps from 2.71 eV to 1.28 eV with good size control and high yields (64%–95%. The resulting nanoparticles were analyzed by XRD, UV-Vis, ICP-OES, XPS, SEM, EDS, and HRTEM. Titration studies by 1H NMR using SSP 1 with 1,2-ethanedithiol and benzyl mercaptan were conducted to elucidate the formation of Chalcopyrite CuInS2 nanoparticles.

  6. Microstructure and Mechanical Properties in Hot-Rolled Extra High-Yield-Strength Steel Plates for Offshore Structure and Shipbuilding

    Science.gov (United States)

    Liu, Dongsheng; Li, Qingliang; Emi, Toshihiko

    2011-05-01

    Key parameters for a thermomechanically controlled processing and accelerated cooling process (TMCP-AcC) were determined for integrated mass production to produce extra high-yield-strength microalloyed low carbon SiMnCrNiCu steel plates for offshore structure and bulk shipbuilding. Confocal scanning microscopy was used to make in-situ observations on the austenite grain growth during reheating. A Gleeble 3800 thermomechanical simulator was employed to investigate the flow stress behavior, static recrystallization (SRX) of austenite, and decomposition behavior of the TMCP conditioned austenite during continuous cooling. The Kocks-Mecking model was employed to describe the constitutive behavior, while the Johnson-Mehl-Avrami-Kolmogorov (JMAK) approach was used to predict the SRX kinetics. The effects of hot rolling schedule and AcC on microstructure and properties were investigated by test-scale rolling trials. The bridging between the laboratory observations and the process parameter determination to optimize the mass production was made by integrated industrial production trials on a set of a 5-m heavy plate mill equipped with an accelerated cooling system. Successful production of 60- and 50-mm-thick plates with yield strength in excess of 460 MPa and excellent toughness at low temperature (213 K (-60 °C)) in the parent metal and the simulated coarse-grained heat affected zone (CGHAZ) provides a useful integrated database for developing advanced high-strength steel plates via TMCP-AcC.

  7. One-step synthesis of high-yield biodiesel from waste cooking oils by a novel and highly methanol-tolerant immobilized lipase.

    Science.gov (United States)

    Wang, Xiumei; Qin, Xiaoli; Li, Daoming; Yang, Bo; Wang, Yonghua

    2017-07-01

    This study reported a novel immobilized MAS1 lipase from marine Streptomyces sp. strain W007 for synthesizing high-yield biodiesel from waste cooking oils (WCO) with one-step addition of methanol in a solvent-free system. Immobilized MAS1 lipase was selected for the transesterification reactions with one-step addition of methanol due to its much more higher biodiesel yield (89.50%) when compared with the other three commercial immobilized lipases (lipase retained approximately 70% of its initial activity after being used for four batch cycles. Finally, the obtained biodiesel was further characterized using FT-IR, 1 H and 13 C NMR spectroscopy. These findings indicated that immobilized MAS1 lipase is a promising catalyst for biodiesel production from WCO with one-step addition of methanol under high methanol concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Determination of NABE in urine of high-yield dairy cows in early lactation in conditions of moderate heat stress

    Directory of Open Access Journals (Sweden)

    Fratrić Natalija

    2010-01-01

    Full Text Available The work presents the results of investigations of the effect of moderate heat stress on the acidobasal status in high-yield dairy cows in early lactation. Improving performance in high-yield dairy cows increases their inclination toward metabolic disorders. The most likely to be affected is the acid-base balance, in particular when cows are exposed to heat stress. Investigations so far have shown that the taking of urine samples and their analysis is the best and fastest way to diagnose disorders in the acid-base balance. Investigations were carried out on 7 clinically healthy cows of the Holstein- Friesian breed in the phase of early lactation, 30 to 40 days (on days 30, 33 and 40 following calving during the summer period, during the month of July, when there were significant variations in daily and nightly temperatures. The cows were in the second and fourth lactation, the annual milk yield was 8000 L milk per cow. The average daily milk production in the early phase of lactation ranged from 35 to 40 L. The cows were fed mixed rations (TMR twice daily. Lucerne hay in limited quantities was given to the cows prior to the mixed feed ration. The ration for this animal category was optimized on the grounds of the daily milk production. The balance of cations and anions in the feed ration stood at 95 mEq/kg DM. The results clearly demonstrate the cows' response to moderate heat stress through the defense parameters in urine (urine pH, NABE (net-acid-base-excretion, acids, bases, ammonium ion (NH4. The determination of the kidney NABE yields more correct data than the urine pH on acidotic conditions. The results of examinations of the urine pH do not show any digressions from physiological values and are approximately the same in all cows during the investigated periods. Normal NABE values are from 100-200 mmol/L. Burdening with acid products results in a NABE range from 0-100mmol/L, and metabolic acidosis results in NAB<0 mmol/L. NABE in the cows

  9. Delivery of RNAi-Based Oligonucleotides by Electropermeabilization

    Directory of Open Access Journals (Sweden)

    Muriel Golzio

    2013-04-01

    Full Text Available For more than a decade, understanding of RNA interference (RNAi has been a growing field of interest. The potent gene silencing ability that small oligonucleotides have offers new perspectives for cancer therapeutics. One of the present limits is that many biological barriers exist for their efficient delivery into target cells or tissues. Electropermeabilization (EP is one of the physical methods successfully used to transfer small oligonucleotides into cells or tissues. EP consists in the direct application of calibrated electric pulses to cells or tissues that transiently permeabilize the plasma membranes, allowing efficient in vitro and in vivo. cytoplasmic delivery of exogenous molecules. The present review reports on the type of therapeutic RNAi-based oligonucleotides that can be electrotransferred, the mechanism(s of their electrotransfer and the technical settings for pre-clinical purposes.

  10. Current progress on aptamer-targeted oligonucleotide therapeutics

    Science.gov (United States)

    Dassie, Justin P; Giangrande, Paloma H

    2014-01-01

    Exploiting the power of the RNAi pathway through the use of therapeutic siRNA drugs has remarkable potential for treating a vast array of human disease conditions. However, difficulties in delivery of these and similar nucleic acid-based pharmacological agents to appropriate organs or tissues, remains a major impediment to their broad clinical application. Synthetic nucleic acid ligands (aptamers) have emerged as effective delivery vehicles for therapeutic oligonucleotides, including siRNAs. In this review, we summarize recent attractive developments in creatively employing cell-internalizing aptamers to deliver therapeutic oligonucleotides (e.g., siRNAs, miRNAs, anti-miRs and antisense oligos) to target cells. We also discuss advancements in aptamer-siRNA chimera technology, as well as, aptamer-functionalized nanoparticles for siRNA delivery. In addition, the challenges and future prospects of aptamer-targeted oligonucleotide drugs for clinical translation are further highlighted. PMID:24304250

  11. Challenges to oligonucleotides-based therapeutics for Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Goyenvalle Aurélie

    2011-02-01

    Full Text Available Abstract Antisense oligonucleotides are short nucleic acids designed to bind to specific messenger RNAs in order to modulate splicing patterns or inhibit protein translation. As such, they represent promising therapeutic tools for many disorders and have been actively developed for more than 20 years as a form of molecular medicine. Although significant progress has been made in developing these agents as drugs, they are yet not recognized as effective therapeutics and several hurdles remain to be overcome. Within the last few years, however, the prospect of successful oligonucleotides-based therapies has moved a step closer, in particular for Duchenne muscular dystrophy. Clinical trials have recently been conducted for this myopathy, where exon skipping is being used to achieve therapeutic outcomes. In this review, the recent developments and clinical trials using antisense oligonucleotides for Duchenne muscular dystrophy are discussed, with emphasis on the challenges ahead for this type of therapy, especially with regards to delivery and regulatory issues.

  12. Fast, high-yield synthesis of amphiphilic Ag nanoclusters and the sensing of Hg(2+) in environmental samples.

    Science.gov (United States)

    Xia, Nan; Yang, Jie; Wu, Zhikun

    2015-06-14

    We report the high-yield (74%) synthesis of Ag30(Capt)18 (abbreviated as Ag30) in a very time-saving fashion (half an hour). The cluster composition was determined by high-resolution mass spectrometry combined with TG analysis, and the structure was probed by 1D and 2D NMR. Interestingly, the nanoclusters can dissolve in water and methanol, as well as in most organic solvents such as ethanol, acetone, acetonitrile, dichloromethane and ethyl acetate with the assistance of acetic acid. Such a good solubility in a range of various polar solvents was not reported previously in nanoclusters' research and is important for applications. An important result from this work is that Ag30 can sense a low concentration of Hg(2+) in environmental samples (including lake water and soil solution), indicating that Ag30 can be a potential colorimetric probe for Hg(2+). The sensing mechanism was revealed to be related to the anti-galvanic reduction process.

