New primer for specific amplification of the CAG repeat in Huntington disease alleles

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

Bond, C.E.; Hodes, M.E.

1994-09-01

Huntington disease is an autosomal dominant neurodegenerative disorder caused by an expansion of a CAG trinucleotide repeat near the 5{prime} end of the gene for Huntington disease (IT15). The CAG repeat is flanked by a variable-length CCG repeat that is included in the amplification product obtained with most currently used primer sets and PCR protocols. Inclusion of this adjacent CCG repeat complicates the accurate assessment of CAG repeat length and interferes with the genotype determination of those individuals carrying alleles in the intermediate range between normal and expanded sized. Due to the GC-rich nature of this region, attempts at designingmore » a protocol for amplification of only the CAG repeat have proved unreliable and difficult to execute. We report here the development of a compatible primer set and PCR protocol that yields consistent amplification of the CAG-repeat region. PCR products can be visualized in ethidium bromide-stained agarose gels for rapid screening or in 6% polyacrylamide gels for determination of exact repeat length. This assay produces bands that can be sized accurately, while eliminating most nonspecific products. Fifty-five specimens examined showed consistency with another well-known method, but one that amplifies the CCG repeats as well. The results we obtained also matched the known carrier status of the donors.« less

Targeting helicase-dependent amplification products with an electrochemical genosensor for reliable and sensitive screening of genetically modified organisms.

PubMed

Moura-Melo, Suely; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Dos Santos Junior, J Ribeiro; da Silva Fonseca, Rosana A; Lobo-Castañón, Maria Jesús

2015-08-18

Cultivation of genetically modified organisms (GMOs) and their use in food and feed is constantly expanding; thus, the question of informing consumers about their presence in food has proven of significant interest. The development of sensitive, rapid, robust, and reliable methods for the detection of GMOs is crucial for proper food labeling. In response, we have experimentally characterized the helicase-dependent isothermal amplification (HDA) and sequence-specific detection of a transgene from the Cauliflower Mosaic Virus 35S Promoter (CaMV35S), inserted into most transgenic plants. HDA is one of the simplest approaches for DNA amplification, emulating the bacterial replication machinery, and resembling PCR but under isothermal conditions. However, it usually suffers from a lack of selectivity, which is due to the accumulation of spurious amplification products. To improve the selectivity of HDA, which makes the detection of amplification products more reliable, we have developed an electrochemical platform targeting the central sequence of HDA copies of the transgene. A binary monolayer architecture is built onto a thin gold film where, upon the formation of perfect nucleic acid duplexes with the amplification products, these are enzyme-labeled and electrochemically transduced. The resulting combined system increases genosensor detectability up to 10(6)-fold, allowing Yes/No detection of GMOs with a limit of detection of ∼30 copies of the CaMV35S genomic DNA. A set of general utility rules in the design of genosensors for detection of HDA amplicons, which may assist in the development of point-of-care tests, is also included. The method provides a versatile tool for detecting nucleic acids with extremely low abundance not only for food safety control but also in the diagnostics and environmental control areas.

[Synthesis of Circular DNA Templates with T4 RNA Ligase for Rolling Circle Amplification].

PubMed

Sakhabutdinova, A R; Maksimova, M A; Garafutdinov, R R

2017-01-01

Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification. The maximum yield of the cyclization products was observed in the presence of 5-10% polyethylene glycol 4000, and the optimum DNA length for the cyclization constituted 50 nucleotides. This highly sensitive method was shown to detect less than 10^(2) circular DNA molecules. The method reliability was proved based on artificially destroyed dsDNA, which suggests its implementation for analyzing any significantly fragmented dsDNA.

78 FR 66940 - Regulatory Requirements for Hearing Aid Devices and Personal Sound Amplification Products; Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-07

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-D-1295] Regulatory Requirements for Hearing Aid Devices and Personal Sound Amplification Products; Draft Guidance for... draft guidance entitled ``Regulatory Requirements for Hearing Aid Devices and Personal Sound...

Quantifying yield gaps in wheat production in Russia

NASA Astrophysics Data System (ADS)

Schierhorn, Florian; Faramarzi, Monireh; Prishchepov, Alexander V.; Koch, Friedrich J.; Müller, Daniel

2014-08-01

Crop yields must increase substantially to meet the increasing demands for agricultural products. Crop yield increases are particularly important for Russia because low crop yields prevail across Russia’s widespread and fertile land resources. However, reliable data are lacking regarding the spatial distribution of potential yields in Russia, which can be used to determine yield gaps. We used a crop growth model to determine the yield potentials and yield gaps of winter and spring wheat at the provincial level across European Russia. We modeled the annual yield potentials from 1995 to 2006 with optimal nitrogen supplies for both rainfed and irrigated conditions. Overall, the results suggest yield gaps of 1.51-2.10 t ha-1, or 44-52% of the yield potential under rainfed conditions. Under irrigated conditions, yield gaps of 3.14-3.30 t ha-1, or 62-63% of the yield potential, were observed. However, recurring droughts cause large fluctuations in yield potentials under rainfed conditions, even when the nitrogen supply is optimal, particularly in the highly fertile black soil areas of southern European Russia. The highest yield gaps (up to 4 t ha-1) under irrigated conditions were detected in the steppe areas in southeastern European Russia along the border of Kazakhstan. Improving the nutrient and water supply and using crop breeds that are adapted to the frequent drought conditions are important for reducing yield gaps in European Russia. Our regional assessment helps inform policy and agricultural investors and prioritize research that aims to increase crop production in this important region for global agricultural markets.

Development of loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Penicillium nordicum in dry-cured meat products.

PubMed

Ferrara, M; Perrone, G; Gallo, A; Epifani, F; Visconti, A; Susca, A

2015-06-02

The need of powerful diagnostic tools for rapid, simple, and cost-effective detection of food-borne fungi has become very important in the area of food safety. Currently, several isothermal nucleic acid amplification methods have been developed as an alternative to PCR-based analyses. Loop-mediated isothermal amplification (LAMP) is one of these innovative methods; it requires neither gel electrophoresis to separate and visualize the products nor expensive laboratory equipment and it has been applied already for detection of pathogenic organisms. In the current study, we developed a LAMP assay for the specific detection of Penicillium nordicum, the major causative agent of ochratoxin A contamination in protein-rich food, especially dry-cured meat products. The assay was based on targeting otapksPN gene, a key gene in the biosynthesis of ochratoxin A (OTA) in P. nordicum. Amplification of DNA during the reaction was detected directly in-tube by color transition of hydroxynaphthol blue from violet to sky blue, visible to the naked eye, avoiding further post amplification analyses. Only DNAs isolated from several P. nordicum strains led to positive results and no amplification was observed from non-target OTA and non OTA-producing strains. The assay was able to detect down to 100 fg of purified targeted genomic DNA or 10(2) conidia/reaction within 60 min. The LAMP assay for detection and identification of P. nordicum was combined with a rapid DNA extraction method set up on serially diluted conidia, providing an alternative rapid, specific and sensitive DNA-based method suitable for application directly "on-site", notably in key steps of dry-cured meat production. Copyright © 2015 Elsevier B.V. All rights reserved.

Pathways between primary production and fisheries yields of large marine ecosystems.

PubMed

Friedland, Kevin D; Stock, Charles; Drinkwater, Kenneth F; Link, Jason S; Leaf, Robert T; Shank, Burton V; Rose, Julie M; Pilskaln, Cynthia H; Fogarty, Michael J

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems.

Pathways between Primary Production and Fisheries Yields of Large Marine Ecosystems

PubMed Central

Friedland, Kevin D.; Stock, Charles; Drinkwater, Kenneth F.; Link, Jason S.; Leaf, Robert T.; Shank, Burton V.; Rose, Julie M.; Pilskaln, Cynthia H.; Fogarty, Michael J.

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems. PMID:22276100

Boosting production yield of biomedical peptides

NASA Technical Reports Server (NTRS)

Manatt, S. L.

1978-01-01

Nuclear magnetic resonance (NMR) technique is employed to monitor synthesis of biomedical peptides. Application of NMR technique may improve production yields of insulin, ACTH, and growth hormones, as well as other synthesized biomedical peptides.

Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio

PubMed Central

Clausson, Carl-Magnus; Arngården, Linda; Ishaq, Omer; Klaesson, Axel; Kühnemund, Malte; Grannas, Karin; Koos, Björn; Qian, Xiaoyan; Ranefall, Petter; Krzywkowski, Tomasz; Brismar, Hjalmar; Nilsson, Mats; Wählby, Carolina; Söderberg, Ola

2015-01-01

Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes. PMID:26202090

Examining the roles that changing harvested areas, closing yield-gaps, and increasing yield ceilings have had on crop production

NASA Astrophysics Data System (ADS)

Johnston, M.; Ray, D. K.; Mueller, N. D.; Foley, J. A.

2011-12-01

With an increasing and increasingly affluent population, there has been tremendous effort to examine strategies for sustainably increasing agricultural production to meet this surging global demand. Before developing new solutions from scratch, though, we believe it is important to consult our recent agricultural history to see where and how agricultural production changes have already taken place. By utilizing the newly created temporal M3 cropland datasets, we can for the first time examine gridded agricultural yields and area, both spatially and temporally. This research explores the historical drivers of agricultural production changes, from 1965-2005. The results will be presented spatially at the global-level (5-min resolution), as well as at the individual country-level. The primary research components of this study are presented below, including the general methodology utilized in each phase and preliminary results for soybean where available. The complete assessment will cover maize, wheat, rice, soybean, and sugarcane, and will include country-specific analysis for over 200 countries, states, territories and protectorates. Phase 1: The first component of our research isolates changes in agricultural production due to variation in planting decisions (harvested area) from changes in production due to intensification efforts (yield). We examine area/yield changes at the pixel-level over 5-year time-steps to determine how much each component has contributed to overall changes in production. Our results include both spatial patterns of changes in production, as well as spatial maps illustrating to what degree the production change is attributed to area and/or yield. Together, these maps illustrate where, why, and by how much agricultural production has changed over time. Phase 2: In the second phase of our research we attempt to determine the impact that area and yield changes have had on agricultural production at the country-level. We calculate a production

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

2015-07-08

We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

Exponential isothermal amplification of nucleic acids and amplified assays for proteins, cells, and enzyme activities.

PubMed

Reid, Michael S; Le, X Chris; Zhang, Hongquan

2018-04-27

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in-situ assay applications. These amplification techniques eliminate the need for temperature cycling required for polymerase chain reaction (PCR) while achieving comparable amplification yield. We highlight here recent advances in exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. We discuss design strategies, enzyme reactions, detection techniques, and key features. Incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from non-specific template interactions, must be addressed to further improve isothermal and exponential amplification techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amplification of chromosomal DNA in situ

DOEpatents

Christian, Allen T.; Coleman, Matthew A.; Tucker, James D.

2002-01-01

Amplification of chromosomal DNA in situ to increase the amount of DNA associated with a chromosome or chromosome region is described. The amplification of chromosomal DNA in situ provides for the synthesis of Fluorescence in situ Hybridization (FISH) painting probes from single dissected chromosome fragments, the production of cDNA libraries from low copy mRNAs and improved in Comparative Genomic Hybridization (CGH) procedures.

Rolling circle amplification of metazoan mitochondrialgenomes

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

Simison, W. Brian; Lindberg, D.R.; Boore, J.L.

2005-07-31

Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

Evidence of high-elevation amplification versus Arctic amplification

NASA Astrophysics Data System (ADS)

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

Elevation-dependent warming in high-elevation regions and Arctic amplification are of tremendous interest to many scientists who are engaged in studies in climate change. Here, using annual mean temperatures from 2781 global stations for the 1961-2010 period, we find that the warming for the world’s high-elevation stations (>500 m above sea level) is clearly stronger than their low-elevation counterparts; and the high-elevation amplification consists of not only an altitudinal amplification but also a latitudinal amplification. The warming for the high-elevation stations is linearly proportional to the temperature lapse rates along altitudinal and latitudinal gradients, as a result of the functional shape of Stefan-Boltzmann law in both vertical and latitudinal directions. In contrast, neither altitudinal amplification nor latitudinal amplification is found within the Arctic region despite its greater warming than lower latitudes. Further analysis shows that the Arctic amplification is an integrated part of the latitudinal amplification trend for the low-elevation stations (≤500 m above sea level) across the entire low- to high-latitude Northern Hemisphere, also a result of the mathematical shape of Stefan-Boltzmann law but only in latitudinal direction.

Evidence of high-elevation amplification versus Arctic amplification

PubMed Central

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

Elevation-dependent warming in high-elevation regions and Arctic amplification are of tremendous interest to many scientists who are engaged in studies in climate change. Here, using annual mean temperatures from 2781 global stations for the 1961–2010 period, we find that the warming for the world’s high-elevation stations (>500 m above sea level) is clearly stronger than their low-elevation counterparts; and the high-elevation amplification consists of not only an altitudinal amplification but also a latitudinal amplification. The warming for the high-elevation stations is linearly proportional to the temperature lapse rates along altitudinal and latitudinal gradients, as a result of the functional shape of Stefan-Boltzmann law in both vertical and latitudinal directions. In contrast, neither altitudinal amplification nor latitudinal amplification is found within the Arctic region despite its greater warming than lower latitudes. Further analysis shows that the Arctic amplification is an integrated part of the latitudinal amplification trend for the low-elevation stations (≤500 m above sea level) across the entire low- to high-latitude Northern Hemisphere, also a result of the mathematical shape of Stefan-Boltzmann law but only in latitudinal direction. PMID:26753547

Production of first generation adenoviral vectors for preclinical protocols: amplification, purification and functional titration.

PubMed

Armendáriz-Borunda, Juan; Bastidas-Ramírez, Blanca Estela; Sandoval-Rodríguez, Ana; González-Cuevas, Jaime; Gómez-Meda, Belinda; García-Bañuelos, Jesús

2011-11-01

Gene therapy represents a promising approach in the treatment of several diseases. Currently, the ideal vector has yet to be designed; though, adenoviral vectors (Ad-v) have provided the most utilized tool for gene transfer due principally to their simple production, among other specific characteristics. Ad-v viability represents a critical variable that may be affected by storage or shipping conditions and therefore it is advisable to be assessed previously to protocol performance. The present work is unique in this matter, as the complete detailed process to obtain Ad-v of preclinical grade is explained. Amplification in permissive HEK-293 cells, purification in CsCl gradients in a period of 10 h, spectrophotometric titration of viral particles (VP) and titration of infectious units (IU), yielding batches of AdβGal, AdGFP, AdHuPA and AdMMP8, of approximately 10¹³-10¹⁴ VP and 10¹²-10¹³ IU were carried out. In vivo functionality of therapeutic AdHuPA and AdMMP8 was evidenced in rats presenting CCl₄-induced fibrosis, as more than 60% of fibrosis was eliminated in livers after systemic delivery through iliac vein in comparison with irrelevant AdβGal. Time required to accomplish the whole Ad-v production steps, including IU titration was 20 to 30 days. We conclude that production of Ad-v following standard operating procedures assuring vector functionality and the possibility to effectively evaluate experimental gene therapy results, leaving aside the use of high-cost commercial kits or sophisticated instrumentation, can be performed in a conventional laboratory of cell culture. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

MemStar: a one-shot Escherichia coli-based approach for high-level bacterial membrane protein production.

PubMed

Lee, Chiara; Kang, Hae Joo; Hjelm, Anna; Qureshi, Abdul Aziz; Nji, Emmanuel; Choudhury, Hassanul; Beis, Konstantinos; de Gier, Jan-Willem; Drew, David

2014-10-16

Optimising membrane protein production yields in Escherichiacoli can be time- and resource-consuming. Here, we present a simple and effective Membrane protein Single shot amplification recipe: MemStar. This one-shot amplification recipe is based on the E. coli strain Lemo21(DE3), the PASM-5052 auto-induction medium and, contradictorily, an IPTG induction step. Using MemStar, production yields for most bacterial membrane proteins tested were improved to reach an average of 5 mg L(-1) per OD600 unit, which is significantly higher than yields obtained with other common production strategies. With MemStar, we have been able to obtain new structural information for several transporters, including the sodium/proton antiporter NapA. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Yield gap analyses to estimate attainable bovine milk yields and evaluate options to increase production in Ethiopia and India.

PubMed

Mayberry, Dianne; Ash, Andrew; Prestwidge, Di; Godde, Cécile M; Henderson, Ben; Duncan, Alan; Blummel, Michael; Ramana Reddy, Y; Herrero, Mario

2017-07-01

Livestock provides an important source of income and nourishment for around one billion rural households worldwide. Demand for livestock food products is increasing, especially in developing countries, and there are opportunities to increase production to meet local demand and increase farm incomes. Estimating the scale of livestock yield gaps and better understanding factors limiting current production will help to define the technological and investment needs in each livestock sector. The aim of this paper is to quantify livestock yield gaps and evaluate opportunities to increase dairy production in Sub-Saharan Africa and South Asia, using case studies from Ethiopia and India. We combined three different methods in our approach. Benchmarking and a frontier analysis were used to estimate attainable milk yields based on survey data. Household modelling was then used to simulate the effects of various interventions on dairy production and income. We tested interventions based on improved livestock nutrition and genetics in the extensive lowland grazing zone and highland mixed crop-livestock zones of Ethiopia, and the intensive irrigated and rainfed zones of India. Our analyses indicate that there are considerable yield gaps for dairy production in both countries, and opportunities to increase production using the interventions tested. In some cases, combined interventions could increase production past currently attainable livestock yields.

Population diversity of ammonium oxidizers investigated by specific PCR amplification

USGS Publications Warehouse

Ward, B.B.; Voytek, M.A.; Witzel, K.-P.

1997-01-01

The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.

Reduced product yield in chemical processes by second law effects

NASA Technical Reports Server (NTRS)

England, C.; Funk, J. E.

1980-01-01

An analysis of second law effects in chemical processes, where product yield is explicitly related to the individual irreversibilities within the process to indicate a maximum theoretical yield, is presented. Examples are given that indicate differences between first and second law approaches toward process efficiency and process yield. This analysis also expresses production capacity in terms of the heating value of a product. As a result, it is particularly convenient in analyzing fuel conversion plants and their potential for improvement. Relationships are also given for the effects of irreversibilities on requirements for process heat and for feedstocks.

Natural genomic amplification of cholinesterase genes in animals.

PubMed

Chatonnet, Arnaud; Lenfant, Nicolas; Marchot, Pascale; Selkirk, Murray E

2017-08-01

Tight control of the concentration of acetylcholine at cholinergic synapses requires precise regulation of the number and state of the acetylcholine receptors, and of the synthesis and degradation of the neurotransmitter. In particular, the cholinesterase activity has to be controlled exquisitely. In the genome of the first experimental models used (man, mouse, zebrafish and drosophila), there are only one or two genes coding for cholinesterases, whereas there are more genes for their closest relatives the carboxylesterases. Natural amplification of cholinesterase genes was first found to occur in some cancer cells and in insect species subjected to evolutionary pressure by insecticides. Analysis of the complete genome sequences of numerous representatives of the various metazoan phyla show that moderate amplification of cholinesterase genes is not uncommon in molluscs, echinoderms, hemichordates, prochordates or lepidosauria. Amplification of acetylcholinesterase genes is also a feature of parasitic nematodes or ticks. In these parasites, over-production of cholinesterase-like proteins in secreted products and the saliva are presumed to have effector roles related to host infection. These amplification events raise questions about the role of the amplified gene products, and the adaptation processes necessary to preserve efficient cholinergic transmission. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. © 2017 International Society for Neurochemistry.

[Principle of LAMP method--a simple and rapid gene amplification method].

PubMed

Ushikubo, Hiroshi

2004-06-01

So far nucleic acid test (NAT) has been employed in various fields, including infectious disease diagnoses. However, due to its complicated procedures and relatively high cost, it has not been widely utilized in many actual diagnostic applications. We have therefore developed a simple and rapid gene amplification technology, Loop-mediated Isothermal Amplification (LAMP) method, which has shown prominent results of surpassing the performance of the conventional gene amplification methods. LAMP method acquires three main features: (1) all reaction can be carried out under isothermal conditions; (2) the amplification efficiency is extremely high and tremendous amount of amplification products can be obtained; and (3) the reaction is highly specific. Furthermore, developed from the standard LAMP method, a rapid LAMP method, by adding in the loop primers, can reduce the amplification time from the previous 1 hour to less than 30 minutes. Enormous amount of white precipitate of magnesium pyrophosphate is produced as a by-product of the amplification, therefore, direct visual detection is possible without using any reaction indicators and detection equipments. We believe LAMP technology, with the integration of these features, can rightly apply to clinical genetic testing, food and environmental analysis, as well as NAT in different fields.

PCR amplification on microarrays of gel immobilized oligonucleotides

DOEpatents

Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

2003-11-04

The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

Comparison of Fission Product Yields and Their Impact

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

S. Harrison

2006-02-01

This memorandum describes the Naval Reactors Prime Contractor Team (NRPCT) Space Nuclear Power Program (SNPP) interest in determining the expected fission product yields from a Prometheus-type reactor and assessing the impact of these species on materials found in the fuel element and balance of plant. Theoretical yield calculations using ORIGEN-S and RACER computer models are included in graphical and tabular form in Attachment, with focus on the desired fast neutron spectrum data. The known fission product interaction concerns are the corrosive attack of iron- and nickel-based alloys by volatile fission products, such as cesium, tellurium, and iodine, and the radiologicalmore » transmutation of krypton-85 in the coolant to rubidium-85, a potentially corrosive agent to the coolant system metal piping.« less

Methods for high yield production of terpenes

DOEpatents

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.

NEANDC specialists meeting on yields and decay data of fission product nuclides

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

Chrien, R.E.; Burrows, T.W.

Separate abstracts were prepared for the 29 papers presented. Workshop reports on decay heat, fission yields, beta- and gamma-ray spectroscopy, and delayed neutrons are included. An appendix contains a survey of the most recent compilations and evaluations containing fission product yield, fission product decay data, and delayed neutron yield information. (WHK)

Measurement of Fission Product Yields from Fast-Neutron Fission

NASA Astrophysics Data System (ADS)

Arnold, C. W.; Bond, E. M.; Bredeweg, T. A.; Fowler, M. M.; Moody, W. A.; Rusev, G.; Vieira, D. J.; Wilhelmy, J. B.; Becker, J. A.; Henderson, R.; Kenneally, J.; Macri, R.; McNabb, D.; Ryan, C.; Sheets, S.; Stoyer, M. A.; Tonchev, A. P.; Bhatia, C.; Bhike, M.; Fallin, B.; Gooden, M. E.; Howell, C. R.; Kelley, J. H.; Tornow, W.

2014-09-01

One of the aims of the Stockpile Stewardship Program is a reduction of the uncertainties on fission data used for analyzing nuclear test data [1,2]. Fission products such as 147Nd are convenient for determining fission yields because of their relatively high yield per fission (about 2%) and long half-life (10.98 days). A scientific program for measuring fission product yields from 235U,238U and 239Pu targets as a function of bombarding neutron energy (0.1 to 15 MeV) is currently underway using monoenergetic neutron beams produced at the 10 MV Tandem Accelerator at TUNL. Dual-fission chambers are used to determine the rate of fission in targets during activation. Activated targets are counted in highly shielded HPGe detectors over a period of several weeks to identify decaying fission products. To date, data have been collected at neutron bombarding energies 4.6, 9.0, 14.5 and 14.8 MeV. Experimental methods and data reduction techniques are discussed, and some preliminary results are presented.

The use of short and long PCR products for improved detection of prunus necrotic ringspot virus in woody plants.

PubMed

Rosner, A; Maslenin, L; Spiegel, S

1997-09-01

The reverse transcriptase-polymerase chain reaction (RT-PCR) was used for detection of prunus necrotic ringspot virus (PNRSV) in dormant peach and almond trees by the application of two different pairs of primers yielding a short and a long product, respectively. The relative amount of the short (200 base pair, bp) product was higher than the longer (785 bp) product. PNRSV was detected better in plant tissues with a low virus concentration (e.g. dormant trees) by amplification of the short PCR product, whereas the long product was product was produced at higher virus titers. Simultaneous amplification of both short and long products was demonstrated using a three-primer mixture in a single reaction tube. In this assay, amplification of either PCR product indicated the presence of PNRSV-specific sequences in the plant tissue examined, thus covering a wide range of virus concentrations in a single test. Dilution of the RNA extracted from infected plant material resulted in a steep decline in the amplification of both short and long PCR products. In contrast, serial dilutions of the intermediate cDNA template differentially affected the amplification patterns: the relative amount of the short product increased whereas that of the long product decreased. These results may explain the preferential amplification of the short PCR product observed in samples containing low virus concentrations.

Controlled Microwave Heating Accelerates Rolling Circle Amplification

PubMed Central

Yoshimura, Takeo; Suzuki, Takamasa; Mineki, Shigeru; Ohuchi, Shokichi

2015-01-01

Rolling circle amplification (RCA) generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same. PMID:26348227

Controlled Microwave Heating Accelerates Rolling Circle Amplification.

PubMed

Yoshimura, Takeo; Suzuki, Takamasa; Mineki, Shigeru; Ohuchi, Shokichi

2015-01-01

Rolling circle amplification (RCA) generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same.

National Variation in Crop Yield Production Functions

NASA Astrophysics Data System (ADS)

Devineni, N.; Rising, J. A.

2017-12-01

A new multilevel model for yield prediction at the county scale using regional climate covariates is presented in this paper. A new crop specific water deficit index, growing degree days, extreme degree days, and time-trend as an approximation of technology improvements are used as predictors to estimate annual crop yields for each county from 1949 to 2009. Every county in the United States is allowed to have unique parameters describing how these weather predictors are related to yield outcomes. County-specific parameters are further modeled as varying according to climatic characteristics, allowing the prediction of parameters in regions where crops are not currently grown and into the future. The structural relationships between crop yield and regional climate as well as trends are estimated simultaneously. All counties are modeled in a single multilevel model with partial pooling to automatically group and reduce estimation uncertainties. The model captures up to 60% of the variability in crop yields after removing the effect of technology, does well in out of sample predictions and is useful in relating the climate responses to local bioclimatic factors. We apply the predicted growing models in a cost-benefit analysis to identify the most economically productive crop in each county.

Greenhouse tomato limited cluster production systems: crop management practices affect yield

NASA Technical Reports Server (NTRS)

Logendra, L. S.; Gianfagna, T. J.; Specca, D. R.; Janes, H. W.

2001-01-01

Limited-cluster production systems may be a useful strategy to increase crop production and profitability for the greenhouse tomato (Lycopersicon esculentum Mill). In this study, using an ebb-and-flood hydroponics system, we modified plant architecture and spacing and determined the effects on fruit yield and harvest index at two light levels. Single-cluster plants pruned to allow two leaves above the cluster had 25% higher fruit yields than did plants pruned directly above the cluster; this was due to an increase in fruit weight, not fruit number. Both fruit yield and harvest index were greater for all single-cluster plants at the higher light level because of increases in both fruit weight and fruit number. Fruit yield for two-cluster plants was 30% to 40% higher than for single-cluster plants, and there was little difference in the dates or length of the harvest period. Fruit yield for three-cluster plants was not significantly different from that of two-cluster plants; moreover, the harvest period was delayed by 5 days. Plant density (5.5, 7.4, 9.2 plants/m2) affected fruit yield/plant, but not fruit yield/unit area. Given the higher costs for materials and labor associated with higher plant densities, a two-cluster crop at 5.5 plants/m2 with two leaves above the cluster was the best of the production system strategies tested.

Protection from feed-forward amplification in an amplified RNAi mechanism

PubMed Central

Pak, Julia; Maniar, Jay Mahesh; Mello, Cecilia Cabral; Fire, Andrew

2012-01-01

SUMMARY The effectiveness of RNA interference (RNAi) in many organisms is potentiated through the signal-amplifying activity of a targeted RNA directed RNA polymerase (RdRP) system that can convert a small population of exogenously-encountered dsRNA fragments into an abundant internal pool of small interfering RNA (siRNA). As for any biological amplification system, we expect an underlying architecture that will limit the ability of a randomly encountered trigger to produce an uncontrolled and self-escalating response. Investigating such limits in C. elegans, we find that feed-forward amplification is limited by a critical biosynthetic and structural distinction at the RNA level between (i) triggers that can produce amplification and (ii) siRNA products of the amplification reaction. By assuring that initial (primary) siRNAs can act as triggers but not templates for activation, and that the resulting (secondary) siRNAs can enforce gene silencing on additional targets without unbridled trigger amplification, the system achieves substantial but fundamentally limited signal amplification. PMID:23141544

Two-dimensional isobutyl acetate production pathways to improve carbon yield

PubMed Central

Tashiro, Yohei; Desai, Shuchi H.; Atsumi, Shota

2015-01-01

For an economically competitive biological process, achieving high carbon yield of a target chemical is crucial. In biochemical production, pyruvate and acetyl-CoA are primary building blocks. When sugar is used as the sole biosynthetic substrate, acetyl-CoA is commonly generated by pyruvate decarboxylation. However, pyruvate decarboxylation during acetyl-CoA formation limits the theoretical maximum carbon yield (TMCY) by releasing carbon, and in some cases also leads to redox imbalance. To avoid these problems, we describe here the construction of a metabolic pathway that simultaneously utilizes glucose and acetate. Acetate is utilized to produce acetyl-CoA without carbon loss or redox imbalance. We demonstrate the utility of this approach for isobutyl acetate (IBA) production, wherein IBA production with glucose and acetate achieves a higher carbon yield than with either sole carbon source. These results highlight the potential for this multiple carbon source approach to improve the TMCY and balance redox in biosynthetic pathways. PMID:26108471

Epstein-Barr Viral Productive Amplification Reprograms Nuclear Architecture, DNA Replication and Histone Deposition

PubMed Central

Chiu, Ya-Fang; Sugden, Arthur U.; Sugden, Bill

2014-01-01

Summary The spontaneous transition of Epstein-Barr Virus (EBV) from latency to productive infection is infrequent, making its analysis in the resulting mixed cell populations difficult. We engineered cells to support this transition efficiently and developed EBV DNA variants that could be visualized and measured as fluorescent signals over multiple cell cycles. This approach revealed that EBV’s productive replication began synchronously for viral DNAs within a cell but asynchronously between cells. EBV DNA amplification was delayed until early S-phase and occurred in factories characterized by the absence of cellular DNA and histones, by a sequential redistribution of PCNA, and by localization away from the nuclear periphery. The earliest amplified DNAs lacked histones accompanying a decline in four histone chaperones. Thus, EBV transitions from being dependent on the cellular replication machinery during latency to commandeering both that machinery and nuclear structure for its own reproductive needs. PMID:24331459

[Investigation of RNA viral genome amplification by multiple displacement amplification technique].

PubMed

Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

2013-06-01

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

Climate-Driven Crop Yield and Yield Variability and Climate Change Impacts on the U.S. Great Plains Agricultural Production.

PubMed

Kukal, Meetpal S; Irmak, Suat

2018-02-22

Climate variability and trends affect global crop yields and are characterized as highly dependent on location, crop type, and irrigation. U.S. Great Plains, due to its significance in national food production, evident climate variability, and extensive irrigation is an ideal region of investigation for climate impacts on food production. This paper evaluates climate impacts on maize, sorghum, and soybean yields and effect of irrigation for individual counties in this region by employing extensive crop yield and climate datasets from 1968-2013. Variability in crop yields was a quarter of the regional average yields, with a quarter of this variability explained by climate variability, and temperature and precipitation explained these in singularity or combination at different locations. Observed temperature trend was beneficial for maize yields, but detrimental for sorghum and soybean yields, whereas observed precipitation trend was beneficial for all three crops. Irrigated yields demonstrated increased robustness and an effective mitigation strategy against climate impacts than their non-irrigated counterparts by a considerable fraction. The information, data, and maps provided can serve as an assessment guide for planners, managers, and policy- and decision makers to prioritize agricultural resilience efforts and resource allocation or re-allocation in the regions that exhibit risk from climate variability.

Investigation of inconsistent ENDF/B-VII.1 independent and cumulative fission product yields with proposed revisions

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

Pigni, Marco T; Francis, Matthew W; Gauld, Ian C

A recent implementation of ENDF/B-VII. independent fission product yields and nuclear decay data identified inconsistencies in the data caused by the use of updated nuclear scheme in the decay sub-library that is not reflected in legacy fission product yield data. Recent changes in the decay data sub-library, particularly the delayed neutron branching fractions, result in calculated fission product concentrations that are incompatible with the cumulative fission yields in the library, and also with experimental measurements. A comprehensive set of independent fission product yields was generated for thermal and fission spectrum neutron induced fission for 235,238U and 239,241Pu in order tomore » provide a preliminary assessment of the updated fission product yield data consistency. These updated independent fission product yields were utilized in the ORIGEN code to evaluate the calculated fission product inventories with experimentally measured inventories, with particular attention given to the noble gases. An important outcome of this work is the development of fission product yield covariance data necessary for fission product uncertainty quantification. The evaluation methodology combines a sequential Bayesian method to guarantee consistency between independent and cumulative yields along with the physical constraints on the independent yields. This work was motivated to improve the performance of the ENDF/B-VII.1 library in the case of stable and long-lived cumulative yields due to the inconsistency of ENDF/B-VII.1 fission p;roduct yield and decay data sub-libraries. The revised fission product yields and the new covariance data are proposed as a revision to the fission yield data currently in ENDF/B-VII.1.« less

An aptasensor for staphylococcus aureus based on nicking enzyme amplification reaction and rolling circle amplification.

PubMed

Xu, Jingguo; Guo, Jia; Maina, Sarah Wanjiku; Yang, Yumeng; Hu, Yimin; Li, Xuanxuan; Qiu, Jiarong; Xin, Zhihong

2018-05-15

An ultra-sensitive aptamer-based biosensor for the detection of staphylococcus aureus was established by adopting the nicking enzyme amplification reaction (NEAR) and the rolling circle amplification (RCA) technologies. Aptamer-probe (AP), containing an aptamer and a probe sequence, was developed to act as the recognition unit of the biosensor, which was specifically bound to S. aureus. The probe was released from AP and initiated into the subsequent DNA amplification reactions where S. aureus was present, converting the detection of S. aureus to the investigation of probe oligonucleotide. The RCA amplification products contained a G-quadruplex motif and formed a three dimensional structure in presence of hemin. The G4/hemin complex showed horseradish peroxidase (HRP)-mimic activity and catalyzed the chemiluminescence reaction of luminol mediated by H 2 O 2 . The results showed that the established biosensor could detect S. aureus specifically with a good linear correlation at 5-10 4  CFU/mL. The signal values based on NEAR-RCA two-step cycle were boosted acutely, much higher than that relied on one-cycle magnification. The limit of detection (LoD) was determined to be as low as 5 CFU/mL. The established aptasensor exhibited a good discrimination of living against dead S. aureus, and can be applied to detect S. aureus in the food industry. Copyright © 2018 Elsevier Inc. All rights reserved.

Investigation of Inconsistent ENDF/B-VII.1 Independent and Cumulative Fission Product Yields with Proposed Revisions

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

Pigni, M.T., E-mail: pignimt@ornl.gov; Francis, M.W.; Gauld, I.C.

A recent implementation of ENDF/B-VII.1 independent fission product yields and nuclear decay data identified inconsistencies in the data caused by the use of updated nuclear schemes in the decay sub-library that are not reflected in legacy fission product yield data. Recent changes in the decay data sub-library, particularly the delayed neutron branching fractions, result in calculated fission product concentrations that do not agree with the cumulative fission yields in the library as well as with experimental measurements. To address these issues, a comprehensive set of independent fission product yields was generated for thermal and fission spectrum neutron-induced fission for {supmore » 235,238}U and {sup 239,241}Pu in order to provide a preliminary assessment of the updated fission product yield data consistency. These updated independent fission product yields were utilized in the ORIGEN code to compare the calculated fission product inventories with experimentally measured inventories, with particular attention given to the noble gases. Another important outcome of this work is the development of fission product yield covariance data necessary for fission product uncertainty quantification. The evaluation methodology combines a sequential Bayesian method to guarantee consistency between independent and cumulative yields along with the physical constraints on the independent yields. This work was motivated to improve the performance of the ENDF/B-VII.1 library for stable and long-lived fission products. The revised fission product yields and the new covariance data are proposed as a revision to the fission yield data currently in ENDF/B-VII.1.« less

Products and yields from O3 photodissociation at 1576 A

NASA Technical Reports Server (NTRS)

Taherian, M. R.; Slanger, T. G.

1985-01-01

An analysis has been made of the primary atomic and molecular products arising from O3 photodissociation at 1576 A. The yield of oxygen atoms is 1.90 + or - 0.30, of which 71 percent are O(3P) and 29 percent are O(1D). Since a primary yield greater than unity can only be a consequence of three-fragment dissociation, these results suggest that fragmentation into three O(3P) atoms, and production of O(1D) plus a singlet oxygen molecule, have comparable yields. Observation of prompt emission in the 7300-8100 A spectral region indicates that the singlet O2 is O2(b 1Sigma + g). Vibrational levels in the range v = 0-6 have been detected, the distribution corresponding to a vibrational temperature of 1000 K.

Pressure-Dependent Yields and Product Branching Ratios in the Broadband Photolysis of Chlorine Nitrate

NASA Technical Reports Server (NTRS)

Nickolaisen, Scott L.; Sander, Stanley P.; Friedl, Randall R.

1996-01-01

The photolysis of chlorine nitrate was studied using broadband flash photolysis coupled with long-path ultraviolet-visible absorption spectroscopy. Branching ratios for the Cl + NO3 and ClO + NO2 product channels were determined from time-dependent measurements of ClO and NO3 concentrations. Yields of the ClO and NO3 products displayed a dependence on the bath gas density and the spectral distribution of the photolysis pulse. Product yields decreased with increasing bath gas density regardless of the spectral distribution of the photolysis pulse; however, the decrease in product yield was much more pronounced when photolysis was limited to longer wavelengths. For photolysis in a quartz cell (lambda > 200 nm) the yield decreased by a factor of 2 over the pressure 10-100 Torr. In a Pyrex cell (lambda > 300 nm), the yield decreased by a factor of 50 over the same pressure range. When photolysis was limited to lambda > 350 nm, the yield decreased by a factor of 250. Branching ratios for the photolysis channels [ClONO2 + h.nu yields ClO + NO2 (1a) and ClONO2 + h.nu yields Cl + NO3 (lb)] were determined from the relative ClO and NO3 product yields at various pressures. Although the absolute product yield displayed a pressure dependence, the branching between the two channels was independent of pressure. The relative branching ratios (assuming negligible contributions from other channels) are 0.61 +/- 0.20 for channel 1a and 0.39 +/- 0.20 for channel lb for photolysis with lambda > 200 nm and 0.44 +/- 0.08 for channel 1a and 0.56 +/- 0.08 for channel 1b for photolysis with lambda > 300 nm. The implications of these results for the chemistry of the lower stratosphere are discussed.

Telomerase Repeated Amplification Protocol (TRAP).

PubMed

Mender, Ilgen; Shay, Jerry W

2015-11-20

Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

Relative fission product yield determination in the USGS TRIGA Mark I reactor

NASA Astrophysics Data System (ADS)

Koehl, Michael A.

Fission product yield data sets are one of the most important and fundamental compilations of basic information in the nuclear industry. This data has a wide range of applications which include nuclear fuel burnup and nonproliferation safeguards. Relative fission yields constitute a major fraction of the reported yield data and reduce the number of required absolute measurements. Radiochemical separations of fission products reduce interferences, facilitate the measurement of low level radionuclides, and are instrumental in the analysis of low-yielding symmetrical fission products. It is especially useful in the measurement of the valley nuclides and those on the extreme wings of the mass yield curve, including lanthanides, where absolute yields have high errors. This overall project was conducted in three stages: characterization of the neutron flux in irradiation positions within the U.S. Geological Survey TRIGA Mark I Reactor (GSTR), determining the mass attenuation coefficients of precipitates used in radiochemical separations, and measuring the relative fission products in the GSTR. Using the Westcott convention, the Westcott flux, modified spectral index, neutron temperature, and gold-based cadmium ratios were determined for various sampling positions in the USGS TRIGA Mark I reactor. The differential neutron energy spectrum measurement was obtained using the computer iterative code SAND-II-SNL. The mass attenuation coefficients for molecular precipitates were determined through experiment and compared to results using the EGS5 Monte Carlo computer code. Difficulties associated with sufficient production of fission product isotopes in research reactors limits the ability to complete a direct, experimental assessment of mass attenuation coefficients for these isotopes. Experimental attenuation coefficients of radioisotopes produced through neutron activation agree well with the EGS5 calculated results. This suggests mass attenuation coefficients of molecular

Yield gaps and yield relationships in US soybean production systems

USDA-ARS?s Scientific Manuscript database

The magnitude of yield gaps (YG) (potential yield – farmer yield) provides some indication of the prospects for increasing crop yield to meet the food demands of future populations. Quantile regression analysis was applied to county soybean [Glycine max (L.) Merrill] yields (1971 – 2011) from Kentuc...

Weak value amplification considered harmful

NASA Astrophysics Data System (ADS)

Ferrie, Christopher; Combes, Joshua

2014-03-01

We show using statistically rigorous arguments that the technique of weak value amplification does not perform better than standard statistical techniques for the tasks of parameter estimation and signal detection. We show that using all data and considering the joint distribution of all measurement outcomes yields the optimal estimator. Moreover, we show estimation using the maximum likelihood technique with weak values as small as possible produces better performance for quantum metrology. In doing so, we identify the optimal experimental arrangement to be the one which reveals the maximal eigenvalue of the square of system observables. We also show these conclusions do not change in the presence of technical noise.

A cascade signal amplification strategy for sensitive and label-free DNA detection based on Exo III-catalyzed recycling coupled with rolling circle amplification.