  13. Freestanding carbon nanodots/poly (vinyl alcohol) films with high photoluminescent quantum yield realized by inverted-pyramid structure

    Science.gov (United States)

    Pang, Linna; Ba, Lixiang; Pan, Wei; Shen, Wenzhong

    2017-02-01

    Carbon nanodots (C-dots) have attracted great attention for their biocompatibility and strong tunable photoluminescence (PL). However, aggregation-induced PL quenching blocks their practical application in solid-state optoelectronics. Here, we report a luminescent C-dots freestanding film with a substantially enhanced high quantum yield (QY) of 72.3%. A facile template method, rather than complicate lithography and etching technique is proposed to fabricate the C-dots composite films with large-area (8 inch × 8 inch) ordered micro-scale inverted-pyramid patterns on the surface. The control experiment and theoretical analysis demonstrate the key success to QY enhancement lies in the separation of C-dots and the pattern of surface inverted-pyramid structure. This work realizes the QY enhancement simply by geometrical optics, not the chemical treatment of luminescent particles. It provides a general approach to fabricate large-area freestanding luminescent composite film with high QY.

  14. Luminescent carbon quantum dots with high quantum yield as a single white converter for white light emitting diodes

    Energy Technology Data Exchange (ETDEWEB)

    Feng, X. T.; Zhang, Y.; Liu, X. G., E-mail: liuxuguang@tyut.edu.cn [Key Laboratory of Interface Science and Engineering in Advanced Materials, Taiyuan University of Technology, Taiyuan 030024 (China); College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Zhang, F.; Wang, Y. L.; Yang, Y. Z., E-mail: yyztyut@126.com [Key Laboratory of Interface Science and Engineering in Advanced Materials, Taiyuan University of Technology, Taiyuan 030024 (China); Research Center on Advanced Materials Science and Technology, Taiyuan University of Technology, Taiyuan 030024 (China)

    2015-11-23

    Carbon quantum dots (CQDs) with high quantum yield (51.4%) were synthesized by a one-step hydrothermal method using thiosalicylic acid and ethylenediamine as precursor. The CQDs have the average diameter of 2.3 nm and possess excitation-independent emission wavelength in the range from 320 to 440 nm excitation. Under an ultraviolet (UV) excitation, the CQDs aqueous solutions emit bright blue fluorescence directly and exhibit broad emission with a high spectral component ratio of 67.4% (blue to red intensity to total intensity). We applied the CQDs as a single white-light converter for white light emitting diodes (WLEDs) using a UV-LED chip as the excitation light source. The resulted WLED shows superior performance with corresponding color temperature of 5227 K and the color coordinates of (0.34, 0.38) belonging to the white gamut.

  15. Effect of a single injection of cabergoline at dry off on udder characteristics in high-yielding dairy cows.

    Science.gov (United States)

    Bertulat, S; Isaka, N; de Prado, A; Lopez, A; Hetreau, T; Heuwieser, W

    2017-04-01

    In recent years, relationships between high milk yield at dry off, higher prevalence for new intramammary infections, and stress were evaluated. Considering increasing milk yield, dry off methods need to be refined to ensure udder health and animal welfare, especially in high-yielding dairy cows. The present work evaluated the effect of a single cabergoline injection (Velactis, Ceva Santé Animale, Libourne, France) at dry off on udder pressure, milk leakage, and signs of udder pain after dry off. A total of 234 high-yielding (≥16 kg of milk/d) dairy cows was enrolled 7 d before and followed up until 14 d after dry off. Cows were dried off without preparation (i.e., no feed change or intermittent milking before dry off) and treated with a single i.m. injection of 5.6 mg of cabergoline (n = 115) or placebo (n = 119) after last milking. Udder characteristics were measured 4 d before (i.e., before and after milking) and 1, 2, 3, 7, 10, and 14 d after dry off. Udder pressure was evaluated utilizing a hand-held dynamometer. Milk leakage and signs of udder pain were noted as binary variables. Whereas udder pressure baseline values after last milking did not differ between treatment groups (0.541 ± 0.15 kg), cabergoline significantly reduced udder pressure in primiparous but not in multiparous cows after dry off. Differences between cabergoline- and placebo-treated primiparous cows could be evaluated until 3 d after dry off. The first day after dry off, udder pressure in placebo- and cabergoline-treated cows increased by 115% and 42.3%, respectively. Whereas pressure values in placebo cows were highest on the first day after dry off (1.16 ± 0.61 kg) and slowly decreased afterward, udder pressure in cows treated with cabergoline had a slower increase and peak only 2 d after dry off (0.94 ± 0.44 kg). Furthermore, cabergoline caused a reduction of milk leakage, a known factor for new intramammary infections. Only 11.3% of cows treated with cabergoline showed milk

  16. Immunomodulation of hematological malignancies using oligonucleotides based-nanomedicines.

    Science.gov (United States)

    Hazan-Halevy, Inbal; Landesman-Milo, Dalit; Rosenblum, Daniel; Mizrahy, Shoshy; Ng, Brandon D; Peer, Dan

    2016-12-28

    Hematological malignancies are a group of diseases characterized by clonal proliferation of blood-forming cells. Malignant blood cells are classified as myeloid or lymphoid cells depending on their stem cell origin. Lymphoid malignancies are characterized by lymphocyte accumulation in the blood stream, in the bone marrow, or in lymphatic nodes and organs. Several of these diseases are associated with chromosomal translocations, which cause gene fusion and amplification of expression, while others are characterized with aberrant expression of oncogenes. Overall, these genes play a major role in development and maintenance of malignant clones. The discovery of antisense oligonucleotides and RNA interference (RNAi) mechanisms offer new tools to specifically manipulate gene expression. Systemic delivery of inhibitory oligonucleotides molecules for manipulation of gene expression in lymphocytes holds a great potential for facilitating the development of an oligonucleotides -based therapy platform for lymphoid blood cancer. However, lymphocytes are among the most difficult targets for oligonucleotides delivery, as they are resistant to conventional transfection reagents and are dispersed throughout the body, making it difficult to successfully localize or deliver oligonucleotides payloads via systemic administration. In this review, we will survey the latest progress in the field of oligonucleotides based nanomedicine in the heterogeneous group of hematological malignancies with special emphasis on RNA based strategies. We will describe the most advanced non-viral nanocarriers for RNA delivery to malignant blood cells. We will also discuss targeted strategies for cell specific delivery of RNA molecules using nanoparticles and the therapeutic benefit of manipulating gene function in hematological malignancies. Finally, we will focus on the ex vivo, in vivo, and clinical trial strategies, that are currently under development in hematological malignancies - strategies that

  17. Hydrated electrons react with high specificity with cisplatin bound to single-stranded DNA.

    Science.gov (United States)

    Behmand, B; Cloutier, P; Girouard, S; Wagner, J R; Sanche, L; Hunting, D J

    2013-12-19

    Short oligonucleotides TTTTTGTGTTT and TTTTTTTGTTT in solution with and without cisplatin (cisPt) bound to the guanine bases were irradiated with γ-rays at doses varying from 0 to 2500 Gy. To determine the effect of hydrated electrons from water radiolysis on the oligonucleotides, we quenched (•)OH radicals with ethylenediaminetetraacetic acid (EDTA) and displaced oxygen, which reacts with hydrated electrons, by bubbling the solution with wet nitrogen. DNA strand breaks and platinum detachment were quantified by gel electrophoresis. Our results demonstrate that hydrated electrons react almost exclusively at the position of the cisPt adduct, where they induce cisPt detachment from one or both guanines in the oligonucleotide. Given the high yield of hydrated electrons in irradiated tissues, this reaction may be an important step in the mechanism of radiosensitization of DNA by cisPt.

  18. A deficiency of manganese ions in the presence of high sugar concentrations is the critical parameter for achieving high yields of itaconic acid by Aspergillus terreus.

    Science.gov (United States)

    Karaffa, Levente; Díaz, Rafael; Papp, Benedek; Fekete, Erzsébet; Sándor, Erzsébet; Kubicek, Christian P

    2015-10-01

    Itaconic acid (IA), an unsaturated dicarboxylic acid with a high potential as a platform for chemicals derived from sugars, is industrially produced by large-scale submerged fermentation by Aspergillus terreus. Although the biochemical pathway and the physiology leading to IA is almost the same as that leading to citric acid production in Aspergillus niger, published data for the volumetric (g L(-1)) and the specific yield (mol/mol carbon source) of IA are significantly lower than for citric acid. Citric acid is known to accumulate to high levels only when a number of nutritional parameters are carefully adjusted, of which the concentration of the carbon source and that of manganese ions in the medium are particularly important. We have therefore investigated whether a variation in these two parameters may enhance IA production and yield by A. terreus. We show that manganese ion concentrations parameters are varied in citric acid production by A. niger, thus showing that the physiology of both processes is widely identical. Consequently, applying the fermentation technology established for citric acid production by A. niger citric acid production to A. terreus should lead to high yields of IA, too.

  19. Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli

    Science.gov (United States)

    George, Kevin W.; Thompson, Mitchell G.; Kang, Aram; Baidoo, Edward; Wang, George; Chan, Leanne Jade G.; Adams, Paul D.; Petzold, Christopher J.; Keasling, Jay D.; Soon Lee, Taek

    2015-01-01

    Branched five carbon (C5) alcohols are attractive targets for microbial production due to their desirable fuel properties and importance as platform chemicals. In this study, we engineered a heterologous isoprenoid pathway in E. coli for the high-yield production of 3-methyl-3-buten-1-ol, 3-methyl-2-buten-1-ol, and 3-methyl-1-butanol, three C5 alcohols that serve as potential biofuels. We first constructed a pathway for 3-methyl-3-buten-1-ol, where metabolite profiling identified NudB, a promiscuous phosphatase, as a likely pathway bottleneck. We achieved a 60% increase in the yield of 3-methyl-3-buten-1-ol by engineering the Shine-Dalgarno sequence of nudB, which increased protein levels by 9-fold and reduced isopentenyl diphosphate (IPP) accumulation by 4-fold. To further optimize the pathway, we adjusted mevalonate kinase (MK) expression and investigated MK enzymes from alternative microbes such as Methanosarcina mazei. Next, we expressed a fusion protein of IPP isomerase and the phosphatase (Idi1~NudB) along with a reductase (NemA) to diversify production to 3-methyl-2-buten-1-ol and 3-methyl-1-butanol. Finally, we used an oleyl alcohol overlay to improve alcohol recovery, achieving final titers of 2.23 g/L of 3-methyl-3-buten-1-ol (~70% of pathway-dependent theoretical yield), 150 mg/L of 3-methyl-2-buten-1-ol, and 300 mg/L of 3-methyl-1-butanol. PMID:26052683

  20. Inhibition of microRNA with antisense oligonucleotides.

    Science.gov (United States)

    Esau, Christine C

    2008-01-01

    Antisense inhibition of microRNA (miRNA) function has been an important tool for uncovering miRNA biology. Chemical modification of anti-miRNA oligonucleotides (AMOs) is necessary to improve affinity for target miRNA, stabilize the AMO to nuclease degradation, and to promote tissue uptake for in vivo delivery. Here I summarize the work done to evaluate the effectiveness of various chemically modified AMOs for use in cultured cells and rodent models, and outline important issues to consider when inhibiting miRNAs with antisense oligonucleotides.

  1. A new high phenyl lactic acid-yielding Lactobacillus plantarum IMAU10124 and a comparative analysis of lactate dehydrogenase gene.

    Science.gov (United States)

    Zhang, Xiqing; Zhang, Shuli; Shi, Yan; Shen, Fadi; Wang, Haikuan

    2014-07-01

    Phenyl lactic acid (PLA) has been widely reported as a new natural antimicrobial compound. In this study, 120 Lactobacillus plantarum strains were demonstrated to produce PLA using high-performance liquid chromatography. Lactobacillus plantarum IMAU10124 was screened with a PLA yield of 0.229 g L(-1) . Compared with all previous reports, this is the highest PLA-producing lactic acid bacteria (LAB) when grown in MRS broth without any optimizing conditions. When 3.0 g L(-1) phenyl pyruvic acid (PPA) was added to the medium as substrate, PLA production reached 2.90 g L(-1) , with the highest 96.05% conversion rate. A lowest PLA-yielding L. plantarum IMAU40105 (0.043 g L(-1) ) was also screened. It was shown that the conversion from PPA to PLA by lactic dehydrogenase (LDH) is the key factor in the improvement of PLA production by LAB. Comparing the LDH gene of two strains, four amino acid mutation sites were found in this study in the LDH of L. plantarum IMAU10124. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  2. Effect of microbiological fertilizer and soil additive on yield of buckwheat (Fagopyrum esculentum Moenchunder high altitude conditions

    Directory of Open Access Journals (Sweden)

    Oljača Snežana

    2012-01-01

    Full Text Available Effect of microbiological fertilizer (Slavol and soil additives (zeolite and hydrogel on buckwheat (Fagopyrum esculentum Moench yield was investigated in this paper. Trial was set up in the village of Radijevići, Serbia in agroecological conditions of mountain Zlatar (altitude 1,065 m during a two-year period 2009 and 2010. A randomized complete block design with four replications was set up. In organic cropping system three combinations of microbiological fertilizer (Slavol with zeolite and hydrogel were used prior to sowing. Different combinations of the microbiological fertilizer and the soil additives gave positive results especially in the second year of the trial. The best combination in organic cropping system was Slavol+hydrogel with foliar application of the microbiological fertilizer, which resulted in the greatest yield of buckwheat and this treatment can be recommended to producers. Buckwheat performed very well under limited conditions of acidic soil on high altitude in organic cropping system and it can be recommended as a very suitable crop for organic producers.

  3. Zhongdanyaozhi No. 1 and Zhongdanyaozhi No. 2 Are Hybrid Cultivars of Salvia miltiorrhiza with High Yield and Active Compounds Content.

    Directory of Open Access Journals (Sweden)

    Meng Chen

    Full Text Available Salvia miltiorrhiza Bunge is an important medicinal plant used for the treatment of cardiovascular disease. Intraspecific hybridization between a male sterile line and inbred lines was followed by 39 F1 crossings. Cultivars "Zhongdanyaozhi No. 1" (ZD1 and "Zhongdanyaozhi No. 2" (ZD2 were obtained. In 2012 and 2013 tests in Beijing, the two cultivars were compared with three widely accepted types, SDCK, SXCK and HNCK from Shandong, Shanxi and Henan provinces. The yield of ZD1 and ZD2 exceeded the three CKs by more than 48.2% and 39.2%, respectively; the composition of the two hybrid cultivars was similar to the control, although the content of some compounds varied to some extent. The content of salvianolic acid B and tanshinone II A of both ZD1 and ZD2 could measure up the requirement of Chinese Pharmacopoeia. The former showed no obvious advantage than the three CKs, while the later's tanshinone II A was 29.6% higher than the three CKs. Taken together, ZD1 is a high yielding and thick-root-type cultivar which is suitable for decoction pieces; while ZD2 is suitable for component especially lipophilic component extraction. ZD1 and ZD2 reported here are the first cultivars obtained by the hybridization of S. miltiorrhiza.