PubMed

Liu, Xingti; Xue, Qingwang; Ding, Yongshun; Zhu, Jing; Wang, Lei; Jiang, Wei

2014-06-07

A sensitive and label-free fluorescence assay for DNA detection has been developed based on cascade signal amplification combining exonuclease III (Exo III)-catalyzed recycling with rolling circle amplification. In this assay, probe DNA hybridized with template DNA was coupled onto magnetic nanoparticles to prepare a magnetic bead-probe (MNB-probe)-template complex. The complex could hybridize with the target DNA, which transformed the protruding 3' terminus of template DNA into a blunt end. Exo III could then digest template DNA, liberating the MNB-probe and target DNA. The intact target DNA then hybridized with other templates and released more MNB-probes. The liberated MNB-probe captured the primer, circular DNA and then initiated the rolling circle amplification (RCA) reaction, realizing a cascade signal amplification. Using this cascade amplification strategy, a sensitive DNA detection method was developed which was superior to many existing Exo III-based signal amplification methods. Moreover, N-methyl mesoporphyrin IX, which had a pronounced structural selectivity for the G-quadruplex, was used to combine with the G-quadruplex RCA products and generate a fluorescence signal, avoiding the need for any fluorophore-label probes. The spike and recovery experiments in a human serum sample indicated that our assay also had great potential for DNA detection in real biological samples.

Digital droplet multiple displacement amplification (ddMDA) for whole genome sequencing of limited DNA samples

DOE PAGES

Rhee, Minsoung; Light, Yooli K.; Meagher, Robert J.; ...

2016-05-04

Here, multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently,more » the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.« less

Digital droplet multiple displacement amplification (ddMDA) for whole genome sequencing of limited DNA samples

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

Rhee, Minsoung; Light, Yooli K.; Meagher, Robert J.

Here, multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently,more » the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.« less

The SPIDER fission fragment spectrometer for fission product yield measurements

DOE PAGES

Meierbachtol, K.; Tovesson, F.; Shields, D.; ...

2015-04-01

We developed the SPectrometer for Ion DEtermination in fission Research (SPIDER) for measuring mass yield distributions of fission products from spontaneous and neutron-induced fission. The 2E–2v method of measuring the kinetic energy (E) and velocity (v) of both outgoing fission products has been utilized, with the goal of measuring the mass of the fission products with an average resolution of 1 atomic mass unit (amu). Moreover, the SPIDER instrument, consisting of detector components for time-of-flight, trajectory, and energy measurements, has been assembled and tested using 229Th and 252Cf radioactive decay sources. For commissioning, the fully assembled system measured fission productsmore » from spontaneous fission of 252Cf. Individual measurement resolutions were met for time-of-flight (250 ps FWHM), spacial resolution (2 mm FHWM), and energy (92 keV FWHM for 8.376 MeV). Finally, these mass yield results measured from 252Cf spontaneous fission products are reported from an E–v measurement.« less

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

NASA Astrophysics Data System (ADS)

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.

Engineering of Corynebacterium glutamicum for high-yield L-valine production under oxygen deprivation conditions.

PubMed

Hasegawa, Satoshi; Suda, Masako; Uematsu, Kimio; Natsuma, Yumi; Hiraga, Kazumi; Jojima, Toru; Inui, Masayuki; Yukawa, Hideaki

2013-02-01

We previously demonstrated efficient L-valine production by metabolically engineered Corynebacterium glutamicum under oxygen deprivation. To achieve the high productivity, a NADH/NADPH cofactor imbalance during the synthesis of l-valine was overcome by engineering NAD-preferring mutant acetohydroxy acid isomeroreductase (AHAIR) and using NAD-specific leucine dehydrogenase from Lysinibacillus sphaericus. Lactate as a by-product was largely eliminated by disrupting the lactate dehydrogenase gene ldhA. Nonetheless, a few other by-products, particularly succinate, were still produced and acted to suppress the L-valine yield. Eliminating these by-products therefore was deemed key to improving theL-valine yield. By additionally disrupting the phosphoenolpyruvate carboxylase gene ppc, succinate production was effectively suppressed, but both glucose consumption and L-valine production dropped considerably due to the severely elevated intracellular NADH/NAD(+) ratio. In contrast, this perturbed intracellular redox state was more than compensated for by deletion of three genes associated with NADH-producing acetate synthesis and overexpression of five glycolytic genes, including gapA, encoding NADH-inhibited glyceraldehyde-3-phosphate dehydrogenase. Inserting feedback-resistant mutant acetohydroxy acid synthase and NAD-preferring mutant AHAIR in the chromosome resulted in higher L-valine yield and productivity. Deleting the alanine transaminase gene avtA suppressed alanine production. The resultant strain produced 1,280 mM L-valine at a yield of 88% mol mol of glucose(-1) after 24 h under oxygen deprivation, a vastly improved yield over our previous best.

Engineering of Corynebacterium glutamicum for High-Yield l-Valine Production under Oxygen Deprivation Conditions

PubMed Central

Hasegawa, Satoshi; Suda, Masako; Uematsu, Kimio; Natsuma, Yumi; Hiraga, Kazumi; Jojima, Toru; Inui, Masayuki

2013-01-01

We previously demonstrated efficient l-valine production by metabolically engineered Corynebacterium glutamicum under oxygen deprivation. To achieve the high productivity, a NADH/NADPH cofactor imbalance during the synthesis of l-valine was overcome by engineering NAD-preferring mutant acetohydroxy acid isomeroreductase (AHAIR) and using NAD-specific leucine dehydrogenase from Lysinibacillus sphaericus. Lactate as a by-product was largely eliminated by disrupting the lactate dehydrogenase gene ldhA. Nonetheless, a few other by-products, particularly succinate, were still produced and acted to suppress the l-valine yield. Eliminating these by-products therefore was deemed key to improving the l-valine yield. By additionally disrupting the phosphoenolpyruvate carboxylase gene ppc, succinate production was effectively suppressed, but both glucose consumption and l-valine production dropped considerably due to the severely elevated intracellular NADH/NAD+ ratio. In contrast, this perturbed intracellular redox state was more than compensated for by deletion of three genes associated with NADH-producing acetate synthesis and overexpression of five glycolytic genes, including gapA, encoding NADH-inhibited glyceraldehyde-3-phosphate dehydrogenase. Inserting feedback-resistant mutant acetohydroxy acid synthase and NAD-preferring mutant AHAIR in the chromosome resulted in higher l-valine yield and productivity. Deleting the alanine transaminase gene avtA suppressed alanine production. The resultant strain produced 1,280 mM l-valine at a yield of 88% mol mol of glucose−1 after 24 h under oxygen deprivation, a vastly improved yield over our previous best. PMID:23241971

Soil Texture and Cultivar Effects on Rice (Oryza sativa, L.) Grain Yield, Yield Components and Water Productivity in Three Water Regimes.

PubMed

Dou, Fugen; Soriano, Junel; Tabien, Rodante E; Chen, Kun

2016-01-01

The objective of this study was to determine the effects of water regime/soil condition (continuous flooding, saturated, and aerobic), cultivar ('Cocodrie' and 'Rondo'), and soil texture (clay and sandy loam) on rice grain yield, yield components and water productivity using a greenhouse trial. Rice grain yield was significantly affected by soil texture and the interaction between water regime and cultivar. Significantly higher yield was obtained in continuous flooding than in aerobic and saturated soil conditions but the latter treatments were comparable to each other. For Rondo, its grain yield has decreased with soil water regimes in the order of continuous flooding, saturated and aerobic treatments. The rice grain yield in clay soil was 46% higher than in sandy loam soil averaged across cultivar and water regime. Compared to aerobic condition, saturated and continuous flooding treatments had greater panicle numbers. In addition, panicle number in clay soil was 25% higher than in sandy loam soil. The spikelet number of Cocodrie was 29% greater than that of Rondo, indicating that rice cultivar had greater effect on spikelet number than soil type and water management. Water productivity was significantly affected by the interaction of water regime and cultivar. Compared to sandy loam soil, clay soil was 25% higher in water productivity. Our results indicated that cultivar selection and soil texture are important factors in deciding what water management option to practice.

Production yield of rare-earth ions implanted into an optical crystal

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

Kornher, Thomas, E-mail: t.kornher@physik.uni-stuttgart.de; Xia, Kangwei; Kolesov, Roman

2016-02-01

Rare-earth (RE) ions doped into desired locations of optical crystals might enable a range of novel integrated photonic devices for quantum applications. With this aim, we have investigated the production yield of cerium and praseodymium by means of ion implantation. As a measure, the collected fluorescence intensity from both implanted samples and single centers was used. With a tailored annealing procedure for cerium, a yield up to 53% was estimated. Praseodymium yield amounts up to 91%. Such high implantation yield indicates a feasibility of creation of nanopatterned rare-earth doping and suggests strong potential of RE species for on-chip photonic devices.

Linear RNA amplification for the production of microarray hybridization probes.

PubMed

Klebes, Ansgar; Kornberg, Thomas B

2008-01-01

To understand Drosophila development and other genetically controlled processes, it is often desirable to identify differences in gene expression levels. An experimental approach to investigate these processes is to catalog the transcriptome by hybridization of mRNA to DNA microbar-rays. In these experiments mRNA-derived hybridization probes are produced and hybridized to an array of DNA spots on a solid support. The labeled cDNAs of the complex hybridization probe will bind to their complementary sequences and provide quantification of the relative concentration of the corresponding transcript in the starting material. However, such approaches are often limited by the scarcity of the experimental sample because standard methods of probe preparation require microgram quantities of mRNA template. Linear RNA amplification can alleviate such limitations to support the generation of microarray hybridization probes from a few 100 pg of mRNA. These smaller quantities can be isolated from a few 100 cells. Here, we present a linear amplification protocol designed to preserve both the relative abundance of transcripts as well as their sequence complexity.

Multiple displacement amplification on single cell and possible PGD applications.

PubMed

Hellani, Ali; Coskun, Serdar; Benkhalifa, Moncef; Tbakhi, Abelghani; Sakati, Nadia; Al-Odaib, Ali; Ozand, Pinar

2004-11-01

Multiple displacement amplification (MDA) is a technique used in the amplification of very low amounts of DNA and reported to yield large quantities of high-quality DNA. We used MDA to amplify the whole genome directly from a single cell. The most common techniques used in PGD are PCR and fluorescent in-situ hybridization (FISH). There are many limitations to these techniques including, the number of chromosomes diagnosed for FISH or the quality of DNA issued from a single cell PCR. This report shows, for the first time, use of MDA for single cell whole genome amplification. A total of 16 short tandem repeats (STRs) were amplified successfully with a similar pattern to the genomic DNA. Furthermore, allelic drop out (ADO) derived from MDA was assessed in 40 single cells by analysing (i) heterozygosity for a known beta globin mutation (IVSI-5 C-G) and by studying (ii) the heterozygous loci present in the STRs. ADO turned out to be 10.25% for the beta globin gene sequencing and 5% for the fluorescent PCR analysis of STRs. Moreover, the amplification accuracy of MDA permitted the detection of trisomy 21 on a single cell using comparative genome hybridization-array. Altogether, these data suggest that MDA can be used for single cell molecular karyotyping and the diagnosis of any single gene disorder in PGD.

Amplification and Attenuation Across USArray Using Ambient Noise Wavefront Tracking

NASA Astrophysics Data System (ADS)

Bowden, Daniel C.; Tsai, Victor C.; Lin, Fan-Chi

2017-12-01

As seismic traveltime tomography continues to be refined using data from the vast USArray data set, it is advantageous to also exploit the amplitude information carried by seismic waves. We use ambient noise cross correlation to make observations of surface wave amplification and attenuation at shorter periods (8-32 s) than can be observed with only traditional teleseismic earthquake sources. We show that the wavefront tracking approach can be successfully applied to ambient noise correlations, yielding results quite similar to those from earthquake observations at periods of overlap. This consistency indicates that the wavefront tracking approach is viable for use with ambient noise correlations, despite concerns of the inhomogeneous and unknown distribution of noise sources. The resulting amplification and attenuation maps correlate well with known tectonic and crustal structure; at the shortest periods, our amplification and attenuation maps correlate well with surface geology and known sedimentary basins, while our longest period amplitudes are controlled by crustal thickness and begin to probe upper mantle materials. These amplification and attenuation observations are sensitive to crustal materials in different ways than traveltime observations and may be used to better constrain temperature or density variations. We also value them as an independent means of describing the lateral variability of observed Rayleigh wave amplitudes without the need for 3-D tomographic inversions.

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification.

PubMed

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-10-21

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of "G-quadruplex" in lantern-like structures. Finally, the continuously enriched "G-quadruplex lanterns" were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10 -17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring.

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification

PubMed Central

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-01-01

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of “G-quadruplex” in lantern-like structures. Finally, the continuously enriched “G-quadruplex lanterns” were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10−17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring. PMID:28335318

Single-molecule dilution and multiple displacement amplification for molecular haplotyping.

PubMed

Paul, Philip; Apgar, Josh

2005-04-01

Separate haploid analysis is frequently required for heterozygous genotyping to resolve phase ambiguity or confirm allelic sequence. We demonstrate a technique of single-molecule dilution followed by multiple strand displacement amplification to haplotype polymorphic alleles. Dilution of DNA to haploid equivalency, or a single molecule, is a simple method for separating di-allelic DNA. Strand displacement amplification is a robust method for non-specific DNA expansion that employs random hexamers and phage polymerase Phi29 for double-stranded DNA displacement and primer extension, resulting in high processivity and exceptional product length. Single-molecule dilution was followed by strand displacement amplification to expand separated alleles to microgram quantities of DNA for more efficient haplotype analysis of heterozygous genes.

High-yield production of herbicidal thaxtomins and analogs in a nonpathogenic Streptomyces strain.

PubMed

Jiang, Guangde; Zhang, Yucheng; Powell, Magan M; Zhang, Peilan; Zuo, Ran; Zhang, Yi; Kallifidas, Dimitrios; Tieu, Albert M; Luesch, Hendrik; Loria, Rosemary; Ding, Yousong

2018-03-30

Thaxtomins are virulence factors of most plant pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the United States Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitro-tryptophan analogs were observed using LC-MS analysis. When culturing the engineered S. albus J1074 in the minimal medium TMDc, the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/L. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized to produce one unnatural fluorinated analog 5-F-thaxtomin A, whose structure was elucidated by a combination of MS and 1D and 2D NMR analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and thereof with high yield, fostering their agricultural applications. IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products but the productivity of native producers is limiting. Heterologous expression of thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap

Yield and yield gaps in central U.S. corn production systems

USDA-ARS?s Scientific Manuscript database

The magnitude of yield gaps (YG) (potential yield – farmer yield) provides some indication of the prospects for increasing crop yield. Quantile regression analysis was applied to county maize (Zea mays L.) yields (1972 – 2011) from Kentucky, Iowa and Nebraska (irrigated) (total of 115 counties) to e...

Gene amplification during myogenic differentiation

PubMed Central

Fischer, Ulrike; Ludwig, Nicole; Raslan, Abdulrahman; Meier, Carola; Meese, Eckart

2016-01-01

Gene amplifications are mostly an attribute of tumor cells and drug resistant cells. Recently, we provided evidence for gene amplifications during differentiation of human and mouse neural progenitor cells. Here, we report gene amplifications in differentiating mouse myoblasts (C2C12 cells) covering a period of 7 days including pre-fusion, fusion and post-fusion stages. After differentiation induction we found an increase in copy numbers of CDK4 gene at day 3, of NUP133 at days 4 and 7, and of MYO18B at day 4. The amplification process was accompanied by gamma-H2AX foci that are indicative of double stand breaks. Amplifications during the differentiating process were also found in primary human myoblasts with the gene CDK4 and NUP133 amplified both in human and mouse myoblasts. Amplifications of NUP133 and CDK4 were also identified in vivo on mouse transversal cryosections at stage E11.5. In the course of myoblast differentiation, we found amplifications in cytoplasm indicative of removal of amplified sequences from the nucleus. The data provide further evidence that amplification is a fundamental mechanism contributing to the differentiation process in mammalians. PMID:26760505

Quality control for quantitative PCR based on amplification compatibility test.

PubMed

Tichopad, Ales; Bar, Tzachi; Pecen, Ladislav; Kitchen, Robert R; Kubista, Mikael; Pfaffl, Michael W

2010-04-01

Quantitative qPCR is a routinely used method for the accurate quantification of nucleic acids. Yet it may generate erroneous results if the amplification process is obscured by inhibition or generation of aberrant side-products such as primer dimers. Several methods have been established to control for pre-processing performance that rely on the introduction of a co-amplified reference sequence, however there is currently no method to allow for reliable control of the amplification process without directly modifying the sample mix. Herein we present a statistical approach based on multivariate analysis of the amplification response data generated in real-time. The amplification trajectory in its most resolved and dynamic phase is fitted with a suitable model. Two parameters of this model, related to amplification efficiency, are then used for calculation of the Z-score statistics. Each studied sample is compared to a predefined reference set of reactions, typically calibration reactions. A probabilistic decision for each individual Z-score is then used to identify the majority of inhibited reactions in our experiments. We compare this approach to univariate methods using only the sample specific amplification efficiency as reporter of the compatibility. We demonstrate improved identification performance using the multivariate approach compared to the univariate approach. Finally we stress that the performance of the amplification compatibility test as a quality control procedure depends on the quality of the reference set. Copyright 2010 Elsevier Inc. All rights reserved.

Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay.

PubMed

Liu, Yang; Wang, Xiao-Yue; Wei, Xue-Min; Gao, Zi-Tong; Han, Jian-Ping

2018-05-22

Species adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.

Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand

PubMed Central

Auburn, Sarah; Serre, David; Pearson, Richard D.; Amato, Roberto; Sriprawat, Kanlaya; To, Sheren; Handayuni, Irene; Suwanarusk, Rossarin; Russell, Bruce; Drury, Eleanor; Stalker, Jim; Miotto, Olivo; Kwiatkowski, Dominic P.; Nosten, Francois; Price, Ric N.

2016-01-01

In regions of coendemicity for Plasmodium falciparum and Plasmodium vivax where mefloquine is used to treat P. falciparum infection, drug pressure mediated by increased copy numbers of the multidrug resistance 1 gene (pvmdr1) may select for mefloquine-resistant P. vivax. Surveillance is not undertaken routinely owing in part to methodological challenges in detection of gene amplification. Using genomic data on 88 P. vivax samples from western Thailand, we identified pvmdr1 amplification in 17 isolates, all exhibiting tandem copies of a 37.6–kilobase pair region with identical breakpoints. A novel breakpoint-specific polymerase chain reaction assay was designed to detect the amplification. The assay demonstrated high sensitivity, identifying amplifications in 13 additional, polyclonal infections. Application to 132 further samples identified the common breakpoint in all years tested (2003–2015), with a decline in prevalence after 2012 corresponding to local discontinuation of mefloquine regimens. Assessment of the structure of pvmdr1 amplification in other geographic regions will yield information about the population-specificity of the breakpoints and underlying amplification mechanisms. PMID:27456706

Limonene ozonolysis in the presence of nitric oxide: Gas-phase reaction products and yields

NASA Astrophysics Data System (ADS)

Ham, Jason E.; Harrison, Joel C.; Jackson, Stephen R.; Wells, J. R.

2016-05-01

The reaction products from limonene ozonolysis were investigated using the new carbonyl derivatization agent, O-tert-butylhydroxylamine hydrochloride (TBOX). With ozone (O3) as the limiting reagent, five carbonyl compounds were detected. The yields of the carbonyl compounds are discussed with and without the presence of a hydroxyl radical (OHrad) scavenger, giving insight into the influence secondary OH radicals have on limonene ozonolysis products. The observed reaction product yields for limonaketone (LimaKet), 7-hydroxyl-6-oxo-3-(prop-1-en-2-yl)heptanal (7H6O), and 2-acetyl-5-oxohexanal (2A5O) were unchanged suggesting OHrad generated by the limonene + O3 reaction does not contribute to their formation. The molar yields of 3-isopropenyl-6-oxo-heptanal (IPOH) and 3-acetyl-6-oxoheptanal (3A6O) decreased by 68% and >95%; respectively, when OHrad was removed. This suggests that OHrad radicals significantly impact the formation of these products. Nitric oxide (NO) did not significantly affect the molar yields of limonaketone or IPOH. However, NO (20 ppb) considerably decreased the molar reaction product yields of 7H6O (62%), 2A5O (63%), and 3A6O (47%), suggesting NO reacted with peroxyl intermediates, generated during limonene ozonolysis, to form other carbonyls (not detected) or organic nitrates. These studies give insight into the transformation of limonene and its reaction products that can lead to indoor exposures.

A Novel Approach for Forecasting Crop Production and Yield Using Remotely Sensed Satellite Images

NASA Astrophysics Data System (ADS)

Singh, R. K.; Budde, M. E.; Senay, G. B.; Rowland, J.

2017-12-01

Forecasting crop production in advance of crop harvest plays a significant role in drought impact management, improved food security, stabilizing food grain market prices, and poverty reduction. This becomes essential, particularly in Sub-Saharan Africa, where agriculture is a critical source of livelihoods, but lacks good quality agricultural statistical data. With increasing availability of low cost satellite data, faster computing power, and development of modeling algorithms, remotely sensed images are becoming a common source for deriving information for agricultural, drought, and water management. Many researchers have shown that the Normalized Difference Vegetation Index (NDVI), based on red and near-infrared reflectance, can be effectively used for estimating crop production and yield. Similarly, crop production and yield have been closely related to evapotranspiration (ET) also as there are strong linkages between production/yield and transpiration based on plant physiology. Thus, we combined NDVI and ET information from remotely sensed images for estimating total production and crop yield prior to crop harvest for Niger and Burkina Faso in West Africa. We identified the optimum time (dekads 23-29) for cumulating NDVI and ET and developed a new algorithm for estimating crop production and yield. We used the crop data from 2003 to 2008 to calibrate our model and the data from 2009 to 2013 for validation. Our results showed that total crop production can be estimated within 5% of actual production (R2 = 0.98) about 30-45 days before end of the harvest season. This novel approach can be operationalized to provide a valuable tool to decision makers for better drought impact management in drought-prone regions of the world.

Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029.

PubMed

Bian, Xiaoying; Tang, Biao; Yu, Yucong; Tu, Qiang; Gross, Frank; Wang, Hailong; Li, Aiying; Fu, Jun; Shen, Yuemao; Li, Yue-Zhong; Stewart, A Francis; Zhao, Guoping; Ding, Xiaoming; Müller, Rolf; Zhang, Youming

2017-07-21

The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L -1 . These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.

Characterization of Edible Pork By-products by Means of Yield and Nutritional Composition

PubMed Central

Moon, Sung Sil

2014-01-01

Basic information regarding the yield and nutritional composition of edible pork by-products, namely heart, liver, lung, stomach, spleen, uterus, pancreas, and small and large intestines, was studied. Our results revealed that the yields varied widely among the pork by-products examined; in particular, liver had the highest yield (1.35%); whereas, spleen had the lowest yield (0.16%). The approximate composition range (minimum to maximum) of these by-products was found to be: moisture 71.59-82.48%; fat 0.28-19.54%; ash 0.155-1.34%, and protein 8.45-22.05%. The highest protein, vitamin A, B2, B6, and total essential amino acid (EAA) contents were found in liver. Large intestine had the highest fat content and lowest EAA content. Heart had the highest vitamin B1 content, whereas pancreas had the highest niacin and vitamin B3 contents. The concentrations of Fe and Zn were highest in liver and pancreas. Total saturated fatty acids (SFA) levels and polyunsaturated fatty acids (PUFA) levels between the by-products ranged from 43.15-50.48%, and 14.92-30.16%, respectively. Furthermore, with the exception of large intestine, all the by-products showed favorable PUFA/SFA ratios. The study indicated that almost all of the pork by-products examined were good sources of important nutrients, and that these data will be of great importance in the promotion of the consumption of edible pork by-products, as well as their utilization in meat processing. PMID:26761170

Linear and exponential TAIL-PCR: a method for efficient and quick amplification of flanking sequences adjacent to Tn5 transposon insertion sites.

PubMed

Jia, Xianbo; Lin, Xinjian; Chen, Jichen

2017-11-02

Current genome walking methods are very time consuming, and many produce non-specific amplification products. To amplify the flanking sequences that are adjacent to Tn5 transposon insertion sites in Serratia marcescens FZSF02, we developed a genome walking method based on TAIL-PCR. This PCR method added a 20-cycle linear amplification step before the exponential amplification step to increase the concentration of the target sequences. Products of the linear amplification and the exponential amplification were diluted 100-fold to decrease the concentration of the templates that cause non-specific amplification. Fast DNA polymerase with a high extension speed was used in this method, and an amplification program was used to rapidly amplify long specific sequences. With this linear and exponential TAIL-PCR (LETAIL-PCR), we successfully obtained products larger than 2 kb from Tn5 transposon insertion mutant strains within 3 h. This method can be widely used in genome walking studies to amplify unknown sequences that are adjacent to known sequences.

Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus.

PubMed

Yanai, Koji; Murakami, Takeshi; Bibb, Mervyn

2006-06-20

Streptomyces kanamyceticus 12-6 is a derivative of the wild-type strain developed for industrial kanamycin (Km) production. Southern analysis and DNA sequencing revealed amplification of a large genomic segment including the entire Km biosynthetic gene cluster in the chromosome of strain 12-6. At 145 kb, the amplifiable unit of DNA (AUD) is the largest AUD reported in Streptomyces. Striking repetitive DNA sequences belonging to the clustered regularly interspaced short palindromic repeats family were found in the AUD and may play a role in its amplification. Strain 12-6 contains a mixture of different chromosomes with varying numbers of AUDs, sometimes exceeding 36 copies and producing an amplified region >5.7 Mb. The level of Km production depended on the copy number of the Km biosynthetic gene cluster, suggesting that DNA amplification occurred during strain improvement as a consequence of selection for increased Km resistance. Amplification of DNA segments including entire antibiotic biosynthetic gene clusters might be a common mechanism leading to increased antibiotic production in industrial strains.

Optimization of Saanen sperm genes amplification: evaluation of standardized protocols in genetically uncharacterized rural goats reared under a subtropical environment.

PubMed

Barbour, Elie K; Saade, Maya F; Sleiman, Fawwak T; Hamadeh, Shady K; Mouneimne, Youssef; Kassaifi, Zeina; Kayali, Ghazi; Harakeh, Steve; Jaber, Lina S; Shaib, Houssam A

2012-10-01

The purpose of this research is to optimize quantitatively the amplification of specific sperm genes in reference genomically characterized Saanen goat and to evaluate the standardized protocols applicability on sperms of uncharacterized genome of rural goats reared under subtropical environment for inclusion in future selection programs. The optimization of the protocols in Saanen sperms included three production genes (growth hormone (GH) exons 2, 3, and 4, αS1-casein (CSN1S1), and α-lactalbumin) and two health genes (MHC class II DRB and prion (PrP)). The optimization was based on varying the primers concentrations and the inclusion of a PCR cosolvent (Triton X). The impact of the studied variables on statistically significant increase in the yield of amplicons was noticed in four out of five (80%) optimized protocols, namely in those related to GH, CSN1S1, α-lactalbumin, and PrP genes (P < 0.05). There was no significant difference in the yield of amplicons related to MHC class II DRB gene, regardless of the variables used (P > 0.05). The applicability of the optimized protocols of Saanen sperm genes on amplification of uncharacterized rural goat sperms revealed a 100% success in tested individuals for amplification of GH, CSN1S1, α-lactalbumin, and MHC class II DRB genes and a 75% success for the PrP gene. The significant success in applicability of the Saanen quantitatively optimized protocols to other uncharacterized genome of rural goats allows for their inclusion in future selection, targeting the sustainability of this farming system in a subtropical environment and the improvement of the farmers livelihood.

Regional crop gross primary production and yield estimation using fused Landsat-MODIS data

NASA Astrophysics Data System (ADS)

He, M.; Kimball, J. S.; Maneta, M. P.; Maxwell, B. D.; Moreno, A.

2017-12-01

Accurate crop yield assessments using satellite-based remote sensing are of interest for the design of regional policies that promote agricultural resiliency and food security. However, the application of current vegetation productivity algorithms derived from global satellite observations are generally too coarse to capture cropland heterogeneity. Merging information from sensors with reciprocal spatial and temporal resolution can improve the accuracy of these retrievals. In this study, we estimate annual crop yields for seven important crop types -alfalfa, barley, corn, durum wheat, peas, spring wheat and winter wheat over Montana, United States (U.S.) from 2008 to 2015. Yields are estimated as the product of gross primary production (GPP) and a crop-specific harvest index (HI) at 30 m spatial resolution. To calculate GPP we used a modified form of the MOD17 LUE algorithm driven by a 30 m 8-day fused NDVI dataset constructed by blending Landsat (5 or 7) and MODIS Terra reflectance data. The fused 30-m NDVI record shows good consistency with the original Landsat and MODIS data, but provides better spatiotemporal information on cropland vegetation growth. The resulting GPP estimates capture characteristic cropland patterns and seasonal variations, while the estimated annual 30 m crop yield results correspond favorably with county-level crop yield data (r=0.96, p<0.05). The estimated crop yield performance was generally lower, but still favorable in relation to field-scale crop yield surveys (r=0.42, p<0.01). Our methods and results are suitable for operational applications at regional scales.

Yield-stress fluids foams: flow patterns and controlled production in T-junction and flow-focusing devices.

PubMed

Laborie, Benoit; Rouyer, Florence; Angelescu, Dan E; Lorenceau, Elise

2016-11-23

We study the formation of yield-stress fluid foams in millifluidic flow-focusing and T-junction devices. First, we provide a phase diagram for the unsteady operating regimes of bubble production when the gas pressure and the yield-stress fluid flow rate are imposed. Three regimes are identified: a co-flow of gas and yield-stress fluid, a transient production of bubble and a flow of yield-stress fluid only. Taking wall slip into account, we provide a model for the pressure at the onset of bubble formation. Then, we detail and compare two simple methods to ensure steady bubble production: regulation of the gas pressure or flow-rate. These techniques, which are easy to implement, thus open pathways for controlled production of dry yield-stress fluid foams as shown at the end of this article.

Biomass changes and trophic amplification of plankton in a warmer ocean.

PubMed

Chust, Guillem; Allen, J Icarus; Bopp, Laurent; Schrum, Corinna; Holt, Jason; Tsiaras, Kostas; Zavatarelli, Marco; Chifflet, Marina; Cannaby, Heather; Dadou, Isabelle; Daewel, Ute; Wakelin, Sarah L; Machu, Eric; Pushpadas, Dhanya; Butenschon, Momme; Artioli, Yuri; Petihakis, George; Smith, Chris; Garçon, Veronique; Goubanova, Katerina; Le Vu, Briac; Fach, Bettina A; Salihoglu, Baris; Clementi, Emanuela; Irigoien, Xabier

2014-07-01

Ocean warming can modify the ecophysiology and distribution of marine organisms, and relationships between species, with nonlinear interactions between ecosystem components potentially resulting in trophic amplification. Trophic amplification (or attenuation) describe the propagation of a hydroclimatic signal up the food web, causing magnification (or depression) of biomass values along one or more trophic pathways. We have employed 3-D coupled physical-biogeochemical models to explore ecosystem responses to climate change with a focus on trophic amplification. The response of phytoplankton and zooplankton to global climate-change projections, carried out with the IPSL Earth System Model by the end of the century, is analysed at global and regional basis, including European seas (NE Atlantic, Barents Sea, Baltic Sea, Black Sea, Bay of Biscay, Adriatic Sea, Aegean Sea) and the Eastern Boundary Upwelling System (Benguela). Results indicate that globally and in Atlantic Margin and North Sea, increased ocean stratification causes primary production and zooplankton biomass to decrease in response to a warming climate, whilst in the Barents, Baltic and Black Seas, primary production and zooplankton biomass increase. Projected warming characterized by an increase in sea surface temperature of 2.29 ± 0.05 °C leads to a reduction in zooplankton and phytoplankton biomasses of 11% and 6%, respectively. This suggests negative amplification of climate driven modifications of trophic level biomass through bottom-up control, leading to a reduced capacity of oceans to regulate climate through the biological carbon pump. Simulations suggest negative amplification is the dominant response across 47% of the ocean surface and prevails in the tropical oceans; whilst positive trophic amplification prevails in the Arctic and Antarctic oceans. Trophic attenuation is projected in temperate seas. Uncertainties in ocean plankton projections, associated to the use of single global and

[Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification].

PubMed

Dovgerd, A P; Zharkov, D O

2014-01-01

PCR amplification of severely degraded DNA, including ancient DNA, forensic samples, and preparations from deeply processed foodstuffs, is a serious problem. Living organisms have a set of enzymes to repair lesions in their DNA. In this work, we have developed and characterized model systems of degraded high-molecular-weight DNA with a predominance of different types of damage. It was shown that depurination and oxidation of the model plasmid DNA template led to a decrease in the PCR efficiency. A set of enzymes performing a full cycle of excision repair of some lesions was determined. The treatment of model-damaged substrates with this set of enzymes resulted in an increased PCR product yield as compared with that of the unrepaired samples.

Development of Local Amplification Factors in the NEAM Region for Production of Regional Tsunami Hazard Maps

NASA Astrophysics Data System (ADS)

Harbitz, C. B.; Glimsdal, S.; Løvholt, F.; Orefice, S.; Romano, F.; Brizuela, B.; Lorito, S.; Hoechner, A.; Babeyko, A. Y.

2016-12-01

The standard way of estimating tsunami inundation is by applying numerical depth-averaged shallow-water run-up models. However, for a regional Probabilistic Tsunami Hazard Assessment (PTHA), applying such inundation models may be too time-consuming. A faster, yet less accurate procedure, is to relate the near-shore surface elevations at offshore points to maximum shoreline water levels by using a set of amplification factors based on the characteristics of the incident wave and the bathymetric slope. The surface elevation at the shoreline then acts as a rough approximation for the maximum inundation height or run-up height along the shoreline. An amplification-factor procedure based on a limited set of idealized broken shoreline segments has previously been applied to estimate the maximum inundation heights globally. Here, we present a study where this technique is developed further, by taking into account the local bathymetric profiles. We extract a large number of local bathymetric transects over a significant part of the North East Atlantic, the Mediterranean and connected seas (NEAM) region. For each bathymetric transect, we compute the wave amplification from an offshore control point to points close to the shoreline using a linear shallow-water model for waves of different period and polarity with a sinusoidal pulse wave as input. The amplification factors are then tabulated. We present maximum water levels from the amplification factor method, and compare these with results from conventional inundation models. Finally, we demonstrate how the amplification factor method can be convolved with PTHA results to provide regional tsunami hazard maps. This work has been supported by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement 603839 (Project ASTARTE), and the TSUMAPS-NEAM Project (http://www.tsumapsneam.eu/), co-financed by the European Union Civil Protection Mechanism, Agreement Number: ECHO/SUB/2015/718568/PREV26.

Development of Local Amplification Factors in the NEAM Region for Production of Regional Tsunami Hazard Maps

NASA Astrophysics Data System (ADS)

Glimsdal, Sylfest; Løvholt, Finn; Bonnevie Harbitz, Carl; Orefice, Simone; Romano, Fabrizio; Brizuela, Beatriz; Lorito, Stefano; Hoechner, Andreas; Babeyko, Andrey

2017-04-01

The standard way of estimating tsunami inundation is by applying numerical depth-averaged shallow-water run-up models. However, for a regional Probabilistic Tsunami Hazard Assessment (PTHA), applying such inundation models may be too time-consuming. A faster, yet less accurate procedure, is to relate the near-shore surface elevations at offshore points to maximum shoreline water levels by using a set of amplification factors based on the characteristics of the incident wave and the bathymetric slope. The surface elevation at the shoreline then acts as a rough approximation for the maximum inundation height or run-up height along the shoreline. An amplification-factor procedure based on a limited set of idealized broken shoreline segments has previously been applied to estimate the maximum inundation heights globally. Here, we present a study where this technique is developed further, by taking into account the local bathymetric profiles. We extract a large number of local bathymetric transects over a significant part of the North East Atlantic, the Mediterranean and connected seas (NEAM region). For each bathymetric transect, we compute the wave amplification from an offshore control point to points close to the shoreline using a linear shallow-water model for waves of different period and polarity with a sinusoidal pulse wave as input. The amplification factors are then tabulated. We present maximum water levels from the amplification factor method, and compare these with results from conventional inundation models. Finally, we demonstrate how the amplification factor method can be convolved with PTHA results to provide regional tsunami hazard maps. This work has been supported by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement 603839 (Project ASTARTE), and the TSUMAPS-NEAM Project (http://www.tsumapsneam.eu/), co-financed by the European Union Civil Protection Mechanism, Agreement Number: ECHO/SUB/2015/718568/PREV26.

Fission product yield measurements using monoenergetic photon beams

NASA Astrophysics Data System (ADS)

Krishichayan; Bhike, M.; Tonchev, A. P.; Tornow, W.

2017-09-01

Measurements of fission products yields (FPYs) are an important source of information on the fission process. During the past couple of years, a TUNL-LANL-LLNL collaboration has provided data on the FPYs from quasi monoenergetic neutron-induced fission on 235U, 238U, and 239Pu and has revealed an unexpected energy dependence of both asymmetric fission fragments at energies below 4 MeV. This peculiar FPY energy dependence was more pronounced in neutron-induced fission of 239Pu. In an effort to understand and compare the effect of the incoming probe on the FPY distribution, we have carried out monoenergetic photon-induced fission experiments on the same 235U, 238U, and 239Pu targets. Monoenergetic photon beams of Eγ = 13.0 MeV were provided by the HIγS facility, the world's most intense γ-ray source. In order to determine the total number of fission events, a dual-fission chamber was used during the irradiation. These irradiated samples were counted at the TUNL's low-background γ-ray counting facility using high efficient HPGe detectors over a period of 10 weeks. Here we report on our first ever photofission product yield measurements obtained with monoenegetic photon beams. These results are compared with neutron-induced FPY data.

Cascade Signal Amplification Based on Copper Nanoparticle-Reported Rolling Circle Amplification for Ultrasensitive Electrochemical Detection of the Prostate Cancer Biomarker.

PubMed

Zhu, Ye; Wang, Huijuan; Wang, Lin; Zhu, Jing; Jiang, Wei

2016-02-03

An ultrasensitive and highly selective electrochemical assay was first attempted by combining the rolling circle amplification (RCA) reaction with poly(thymine)-templated copper nanoparticles (CuNPs) for cascade signal amplification. As proof of concept, prostate specific antigen (PSA) was selected as a model target. Using a gold nanoparticle (AuNP) as a carrier, we synthesized the primer-AuNP-aptamer bioconjugate for signal amplification by increasing the primer/aptamer ratio. The specific construction of primer-AuNP-aptamer/PSA/anti-PSA sandwich structure triggered the effective RCA reaction, in which thousands of tandem poly(thymine) repeats were generated and directly served as the specific templates for the subsequent CuNP formation. The signal readout was easily achieved by dissolving the RCA product-templated CuNPs and detecting the released copper ions with differential pulse stripping voltammetry. Because of the designed cascade signal amplification strategy, the newly developed method achieved a linear range of 0.05-500 fg/mL, with a remarkable detection limit of 0.020 ± 0.001 fg/mL PSA. Finally, the feasibility of the developed method for practical application was investigated by analyzing PSA in the real clinical human serum samples. The ultrasensitivity, specificity, convenience, and capability for analyzing the clinical samples demonstrate that this method has great potential for practical disease diagnosis applications.

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

PubMed

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.

Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS).

PubMed

Sharma, Nidhi; Hoshika, Shuichi; Hutter, Daniel; Bradley, Kevin M; Benner, Steven A

2014-10-13

Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand.

PubMed

Auburn, Sarah; Serre, David; Pearson, Richard D; Amato, Roberto; Sriprawat, Kanlaya; To, Sheren; Handayuni, Irene; Suwanarusk, Rossarin; Russell, Bruce; Drury, Eleanor; Stalker, Jim; Miotto, Olivo; Kwiatkowski, Dominic P; Nosten, Francois; Price, Ric N

2016-10-15

In regions of coendemicity for Plasmodium falciparum and Plasmodium vivax where mefloquine is used to treat P. falciparum infection, drug pressure mediated by increased copy numbers of the multidrug resistance 1 gene (pvmdr1) may select for mefloquine-resistant P. vivax Surveillance is not undertaken routinely owing in part to methodological challenges in detection of gene amplification. Using genomic data on 88 P. vivax samples from western Thailand, we identified pvmdr1 amplification in 17 isolates, all exhibiting tandem copies of a 37.6-kilobase pair region with identical breakpoints. A novel breakpoint-specific polymerase chain reaction assay was designed to detect the amplification. The assay demonstrated high sensitivity, identifying amplifications in 13 additional, polyclonal infections. Application to 132 further samples identified the common breakpoint in all years tested (2003-2015), with a decline in prevalence after 2012 corresponding to local discontinuation of mefloquine regimens. Assessment of the structure of pvmdr1 amplification in other geographic regions will yield information about the population-specificity of the breakpoints and underlying amplification mechanisms. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.

Adsorption-induced auto-amplification of enantiomeric excess on an achiral surface

NASA Astrophysics Data System (ADS)

Yun, Yongju; Gellman, Andrew J.

2015-06-01

The homochirality of biomolecules is a signature of life on Earth and has significant implications in, for example, the production of pharmaceutical compounds. It has been suggested that biomolecular homochirality may have arisen from the amplification of a spontaneously formed small enantiomeric excess (e.e.). Many minerals exhibit naturally chiral surfaces and so adsorption has been proposed as one possible mechanism for such an amplification of e.e. Here we show that when gas-phase mixtures of D- and L-aspartic acid are exposed to an achiral Cu(111) surface, a small e.e. in the gas phase, e.e.g, leads to an amplification of the e.e. on the surface, e.e.s, under equilibrium conditions. Adsorption-induced amplification of e.e. does not require a chiral surface. The dependence of e.e.s on e.e.g has been modelled successfully using a Langmuir-like adsorption isotherm that incorporates the formation of homochiral adsorbate clusters on the surface.

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

PubMed

Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

2008-10-01

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs

PubMed Central

Morisset, Dany; Dobnik, David; Hamels, Sandrine; Žel, Jana; Gruden, Kristina

2008-01-01

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1–25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification. PMID:18710880

Graphene Nanoprobes for Real-Time Monitoring of Isothermal Nucleic Acid Amplification.

PubMed

Li, Fan; Liu, Xiaoguo; Zhao, Bin; Yan, Juan; Li, Qian; Aldalbahi, Ali; Shi, Jiye; Song, Shiping; Fan, Chunhai; Wang, Lihua

2017-05-10

Isothermal amplification is an efficient way to amplify DNA with high accuracy; however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, a graphene oxide (GO)-based nanoprobe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two-, and three-dimensional structures. It was found that the high rigid structures exhibited much lower affinity with GO than soft ssDNA, and generally the rigidity was dependent on the length of targets and the hybridization position with probe DNA. On the basis of these results, we successfully monitored HCR amplification process, RCA process, and the enzyme restriction of RCA products with GO nanoprobe; other applications including the detection of the assembly/disassembly of DNA 3-helix structures were also performed. Compared to the widely used end-point detection methods, the GO-based sensing platform is simple, sensitive, cost-effective, and especially in a real-time monitoring mode. We believe such studies can provide comprehensive understandings and evocation on design of GO-based biosensors for broad application in various fields.