  4. High-yield enzymatic bioconversion of hydroquinone to α-arbutin, a powerful skin lightening agent, by amylosucrase.

    Science.gov (United States)

    Seo, Dong-Ho; Jung, Jong-Hyun; Ha, Suk-Jin; Cho, Hyun-Kug; Jung, Dong-Hyun; Kim, Tae-Jip; Baek, Nam-In; Yoo, Sang-Ho; Park, Cheon-Seok

    2012-06-01

    α-Arbutin (α-Ab) is a powerful skin whitening agent that blocks epidermal melanin biosynthesis by inhibiting the enzymatic oxidation of tyrosine and L-3,4-dihydroxyphenylalanine (L-DOPA). α-Ab was effectively synthesized from hydroquinone (HQ) by enzymatic biotransformation using amylosucrase (ASase). The ASase gene from Deinococcus geothermalis (DGAS) was expressed and efficiently purified from Escherichia coli using a constitutive expression system. The expressed DGAS was functional and performed a glycosyltransferase reaction using sucrose as a donor and HQ as an acceptor. The presence of a single HQ bioconversion product was confirmed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). The HQ bioconversion product was isolated by silica gel open column chromatography and its chemical structure determined by 1H and 13C nuclear magnetic resonance (NMR). The product was determined to be hydroquinone-O-α-D-glucopyranoside with a glucose molecule linked to HQ through an α-glycosidic bond. However, the production yield of the transfer reaction was significantly low (1.3%) due to the instability of HQ in the reaction mixture. The instability of HQ was considerably improved by antioxidant agents, particularly ascorbic acid, implying that HQ is labile to oxidation. A maximum yield of HQ transfer product of 90% was obtained at a 10:1 molar ratio of donor (sucrose) and acceptor (HQ) molecules in the presence of 0.2 mM ascorbic acid.

  5. Powder, paper and foam of few-layer graphene prepared in high yield by electrochemical intercalation exfoliation of expanded graphite.

    Science.gov (United States)

    Wu, Liqiong; Li, Weiwei; Li, Peng; Liao, Shutian; Qiu, Shengqiang; Chen, Mingliang; Guo, Yufen; Li, Qi; Zhu, Chao; Liu, Liwei

    2014-04-09

    A facile and high-yield approach to the preparation of few-layer graphene (FLG) by electrochemical intercalation exfoliation (EIE) of expanded graphite in sulfuric acid electrolyte is reported. Stage-1 H2SO4-graphite intercalation compound is used as a key intermediate in EIE to realize the efficient exfoliation. The yield of the FLG sheets (flakes enables them to disperse effectively, which contributes to the film-forming characteristics of the FLG flakes. These electrochemically exfoliated FLG flakes are integrated into several kinds of macroscopic graphene structures. Flexible and freestanding graphene papers made of the FLG flakes retain excellent conductivity (≈24,500 S m(-1)). Three-dimensional (3D) graphene foams with light weight are fabricated from the FLG flakes by the use of Ni foams as self-sacrifice templates. Furthermore, 3D graphene/Ni foams without any binders, which are used as supercapacitor electrodes in aqueous electrolyte, provide the specific capacitance of 113.2 F g(-1) at a current density of 0.5 A g(-1), retaining 90% capacitance after 1000 cycles. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. High quantum yield graphene quantum dots decorated TiO{sub 2} nanotubes for enhancing photocatalytic activity

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Ailan, E-mail: qal67@163.com; Xie, Haolong; Xu, Xinmei; Zhang, Yangyu; Wen, Shengwu; Cui, Yifan

    2016-07-01

    Highlights: • High concentration yellow GQDs and TiO{sub 2} nanotubes were achieved by a simple and green method. • High quantum yield GQDs enhanced the photodegradation capacity of TiO{sub 2} nanotube. • The catalytic performance of GQDs/TiO{sub 2} depends on the GQDs loading. • The improved photocatalytic activity of GQDs/TiO{sub 2} was attributed to three aspects. - Abstract: Graphene quantum dots (GQDs) with high quantum yield (about 23.6% at an excitation wavelength of 320 nm) and GQDs/TiO{sub 2} nanotubes (GQDs/TiO{sub 2} NTs) composites were achieved by a simple hydrothermal method at low temperature. Photoluminescence characterization showed that the GQDs exhibited the down-conversion PL features at excitation from 300 to 420 nm and up-conversion photoluminescence in the range of 600–800 nm. The photocatalytic activity of prepared GQDs/TiO{sub 2} NTs composites on the degradation of methyl orange (MO) was significantly enhanced compared with that of pure TiO{sub 2} nanotubes (TiO{sub 2} NTs). For the composites coupling with 1.5%, 2.5% and 3.5% GQDs, the degradation of MO after 20 min irradiation under UV–vis light irradiation (λ = 380–780 nm) were 80.52%, 94.64% and 51.91%, respectively, which are much higher than that of pure TiO{sub 2} NTs (35.41%). It was inferred from the results of characterization that the improved photocatalytic activity of the GQDs/TiO{sub 2} NTs composites was attributed to the synergetic effect of up-conversion properties of the GQDs, enhanced visible light absorption and efficient separation of photogenerated electron-holes of the GQDs/TiO{sub 2} composite.

  7. Rapid transient production in plants by replicating and non-replicating vectors yields high quality functional anti-HIV antibody.

    Science.gov (United States)

    Sainsbury, Frank; Sack, Markus; Stadlmann, Johannes; Quendler, Heribert; Fischer, Rainer; Lomonossoff, George P

    2010-11-12

    The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product. To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV) RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue) of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER). Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO) cell-produced 2G12. Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for biopharmaceutical development

  8. Rapid transient production in plants by replicating and non-replicating vectors yields high quality functional anti-HIV antibody.

    Directory of Open Access Journals (Sweden)

    Frank Sainsbury

    2010-11-01

    Full Text Available The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product.To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER. Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO cell-produced 2G12.Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for

  9. Reduced fertility in high-yielding dairy cows: are the oocyte and embryo in danger? Part II. Mechanisms linking nutrition and reduced oocyte and embryo quality in high-yielding dairy cows.

    Science.gov (United States)

    Leroy, J L M R; Van Soom, A; Opsomer, G; Goovaerts, I G F; Bols, P E J

    2008-10-01

    Dairy cow fertility has been declining during since the mid-80s and this has given rise to numerous scientific studies in which important parts of the pathogenesis are elucidated. Reduced oocyte and embryo quality are acknowledged as major factors in the widely described low conception rates and in the high prevalence of early embryonic mortality. Apart from the importance of the negative energy balance (NEB) and the associated endocrine and metabolic consequences, there is a growing attention towards the effect of the milk yield promoting diets which are rich in energy and protein. Starch-rich diets can improve the energy status and thus the ovarian activity in the early postpartum period but the oocyte and embryo quality can suffer from such insulinogenic diets. Supplementation of dietary fat has a similar dual effect with a beneficial stimulation of the ovarian steroid production while the oocyte and the embryo display an altered energy metabolism and excessive lipid accumulation. High-protein diets can elevate the ammonia and urea concentrations in the blood, leading to changed intrafollicular, oviductal and uterine environments. Oocytes and embryos are highly sensitive to such changes in their microenvironment, possibly leading to a disturbed maturation, fertilization or early cleavage. Several nutrition-linked mechanisms, through which oocyte and/or embryo quality can be affected in modern dairy cows, well after the period of NEB, are proposed and comprehensively reviewed in the present report.

  10. Changes in Soil Chemical Properties and Lettuce Yield Response Following Incorporation of Biochar and Cow Dung to Highly Weathered Acidic Soils

    DEFF Research Database (Denmark)

    Agyei Frimpong, Kwame; Amoakwah, Emmanuel; Osei, Benjamin A

    2016-01-01

    imposed on two highly weathered, acidic soils from the coastal savanna and tropical rainforest agroecological zones of Ghana, respectively, to elucidate their effect on yield of lettuce. The study showed that application of biochar solely or in combination with cow dung increased soil pH, total organic...... improve soil chemical properties and lettuce yield if applied solely or in combination with cow dung....

  11. 1H NMR studies of the bis-intercalation of a homodimeric oxazole yellow dye in DNA oligonucleotides.