Highly Efficient Protein Misfolding Cyclic Amplification

PubMed Central

Ostapchenko, Valeriy G.; Savtchenk, Regina; Alexeeva, Irina; Rohwer, Robert G.; Baskakov, Ilia V.

2011-01-01

Protein misfolding cyclic amplification (PMCA) provides faithful replication of mammalian prions in vitro and has numerous applications in prion research. However, the low efficiency of conversion of PrPC into PrPSc in PMCA limits the applicability of PMCA for many uses including structural studies of infectious prions. It also implies that only a small sub-fraction of PrPC may be available for conversion. Here we show that the yield, rate, and robustness of prion conversion and the sensitivity of prion detection are significantly improved by a simple modification of the PMCA format. Conducting PMCA reactions in the presence of Teflon beads (PMCAb) increased the conversion of PrPC into PrPSc from ∼10% to up to 100%. In PMCAb, a single 24-hour round consistently amplified PrPSc by 600-700-fold. Furthermore, the sensitivity of prion detection in one round (24 hours) increased by 2-3 orders of magnitude. Using serial PMCAb, a 1012-fold dilution of scrapie brain material could be amplified to the level detectible by Western blotting in 3 rounds (72 hours). The improvements in amplification efficiency were observed for the commonly used hamster 263K strain and for the synthetic strain SSLOW that otherwise amplifies poorly in PMCA. The increase in the amplification efficiency did not come at the expense of prion replication specificity. The current study demonstrates that poor conversion efficiencies observed previously have not been due to the scarcity of a sub-fraction of PrPC susceptible to conversion nor due to limited concentrations of essential cellular cofactors required for conversion. The new PMCAb format offers immediate practical benefits and opens new avenues for developing fast ultrasensitive assays and for producing abundant quantities of PrPSc in vitro. PMID:21347353

Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture.

PubMed

Cassman, K G

1999-05-25

Wheat (Triticum aestivum L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide about two-thirds of all energy in human diets, and four major cropping systems in which these cereals are grown represent the foundation of human food supply. Yield per unit time and land has increased markedly during the past 30 years in these systems, a result of intensified crop management involving improved germplasm, greater inputs of fertilizer, production of two or more crops per year on the same piece of land, and irrigation. Meeting future food demand while minimizing expansion of cultivated area primarily will depend on continued intensification of these same four systems. The manner in which further intensification is achieved, however, will differ markedly from the past because the exploitable gap between average farm yields and genetic yield potential is closing. At present, the rate of increase in yield potential is much less than the expected increase in demand. Hence, average farm yields must reach 70-80% of the yield potential ceiling within 30 years in each of these major cereal systems. Achieving consistent production at these high levels without causing environmental damage requires improvements in soil quality and precise management of all production factors in time and space. The scope of the scientific challenge related to these objectives is discussed. It is concluded that major scientific breakthroughs must occur in basic plant physiology, ecophysiology, agroecology, and soil science to achieve the ecological intensification that is needed to meet the expected increase in food demand.

Signal amplification of microRNAs with modified strand displacement-based cycling probe technology.

PubMed

Jia, Huning; Bu, Ying; Zou, Bingjie; Wang, Jianping; Kumar, Shalen; Pitman, Janet L; Zhou, Guohua; Song, Qinxin

2016-10-24

Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis. Therefore, miRNAs are potentially a powerful marker for monitoring cancer and diagnosis. Here, we present sensitive signal amplification for miRNAs based on modified cycling probe technology with strand displacement amplification. miRNA was captured by the template coupled with beads, and then the first cycle based on SDA was repeatedly extended to the nicking end, which was produced by the extension reaction of miRNA. The products generated by SDA are captured by a molecular beacon (MB), which is designed to initiate the second amplification cycle, with a similar principle to the cycling probe technology (CPT), which is based on repeated digestion of the DNA-RNA hybrid by the RNase H. After one sample enrichment and two steps of signal amplification, 0.1 pM of let-7a can be detected. The miRNA assay exhibits a great dynamic range of over 100 orders of magnitude and high specificity to clearly discriminate a single base difference in miRNA sequences. This isothermal amplification does not require any special temperature control instrument. The assay is also about signal amplification rather than template amplification, therefore minimising contamination issues. In addition, there is no need for the reverse transcription (RT) process. Thus the amplification is suitable for miRNA detection.

Multiscale image contrast amplification (MUSICA)

NASA Astrophysics Data System (ADS)

Vuylsteke, Pieter; Schoeters, Emile P.

1994-05-01

This article presents a novel approach to the problem of detail contrast enhancement, based on multiresolution representation of the original image. The image is decomposed into a weighted sum of smooth, localized, 2D basis functions at multiple scales. Each transform coefficient represents the amount of local detail at some specific scale and at a specific position in the image. Detail contrast is enhanced by non-linear amplification of the transform coefficients. An inverse transform is then applied to the modified coefficients. This yields a uniformly contrast- enhanced image without artefacts. The MUSICA-algorithm is being applied routinely to computed radiography images of chest, skull, spine, shoulder, pelvis, extremities, and abdomen examinations, with excellent acceptance. It is useful for a wide range of applications in the medical, graphical, and industrial area.

Miniaturized isothermal nucleic acid amplification, a review.

PubMed

Asiello, Peter J; Baeumner, Antje J

2011-04-21

Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

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

PubMed

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.

Amplification in the rehabilitation of unilateral deafness: speech in noise and directional hearing effects with bone-anchored hearing and contralateral routing of signal amplification.

PubMed

Lin, Li-Mei; Bowditch, Stephen; Anderson, Michael J; May, Bradford; Cox, Kenneth M; Niparko, John K

2006-02-01

Vibromechanical stimulation with a semi-implantable bone conductor (Entific BAHA device) overcomes some of the head-shadow effects in unilateral deafness. What specific rehabilitative benefits are observed when the functional ear exhibits normal hearing versus moderate sensorineural hearing loss (SNHL)? The authors conducted a prospective trial of subjects with unilateral deafness in a tertiary care center. This study comprised adults with unilateral deafness (pure-tone average [PTA] > 90 dB; Sp.D. < 20%) and either normal monaural hearing (n = 18) or moderate SNHL (PTA = 25-50 dB: Sp.D. > 75%) in the contralateral functional ear (n = 5). Subjects were fit with contralateral routing of signal (CROS) devices for 1 month and tested before (mastoid) implantation, fitting, and testing with a bone-anchored hearing aid (BAHA). Outcome measures were: 1) subjective benefit; 2) source localization tests (Source Azimuth Identification in Noise Test [SAINT]); 3) speech discrimination in quiet and in noise assessed with Hearing In Noise Test (HINT) protocols. There was consistent satisfaction with BAHA amplification and poor acceptance of CROS amplification. General directional hearing decreased with CROS use and was unchanged by BAHA and directional microphone aids. Relative to baseline and CROS, BAHA produced significantly better speech recognition in noise. Twenty-two of 23 subjects followed up in this study continue to use their BAHA device over an average follow-up period of 30.24 months (range, 51-12 months). BAHA amplification on the side of a deaf ear yields greater benefit in subjects with monaural hearing than does CROS amplification. Advantages likely related to averting the interference of speech signals delivered to the better ear, as occurs with conventional CROS amplification, while alleviating the negative head-shadow effects of unilateral deafness. The advantages of head-shadow reduction in enhancing speech recognition with noise in the hearing ear outweigh

NASBA: A detection and amplification system uniquely suited for RNA

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

Sooknanan, R.; Malek, L.T.

1995-06-01

The invention of PCR (polymerase chain reaction) has revolutionized our ability to amplify and manipulate a nucleic acid sequence in vitro. The commercial rewards of this revolution have driven the development of other nuclei acid amplification and detection methodologies. This has created an alphabet soup of technologies that use different amplification methods, including NASBA (nucleic acid sequence-based amplification), LCR (ligase chain reaction), SDA (strand displacement amplification), QBR (Q-beta replicase), CPR (cycling probe reaction), and bDNA (branched DNA). Despite the differences in their processes, these amplification systems can be separated into two broad categories based on how they achieve their goal:more » sequence-based amplification systems, such as PCR, NASBA, and SDA, amplify a target nucleic acid sequence. Signal-based amplification systems, such as LCR, QBR, CPR and bDNA, amplify or alter a signal from a detection reaction that is target-dependent. While the various methods have relative strengths and weaknesses, only NASBA offers the unique ability to homogeneously amplify an RNA analyte in the presence of homologous genomic DNA under isothermal conditions. Since the detection of RNA sequences almost invariably measures biological activity, it is an excellent prognostic indicator of activities as diverse as virus production, gene expression, and cell viability. The isothermal nature of the reaction makes NASBA especially suitable for large-scale manual screening. These features extend NASBA`s application range from research to commercial diagnostic applications. Field test kits are presently under development for human diagnostics as well as the burgeoning fields of food and environmental diagnostic testing. These developments suggest future integration of NASBA into robotic workstations for high-throughput screening as well. 17 refs., 1 tab.« less

Observational Evidence for Desert Amplification Using Multiple Satellite Datasets.

PubMed

Wei, Nan; Zhou, Liming; Dai, Yongjiu; Xia, Geng; Hua, Wenjian

2017-05-17

Desert amplification identified in recent studies has large uncertainties due to data paucity over remote deserts. Here we present observational evidence using multiple satellite-derived datasets that desert amplification is a real large-scale pattern of warming mode in near surface and low-tropospheric temperatures. Trend analyses of three long-term temperature products consistently confirm that near-surface warming is generally strongest over the driest climate regions and this spatial pattern of warming maximizes near the surface, gradually decays with height, and disappears in the upper troposphere. Short-term anomaly analyses show a strong spatial and temporal coupling of changes in temperatures, water vapor and downward longwave radiation (DLR), indicating that the large increase in DLR drives primarily near surface warming and is tightly associated with increasing water vapor over deserts. Atmospheric soundings of temperature and water vapor anomalies support the results of the long-term temperature trend analysis and suggest that desert amplification is due to comparable warming and moistening effects of the troposphere. Likely, desert amplification results from the strongest water vapor feedbacks near the surface over the driest deserts, where the air is very sensitive to changes in water vapor and thus efficient in enhancing the longwave greenhouse effect in a warming climate.

Chemical Amplification with Encapsulated Reagents

NASA Technical Reports Server (NTRS)

Chen, Jian; Koemer, Steffi; Craig, Stephen; Lin, Shirley; Rudkevich, Dmitry M.; Rebek, Julius, Jr.

2002-01-01

Autocatalysis and chemical amplification are characteristic properties of living systems, and they give rise to behaviors such as increased sensitivity, responsiveness, and self-replication. Here we report a synthetic system in which a unique form of compartmentalization leads to nonlinear, autocatalytic behavior. The compartment is a reversibly formed capsule in which a reagent is sequestered. Reaction products displace the reagent from the capsule into solution and the reaction rate is accelerated. The resulting self-regulation is sensitive to the highly selective molecular recognition properties of the capsule.

Multiple Cross Displacement Amplification Combined with Gold Nanoparticle-Based Lateral Flow Biosensor for Detection of Vibrio parahaemolyticus

PubMed Central

Wang, Yi; Li, Hui; Li, Dongxun; Li, Kewei; Wang, Yan; Xu, Jianguo; Ye, Changyun

2016-01-01

Vibrio parahaemolyticus (V. parahaemolyticus) is a marine seafood-borne pathogen causing severe illnesses in humans and aquatic animals. In the present study, multiple cross displacement amplification was combined with a lateral flow biosensor (MCDA-LFB) to detect the toxR gene of V. parahaemolyticus in DNA extracts from pure cultures and spiked oyster homogenates. Amplification was carried out at a constant temperature (62°C) for only 30 min, and amplification products were directly applied to the biosensor. The entire process, including oyster homogenate processing (30 min), isothermal amplification (30 min) and results indicating (∼2 min), could be completed within 65 min. Amplification product was detectable from as little as 10 fg of pure V. parahaemolyticus DNA and from approximately 4.2 × 102 CFU in 1 mL of oyster homogenate. No cross-reaction with other Vibrio species and with non-Vibrio species was observed. Therefore, the MCDA-LFB method established in the current report is suitable for the rapid screening of V. parahaemolyticus in clinical, food, and environmental samples. PMID:28066368

Dynamics and control of DNA sequence amplification

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

Marimuthu, Karthikeyan; Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu; Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054

2014-10-28

DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reactionmore » are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.« less

Questioning cochlear amplification

NASA Astrophysics Data System (ADS)

van der Heijden, Marcel; Versteegh, Corstiaen P. C.

2015-12-01

Thirty years ago it was hypothesized that motile processes inject mechanical energy into cochlear traveling waves. This mechanical amplification, alternatively described as negative damping, is invoked to explain both the sensitivity and the nonlinear compression of cochlear responses. There is a recent trend to present cochlear amplification as an established fact, even though the evidence is at most circumstantial and several thorny problems have remained unresolved. We analyze several of these issues, and present new basilar membrane recordings that allowed us to quantify cochlear energy flow. Specifically, we address the following questions: (1) Does auditory sensitivity require narrowband amplification? (2) Has the "RC problem" (lowpass filtering of outer hair cell receptor potential) been resolved? (3) Can OHC motility improve auditory sensitivity? (4) Is there a net power gain between neighboring locations on the basilar membrane? The analyses indicate that mechanical amplification in the cochlea is neither necessary nor useful, and that realizing it by known forms of motility would reduce sensitivity rather than enhance it. Finally, our experimental data show that the peaking of the traveling wave is realized by focusing the acoustic energy rather than amplifying it. (Abbreviations. BM: basilar membrane; CF: characteristic frequency; IHC: inner hair cell; ME: middle ear; MT; mechanotransducer; OHC: outer hair cell; SPL: sound pressure level.)

Biomaterials in light amplification

NASA Astrophysics Data System (ADS)

Mysliwiec, Jaroslaw; Cyprych, Konrad; Sznitko, Lech; Miniewicz, Andrzej

2017-03-01

Biologically produced or inspired materials can serve as optical gain media, i.e. they can exhibit the phenomenon of light amplification. Some of these materials, under suitable dye-doping and optical pumping conditions, show lasing phenomena. The emerging branch of research focused on obtaining lasing action in highly disordered and highly light scattering materials, i.e. research on random lasing, is perfectly suited for biological materials. The use of biomaterials in light amplification has been extensively reported in the literature. In this review we attempt to report on progress in the development of biologically derived systems able to show the phenomena of light amplification and random lasing together with the contribution of our group to this field. The rich world of biopolymers modified with molecular aggregates and nanocrystals, and self-organized at the nanoscale, offers a multitude of possibilities for tailoring luminescent and light scattering properties that are not easily replicated in conventional organic or inorganic materials. Of particular importance and interest are light amplification and lasing, or random lasing studies in biological cells and tissues. In this review we will describe nucleic acids and their complexes employed as gain media due to their favorable optical properties and ease of manipulation. We will report on research conducted on various biomaterials showing structural analogy to nucleic acids such as fluorescent proteins, gelatins in which the first distributed feedback laser was realized, and also amyloids or silks, which, due to their dye-doped fiber-like structure, allow for light amplification. Other materials that were investigated in that respect include polysaccharides, like starch exhibiting favorable photostability in comparison to other biomaterials, and chitosan, which forms photonic crystals or cellulose. Light amplification and random lasing was not only observed in processed biomaterials but also in living

Catechol-chitosan redox capacitor for added amplification in electrochemical immunoanalysis.

PubMed

Yan, Kun; Liu, Yi; Guan, Yongguang; Bhokisham, Narendranath; Tsao, Chen-Yu; Kim, Eunkyoung; Shi, Xiao-Wen; Wang, Qin; Bentley, William E; Payne, Gregory F

2018-05-22

Antibodies are common recognition elements for molecular detection but often the signals generated by their stoichiometric binding must be amplified to enhance sensitivity. Here, we report that an electrode coated with a catechol-chitosan redox capacitor can amplify the electrochemical signal generated from an alkaline phosphatase (AP) linked immunoassay. Specifically, the AP product p-aminophenol (PAP) undergoes redox-cycling in the redox capacitor to generate amplified oxidation currents. We estimate an 8-fold amplification associated with this redox-cycling in the capacitor (compared to detection by a bare electrode). Importantly, this capacitor-based amplification is generic and can be coupled to existing amplification approaches based on enzyme-linked catalysis or magnetic nanoparticle-based collection/concentration. Thus, the capacitor should enhance sensitivities in conventional immunoassays and also provide chemical to electrical signal transduction for emerging applications in molecular communication. Copyright © 2018 Elsevier B.V. All rights reserved.

Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers.

PubMed

Caetano-Anollés, G; Gresshoff, P M

1996-06-01

DNA amplification fingerprinting (DAF) with mini-hairpins harboring arbitrary "core" sequences at their 3' termini were used to fingerprint a variety of templates, including PCR products and whole genomes, to establish genetic relationships between plant tax at the interspecific and intraspecific level, and to identify closely related fungal isolates and plant accessions. No correlation was observed between the sequence of the arbitrary core, the stability of the mini-hairpin structure and DAF efficiency. Mini-hairpin primers with short arbitrary cores and primers complementary to simple sequence repeats present in microsatellites were also used to generate arbitrary signatures from amplification profiles (ASAP). The ASAP strategy is a dual-step amplification procedure that uses at least one primer in each fingerprinting stage. ASAP was able to reproducibly amplify DAF products (representing about 10-15 kb of sequence) following careful optimization of amplification parameters such as primer and template concentration. Avoidance of primer sequences partially complementary to DAF product termini was necessary in order to produce distinct fingerprints. This allowed the combinatorial use of oligomers in nucleic acid screening, with numerous ASAP fingerprinting reactions based on a limited number of primer sequences. Mini-hairpin primers and ASAP analysis significantly increased detection of polymorphic DNA, separating closely related bermudagrass (Cynodon) cultivars and detecting putatively linked markers in bulked segregant analysis of the soybean (Glycine max) supernodulation (nitrate-tolerant symbiosis) locus.

Ferrocenemonocarboxylic-HRP@Pt nanoparticles labeled RCA for multiple amplification of electro-immunosensing.

PubMed

Su, Huilan; Yuan, Ruo; Chai, Yaqin; Mao, Li; Zhuo, Ying

2011-07-15

A multiple amplification immunoassay was proposed to detect alpha-fetoprotein (AFP), which was based on ferrocenemonocarboxylic-HRP conjugated on Pt nanoparticles as labels for rolling circle amplification (RCA). Firstly, the capture antibody (anti-AFP) was immobilized on glass carbon electrode (GCE) deposited nano-sized gold particles. After a typical immuno-sandwich protocol, primary DNA was immobilized by labeling secondary antibody, which acted as a precursor to initiate RCA. The products of RCA provide large amount of sites to link detection DNAs, which were labeled by signal probes (ferrocenemonocarboxylic) and horseradish peroxidase (HRP). Moreover, the enzymatic amplification signals could be produced by the catalysis of HRP and Pt nanoparticles with the addition of H₂O₂. These lead to multiple amplification signals monitoring by electrochemical instrument and further resulted in high sensitivity of the immunoassay with the detection limit of 1.7 pg/mL. Copyright © 2011 Elsevier B.V. All rights reserved.

Reducing uncertainties for short lived cumulative fission product yields

DOE PAGES

Stave, Sean; Prinke, Amanda; Greenwood, Larry; ...

2015-09-05

Uncertainties associated with short lived (halflives less than 1 day) fission product yields listed in databases such as the National Nuclear Data Center’s ENDF/B-VII are large enough for certain isotopes to provide an opportunity for new precision measurements to offer significant uncertainty reductions. A series of experiments has begun where small samples of 235U are irradiated with a pulsed, fission neutron spectrum at the Nevada National Security Site and placed between two broad-energy germanium detectors. The amount of various isotopes present immediately following the irradiation can be determined given the total counts and the calibrated properties of the detector system.more » The uncertainty on the fission yields for multiple isotopes has been reduced by nearly an order of magnitude.« less

Breed of cow and herd productivity affect milk nutrient recovery in curd, and cheese yield, efficiency and daily production.

PubMed

Stocco, G; Cipolat-Gotet, C; Gasparotto, V; Cecchinato, A; Bittante, G

2018-02-01

Little is known about cheese-making efficiency at the individual cow level, so our objective was to study the effects of herd productivity, individual herd within productivity class and breed of cow within herd by producing, then analyzing, 508 model cheeses from the milk of 508 cows of six different breeds reared in 41 multi-breed herds classified into two productivity classes (high v. low). For each cow we obtained six milk composition traits; four milk nutrient (fat, protein, solids and energy) recovery traits (REC) in curd; three actual % cheese yield traits (%CY); two theoretical %CYs (fresh cheese and cheese solids) calculated from milk composition; two overall cheese-making efficiencies (% ratio of actual to theoretical %CYs); daily milk yield (dMY); and three actual daily cheese yield traits (dCY). The aforementioned phenotypes were analyzed using a mixed model which included the fixed effects of herd productivity, parity, days in milk (DIM) and breed; the random effects were the water bath, vat, herd and residual. Cows reared in high-productivity herds yielded more milk with higher nutrient contents and more cheese per day, had greater theoretical %CY, and lower cheese-making efficiency than low-productivity herds, but there were no differences between them in terms of REC traits. Individual herd within productivity class was an intermediate source of total variation in REC, %CY and efficiency traits (10.0% to 17.2%), and a major source of variation in milk yield and dCY traits (43.1% to 46.3%). Parity of cows was an important source of variation for productivity traits, whereas DIM affected almost all traits. Breed within herd greatly affected all traits. Holsteins produced more milk, but Brown Swiss cows produced milk with higher actual and theoretical %CYs and cheese-making efficiency, so that the two large-framed breeds had the same dCY. Compared with the two large-framed breeds, the small Jersey cows produced much less milk, but with greater actual

Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi by Recombinase Polymerase Amplification.

PubMed

Prescott, Meagan A; Reed, Aimee N; Jin, Ling; Pastey, Manoj K

2016-09-01

Since the emergence of cyprinid herpesvirus 3 (CyHV-3), outbreaks have been devastating to Common Carp Cyprinus carpio and koi (a variant of Common Carp), leading to high economic losses. Current diagnostics for detecting CyHV-3 are limited in sensitivity and are further complicated by latency. Here we describe the detection of CyHV-3 by recombinase polymerase amplification (RPA). The RPA assay can detect as low as 10 copies of the CyHV-3 genome by an isothermal reaction and yields results in approximately 20 min. Using the RPA assay, the CyHV-3 genome can be detected in the total DNA of white blood cells isolated from koi latently infected with CyHV-3, while less than 10% of the latently infected koi can be detected by a real-time PCR assay in the total DNA of white blood cells. In addition, RPA products can be detected in a lateral flow device that is cheap and fast and can be used outside of the diagnostic lab. The RPA assay and lateral flow device provide for the rapid, sensitive, and specific amplification of CyHV-3 that with future modifications for field use and validation could lead to enhanced surveillance and early diagnosis of CyHV-3 in the laboratory and field. Received September 14, 2015; accepted April 9, 2016.

Amplification of terahertz pulses in gases beyond thermodynamic equilibrium

NASA Astrophysics Data System (ADS)

Schwaab, G. W.; Schroeck, K.; Havenith, M.

2007-03-01

In Ebbinghaus [Plasma Sources Sci. Technol. 15, 72 (2006)] we reported terahertz time-domain spectroscopy in a plasma at low pressure, we observed a simultaneous absorption and amplification process within each single rotational transition. Here we show that this observation is a direct consequence of the short interaction time of the pulsed terahertz radiation with the plasma, which is shorter than the average collision time between the molecules. Thus, during the measurement time the molecular states may be considered entangled. Solution of the time-dependent Schrödinger equation yields a linear term that may be neglected for long observation times, large frequencies, or nonentangled states. We determine the restrictions for the observation of this effect and calculate the spectrum of a simple diatomic molecule. Using this model we are able to explain the spectral features showing a change from emission to absorption as observed previously. In addition we find that the amplification and absorption do not follow the typical Lambert-Beer exponential law but an approximate square law.

Unusual isothermal multimerization and amplification by the strand-displacing DNA polymerases with reverse transcription activities.

PubMed

Wang, Guoping; Ding, Xiong; Hu, Jiumei; Wu, Wenshuai; Sun, Jingjing; Mu, Ying

2017-10-24

Existing isothermal nucleic acid amplification (INAA) relying on the strand displacement activity of DNA polymerase usually requires at least two primers. However, in this paper, we report an unusual isothermal multimerization and amplification (UIMA) which only needs one primer and is efficiently initiated by the strand-displacing DNA polymerases with reverse transcription activities. On electrophoresis, the products of UIMA present a cascade-shape band and they are confirmed to be multimeric DNAs with repeated target sequences. In contrast to current methods, UIMA is simple to product multimeric DNA, due to the independent of multiple primers and rolling circle structures. Through assaying the synthesized single-stranded DNA targets, UIMA performs high sensitivity and specificity, as well as the universality. In addition, a plausible mechanism of UIMA is proposed, involving short DNA bending, mismatch extension, and template slippage. UIMA is a good explanation for why nonspecific amplification easily happens in existing INAAs. As the simplest INAA till now, UIMA provides a new insight for deeply understanding INAA and opens a new avenue for thoroughly addressing nonspecific amplification.

Characterization of different biological types of steers (cycle IV): wholesale, subprimal, and retail product yields.

PubMed

Wheeler, T L; Cundiff, L V; Koch, R M; Dikeman, M E; Crouse, J D

1997-09-01

Carcass cut-out yields of 888 steers obtained from mating Hereford and Angus cows to Hereford or Angus (HA), Charolais (Ch), Gelbvieh (Gb), Pinzgauer (Pz), Shorthorn (Sh), Galloway (Gw), Longhorn (Lh), Nellore (Ne), Piedmontese (Pm), and Salers (Sa) sires were compared. Data were evaluated at constant age (426 d), carcass weight (324 kg), fat thickness (1.2 cm), fat trim percentage (23%), and marbling (Small(00)) end points. Piedmontese-sired steers excelled in total retail product and fat trim percentages at all slaughter end points except at the 23% fat trim end point. At an age end point, percentage of retail product was greater in steers sired by Continental European breeds (Gb, Ch, Sa, Pz; 63.3 to 65.5% at 0 cm trim) than in steers sired by British breeds (Sh, HA; 60.1 to 61.0%). Piedmontese-sired steers, which were expected to carry one copy of a major gene for muscle hypertrophy, had the highest (P < .05) retail product yields at an age end point (69.7%). At an age end point, although carcass weights were significantly heavier (P < .05) for Charolais-sired steers than for Piedmontese-sired steers, lean growth rate, as reflected by totally trimmed retail product at 426 d, was similar (P > .05) for Piedmontese and Charolais-sired steers. Differences among sire breeds were small for retail product percentage at marbling, fat thickness, and fat trim end points. Ranking of sire breeds for age-constant weight of retail product was as follows: Ch, Pm, Gb, Sa, Ne, Pz, HA, Sh, Gw, and Lh. Sire breed differences in wholesale and subprimal cut yields were similar to total retail product differences. Piedmontese-sired steers produced the most muscular, leanest, and highest-yielding carcasses, and HA- and Sh-sired steers produced the fattest, lowest-yielding carcasses.

Ozone deposition velocities, reaction probabilities and product yields for green building materials

NASA Astrophysics Data System (ADS)

Lamble, S. P.; Corsi, R. L.; Morrison, G. C.

2011-12-01

Indoor surfaces can passively remove ozone that enters buildings, reducing occupant exposure without an energy penalty. However, reactions between ozone and building surfaces can generate and release aerosols and irritating and carcinogenic gases. To identify desirable indoor surfaces the deposition velocity, reaction probability and carbonyl product yields of building materials considered green (listed, recycled, sustainable, etc.) were quantified. Nineteen separate floor, wall or ceiling materials were tested in a 10 L, flow-through laboratory reaction chamber. Inlet ozone concentrations were maintained between 150 and 200 ppb (generally much lower in chamber air), relative humidity at 50%, temperature at 25 °C and exposure occurred over 24 h. Deposition velocities ranged from 0.25 m h -1 for a linoleum style flooring up to 8.2 m h -1 for a clay based paint; reaction probabilities ranged from 8.8 × 10 -7 to 6.9 × 10 -5 respectively. For all materials, product yields of C 1 thru C 12 saturated n-aldehydes, plus acetone ranged from undetectable to greater than 0.70 The most promising material was a clay wall plaster which exhibited a high deposition velocity (5.0 m h -1) and a low product yield (

Acrolein Yields in Mainstream Smoke From Commercial Cigarette and Little Cigar Tobacco Products.

PubMed

Cecil, Todd L; Brewer, Tim M; Young, Mimy; Holman, Matthew R

2017-07-01

Many carbonyls are produced from the combustion of tobacco products and many of these carbonyls are harmful or potentially harmful constituents of mainstream cigarette smoke. One carbonyl of particular interest is acrolein, which is formed from the incomplete combustion of organic matter and the most significant contributor to non-cancer respiratory effects from cigarette smoke. Sheet-wrapped cigars, also known as "little cigars," are a type of tobacco products that have not been extensively investigated in literature. This study uses standard cigarette testing protocols to determine the acrolein yields from sheet-wrapped cigars. Sheet-wrapped cigar and cigarette products were tested by derivatizing the mainstream smoke with 2,4-dinitrophenylhydrazine (DNPH) solution and then quantifying the derivatives using conventional analytical systems. The results demonstrate that sheet-wrapped cigars can be tested for acrolein yields in mainstream smoke using the same methods used for the evaluation of cigarettes. The variability in the sheet-wrapped cigars and cigarettes under the International Organization for Standardization smoking regimen is statistically similar at the 95% confidence interval; however, increased variability is observed for sheet-wrapped cigar products under the Health Canada Intense (CI) smoking regimen. The amount of acrolein released by smoking sheet-wrapped cigars can be measured using standard smoking regimen currently used for cigarettes. The sheet-wrapped cigars were determined to yield similar quantity of acrolein from commercial cigarette products using two standard smoking regimens. This article reports on the measured quantity of acrolein from 15 commercial sheet-wrapped cigars using a validated standard smoking test method that derivatizes acrolein in the mainstream smoke with DNPH solution, and uses Liquid Chromatography/Ultra-Violet Detection (LC/UV) for separation and detection. These acrolein yields were similar to the levels found in

Estimation efficiency of usage satellite derived and modelled biophysical products for yield forecasting

NASA Astrophysics Data System (ADS)

Kolotii, Andrii; Kussul, Nataliia; Skakun, Sergii; Shelestov, Andrii; Ostapenko, Vadim; Oliinyk, Tamara

2015-04-01

Efficient and timely crop monitoring and yield forecasting are important tasks for ensuring of stability and sustainable economic development [1]. As winter crops pay prominent role in agriculture of Ukraine - the main focus of this study is concentrated on winter wheat. In our previous research [2, 3] it was shown that usage of biophysical parameters of crops such as FAPAR (derived from Geoland-2 portal as for SPOT Vegetation data) is far more efficient for crop yield forecasting to NDVI derived from MODIS data - for available data. In our current work efficiency of usage such biophysical parameters as LAI, FAPAR, FCOVER (derived from SPOT Vegetation and PROBA-V data at resolution of 1 km and simulated within WOFOST model) and NDVI product (derived from MODIS) for winter wheat monitoring and yield forecasting is estimated. As the part of crop monitoring workflow (vegetation anomaly detection, vegetation indexes and products analysis) and yield forecasting SPIRITS tool developed by JRC is used. Statistics extraction is done for landcover maps created in SRI within FP-7 SIGMA project. Efficiency of usage satellite based and modelled with WOFOST model biophysical products is estimated. [1] N. Kussul, S. Skakun, A. Shelestov, O. Kussul, "Sensor Web approach to Flood Monitoring and Risk Assessment", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 815-818. [2] F. Kogan, N. Kussul, T. Adamenko, S. Skakun, O. Kravchenko, O. Kryvobok, A. Shelestov, A. Kolotii, O. Kussul, and A. Lavrenyuk, "Winter wheat yield forecasting in Ukraine based on Earth observation, meteorological data and biophysical models," International Journal of Applied Earth Observation and Geoinformation, vol. 23, pp. 192-203, 2013. [3] Kussul O., Kussul N., Skakun S., Kravchenko O., Shelestov A., Kolotii A, "Assessment of relative efficiency of using MODIS data to winter wheat yield forecasting in Ukraine", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 3235 - 3238.

Enhancing enterovirus A71 vaccine production yield by microcarrier profusion bioreactor culture.

PubMed

Liu, Chia-Chyi; Wu, Suh-Chin; Wu, Shang-Rung; Lin, Hsiao-Yu; Guo, Meng-Shin; Yung-Chih Hu, Alan; Chow, Yen-Hung; Chiang, Jen-Ron; Shieh, Dar-Bin; Chong, Pele

2018-05-24

Hand, foot and mouth diseases (HFMD) are mainly caused by Enterovirus A71 (EV-A71) infections. Clinical trials in Asia conducted with formalin-inactivated EV-A71 vaccine candidates produced from serum-free Vero cell culture using either roller bottle or cell factory technology, are found to be safe and highly efficacious. To increase vaccine yields and reduce the production costs, the bioprocess improvement for EV-A71 vaccine manufacturing is currently being investigated. The parameters that could affect and enhance the production yields of EV-A71 virus growth in the microcarrier bioreactor were investigated. The medium replacement culture strategy included a multi-harvested semi-batch process and perfusion technology and was found to increase the production yields more than 7-14 folds. Based on the western blot and cryo-EM analyses of the EV-A71 virus particles produced from either the multi-harvested semi-batch (MHSBC) or perfusion cultures were found to be similar to those virus particles obtained from the single batch culture. Mouse immunogenicity studies indicate that the EV-A71 vaccine candidates produced from the perfusion culture have similar potency to those obtained from single batch bioprocess. The physical structures of the EV-A71 particles revealed by the cryo-EM analysis were found to be spherical capsid particles. These results provide feasible technical bioprocesses for increasing virus yields and the scale up of EV-A71 vaccine manufacturing using the bioreactor cell culture methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi (Cyprinus carpio) by Recombinase Polymerase Amplification

PubMed Central

Prescott, Meagan A.; Reed, Aimee N.; Jin, Ling; Pastey, Manoj K.

2018-01-01

Since the emergence of cyprinid herpes virus 3 (CyHV-3), outbreaks have been devastating to koi and common carp leading to high economic losses. Current diagnostics for detecting CyHV-3 are limited in sensitivity and are further complicated by latency. Here we describe the detection of CyHV-3 by recombinase polymerase amplification (RPA). The RPA assay can detect as low as 10 copies of CyHV-3 genome by an isothermal reaction and yields results in approximately 20 minutes. Using the RPA assay, CyHV-3 genome can be detected in total DNA of white blood cells isolated from koi latently infected with CyHV-3, while less than 10% of the latently infected koi can be detected by a real-time PCR assay in total DNA of white blood cells. In addition, RPA products can be detected in a lateral flow device that is cheap, fast, and can be used outside of the diagnostic lab. The RPA assay and lateral flow device provide for the rapid, sensitive, and specific amplification of CyHV-3 that with future modifications for field use and validation could lead to enhanced surveillance and early diagnosis of CyHV-3 in the laboratory and field. PMID:27485254

Three-input majority function as the unique optimal function for the bias amplification using nonlocal boxes

NASA Astrophysics Data System (ADS)

Mori, Ryuhei

2016-11-01

Brassard et al. [Phys. Rev. Lett. 96, 250401 (2006), 10.1103/PhysRevLett.96.250401] showed that shared nonlocal boxes with a CHSH (Clauser, Horne, Shimony, and Holt) probability greater than 3/+√{6 } 6 yield trivial communication complexity. There still exists a gap with the maximum CHSH probability 2/+√{2 } 4 achievable by quantum mechanics. It is an interesting open question to determine the exact threshold for the trivial communication complexity. Brassard et al.'s idea is based on recursive bias amplification by the three-input majority function. It was not obvious if another choice of function exhibits stronger bias amplification. We show that the three-input majority function is the unique optimal function, so that one cannot improve the threshold 3/+√{6 } 6 by Brassard et al.'s bias amplification. In this work, protocols for computing the function used for the bias amplification are restricted to be nonadaptive protocols or a particular adaptive protocol inspired by Pawłowski et al.'s protocol for information causality [Nature (London) 461, 1101 (2009), 10.1038/nature08400]. We first show an adaptive protocol inspired by Pawłowski et al.'s protocol, and then show that the adaptive protocol improves upon nonadaptive protocols. Finally, we show that the three-input majority function is the unique optimal function for the bias amplification if we apply the adaptive protocol to each step of the bias amplification.

Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification

PubMed Central

Dean, Frank B.; Nelson, John R.; Giesler, Theresa L.; Lasken, Roger S.

2001-01-01

We describe a simple method of using rolling circle amplification to amplify vector DNA such as M13 or plasmid DNA from single colonies or plaques. Using random primers and φ29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours. This procedure removes the need for lengthy growth periods and traditional DNA isolation methods. Reaction products can be used directly for DNA sequencing after phosphatase treatment to inactivate unincorporated nucleotides. Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications. PMID:11381035

Meteorological fluctuations define long-term crop yield patterns in conventional and organic production systems

USDA-ARS?s Scientific Manuscript database

Periodic variability in meteorological patterns presents significant challenges to crop production consistency and yield stability. Meteorological influences on corn and soybean grain yields were analyzed over an 18-year period at a long-term experiment in Beltsville, Maryland, U.S.A., comparing c...

Associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions

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

Xie Jujun; Department of Physics, Zhengzhou University, Zhengzhou, Henan 450001; Wilkin, Colin

2010-08-15

The total and differential cross sections for associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions have been studied in a unified approach using an effective Lagrangian model. It is assumed that both the K{sup -}p and {pi}{sup 0{Sigma}0} final states originate from the decay of the {Lambda}(1405) that was formed in the production chain pp{yields}p(N*(1535){yields}K{sup +{Lambda}}(1405)). The available experimental data are well reproduced, especially the ratio of the two total cross sections, which is much less sensitive to the particular model of the entrance channel. The significant coupling of the N*(1535) to {Lambda}(1405)K is further evidencemore » for large ss-bar components in the quark wave function of the N*(1535).« less

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

PubMed

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

Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli.

PubMed

Zhu, Xinna; Tan, Zaigao; Xu, Hongtao; Chen, Jing; Tang, Jinlei; Zhang, Xueli

2014-07-01

Reducing equivalents are an important cofactor for efficient synthesis of target products. During metabolic evolution to improve succinate production in Escherichia coli strains, two reducing equivalent-conserving pathways were activated to increase succinate yield. The sensitivity of pyruvate dehydrogenase to NADH inhibition was eliminated by three nucleotide mutations in the lpdA gene. Pyruvate dehydrogenase activity increased under anaerobic conditions, which provided additional NADH. The pentose phosphate pathway and transhydrogenase were activated by increased activities of transketolase and soluble transhydrogenase SthA. These data suggest that more carbon flux went through the pentose phosphate pathway, thus leading to production of more reducing equivalent in the form of NADPH, which was then converted to NADH through soluble transhydrogenase for succinate production. Reverse metabolic engineering was further performed in a parent strain, which was not metabolically evolved, to verify the effects of activating these two reducing equivalent-conserving pathways for improving succinate yield. Activating pyruvate dehydrogenase increased succinate yield from 1.12 to 1.31mol/mol, whereas activating the pentose phosphate pathway and transhydrogenase increased succinate yield from 1.12 to 1.33mol/mol. Activating these two pathways in combination led to a succinate yield of 1.5mol/mol (88% of theoretical maximum), suggesting that they exhibited a synergistic effect for improving succinate yield. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Succinic acid production with Actinobacillus succinogenes: rate and yield analysis of chemostat and biofilm cultures.

PubMed

Brink, Hendrik Gideon; Nicol, Willie

2014-08-19

Succinic acid is well established as bio-based platform chemical with production quantities expecting to increase exponentially within the next decade. Actinobacillus succinogenes is by far the most studied wild organism for producing succinic acid and is known for high yield and titre during production on various sugars in batch culture. At low shear conditions continuous fermentation with A. succinogenes results in biofilm formation. In this study, a novel shear controlled fermenter was developed that enabled: 1) chemostat operation where self-immobilisation was opposed by high shear rates and, 2) in-situ removal of biofilm by increasing shear rates and subsequent analysis thereof. The volumetric productivity of the biofilm fermentations were an order of magnitude more than the chemostat runs. In addition the biofilm runs obtained substantially higher yields. Succinic acid to acetic acid ratios for chemostat runs were 1.28±0.2 g.g(-1), while the ratios for biofilm runs started at 2.4 g.g(-1) and increased up to 3.3 g.g(-1) as glucose consumption increased. This corresponded to an overall yield on glucose of 0.48±0.05 g.g(-1) for chemostat runs, while the yields varied between 0.63 g.g(-1) and 0.74 g.g(-1) for biofilm runs. Specific growth rates (μ) were shown to be severely inhibited by the formation of organic acids, with μ only 12% of μ(max) at a succinic acid titre of 7 g.L(-1). Maintenance production of succinic acid was shown to be dominant for the biofilm runs with cell based production rates (extracellular polymeric substance removed) decreasing as SA titre increases. The novel fermenter allowed for an in-depth bioreaction analysis of A. succinogenes. Biofilm cells achieve higher SA yields than suspended cells and allow for operation at higher succinic acid titre. Both growth and maintenance rates were shown to drastically decrease with succinic acid titre. The A. succinogenes biofilm process has vast potential, where self-induced high cell densities

Unexpected high yields of carbonyl and peroxide products of aqueous isoprene ozonolysis and implications

NASA Astrophysics Data System (ADS)

Wang, H. L.; Huang, D.; Zhang, X.; Zhao, Y.; Chen, Z. M.

2012-03-01

The aqueous phase reaction of volatile organic compounds (VOCs) has not been considered in most analyses of atmospheric chemical processes. However, some experimental evidence has shown that, compared to the corresponding gas phase reaction, the aqueous chemical processes of VOCs in the bulk solutions and surfaces of ambient wet particles (cloud, fog, and wet aerosols) may potentially contribute to the products and formation of secondary organic aerosol (SOA). In the present study, we performed a laboratory experiment of the aqueous ozonolysis of isoprene at different pHs (3-7) and temperatures (4-25 °C). We detected three important kinds of products, including carbonyl compounds, peroxide compounds, and organic acids. Our results showed that the molar yields of these products were nearly independent of the investigated pHs and temperatures. These products included (1) carbonyls: 56.7 ± 6.7% formaldehyde, 42.8 ± 2.5% methacrolein (MAC), and 57.7 ± 3.4% methyl vinyl ketone (MVK); (2) peroxides: 53.4 ± 4.1% hydrogen peroxide (H2O2) and 15.1 ± 3.1% hydroxylmethyl hydroperoxide (HMHP); and (3) organic acids: undetectable (< 1% estimated by the detection limit). Based on the amounts of products formed and the isoprene consumed, the total carbon yield was estimated to be 95 ± 4%. This implied that most of the products in the reaction system were detected. Of note, the combined yields of both MAC + MVK and H2O2 + HMHP in the aqueous isoprene ozonolysis were much higher than those observed in the corresponding gas phase reaction. We suggested that these unexpected high yields of carbonyls and peroxides were related to the greater capability of condensed water, compared to water vapor, to stabilize energy-rich Criegee radicals. This aqueous ozonolysis of isoprene (and possibly other biogenic VOCs) could potentially occur on the surfaces of ambient wet particles and plants. Moreover, the high-yield carbonyl and peroxide products might provide a considerable source of

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

PubMed Central

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

Rapid DNA Amplification Using a Battery-Powered Thin-Film Resistive Thermocycler

PubMed Central

Herold, Keith E.; Sergeev, Nikolay; Matviyenko, Andriy; Rasooly, Avraham

2010-01-01

Summary A prototype handheld, compact, rapid thermocycler was developed for multiplex analysis of nucleic acids in an inexpensive, portable configuration. Instead of the commonly used Peltier heating/cooling element, electric thin-film resistive heater and a miniature fan enable rapid heating and cooling of glass capillaries leading to a simple, low-cost Thin-Film Resistive Thermocycler (TFRT). Computer-based pulse width modulation control yields heating rates of 6–7 K/s and cooling rates of 5 K/s. The four capillaries are closely coupled to the heater, resulting in low power consumption. The energy required by a nominal PCR cycle (20 s at each temperature) was found to be 57 ± 2 J yielding an average power of approximately 1.0 W (not including the computer and the control system). Thus the device can be powered by a standard 9 V alkaline battery (or other 9 V power supply). The prototype TFRT was demonstrated (in a benchtop configuration) for detection of three important food pathogens (E. coli ETEC, Shigella dysenteriae, and Salmonella enterica). PCR amplicons were analyzed by gel electrophoresis. The 35 cycle PCR protocol using a single channel was completed in less then 18 min. Simple and efficient heating/cooling, low cost, rapid amplification, and low power consumption make the device suitable for portable DNA amplification applications including clinical point of care diagnostics and field use. PMID:19159110

Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases.

PubMed

Sahoo, Pravas Ranjan; Sethy, Kamadev; Mohapatra, Swagat; Panda, Debasis

2016-05-01

India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.

Radiation use efficiency, biomass production, and grain yield in two maize hybrids differing in drought tolerance

USDA-ARS?s Scientific Manuscript database

Drought tolerant (DT) maize (Zea mays L.) hybrids have potential to increase yield under drought conditions. However, little information is known about the physiological determinations of yield in DT hybrids. Our objective was to assess radiation use efficiency (RUE), biomass production, and yield ...

Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content.

PubMed

Waclawovsky, Alessandro J; Sato, Paloma M; Lembke, Carolina G; Moore, Paul H; Souza, Glaucia M

2010-04-01

An increasing number of plant scientists, including breeders, agronomists, physiologists and molecular biologists, are working towards the development of new and improved energy crops. Research is increasingly focused on how to design crops specifically for bioenergy production and increased biomass generation for biofuel purposes. The most important biofuel to date is bioethanol produced from sugars (sucrose and starch). Second generation bioethanol is also being targeted for studies to allow the use of the cell wall (lignocellulose) as a source of carbon. If a crop is to be used for bioenergy production, the crop should be high yielding, fast growing, low lignin content and requiring relatively small energy inputs for its growth and harvest. Obtaining high yields in nonprime agricultural land is a key for energy crop development to allow sustainability and avoid competition with food production. Sugarcane is the most efficient bioenergy crop of tropical and subtropical regions, and biotechnological tools for the improvement of this crop are advancing rapidly. We focus this review on the studies of sugarcane genes associated with sucrose content, biomass and cell wall metabolism and the preliminary physiological characterization of cultivars that contrast for sugar and biomass yield.

Growth, yield and compositional characteristics of Jerusalem artichoke as it relates to biomass production

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

Stauffer, M.D.; Chubey, B.B.; Dorrell, D.G.

1980-01-01

Jerusalem artichoke (Helianthus tuberosus L.) has shown excellent potential as a carbohydrate-rich crop. Initial investigations determined inulin and tuber yields; however, when additional studies showed that good quality pulp remained after inulin extraction and high forage yields per hectare were obtainable, the scope of investigation was broadened to assess utilization of the total plant. Plant growth, yield and compositional characteristics of Jerusalem artichoke as they relate to biomass production will be reported.

Photofission product yields of 238U and 239Pu with 22-MeV bremsstrahlung

NASA Astrophysics Data System (ADS)

Wen, Xianfei; Yang, Haori

2016-06-01

In homeland security and nuclear safeguards applications, non-destructive techniques to identify and quantify special nuclear materials are in great demand. Although nuclear materials naturally emit characteristic radiation (e.g. neutrons, γ-rays), their intensity and energy are normally low. Furthermore, such radiation could be intentionally shielded with ease or buried in high-level background. Active interrogation techniques based on photofission have been identified as effective assay approaches to address this issue. In designing such assay systems, nuclear data, like photofission product yields, plays a crucial role. Although fission yields for neutron-induced reactions have been well studied and readily available in various nuclear databases, data on photofission product yields is rather scarce. This poses a great challenge to the application of photofission techniques. In this work, short-lived high-energy delayed γ-rays from photofission of 238U were measured in between linac pulses. In addition, a list-mode system was developed to measure relatively long-lived delayed γ-rays from photofission of 238U and 239Pu after the irradiation. Time and energy information of each γ-ray event were simultaneously recorded by this system. Cumulative photofission product yields were then determined using the measured delayed γ-ray spectra.

Plant-based assessment of inherent soil productivity and contributions to China's cereal crop yield increase since 1980.

PubMed

Fan, Mingsheng; Lal, Rattan; Cao, Jian; Qiao, Lei; Su, Yansen; Jiang, Rongfeng; Zhang, Fusuo

2013-01-01

China's food production has increased 6-fold during the past half-century, thanks to increased yields resulting from the management intensification, accomplished through greater inputs of fertilizer, water, new crop strains, and other Green Revolution's technologies. Yet, changes in underlying quality of soils and their effects on yield increase remain to be determined. Here, we provide a first attempt to quantify historical changes in inherent soil productivity and their contributions to the increase in yield. The assessment was conducted based on data-set derived from 7410 on-farm trials, 8 long-term experiments and an inventory of soil organic matter concentrations of arable land. Results show that even without organic and inorganic fertilizer addition crop yield from on-farm trials conducted in the 2000s was significantly higher compared with those in the 1980s - the increase ranged from 0.73 to 1.76 Mg/ha for China's major irrigated cereal-based cropping systems. The increase in on-farm yield in control plot since 1980s was due primarily to the enhancement of soil-related factors, and reflected inherent soil productivity improvement. The latter led to higher and stable yield with adoption of improved management practices, and contributed 43% to the increase in yield for wheat and 22% for maize in the north China, and, 31%, 35% and 22% for early and late rice in south China and for single rice crop in the Yangtze River Basin since 1980. Thus, without an improvement in inherent soil productivity, the 'Agricultural Miracle in China' would not have happened. A comprehensive strategy of inherent soil productivity improvement in China, accomplished through combining engineering-based measures with biological-approaches, may be an important lesson for the developing world. We propose that advancing food security in 21st century for both China and other parts of world will depend on continuously improving inherent soil productivity.

Integrated bioethanol production to boost low-concentrated cellulosic ethanol without sacrificing ethanol yield.

PubMed

Xu, Youjie; Zhang, Meng; Roozeboom, Kraig; Wang, Donghai

2018-02-01

Four integrated designs were proposed to boost cellulosic ethanol titer and yield. Results indicated co-fermentation of corn flour with hydrolysate liquor from saccharified corn stover was the best integration scheme and able to boost ethanol titers from 19.9 to 123.2 g/L with biomass loading of 8% and from 36.8 to 130.2 g/L with biomass loadings of 16%, respectively, while meeting the minimal ethanol distillation requirement of 40 g/L and achieving high ethanol yields of above 90%. These results indicated integration of first and second generation ethanol production could significantly accelerate the commercialization of cellulosic biofuel production. Co-fermentation of starchy substrate with hydrolysate liquor from saccharified biomass is able to significantly enhance ethanol concentration to reduce energy cost for distillation without sacrificing ethanol yields. This novel method could be extended to any pretreatment of biomass from low to high pH pretreatment as demonstrated in this study. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relationships between primary production and crop yields in semi-arid and arid irrigated agro-ecosystems

NASA Astrophysics Data System (ADS)

Jaafar, H. H.; Ahmad, F. A.

2015-04-01

In semi-arid areas within the MENA region, food security problems are the main problematic imposed. Remote sensing can be a promising too early diagnose food shortages and further prevent the population from famine risks. This study is aimed at examining the possibility of forecasting yield before harvest from remotely sensed MODIS-derived Enhanced Vegetation Index (EVI), Net photosynthesis (net PSN), and Gross Primary Production (GPP) in semi-arid and arid irrigated agro-ecosystems within the conflict affected country of Syria. Relationships between summer yield and remotely sensed indices were derived and analyzed. Simple regression spatially-based models were developed to predict summer crop production. The validation of these models was tested during conflict years. A significant correlation (p<0.05) was found between summer crop yield and EVI, GPP and net PSN. Results indicate the efficiency of remotely sensed-based models in predicting summer yield, mostly for cotton yields and vegetables. Cumulative summer EVI-based model can predict summer crop yield during crisis period, with deviation less than 20% where vegetables are the major yield. This approach prompts to an early assessment of food shortages and lead to a real time management and decision making, especially in periods of crisis such as wars and drought.

Other Products and Devices to Improve Hearing

MedlinePlus

... and Consumer Devices Consumer Products Hearing Aids Other Products and Devices to Improve Hearing Share Tweet Linkedin ... no hearing in one ear. Personal Sound Amplification Products Personal Sound Amplification Products (PSAPs), or sound amplifiers, ...

Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security

PubMed Central

Li, Xiaoyun; Liu, Nianjie; You, Liangzhi; Ke, Xinli; Liu, Haijun; Huang, Malan; Waddington, Stephen R.

2016-01-01

After a remarkable 86% increase in cereal production from 1980 to 2005, recent crop yield growth in China has been slow. County level crop production data between 1980 and 2010 from eastern and middle China were used to analyze spatial and temporal patterns of rice, wheat and maize yield in five major farming systems that include around 90% of China's cereal production. Site-specific yield trends were assessed in areas where those crops have experienced increasing yield or where yields have stagnated or declined. We find that rice yields have continued to increase on over 12.3 million hectares (m. ha) or 41.8% of the rice area in China between 1980 and 2010. However, yields stagnated on 50% of the rice area (around 14.7 m. ha) over this time period. Wheat yields increased on 13.8 m. ha (58.2% of the total harvest area), but stagnated on around 3.8 m. ha (15.8% of the harvest area). Yields increased on a smaller proportion of the maize area (17.7% of harvest area, 5.3 m. ha), while yields have stagnated on over 54% (16.3 m. ha). Many parts of the lowland rice and upland intensive sub-tropical farming systems were more prone to stagnation with rice, the upland intensive sub-tropical system with wheat, and maize in the temperate mixed system. Large areas where wheat yield continues to rise were found in the lowland rice and temperate mixed systems. Land and water constraints, climate variability, and other environmental limitations undermine increased crop yield and agricultural productivity in these systems and threaten future food security. Technology and policy innovations must be implemented to promote crop yields and the sustainable use of agricultural resources to maintain food security in China. In many production regions it is possible to better match the crop with input resources to raise crop yields and benefits. Investments may be especially useful to intensify production in areas where yields continue to improve. For example, increased support to maize

Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification.

PubMed

Ma, Youlong; Teng, Feiyue; Libera, Matthew

2018-06-05

Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here, we demonstrate the concept of solid-phase nucleic acid sequence-based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency. SP-NASBA involves two enzymes, avian myeloblastosis virus reverse transcriptase (AMV-RT) and RNase H, to convert tethered forward and reverse primers into tethered double-stranded DNA (ds-DNA) bridges from which RNA - amplicons can be generated by a third enzyme, T7 RNA polymerase. We create microgels on silicon surfaces using electron-beam patterning of thin-film blends of hydroxyl-terminated and biotin-terminated poly(ethylene glycol) (PEG-OH, PEG-B). The tethering density is linearly related to the PEG-B concentration, and biotinylated primers and molecular beacon detection probes are tethered to streptavidin-activated microgels. While SP-NASBA is very efficient at low tethering densities, the efficiency decreases dramatically with increasing tethering density due to three effects: (a) a reduced hybridization efficiency of tethered molecular beacon detection probes; (b) a decrease in T7 RNA polymerase efficiency; (c) inhibition of T7 RNA polymerase activity by AMV-RT.

Exploratory study of fission product yield determination from photofission of Pu 239 at 11 MeV with monoenergetic photons

DOE PAGES

Bhike, Megha; Tornow, W.; Krishichayan, -; ...

2017-02-14

Here, measurements of fission product yields play an important role for the understanding of fundamental aspects of the fission process. Recently, neutron-induced fission product-yield data of  239Pu at energies below 4 MeV revealed an unexpected energy dependence of certain fission fragments. In order to investigate whether this observation is prerogative to neutron-induced fission, a program has been initiated to measure fission product yields in photoinduced fission. Here we report on the first ever photofission product yield measurement with monoenergetic photons produced by Compton back-scattering of FEL photons. The experiment was performed at the High-Intensity Gamma-ray Source at Triangle Universities Nuclear Laboratorymore » on  239Pu at E γ = 11 MeV. In this exploratory study the yield of eight fission products ranging from  91Sr to  143Ce has been obtained.« less

Exploratory study of fission product yield determination from photofission of Pu 239 at 11 MeV with monoenergetic photons

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

Bhike, Megha; Tornow, W.; Krishichayan, -

Here, measurements of fission product yields play an important role for the understanding of fundamental aspects of the fission process. Recently, neutron-induced fission product-yield data of  239Pu at energies below 4 MeV revealed an unexpected energy dependence of certain fission fragments. In order to investigate whether this observation is prerogative to neutron-induced fission, a program has been initiated to measure fission product yields in photoinduced fission. Here we report on the first ever photofission product yield measurement with monoenergetic photons produced by Compton back-scattering of FEL photons. The experiment was performed at the High-Intensity Gamma-ray Source at Triangle Universities Nuclear Laboratorymore » on  239Pu at E γ = 11 MeV. In this exploratory study the yield of eight fission products ranging from  91Sr to  143Ce has been obtained.« less

Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum

DOE PAGES

Papanek, Beth A.; Biswas, Ranjita; Rydzak, Thomas; ...

2015-09-12

Clostridium thermocellum has the natural ability to convert cellulose to ethanol, making it a promising candidate for consolidated bioprocessing (CBP) of cellulosic biomass to biofuels. To further improve its CBP capabilities, we study a mutant strain of C. thermocellum that was constructed (strain AG553; C. thermocellum Δhpt ΔhydG Δldh Δpfl Δpta-ack) to increase flux to ethanol by removing side product formation. Strain AG553 showed a two- to threefold increase in ethanol yield relative to the wild type on all substrates tested. On defined medium, strain AG553 exceeded 70% of theoretical ethanol yield on lower loadings of the model crystalline cellulosemore » Avicel, effectively eliminating formate, acetate, and lactate production and reducing H 2 production by fivefold. On 5 g/L Avicel, strain AG553 reached an ethanol yield of 63.5% of the theoretical maximum compared with 19.9% by the wild type, and it showed similar yields on pretreated switchgrass and poplar. The elimination of organic acid production suggested that the strain might be capable of growth under higher substrate loadings in the absence of pH control. Final ethanol titer peaked at 73.4 mM in mutant AG553 on 20 g/L Avicel, at which point the pH decreased to a level that does not allow growth of C. thermocellum, likely due to CO 2 accumulation. In comparison, the maximum titer of wild type C. thermocellum was 14.1 mM ethanol on 10 g/L Avicel. In conclusion, with the elimination of the metabolic pathways to all traditional fermentation products other than ethanol, AG553 is the best ethanol-yielding CBP strain to date and will serve as a platform strain for further metabolic engineering for the bioconversion of lignocellulosic biomass.« less

Optimizing cropland cover for stable food production in Sub-Saharan Africa using simulated yield and Modern Portfolio Theory

NASA Astrophysics Data System (ADS)

Bodin, P.; Olin, S.; Pugh, T. A. M.; Arneth, A.

2014-12-01

Food security can be defined as stable access to food of good nutritional quality. In Sub Saharan Africa access to food is strongly linked to local food production and the capacity to generate enough calories to sustain the local population. Therefore it is important in these regions to generate not only sufficiently high yields but also to reduce interannual variability in food production. Traditionally, climate impact simulation studies have focused on factors that underlie maximum productivity ignoring the variability in yield. By using Modern Portfolio Theory, a method stemming from economics, we here calculate optimum current and future crop selection that maintain current yield while minimizing variance, vs. maintaining variance while maximizing yield. Based on simulated yield using the LPJ-GUESS dynamic vegetation model, the results show that current cropland distribution for many crops is close to these optimum distributions. Even so, the optimizations displayed substantial potential to either increase food production and/or to decrease its variance regionally. Our approach can also be seen as a method to create future scenarios for the sown areas of crops in regions where local food production is important for food security.

Homogeneous and label-free detection of microRNAs using bifunctional strand displacement amplification-mediated hyperbranched rolling circle amplification.

PubMed

Zhang, Li-rong; Zhu, Guichi; Zhang, Chun-yang

2014-07-01

MicroRNAs (miRNAs) are an emerging class of biomarkers and therapeutic targets for various diseases including cancers. Here, we develop a homogeneous and label-free method for sensitive detection of let-7a miRNA based on bifunctional strand displacement amplification (SDA)-mediated hyperbranched rolling circle amplification (HRCA). The binding of target miRNA with the linear template initiates the bifunctional SDA reaction, generating two different kinds of triggers which can hybridize with the linear template to initiate new rounds of SDA reaction for the production of more and more triggers. In the meantime, the released two different kinds of triggers can function as the first and the second primers, respectively, to initiate the HRCA reaction whose products can be simply monitored by a standard fluorometer with SYBR Green I as the fluorescent indicator. The proposed method exhibits high sensitivity with a detection limit of as low as 1.8 × 10(-13) M and a large dynamic range of 5 orders of magnitude from 0.1 pM to 10 nM, and it can even discriminate the single-base difference among the miRNA family members. Moreover, this method can be used to analyze the total RNA samples from the human lung tissues and might be further applied for sensitive detection of various proteins, small molecules, and metal ions in combination with specific aptamers.

Assessing wheat yield, Biomass, and water productivity responses to growth stage based irrigation water allocation

USDA-ARS?s Scientific Manuscript database

Increasing irrigated wheat yields is important to the overall profitability of limited-irrigation cropping systems in western Kansas. A simulation study was conducted to (1) validate APSIM's (Agricultural Production Systems sIMulator) ability to simulate wheat growth and yield in Kansas, and (2) app...

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification

PubMed Central

Schouten, Jan P.; McElgunn, Cathal J.; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-01-01

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down’s syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50–70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences. PMID:12060695

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.

PubMed

Schouten, Jan P; McElgunn, Cathal J; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-06-15

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down's syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

Evaluation of preservation methods for improving biogas production and enzymatic conversion yields of annual crops

PubMed Central

2011-01-01

Background The use of energy crops and agricultural residues is expected to increase to fulfil the legislative demands of bio-based components in transport fuels. Ensiling methods, adapted from the feed sector, are suitable storage methods to preserve fresh crops throughout the year for, for example, biogas production. Various preservation methods, namely ensiling with and without acid addition for whole crop maize, fibre hemp and faba bean were investigated. For the drier fibre hemp, alkaline urea treatment was studied as well. These treatments were also explored as mild pretreatment methods to improve the disassembly and hydrolysis of these lignocellulosic substrates. Results The investigated storage treatments increased the availability of the substrates for biogas production from hemp and in most cases from whole maize but not from faba bean. Ensiling of hemp, without or with addition of formic acid, increased methane production by more than 50% compared to fresh hemp. Ensiling resulted in substantially increased methane yields also from maize, and the use of formic acid in ensiling of maize further enhanced methane yields by 16%, as compared with fresh maize. Ensiled faba bean, in contrast, yielded somewhat less methane than the fresh material. Acidic additives preserved and even increased the amount of the valuable water-soluble carbohydrates during storage, which affected most significantly the enzymatic hydrolysis yield of maize. However, preservation without additives decreased the enzymatic hydrolysis yield especially in maize, due to its high content of soluble sugars that were already converted to acids during storage. Urea-based preservation significantly increased the enzymatic hydrolysability of hemp. Hemp, preserved with urea, produced the highest carbohydrate increase of 46% in enzymatic hydrolysis as compared to the fresh material. Alkaline pretreatment conditions of hemp improved also the methane yields. Conclusions The results of the present

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Optimizing rice yields while minimizing yield-scaled global warming potential.

PubMed

Pittelkow, Cameron M; Adviento-Borbe, Maria A; van Kessel, Chris; Hill, James E; Linquist, Bruce A

2014-05-01

To meet growing global food demand with limited land and reduced environmental impact, agricultural greenhouse gas (GHG) emissions are increasingly evaluated with respect to crop productivity, i.e., on a yield-scaled as opposed to area basis. Here, we compiled available field data on CH4 and N2 O emissions from rice production systems to test the hypothesis that in response to fertilizer nitrogen (N) addition, yield-scaled global warming potential (GWP) will be minimized at N rates that maximize yields. Within each study, yield N surplus was calculated to estimate deficit or excess N application rates with respect to the optimal N rate (defined as the N rate at which maximum yield was achieved). Relationships between yield N surplus and GHG emissions were assessed using linear and nonlinear mixed-effects models. Results indicate that yields increased in response to increasing N surplus when moving from deficit to optimal N rates. At N rates contributing to a yield N surplus, N2 O and yield-scaled N2 O emissions increased exponentially. In contrast, CH4 emissions were not impacted by N inputs. Accordingly, yield-scaled CH4 emissions decreased with N addition. Overall, yield-scaled GWP was minimized at optimal N rates, decreasing by 21% compared to treatments without N addition. These results are unique compared to aerobic cropping systems in which N2 O emissions are the primary contributor to GWP, meaning yield-scaled GWP may not necessarily decrease for aerobic crops when yields are optimized by N fertilizer addition. Balancing gains in agricultural productivity with climate change concerns, this work supports the concept that high rice yields can be achieved with minimal yield-scaled GWP through optimal N application rates. Moreover, additional improvements in N use efficiency may further reduce yield-scaled GWP, thereby strengthening the economic and environmental sustainability of rice systems. © 2013 John Wiley & Sons Ltd.

Improved multiple displacement amplification (iMDA) and ultraclean reagents.

PubMed

Motley, S Timothy; Picuri, John M; Crowder, Chris D; Minich, Jeremiah J; Hofstadler, Steven A; Eshoo, Mark W

2014-06-06

Next-generation sequencing sample preparation requires nanogram to microgram quantities of DNA; however, many relevant samples are comprised of only a few cells. Genomic analysis of these samples requires a whole genome amplification method that is unbiased and free of exogenous DNA contamination. To address these challenges we have developed protocols for the production of DNA-free consumables including reagents and have improved upon multiple displacement amplification (iMDA). A specialized ethylene oxide treatment was developed that renders free DNA and DNA present within Gram positive bacterial cells undetectable by qPCR. To reduce DNA contamination in amplification reagents, a combination of ion exchange chromatography, filtration, and lot testing protocols were developed. Our multiple displacement amplification protocol employs a second strand-displacing DNA polymerase, improved buffers, improved reaction conditions and DNA free reagents. The iMDA protocol, when used in combination with DNA-free laboratory consumables and reagents, significantly improved efficiency and accuracy of amplification and sequencing of specimens with moderate to low levels of DNA. The sensitivity and specificity of sequencing of amplified DNA prepared using iMDA was compared to that of DNA obtained with two commercial whole genome amplification kits using 10 fg (~1-2 bacterial cells worth) of bacterial genomic DNA as a template. Analysis showed >99% of the iMDA reads mapped to the template organism whereas only 0.02% of the reads from the commercial kits mapped to the template. To assess the ability of iMDA to achieve balanced genomic coverage, a non-stochastic amount of bacterial genomic DNA (1 pg) was amplified and sequenced, and data obtained were compared to sequencing data obtained directly from genomic DNA. The iMDA DNA and genomic DNA sequencing had comparable coverage 99.98% of the reference genome at ≥1X coverage and 99.9% at ≥5X coverage while maintaining both balance

External and semi-internal controls for PCR amplification of homologous sequences in mixed templates.

PubMed

Kalle, Elena; Gulevich, Alexander; Rensing, Christopher

2013-11-01

In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance. This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples. The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products. © 2013 Elsevier B.V. All rights reserved.

Agronomic Characteristics Related to Grain Yield and Nutrient Use Efficiency for Wheat Production in China

PubMed Central

Zheng, Huaiguo; Xu, Xinpeng

2016-01-01

In order to make clear the recent status and trend of wheat (Triticum aestivum L.) production in China, datasets from multiple field experiments and published literature were collected to study the agronomic characteristics related to grain yield, fertilizer application and nutrient use efficiency from the year 2000 to 2011. The results showed that the mean grain yield of wheat in 2000–2011 was 5950 kg/ha, while the N, P2O5 and K2O application rates were 172, 102 and 91 kg/ha on average, respectively. The decrease in N and P2O5 and increase in K2O balanced the nutrient supply and was the main reason for yield increase. The partial factor productivity (PFP, kg grain yield produced per unit of N, P2O5 or K2O applied) values of N (PFP-N), P (PFP-P) and K (PFP-K) were in the ranges of 29.5~39.6, 43.4~74.9 and 44.1~76.5 kg/kg, respectively. While PFP-N showed no significant changes from 2000 to 2010, both PFP-P and PFP-K showed an increased trend over this period. The mean agronomic efficiency (AE, kg grain yield increased per unit of N, P2O5 or K2O applied) values of N (AEN), P (AEP) and K (AEK) were 9.4, 10.2 and 6.5 kg/kg, respectively. The AE values demonstrated marked inter-annual fluctuations, with the amplitude of fluctuation for AEN greater than those for AEP and AEK. The mean fertilizer recovery efficiency (RE, the fraction of nutrient uptake in aboveground plant dry matter to the nutrient of fertilizer application) values of N, P and K in the aboveground biomass were 33.1%, 24.3% and 28.4%, respectively. It was also revealed that different wheat ecological regions differ greatly in wheat productivity, fertilizer application and nutrient use efficiency. In summary, it was suggested that best nutrient management practices, i.e. fertilizer recommendation applied based on soil testing or yield response, with strategies to match the nutrient input with realistic yield and demand, or provided with the 4R’s nutrient management (right time, right rate, right site

Brazilian Soybean Yields and Yield Gaps Vary with Farm Size

NASA Astrophysics Data System (ADS)

Jeffries, G. R.; Cohn, A.; Griffin, T. S.; Bragança, A.

2017-12-01

Understanding the farm size-specific characteristics of crop yields and yield gaps may help to improve yields by enabling better targeting of technical assistance and agricultural development programs. Linking remote sensing-based yield estimates with property boundaries provides a novel view of the relationship between farm size and yield structure (yield magnitude, gaps, and stability over time). A growing literature documents variations in yield gaps, but largely ignores the role of farm size as a factor shaping yield structure. Research on the inverse farm size-productivity relationship (IR) theory - that small farms are more productive than large ones all else equal - has documented that yield magnitude may vary by farm size, but has not considered other yield structure characteristics. We examined farm size - yield structure relationships for soybeans in Brazil for years 2001-2015. Using out-of-sample soybean yield predictions from a statistical model, we documented 1) gaps between the 95th percentile of attained yields and mean yields within counties and individual fields, and 2) yield stability defined as the standard deviation of time-detrended yields at given locations. We found a direct relationship between soy yields and farm size at the national level, while the strength and the sign of the relationship varied by region. Soybean yield gaps were found to be inversely related to farm size metrics, even when yields were only compared to farms of similar size. The relationship between farm size and yield stability was nonlinear, with mid-sized farms having the most stable yields. The work suggests that farm size is an important factor in understanding yield structure and that opportunities for improving soy yields in Brazil are greatest among smaller farms.

Mineral Nutritional Yield and Nutrient Density of Locally Adapted Wheat Genotypes under Organic Production

PubMed Central

Moreira-Ascarrunz, Sergio Daniel; Larsson, Hans; Prieto-Linde, Maria Luisa; Johansson, Eva

2016-01-01

The aim of the present investigation was to investigate the nutritional yield, nutrient density, stability, and adaptability of organically produced wheat for sustainable and nutritional high value food production. This study evaluated the nutritional yield of four minerals (Fe, Zn, Cu, and Mg) in 19 wheat genotypes, selected as being locally adapted under organic agriculture conditions. The new metric of nutritional yield was calculated for each genotype and they were evaluated for stability using the Additive Main effects and Multiplicative Interaction (AMMI) stability analysis and for genotypic value, stability, and adaptability using the Best Linear Unbiased Prediction (BLUP procedure). The results indicated that there were genotypes suitable for production under organic agriculture conditions with satisfactory yields (>4000 kg·ha−1). Furthermore, these genotypes showed high nutritional yield and nutrient density for the four minerals studied. Additionally, since these genotypes were stable and adaptable over three environmentally different years, they were designated “balanced genotypes” for the four minerals and for the aforementioned characteristics. Selection and breeding of such “balanced genotypes” may offer an alternative to producing nutritious food under low-input agriculture conditions. Furthermore, the type of evaluation presented here may also be of interest for implementation in research conducted in developing countries, following the objectives of producing enough nutrients for a growing population. PMID:28231184

Biologically relevant effects of mRNA amplification on gene expression profiles.

PubMed

van Haaften, Rachel I M; Schroen, Blanche; Janssen, Ben J A; van Erk, Arie; Debets, Jacques J M; Smeets, Hubert J M; Smits, Jos F M; van den Wijngaard, Arthur; Pinto, Yigal M; Evelo, Chris T A

2006-04-11

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results. In the present study we compared microarray data obtained from amplified mRNA derived from biopsies of rat cardiac left ventricle and non-amplified mRNA derived from the same organ. Biopsies were linearly amplified to acquire enough material for a microarray experiment. Both amplified and unamplified samples were hybridized to the Rat Expression Set 230 Array of Affymetrix. Analysis of the microarray data showed that unamplified material of two different left ventricles had 99.6% identical gene expression. Gene expression patterns of two biopsies obtained from the same parental organ were 96.3% identical. Similarly, gene expression pattern of two biopsies from dissimilar organs were 92.8% identical to each other.Twenty-one percent of reporters called present in parental left ventricular tissue disappeared after amplification in the biopsies. Those reporters were predominantly seen in the low intensity range. Sequence analysis showed that reporters that disappeared after amplification had a GC-content of 53.7+/-4.0%, while reporters called present in biopsy- and whole LV-samples had an average GC content of 47.8+/-5.5% (P <0.001). Those reporters were also predicted to form significantly more (0.76+/-0.07 versus 0.38+/-0.1) and longer (9.4+/-0.3 versus 8.4+/-0.4) hairpins as compared to representative control reporters present before and after amplification. This study establishes that the gene expression profile obtained after amplification of mRNA of left ventricular

Biologically relevant effects of mRNA amplification on gene expression profiles

PubMed Central

van Haaften, Rachel IM; Schroen, Blanche; Janssen, Ben JA; van Erk, Arie; Debets, Jacques JM; Smeets, Hubert JM; Smits, Jos FM; van den Wijngaard, Arthur; Pinto, Yigal M; Evelo, Chris TA

2006-01-01

Background Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results. In the present study we compared microarray data obtained from amplified mRNA derived from biopsies of rat cardiac left ventricle and non-amplified mRNA derived from the same organ. Biopsies were linearly amplified to acquire enough material for a microarray experiment. Both amplified and unamplified samples were hybridized to the Rat Expression Set 230 Array of Affymetrix. Results Analysis of the microarray data showed that unamplified material of two different left ventricles had 99.6% identical gene expression. Gene expression patterns of two biopsies obtained from the same parental organ were 96.3% identical. Similarly, gene expression pattern of two biopsies from dissimilar organs were 92.8% identical to each other. Twenty-one percent of reporters called present in parental left ventricular tissue disappeared after amplification in the biopsies. Those reporters were predominantly seen in the low intensity range. Sequence analysis showed that reporters that disappeared after amplification had a GC-content of 53.7+/-4.0%, while reporters called present in biopsy- and whole LV-samples had an average GC content of 47.8+/-5.5% (P <0.001). Those reporters were also predicted to form significantly more (0.76+/-0.07 versus 0.38+/-0.1) and longer (9.4+/-0.3 versus 8.4+/-0.4) hairpins as compared to representative control reporters present before and after amplification. Conclusion This study establishes that the gene expression profile obtained after

Optical chirped beam amplification and propagation

DOEpatents

Barty, Christopher P.

2004-10-12

A short pulse laser system uses dispersive optics in a chirped-beam amplification architecture to produce high peak power pulses and high peak intensities without the potential for intensity dependent damage to downstream optical components after amplification.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification

PubMed Central

Maruyama, Toru; Yamagishi, Keisuke; Mori, Tetsushi; Takeyama, Haruko

2015-01-01

Whole genome amplification (WGA) is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA), using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 105 droplets (67 pL) within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single Escherichia coli cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples. PMID:26389587

Slow pyrolysis polygeneration of bamboo (Phyllostachys pubescens): Product yield prediction and biochar formation mechanism.

PubMed

Wang, Huihui; Wang, Xin; Cui, Yanshan; Xue, Zhongcai; Ba, Yuxin

2018-05-11

Slow pyrolysis of bamboo was conducted at 400-600 °C and pyrolysis products were characterized with FTIR, BET, XRD, SEM, EDS and GC to establish a pyrolysis product yield prediction model and biochar formation mechanism. Pyrolysis biochar yield was predicted based on content of cellulose, hemicellulose and lignin in biomass with their carbonization index of 0.20, 0.35 and 0.45. The formation mechanism of porous structure in pyrolysis biochar was established based on its physicochemical property evolution and emission characteristics of pyrolysis gas. The main components (cellulose, hemicellulose and lignin) had different pyrolysis or chemical reaction pathways to biochar. Lignin had higher aromatic structure, which resulted higher biochar yield. It was the main biochar precursor during biomass pyrolysis. Cellulose was likely to improve porous structure of pyrolysis biochar due to its high mass loss percentage. Higher pyrolysis temperatures (600 °C) promoted inter- and intra-molecular condensation reactions and aromaticity in biochar. Copyright © 2018 Elsevier Ltd. All rights reserved.

Zygotic amplification of secondary piRNAs during silkworm embryogenesis

PubMed Central

Kawaoka, Shinpei; Arai, Yuji; Kadota, Koji; Suzuki, Yutaka; Hara, Kahori; Sugano, Sumio; Shimizu, Kentaro; Tomari, Yukihide; Shimada, Toru; Katsuma, Susumu

2011-01-01

PIWI-interacting RNAs (piRNAs) are 23–30-nucleotide-long small RNAs that act as sequence-specific silencers of transposable elements in animal gonads. In flies, genetics and deep sequencing data have led to a hypothesis for piRNA biogenesis called the ping-pong cycle, where antisense primary piRNAs initiate an amplification loop to generate sense secondary piRNAs. However, to date, the process of the ping-pong cycle has never been monitored at work. Here, by large-scale profiling of piRNAs from silkworm ovary and embryos of different developmental stages, we demonstrate that maternally inherited antisense-biased piRNAs trigger acute amplification of secondary sense piRNA production in zygotes, at a time coinciding with zygotic transcription of sense transposon mRNAs. These results provide on-site evidence for the ping-pong cycle. PMID:21628432

Empirical evidence for acceleration-dependent amplification factors

USGS Publications Warehouse

Borcherdt, R.D.

2002-01-01

Site-specific amplification factors, Fa and Fv, used in current U.S. building codes decrease with increasing base acceleration level as implied by the Loma Prieta earthquake at 0.1g and extrapolated using numerical models and laboratory results. The Northridge earthquake recordings of 17 January 1994 and subsequent geotechnical data permit empirical estimates of amplification at base acceleration levels up to 0.5g. Distance measures and normalization procedures used to infer amplification ratios from soil-rock pairs in predetermined azimuth-distance bins significantly influence the dependence of amplification estimates on base acceleration. Factors inferred using a hypocentral distance norm do not show a statistically significant dependence on base acceleration. Factors inferred using norms implied by the attenuation functions of Abrahamson and Silva show a statistically significant decrease with increasing base acceleration. The decrease is statistically more significant for stiff clay and sandy soil (site class D) sites than for stiffer sites underlain by gravely soils and soft rock (site class C). The decrease in amplification with increasing base acceleration is more pronounced for the short-period amplification factor, Fa, than for the midperiod factor, Fv.

Sensitive Detection Using Microfluidics and Nonlinear Amplification

DTIC Science & Technology

2011-07-22

Quantification of Nucleic Acids via Simultaneous Chemical Initiation of Recombinase Polymerase Amplification Reactions on SlipChip" 2011, 83, 3533... Amplification 5a. CONTRACT NUMBER 5b. GRANT NUMBER N00014-08-1-0936 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Rustem F. Ismagilov 5d. PROJECT NUMBER 5e...concentrations by combining controlled chemical autocatalytic amplification and stochastic confinement of small particles with the microfluidic

Four photon parametric amplification. [in unbiased Josephson junction

NASA Technical Reports Server (NTRS)

Parrish, P. T.; Feldman, M. J.; Ohta, H.; Chiao, R. Y.

1974-01-01

An analysis is presented describing four-photon parametric amplification in an unbiased Josephson junction. Central to the theory is the model of the Josephson effect as a nonlinear inductance. Linear, small signal analysis is applied to the two-fluid model of the Josephson junction. The gain, gain-bandwidth product, high frequency limit, and effective noise temperature are calculated for a cavity reflection amplifier. The analysis is extended to multiple (series-connected) junctions and subharmonic pumping.

Simulation of Biomass Yield and Soil Organic Carbon under Bioenergy Sorghum Production

PubMed Central

Dou, Fugen; Wight, Jason P.; Wilson, Lloyd T.; Storlien, Joseph O.; Hons, Frank M.

2014-01-01

Developing sustainable management practices including appropriate residue removal and nitrogen (N) fertilization for bioenergy sorghum is critical. However, the effects of residue removal and N fertilization associated with bioenergy sorghum production on soil organic carbon (SOC) are less studied compared to other crops. The objective of our research was to assess the impacts of residue removal and N fertilization on biomass yield and SOC under biomass sorghum production. Field measurements were used to calibrate the DNDC model, then verified the model by comparing simulated results with measured results using the field management practices as agronomic inputs. Both residue removal and N fertilization affected bioenergy sorghum yields in some years. The average measured SOC at 0–50 cm across the treatments and the time-frame ranged from 47.5 to 78.7 Mg C ha−1, while the simulated SOC was from 56.3 to 67.3 Mg C ha−1. The high correlation coefficients (0.65 to 0.99) and low root mean square error (3 to 18) between measured and simulated values indicate the DNDC model accurately simulated the effects of residue removal with N fertilization on bioenergy sorghum production and SOC. The model predictions revealed that there is, in the long term, a trend for higher SOC under bioenergy sorghum production regardless of residue management. PMID:25531758

Parametric amplification in MoS2 drum resonator.

PubMed

Prasad, Parmeshwar; Arora, Nishta; Naik, A K

2017-11-30

Parametric amplification is widely used in diverse areas from optics to electronic circuits to enhance low level signals by varying relevant system parameters. Parametric amplification has also been performed in several micro-nano resonators including nano-electromechanical system (NEMS) resonators based on a two-dimensional (2D) material. Here, we report the enhancement of mechanical response in a MoS 2 drum resonator using degenerate parametric amplification. We use parametric pumping to modulate the spring constant of the MoS 2 resonator and achieve a 10 dB amplitude gain. We also demonstrate quality factor enhancement in the resonator with parametric amplification. We investigate the effect of cubic nonlinearity on parametric amplification and show that it limits the gain of the mechanical resonator. Amplifying ultra-small displacements at room temperature and understanding the limitations of the amplification in these devices is key for using these devices for practical applications.

Direct duplex real-time loop mediated isothermal amplification assay for the simultaneous detection of cow and goat species origin of milk and yogurt products for field use.

PubMed

Kim, Mi-Ju; Kim, Hae-Yeong

2018-04-25

A multiple loop-mediated isothermal amplification (LAMP) method was developed to detect cow and goat milk in the field using a portable fluorescence device. For rapid on-site detection, this duplex LAMP assay was used in combination with direct amplification, without DNA extraction. The cow- and goat-specific LAMP primer sets were designed based on the mitochondrial cytochrome b gene, and showed specificity against 13 other animal species in the reactions. The sensitivity of the duplex LAMP assay for cow and goat was 0.1 and 1 pg, respectively. The detection limit for both target species in milk mixtures was 2%. This assay successfully amplified and identified the two target species in 24 samples of commercial milk and yogurt products, with 30 min sampling-to-result analysis time. Therefore, this direct duplex real-time LAMP assay is useful for on-site simultaneous detection of cow and goat milk in commercial products, a capability needed to confirm accurate labeling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sediment-induced amplification and the collapse of the Nimitz Freeway

USGS Publications Warehouse

Hough, S.E.; Friberg, P.A.; Busby, R.; Field, E.F.; Jacob, K.H.; Borcherdt, R.D.