    Science.gov (United States)

    Johansen, F; Jacobsen, J P

    1998-10-01

    We have used one and two dimensional 1H NMR spectroscopy to characterize the binding of a homodimeric oxazole yellow dye, 1,1'-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-bis-4-( 3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-2-methylidene)-quinoliniu m tetraiodide (YOYO), to oligonucleotides containing the (5'-CTAG-3')2 and the (5'-CCGG-3')2 binding sites in either different oligonucleotides or in the same oligonucleotide. YOYO bis-intercalates strongly in all the oligonucleotides used and binds preferentially to a (5'-CTAG-3')2 binding site in the oligonucleotide d(CGCTAGCG)2 (1). YOYO also binds preferentially to a (5'-CCGG-3')2 sequence in the oligonucleotide d(CGCCGGCG)2 (2) but slightly less favorably than to the (5'- CTAG-3')2 sequence in 1. The binding of YOYO to the d(CGCTAGCCGGCG):d(CGCCGGCTAGCG) (3) oligonucleotide, containing two preferential binding sites, was also examined. YOYO forms mixtures of 1:1 and 1:2 complexes with oligonucleotide 3 in ratios dependent on the relative amount of YOYO and the oligonucleotides in the sample. The binding of YOYO to the oligonucleotide 3 occur sequence selective in the (5'-CTAG-3')2 site and the (5'- CCGG-3')2 site. We have also used two dimensional 1H NMR spectroscopy to determine the solution structure of the DNA oligonucleotide d(5'-CGCTAGCG-3')2 complexed with YOYO. The determination of the structure was based on a total relaxation matrix analysis of the NOESY cross peaks intensities. DQF-COSY spectra were used to obtain coupling constants for the deoxyribose ring protons. The coupling constants were transformed into angle estimates. The NOE derived distance and dihedral restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the YOYO-complex from both A-form and B-form dsDNA starting structures giving a total of 40 final structures. Since many NOE contacts were observed between YOYO and dsDNA the resulting structure has a fairly high resolution and

  12. Anti sense and sensibility : renal and skin effects of (antisense) oligonucleotides

    NARCIS (Netherlands)

    Meer, van L.

    2017-01-01

    This thesis describes the clinical investigation of a novel treatment strategy for type 2 diabetes mellitus (t2dm) using an antisense oligonucleotide(aon)to inhibit the sglt2 receptor. Furthermore it describes skin effects of oligonucleotides

  13. High-yield production of short GpppA- and 7MeGpppA-capped RNAs and HPLC-monitoring of methyltransfer reactions at the guanine-N7 and adenosine-2'O positions.

    Science.gov (United States)

    Peyrane, F; Selisko, B; Decroly, E; Vasseur, J J; Benarroch, D; Canard, B; Alvarez, K

    2007-01-01

    Many eukaryotic and viral mRNAs, in which the first transcribed nucleotide is an adenosine, are decorated with a cap-1 structure, (7Me)G5'-ppp5'-A(2'OMe). The positive-sense RNA genomes of flaviviruses (Dengue, West Nile virus) for example show strict conservation of the adenosine. We set out to produce GpppA- and (7Me)GpppA-capped RNA oligonucleotides for non-radioactive mRNA cap methyltransferase assays and, in perspective, for studies of enzyme specificity in relation to substrate length as well as for co-crystallization studies. This study reports the use of a bacteriophage T7 DNA primase fragment to synthesize GpppAC(n) and (7Me)GpppAC(n) (1 < or = n < or = 9) in a one-step enzymatic reaction, followed by direct on-line cleaning HPLC purification. Optimization studies show that yields could be modulated by DNA template, enzyme and substrate concentration adjustments and longer reaction times. Large-scale synthesis rendered pure (in average 99%) products (1 < or = n < or = 7) in quantities of up to 100 nmol starting from 200 nmol cap analog. The capped RNA oligonucleotides were efficient substrates of Dengue virus (nucleoside-2'-O-)-methyltransferase, and human (guanine-N7)-methyltransferase. Methyltransfer reactions were monitored by a non-radioactive, quantitative HPLC assay. Additionally, the produced capped RNAs may serve in biochemical, inhibition and structural studies involving a variety of eukaryotic and viral methyltransferases and guanylyltransferases.

  14. Simulation of the electron collection efficiency of a PMT based on the MCP coated with high secondary yield material

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Lin, E-mail: chenlin@opt.cn [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Graduate School of Chinese Academy of Sciences (CAS), Beijing 100049 (China); Xi' an Jiaotong University, Xi' an 710049 (China); Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006 (China); Tian, Jinshou [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006 (China); Zhao, Tianchi [Institute of High Energy Physics (IHEP) of CAS, Beijing 100049 (China); Liu, Chunliang [Xi' an Jiaotong University, Xi' an 710049 (China); Liu, Hulin; Wei, Yonglin; Sai, Xiaofeng [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Chen, Ping [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Graduate School of Chinese Academy of Sciences (CAS), Beijing 100049 (China); Wang, Xing; Lu, Yu [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Hui, Dandan [State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics (XIOPM), Chinese Academy of Sciences (CAS), Xi' an 710119 (China); Graduate School of Chinese Academy of Sciences (CAS), Beijing 100049 (China)

    2016-11-01

    Owning to the serious loss of photoelectrons striking at the input electrode of traditional microchannel plate (MCP), photoelectron collection efficiency (CE) of photomultiplier tubes based on MCP (MCP-PMTs) fluctuates around the MCP open area fraction and cannot make a breakthrough. Depositing a thin film of high secondary electron yield material on the MCP is proposed as an effective approach to improve the CE. The available simulation and experimental data to validate it, however, is sparse. In our work, a three-dimensional small area MCP model is developed in CST Studio Suite to evaluate the collection efficiencies of PMTs based on the traditional MCP and the coated one, respectively. Results predict that CE of the PMT based on the coated MCP has a significant increase and a better uniformity, which is expected to reach 100%.

  15. Impact of ovarian and uterine conditions on some diagnostic tests output of endometritis in postpartum high-yielding dairy cows.

    Science.gov (United States)

    Senosy, W; Uchiza, M; Tameoka, N; Izaike, Y; Osawa, T

    2011-10-01

    The effect of ovarian predominating structures and uterine condition on the result of some diagnostic tools for the evaluation of endometritis was studied in postpartum (pp) Holstein-Friesian dairy cows (n = 58). Endometrial cytology (EC) and the evaluation of vaginal mucus by vaginoscopy or Metricheck were performed weekly from week 3 to 7 pp. The ovarian studies involved the predominating structures including cystic follicles with plasma progesterone (P(4) ; more or 23 mm), corpus luteum (CL), pre-ovulatory follicles (10-23 mm) and small follicles (follicular cysts with low progesterone (P(4) ovarian structures and uterine condition in early pp high-yielding dairy cows. © 2011 Blackwell Verlag GmbH.

  16. Continuous high-yield production of vertically aligned carbon nanotubes on 2D and 3D substrates.

    Science.gov (United States)

    Guzmán de Villoria, Roberto; Hart, A John; Wardle, Brian L

    2011-06-28

    Vertically aligned carbon nanotubes (VACNTs) have certain advantages over bulk CNT powders and randomly oriented CNT mats for applications in flexible electronic devices, filtration membranes, biosensors and multifunctional aerospace materials. Here, a machine and a process to synthesize VACNTs in a continuous manner are presented showing uniform growth on 2D and 3D substrates, including alumina fibers, silicon wafer pieces, and stainless steel foils. Aligned multiwalled carbon nanotubes (MWNT) are synthesized at substrate feed rates of up to 6.8 cm/min, and the CNTs reach up to 60 μm in length depending on residence time in the reactor. In addition to the aligned morphology indicative of high yield growth, transmission electron microscopy and Raman spectroscopy reveal that the CNTs are of comparable quality to CNTs grown via a similar batch process. A significant reduction in time, reaction products, gases, and energy is demonstrated relative to batch processing, paving the way for industrial production of VACNTs.

  17. High yielding tropical energy crops for bioenergy production: Effects of plant components, harvest years and locations on biomass composition.

    Science.gov (United States)

    Surendra, K C; Ogoshi, Richard; Zaleski, Halina M; Hashimoto, Andrew G; Khanal, Samir Kumar

    2017-12-18

    The composition of lignocellulosic feedstock, which depends on crop type, crop management, locations and plant parts, significantly affects the conversion efficiency of biomass into biofuels and biobased products. Thus, this study examined the composition of different parts of two high yielding tropical energy crops, Energycane and Napier grass, collected across three locations and years. Significantly higher fiber content was found in the leaves of Energycane than stems, while fiber content was significantly higher in the stems than the leaves of Napier grass. Similarly, fiber content was higher in Napier grass than Energycane. Due to significant differences in biomass composition between the plant parts within a crop type, neither biological conversion, including anaerobic digestion, nor thermochemical pretreatment alone is likely to efficiently convert biomass components into biofuels and biobased products. However, combination of anaerobic digestion with thermochemical conversion technologies could efficiently utilize biomass components in generating biofuels and biobased products. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. A comparison of enzymatic digestion for the quantitation of an oligonucleotide by liquid chromatography-isotope dilution mass spectrometry.

    Science.gov (United States)

    Donald, Carol E; Stokes, Peter; O'Connor, Gavin; Woolford, Alison J

    2005-03-25

    DNA is a universal analyte found in almost every organism. It is the code that dictates our genetic make-up and it provides a vast library of information. DNA sequences can indicate genetic modification of foodstuffs, how we may metabolise pharmaceuticals and the likelihood of suffering particular diseases. The basis for many of these genetic tests would benefit greatly from procedures that can accurately quantitate DNA in an absolute manner. This would then provide a sound and universally consistent foundation for regulatory and diagnostic decision making. This work compares two different enzymatic digestion systems as precursor steps to high accuracy isotope dilution mass spectrometry (IDMS) quantitation of a 20mer oligonucleotide. In the first approach, snake venom phosphodiesterase (SVP) digests the oligonucleotide to its constituent deoxynucleotides (dNMPs), followed by liquid chromatography-IDMS (LC-IDMS) quantitation. The second enzyme digestion approach used a combination of snake venom phosphodiesterase and shrimp alkaline phosphatase (SAP) which reduces the oligonucleotide to its constituent deoxynucleosides (dNs). This was then followed by an alternative LC separation and equivalent IDMS measurements. Total phosphorous content of the 20mer oligonucleotide was measured by inductively coupled plasma optical emission spectroscopy (ICP-OES). This provided independent data for comparison with the two enzyme digestion-IDMS based procedures. The most appropriate method of quantitation was found to be the combined SVP and SAP digestion. This approach negates the need to consider and/or account for the lack of a 5' terminal phosphate residue. It also enables the use of positive ion mass spectrometry which simplifies the chromatographic requirements. Based on the exact matched IDMS of the adenine deoxynucleoside, the concentration of the original 20mer oligonucleotide was found to be 110+/-9 microg g(-1). This showed good agreement with the ICP-OES data based on

  19. Assessment of production conditions for efficient use of Escherichia coli in high-yield heterologous recombinant selenoprotein synthesis.

    Science.gov (United States)

    Rengby, Olle; Johansson, Linda; Carlson, Lars A; Serini, Elena; Vlamis-Gardikas, Alexios; Kårsnäs, Per; Arnér, Elias S J

    2004-09-01

    The production of heterologous selenoproteins in Escherichia coli necessitates the design of a secondary structure in the mRNA forming a selenocysteine insertion sequence (SECIS) element compatible with SelB, the elongation factor for selenocysteine insertion at a predefined UGA codon. SelB competes with release factor 2 (RF2) catalyzing translational termination at UGA. Stoichiometry between mRNA, the SelB elongation factor, and RF2 is thereby important, whereas other expression conditions affecting the yield of recombinant selenoproteins have been poorly assessed. Here we expressed the rat selenoprotein thioredoxin reductase, with titrated levels of the selenoprotein mRNA under diverse growth conditions, with or without cotransformation of the accessory bacterial selA, selB, and selC genes. Titration of the selenoprotein mRNA with a pBAD promoter was performed in both TOP10 and BW27783 cells, which unexpectedly could not improve yield or specific activity compared to that achieved in our prior studies. Guided by principal component analysis, we instead discovered that the most efficient bacterial selenoprotein production conditions were obtained with the high-transcription T7lac-driven pET vector system in presence of the selA, selB, and selC genes, with induction of production at late exponential phase. About 40 mg of rat thioredoxin reductase with 50% selenocysteine content could thereby be produced per liter bacterial culture. These findings clearly illustrate the ability of E. coli to upregulate the selenocysteine incorporation machinery on demand and that this is furthermore strongly augmented in late exponential phase. This study also demonstrates that E. coli can indeed be utilized as cell factories for highly efficient production of heterologous selenoproteins such as rat thioredoxin reductase.

  20. The Potential of Lr19 and Bdv2 Translocations to Improve Yield and Disease Resistance in the High Rainfall Wheat Zones of Australia

    Directory of Open Access Journals (Sweden)

    Garry Rosewarne

    2015-02-01

    Full Text Available Chromosomal translocations in wheat derived from alien species are a valuable source of genetic diversity that have provided increases in resistance to various diseases and improved tolerance to abiotic stresses in wheat. These alien genomic segments can also affect multiple traits, with a concomitant ability to alter yield potential in either a positive or negative fashion. The aim of this work was to characterize the effects on yield of two types of translocations, namely T4-derived translocations from Thinopyrum ponticum, carrying the leaf rust resistance gene Lr19, and the TC14 translocation from Th. intermedium, carrying the barley yellow dwarf virus resistance gene Bdv2, in Australian adapted genetic backgrounds and under Australian conditions. A large range of germplasm was developed by crossing donor sources of the translocations into 24 Australian adapted varieties producing 340 genotypes. Yield trials were conducted in 14 environments to identify effects on yield and yield components. The T4 translocations had a positive effect on yield in one high yielding environment, but negatively affected yield in low-yielding environments. The TC14 translocation was generally benign, however, it was associated with a negative impact on yield and reduced height in two genetic backgrounds. The translocation was also associated with a delayed maturity in several backgrounds. The T4 translocations results were consistent with previously published data, whilst this is the first time that such an investigation has been undertaken on the TC14 translocation. Our data suggests a limited role for each of these translocations in Australia. The T4 translocations may be useful in high yielding environments, such as under irrigation in NSW and in the more productive high rainfall regions of south-eastern Australia. Traits associated with the TC14 translocation, such as BYDV resistance and delayed maturity, would make this translocation useful in BYDV

  1. A dual-colored ratiometric-fluorescent oligonucleotide probe for the detection of human telomerase RNA in cell extracts.

    Science.gov (United States)

    Ning, Dianhua; He, Changtian; Liu, Zhengjie; Liu, Cui; Wu, Qilong; Zhao, TingTing; Liu, Renyong

    2017-05-21

    Human telomerase RNA (hTR), which is one component of telomerase, was deemed to be a biomarker to monitor tumor cells due to its different expression levels in tumor cells and normal somatic cells. Thus far, plentiful fluorescent probes have been designed to investigate nucleic acids. However, most of them are limited since they are time-consuming, require professional operators and even result in false positive signals in the cellular environment. Herein, we report a dual-colored ratiometric-fluorescent oligonucleotide probe to achieve the reliable detection of human telomerase RNA in cell extracts. The probe is constructed using a dual-labeled fluorescent oligonucleotide hybridized with target-complemented Dabcyl-labeled oligonucleotide. In the presence of the target, the dual-labeled fluorescent oligonucleotide translates into a hairpin structure, which leads to the generation of the fluorescence resonance energy transfer (FRET) phenomenon under UV excitation. Compared to conventional methods, this strategy could effectively avoid false positive signals, and it not only possesses the advantages of simplicity and high specificity but also has the merits of signal stability and distinguishable color variation. Moreover, the quantitative assay of hTR would have a far-reaching impact on the telomerase mechanism and even tumor diagnosis research.

  2. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles

    DEFF Research Database (Denmark)

    Cogoi, S; Jakobsen, U; Pedersen, E B

    2016-01-01

    factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated...

  3. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

    Directory of Open Access Journals (Sweden)

    Tatyana V. Abramova

    2014-05-01

    Full Text Available An efficient solid-phase-supported peptide synthesis (SPPS of morpholinoglycine oligonucleotide (MorGly mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.

  4. Chromosome-specific painting in Cucumis species using bulked oligonucleotides

    Science.gov (United States)

    Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a sing...

  5. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence

    DEFF Research Database (Denmark)

    Taskova, Maria; Uhd, Jesper; Miotke, Laura

    2017-01-01

    opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA...

  6. Fragmentation of protonated oligonucleotides by energetic photons and Cq+ ions

    NARCIS (Netherlands)

    Gonzalez-Magana, O.; Tiemens, M.; Reitsma, G.; Boschman, L.; Door, M.; Bari, S.; Lahaie, P. O.; Wagner, J. R.; Huels, M. A.; Hoekstra, R.; Schlathölter, Thomas

    2013-01-01

    The ionization and fragmentation of trapped protonated dGCAT oligonucleotides upon interaction with energetic photons (h nu = 10-570 eV) and keV Cq+ ions was investigated by means of time-of-flight mass spectrometry. The observed fragmentation patterns are dominated by protonated and nonprotonated

  7. Chemically modified oligonucleotides with efficient RNase H response

    DEFF Research Database (Denmark)

    Vester, Birte; Boel, Anne Marie; Lobedanz, Sune

    2008-01-01

    Ten different chemically modified nucleosides were incorporated into short DNA strands (chimeric oligonucleotides ON3-ON12 and ON15-ON24) and then tested for their capacity to mediate RNAse H cleavage of the complementary RNA strand. The modifications were placed at two central positions directly...