1990-01-01

THE amplification of ground motion by low-seismic-velocity surface sediments is an important factor in determining the seismic hazard specific to a given site. The Ms = 7.1 Loma Prieta earthquake of 17 October 1989 was the largest event in the contiguous United States in 37 years, and yielded an unparalleled volume of seismic data from the main shock and aftershock sequence1. These data can be used to image the seismic source, to study detailed Earth structure, and to study the propagation of seismic waves both through bedrock at depth and through sediment layers near the surface. Near the edge of San Francisco Bay, site conditions vary considerably on scales of hundreds of metres. The collapsed section of the two-tiered Nimitz Freeway in Oakland was built on San Francisco Bay mud, whereas stiffer alluvial sediments underlie a southern section that was damaged but did not collapse. Here we analyse high-quality, digital aftershock recordings from several sites near the Nimitz Freeway, and conclude that soil conditions and resulting ground-motion amplification may have contributed significantly to the failure of the structure.

[Prediction of the side-cut product yield of atmospheric/vacuum distillation unit by NIR crude oil rapid assay].

PubMed

Wang, Yan-Bin; Hu, Yu-Zhong; Li, Wen-Le; Zhang, Wei-Song; Zhou, Feng; Luo, Zhi

2014-10-01

In the present paper, based on the fast evaluation technique of near infrared, a method to predict the yield of atmos- pheric and vacuum line was developed, combined with H/CAMS software. Firstly, the near-infrared (NIR) spectroscopy method for rapidly determining the true boiling point of crude oil was developed. With commercially available crude oil spectroscopy da- tabase and experiments test from Guangxi Petrochemical Company, calibration model was established and a topological method was used as the calibration. The model can be employed to predict the true boiling point of crude oil. Secondly, the true boiling point based on NIR rapid assay was converted to the side-cut product yield of atmospheric/vacuum distillation unit by H/CAMS software. The predicted yield and the actual yield of distillation product for naphtha, diesel, wax and residual oil were compared in a 7-month period. The result showed that the NIR rapid crude assay can predict the side-cut product yield accurately. The near infrared analytic method for predicting yield has the advantages of fast analysis, reliable results, and being easy to online operate, and it can provide elementary data for refinery planning optimization and crude oil blending.

Planting pattern and weed control method influence on yield production of corn (Zea mays L.)

NASA Astrophysics Data System (ADS)

Purba, E.; Nasution, D. P.

2018-02-01

Field experiment was carried out to evaluate the influence of planting patterns and weed control methods on the growth and yield of corn. The effect of the planting pattern and weed control method was studied in a split plot design. The main plots were that of planting pattern single row (25cm x 60cm), double row (25cm x 25cm x 60cm) and triangle row ( 25cm x 25cm x 25cm). Subplot was that of weed control method consisted five methods namely weed free throughout the growing season, hand weeding, sprayed with glyphosate, sprayed with paraquat, and no weeding.. Result showed that both planting pattern and weed control method did not affect the growth of corn. However, planting pattern and weed control method significantly affected yield production. Yield resulted from double row and triangle planting pattern was 14% and 41% higher, consecutively, than that of single row pattern. The triangle planting pattern combined with any weed control method produced the highest yield production of corn.

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

PubMed

Su, Jialei; Shen, Feng; Qiu, Mo; Qi, Xinhua

2017-02-14

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.

A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection

PubMed Central

Veigas, Bruno; Águas, Hugo; Fortunato, Elvira; Martins, Rodrigo; Baptista, Pedro Viana; Igreja, Rui

2017-01-01

Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate). This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions. PMID:29144379

High-yield production of pure tagatose from fructose by a three-step enzymatic cascade reaction.

PubMed

Lee, Seon-Hwa; Hong, Seung-Hye; Kim, Kyoung-Rok; Oh, Deok-Kun

2017-08-01

To produce tagatose from fructose with a high conversion rate and to establish a high-yield purification method of tagatose from the reaction mixture. Fructose at 1 M (180 g l -1 ) was converted to 0.8 M (144 g l -1 ) tagatose by a three-step enzymatic cascade reaction, involving hexokinase, plus ATP, fructose-1,6-biphosphate aldolase, phytase, over 16 h with a productivity of 9 g l -1 h -1 . No byproducts were detected. Tagatose was recrystallized from ethanol to a purity of 99.9% and a yield of 96.3%. Overall, tagatose at 99.9% purity was obtained from fructose with a yield of 77%. This is the first biotechnological production of tagatose from fructose and the first application of solvent recrystallization for the purification of rare sugars.

Boosting autofermentation rates and product yields with sodium stress cycling: application to production of renewable fuels by cyanobacteria.

PubMed

Carrieri, Damian; Momot, Dariya; Brasg, Ian A; Ananyev, Gennady; Lenz, Oliver; Bryant, Donald A; Dismukes, G Charles

2010-10-01

Sodium concentration cycling was examined as a new strategy for redistributing carbon storage products and increasing autofermentative product yields following photosynthetic carbon fixation in the cyanobacterium Arthrospira (Spirulina) maxima. The salt-tolerant hypercarbonate strain CS-328 was grown in a medium containing 0.24 to 1.24 M sodium, resulting in increased biosynthesis of soluble carbohydrates to up to 50% of the dry weight at 1.24 M sodium. Hypoionic stress during dark anaerobic metabolism (autofermentation) was induced by resuspending filaments in low-sodium (bi)carbonate buffer (0.21 M), which resulted in accelerated autofermentation rates. For cells grown in 1.24 M NaCl, the fermentative yields of acetate, ethanol, and formate increase substantially to 1.56, 0.75, and 1.54 mmol/(g [dry weight] of cells·day), respectively (36-, 121-, and 6-fold increases in rates relative to cells grown in 0.24 M NaCl). Catabolism of endogenous carbohydrate increased by approximately 2-fold upon hypoionic stress. For cultures grown at all salt concentrations, hydrogen was produced, but its yield did not correlate with increased catabolism of soluble carbohydrates. Instead, ethanol excretion becomes a preferred route for fermentative NADH reoxidation, together with intracellular accumulation of reduced products of acetyl coenzyme A (acetyl-CoA) formation when cells are hypoionically stressed. In the absence of hypoionic stress, hydrogen production is a major beneficial pathway for NAD(+) regeneration without wasting carbon intermediates such as ethanol derived from acetyl-CoA. This switch presumably improves the overall cellular economy by retaining carbon within the cell until aerobic conditions return and the acetyl unit can be used for biosynthesis or oxidized via respiration for a much greater energy return.

Chronic centrosome amplification without tumorigenesis

PubMed Central

Vitre, Benjamin; Holland, Andrew J.; Kulukian, Anita; Shoshani, Ofer; Hirai, Maretoshi; Wang, Yin; Maldonado, Marcus; Cho, Thomas; Boubaker, Jihane; Swing, Deborah A.; Tessarollo, Lino; Evans, Sylvia M.; Fuchs, Elaine; Cleveland, Don W.

2015-01-01

Centrosomes are microtubule-organizing centers that facilitate bipolar mitotic spindle assembly and chromosome segregation. Recognizing that centrosome amplification is a common feature of aneuploid cancer cells, we tested whether supernumerary centrosomes are sufficient to drive tumor development. To do this, we constructed and analyzed mice in which centrosome amplification can be induced by a Cre-recombinase–mediated increase in expression of Polo-like kinase 4 (Plk4). Elevated Plk4 in mouse fibroblasts produced supernumerary centrosomes and enhanced the expected mitotic errors, but proliferation continued only after inactivation of the p53 tumor suppressor. Increasing Plk4 levels in mice with functional p53 produced centrosome amplification in liver and skin, but this did not promote spontaneous tumor development in these tissues or enhance the growth of chemically induced skin tumors. In the absence of p53, Plk4 overexpression generated widespread centrosome amplification, but did not drive additional tumors or affect development of the fatal thymic lymphomas that arise in animals lacking p53. We conclude that, independent of p53 status, supernumerary centrosomes are not sufficient to drive tumor formation. PMID:26578792

A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers

NASA Astrophysics Data System (ADS)

Du, Yan; Hughes, Randall A.; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.; Li, Bingling

2015-06-01

Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20-100 copies/μl, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device.

Plant-Based Assessment of Inherent Soil Productivity and Contributions to China’s Cereal Crop Yield Increase since 1980

PubMed Central

Fan, Mingsheng; Lal, Rattan; Cao, Jian; Qiao, Lei; Su, Yansen; Jiang, Rongfeng; Zhang, Fusuo

2013-01-01

Objective China’s food production has increased 6-fold during the past half-century, thanks to increased yields resulting from the management intensification, accomplished through greater inputs of fertilizer, water, new crop strains, and other Green Revolution’s technologies. Yet, changes in underlying quality of soils and their effects on yield increase remain to be determined. Here, we provide a first attempt to quantify historical changes in inherent soil productivity and their contributions to the increase in yield. Methods The assessment was conducted based on data-set derived from 7410 on-farm trials, 8 long-term experiments and an inventory of soil organic matter concentrations of arable land. Results Results show that even without organic and inorganic fertilizer addition crop yield from on-farm trials conducted in the 2000s was significantly higher compared with those in the 1980s — the increase ranged from 0.73 to 1.76 Mg/ha for China’s major irrigated cereal-based cropping systems. The increase in on-farm yield in control plot since 1980s was due primarily to the enhancement of soil-related factors, and reflected inherent soil productivity improvement. The latter led to higher and stable yield with adoption of improved management practices, and contributed 43% to the increase in yield for wheat and 22% for maize in the north China, and, 31%, 35% and 22% for early and late rice in south China and for single rice crop in the Yangtze River Basin since 1980. Conclusions Thus, without an improvement in inherent soil productivity, the ‘Agricultural Miracle in China’ would not have happened. A comprehensive strategy of inherent soil productivity improvement in China, accomplished through combining engineering-based measures with biological-approaches, may be an important lesson for the developing world. We propose that advancing food security in 21st century for both China and other parts of world will depend on continuously improving inherent soil

Optimization of grapevine yield by applying mathematical models to obtain quality wine products

NASA Astrophysics Data System (ADS)

Alina, Dobrei; Alin, Dobrei; Eleonora, Nistor; Teodor, Cristea; Marius, Boldea; Florin, Sala

2016-06-01

Relationship between the crop load and the grape yield and quality is a dynamic process, specific for wine cultivars and for fresh consumption varieties. Modeling these relations is important for the improvement of technological works. This study evaluated the interrelationship of crop load (B - buds number) and several production parameters (Y - yield; S - sugar; A - acidity; GaI - Glucoacidimetric index; AP - alcoholic potential; F - flavorings, WA - wine alcohol; SR - sugar residue, in Muscat Ottonel wine cultivar and Y - yield; S - sugar; A - acidity; GaI - Glucoacidimetric Index; CP - commercial production; BS - berries size in the Victoria table grape cultivar). In both varieties have been identified correlations between the independent variable (B - buds number as a result of pruning and training practices) and quality parameters analyzed (r = -0.699 for B vsY relationship; r = 0.961 for the relationship B vs S; r = -0.959 for B vs AP relationship; r = 0.743 for the relationship Y vs S, p <0.01, in the Muscat Ottonel cultivar, respectively r = -0.907 for relationship B vs Y; r = -0.975 for B vs CP relationship; r = -0.971 for relationship B vs BS; r = 0.990 for CP vs BS relationship in the Victoria cultivar. Through regression analysis were obtained models that describe the variation concerning production and quality parameters in relation to the independent variable (B - buds number) with statistical significance results.

Production of scandium-44 m and scandium-44 g with deuterons on calcium-44: cross section measurements and production yield calculations.

PubMed

Duchemin, C; Guertin, A; Haddad, F; Michel, N; Métivier, V

2015-09-07

HIGHLIGHTS • Production of Sc-44 m, Sc-44 g and contaminants. • Experimental values determined using the stacked-foil technique. • Thick-Target production Yield (TTY) calculations. • Comparison with the TALYS code version 1.6.Among the large number of radionuclides of medical interest, Sc-44 is promising for PET imaging. Either the ground-state Sc-44 g or the metastable-state Sc-44 m can be used for such applications, depending on the molecule used as vector. This study compares the production rates of both Sc-44 states, when protons or deuterons are used as projectiles on an enriched Calcium-44 target. This work presents the first set of data for the deuteron route. The results are compared with the TALYS code. The Thick-Target production Yields of Sc-44 m and Sc-44 g are calculated and compared with those for the proton route for three different scenarios: the production of Sc-44 g for conventional PET imaging, its production for the new 3 γ imaging technique developed at the SUBATECH laboratory and the production of a Sc-44 m/Sc-44 g in vivo generator for antibody labelling.

Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database.

PubMed

Niu, Mutian; Kebreab, Ermias; Hristov, Alexander N; Oh, Joonpyo; Arndt, Claudia; Bannink, André; Bayat, Ali R; Brito, André F; Boland, Tommy; Casper, David; Crompton, Les A; Dijkstra, Jan; Eugène, Maguy A; Garnsworthy, Phil C; Haque, Md Najmul; Hellwing, Anne L F; Huhtanen, Pekka; Kreuzer, Michael; Kuhla, Bjoern; Lund, Peter; Madsen, Jørgen; Martin, Cécile; McClelland, Shelby C; McGee, Mark; Moate, Peter J; Muetzel, Stefan; Muñoz, Camila; O'Kiely, Padraig; Peiren, Nico; Reynolds, Christopher K; Schwarm, Angela; Shingfield, Kevin J; Storlien, Tonje M; Weisbjerg, Martin R; Yáñez-Ruiz, David R; Yu, Zhongtang

2018-02-16

Enteric methane (CH 4 ) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH 4 is complex, expensive, and impractical at large scales; therefore, models are commonly used to predict CH 4 production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH 4 production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH 4 production (g/day per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH 4 prediction accuracy. The intercontinental database covered Europe (EU), the United States (US), and Australia (AU). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6%, 14.7%, and 19.8% for intercontinental, EU, and United States regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH 4 production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH 4 emission conversion factors for specific regions are required to improve CH 4 production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and

Classroom Amplification Technology: Theory and Practice.

ERIC Educational Resources Information Center

Crandell, Carl C.; Smaldino, Joseph J.

2000-01-01

This article reviews some relevant events in the development of acoustical standards for classrooms, describes classroom challenges to providing clear acoustical signals to children in classrooms, and outlines amplification solutions to some of those classroom challenges. Solutions include personal amplification devices and use of signal-to-noise…

Advanced model for the prediction of the neutron-rich fission product yields

NASA Astrophysics Data System (ADS)

Rubchenya, V. A.; Gorelov, D.; Jokinen, A.; Penttilä, H.; Äystö, J.

2013-12-01

The consistent models for the description of the independent fission product formation cross sections in the spontaneous fission and in the neutron and proton induced fission at the energies up to 100 MeV is developed. This model is a combination of new version of the two-component exciton model and a time-dependent statistical model for fusion-fission process with inclusion of dynamical effects for accurate calculations of nucleon composition and excitation energy of the fissioning nucleus at the scission point. For each member of the compound nucleus ensemble at the scission point, the primary fission fragment characteristics: kinetic and excitation energies and their yields are calculated using the scission-point fission model with inclusion of the nuclear shell and pairing effects, and multimodal approach. The charge distribution of the primary fragment isobaric chains was considered as a result of the frozen quantal fluctuations of the isovector nuclear matter density at the scission point with the finite neck radius. Model parameters were obtained from the comparison of the predicted independent product fission yields with the experimental results and with the neutron-rich fission product data measured with a Penning trap at the Accelerator Laboratory of the University of Jyväskylä (JYFLTRAP).

HER-2 amplification in tubular carcinoma of the breast.

PubMed

Oakley, Gerard J; Tubbs, Raymond R; Crowe, Joseph; Sebek, Bruce; Budd, G Thomas; Patrick, Rebecca J; Procop, Gary W

2006-07-01

The prognostic and therapeutic implications of HER-2 gene amplification and estrogen and progesterone receptor status in breast cancer are well described. To address the relative paucity of information concerning HER-2 amplification for tubular carcinomas, we assessed the frequency of gene amplification in 55 tubular carcinomas of the breast from 54 patients, 5 of which had axillary node metastases. The HER-2 gene copy number was assessed by fluorescence in situ hybridization for the majority of tumors analyzed, whereas estrogen and progesterone receptor status was achieved by immunohistochemical analysis. HER-2 gene amplification was not observed in any of the tumors examined, and most were estrogen receptor-positive. This HER-2 gene amplification frequency was significantly lower than the frequency of gene amplification previously reported for all invasive ductal carcinoma of no special type (P < .01). HER-2 gene amplification likely occurs infrequently, or not at all, in tubular carcinomas of the breast, whereas most express estrogen receptors.

Characterization of Hanwoo Bovine By-products by Means of Yield, Physicochemical and Nutritional Compositions

PubMed Central

Moon, Sung Sil

2014-01-01

Though the edible bovine by-products are widely used for human consumption in most countries worldwide but the scientific information regarding the nutritional quality of these by-products is scarce. In the present study, the basic information regarding the yields, physicochemical and nutritional compositions of edible Hanwoo bovine by-products was studied. Our results showed that the yields, physicochemical and nutritional composition widely varied between the by-products examined. The highest pH values were found in rumen, reticulum, omasum and reproductive organ. Heart, liver, kidney and spleen had the lowest CIE L* values and highest CIE a* values. Liver had the highest vitamin A, B2 and niacin contents whereas the highest B1 and B5 contents were found in kidney. The highest Ca content was found in rumen, reticulum, omasum, head and leg while the highest Mn and Fe contents were found in rumen, omasum and spleen, respectively. Liver had the highest Cu content. Total essential amino acids (EAA)/amino acids (AA) ratios ranged between the by-products from 38.37% to 47.41%. Total polyunsaturated fatty acids (PUFA) levels ranged between the by-products from 2.26% to 26.47%, and most by-products showed favorable PUFA/SFA ratios. It is concluded that most of by-products examined are good sources of essential nutrients and these data will be of great importance for promotion of consumption and utilization of beef by-products in future. PMID:26761281

Excessive by-product formation: A key contributor to low isobutanol yields of engineered Saccharomyces cerevisiae strains.

PubMed

Milne, N; Wahl, S A; van Maris, A J A; Pronk, J T; Daran, J M

2016-12-01

It is theoretically possible to engineer Saccharomyces cerevisiae strains in which isobutanol is the predominant catabolic product and high-yielding isobutanol-producing strains are already reported by industry. Conversely, isobutanol yields of engineered S. cerevisiae strains reported in the scientific literature typically remain far below 10% of the theoretical maximum. This study explores possible reasons for these suboptimal yields by a mass-balancing approach. A cytosolically located, cofactor-balanced isobutanol pathway, consisting of a mosaic of bacterial enzymes whose in vivo functionality was confirmed by complementation of null mutations in branched-chain amino acid metabolism, was expressed in S. cerevisiae . Product formation by the engineered strain was analysed in shake flasks and bioreactors. In aerobic cultures, the pathway intermediate isobutyraldehyde was oxidized to isobutyrate rather than reduced to isobutanol. Moreover, significant concentrations of the pathway intermediates 2,3-dihydroxyisovalerate and α-ketoisovalerate, as well as diacetyl and acetoin, accumulated extracellularly. While the engineered strain could not grow anaerobically, micro-aerobic cultivation resulted in isobutanol formation at a yield of 0.018±0.003 mol/mol glucose. Simultaneously, 2,3-butanediol was produced at a yield of 0.649±0.067 mol/mol glucose. These results identify massive accumulation of pathway intermediates, as well as overflow metabolites derived from acetolactate, as an important, previously underestimated contributor to the suboptimal yields of 'academic' isobutanol strains. The observed patterns of by-product formation is consistent with the notion that in vivo activity of the iron-sulphur-cluster-requiring enzyme dihydroxyacid dehydratase is a key bottleneck in the present and previously described 'academic' isobutanol-producing yeast strains.

Microreactor-based mixing strategy suppresses product inhibition to enhance sugar yields in enzymatic hydrolysis for cellulosic biofuel production.

PubMed

Chakraborty, Saikat; Singh, Prasun Kumar; Paramashetti, Pawan

2017-08-01

A novel microreactor-based energy-efficient process of using complete convective mixing in a macroreactor till an optimal mixing time followed by no mixing in 200-400μl microreactors enhances glucose and reducing sugar yields by upto 35% and 29%, respectively, while saving 72-90% of the energy incurred on reactor mixing in the enzymatic hydrolysis of cellulose. Empirical exponential relations are provided for determining the optimal mixing time, during which convective mixing in the macroreactor promotes mass transport of the cellulase enzyme to the solid Avicel substrate, while the latter phase of no mixing in the microreactor suppresses product inhibition by preventing the inhibitors (glucose and cellobiose) from homogenizing across the reactor. Sugar yield increases linearly with liquid to solid height ratio (r h ), irrespective of substrate loading and microreactor size, since large r h allows the inhibitors to diffuse in the liquid away from the solids, thus reducing product inhibition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ® swabs.

PubMed

Ambers, Angie; Wiley, Rachel; Novroski, Nicole; Budowle, Bruce

2018-01-01

Previous studies have shown that nylon flocked swabs outperform traditional fiber swabs in DNA recovery due to their innovative design and lack of internal absorbent core to entrap cellular materials. The microFLOQ ® Direct swab, a miniaturized version of the 4N6 FLOQSwab ® , has a small swab head that is treated with a lysing agent which allows for direct amplification and DNA profiling from sample collection to final result in less than two hours. Additionally, the microFLOQ ® system subsamples only a minute portion of a stain and preserves the vast majority of the sample for subsequent testing or re-analysis, if desired. The efficacy of direct amplification of DNA from dilute bloodstains, saliva stains, and touch samples was evaluated using microFLOQ ® Direct swabs and the GlobalFiler™ Express system. Comparisons were made to traditional methods to assess the robustness of this alternate workflow. Controlled studies with 1:19 and 1:99 dilutions of bloodstains and saliva stains consistently yielded higher STR peak heights than standard methods with 1ng input DNA from the same samples. Touch samples from common items yielded single source and mixed profiles that were consistent with primary users of the objects. With this novel methodology/workflow, no sample loss occurs and therefore more template DNA is available during amplification. This approach may have important implications for analysis of low quantity and/or degraded samples that plague forensic casework. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

End product yields from the extraruminal fermentation of various polysaccharide, protein and nucleic acid components of biofuels feedstocks.

PubMed

Weimer, Paul J

2011-02-01

"Extraruminal" fermentations employing in vitro incubation of mixed ruminal bacterial consortia, are capable of converting a complex array of biomass materials to mixtures of volatile fatty acids (VFA), methane, and carbon dioxide. Most of the potential energy in the biomass feedstock is retained in the VFA products, which are potential reactants for electrochemical conversion to hydrocarbon fuels. Quantitative data on VFA yields and proportions from biomass components are necessary for determining industrial feasibility, but such measurements have not been systematically reported. VFA yields and proportions were determined for a variety of carbohydrates, proteins and nucleic acids. Carbohydrates yielded primarily acetic and propionic acids, while proteins also yielded a more favorable product mix (longer average chain length and branched chain VFAs). Addition of certain co-substrates (e.g., glycerol) favorably improved the VFA product mix. The results have implications for hydrocarbon fuel generation from biomass materials by hybrid fermentation/chemical processes. Published by Elsevier Ltd.

Influence of solid-liquid separation strategy on biogas yield from a stratified swine production system.

PubMed

Cestonaro do Amaral, André; Kunz, Airton; Radis Steinmetz, Ricardo Luis; Scussiato, Lucas Antunes; Tápparo, Deisi Cristina; Gaspareto, Taís Carla

2016-03-01

As the fourth largest swine producer and exporter, Brazil has increased its participation in the global swine production market. Generally, these units concentrate a large number of animals and generate effluents that must be correctly managed to prevent environmental impacts, being anaerobic digestion is an interesting alternative for treating these effluents. The low-volatile solid concentration in the manure suggests the need for solid-liquid separation as a tool to improve the biogas generation capacity. This study aimed to determine the influence of simplified and inexpensive solid-liquid separation strategies (screening and settling) and the different manures produced during each swine production phase (gestating and farrowing sow houses, nursery houses and finishing houses) on biogas and methane yield. We collected samples in two gestating sow houses (GSH-a and GSH-b), two farrowing sow houses (FSH-a and FSH-b), a nursery house (NH) and a finishing house (FH). Biochemical methane potential (BMP) tests were performed according to international standard procedures. The settled sludge fraction comprised 20-30% of the raw manure volume, which comprises 40-60% of the total methane yield. The methane potential of the settled sludge fraction was approximately two times higher than the methane potential of the supernatant fraction. The biogas yield differed among the raw manures from different swine production phases (GSH-a 326.4 and GSH-b 577.1; FSH-a 860.1 and FSH-b 479.2; NH -970.2; FH 474.5 NmLbiogas.gVS(-1)). The differences were relative to the production phase (feed type and feeding techniques) and the management of the effluent inside the facilities (water management). Brazilian swine production has increased his participation in the global market, been the fourth producer and the fourth exporter. The segregation of swine production in multiple sites has increased its importance, due to the possibilities to have more specialized units. Generally, these units

Microwave amplification with nanomechanical resonators.

PubMed

Massel, F; Heikkilä, T T; Pirkkalainen, J-M; Cho, S U; Saloniemi, H; Hakonen, P J; Sillanpää, M A

2011-12-14

The sensitive measurement of electrical signals is at the heart of modern technology. According to the principles of quantum mechanics, any detector or amplifier necessarily adds a certain amount of noise to the signal, equal to at least the noise added by quantum fluctuations. This quantum limit of added noise has nearly been reached in superconducting devices that take advantage of nonlinearities in Josephson junctions. Here we introduce the concept of the amplification of microwave signals using mechanical oscillation, which seems likely to enable quantum-limited operation. We drive a nanomechanical resonator with a radiation pressure force, and provide an experimental demonstration and an analytical description of how a signal input to a microwave cavity induces coherent stimulated emission and, consequently, signal amplification. This generic scheme, which is based on two linear oscillators, has the advantage of being conceptually and practically simpler than the Josephson junction devices. In our device, we achieve signal amplification of 25 decibels with the addition of 20 quanta of noise, which is consistent with the expected amount of added noise. The generality of the model allows for realization in other physical systems as well, and we anticipate that near-quantum-limited mechanical microwave amplification will soon be feasible in various applications involving integrated electrical circuits.

Quantum yield for carbon monoxide production in the 248 nm photodissociation of carbonyl sulfide (OCS)

NASA Technical Reports Server (NTRS)

Zhao, Z.; Stickel, R. E.; Wine, P. H.

1995-01-01

Tunable diode laser absorption spectroscopy has been coupled with excimer laser flash photolysis to measure the quantum yield for CO production from 248 nm photodissociation of carbonyl sulfide (OCS) relative to the well-known quantum yield for CO production from 248 nm photolysis of phosgene (Cl2CO2). The temporal resolution of the experiments was sufficient to distinguish CO formed directly by photodissociation from that formed by subsequent S((sup 3)P(sub J)) reaction with OCS. Under the experimental conditions employed, CO formation via the fast S((sup 1)D(sub 2)) + OCS reaction was minimal. Measurements at 297K and total pressures from 4 to 100 Torr N2 + N2O show the CO yield to be greater than 0.95 and most likely unity. This result suggests that the contribution of OCS as a precursor to the lower stratospheric sulfate aerosol layer is somewhat larger than previously thought.

Amplification of the Gp41 gene for detection of mutations conferring resistance to HIV-1 fusion inhibitors on genotypic assay

NASA Astrophysics Data System (ADS)

Tanumihardja, J.; Bela, B.

2017-08-01

Fusion inhibitors have potential for future use in HIV control programs in Indonesia, so the capacity to test resistance to such drugs needs to be developed. Resistance-detection with a genotypic assay began with amplification of the target gene, gp41. Based on the sequence of the two most common HIV subtypes in Indonesia, AE and B, a primer pair was designed. Plasma samples containing both subtypes were extracted to obtain HIV RNA. Using PCR, the primer pair was used to produce the amplification product, the identity of which was checked based on length under electrophoresis. Eleven plasma samples were included in this study. One-step PCR using the primer pair was able to amplify gp41 from 54.5% of the samples, and an unspecific amplification product was seen in 1.1% of the samples. Amplification failed in 36.4% of the samples, which may be due to an inappropriate primer sequence. It was also found that the optimal annealing temperature for producing the single expected band was 57.2 °C. With one-step PCR, the designed primer pair amplified the HIV-1 gp41 gene from subtypes AE and B. However, further research should be done to determine the conditions that will increase the sensitivity and specificity of the amplification process.

Analysis of the trade-off between high crop yield and low yield instability at the global scale

NASA Astrophysics Data System (ADS)

Ben-Ari, Tamara; Makowski, David

2016-10-01

Yield dynamics of major crops species vary remarkably among continents. Worldwide distribution of cropland influences both the expected levels and the interannual variability of global yields. An expansion of cultivated land in the most productive areas could theoretically increase global production, but also increase global yield instability if the most productive regions are characterized by high interannual yield variability. In this letter, we use portfolio analysis to quantify the tradeoff between the expected values and the interannual variance of global yield. We compute optimal frontiers for four crop species i.e., maize, rice, soybean and wheat and show how the distribution of cropland among large world regions can be optimized to either increase expected global crop production or decrease its interannual variability. We also show that a preferential allocation of cropland in the most productive regions can increase global expected yield at the expense of yield stability. Theoretically, optimizing the distribution of a small fraction of total cultivated areas can help find a good compromise between low instability and high crop yields at the global scale.

Peroxy Radical Measurements during the IRRONIC Field Project by C2H6 - NO Chemical Amplification

NASA Astrophysics Data System (ADS)

Wood, E. C. D.; Kundu, S.; Deming, B.; Lew, M.; Stevens, P. S.; Sklaveniti, S.; Dusanter, S.

2015-12-01

We present measurements of total peroxy radicals (HO2 + RO2) during the Indiana Radical, Reactivity and Ozone Production Intercomparison (IRRONIC) field project in Bloomington, Indiana during July 2015. Peroxy radicals were measured by chemical amplification using ethane and nitric oxide in dual PFA reaction chambers, and the amplification product NO2 was quantified by cavity attenuated phase shift spectroscopy. On sunny days mid-day peroxy radical mixing ratios were typically between 20 and 70 ppt and were well correlated with "HO2*" measured by the Indiana University Laser-Induced Fluorescence with Fluorescence Assay by Gas Expansion (IU-FAGE) instrument. The ratio of total peroxy radicals (UMass) to the IU-FAGE HO2* measurements was greater than two. We also describe results from an informal intercomparison of the two instruments' calibration sources, which are based on acetone photolysis (UMass) and water photolysis (IU). In addition to sampling the IU calibration source in "amplification" mode, the UMass instrument also separately quantified the HO2 mixing ratio in the IU calibration gas by reaction with excess NO and subsequent quantification of the NO2 produced.

Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification.

PubMed

Ebai, Tonge; Souza de Oliveira, Felipe Marques; Löf, Liza; Wik, Lotta; Schweiger, Caroline; Larsson, Anders; Keilholtz, Ulrich; Haybaeck, Johannes; Landegren, Ulf; Kamali-Moghaddam, Masood

2017-09-01

Detecting proteins at low concentrations in plasma is crucial for early diagnosis. Current techniques in clinical routine, such as sandwich ELISA, provide sensitive protein detection because of a dependence on target recognition by pairs of antibodies, but detection of still lower protein concentrations is often called for. Proximity ligation assay with rolling circle amplification (PLARCA) is a modified proximity ligation assay (PLA) for analytically specific and sensitive protein detection via binding of target proteins by 3 antibodies, and signal amplification via rolling circle amplification (RCA) in microtiter wells, easily adapted to instrumentation in use in hospitals. Proteins captured by immobilized antibodies were detected using a pair of oligonucleotide-conjugated antibodies. Upon target recognition these PLA probes guided oligonucleotide ligation, followed by amplification via RCA of circular DNA strands that formed in the reaction. The RCA products were detected by horseradish peroxidase-labeled oligonucleotides to generate colorimetric reaction products with readout in an absorbance microplate reader. We compared detection of interleukin (IL)-4, IL-6, IL-8, p53, and growth differentiation factor 15 (GDF-15) by PLARCA and conventional sandwich ELISA or immuno-RCA. PLARCA detected lower concentrations of proteins and exhibited a broader dynamic range compared to ELISA and iRCA using the same antibodies. IL-4 and IL-6 were detected in clinical samples at femtomolar concentrations, considerably lower than for ELISA. PLARCA offers detection of lower protein levels and increased dynamic ranges compared to ELISA. The PLARCA procedure may be adapted to routine instrumentation available in hospitals and research laboratories. © 2017 American Association for Clinical Chemistry.

New methods to characterize site amplification

USGS Publications Warehouse

Safak, Erdal

1993-01-01

Methods alternative to spectral ratios are introduced to characterize site amplification. The methods are developed by using a range of models, from the simple constant amplification model to the time-varying filter model. Examples are given for each model by using a pair of rock- and soil-site recordings from the Loma Prieta earthquake.

A cascade signal amplification strategy for surface enhanced Raman spectroscopy detection of thrombin based on DNAzyme assistant DNA recycling and rolling circle amplification.

PubMed

Gao, Fenglei; Du, Lili; Tang, Daoquan; Lu, Yao; Zhang, Yanzhuo; Zhang, Lixian

2015-04-15

A sensitive protocol for surface enhanced Raman spectroscopy (SERS) detection of thrombin is designed with R6G-Ag NPs as a signal tag by combining DNAzyme assistant DNA recycling and rolling circle amplification (RCA). Molecular beacon (MB) as recognition probe immobilizes on the glass slides and performs the amplification procedure. After thrombin-induced structure-switching DNA hairpins of probe 1, the DNAzyme is liberated from the caged structure, which hybridizes with the MB for cleavage of the MB in the presence of cofactor Zn(2+) and initiates the DNA recycling process, leading to the cleavage of a large number of MB and the generation of numerous primers for triggering RCA reaction. The long amplified RCA product which contained hundreds of tandem-repeat sequences, which can bind with oligonucleotide functionalized Ag NPs reporters. The attached signal tags can be easily read out by SERS. Because of the cascade signal amplification, these newly designed protocols provides a sensitive SERS detection of thrombin down to the femolar level (2.3fM) with a linear range of 5 orders of magnitude (from 10(-14) to 10(-9)M) and have high selectivity toward its target protein. The proposed method is expected to be a good clinical tool for the diagnosis of a thrombotic disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Proximity-dependent isothermal cycle amplification for small-molecule detection based on surface enhanced Raman scattering.

PubMed

Li, Ying; Zeng, Yan; Mao, Yaning; Lei, Chengcun; Zhang, Shusheng

2014-01-15

A novel proximity-dependent isothermal cycle amplification (PDICA) strategy has been proposed and successfully used for the determination of cocaine coupled with surface enhanced Raman scattering (SERS). For enhancing the SERS signal, Raman dye molecules modified bio-barcode DNA and gold nanoparticles (AuNPs) are used to prepare the Raman probes. Magnetic beads (MBs) are used as the carrier of amplification template and signal output products for circumventing the problem of high background induced by excess bio-barcode DNA. In the presence of target molecules, two label-free proximity probes can hybridize with each other and subsequently opens the hairpin connector-probe to perform the PDICA reaction including the target recycling amplification and strand-displacement amplification. As a result, abundant AuNPs Raman probes can be anchored on the surface of MBs and a low detection limit of 0.1 nM for cocaine is obtained. This assay also exhibits an excellent selectivity and has been successfully performed in human serum, which confirms the reliability and practicality of this protocol. © 2013 Elsevier B.V. All rights reserved.

Molecular analysis of single oocyst of Eimeria by whole genome amplification (WGA) based nested PCR.

PubMed

Wang, Yunzhou; Tao, Geru; Cui, Yujuan; Lv, Qiyao; Xie, Li; Li, Yuan; Suo, Xun; Qin, Yinghe; Xiao, Lihua; Liu, Xianyong

2014-09-01

PCR-based molecular tools are widely used for the identification and characterization of protozoa. Here we report the molecular analysis of Eimeria species using combined methods of whole genome amplification (WGA) and nested PCR. Single oocyst of Eimeria stiedai or Eimeriamedia was directly used for random amplification of the genomic DNA with either primer extension preamplification (PEP) or multiple displacement amplification (MDA), and then the WGA product was used as template in nested PCR with species-specific primers for ITS-1, 18S rDNA and 23S rDNA of E. stiedai and E. media. WGA-based PCR was successful for the amplification of these genes from single oocyst. For the species identification of single oocyst isolated from mixed E. stiedai or E. media, the results from WGA-based PCR were exactly in accordance with those from morphological identification, suggesting the availability of this method in molecular analysis of eimerian parasites at the single oocyst level. WGA-based PCR method can also be applied for the identification and genetic characterization of other protists. Copyright © 2014 Elsevier Inc. All rights reserved.

High-throughput amplification of mature microRNAs in uncharacterized animal models using polyadenylated RNA and stem-loop reverse transcription polymerase chain reaction.

PubMed

Biggar, Kyle K; Wu, Cheng-Wei; Storey, Kenneth B

2014-10-01

This study makes a significant advancement on a microRNA amplification technique previously used for expression analysis and sequencing in animal models without annotated mature microRNA sequences. As research progresses into the post-genomic era of microRNA prediction and analysis, the need for a rapid and cost-effective method for microRNA amplification is critical to facilitate wide-scale analysis of microRNA expression. To facilitate this requirement, we have reoptimized the design of amplification primers and introduced a polyadenylation step to allow amplification of all mature microRNAs from a single RNA sample. Importantly, this method retains the ability to sequence reverse transcription polymerase chain reaction (RT-PCR) products, validating microRNA-specific amplification. Copyright © 2014 Elsevier Inc. All rights reserved.

Destiny-yield relationship for channel catfish reared in a biofloc technology production system

USDA-ARS?s Scientific Manuscript database

The effect of stocking density on yield of stocker channel catfish and water quality in a biofloc technology production system was studied in this completely randomized design experiment. Fingerling channel catfish (Ictalurus punctatus; 48.0 g/fish, 17.8 cm/fish) were stocked into nine continuously ...

Flux amplification in helicity injected spherical tori

NASA Astrophysics Data System (ADS)

Tang, X. Z.; Boozer, A. H.

2005-04-01

An important measure of the effective current drive by helicity injection into spheromaks and spherical tori is provided by the flux amplification factor, defined as the ratio between the closed poloidal flux in the relaxed mean field and the initial injector vacuum poloidal flux. Flux amplification in magnetic helicity injection is governed by a resonant behavior for Taylor-relaxed plasmas satisfying j =kB. Under the finite net toroidal flux constraint in a spherical torus (ST), the constrained linear resonance k1c is upshifted substantially from the primary Jensen-Chu resonance k1 that was known to be responsible for flux amplification in spheromak formation. Standard coaxial helicity injection into a ST operates at large M, with M the characteristic dimensionless parameter defined as the ratio between the toroidal flux in the discharge chamber and the injector poloidal flux. Meaningful flux amplification for ST plasmas is limited by a critical kr at which edge toroidal field reverses its direction. The kr is downshifted from k1 by a small amount inversely proportional to M. The maximum flux amplification factor Ar≡A(k=kr) scales linearly with M. At the other end of k, substantial flux amplification A(k =ko)˜1 becomes available for ko that scales inversely proportional to M, a significant departure from that in spheromak formation. These important parameters follow the inequality koamplification factor in a ST to be smaller than M. The scaling laws are given analytically in the asymptotic limit of M ≫1, but numerical solutions indicate that they are useful even for M ˜1.

Amplification of Angular Rotations Using Weak Measurements

NASA Astrophysics Data System (ADS)

Magaña-Loaiza, Omar S.; Mirhosseini, Mohammad; Rodenburg, Brandon; Boyd, Robert W.

2014-05-01

We present a weak measurement protocol that permits a sensitive estimation of angular rotations based on the concept of weak-value amplification. The shift in the state of a pointer, in both angular position and the conjugate orbital angular momentum bases, is used to estimate angular rotations. This is done by an amplification of both the real and imaginary parts of the weak-value of a polarization operator that has been coupled to the pointer, which is a spatial mode, via a spin-orbit coupling. Our experiment demonstrates the first realization of weak-value amplification in the azimuthal degree of freedom. We have achieved effective amplification factors as large as 100, providing a sensitivity that is on par with more complicated methods that employ quantum states of light or extremely large values of orbital angular momentum.

DNA-based identification of spices: DNA isolation, whole genome amplification, and polymerase chain reaction.

PubMed

Focke, Felix; Haase, Ilka; Fischer, Markus

2011-01-26

Usually spices are identified morphologically using simple methods like magnifying glasses or microscopic instruments. On the other hand, molecular biological methods like the polymerase chain reaction (PCR) enable an accurate and specific detection also in complex matrices. Generally, the origins of spices are plants with diverse genetic backgrounds and relationships. The processing methods used for the production of spices are complex and individual. Consequently, the development of a reliable DNA-based method for spice analysis is a challenging intention. However, once established, this method will be easily adapted to less difficult food matrices. In the current study, several alternative methods for the isolation of DNA from spices have been developed and evaluated in detail with regard to (i) its purity (photometric), (ii) yield (fluorimetric methods), and (iii) its amplifiability (PCR). Whole genome amplification methods were used to preamplify isolates to improve the ratio between amplifiable DNA and inhibiting substances. Specific primer sets were designed, and the PCR conditions were optimized to detect 18 spices selectively. Assays of self-made spice mixtures were performed to proof the applicability of the developed methods.

Novel rolling circle amplification and DNA origami-based DNA belt-involved signal amplification assay for highly sensitive detection of prostate-specific antigen (PSA).