  8. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  9. High yield purification and characterization of engineered human P450 1A2 and generation of immuno-inhibitor antibodies.

    Science.gov (United States)

    Louërat-Oriou, B; Flinois, J P; Beaune, P H; Pompon, D

    1999-02-01

    P450 S12, an engineered human P450 1A2 containing the 88-first amino-acids of the P450 1A1, demonstrates particularly high expression level in yeast while exhibiting catalytic properties very similar to the moderately expressed natural human P450 1A2. To facilitate P450 purification by nickel chelate chromatography, C-terminal extensions including histidine tags were tested. The -G(H)4 extension was found to be particularly efficient for permitting high expression levels without any catalytic alteration. This engineered P450 was purified to electrophoretic homogeneity (18 nmol/mg of protein) at a very high yield (87%) without any detectable formation of P420. P450 S12 activities were reconstituted in the presence of yeast and Arabidopsis thaliana (ATR1) NADPH-P450 reductases. The plant reductase supported better ethoxyresorufin-, methoxyresorufin- and phenacetin-O-dealkylase activities than the yeast reductase in reconstituted systems. Interestingly, polyclonal antibodies raised against purified P450 S12 selectively recognized in Western blot and fully immuno-inhibited the natural or recombinant P450 1A2 with very limited or no cross-reaction with P450 1A1 and other isoenzymes.

  10. Highly Luminescent Phase-Stable CsPbI3 Perovskite Quantum Dots Achieving Near 100% Absolute Photoluminescence Quantum Yield.

    Science.gov (United States)

    Liu, Feng; Zhang, Yaohong; Ding, Chao; Kobayashi, Syuusuke; Izuishi, Takuya; Nakazawa, Naoki; Toyoda, Taro; Ohta, Tsuyoshi; Hayase, Shuzi; Minemoto, Takashi; Yoshino, Kenji; Dai, Songyuan; Shen, Qing

    2017-10-24

    Perovskite quantum dots (QDs) as a new type of colloidal nanocrystals have gained significant attention for both fundamental research and commercial applications owing to their appealing optoelectronic properties and excellent chemical processability. For their wide range of potential applications, synthesizing colloidal QDs with high crystal quality is of crucial importance. However, like most common QD systems such as CdSe and PbS, those reported perovskite QDs still suffer from a certain density of trapping defects, giving rise to detrimental nonradiative recombination centers and thus quenching luminescence. In this paper, we show that a high room-temperature photoluminescence quantum yield of up to 100% can be obtained in CsPbI3 perovskite QDs, signifying the achievement of almost complete elimination of the trapping defects. This is realized with our improved synthetic protocol that involves introducing organolead compound trioctylphosphine-PbI2 (TOP-PbI2) as the reactive precursor, which also leads to a significantly improved stability for the resulting CsPbI3 QD solutions. Ultrafast kinetic analysis with time-resolved transient absorption spectroscopy evidence the negligible electron or hole-trapping pathways in our QDs, which explains such a high quantum efficiency. We expect the successful synthesis of the "ideal" perovskite QDs will exert profound influence on their applications to both QD-based light-harvesting and -emitting devices.

  11. Ultrasensitive electrochemical biosensor based on the oligonucleotide self-assembled monolayer-mediated immunosensing interface

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Dengyou; Luo, Qimei [Science College of Hunan Agricultural University, Changsha 410128 (China); Deng, Fawen [The Fourth Hospital of Chansha, Changsha 410006 (China); Li, Zhen [Science College of Hunan Agricultural University, Changsha 410128 (China); Li, Benxiang, E-mail: 172170960@qq.com [Science College of Hunan Agricultural University, Changsha 410128 (China); Shen, Zhifa, E-mail: shenzhifa@wmu.edu.cn [Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035 (China)

    2017-06-08

    Highly sensitive and selective quantitation of a variety of proteins over a wide concentration range is highly desirable for increased accuracy of biomarker detection or for multidisease diagnostics. In the present contribution, using human immunoglobulin G (HIgG) as the model target protein, an electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer-mediated (OSAM) sensing interface. For this immunosensor, the “signal-on” signaling mechanism and enzymatic signal amplification effect were integrated into one sensing architecture. Moreover, the thiolated flexible single-stranded DNAs immobilized onto gold electrode surface not only performs the wobbling motion to facilitate the electron transfer between the electrode surface and biosensing layer but also fundamentally prohibiting the direct interaction of proteins with gold substrate. Thus, the electrochemical signal could be efficiently enhanced and the unspecific adsorption or cross-reaction might be eliminated. As a result, utilizing the newly-proposed immunosensor, the HIgG can be detected down to 0.5 ng/mL, and the high detection specificity is offered. The successful design of OSAM and the highly desirable detection capability of new immunosensor are expected to provide a perspective for fabricating new robust immunosensing platform and for promising potential of oligonucleotide probe in biological research and biomedical diagnosis. - Highlights: • An electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer (OASM). • OASM severs as a flexible monolayer to promote electron transfer and prohibits the direct interaction of proteins with gold substrate. • The electrochemical signal is efficiently enhanced and the unspecific adsorption or cross-reaction is eliminated. • Target protein can be detected down to 0.5 ng/mL, and the high detection specificity can be obtained.

  12. Preparation of carbon-encapsulated iron nanoparticles in high yield by DC arc discharge and their characterization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fan [Department of Chemistry, School of Science, Tianjin University, Tianjin 300072 (China); Cui, Lan; Lin, Kui [Center of Analysis, Tianjin University, Tianjin 300072 (China); Jin, Feng-min; Wang, Bin [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Shi, Shu-xiu [Department of Chemistry, School of Science, Tianjin University, Tianjin 300072 (China); Yang, De-an [School of Materials Science and Engineering, Tianjin University, Tianjin 300072 (China); Wang, Hui [Center of Analysis, Tianjin University, Tianjin 300072 (China); He, Fei [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Chen, Xiao-ping [Center of Analysis, Tianjin University, Tianjin 300072 (China); Cui, Shen, E-mail: cuishen@tju.edu.cn [Department of Chemistry, School of Science, Tianjin University, Tianjin 300072 (China)

    2013-03-15

    Highlights: ► CEINPs with core–shell structure and high Fe content were prepared in high yield by DC arc discharge. ► The anode II with a mass ratio of total iron to carbon 8:1 was used in DC arc discharge. ► The possible process of formation of CEINPs is briefly discussed. ► The uniformity of composition of anode is very important for the formation of CEINPs. ► The MEF and MMF of iron element may also play an important role in the formation of CEINPs. -- Abstract: Carbon-encapsulated iron nanoparticles (CEINPs) were prepared by DC arc discharge under nitrogen atmosphere of high temperature. The products were characterized by transmission electron microscope (TEM), high-resolution transmission electron microscope (HRTEM), X-ray diffractometer (XRD), energy dispersive X-ray (EDX) spectroscope, and X-ray photoelectron spectroscope (XPS), and their magnetic properties were measured by physical property measurement system (PPMS). The product B{sub I}, obtained from the anode I, contains the nanoparticles of iron and iron carbide, and carbon coating with imperfect and disordered layer structure. The product B{sub II}, obtained from the anode II, mainly consists of CEINPs, whose cores mainly consist of iron and iron carbide and shells contain about 3–7 graphitic layers. The iron contents in the products B{sub I} and B{sub II} are 44.8 and 82.6 wt.%, respectively. The products B{sub I} and B{sub II} have similar phase composition which includes carbon, iron, iron carbide, ferrous and ferric oxide, iron nitride, and carbon nitride. The saturation magnetization (Ms) of the products B{sub I} and B{sub II} are 29.35 and 88.66 emu/g and their coercivity (Hc) are 220 and 240 Oe, respectively. The total yields of all the products formed in the arc discharge chamber from anodes I and II, except for the cylinder-shaped deposits formed on the top of the cathode, are 25.8 and 22.3 wt.%, respectively. The possible process of formation of CEINPs is briefly discussed on

  13. Advanced aqueous-phase phosphoramidation reactions for effectively synthesizing peptide-oligonucleotide conjugates trafficked into a human cell line.