PubMed

Yan, Juan; Hu, Chongya; Wang, Ping; Liu, Rui; Zuo, Xiaolei; Liu, Xunwei; Song, Shiping; Fan, Chunhai; He, Dannong; Sun, Gang

2014-11-26

Prostate-specific antigen (PSA) is one of the most important biomarkers for the early diagnosis and prognosis of prostate cancer. Although many efforts have been made to achieve significant progress for the detection of PSA, challenges including relative low sensitivity, complicated operation, sophisticated instruments, and high cost remain unsolved. Here, we have developed a strategy combining rolling circle amplification (RCA)-based DNA belts and magnetic bead-based enzyme-linked immunosorbent assay (ELISA) for the highly sensitive and specific detection of PSA. At first, a 96-base circular DNA template was designed and prepared for the following RCA. Single stranded DNA (ssDNA) products from RCA were used as scaffold strand for DNA origami, which was hybridized with three staple strands of DNA. The resulting DNA belts were conjugated with multiple enzymes for signal amplification and then employed to magnetic bead based ELISA for PSA detection. Through our strategy, as low as 50 aM of PSA can be detected with excellent specificity.

Diagnostic devices for isothermal nucleic acid amplification.

PubMed

Chang, Chia-Chen; Chen, Chien-Cheng; Wei, Shih-Chung; Lu, Hui-Hsin; Liang, Yang-Hung; Lin, Chii-Wann

2012-01-01

Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.

Diagnostic Devices for Isothermal Nucleic Acid Amplification

PubMed Central

Chang, Chia-Chen; Chen, Chien-Cheng; Wei, Shih-Chung; Lu, Hui-Hsin; Liang, Yang-Hung; Lin, Chii-Wann

2012-01-01

Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development. PMID:22969402

Rapid detection of microbial DNA by a novel isothermal genome exponential amplification reaction (GEAR) assay.

PubMed

Prithiviraj, Jothikumar; Hill, Vincent; Jothikumar, Narayanan

2012-04-20

In this study we report the development of a simple target-specific isothermal nucleic acid amplification technique, termed genome exponential amplification reaction (GEAR). Escherichia coli was selected as the microbial target to demonstrate the GEAR technique as a proof of concept. The GEAR technique uses a set of four primers; in the present study these primers targeted 5 regions on the 16S rRNA gene of E. coli. The outer forward and reverse Tab primer sequences are complementary to each other at their 5' end, whereas their 3' end sequences are complementary to their respective target nucleic acid sequences. The GEAR assay was performed at a constant temperature 60 °C and monitored continuously in a real-time PCR instrument in the presence of an intercalating dye (SYTO 9). The GEAR assay enabled amplification of as few as one colony forming units of E. coli per reaction within 30 min. We also evaluated the GEAR assay for rapid identification of bacterial colonies cultured on agar media directly in the reaction without DNA extraction. Cells from E. coli colonies were picked and added directly to GEAR assay mastermix without prior DNA extraction. DNA in the cells could be amplified, yielding positive results within 15 min. Published by Elsevier Inc.

Steam gasification of waste tyre: Influence of process temperature on yield and product composition

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

Portofino, Sabrina, E-mail: sabrina.portofino@enea.it; Donatelli, Antonio; Iovane, Pierpaolo

Highlights: ► Steam gasification of waste tyre as matter and energy recovery treatment. ► Process temperature affects products yield and gas composition. ► High temperature promotes hydrogen production. ► Char exploitation as activated carbon or carbon source. - Abstract: An experimental survey of waste tyre gasification with steam as oxidizing agent has been conducted in a continuous bench scale reactor, with the aim of studying the influence of the process temperature on the yield and the composition of the products; the tests have been performed at three different temperatures, in the range of 850–1000 °C, holding all the other operationalmore » parameters (pressure, carrier gas flow, solid residence time). The experimental results show that the process seems promising in view of obtaining a good quality syngas, indicating that a higher temperature results in a higher syngas production (86 wt%) and a lower char yield, due to an enhancement of the solid–gas phase reactions with the temperature. Higher temperatures clearly result in higher hydrogen concentrations: the hydrogen content rapidly increases, attaining values higher than 65% v/v, while methane and ethylene gradually decrease over the range of the temperatures; carbon monoxide and dioxide instead, after an initial increase, show a nearly constant concentration at 1000 °C. Furthermore, in regards to the elemental composition of the synthesis gas, as the temperature increases, the carbon content continuously decreases, while the oxygen content increases; the hydrogen, being the main component of the gas fraction and having a small atomic weight, is responsible for the progressive reduction of the gas density at higher temperature.« less

Oncogene-like induction of cellular invasion from centrosome amplification

PubMed Central

Godinho, Susana A.; Picone, Remigio; Burute, Mithila; Dagher, Regina; Su, Ying; Leung, Cheuk T.; Polyak, Kornelia; Brugge, Joan S.; Thery, Manuel; Pellman, David

2014-01-01

Centrosome amplification has long been recognized as a feature of human tumors, however its role in tumorigenesis remains unclear1. Centrosome amplification is poorly tolerated by non-transformed cells, and, in the absence of selection, extra centrosomes are spontaneously lost2. Thus, the high frequency of centrosome amplification, particularly in more aggressive tumors3, raises the possibility that extra centrosomes could, in some contexts, confer advantageous characteristics that promote tumor progression. Using a three-dimensional model system and other approaches to culture human mammary epithelial cells, we find that centrosome amplification triggers cell invasion. This invasive behavior is similar to that induced by overexpression of the breast cancer oncogene ErbB24 and indeed enhances invasiveness triggered by ErbB2. We show that, through increased centrosomal microtubule nucleation, centrosome amplification increases Rac1 activity, which disrupts normal cell-cell adhesion and promotes invasion. These findings demonstrate that centrosome amplification, a structural alteration of the cytoskeleton, can promote features of malignant transformation. PMID:24739973

Product yield-detected ESR on magnetic field-dependent photoreduction of quinones in SDS micellar solution

NASA Astrophysics Data System (ADS)

Okazaki, M.; Sakata, S.; Konaka, R.; Shiga, T.

1987-06-01

Transient free radicals in the magnetic field-dependent photoreduction of quinones (menadione or anthraquinone) in a sodium dodecyl sulfate (SDS) micellar solution, were converted to stable nitroxide radicals by the ``spin trapping'' technique with or without the microwave irradiation. Upon irradiating the microwave at 160 mW, the product yield (``spin adduct'' of the alkyl radical generated from SDS molecule) decreased by up to 14% at certain magnetic fields in a resonant manner. Although only one component of the postulated radical pair was converted to the spin adduct, the decrease in the yield as a function of external magnetic field revealed the ESR spectra of both component radicals of the radical pair, i.e., the semiquinone radical and the alkyl radical from SDS. This experiment not only gives the direct evidence for the radical pair model, but also suggests the possibility for this method to be applied in controlling the chemical reactions by the microwave. A simple calculation was made to simulate the observed ``product yield-detected ESR.'' Agreements were achieved semiquantitatively between the observed reductions in the spin adduct yields and those calculated. The estimated exchange interaction between the component radicals in the radical pair of the present systems was lower than 0.3 mT.

Quality assurance after process changes of the production of a therapeutic antibody.

PubMed

Brass, J M; Krummen, K; Moll-Kaufmann, C

1996-12-01

Process development for the production of a therapeutic humanised antibody is a very complex operation. It involves recombinant genetics, verification of a strong expression system, gene amplification, characterisation of a stable host cell expression system, optimisation and design of the mammalian cell culture fermentation system and development of an efficient recovery process resulting in high yields and product quality. Rapid progress in the field and the wish of some pharmaceutical companies for outsourcing their production are the driving forces for process changes relatively late in the development phase. This literature survey is aimed at identifying the limits of acceptable process changes in up scaling of the fermentation and down stream processing of biopharmaceuticals and defining the demand in production validation to prove product equivalency and identity of the isolated, purified therapeutic antibody.

Development of microsatellite markers in Cordia bifurcata (Boraginaceae) and cross-species amplification in Cordia inermis and Cordia pringlei.

PubMed

Spoon, Tracey R; Kesseli, Rick V

2008-09-01

We developed 16 microsatellite markers in Cordia bifurcata, a Central and South American shrub. The markers show low polymorphism in C. bifurcata, a species suspected of self-fertilization or apomixis. Of four polymorphic loci, three had only two alleles. However, current research indicates that these markers hold value for interpopulational comparisons of C. bifurcata and for analyses of congeners. In Cordia inermis, a dioecious or subdioecious shrub, seven of the markers produced interpretable amplification products of which five showed polymorphism. In Cordia pringlei, a distylous shrub, nine of the markers produced interpretable amplification products of which six showed polymorphism. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Desert Amplification in a Warming Climate

PubMed Central

Zhou, Liming

2016-01-01

Here I analyze the observed and projected surface temperature anomalies over land between 50°S-50°N for the period 1950–2099 by large-scale ecoregion and find strongest warming consistently and persistently seen over driest ecoregions such as the Sahara desert and the Arabian Peninsula during various 30-year periods, pointing to desert amplification in a warming climate. This amplification enhances linearly with the global mean greenhouse gases(GHGs) radiative forcing and is attributable primarily to a stronger GHGs-enhanced downward longwave radiation forcing reaching the surface over drier ecoregions as a consequence of a warmer and thus moister atmosphere in response to increasing GHGs. These results indicate that desert amplification may represent a fundamental pattern of global warming associated with water vapor feedbacks over land in low- and mid- latitudes where surface warming rates depend inversely on ecosystem dryness. It is likely that desert amplification might involve two types of water vapor feedbacks that maximize respectively in the tropical upper troposphere and near the surface over deserts, with both being very dry and thus extremely sensitive to changes of water vapor. PMID:27538725

Yoctomole electrochemical genosensing of Ebola virus cDNA by rolling circle and circle to circle amplification.

PubMed

Carinelli, S; Kühnemund, M; Nilsson, M; Pividori, M I

2017-07-15

This work addresses the design of an Ebola diagnostic test involving a simple, rapid, specific and highly sensitive procedure based on isothermal amplification on magnetic particles with electrochemical readout. Ebola padlock probes were designed to detect a specific L-gene sequence present in the five most common Ebola species. Ebola cDNA was amplified by rolling circle amplification (RCA) on magnetic particles. Further re-amplification was performed by circle-to-circle amplification (C2CA) and the products were detected in a double-tagging approach using a biotinylated capture probe for immobilization on magnetic particles and a readout probe for electrochemical detection by square-wave voltammetry on commercial screen-printed electrodes. The electrochemical genosensor was able to detect as low as 200 ymol, corresponding to 120 cDNA molecules of L-gene Ebola virus with a limit of detection of 33 cDNA molecules. The isothermal double-amplification procedure by C2CA combined with the electrochemical readout and the magnetic actuation enables the high sensitivity, resulting in a rapid, inexpensive, robust and user-friendly sensing strategy that offers a promising approach for the primary care in low resource settings, especially in less developed countries. Copyright © 2016 Elsevier B.V. All rights reserved.

Optimization of the yield of dark microaerobic production of hydrogen from lactate by Rhodopseudomonas palustris.

PubMed

Lazaro, Carolina Zampol; Hitit, Zeynep Yilmazer; Hallenbeck, Patrick C

2017-12-01

Hydrogen yields of dark fermentation are limited due to the need to also produce reduced side products, and photofermentation, an alternative, is limited by the need for light. A relatively new strategy, dark microaerobic fermentation, could potentially overcome both these constraints. Here, application of this strategy demonstrated for the first time significant hydrogen production from lactate by a single organism in the dark. Response surface methodology (RSM) was used to optimize substrate and oxygen concentration as well as inoculum using both (1) regular batch and (2) O 2 fed batch cultures. The highest hydrogen yield (HY) was observed under regular batch (1.4±0.1molH 2 /mollactate) and the highest hydrogen production (HP) (173.5µmolH 2 ) was achieved using O 2 fed batch. This study has provided proof of principal for the ability of microaerobic fermentation to drive thermodynamically difficult reactions, such as the conversion of lactate to hydrogen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Can Anomalous Amplification be Attained without Postselection?

PubMed

Martínez-Rincón, Julián; Liu, Wei-Tao; Viza, Gerardo I; Howell, John C

2016-03-11

We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without discarding of data, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected. A tunable phase controls the strength of the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. We show that in the presence of technical noise the effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique.

Can Anomalous Amplification be Attained without Postselection?

NASA Astrophysics Data System (ADS)

Martínez-Rincón, Julián; Liu, Wei-Tao; Viza, Gerardo I.; Howell, John C.

2016-03-01

We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without discarding of data, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected. A tunable phase controls the strength of the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. We show that in the presence of technical noise the effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique.

Lidar using the backscatter amplification effect

NASA Astrophysics Data System (ADS)

Razenkov, Igor A.; Banakh, Victor A.

2018-04-01

Experimental data proving the possibility of lidar measurement of the refractive turbulence strength based on the effect of backscatter amplification (BSA) are reported. It is shown that the values of the amplification factor correlate with the variance of random jitter of optical image of an incoherent light source depending on the value of the structure constant of the air refractive index turbulent fluctuations averaged over the probing path. This paper presents the results of measurements of the BSA factor in comparison with the simultaneous measurements of the BSA peak, which is very narrow and only occurs on the laser beam axis. It is constructed the range-time images of the derivative of the amplification factor gives a comprehensive picture of the location of turbulent zones and their temporal dynamics.

Amplification, Technology, and Cochlear Implants for Infants.

ERIC Educational Resources Information Center

Adam, Arlie J.

1993-01-01

Early amplification is crucial to efficient habilitation and development of oral communication skills in hearing-impaired infants. Initial evaluation and fitting of amplification is a joint effort by the audiologist, therapist, and parents, whether the child uses traditional hearing aids or cochlear implants, and should be supplemented by a…

Detection of periodontal pathogen Porphyromonas gingivalis by loop-mediated isothermal amplification method.

PubMed

Maeda, Hiroshi; Kokeguchi, Susumu; Fujimoto, Chiyo; Tanimoto, Ichiro; Yoshizumi, Wakako; Nishimura, Fusanori; Takashiba, Shogo

2005-02-01

A method for nucleic acid amplification, loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for periodontal pathogen, Porphyromonas gingivalis. A set of six primers was designed by targeting the 16S ribosomal RNA gene. By the detection system, target DNA was amplified and visualized on agarose gel within 30 min under isothermal condition at 64 degrees C with a detection limit of 20 cells of P. gingivalis. Without gel electrophoresis, the LAMP amplicon was directly visualized in the reaction tube by addition of SYBR Green I for a naked-eye inspection. The LAMP reaction was also assessed by white turbidity of magnesium pyrophosphate (a by-product of LAMP) in the tube. Detection limits of these naked-eye inspections were 20 cells and 200 cells, respectively. Although false-positive DNA amplification was observed from more than 10(7) cells of Porphyromonas endodontalis, no amplification was observed in other five related oral pathogens. Further, quantitative detection of P. gingivalis was accomplished by a real-time monitoring of the LAMP reaction using SYBR Green I with linearity over a range of 10(2)-10(6) cells. The real-time LAMP was then applied to clinical samples of dental plaque and demonstrated almost identical results to the conventional real-time PCR with an advantage of rapidity. These findings indicate the potential usefulness of LAMP for detecting and quantifying P. gingivalis, especially in its rapidity and simplicity.

Assessing the Effects of Climate Variability on Orange Yield in Florida to Reduce Production Forecast Errors

NASA Astrophysics Data System (ADS)

Concha Larrauri, P.

2015-12-01

Orange production in Florida has experienced a decline over the past decade. Hurricanes in 2004 and 2005 greatly affected production, almost to the same degree as strong freezes that occurred in the 1980's. The spread of the citrus greening disease after the hurricanes has also contributed to a reduction in orange production in Florida. The occurrence of hurricanes and diseases cannot easily be predicted but the additional effects of climate on orange yield can be studied and incorporated into existing production forecasts that are based on physical surveys, such as the October Citrus forecast issued every year by the USDA. Specific climate variables ocurring before and after the October forecast is issued can have impacts on flowering, orange drop rates, growth, and maturation, and can contribute to the forecast error. Here we present a methodology to incorporate local climate variables to predict the USDA's orange production forecast error, and we study the local effects of climate on yield in different counties in Florida. This information can aid farmers to gain an insight on what is to be expected during the orange production cycle, and can help supply chain managers to better plan their strategy.

Beam cleaning of an incoherent laser via plasma Raman amplification

DOE PAGES

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.; ...

2017-09-25

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Beam cleaning of an incoherent laser via plasma Raman amplification

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

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Chemical amplification based on fluid partitioning

DOEpatents

Anderson, Brian L [Lodi, CA; Colston, Jr., Billy W.; Elkin, Chris [San Ramon, CA

2006-05-09

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

Exploratory study of fission product yield determination from photofission of 239Pu at 11 MeV with monoenergetic photons

NASA Astrophysics Data System (ADS)

Bhike, Megha; Tornow, W.; Krishichayan, Tonchev, A. P.

2017-02-01

Measurements of fission product yields play an important role for the understanding of fundamental aspects of the fission process. Recently, neutron-induced fission product-yield data of 239Pu at energies below 4 MeV revealed an unexpected energy dependence of certain fission fragments. In order to investigate whether this observation is prerogative to neutron-induced fission, a program has been initiated to measure fission product yields in photoinduced fission. Here we report on the first ever photofission product yield measurement with monoenergetic photons produced by Compton back-scattering of FEL photons. The experiment was performed at the High-Intensity Gamma-ray Source at Triangle Universities Nuclear Laboratory on 239Pu at Eγ=11 MeV. In this exploratory study the yield of eight fission products ranging from 91Sr to 143Ce has been obtained.

Explanatory model for sound amplification in a stethoscope

NASA Astrophysics Data System (ADS)

Eshach, H.; Volfson, A.

2015-01-01

In the present paper we suggest an original physical explanatory model that explains the mechanism of the sound amplification process in a stethoscope. We discuss the amplification of a single pulse, a continuous wave of certain frequency, and finally we address the resonant frequencies. It is our belief that this model may provide students with opportunities to not only better understand the amplification mechanism of a stethoscope, but also to strengthen their understanding of sound, pressure, waves, resonance modes, etc.

Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming.

PubMed

Martineau, Rhett L; Murray, Sarah A; Ci, Shufang; Gao, Weimin; Chao, Shih-Hui; Meldrum, Deirdre R

2017-01-03

This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.

Biomass production of 12 winter cereal cover crop cultivars and their effect on subsequent no-till corn yield

USDA-ARS?s Scientific Manuscript database

Cover crops can improve the sustainability and resilience of corn and soybean production systems. However, there have been isolated reports of corn yield reductions following winter rye cover crops. Although there are many possible causes of corn yield reductions following winter cereal cover crops,...

Dual-fission chamber and neutron beam characterization for fission product yield measurements using monoenergetic neutrons

NASA Astrophysics Data System (ADS)

Bhatia, C.; Fallin, B.; Gooden, M. E.; Howell, C. R.; Kelley, J. H.; Tornow, W.; Arnold, C. W.; Bond, E. M.; Bredeweg, T. A.; Fowler, M. M.; Moody, W. A.; Rundberg, R. S.; Rusev, G.; Vieira, D. J.; Wilhelmy, J. B.; Becker, J. A.; Macri, R.; Ryan, C.; Sheets, S. A.; Stoyer, M. A.; Tonchev, A. P.

2014-09-01

A program has been initiated to measure the energy dependence of selected high-yield fission products used in the analysis of nuclear test data. We present out initial work of neutron activation using a dual-fission chamber with quasi-monoenergetic neutrons and gamma-counting method. Quasi-monoenergetic neutrons of energies from 0.5 to 15 MeV using the TUNL 10 MV FM tandem to provide high-precision and self-consistent measurements of fission product yields (FPY). The final FPY results will be coupled with theoretical analysis to provide a more fundamental understanding of the fission process. To accomplish this goal, we have developed and tested a set of dual-fission ionization chambers to provide an accurate determination of the number of fissions occurring in a thick target located in the middle plane of the chamber assembly. Details of the fission chamber and its performance are presented along with neutron beam production and characterization. Also presented are studies on the background issues associated with room-return and off-energy neutron production. We show that the off-energy neutron contribution can be significant, but correctable, while room-return neutron background levels contribute less than <1% to the fission signal.

Detection of Giardia in environmental waters by immuno-PCR amplification methods.

PubMed

Mahbubani, M H; Schaefer, F W; Jones, D D; Bej, A K

1998-02-01

Genomic DNA was extracted either directly from Giardia muris cysts seeded into environmental surface waters or from cysts isolated by immunomagnetic beads (IMB). A 0.171-kbp segment of the giardin gene was PCR-amplified following "direct extraction" of Giardia DNA from seeded Cahaba river water concentrate with moderate turbidity (780 JTU's), but DNA purified from seeded Colorado river water concentrates with high turbidity (2 x 10(5) JTUs) failed to amplify. However, if the cysts were first separated by the IMB approach from seeded Cahaba or Colorado river waters, and the DNA released by a freeze-boil Chelex(R)100 treatment, detection of G. muris by PCR amplification could be achieved at a sensitivity of 3 x 10(0) or 3 x 10(1) cysts/ml, respectively. If, however, the G. muris cysts used to seed even moderately turbid river waters (780 JTUs) were formalin treated (which is conventionally used for microscopic examination), neither direct extraction nor IMB purification methods yielded amplifiable DNA. Use of immunomagnetic beads to separate Giardia cysts from complex matrices of environmental surface waters followed by DNA release and PCR amplification of the target giardin gene improved the reliability of detection of this pathogen with the required sensitivity.

High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling.

PubMed

Rollin, Joseph A; Martin del Campo, Julia; Myung, Suwan; Sun, Fangfang; You, Chun; Bakovic, Allison; Castro, Roberto; Chandrayan, Sanjeev K; Wu, Chang-Hao; Adams, Michael W W; Senger, Ryan S; Zhang, Y-H Percival

2015-04-21

The use of hydrogen (H2) as a fuel offers enhanced energy conversion efficiency and tremendous potential to decrease greenhouse gas emissions, but producing it in a distributed, carbon-neutral, low-cost manner requires new technologies. Herein we demonstrate the complete conversion of glucose and xylose from plant biomass to H2 and CO2 based on an in vitro synthetic enzymatic pathway. Glucose and xylose were simultaneously converted to H2 with a yield of two H2 per carbon, the maximum possible yield. Parameters of a nonlinear kinetic model were fitted with experimental data using a genetic algorithm, and a global sensitivity analysis was used to identify the enzymes that have the greatest impact on reaction rate and yield. After optimizing enzyme loadings using this model, volumetric H2 productivity was increased 3-fold to 32 mmol H2⋅L(-1)⋅h(-1). The productivity was further enhanced to 54 mmol H2⋅L(-1)⋅h(-1) by increasing reaction temperature, substrate, and enzyme concentrations--an increase of 67-fold compared with the initial studies using this method. The production of hydrogen from locally produced biomass is a promising means to achieve global green energy production.

High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling

PubMed Central

Rollin, Joseph A.; Martin del Campo, Julia; Myung, Suwan; Sun, Fangfang; You, Chun; Bakovic, Allison; Castro, Roberto; Chandrayan, Sanjeev K.; Wu, Chang-Hao; Adams, Michael W. W.; Senger, Ryan S.; Zhang, Y.-H. Percival

2015-01-01

The use of hydrogen (H2) as a fuel offers enhanced energy conversion efficiency and tremendous potential to decrease greenhouse gas emissions, but producing it in a distributed, carbon-neutral, low-cost manner requires new technologies. Herein we demonstrate the complete conversion of glucose and xylose from plant biomass to H2 and CO2 based on an in vitro synthetic enzymatic pathway. Glucose and xylose were simultaneously converted to H2 with a yield of two H2 per carbon, the maximum possible yield. Parameters of a nonlinear kinetic model were fitted with experimental data using a genetic algorithm, and a global sensitivity analysis was used to identify the enzymes that have the greatest impact on reaction rate and yield. After optimizing enzyme loadings using this model, volumetric H2 productivity was increased 3-fold to 32 mmol H2⋅L−1⋅h−1. The productivity was further enhanced to 54 mmol H2⋅L−1⋅h−1 by increasing reaction temperature, substrate, and enzyme concentrations—an increase of 67-fold compared with the initial studies using this method. The production of hydrogen from locally produced biomass is a promising means to achieve global green energy production. PMID:25848015

High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling

DOE PAGES

Rollin, Joseph A.; Martin del Campo, Julia; Myung, Suwan; ...

2015-04-06

The use of hydrogen (H 2) as a fuel offers enhanced energy conversion efficiency and tremendous potential to decrease greenhouse gas emissions, but producing it in a distributed, carbon-neutral, low-cost manner requires new technologies. Herein we demonstrate the complete conversion of glucose and xylose from plant biomass to H 2 and CO 2 based on an in vitro synthetic enzymatic pathway. Glucose and xylose were simultaneously converted to H 2 with a yield of two H 2 per carbon, the maximum possible yield. Parameters of a nonlinear kinetic model were fitted with experimental data using a genetic algorithm, and amore » global sensitivity analysis was used to identify the enzymes that have the greatest impact on reaction rate and yield. After optimizing enzyme loadings using this model, volumetric H 2 productivity was increased 3-fold to 32 mmol H 2∙L ₋1∙h ₋1. The productivity was further enhanced to 54 mmol H 2∙L ₋1∙h ₋1 by increasing reaction temperature, substrate, and enzyme concentrations—an increase of 67-fold compared with the initial studies using this method. The production of hydrogen from locally produced biomass is a promising means to achieve global green energy production.« less

High yield production of extracellular recombinant levansucrase by Bacillus megaterium.

PubMed

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.

Ultrabright multikilovolt x-ray source: saturated amplification on noble gas transition arrays from hollow atom states

DOEpatents

Rhodes, Charles K.; Boyer, Keith

2004-02-17

An apparatus and method for the generation of ultrabright multikilovolt x-rays from saturated amplification on noble gas transition arrays from hollow atom states is described. Conditions for x-ray amplification in this spectral region combine the production of cold, high-Z matter, with the direct, selective multiphoton excitation of hollow atoms from clusters using ultraviolet radiation and a nonlinear mode of confined, self-channeled propagation in plasmas. Data obtained is consistent with the presence of saturated amplification on several transition arrays of the hollow atom Xe(L) spectrum (.lambda..about.2.9 .ANG.). An estimate of the peak brightness achieved is .about.10.sup.29 .gamma..multidot.s.sup.-1.multidot.mm.sup.-2.multidot.mr.sup.-2 (0.1% Bandwidth).sup.-1, that is .about.10.sup.5 -fold higher than presently available synchotron technology.

Detection of the 35S promoter in transgenic maize via various isothermal amplification techniques: a practical approach.

PubMed

Zahradnik, Celine; Kolm, Claudia; Martzy, Roland; Mach, Robert L; Krska, Rudolf; Farnleitner, Andreas H; Brunner, Kurt

2014-11-01

In 2003 the European Commission introduced a 0.9% threshold for food and feed products containing genetically modified organism (GMO)-derived components. For commodities containing GMO contents higher than this threshold, labelling is mandatory. To provide a DNA-based rapid and simple detection method suitable for high-throughput screening of GMOs, several isothermal amplification approaches for the 35S promoter were tested: strand displacement amplification, nicking-enzyme amplification reaction, rolling circle amplification, loop-mediated isothermal amplification (LAMP) and helicase-dependent amplification (HDA). The assays developed were tested for specificity in order to distinguish between samples containing genetically modified (GM) maize and non-GM maize. For those assays capable of this discrimination, tests were performed to determine the lower limit of detection. A false-negative rate was determined to rule out whether GMO-positive samples were incorrectly classified as GMO-negative. A robustness test was performed to show reliable detection independent from the instrument used for amplification. The analysis of three GM maize lines showed that only LAMP and HDA were able to differentiate between the GMOs MON810, NK603, and Bt11 and non-GM maize. Furthermore, with the HDA assay it was possible to realize a detection limit as low as 0.5%. A false-negative rate of only 5% for 1% GM maize for all three maize lines shows that HDA has the potential to be used as an alternative strategy for the detection of transgenic maize. All results obtained with the LAMP and HDA assays were compared with the results obtained with a previously reported real-time PCR assay for the 35S promoter in transgenic maize. This study presents two new screening assays for detection of the 35S promoter in transgenic maize by applying the isothermal amplification approaches HDA and LAMP.

MET amplification as a potential therapeutic target in gastric cancer

PubMed Central

Kawakami, Hisato; Okamoto, Isamu; Arao, Tokuzo; Okamoto, Wataru; Matsumoto, Kazuko; Taniguchi, Hirokazu; Kuwata, Kiyoko; Yamaguchi, Haruka; Nishio, Kazuto; Nakagawa, Kazuhiko; Yamada, Yasuhide

2013-01-01

Our aim was to investigate both the prevalence of MET amplification in gastric cancer as well as the potential of this genetic alteration to serve as a therapeutic target in gastric cancer. MET amplification was assessed by initial screening with a PCR-based copy number assay followed by confirmatory FISH analysis in formalin-fixed, paraffin-embedded specimens of gastric cancer obtained at surgery. The effects of MET tyrosine kinase inhibitors (MET-TKIs) in gastric cancer cells with or without MET amplification were also examined. The median MET copy number in 266 cases of gastric cancer was 1.7, with a range of 0.41 to 21.3. We performed FISH analysis for the 15 cases with the highest MET copy numbers. MET amplification was confirmed in the four assessable cases with a MET copy number of at least 4, whereas MET amplification was not detected in those with a gene copy number of <4. The prevalence of MET amplification was thus 1.5% (4 out of 266 cases). Inhibition of MET by MET-TKIs resulted in the induction of apoptosis accompanied by attenuation of downstream MET signaling in gastric cancer cell lines with MET amplification but not in those without this genetic change. MET amplification identifies a small but clinically important subgroup of gastric cancer patients who are likely to respond to MET-TKIs. Furthermore, screening with a PCR-based copy number assay is an efficient way to reduce the number of patients requiring confirmation of MET amplification by FISH analysis. PMID:23327903

Problems encountered when defining Arctic amplification as a ratio.

PubMed

Hind, Alistair; Zhang, Qiong; Brattström, Gudrun

2016-07-27

In climate change science the term 'Arctic amplification' has become synonymous with an estimation of the ratio of a change in Arctic temperatures compared with a broader reference change under the same period, usually in global temperatures. Here, it is shown that this definition of Arctic amplification comes with a suite of difficulties related to the statistical properties of the ratio estimator itself. Most problematic is the complexity of categorizing uncertainty in Arctic amplification when the global, or reference, change in temperature is close to 0 over a period of interest, in which case it may be impossible to set bounds on this uncertainty. An important conceptual distinction is made between the 'Ratio of Means' and 'Mean Ratio' approaches to defining a ratio estimate of Arctic amplification, as they do not only possess different uncertainty properties regarding the amplification factor, but are also demonstrated to ask different scientific questions. Uncertainty in the estimated range of the Arctic amplification factor using the latest global climate models and climate forcing scenarios is expanded upon and shown to be greater than previously demonstrated for future climate projections, particularly using forcing scenarios with lower concentrations of greenhouse gases.

Detection of mycobacterium tuberculosis in paraffin-embedded pleural biopsy specimens by commercial ribosomal RNA and DNA amplification kits.

PubMed

Ruiz-Manzano, J; Manterola, J M; Gamboa, F; Calatrava, A; Monsó, E; Martínez, C; Ausina, V

2000-09-01

To evaluate the utility of two gene amplification systems in historical paraffin-embedded pleural biopsy (PEB) tissues from patients with pleural tuberculosis, and to compare the results to those obtained with conventional histologic and microbiological methods. A retrospective study. Seventy-four formalin-fixed PEB tissues collected and stored over 12 years (1984 through 1995) were retrieved. Gene amplifications were performed in 57 tissues from patients with diagnoses of pleural tuberculosis and in 17 from patients with carcinoma as controls, using the first version of the Amplified Mycobacterium tuberculosis Direct Test (AMTDT; Gen-Probe; San Diego, CA) and the LCx Mycobacterium tuberculosis Assay (LCxMTB; Abbott Laboratories; Abbott Park, IL). The sensitivities of the AMTDT and LCxMTB were 52.6% and 63.2%, respectively (p = not statistically significant). The specificity of both tests was 100%. Twenty tissue samples (35.1%) were positive by both systems, and 10 tissues (17.5%) were positive only by the AMTDT, while 16 tissues (28.1%) were positive only by the LCxMTB. Both tests gave negative results for 11 specimens (19.3%). When both tests were used, a positive diagnosis was achieved in 80.7% of the samples. Diagnosis of 73.7% of patient conditions had previously been made by smear examination of pleural biopsy and sputum, pleural liquid, or biopsy culture. The overall diagnostic yield with both culture and amplification techniques was 96.5% (55 of 57 patients) for pleural tuberculosis, with amplification techniques adding 22.8% of the diagnoses. Amplification techniques are useful in archival PEB tissues, providing additional diagnoses beyond culturing, although the sensitivity should be improved, possibly by standardizing protocols.

Amplification of seismic waves by the Seattle basin, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.; Weaver, C.S.; Creager, K.C.; Snelson, C.M.; Crosson, R.S.; Miller, K.C.; Trehu, A.M.

2003-01-01

Recordings of the 1999 Mw 7.6 Chi-Chi (Taiwan) earthquake, two local earthquakes, and five blasts show seismic-wave amplification over a large sedimentary basin in the U.S. Pacific Northwest. For weak ground motions from the Chi-Chi earthquake, the Seattle basin amplified 0.2- to 0.8-Hz waves by factors of 8 to 16 relative to bedrock sites west of the basin. The amplification and peak frequency change during the Chi-Chi coda: the initial S-wave arrivals (0-30 sec) had maximum amplifications of 12 at 0.5-0.8 Hz, whereas later arrivals (35-65 sec) reached amplifications of 16 at 0.3-0.5 Hz. Analysis of local events in the 1.0- to 10.0-Hz frequency range show fourfold amplifications for 1.0-Hz weak ground motion over the Seattle basin. Amplifications decrease as frequencies increase above 1.0 Hz, with frequencies above 7 Hz showing lower amplitudes over the basin than at bedrock sites. Modeling shows that resonance in low-impedance deposits forming the upper 550 m of the basin beneath our profile could cause most of the observed amplification, and the larger amplification at later arrival times suggests surface waves also play a substantial role. These results emphasize the importance of shallow deposits in determining ground motions over large basins.

Fission yield measurements at IGISOL

NASA Astrophysics Data System (ADS)

Lantz, M.; Al-Adili, A.; Gorelov, D.; Jokinen, A.; Kolhinen, V. S.; Mattera, A.; Moore, I.; Penttilä, H.; Pomp, S.; Prokofiev, A. V.; Rakopoulos, V.; Rinta-Antila, S.; Simutkin, V.; Solders, A.

2016-06-01

The fission product yields are an important characteristic of the fission process. In fundamental physics, knowledge of the yield distributions is needed to better understand the fission process. For nuclear energy applications good knowledge of neutroninduced fission-product yields is important for the safe and efficient operation of nuclear power plants. With the Ion Guide Isotope Separator On-Line (IGISOL) technique, products of nuclear reactions are stopped in a buffer gas and then extracted and separated by mass. Thanks to the high resolving power of the JYFLTRAP Penning trap, at University of Jyväskylä, fission products can be isobarically separated, making it possible to measure relative independent fission yields. In some cases it is even possible to resolve isomeric states from the ground state, permitting measurements of isomeric yield ratios. So far the reactions U(p,f) and Th(p,f) have been studied using the IGISOL-JYFLTRAP facility. Recently, a neutron converter target has been developed utilizing the Be(p,xn) reaction. We here present the IGISOL-technique for fission yield measurements and some of the results from the measurements on proton induced fission. We also present the development of the neutron converter target, the characterization of the neutron field and the first tests with neutron-induced fission.

Strand Invasion Based Amplification (SIBA®): a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

PubMed

Hoser, Mark J; Mansukoski, Hannu K; Morrical, Scott W; Eboigbodin, Kevin E

2014-01-01

Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR) in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA). SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO) into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

Influence of biochemical composition during hydrothermal liquefaction of algae on product yields and fuel properties.

PubMed

Shakya, Rajdeep; Adhikari, Sushil; Mahadevan, Ravishankar; Shanmugam, Saravanan R; Nam, Hyungseok; Hassan, El Barbary; Dempster, Thomas A

2017-11-01

Hydrothermal liquefaction (HTL) of nine algae species were performed at two reaction temperatures (280 and 320°C) to compare the effect of their biomass composition on product yields and properties. Results obtained after HTL indicate large variations in terms of bio-oil yields and its properties. The maximum bio-oil yield (66wt%) was obtained at 320°C with a high lipid containing algae Nannochloropsis. The higher heating value of bio-oils ranged from 31 to 36MJ/kg and around 50% of the bio-oils was in the vacuum gas oil range while high lipid containing algae Nannochloropsis contained a significant portion (33-42%) in the diesel range. A predictive relationship between bio-oil yields and biochemical compositions was developed and showed a broad agreement between predictive and experimental yields. The aqueous phases obtained had high amount of TOC (12-43g/L), COD (35-160g/L), TN (1-18g/L), ammonium (0.34-12g/L) and phosphate (0.7-12g/L). Copyright © 2017 Elsevier Ltd. All rights reserved.

Breeding cassava for higher yield

USDA-ARS?s Scientific Manuscript database

Cassava is a root crop grown for food and for starch production. Breeding progress is slowed by asexual production and high levels of heterozygosity. Germplasm resources are rich and accessible to breeders through genebanks worldwide. Breeding objectives include high root yield, yield stability, dis...

Sequence independent amplification of DNA

DOEpatents

Bohlander, S.K.

1998-03-24

The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

Sequence independent amplification of DNA

DOEpatents

Bohlander, Stefan K.

1998-01-01

The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

Yields of short-lived fission products produced following {sup 235}U(n{sub th},f)

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

Tipnis, S.V.; Campbell, J.M.; Couchell, G.P.

1998-08-01

Measurements of gamma-ray spectra, following the thermal neutron fission of {sup 235}U have been made using a high purity germanium detector at the University of Massachusetts Lowell (UML) Van de Graaff facility. The gamma spectra were measured at delay times ranging from 0.2 s to nearly 10thinsp000 s following the rapid transfer of the fission fragments with a helium-jet system. On the basis of the known gamma transitions, forty isotopes have been identified and studied. By measuring the relative intensities of these transitions, the relative yields of the various precursor nuclides have been calculated. The results are compared with themore » recommended values listed in the ENDF/B-VI fission product data base (for the lifetimes and the relative yields) and those published in the Nuclear Data Sheets (for the beta branching ratios). This information is particularly useful for the cases of short-lived fission products with lifetimes of the order of fractions of a second or a few seconds. Independent yields of many of these isotopes have rather large uncertainties, some of which have been reduced by the present study. {copyright} {ital 1998} {ital The American Physical Society}« less

Rapid and Sensitive Detection of Norovirus Genomes in Oysters by a Two-Step Isothermal Amplification Assay System Combining Nucleic Acid Sequence-Based Amplification and Reverse Transcription-Loop-Mediated Isothermal Amplification Assays▿

PubMed Central

Fukuda, Shinji; Sasaki, Yukie; Seno, Masato

2008-01-01

We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h. PMID:18456857

HARP targets pion production cross section and yield measurements: Implications for MiniBooNE neutrino flux

NASA Astrophysics Data System (ADS)

Wickremasinghe, Don Athula Abeyarathna

The prediction of the muon neutrino flux from a 71.0 cm long beryllium target for the MiniBooNE experiment is based on a measured pion production cross section which was taken from a short beryllium target (2.0 cm thick - 5% nuclear interaction length) in the Hadron Production (HARP) experiment at CERN. To verify the extrapolation to our longer target, HARP also measured the pion production from 20.0 cm and 40.0 cm beryllium targets. The measured production yields on targets of 50% and 100% nuclear interaction lengths in the kinematic rage of momentum from 0.75 GeV/c to 6.5 GeV/c and the range of angle from 30 mrad to 210 mrad are presented along with an update of the short target cross sections. The best fitted extended Sanford-Wang (SW) model parameterization for updated short beryllium target positive pion production cross section is presented. Yield measurements for all three targets are also compared with that from the Monte Carlo predictions in the MiniBooNE experiment for different SW parameterization. The comparisons of muon neutrino flux predictions for updated SW model is presented.

How changes of climate extremes affect summer and winter crop yields and water productivity in the southeast USA

NASA Astrophysics Data System (ADS)

Tian, D.; Cammarano, D.

2017-12-01

Modeling changes of crop production at regional scale is important to make adaptation measures for sustainably food supply under global change. In this study, we explore how changing climate extremes in the 20th and 21st century affect maize (summer crop) and wheat (winter crop) yields in an agriculturally important region: the southeast United States. We analyze historical (1950-1999) and projected (2006-2055) precipitation and temperature extremes by calculating the changes of 18 climate extreme indices using the statistically downscaled CMIP5 data from 10 general circulation models (GCMs). To evaluate how these climate extremes affect maize and wheat yields, historical baseline and projected maize and wheat yields under RCP4.5 and RCP8.5 scenarios are simulated using the DSSAT-CERES maize and wheat models driven by the same downscaled GCMs data. All of the changes are examined at 110 locations over the study region. The results show that most of the precipitation extreme indices do not have notable change; mean precipitation, precipitation intensity, and maximum 1-day precipitation are generally increased; the number of rainy days is decreased. The temperature extreme indices mostly showed increased values on mean temperature, number of high temperature days, diurnal temperature range, consecutive high temperature days, maximum daily maximum temperature, and minimum daily minimum temperature; the number of low temperature days and number of consecutive low temperature days are decreased. The conditional probabilistic relationships between changes in crop yields and changes in extreme indices suggested different responses of crop yields to climate extremes during sowing to anthesis and anthesis to maturity periods. Wheat yields and crop water productivity for wheat are increased due to an increased CO2 concentration and minimum temperature; evapotranspiration, maize yields, and crop water productivity for wheat are decreased owing to the increased temperature

High yield cell-free production of integral membrane proteins without refolding or detergents.

PubMed

Wuu, Jessica J; Swartz, James R

2008-05-01

Integral membrane proteins act as critical cellular components and are important drug targets. However, difficulties in producing membrane proteins have hampered investigations of structure and function. In vivo production systems are often limited by cell toxicity, and previous in vitro approaches have required unnatural folding pathways using detergents or lipid solutions. To overcome these limitations, we present an improved cell-free expression system which produces high yields of integral membrane proteins without the use of detergents or refolding steps. Our cell-free reaction activates an Escherichia coli-derived cell extract for transcription and translation. Purified E. coli inner membrane vesicles supply membrane-bound components and the lipid environment required for insertion and folding. Using this system, we demonstrated successful synthesis of two complex integral membrane transporters, the tetracycline pump (TetA) and mannitol permease (MtlA), in yields of 570+/-50 microg/mL and 130+/-30 microg/mL of vesicle-associated protein, respectively. These yields are up to 400 times typical in vivo concentrations. Insertion and folding of these proteins are verified by sucrose flotation, protease digestion, and activity assays. Whereas TetA incorporates efficiently into vesicle membranes with over two-thirds of the synthesized protein being inserted, MtlA yields appear to be limited by insufficient concentrations of a membrane-associated chaperone.