    Science.gov (United States)

    Wang, Tzu-Pin; Ko, Ni Chien; Su, Yu-Chih; Wang, Eng-Chi; Severance, Scott; Hwang, Chi-Ching; Shih, Ying Ting; Wu, Min Hui; Chen, Yen-Hsu

    2012-12-19

    Peptide-oligonucleotide conjugates (POCs) have held promise as effective therapeutic agents in treating microbial infections and human genetic diseases including cancers. In clinical applications, POCs are especially useful to circumvent cellular delivery and specificity problems of oligonucleotides. We previously reported that nucleic acid phosphoramidation reactions performed in aqueous solutions have the potential for facile POC synthesis. Here, we carried out further studies to significantly improve aqueous-phase two-step phosphoramidation reaction yield. Optimized reactions were employed to effectively synthesize POCs for delivery into human A549 cells. We achieved optimization of aqueous-phase two-step phosphoramidation reaction and improved reaction yield by (1) determining appropriate co-solutes and co-solute concentrations to acquire higher reaction yields, (2) exploring a different nucleophilicity of imidazole and its derivatives to stabilize essential nucleic acid phosphorimidazolide intermediates prior to POC formation, and (3) enhancing POC synthesis by increasing reactant nucleophilicity. The advanced two-step phosphoramidation reaction was exploited to effectively conjugate a well-studied cell penetrating peptide, the Tat(48-57) peptide, with oligonucleotides, bridged by either no linkers or a disulfide-containing linker, to have the corresponding POC yields of 47-75%. Phosphoramidation-synthesized POCs showed no cytotoxicity to human A549 cells at studied POC concentrations after 24 h inoculation and were successfully trafficked into the human A549 cell line as demonstrated by flow cytometry, fluorescent microscopy, and confocal laser scanning microscopy study. The current report provides insight into aqueous-phase phosphoramidation reactions, the knowledge of which was used to develop effective strategies for synthesizing POCs with crucial applications including therapeutic agents for medicine.

  14. High yield production and refolding of the double-knot toxin, an activator of TRPV1 channels.

    Directory of Open Access Journals (Sweden)

    Chanhyung Bae

    Full Text Available A unique peptide toxin, named double-knot toxin (DkTx, was recently purified from the venom of the tarantula Ornithoctonus huwena and was found to stably activate TRPV1 channels by targeting the outer pore domain. DkTx has been shown to consist of two inhibitory cysteine-knot (ICK motifs, referred to as K1 and K2, each containing six cysteine residues. Beyond this initial characterization, however, the structural and functional details about DkTx remains elusive in large part due to the lack of a high yielding methodology for the synthesis and folding of this cysteine-rich peptide. Here, we overcome this obstacle by generating pure DkTx in quantities sufficient for structural and functional analyses. Our methodology entails expression of DkTx in E. coli followed by oxidative folding of the isolated linear peptide. Upon screening of various oxidative conditions for optimizing the folding yield of the toxin, we observed that detergents were required for efficient folding of the linear peptide. Our synthetic DkTx co-eluted with the native toxin on HPLC, and irreversibly activated TRPV1 in a manner identical to native DkTx. Interestingly, we find that DkTx has two interconvertible conformations present in a 1∶6 ratio at equilibrium. Kinetic analysis of DkTx folding suggests that the K1 and K2 domains influence each other during the folding process. Moreover, the CD spectra of the toxins shows that the secondary structures of K1 and K2 remains intact even after separating the two knots. These findings provide a starting point for detailed studies on the structural and functional characterization of DkTx and utilization of this toxin as a tool to explore the elusive mechanisms underlying the polymodal gating of TRPV1.

  15. Differential expression pattern of rubber elongation factor (REF) mRNA transcripts from high and low yielding clones of rubber tree (Hevea brasiliensis Muell. Arg.).

    Science.gov (United States)

    Priya, P; Venkatachalam, P; Thulaseedharan, A

    2007-10-01

    In Hevea tree, rubber elongation factor (REF) is a key gene involved in rubber biosynthesis. Since the immaturity period for Hevea is 6 years, identification of molecular marker for latex yield potential will be beneficial for early selection of high yielding clones. The main objective of this research is to study the expression pattern of the REF gene in contrasting latex yield rubber clones (high and low yielding) by Northern blot as well as RT-PCR analysis. Accumulation of REF mRNA transcripts was significantly higher in latex cells compared to other cells of seedlings and mature Hevea trees. Northern results revealed that the level of REF gene expression in latex cells of high yielding rubber clones was significantly higher than in low yielders. According to RT-PCR results, the abundance of REF mRNA transcripts in latex cells was fivefold higher in the RRII105 clone, one of the most high yielding rubber clones. It is evident from the results that both tapping and ethephon treatment had a direct effect on induction of REF gene expression. Results demonstrate a positive correlation between REF gene expression pattern and latex yield.

  16. Display of cellulases on the cell surface of Saccharomyces cerevisiae for high yield ethanol production from high-solid lignocellulosic biomass.

    Science.gov (United States)

    Matano, Yuki; Hasunuma, Tomohisa; Kondo, Akihiko

    2012-03-01

    Economically feasible processes for industrial cellulosic ethanol production requires increasing the final ethanol titer during fermentation due to the high energy demands of the subsequent ethanol distillation. In the present study, high-yield ethanol production was achieved by short-term liquefaction and fermentation of lignocellulose biomass in a novel drum-type rotary fermentation system using a yeast strain developed for cell-surface display of fungal endoglucanase, cellobiohydrolase, and β-glucosidase. In the presence of 10 FPU/g-biomass cellulase added, the recombinant cellulolytic strain produced 1.4-fold higher ethanol (89% of theoretical yield) from high-solid (200 g-dry weight/L) rice straw within 72 h of fermentation than wild type strain. Cell-surface engineering successfully reduced the amount of commercial enzyme required for the fermentation of cellulose. This study demonstrates that cellulases displayed on the yeast cell surface are capable of hydrolyzing cellulose that was not hydrolyzed by commercial cellulases, leading to increased sugar utilization for improved ethanol production. Copyright © 2012. Published by Elsevier Ltd.

  17. Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

    Science.gov (United States)

    Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

    2014-08-20

    DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.

  18. High yield purification of full-length functional hERG K+ channels produced in Saccharomyces cerevisiae.

    Science.gov (United States)

    Molbaek, Karen; Scharff-Poulsen, Peter; Helix-Nielsen, Claus; Klaerke, Dan A; Pedersen, Per Amstrup

    2015-02-07

    The hERG potassium channel is essential for repolarization of the cardiac action potential. Due to this vital function, absence of unintended and potentially life-threatening interactions with hERG is required for approval of new drugs. The structure of hERG is therefore one of the most sought-after. To provide purified hERG for structural studies and new hERG biomimetic platforms for detection of undesirable interactions, we have developed a hERG expression platform generating unprecedented amounts of purified and functional hERG channels. Full-length hERG, with or without a C-terminally fused green fluorescent protein (GFP) His 8-tag was produced from a codon-optimized hERG cDNA in Saccharomyces cerevisiae. Both constructs complemented the high potassium requirement of a knock-out Saccharomyces cerevisiae strain, indicating correct tetramer assembly in vivo. Functionality was further demonstrated by Astemizole binding to membrane embedded hERG-GFP-His 8 with a stoichiometry corresponding to tetramer assembly. The 156 kDa hERG-GFP protein accumulated to a membrane density of 1.6%. Fluorescence size exclusion chromatography of hERG-GFP-His 8 solubilized in Fos-Choline-12 supplemented with cholesteryl-hemisuccinate and Astemizole resulted in a monodisperse elution profile demonstrating a high quality of the hERG channels. hERG-GFP-His 8 purified by Ni-affinity chromatography maintained the ability to bind Astemizole with the correct stoichiometry indicating that the native, tetrameric structure was preserved. To our knowledge this is the first reported high-yield production and purification of full length, tetrameric and functional hERG. This significant breakthrough will be paramount in obtaining hERG crystal structures, and in establishment of new high-throughput hERG drug safety screening assays.