THE GAS PHASE REACTION OF OZONE WITH 1,3-BUTADIENE: FORMATION YIELDS OF SOME TOXIC PRODUCTS. (R826236)

EPA Science Inventory

The formation yields of acrolein, 1,2-epoxy-3-butene and OH radicals have been measured from reaction of ozone with 1,3-butadiene at room temperature and atmosphere pressure. 1,3,5-Trimethyl benzene was added to scavenge OH radicals in measurements of product yields. In separa...

Topographical and geological amplification: case studies and engineering implications

USGS Publications Warehouse

Celebi, M.

1991-01-01

Topographical and geological amplification that occurred during past earthquakes are quantified using spectral ratios of recorded motions. Several cases are presented from the 1985 Chilean and Mexican earthquakes as well as the 1983 Coalinga (California) and 1987 Supersition Hills (California) earthquake. The strong motions recorded in Mexico City during the 1985 Michoacan earthquake are supplemented by ambient motions recorded within Mexico City to quantify the now well known resonating frequencies of the Mexico City lakebed. Topographical amplification in Canal Beagle (Chile), Coalinga and Superstition Hills (California) are quantified using the ratios derived from the aftershocks following the earthquakes. A special dense array was deployed to record the aftershocks in each case. The implications of both geological and topographical amplification are discussed in light of current code provisions. The observed geological amplifications has already influenced the code provisions. Suggestions are made to the effect that the codes should include further provisions to take the amplification due to topography into account. ?? 1991.

Embryo Sexing and Sex Chromosomal Chimerism Analysis by Loop-Mediated Isothermal Amplification in Cattle and Water Buffaloes

PubMed Central

HIRAYAMA, Hiroki; KAGEYAMA, Soichi; MORIYASU, Satoru; SAWAI, Ken; MINAMIHASHI, Akira

2013-01-01

Abstract In domestic animals of the family Bovidae, sex preselection of offspring has been demanded for convenience of milk/beef production and animal breeding. Development of the nonsurgical embryo transfer technique and sexing methods of preimplantation embryos made it possible. Sexing based on detection of Y chromosome-specific DNA sequences is considered the most reliable method to date. PCR enables amplification of a target sequence from a small number of blastomeres. However, it requires technical skill and is time consuming. Furthermore, PCR has the risk of false positives because of DNA contamination during handling of the PCR products in duplicate PCR procedures and/or electrophoresis. Therefore, for embryo sexing to become widely used in the cattle embryo transfer industry, a simple, rapid and precise sexing method needs to be developed. Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method, and the reaction is carried out under isothermal conditions (range, 60 to 65 C) using DNA polymerase with strand displacement activity. When the target DNA is amplified by LAMP, a white precipitate derived from magnesium pyrophosphate (a by-product of the LAMP reaction) is observed. It is noteworthy that LAMP does not need special reagents or electrophoresis to detect the amplified DNA. This review describes the development and application of an embryo sexing method using LAMP in cattle and water buffaloes. PMID:23965599

Monash Chemical Yields Project (Monχey) Element production in low- and intermediate-mass stars

NASA Astrophysics Data System (ADS)

Doherty, Carolyn; Lattanzio, John; Angelou, George; Campbell, Simon W.; Church, Ross; Constantino, Thomas; Cristallo, Sergio; Gil-Pons, Pilar; Karakas, Amanda; Lugaro, Maria; Stancliffe, Richard

The Monχey project will provide a large and homogeneous set of stellar yields for the low- and intermediate- mass stars and has applications particularly to galactic chemical evolution modelling. We describe our detailed grid of stellar evolutionary models and corresponding nucleosynthetic yields for stars of initial mass 0.8 M⊙ up to the limit for core collapse supernova (CC-SN) ~ 10 M⊙. Our study covers a broad range of metallicities, ranging from the first, primordial stars (Z = 0) to those of super-solar metallicity (Z = 0.04). The models are evolved from the zero-age main-sequence until the end of the asymptotic giant branch (AGB) and the nucleosynthesis calculations include all elements from H to Bi. A major innovation of our work is the first complete grid of heavy element nucleosynthetic predictions for primordial AGB stars as well as the inclusion of extra-mixing processes (in this case thermohaline) during the red giant branch. We provide a broad overview of our results with implications for galactic chemical evolution as well as highlight interesting results such as heavy element production in dredge-out events of super-AGB stars. We briefly introduce our forthcoming web-based database which provides the evolutionary tracks, structural properties, internal/surface nucleosynthetic compositions and stellar yields. Our web interface includes user- driven plotting capabilities with output available in a range of formats. Our nucleosynthetic results will be available for further use in post processing calculations for dust production yields.

Direct Fluorescence Detection of Allele-Specific PCR Products Using Novel Energy-Transfer Labeled Primers.

PubMed

Winn-Deen

1998-12-01

Background: Currently analysis of point mutations can be done by allele-specific polymerase chain reaction (PCR) followed by gel analysis or by gene-specific PCR followed by hybridization with an allele-specific probe. Both of these mutation detection methods require post-PCR laboratory time and run the risk of contaminating subsequent experiments with the PCR product liberated during the detection step. The author has combined the PCR amplification and detection steps into a single procedure suitable for closed-tube analysis. Methods and Results: Allele-specific PCR primers were designed as Sunrise energy-transfer primers and contained a 3' terminal mismatch to distinguish between normal and mutant DNA. Cloned normal (W64) and mutant (R64) templates of the beta3-adrenergic receptor gene were tested to verify amplification specificity and yield. A no-target negative control was also run with each reaction. After PCR, each reaction was tested for fluorescence yield by measuring fluorescence on a spectrofluorimeter or fluorescent microtitreplate reader. The cloned controls and 24 patient samples were tested for the W64R mutation by two methods. The direct fluorescence results with the Sunrise allele-specific PCR method gave comparable genotypes to those obtained with the PCR/ restriction digest/gel electrophoresis control method. No PCR artifacts were observed in the negative controls or in the PCR reactions run with the mismatched target. Conclusions: The results of this pilot study indicate good PCR product and fluorescence yield from allele-specific energy-transfer labeled primers, and the capability of distinguishing between normal and mutant alleles based on fluorescence alone, without the need for restriction digestion, gel electrophoresis, or hybridization with an allele-specific probe.

Point of care nucleic acid detection of viable pathogenic bacteria with isothermal RNA amplification based paper biosensor

NASA Astrophysics Data System (ADS)

Liu, Hongxing; Xing, Da; Zhou, Xiaoming

2014-09-01

Food-borne pathogens such as Listeria monocytogenes have been recognized as a major cause of human infections worldwide, leading to substantial health problems. Food-borne pathogen identification needs to be simpler, cheaper and more reliable than the current traditional methods. Here, we have constructed a low-cost paper biosensor for the detection of viable pathogenic bacteria with the naked eye. In this study, an effective isothermal amplification method was used to amplify the hlyA mRNA gene, a specific RNA marker in Listeria monocytogenes. The amplification products were applied to the paper biosensor to perform a visual test, in which endpoint detection was performed using sandwich hybridization assays. When the RNA products migrated along the paper biosensor by capillary action, the gold nanoparticles accumulated at the designated Test line and Control line. Under optimized experimental conditions, as little as 0.5 pg/μL genomic RNA from Listeria monocytogenes could be detected. The whole assay process, including RNA extraction, amplification, and visualization, can be completed within several hours. The developed method is suitable for point-of-care applications to detect food-borne pathogens, as it can effectively overcome the false-positive results caused by amplifying nonviable Listeria monocytogenes.

Describing Site Amplification for Surface Waves in Realistic Basins

NASA Astrophysics Data System (ADS)

Bowden, D. C.; Tsai, V. C.

2017-12-01

Standard characterizations of site-specific site response assume a vertically-incident shear wave; given a 1D velocity profile, amplification and resonances can be calculated based on conservation of energy. A similar approach can be applied to surface waves, resulting in an estimate of amplification relative to a hard rock site that is different in terms of both amount of amplification and frequency. This prediction of surface-wave site amplification has been well validated through simple simulations, and in this presentation we explore the extent to which a 1D profile can explain observed amplifications in more realistic scenarios. Comparisons of various simple 2D and 3D simulations, for example, allow us to explore the effect of different basin shapes and the relative importance of effects such as focusing, conversion of wave-types and lateral surface wave resonances. Additionally, the 1D estimates for vertically-incident shear waves and for surface waves are compared to spectral ratios of historic events in deep sedimentary basins to demonstrate the appropriateness of the two different predictions. This difference in amplification responses between the wave types implies that a single measurement of site response, whether analytically calculated from 1D models or empirically observed, is insufficient for regions where surface waves play a strong role.

Whole-genome multiple displacement amplification from single cells.

PubMed

Spits, Claudia; Le Caignec, Cédric; De Rycke, Martine; Van Haute, Lindsey; Van Steirteghem, André; Liebaers, Inge; Sermon, Karen

2006-01-01

Multiple displacement amplification (MDA) is a recently described method of whole-genome amplification (WGA) that has proven efficient in the amplification of small amounts of DNA, including DNA from single cells. Compared with PCR-based WGA methods, MDA generates DNA with a higher molecular weight and shows better genome coverage. This protocol was developed for preimplantation genetic diagnosis, and details a method for performing single-cell MDA using the phi29 DNA polymerase. It can also be useful for the amplification of other minute quantities of DNA, such as from forensic material or microdissected tissue. The protocol includes the collection and lysis of single cells, and all materials and steps involved in the MDA reaction. The whole procedure takes 3 h and generates 1-2 microg of DNA from a single cell, which is suitable for multiple downstream applications, such as sequencing, short tandem repeat analysis or array comparative genomic hybridization.

7 CFR 1437.102 - Yield determinations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Determining Yield Coverage Using Actual Production History § 1437.102 Yield determinations. (a) An actual... used in the actual production history base period when less than four consecutive crop years of actual... calculated, in the actual production history base period when the producer reports acreage for the crop but...

7 CFR 1437.102 - Yield determinations.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Determining Yield Coverage Using Actual Production History § 1437.102 Yield determinations. (a) An actual... used in the actual production history base period when less than four consecutive crop years of actual... calculated, in the actual production history base period when the producer reports acreage for the crop but...

7 CFR 1437.102 - Yield determinations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Determining Yield Coverage Using Actual Production History § 1437.102 Yield determinations. (a) An actual... used in the actual production history base period when less than four consecutive crop years of actual... calculated, in the actual production history base period when the producer reports acreage for the crop but...

ESR1 gene amplification in endometrial carcinomas: a clinicopathological analysis.

PubMed

Rahman, Mohammed Tanjimur; Nakayama, Kentaro; Rahman, Munmun; Ishikawa, Masako; Katagiri, Hiroshi; Katagiri, Atsuko; Ishibashi, Tomoka; Sato, Emi; Iida, Kouji; Ishikawa, Noriyuki; Nakayama, Naomi; Miyazaki, Kohji

2013-09-01

This study investigated the clinicopathological significance of estrogen receptor 1 (ESR1) gene amplification and its relationship to phosphatase and tensin homolog (PTEN), human epidermal growth factor receptor 2 (HER2), MutL homolog 1 (MLH1), p53, and AT rich interactive domain 1A (ARID1A) expression in endometrial carcinomas. ESR1 amplification and expression were assessed by fluorescence in situ hybridization and immunohistochemistry. Clinical data were collected by retrospective chart review. ESR1 amplification was identified in 13 out of 111 (11.7%) endometrial carcinomas. No significant association was observed between ESR1 amplification and International Federation of Gynecology and Obstetrics (FIGO) stage (p=0.17), histological grade (p=0.35), lymph node metastasis (p=0.51), or deep myometrial invasion (p=0.46). ESR1 amplification was independent of PTEN, p53, HER2, MLH1, and ARID1A protein expression. Patients without estrogen receptor (ER) or progesterone receptor (PR) expression had shorter progression-free and overall survival than those with ER or PR expression (p<0.01). ESR1 amplification is independent of known clinicopathological factors related to poor prognosis and PTEN, p53, HER2, MLH1, and ARID1A protein expression, suggesting ESR1 amplification may be an early event in endometrial carcinoma development.

Water productivity, yield, and berry composition in sustained versus regulated deficit irrigation of Merlot grapevines

USDA-ARS?s Scientific Manuscript database

The wine grape cultivar Merlot (Vitis vinifera L.) was irrigated at incremental fractions of estimated crop evapotranspiration or a regulated deficit (RDI) regime to identify which practice best optimized water productivity and berry composition without compromising yield. Three severities of susta...

Dry matter yields and quality of forages derived from grass species and organic production methods (year 111).

PubMed

Pholsen, S; Rodchum, P; Higgs, D E B

2014-07-01

This third year work was carried on at Khon Kaen University during the 2008-2009 to investigate dry matter yields of grass, grass plus legumes, grown on Korat soil series (Oxic Paleustults). The experiment consisted of twelve-treatment combinations of a 3x4 factorial arranged in a Randomized Complete Block Design (RCBD) with four replications. The results showed that Dry Matter Yields (DMY) of Ruzi and Guinea grass were similar with mean values of 6,585 and 6,130 kg ha(-1) whilst Napier gave the lowest (884 kg ha(-1)). With grass plus legume, grass species and production methods gave highly significant dry matter yields where Guinea and Ruzi gave dry matter yields of 7,165 and 7,181 kg ha(-1), respectively and Napier was the least (2,790 kg ha(-1)). The production methods with the use of cattle manure gave the highest DMY (grass alone) of 10,267 kg ha(-1) followed by Wynn and Verano with values of 6,064 and 3,623 kg ha(-1), respectively. Guinea plus cattle manure gave the highest DMY of 14,599 kg ha(-1) whilst Ruzi gave 12,977 kg ha(-1). Guinea plus Wynn gave DMY of 7,082 kg ha(-1). Ruzi plus Verano gave DMY of 6,501 kg ha(-1). Forage qualities of crude protein were highest with those grown with grass plus legumes. Some prospects in improving production were discussed.

Label-free thioflavin T/G-quadruplex-based real-time strand displacement amplification for biosensing applications.

PubMed

Du, Yi-Chen; Zhu, Li-Na; Kong, De-Ming

2016-12-15

To promote application of strand-displacement amplification (SDA) techniques in biosensing, a label-free, real-time monitoring strategy for isothermal nucleic acid amplification reactions was designed. G-quadruplex structures were introduced into SDA products using specific recognition of G-quadruplexes by the fluorogenic dye thioflavin T. Performance was good for real-time monitoring of traditional SDA by a linear-amplification mechanism and for exponential cross-triggered SDA amplification. The strategy worked on a commercial real-time PCR instrument, making it suitable for biosensing platforms. As examples, two highly sensitive and specific biosensors were designed for analysis of the activity of uracil-DNA glycosylase (UDG) and the restriction endonuclease EcoRI. Detection limits were 6×10(-5)U/mL for UDG and 0.016U/mL for EcoRI. Detection of corresponding targets in complex matrices such as cell lysates or human serum was also demonstrated. Compared to traditional end-point detection methods, real-time SDA-based approaches have the advantages of simple, fast operation; high sensitivity; low risk of carryover contamination; and very high throughput. The introduction of real-time monitoring strategies may promote application of SDA reactions in biosensor design. Copyright © 2016 Elsevier B.V. All rights reserved.

A comprehensive assessment of the correlations between field crop yields and commonly used MODIS products

NASA Astrophysics Data System (ADS)

Johnson, David M.

2016-10-01

An exploratory assessment was undertaken to determine the correlation strength and optimal timing of several commonly used Moderate Resolution Imaging Spectroradiometer (MODIS) composited imagery products against crop yields for 10 globally significant agricultural commodities. The crops analyzed included barley, canola, corn, cotton, potatoes, rice, sorghum, soybeans, sugarbeets, and wheat. The MODIS data investigated included the Normalized Difference Vegetation Index (NDVI), Fraction of Photosynthetically Active Radiation (FPAR), Leaf Area Index (LAI), and Gross Primary Production (GPP), in addition to daytime Land Surface Temperature (DLST) and nighttime LST (NLST). The imagery utilized all had 8-day time intervals, but NDVI had a 250 m spatial resolution while the other products were 1000 m. These MODIS datasets were also assessed from both the Terra and Aqua satellites, with their differing overpass times, to document any differences. A follow-on analysis, using the Terra 250 m NDVI data as a benchmark, looked at the yield prediction utility of NDVI at two spatial scales (250 m vs. 1000 m), two time precisions (8-day vs. 16-day), and also assessed the Enhanced Vegetation Index (EVI, at 250 m, 16-day). The analyses spanned the major farming areas of the United States (US) from the summers of 2008-2013 and used annual county-level average crop yield data from the US Department of Agriculture as a basis. All crops, except rice, showed at least some positive correlations to each of the vegetation related indices in the middle of the growing season, with NDVI performing slightly better than FPAR. LAI was somewhat less strongly correlated and GPP weak overall. Conversely, some of the crops, particularly canola, corn, and soybeans, also showed negative correlations to DLST mid-summer. NLST, however, was never correlated to crop yield, regardless of the crop or seasonal timing. Differences between the Terra and Aqua results were found to be minimal. The 1000 m

Backward Raman amplification in the long-wavelength infrared

NASA Astrophysics Data System (ADS)

Johnson, L. A.; Gordon, D. F.; Palastro, J. P.; Hafizi, B.

2017-03-01

The wealth of work in backward Raman amplification in plasma has focused on the extreme intensity limit; however, backward Raman amplification may also provide an effective and practical mechanism for generating intense, broad bandwidth, long-wavelength infrared radiation (LWIR). An electromagnetic simulation coupled with a relativistic cold fluid plasma model is used to demonstrate the generation of picosecond pulses at a wavelength of 10 μm with terawatt powers through backward Raman amplification. The effects of collisional damping, Landau damping, pump depletion, and wave breaking are examined, as well as the resulting design considerations for an LWIR Raman amplifier.

Fission Product Yields from {sup 232}Th, {sup 238}U, and {sup 235}U Using 14 MeV Neutrons

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

Pierson, B.D., E-mail: bpnuke@umich.edu; Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352; Greenwood, L.R.

Neutron-induced fission yield studies using deuterium-tritium fusion-produced 14 MeV neutrons have not yet directly measured fission yields from fission products with half-lives on the order of seconds (far from the line of nuclear stability). Fundamental data of this nature are important for improving and validating the current models of the nuclear fission process. Cyclic neutron activation analysis (CNAA) was performed on three actinide targets–thorium-oxide, depleted uranium metal, and highly enriched uranium metal–at the University of Michigan's Neutron Science Laboratory (UM-NSL) using a pneumatic system and Thermo-Scientific D711 accelerator-based fusion neutron generator. This was done to measure the fission yields ofmore » short-lived fission products and to examine the differences between the delayed fission product signatures of the three actinides. The measured data were compared against previously published results for {sup 89}Kr, −90, and −92 and {sup 138}Xe, −139, and −140. The average percent deviation of the measured values from the Evaluated Nuclear Data Files VII.1 (ENDF/B-VII.1) for thorium, depleted-uranium, and highly-enriched uranium were −10.2%, 4.5%, and −12.9%, respectively. In addition to the measurements of the six known fission products, 23 new fission yield measurements from {sup 84}As to {sup 146}La are presented.« less

Amplification, Redundancy, and Quantum Chernoff Information

NASA Astrophysics Data System (ADS)

Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

2014-04-01

Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the "collapse of the wave packet," and a way to avoid embarrassing problems exemplified by Schrödinger's cat. Such a bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen interpretation. Quantum Darwinism views amplification as replication, in many copies, of the information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. This leads to objective reality via the presence of robust and widely accessible records of selected quantum states. The resulting redundancy (the number of copies deposited in the environment) follows from the quantum Chernoff information that quantifies the information transmitted by a typical elementary subsystem of the environment.

Amplification of hofmeister effect by alcohols.

PubMed

Xu, Yun; Liu, Guangming

2014-07-03

We have demonstrated that Hofmeister effect can be amplified by adding alcohols to aqueous solutions. The lower critical solution temperature behavior of poly(N-isopropylacrylamide) has been employed as the model system to study the amplification of Hofmeister effect. The alcohols can more effectively amplify the Hofmeister effect following the series methanol < ethanol < 1-propanol < 2-propanol for the monohydric alcohols and following the series d-sorbitol ≈ xylitol ≈ meso-erythritol < glycerol < ethylene glycol < methanol for the polyhydric alcohols. Our study reveals that the relative extent of amplification of Hofmeister effect is determined by the stability of the water/alcohol complex, which is strongly dependent on the chemical structure of alcohols. The more stable solvent complex formed via stronger hydrogen bonds can more effectively differentiate the anions through the anion-solvent complex interactions, resulting in a stronger amplification of Hofmeister effect. This study provides an alternative method to tune the relative strength of Hofmeister effect besides salt concentration.

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection.

PubMed

Barreda-García, Susana; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Lobo-Castañón, María Jesús

2018-01-01

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Graphical Abstract Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA).

Stellar feedback strongly alters the amplification and morphology of galactic magnetic fields

NASA Astrophysics Data System (ADS)

Su, Kung-Yi; Hayward, Christopher C.; Hopkins, Philip F.; Quataert, Eliot; Faucher-Giguère, Claude-André; Kereš, Dušan

2018-01-01

Using high-resolution magnetohydrodynamic simulations of idealized, non-cosmological galaxies, we investigate how cooling, star formation and stellar feedback affect galactic magnetic fields. We find that the amplification histories, saturation values and morphologies of the magnetic fields vary considerably depending on the baryonic physics employed, primarily because of differences in the gas density distribution. In particular, adiabatic runs and runs with a subgrid (effective equation of state) stellar feedback model yield lower saturation values and morphologies that exhibit greater large-scale order compared with runs that adopt explicit stellar feedback and runs with cooling and star formation but no feedback. The discrepancies mostly lie in gas denser than the galactic average, which requires cooling and explicit fragmentation to capture. Independent of the baryonic physics included, the magnetic field strength scales with gas density as B ∝ n2/3, suggesting isotropic flux freezing or equipartition between the magnetic and gravitational energies during the field amplification. We conclude that accurate treatments of cooling, star formation and stellar feedback are crucial for obtaining the correct magnetic field strength and morphology in dense gas, which, in turn, is essential for properly modelling other physical processes that depend on the magnetic field, such as cosmic ray feedback.

HARP targets pion production cross section and yield measurements. Implications for MiniBooNE neutrino flux

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

Wickremasinghe, Don Athula Abeyarathna

2015-07-01

The prediction of the muon neutrino flux from a 71.0 cm long beryllium target for the MiniBooNE experiment is based on a measured pion production cross section which was taken from a short beryllium target (2.0 cm thick - 5% nuclear interaction length) in the Hadron Production (HARP) experiment at CERN. To verify the extrapolation to our longer target, HARP also measured the pion production from 20.0 cm and 40.0 cm beryllium targets. The measured production yields, d 2N π± (p; θ )=dpd Ω, on targets of 50% and 100% nuclear interaction lengths in the kinematic rage of momentum frommore » 0.75 GeV/c to 6.5 GeV/c and the range of angle from 30 mrad to 210 mrad are presented along with an update of the short target cross sections. The best fitted extended Sanford-Wang (SW) model parameterization for updated short beryllium target π + production cross section is presented. Yield measurements for all three targets are also compared with that from the Monte Carlo predictions in the MiniBooNE experiment for different SW parameterization. The comparisons of v μ flux predictions for updated SW model is presented.« less

Evaluating a satellite-based seasonal evapotranspiration product and identifying its relationship with other satellite-derived products and crop yield: A case study for Ethiopia

USGS Publications Warehouse

Tadesse, Tsegaye; Senay, Gabriel B.; Berhan, Getachew; Regassa, Teshome; Beyene, Shimelis

2015-01-01

Satellite-derived evapotranspiration anomalies and normalized difference vegetation index (NDVI) products from Moderate Resolution Imaging Spectroradiometer (MODIS) data are currently used for African agricultural drought monitoring and food security status assessment. In this study, a process to evaluate satellite-derived evapotranspiration (ETa) products with a geospatial statistical exploratory technique that uses NDVI, satellite-derived rainfall estimate (RFE), and crop yield data has been developed. The main goal of this study was to evaluate the ETa using the NDVI and RFE, and identify a relationship between the ETa and Ethiopia’s cereal crop (i.e., teff, sorghum, corn/maize, barley, and wheat) yields during the main rainy season. Since crop production is one of the main factors affecting food security, the evaluation of remote sensing-based seasonal ETa was done to identify the appropriateness of this tool as a proxy for monitoring vegetation condition in drought vulnerable and food insecure areas to support decision makers. The results of this study showed that the comparison between seasonal ETa and RFE produced strong correlation (R2 > 0.99) for all 41 crop growing zones in Ethiopia. The results of the spatial regression analyses of seasonal ETa and NDVI using Ordinary Least Squares and Geographically Weighted Regression showed relatively weak yearly spatial relationships (R2 < 0.7) for all cropping zones. However, for each individual crop zones, the correlation between NDVI and ETa ranged between 0.3 and 0.84 for about 44% of the cropping zones. Similarly, for each individual crop zones, the correlation (R2) between the seasonal ETa anomaly and de-trended cereal crop yield was between 0.4 and 0.82 for 76% (31 out of 41) of the crop growing zones. The preliminary results indicated that the ETa products have a good predictive potential for these 31 identified zones in Ethiopia. Decision makers may potentially use ETa products for monitoring cereal

Evaluating a satellite-based seasonal evapotranspiration product and identifying its relationship with other satellite-derived products and crop yield: A case study for Ethiopia

NASA Astrophysics Data System (ADS)

Tadesse, Tsegaye; Senay, Gabriel B.; Berhan, Getachew; Regassa, Teshome; Beyene, Shimelis

2015-08-01

Satellite-derived evapotranspiration anomalies and normalized difference vegetation index (NDVI) products from Moderate Resolution Imaging Spectroradiometer (MODIS) data are currently used for African agricultural drought monitoring and food security status assessment. In this study, a process to evaluate satellite-derived evapotranspiration (ETa) products with a geospatial statistical exploratory technique that uses NDVI, satellite-derived rainfall estimate (RFE), and crop yield data has been developed. The main goal of this study was to evaluate the ETa using the NDVI and RFE, and identify a relationship between the ETa and Ethiopia's cereal crop (i.e., teff, sorghum, corn/maize, barley, and wheat) yields during the main rainy season. Since crop production is one of the main factors affecting food security, the evaluation of remote sensing-based seasonal ETa was done to identify the appropriateness of this tool as a proxy for monitoring vegetation condition in drought vulnerable and food insecure areas to support decision makers. The results of this study showed that the comparison between seasonal ETa and RFE produced strong correlation (R2 > 0.99) for all 41 crop growing zones in Ethiopia. The results of the spatial regression analyses of seasonal ETa and NDVI using Ordinary Least Squares and Geographically Weighted Regression showed relatively weak yearly spatial relationships (R2 < 0.7) for all cropping zones. However, for each individual crop zones, the correlation between NDVI and ETa ranged between 0.3 and 0.84 for about 44% of the cropping zones. Similarly, for each individual crop zones, the correlation (R2) between the seasonal ETa anomaly and de-trended cereal crop yield was between 0.4 and 0.82 for 76% (31 out of 41) of the crop growing zones. The preliminary results indicated that the ETa products have a good predictive potential for these 31 identified zones in Ethiopia. Decision makers may potentially use ETa products for monitoring cereal crop

Effect of different liming levels on the biomass production and essential oil extraction yield of Cunila galioides Benth.

PubMed

Mossi, A J; Pauletti, G F; Rota, L; Echeverrigaray, S; Barros, I B I; Oliveira, J V; Paroul, N; Cansian, R L

2012-11-01

Poejo is an aromatic and medicinal plant native to highland areas of south Brazil, in acid soils with high Al3+ concentration. The main objective of the present work was to evaluate the effect of liming on the extraction yield of essential oil of three chemotypes of poejo (Cunila galioides Benth). For this purpose, the experiments were performed in a greenhouse, using 8-litre pots. The treatments were four dosages of limestone (0, 3.15, 12.5, and 25 g.L(-1)) and a completely random experimental design was used, with four replications and three chemotypes, set up in a 3 × 4 factorial arrangement. The parameters evaluated were dry weight of aerial parts, essential oil content and chemical composition of essential oil. Results showed that liming affects the biomass production, essential oil yield and chemical composition, with cross interaction verified between chemotype and limestone dosage. For the higher dosage lower biomass production, lower yield of essential oil as well as the lowest content of citral (citral chemotype) and limonene (menthene chemotype) was observed. In the ocimene chemotype, no liming influence was observed on the essential oil yield and on the content of major compounds. The dosage of 3.15 g.L(-1) can be considered the best limestone dosage for the production of poejo for the experimental conditions evaluated.

Water consumption, grain yield, and water productivity in response to field water management in double rice systems in China.

PubMed

Wu, Xiao Hong; Wang, Wei; Yin, Chun Mei; Hou, Hai Jun; Xie, Ke Jun; Xie, Xiao Li

2017-01-01

Rice cultivation has been challenged by increasing food demand and water scarcity. We examined the responses of water use, grain yield, and water productivity to various modes of field water managements in Chinese double rice systems. Four treatments were studied in a long-term field experiment (1998-2015): continuous flooding (CF), flooding-midseason drying-flooding (F-D-F), flooding-midseason drying-intermittent irrigation without obvious standing water (F-D-S), and flooding-rain-fed (F-RF). The average precipitation was 483 mm in early-rice season and 397 mm in late-rice season. The irrigated water for CF, F-D-F, F-D-S, and F-RF, respectively, was 263, 340, 279, and 170 mm in early-rice season, and 484, 528, 422, and 206 mm in late-rice season. Grain yield for CF, F-D-F, F-D-S, and F-RF, respectively, was 4,722, 4,597, 4,479, and 4,232 kgha-1 in early-rice season, and 5,420, 5,402, 5,366, and 4,498 kgha-1 in late-rice season. Compared with CF, F-D-F consumed more irrigated water, which still decreased grain yield, leading to a decrease in water productivity by 25% in early-rice season and by 8% in late-rice season. Compared with F-D-F, F-D-S saved much irrigated water with a small yield reduction, leading to an increase in water productivity by 22% in early-rice season and by 26% in late-rice season. The results indicate that CF is best for early-rice and FDS is best for late-rice in terms of grain yield and water productivity.

[Prognostic significance of MYCN amplification in children neuroblastic tumors].

PubMed

Niu, Huilin; Xu, Tao; Wang, Fenghua; Chen, Zhengrong; Gao, Qiu; Yi, Peng; Xia, Jianqing

2015-02-01

To summarize the clinicopathologic features of neuroblastic tumors (NT), and to explore the prognostic significance of MYCN amplification in NT. The clinicopathologic data of 267 NT were reviewed. MYCN gene amplification was detected by fluorescence in situ hybridization (FISH) in 119 cases and the relationship with pathological characteristics and prognostic significance were analyzed. The study included 267 cases of children NT from patients aged from 1 day to 13 years (median 27 months). The male to female ratio was 1.43. There were 38 cases (14.2%), 43 cases (16.1%), 71 cases (26.6%), and 115 cases (43.1%) of INSS stages I, II, III and IV respectively.Favorable histology group had 157 cases (59.9%); unfavorable histology group had 110 cases (40.1%).Of the 119 NT cases with MYCN FISH performed, 18 cases (15.1%) showed amplification and the signal ratio of MYCN to CEP2 was 4.08-43.29. One hundred and one cases of non-amplified MYCN included MYCN gain in 79 cases (66.3%) and MYCN negative in 22 cases (18.5%). MYCN expression showed significant difference (P = 0.000) between ages, gender, NT type and MKI, but not INPC and clinical stage (P > 0.05).Of the 18 cases with MYCN amplification, 3 were undifferentiated, and 15 poorly differentiated; 17 had high MKI and one moderate MKI. All 18 cases were in unfavorable histology group; the overall survival rate was 3/18, with an average survival time of (17.9 ± 2.4) months.Of the 101 MYCN non-amplification cases, the overall survival rate was 68.3% (69/101), with an average survival time of (29.8 ± 1.3) months. Survival analysis showed the cases with MYCN amplification had worse prognosis (P < 0.05). NT were commonly diagnosed in early ages and easily to metastasize. Most of cases with favorable histology. The cases of MYCN amplification showed unfavorable histology, and the majority cases with high MKI; The patients with MYCN gene amplification had poor prognosis.

Increasing plant density in eastern United States broccoli production systems to maximize marketable head yields

USDA-ARS?s Scientific Manuscript database

Increased demand for fresh market broccoli (Brassica oleracea L. var. italica) has led to increased production along the eastern seaboard of the United States. Maximizing broccoli yields is a primary concern for quickly expanding eastern commercial markets. Thus, a plant density study was carried ...

Whole genome amplification of DNA extracted from FFPE tissues.

PubMed

Bosso, Mira; Al-Mulla, Fahd

2011-01-01

Whole genome amplification systems were developed to meet the increasing research demands on DNA resources and to avoid DNA shortage. The technology enables amplification of nanogram amounts of DNA into microgram quantities and is increasingly used in the amplification of DNA from multiple origins such as blood, fresh frozen tissue, formalin-fixed paraffin-embedded tissues, saliva, buccal swabs, bacteria, and plant and animal sources. This chapter focuses on the use of GenomePlex(®) tissue Whole Genome Amplification Kit, to amplify DNA directly from archived tissue. In addition, this chapter documents our unique experience with the utilization of GenomePlex(®) amplified DNA using several molecular techniques including metaphase Comparative Genomic Hybridization, array Comparative Genomic Hybridization, and real-time quantitative polymerase chain reaction assays. GenomePlex(®) is a registered trademark of Rubicon Genomics Incorporation.

The focusing effect in backward Raman amplification in plasma

NASA Astrophysics Data System (ADS)

Li, Zhaoli; Peng, Hao; Zuo, Yanlei; Su, Jingxin; Yang, Suhui

2018-04-01

In this paper, the focusing effect on backward Raman amplification in plasma is investigated. A fluid model, used to simulate the backward Raman amplification and including the relativistic, ponderomotive, and thermal self-focusing and the mutual-focusing effect simultaneously, is proposed and investigated. The focusing effect is shown to severely distort the profile of the seed when the seed intensity was as high as 10 17 W/cm2. Reducing the plasma density can relax the focusing effect, but at the cost of decreasing the amplification efficiency. Changing the profile of the seed has a limited effect on mitigating the focusing effect. A Gaussian profile of the pump and a defocusing shape of the plasma density seem to be an effective way to mitigate the focusing effect without decreasing the amplification efficiency.

Preparation of DNA-containing extract for PCR amplification

DOEpatents

Dunbar, John M.; Kuske, Cheryl R.

2006-07-11

Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

Raman amplification in the coherent wave-breaking regime.

PubMed

Farmer, J P; Pukhov, A

2015-12-01

In regimes far beyond the wave-breaking threshold of Raman amplification, we show that significant amplification can occur after the onset of wave breaking, before phase mixing destroys the coherent coupling between pump, probe, and plasma wave. Amplification in this regime is therefore a transient effect, with the higher-efficiency "coherent wave-breaking" (CWB) regime accessed by using a short, intense probe. Parameter scans illustrate the marked difference in behavior between below wave breaking, in which the energy-transfer efficiency is high but total energy transfer is low, wave breaking, in which efficiency is low, and CWB, in which moderate efficiencies allow the highest total energy transfer.

Comparison of three DNA extraction kits to establish maximum yield and quality of coral-associated microbial DNA

USGS Publications Warehouse

Baker, Erin J.; Kellogg, Christina A.

2014-01-01

Coral microbiology is an expanding field, yet there is no standard DNA extraction protocol. Although many researchers depend on commercial extraction kits, no specific kit has been optimized for use with coral samples. Both soil and plant DNA extraction kits from MO BIO Laboratories, Inc., have been used by many research groups for this purpose. MO BIO recently replaced their PowerPlant® kit with an improved PowerPlantPro kit, but it was unclear how these changes would affect the kit’s use with coral samples. In order to determine which kit produced the best results, we conducted a comparison between the original PowerPlant kit, the new PowerPlantPro kit, and an alternative kit, PowerSoil, using samples from several different coral genera. The PowerPlantPro kit had the highest DNA yields, but the lack of 16S rRNA gene amplification in many samples suggests that much of the yield may be coral DNA rather than microbial DNA. The most consistent positive amplifications came from the PowerSoil kit.

Topoisomerase expression and amplification in solid tumours: Analysis of 24,262 patients

PubMed Central

Heestand, Gregory M.; Schwaederle, Maria; Gatalica, Zoran; Arguello, David; Kurzrock, Razelle

2017-01-01

Background Topoisomerase I (TOPO1) and topoisomerase IIα (TOP2A) are specific targets of multiple chemotherapy drugs. Increased expression of TOPO1 protein and amplification of the TOP2A gene have been associated with treatment response in colorectal and breast cancers, respectively. TOPO1 and TOP2A may be potential therapeutic targets in other malignancies as well. Summary of methods We analysed TOPO1 protein expression and TOP2A gene amplification in patients (n = 24,262 specimens) with diverse cancers. Since HER2 and TOP2A co-amplification have been investigated for predictive value regarding anthracycline benefit, we analysed specimens for HER2 amplification as well. Results Overexpressed TOPO1 protein was present in 51% of the tumours. Four percent of the tumours had TOP2A amplification, with gallbladder tumours and gastroesophageal/oesophageal tumours having rates over 10%. Overall, 4903 specimens were assessed for both TOP2A and HER2 amplification; 129 (2.6%) had co-amplification. High rates (>40%) of HER2 amplification were seen in patients with TOP2A amplification in breast, ovarian, gastroesophageal/oesophageal and pancreatic cancer. Conclusion Our data indicate that increased TOPO1 expression and TOP2A amplification, as well as HER2 co-alterations, are present in multiple malignancies. The implications of these observations regarding sensitivity to chemotherapy not traditionally administered to these tumour types merits investigation. PMID:28728050

Hybrid chirped pulse amplification system

DOEpatents

Barty, Christopher P.; Jovanovic, Igor

2005-03-29

A hybrid chirped pulse amplification system wherein a short-pulse oscillator generates an oscillator pulse. The oscillator pulse is stretched to produce a stretched oscillator seed pulse. A pump laser generates a pump laser pulse. The stretched oscillator seed pulse and the pump laser pulse are directed into an optical parametric amplifier producing an optical parametric amplifier output amplified signal pulse and an optical parametric amplifier output unconverted pump pulse. The optical parametric amplifier output amplified signal pulse and the optical parametric amplifier output laser pulse are directed into a laser amplifier producing a laser amplifier output pulse. The laser amplifier output pulse is compressed to produce a recompressed hybrid chirped pulse amplification pulse.

Benefits of the fiber optic versus the electret microphone in voice amplification.

PubMed

Kyriakou, Kyriaki; Fisher, Hélène R

2013-01-01

Voice disorders that result in reduced loudness may cause difficulty in communicating, socializing and participating in occupational activities. Amplification is often recommended in order to facilitate functional communication, reduce vocal load and avoid developing maladaptive compensatory behaviours. The most common microphone used with amplification systems is the electret microphone. One alternate form of microphone is the fiber optic microphone. To examine the benefits of the fiber optic (1190S) versus the electret (M04) microphone as measured by objective and subjective parameters in the amplification of a patient's voice with reduced loudness caused by neurological and/or respiratory-based problems. Eighteen patients with vocal fold paralysis, Parkinson's disease and/or chronic obstructive pulmonary disease (COPD) participated in the study. The study contained a measurement of intensity, amplitude perturbation and signal-to-noise ratio during a sustained vowel production and a measurement of intensity during conversation with the use of the two microphones simultaneously. It also included the completion of a questionnaire indicating the patient's satisfaction with each microphone. The fiber optic (1190S) microphone had better objective acoustic performance (i.e. lower amplitude perturbation, higher signal-to-noise ratio and higher intensity) than the electret (M04) microphone. It also had better patient subjective satisfaction (i.e. less conspicuousness, more voice clarity, less acoustic feedback, more loudness and more utilization) than the electret microphone. Patients with neurological and/or respiratory-based voice problems may more confidently and frequently use the fiber optic microphone to communicate, socialize and participate in occupational activities more easily. Speech-language pathologists may more confidently use or recommend the fiber optic microphone with amplification systems. © 2012 Royal College of Speech and Language Therapists.

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification

PubMed Central

Kulshreshtha, Deepika; Gupta, Sangeeta; Singh, Kartar; Bhardwaj, Subhash C.

2018-01-01

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification.

PubMed

Manjunatha, C; Sharma, Sapna; Kulshreshtha, Deepika; Gupta, Sangeeta; Singh, Kartar; Bhardwaj, Subhash C; Aggarwal, Rashmi

2018-01-01

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in

Approaches to Selection and Fitting of Amplification for Infants and Toddlers.

ERIC Educational Resources Information Center

Beauchaine, Kathryn L.

This paper addresses three areas related to amplification for infants and toddlers with hearing impairments: (1) identification issues as they relate to early amplification; (2) selection of amplification; and (3) assessment of aided function. Identification issues discussed include the goal of early identification of hearing loss and the impact…

Yield: it's now an entitlement

NASA Astrophysics Data System (ADS)

George, Bill

1994-09-01

Only a few years ago, the primary method of cost reduction and productivity improvement in the semiconductor industry was increasing manufacturing yields throughout the process. Many of the remarkable reliability improvements realized over the past decade have come about as a result of actions that were originally taken primarily to improve device yields. Obviously, the practice of productivity improvement through yield enhancement is limited to the attainment of 100% yield, at which point some other mechanism must be employed. Traditionally, new products have been introduced to manufacturing at a point of relative immaturity, and semiconductor producers have relied on the traditional `learning curve' method of yield improvement to attain profitable levels of manufacturing yield. Recently, results of a survey of several fabs by a group of University of California at Berkeley researchers in the Competitive Semiconductor Manufacturing Program indicate that most factories learn at about the same rate after startup, in terms of both line yield and defectivity. If this is indeed generally true, then the most competitive factor is the one that starts with the highest yield, and it is difficult to displace a leader once his lead has been established. The two observations made above carry enormous implications for the semiconductor development or manufacturing professional. First, one must achieve very high yields in order to even play the game. Second, the achievement of competitive yields over time in the life of a factory is determined even before the factory is opened, in the planning and development phase. Third, and perhaps most uncomfortable for those of us who have relied on yield improvement as a cost driver, the winners of the nineties will find new levers to drive costs down, having already gotten the benefit of very high yield. This paper looks at the question of how the winners will achieve the critical measures of success, high initial yield and utilization

Problems encountered when defining Arctic amplification as a ratio

PubMed Central

Hind, Alistair; Zhang, Qiong; Brattström, Gudrun

2016-01-01

In climate change science the term ‘Arctic amplification’ has become synonymous with an estimation of the ratio of a change in Arctic temperatures compared with a broader reference change under the same period, usually in global temperatures. Here, it is shown that this definition of Arctic amplification comes with a suite of difficulties related to the statistical properties of the ratio estimator itself. Most problematic is the complexity of categorizing uncertainty in Arctic amplification when the global, or reference, change in temperature is close to 0 over a period of interest, in which case it may be impossible to set bounds on this uncertainty. An important conceptual distinction is made between the ‘Ratio of Means’ and ‘Mean Ratio’ approaches to defining a ratio estimate of Arctic amplification, as they do not only possess different uncertainty properties regarding the amplification factor, but are also demonstrated to ask different scientific questions. Uncertainty in the estimated range of the Arctic amplification factor using the latest global climate models and climate forcing scenarios is expanded upon and shown to be greater than previously demonstrated for future climate projections, particularly using forcing scenarios with lower concentrations of greenhouse gases. PMID:27461918

Limits on amplification by Aharonov-Albert-Vaidman weak measurement

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

Koike, Tatsuhiko; Tanaka, Saki

2011-12-15

We analyze the amplification by the Aharonov-Albert-Vaidman weak quantum measurement on a Sagnac interferometer [Dixon et al., Phys. Rev. Lett. 102, 173601 (2009)] up to all orders of the coupling strength between the measured system and the measuring device. The amplifier transforms a small tilt of a mirror into a large transverse displacement of the laser beam. The conventional analysis has shown that the measured value is proportional to the weak value, so that the amplification can be made arbitrarily large in the cost of decreasing output laser intensity. It is shown that the measured displacement and the amplification factormore » are in fact not proportional to the weak value and rather vanish in the limit of infinitesimal output intensity. We derive the optimal overlap of the pre- and postselected states with which the amplification become maximum. We also show that the nonlinear effects begin to arise in the performed experiments so that any improvements in the experiment, typically with an amplification greater than 100, should require the nonlinear theory in translating the observed value to the original displacement.« less

Microarray-based comparison of three amplification methods for nanogram amounts of total RNA

PubMed Central

Singh, Ruchira; Maganti, Rajanikanth J.; Jabba, Sairam V.; Wang, Martin; Deng, Glenn; Heath, Joe Don; Kurn, Nurith; Wangemann, Philine

2007-01-01

Gene expression profiling using microarrays requires microgram amounts of RNA, which limits its direct application for the study of nanogram RNA samples obtained using microdissection, laser capture microscopy, or needle biopsy. A novel system based on Ribo-SPIA technology (RS, Ovation-Biotin amplification and labeling system) was recently introduced. The utility of the RS system, an optimized prototype system for picogram RNA samples (pRS), and two T7-based systems involving one or two rounds of amplification (OneRA, Standard Protocol, or TwoRA, Small Sample Prototcol, version II) were evaluated in the present study. Mouse kidney (MK) and mouse universal reference (MUR) RNA samples, 0.3 ng to 10 μg, were analyzed using high-density Affymetrix Mouse Genome 430 2.0 GeneChip arrays. Call concordance between replicates, correlations of signal intensity, signal intensity ratios, and minimal fold increase necessary for significance were determined. All systems amplified partially overlapping sets of genes with similar signal intensity correlations. pRS amplified the highest number of genes from 10-ng RNA samples. We detected 24 of 26 genes verified by RT-PCR in samples prepared using pRS. TwoRA yielded somewhat higher call concordances than did RS and pRS (91.8% vs. 89.3% and 88.1%, respectively). Although all target preparation methods were suitable, pRS amplified the highest number of targets and was found to be suitable for amplification of as little as 0.3 ng of total RNA. In addition, RS and pRS were faster and simpler to use than the T7-based methods and resulted in the generation of cDNA, which is more stable than cRNA. PMID:15613496

Mass-yield distributions of fission products in bremsstrahlung-induced fission of 232Th

NASA Astrophysics Data System (ADS)

Naik, H.; Kim, G. N.; Kim, K.

2018-01-01

The cumulative yields of various fission products within the 77-153 mass regions in the 2.5-GeV bremsstrahlung-induced fission of 232Th have been determined by using the recoil catcher and an off-line γ-ray spectrometric technique at the Pohang Accelerator Laboratory, Korea. The mass-yield distributions were obtained from the cumulative yields after charge-distribution corrections. The peak-to-valley (P /V ) ratio, the average value of light mass ( ) and heavy mass ( ), and the average postfission number of neutrons ( expt) were obtained from the mass yield of the 232Th(γ ,f ) reaction. The present and literature data in the 232Th(γ ,f ) reaction were compared with the similar data in the 238U(γ ,f ) reaction at various excitation energies to examine the role of potential energy surface and the effect of standard I and standard II asymmetric modes of fission. It was found that (i) even at the bremsstrahlung end-point energy of 2.5 GeV, the mass-yield distribution in the 232Th(γ ,f ) reaction is triple humped, unlike 238U(γ ,f ) reaction, where it is double humped. (ii) The peak-to-valley (P /V ) ratio decreases with the increase of excitation energies. However, the P /V ratio of the 232Th(γ ,f ) reaction is always lower than that of the 238U(γ ,f ) reaction due to the presence of a third peak in the former. (iii) In both the 232Th(γ ,f ) and 238U(γ ,f ) reactions, the nuclear structure effect almost vanishes at the bremsstrahlung end-point energies of 2.5-3.5 GeV.

Accelerated isothermal nucleic acid amplification in betaine-free reaction.

PubMed

Ma, Cuiping; Wang, Yifan; Zhang, Pansong; Shi, Chao

2017-08-01

Betaine was used as a common additive to isothermal nucleic acid amplification reactions because of lowering the melting temperature (Tm) of DNA. Herein, we reported a novel finding that betaine was inhibiting the reaction efficiency of isothermal amplification reactions. In this work, we have verified this finding by classical loop-mediated isothermal amplification that the addition of 0.8 M betaine inhibited the efficiency of reaction dropping to approximately 1%. Additionally, we clarified the mechanism of betaine hindering isothermal amplification reactions with a molecular barrier to lower associate rate constant K1 for intermolecular hybridization. This finding would be very significant for studies on the interaction between small molecule substance and DNA, and the development of point-of-care testing because of simplifying reaction system and increasing reaction efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

High Yields of Hydrogen Production Induced by Meta-Substituted Dichlorophenols Biodegradation from the Green Alga Scenedesmus obliquus

PubMed Central

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

Explanatory Model for Sound Amplification in a Stethoscope

ERIC Educational Resources Information Center

Eshach, H.; Volfson, A.

2015-01-01

In the present paper we suggest an original physical explanatory model that explains the mechanism of the sound amplification process in a stethoscope. We discuss the amplification of a single pulse, a continuous wave of certain frequency, and finally we address the resonant frequencies. It is our belief that this model may provide students with…

Detection and signal amplification in zebrafish RNA FISH.

PubMed

Hauptmann, Giselbert; Lauter, Gilbert; Söll, Iris

2016-04-01

In situ hybridization (ISH) has become an invaluable tool for the detection of RNA in cells, tissues and organisms. Due to improvements in target and signal amplification and in probe design remarkable progress has been made concerning sensitivity, specificity and resolution of chromogenic and fluorescent ISH (FISH). These advancements allow for exquisite cellular and sub-cellular resolution and for detecting multiple RNA species at a time by multiplexing. In zebrafish (F)ISH non-enzymatic and enzymatic amplification systems have been employed to obtain enhanced signal intensities and signal-to-noise ratios. These amplification strategies include branched DNA-based RNAscope and in situ hybridization chain reaction (HCR) techniques, as well as alkaline phosphatase (AP)- and horseradish peroxidase (PO)-based immunoassays. For practical application, we provide proven multiplex FISH protocols for AP- and PO-based visualization of mRNAs at high resolution. The protocols take advantage of optimized tyramide signal amplification (TSA) conditions of the PO assay and long-lasting high signal-to-noise ratio of the AP reaction, thereby enabling detection of less abundant transcripts. Copyright © 2016 Elsevier Inc. All rights reserved.

Graphene Ambipolar Nanoelectronics for High Noise Rejection Amplification.

PubMed

Liu, Che-Hung; Chen, Qi; Liu, Chang-Hua; Zhong, Zhaohui

2016-02-10

In a modern wireless communication system, signal amplification is critical for overcoming losses during multiple data transformations/processes and long-distance transmission. Common mode and differential mode are two fundamental amplification mechanisms, and they utilize totally different circuit configurations. In this paper, we report a new type of dual-gate graphene ambipolar device with capability of operating under both common and differential modes to realize signal amplification. The signal goes through two stages of modulation where the phase of signal can be individually modulated to be either in-phase or out-of-phase at two stages by exploiting the ambipolarity of graphene. As a result, both common and differential mode amplifications can be achieved within one single device, which is not possible in the conventional circuit configuration. In addition, a common-mode rejection ratio as high as 80 dB can be achieved, making it possible for low noise circuit application. These results open up new directions of graphene-based ambipolar electronics that greatly simplify the RF circuit complexity and the design of multifunction device operation.

Detection of MET amplification in gastroesophageal tumor specimens using IQFISH

PubMed Central

Nielsen, Karsten Bork; Mollerup, Jens; Jepsen, Anna; Go, Ning

2017-01-01

Background The gene mesenchymal epithelial transition factor (MET) is a proto-oncogene that encodes a transmembrane receptor with intrinsic tyrosine kinase activity known as Met or cMet. MET is found to be amplified in several human cancers including gastroesophageal cancer. Methods Here we report the MET amplification prevalence data from 159 consecutive tumor specimens from patients with gastric (G), gastroesophageal junction (GEJ) and esophageal (E) adenocarcinoma, using a novel fluorescence in situ hybridization (FISH) assay, MET/CEN-7 IQFISH Probe Mix [an investigational use only (IUO) assay]. MET amplification was defined as a MET/CEN-7 ratio ≥2.0. Furthermore, the link between the MET signal distribution and amplification status was investigated. Results The prevalence of MET amplification was found to be 6.9%. The FISH assay demonstrated a high inter-observer reproducibility. The inter-observer results showed a 100% overall agreement with respect to the MET status (amplified/non-amplified). The inter-observer CV was estimated to 11.8% (95% CI: 10.2–13.4). For the signal distribution, the inter-observer agreement was reported to be 98.7%. We also report an association of MET amplification and a unique signal distribution pattern in the G/GEJ/E tumor specimens. We found that the prevalence of MET amplification was markedly higher in tumors specimens with a heterogeneous (66.7%) versus homogeneous (2.0%) signal distribution. Furthermore, specimens with a heterogeneous signal distribution had a statically significantly higher median MET/CEN-7 ratio (2.35 versus 1.04; P<0.0001). Conclusions The novel FISH assay showed a high inter-observer reproducibility both with respect to amplification status and signal distribution. Based on the finding in the study it is suggested that MET amplification mainly is associated with tumor cells that is represented by a heterogonous growth pattern. PMID:29285491

Detection of MET amplification in gastroesophageal tumor specimens using IQFISH.

PubMed

Jørgensen, Jan Trøst; Nielsen, Karsten Bork; Mollerup, Jens; Jepsen, Anna; Go, Ning

2017-12-01

The gene mesenchymal epithelial transition factor ( MET ) is a proto-oncogene that encodes a transmembrane receptor with intrinsic tyrosine kinase activity known as Met or cMet. MET is found to be amplified in several human cancers including gastroesophageal cancer. Here we report the MET amplification prevalence data from 159 consecutive tumor specimens from patients with gastric (G), gastroesophageal junction (GEJ) and esophageal (E) adenocarcinoma, using a novel fluorescence in situ hybridization (FISH) assay, MET /CEN-7 IQFISH Probe Mix [an investigational use only (IUO) assay]. MET amplification was defined as a MET /CEN-7 ratio ≥2.0. Furthermore, the link between the MET signal distribution and amplification status was investigated. The prevalence of MET amplification was found to be 6.9%. The FISH assay demonstrated a high inter-observer reproducibility. The inter-observer results showed a 100% overall agreement with respect to the MET status (amplified/non-amplified). The inter-observer CV was estimated to 11.8% (95% CI: 10.2-13.4). For the signal distribution, the inter-observer agreement was reported to be 98.7%. We also report an association of MET amplification and a unique signal distribution pattern in the G/GEJ/E tumor specimens. We found that the prevalence of MET amplification was markedly higher in tumors specimens with a heterogeneous (66.7%) versus homogeneous (2.0%) signal distribution. Furthermore, specimens with a heterogeneous signal distribution had a statically significantly higher median MET /CEN-7 ratio (2.35 versus 1.04; P<0.0001). The novel FISH assay showed a high inter-observer reproducibility both with respect to amplification status and signal distribution. Based on the finding in the study it is suggested that MET amplification mainly is associated with tumor cells that is represented by a heterogonous growth pattern.

Active frequency matching in stimulated Brillouin amplification for production of a 2.4  J, 200  ps laser pulse.

PubMed

Yuan, Hang; Wang, Yulei; Lu, Zhiwei; Zheng, Zhenxing

2018-02-01

A frequency matching Brillouin amplification in high-power solid-state laser systems is proposed. The energy extraction efficiency could be maintained at a high level in a non-collinear Brillouin amplification structure using an exact Stokes frequency shift. Laser pulses having a width of 200 ps and energy of 2.4 J were produced. This method can be used to transfer energy from a long pulse to a short pulse through a high-power solid-state laser system.

Development and evaluation of a rapid recombinase polymerase amplification assay for detection of coxsackievirus A6.

PubMed

Wang, Kaifeng; Wu, Yue; Yin, Dan; Tang, Shixing; Hu, Guifang; He, Yaqing

2017-01-01

Coxsackievirus A6 (CV-A6) is an important pathogen causing hand, foot and mouth disease (HFMD). The aim of this study was to develop and evaluate a rapid real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of CV-A6. The sensitivity of this assay was 202 copies/reaction, with 100 % specificity. Furthermore, this assay yielded consistent results comparable with a commercial qRT-PCR diagnostic kit. This assay is therefore potentially useful for surveillance of CV-A6 infections and outbreak control.

The reaction between CH 3O 2 and OH radicals: Product yields and atmospheric implications

DOE PAGES

Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa; ...

2017-01-25

The reaction between CH 3O 2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH 3O 2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO 2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH 3O 2, OH, and HO 2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of Φ HO2more » = (0.8 ± 0.2) and an upper limit for Φ Criegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH 3O 2+OH reaction into the model results in up to 30% decrease in the CH 3O 2 radical concentration while the HO 2 concentration increased by up to 20%. Finally, production and destruction of O 3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH 3O 2 and OH leads to a 6% decrease of O 3.« less

The reaction between CH 3O 2 and OH radicals: Product yields and atmospheric implications

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

Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa

The reaction between CH 3O 2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH 3O 2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO 2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH 3O 2, OH, and HO 2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of Φ HO2more » = (0.8 ± 0.2) and an upper limit for Φ Criegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH 3O 2+OH reaction into the model results in up to 30% decrease in the CH 3O 2 radical concentration while the HO 2 concentration increased by up to 20%. Finally, production and destruction of O 3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH 3O 2 and OH leads to a 6% decrease of O 3.« less

New measurements on isobaric fission product yields and mean kinetic energy for 241Pu thermal neutron-induced fission

NASA Astrophysics Data System (ADS)

Julien-Laferrière, Sylvain; Kessedjian, Grégoire; Serot, Olivier; Chebboubi, Abdelaziz; Bernard, David; Blanc, Aurélien; Köster, Ulli; Litaize, Olivier; Materna, Thomas; Meplan, Olivier; Rapala, Michal; Sage, Christophe

2018-03-01

Nuclear fission yields data measurements for thermal neutron induced fission of 241Pu have been carried out at the Institut Laue Langevin (ILL) in Grenoble, using the Lohengrin mass spectrometer. Mass, isotopic and isomeric yields have been extracted for the last measurements. A focus is given in this document to the mass yield results which are obtained for almost the entire heavy peak and most of the light high yields masses, along with the covariance matrix. The mean kinetic energy as a function of the fission product mass has also been extracted from the measurements. The total mean kinetic energy pre and post neutron emission have been assessed and compared to other works showing a rather good agreement.

Systematization of the yields of products of photonuclear reactions on enriched-tin targets at the bremsstrahlung-photon endpoint energy of 4.5 GeV

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

Balabekyan, A. R., E-mail: balabekyan@ysu.a

2008-11-15

Yields of photonuclear-reaction products formed in targets from separated tin isotopes under the effect of beams of bremsstrahlung photons whose endpoint energy is 4.5 GeV were investigated. The systematization performed on this basis revealed an isoscaling character of the behavior of the production yields for various regions of reaction-product masses.

Eco-efficient agriculture for producing higher yields with lower greenhouse gas emissions: a case study of intensive irrigation wheat production in China

NASA Astrophysics Data System (ADS)

Cui, Z. L.; Ye, Y. L.; Ma, W. Q.; Chen, X. P.; Zhang, F. S.

2013-10-01

Although the concept of producing higher yields with reduced greenhouse gas (GHG) emissions is a goal that attracts increasing public and scientific attention, the tradeoff between crop productivity and GHG emissions in intensive agricultural production is not well understood. In this study, we investigated 33 sites of on-farm experiments to evaluate the tradeoff between grain yield and GHG emissions using two systems (conventional practice, CP; high-yielding systems, HY) of intensive irrigation wheat (Triticum aestivum L.) in China. Furthermore, we discussed the potential to produce higher yields with lower GHG emissions based on a survey of 2938 farmers. However, in both the HY and CP systems, wheat grain yield response to GHG emissions fit a linear-plateau model, whereas the curve for grain yield from the HY system was always higher than that from the CP system. Compared to the CP system, grain yield was 44% (2.6 Mg ha-1) higher in the HY system, while GHG emissions increased by only 2.5%, and GHG emission intensity was reduced by 29%. The current intensive irrigation wheat system with farmers' practice had a median yield and maximum GHG emission rate of 6.05 Mg ha-1 and 4783 kg CO2 eq ha-1, respectively; however, this system can be transformed to maintain yields while reducing GHG emissions by 40% (5.96 Mg ha-1, and 2890 kg CO2 eq ha-1). Further, the HY system was found to increase grain yield by 41% with a simultaneous reduction in GHG emissions by 38% (8.55 Mg ha-1, and 2961 kg CO2 eq ha-1, respectively). In the future, we suggest moving the tradeoff relationships and calculations from grain yield and GHG emissions, to new measures of productivity and environmental protection using innovative management technologies. This shift in focus is critical to achieve food and environmental security.

A surface-confined DNA assembly amplification strategy on DNA nanostructural scaffold for electrochemiluminescence biosensing.

PubMed

Feng, Qiu-Mei; Guo, Yue-Hua; Xu, Jing-Juan; Chen, Hong-Yuan

2018-02-15

A critical challenge in surface-based DNA assembly amplification is the reduced accessibility of DNA strands arranged on a heterogeneous surface compared to that in homogeneous solution. Here, a novel in situ surface-confined DNA assembly amplification electrochemiluminescence (ECL) biosensor based on DNA nanostructural scaffold was presented. In this design, a stem-loop structural DNA segment (Hairpin 1) was constructed on the vertex of DNA nanostructural scaffold as recognition probe. In the present of target DNA, the hairpin structure changed to rod-like through complementary hybridization with target DNA, resulting in the formation of Hairpin 1:target DNA. When the obtained Hairpin 1:target DNA met Hairpin 2 labeled with glucose oxidase (GOD), the DNA cyclic amplification was activated, releasing target DNA into homogeneous solution for the next recycling. Thus, the ECL signal of Ru(bpy) 3 2+ -TPrA system was quenched by H 2 O 2 , the product of GOD catalyzing glucose. As a result, this proposed method achieved a linear range response from 50 aM to 10 pM with lower detection limit of 20 aM. Copyright © 2017 Elsevier B.V. All rights reserved.

Loop mediated isothermal amplification (LAMP) assay for detection of coconut root wilt disease and arecanut yellow leaf disease phytoplasma.

PubMed

Nair, Smita; Manimekalai, Ramaswamy; Ganga Raj, Palliyath; Hegde, Vinayaka

2016-07-01

The coconut root wilt disease (RWD) and the arecanut yellow leaf disease (YLD) are two major phytoplasma associated diseases affecting palms in South India. Greatly debilitating the palm health, these diseases cause substantial yield reduction and economic loss to farmers. A rapid and robust diagnostic technique is crucial in efficient disease management. We established phytoplasma 16S rDNA targeted loop mediated isothermal amplification (LAMP) and real time LAMP based diagnostics for coconut RWD and arecanut YLD. The LAMP reaction was set at 65 °C and end point detection made using hydroxynaphthol blue (HNB) and agarose gel electrophoresis. Molecular typing of LAMP products were made with restriction enzyme HpyCH4 V. Conventional PCR with LAMP external primers and sequencing of amplicons was carried out. Real time LAMP was performed on the Genei II platform (Optigene Ltd., UK). An annealing curve analysis was programmed at the end of the incubation to check the fidelity of the amplicons. The phytoplasma positive samples produced typical ladder like bands on agarose gel, showed colour change from violet to blue with HNB and produced unique annealing peak at 85 ± 0.5 °C in the real time detection. Restriction digestion produced predicted size fragments. Sequencing and BLASTN analysis confirmed that the amplification corresponded to phytoplasma 16S rRNA gene. LAMP method devised here was found to be more robust compared to conventional nested PCR and hence has potential applications in detection of phytoplasma from symptomatic palm samples and in rapid screening of healthy seedlings.

Visual Biopsy by Hydrogen Peroxide-Induced Signal Amplification.

PubMed

Zhao, Wenjie; Yang, Sheng; Yang, Jinfeng; Li, Jishan; Zheng, Jing; Qing, Zhihe; Yang, Ronghua

2016-11-01

Visual biopsy has attracted special interest by surgeons due to its simplicity and practicality; however, the limited sensitivity of the technology makes it difficult to achieve an early diagnosis. To circumvent this problem, herein, we report a visual signal amplification strategy for establishing a marker-recognizable biopsy that enables early cancer diagnosis. In our proposed approach, hydrogen peroxide (H 2 O 2 ) was selected as a potential underlying marker for its compact relationship in cancer progression. For selective recognition of H 2 O 2 in the process of visual biopsy, a benzylbenzeneboronic acid pinacol ester-decorated copolymer, namely, PMPC-Bpe, was synthesized, affording the final formation of the H 2 O 2 -responsive micelles in which amylose was trapped. The presence of H 2 O 2 activates the boronate ester recognition site and induces it releasing abundant indicator amylose, leading to signal amplification. The indicator came across the solution of KI/I 2 added to the sample, and the formative amylose-KI/I 2 complex has a distinct blue color at 574 nm for visual amplification detection. The feasibility of the proposed method is demonstrated by visualizing the H 2 O 2 content of cancer at different stages and three kinds of actual cancerous samples. As far as we know, this is the first paradigm to rationally design a signaling amplification-based molecular recognizable biopsy for visual and sensitive disease identification, which will extend new possibilities for marker-recognition and signal amplification-based biopsy in disease progressing.

CDK4 Amplification Predicts Recurrence of Well-Differentiated Liposarcoma of the Abdomen

PubMed Central

Ha, Sang Yun; Paik, Kwang Yeol; Lee, Seung Eun; Kim, Jong Man; Park, Jae Berm; Kwon, Choon Hyuck David; Joh, Jae-Won; Choi, Yoon-La; Kim, Sung Joo

2014-01-01

Background The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD) and dedifferentiated (DD) liposarcomas. Methods From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR). Results There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05). Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7%) and MDM2 amplification in 46 cases (95.8%). WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041). High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54) was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012) and multivariate analyses (P = 0.020). Conclusions Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection. PMID:25121597

Fission Product Yield Study of 235U, 238U and 239Pu Using Dual-Fission Ionization Chambers

NASA Astrophysics Data System (ADS)

Bhatia, C.; Fallin, B.; Howell, C.; Tornow, W.; Gooden, M.; Kelley, J.; Arnold, C.; Bond, E.; Bredeweg, T.; Fowler, M.; Moody, W.; Rundberg, R.; Rusev, G.; Vieira, D.; Wilhelmy, J.; Becker, J.; Macri, R.; Ryan, C.; Sheets, S.; Stoyer, M.; Tonchev, A.

2014-05-01

To resolve long-standing differences between LANL and LLNL regarding the correct fission basis for analysis of nuclear test data [M.B. Chadwick et al., Nucl. Data Sheets 111, 2891 (2010); H. Selby et al., Nucl. Data Sheets 111, 2891 (2010)], a collaboration between TUNL/LANL/LLNL has been established to perform high-precision measurements of neutron induced fission product yields. The main goal is to make a definitive statement about the energy dependence of the fission yields to an accuracy better than 2-3% between 1 and 15 MeV, where experimental data are very scarce. At TUNL, we have completed the design, fabrication and testing of three dual-fission chambers dedicated to 235U, 238U, and 239Pu. The dual-fission chambers were used to make measurements of the fission product activity relative to the total fission rate, as well as for high-precision absolute fission yield measurements. The activation method was employed, utilizing the mono-energetic neutron beams available at TUNL. Neutrons of 4.6, 9.0, and 14.5 MeV were produced via the 2H(d,n)3He reaction, and for neutrons at 14.8 MeV, the 3H(d,n)4He reaction was used. After activation, the induced γ-ray activity of the fission products was measured for two months using high-resolution HPGe detectors in a low-background environment. Results for the yield of seven fission fragments of 235U, 238U, and 239Pu and a comparison to available data at other energies are reported. For the first time results are available for neutron energies between 2 and 14 MeV.

Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices

PubMed Central

Zanoli, Laura Maria; Spoto, Giuseppe

2012-01-01

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. PMID:25587397

Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

PubMed

Cimino, Matthew T

2010-03-01

Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements. (c) Georg Thieme Verlag KG Stuttgart . New York.

Identification of Genetic Elements Associated with EPSPS Gene Amplification

PubMed Central

Gaines, Todd A.; Wright, Alice A.; Molin, William T.; Lorentz, Lothar; Riggins, Chance W.; Tranel, Patrick J.; Beffa, Roland; Westra, Philip; Powles, Stephen B.

2013-01-01

Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world’s most important herbicide. However, the gene amplification mechanism is unknown. We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences. The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns. The gene amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified sequence is at least 30 kb in length. Our data support the presence of two EPSPS loci in susceptible (S) A. palmeri, and that only one of these was amplified in glyphosate-resistant (R) A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs) were identified next to EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac) transposase and a repetitive sequence region were associated with amplified EPSPS genes. The mechanism controlling this DNA-mediated amplification remains unknown. Further investigation is necessary to determine if the gene amplification may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene. PMID:23762434

Uniform amplification of phage display libraries in monodisperse emulsions.

PubMed

Matochko, Wadim L; Ng, Simon; Jafari, Mohammad R; Romaniuk, Joseph; Tang, Sindy K Y; Derda, Ratmir

2012-09-01

In this paper, we describe a complete experimental setup for the uniform amplification of libraries of phage. Uniform amplification, which multiplies every phage clone by the same amount irrespective of the growth rate of the clone is essential for phage-display screening. Amplification of phage libraries in a common solution is often non-uniform: it favors fast-growing clones and eliminates those that grow slower. This competition leads to elimination of many useful binding clones, and it is a major barrier to identification of ligands for targets with multiple binding sites such as cells, tissues, or mixtures of proteins. Uniform amplification is achieved by encapsulating individual phage clones into isolated compartments (droplets) of identical volume. Each droplet contains culture medium and an excess of host (Escherichia coli). Here, we describe microfluidics devices that generate mono-disperse droplet-based compartments, and optimal conditions for amplification of libraries of different size. We also describe the detailed synthesis of a perfluoro surfactant, which gives droplets exceptional stability. Droplets stabilized by this compound do not coalesce after many hours in shaking culture. We identified a commercially available compound (Krytox), which destabilizes these droplets to recover the amplified libraries. Overall, uniform amplification is a sequence of three simple steps: (1) encapsulation of mixture of phage and bacteria in droplets using microfluidics; (2) incubation of droplets in a shaking culture; (3) destabilization of droplets to harvest the amplified phage. We anticipate that this procedure can be easily adapted in any academic or industrial laboratory that uses phage display. Copyright © 2012 Elsevier Inc. All rights reserved.

High-power parametric amplification of 11.8-fs laser pulses with carrier-envelope phase control.

PubMed

Zinkstok, R Th; Witte, S; Hogervorst, W; Eikema, K S E

2005-01-01

Phase-stable parametric chirped-pulse amplification of ultrashort pulses from a carrier-envelope phase-stabilized mode-locked Ti:sapphire oscillator (11.0 fs) to 0.25 mJ/pulse at 1 kHz is demonstrated. Compression with a grating compressor and a LCD shaper yields near-Fourier-limited 11.8-fs pulses with an energy of 0.12 mJ. The amplifier is pumped by 532-nm pulses from a synchronized mode-locked laser, Nd:YAG amplifier system. This approach is shown to be promising for the next generation of ultrafast amplifiers aimed at producing terawatt-level phase-controlled few-cycle laser pulses.

Weak-value amplification and optimal parameter estimation in the presence of correlated noise

NASA Astrophysics Data System (ADS)

Sinclair, Josiah; Hallaji, Matin; Steinberg, Aephraim M.; Tollaksen, Jeff; Jordan, Andrew N.

2017-11-01

We analytically and numerically investigate the performance of weak-value amplification (WVA) and related parameter estimation methods in the presence of temporally correlated noise. WVA is a special instance of a general measurement strategy that involves sorting data into separate subsets based on the outcome of a second "partitioning" measurement. Using a simplified correlated noise model that can be analyzed exactly together with optimal statistical estimators, we compare WVA to a conventional measurement method. We find that WVA indeed yields a much lower variance of the parameter of interest than the conventional technique does, optimized in the absence of any partitioning measurements. In contrast, a statistically optimal analysis that employs partitioning measurements, incorporating all partitioned results and their known correlations, is found to yield an improvement—typically slight—over the noise reduction achieved by WVA. This result occurs because the simple WVA technique is not tailored to any specific noise environment and therefore does not make use of correlations between the different partitions. We also compare WVA to traditional background subtraction, a familiar technique where measurement outcomes are partitioned to eliminate unknown offsets or errors in calibration. Surprisingly, for the cases we consider, background subtraction turns out to be a special case of the optimal partitioning approach, possessing a similar typically slight advantage over WVA. These results give deeper insight into the role of partitioning measurements (with or without postselection) in enhancing measurement precision, which some have found puzzling. They also resolve previously made conflicting claims about the usefulness of weak-value amplification to precision measurement in the presence of correlated noise. We finish by presenting numerical results to model a more realistic laboratory situation of time-decaying correlations, showing that our conclusions hold

Impacts of climate change on rice production in Africa and causes of simulated yield changes.

PubMed

van Oort, Pepijn A J; Zwart, Sander J

2018-03-01

This study is the first of its kind to quantify possible effects of climate change on rice production in Africa. We simulated impacts on rice in irrigated systems (dry season and wet season) and rainfed systems (upland and lowland). We simulated the use of rice varieties with a higher temperature sum as adaptation option. We simulated rice yields for 4 RCP climate change scenarios and identified causes of yield declines. Without adaptation, shortening of the growing period due to higher temperatures had a negative impact on yields (-24% in RCP 8.5 in 2070 compared with the baseline year 2000). With varieties that have a high temperature sum, the length of the growing period would remain the same as under the baseline conditions. With this adaptation option rainfed rice yields would increase slightly (+8%) but they remain subject to water availability constraints. Irrigated rice yields in East Africa would increase (+25%) due to more favourable temperatures and due to CO2 fertilization. Wet season irrigated rice yields in West Africa were projected to change by -21% or +7% (without/with adaptation). Without adaptation irrigated rice yields in West Africa in the dry season would decrease by -45% with adaptation they would decrease significantly less (-15%). The main cause of this decline was reduced photosynthesis at extremely high temperatures. Simulated heat sterility hardly increased and was not found a major cause for yield decline. The implications for these findings are as follows. For East Africa to benefit from climate change, improved water and nutrient management will be needed to benefit fully from the more favourable temperatures and increased CO2 concentrations. For West Africa, more research is needed on photosynthesis processes at extreme temperatures and on adaptation options such as shifting sowing dates. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP).

PubMed

Nkere, Chukwuemeka K; Oyekanmi, Joshua O; Silva, Gonçalo; Bömer, Moritz; Atiri, Gabriel I; Onyeka, Joseph; Maroya, Norbert G; Seal, Susan E; Kumar, P Lava

2018-04-01

A closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP) assay was developed for the detection of yam mosaic virus (YMV, genus Potyvirus) infecting yam (Dioscorea spp.). The assay uses a set of six oligonucleotide primers targeting the YMV coat protein region, and the amplification products in YMV-positive samples are visualized by chromogenic detection with SYBR Green I dye. The CT-RT-LAMP assay detected YMV in leaf and tuber tissues of infected plants. The assay is 100 times more sensitive in detecting YMV than standard RT-PCR, while maintaining the same specificity.

Gold nanoparticles production using reactor and cyclotron based methods in assessment of (196,198)Au production yields by (197)Au neutron absorption for therapeutic purposes.

PubMed

Khorshidi, Abdollah

2016-11-01

Medical nano-gold radioisotopes is produced regularly using high-flux nuclear reactors, and an accelerator-driven neutron activator can turn out higher yield of (197)Au(n,γ)(196,198)Au reactions. Here, nano-gold production via radiative/neutron capture was investigated using irradiated Tehran Research Reactor flux and also simulated proton beam of Karaj cyclotron in Iran. (197)Au nano-solution, including 20nm shaped spherical gold and water, was irradiated under Tehran reactor flux at 2.5E+13n/cm(2)/s for (196,198)Au activity and production yield estimations. Meanwhile, the yield was examined using 30MeV proton beam of Karaj cyclotron via simulated new neutron activator containing beryllium target, bismuth moderator around the target, and also PbF2 reflector enclosed the moderator region. Transmutation in (197)Au nano-solution samples were explored at 15 and 25cm distances from the target. The neutron flux behavior inside the water and bismuth moderators was investigated for nano-gold particles transmutation. The transport of fast neutrons inside bismuth material as heavy nuclei with a lesser lethargy can be contributed in enhanced nano-gold transmutation with long duration time than the water moderator in reactor-based method. Cyclotron-driven production of βeta-emitting radioisotopes for brachytherapy applications can complete the nano-gold production technology as a safer approach as compared to the reactor-based method. Copyright © 2016 Elsevier B.V. All rights reserved.

Production of N(+)-asterisk from N2 + hnu - Effective EUV emission yields from laboratory and dayglow data

NASA Technical Reports Server (NTRS)

Meier, R. R.; Samson, James A. R.; Chung, Y.; Lee, E.-M.; He, Z.-X.

1991-01-01

Photodissociative ionization of N2 into the unbound N2(+) H 2Sigma-g(+) state is identified as the parentage of a number of N(+) and N-excited states that contribute to the u.v. dayglow. Yields have been obtained for the production of extreme ultraviolet emission lines of N(+) and N from a laboratory experiment using a broadband synchrotron radiation source with fluorescence spectroscopy. The yields are termed 'effective', in that they are constant percentages of the H state cross section. These are compared wih effective yields needed to reproduce N II 1085 and 916 A lines from four dayglow observations using a model of solar energy deposition and photoelectron production and loss in the earth's thermosphere. The 1085 A effective yield measured in the laboratory (18 percent) agrees with that from the dayglow data (average of 17 percent) to well within experimental uncertainties. Thus, it is concluded that photodissociative ionization of N2 is the primary source of the N II 1085 A dayglow. However, there is an order of magnitude discrepancy among the various dayglow observations of the 1085/916 intensity ratio, only one of which is consistent with the laboratory observation of 4.4. Neither contamination by other dayglow features nor atmospheric extinction can account for the disparities. Laboratory measurements of N2 and O2 absorption cross sections at these wavelengths are also reported.

Isothermal amplification detection of nucleic acids by a double-nicked beacon.

PubMed

Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

2016-03-01

Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use. Copyright © 2015 Elsevier Inc. All rights reserved.

Amplification of Information by Photons and the Quantum Chernoff Bound

NASA Astrophysics Data System (ADS)

Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

2014-03-01

Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the ``collapse of the wavepacket,'' and a way to avoid embarrassing problems exemplified by Schrödinger's cat. This bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen Interpretation. Quantum Darwinism views amplification as replication, in many copies, of information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. The resultant amplification is huge, proportional to # ξQCB . Here, #  is the environment size and ξQCB is the ``typical'' Quantum Chernoff Information, which quantifies the efficiency of the amplification. The information communicated though the environment is imprinted in the states of individual environment subsystems, e.g., in single photons, which document the transfer of information into the environment and result in the emergence of the classical world. See, http://mike.zwolak.org

Parametric Amplification For Detecting Weak Optical Signals

NASA Technical Reports Server (NTRS)

Hemmati, Hamid; Chen, Chien; Chakravarthi, Prakash

1996-01-01

Optical-communication receivers of proposed type implement high-sensitivity scheme of optical parametric amplification followed by direct detection for reception of extremely weak signals. Incorporates both optical parametric amplification and direct detection into optimized design enhancing effective signal-to-noise ratios during reception in photon-starved (photon-counting) regime. Eliminates need for complexity of heterodyne detection scheme and partly overcomes limitations imposed on older direct-detection schemes by noise generated in receivers and by limits on quantum efficiencies of photodetectors.

Self-locked aptamer probe mediated cascade amplification strategy for highly sensitive and selective detection of protein and small molecule.

PubMed

Li, Wei; Jiang, Wei; Wang, Lei

2016-10-12

In this work, a novel self-locked aptamer probe mediated cascade amplification strategy has been constructed for highly sensitive and specific detection of protein. First, the self-locked aptamer probe was designed with three functions: one was specific molecular recognition attributed to the aptamer sequence, the second was signal transduction owing to the transduction sequence, and the third was self-locking through the hybridization of the transduction sequence and part of the aptamer sequence. Then, the aptamer sequence specific recognized the target and folded into a three-way helix junction, leading to the release of the transduction sequence. Next, the 3'-end of this three-way junction acted as primer to trigger the strand displacement amplification (SDA), yielding a large amount of primers. Finally, the primers initiated the dual-exponential rolling circle amplification (DE-RCA) and generated numerous G-quadruples sequences. By inserting the fluorescent dye N-methyl mesoporphyrin IX (NMM), enhanced fluorescence signal was achieved. In this strategy, the self-locked aptamer probe was more stable to reduce the interference signals generated by the uncontrollable folding in unbounded state. Through the cascade amplification of SDA and DE-RCA, the sensitivity was further improved with a detection limit of 3.8 × 10(-16) mol/L for protein detection. Furthermore, by changing the aptamer sequence of the probe, sensitive and selective detection of adenosine has been also achieved, suggesting that the proposed strategy has good versatility and can be widely used in sensitive and selective detection of biomolecules. Copyright © 2016 Elsevier B.V. All rights reserved.

Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

ERIC Educational Resources Information Center

Esernio-Jenssen, Debra; Barnes, Marilyn

2011-01-01

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

Metabolic engineering for the high-yield production of isoprenoid-based C 5 alcohols in E. coli

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

George, Kevin W.; Thompson, Mitchell G.; Kang, Aram

2015-06-08

Branched five carbon (C 5) 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 C 5 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 diphosphatemore » (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. Lastly, 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.« less

Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli

PubMed Central

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

MET expression and amplification in patients with localized gastric cancer

PubMed Central

Janjigian, Yelena Y.; Tang, Laura H.; Coit, Daniel G.; Kelsen, David P.; Francone, Todd D.; Weiser, Martin R.; Jhanwar, Suresh C.; Shah, Manish A.

2013-01-01

Background MET, the receptor for hepatocyte growth factor has been proposed as a therapeutic target in gastric cancer. This study assessed the incidence of MET expression and gene amplification in tumors of Western patients with gastric cancer. Methods Tumor specimens from patients enrolled on a preoperative chemotherapy study (NCI 5700) were examined for presence of MET gene amplification by fluorescence in situ hybridization (FISH), MET mRNA expression by quantitative polymerase chain reaction, MET overexpression by immunohistochemistry (IHC), and for evidence of MET pathway activation by p-MET IHC. Results Although high-level of MET protein and mRNA were commonly encountered (in 63% and 50% of resected tumor specimens, respectively), none of these tumors had MET gene amplification by FISH, and only 6.6% had evidence of MET tyrosine kinase activity by p-MET IHC. Conclusions In this cohort of patients with localized gastric cancer, the presence of high MET protein and RNA expression does not correlate with MET gene amplification or pathway activation as evidenced by the absence of amplification by FISH and negative p-MET IHC analysis. Impact This paper demonstrates a lack of MET amplification and pathway activation in a cohort of 38 patients with localized gastric cancer, suggesting that MET-driven gastric cancers are relatively rare in Western patients. PMID:21393565

Development of a rapid assay for the diagnosis of Myxobolus cerebralis in fish and oligochaetes using loop-mediated isothermal amplification.

PubMed

El-Matbouli, M; Soliman, H

2005-09-01

A loop-mediated isothermal amplification assay was developed for the rapid detection of Myxobolus cerebralis in both fish and oligochaete hosts. The assay was optimized to amplify parasitic DNA by incubation with Bst DNA polymerase and a set of six specially constructed primers at 65 degrees C for 60 min. The amplification products were detected visually using SYBR Green I dye which gave identical results to gel electrophoresis analysis. Parasite DNA was detected from infected oligochaetes, and from the anal fin, caudal fin, dorsal fin and operculum of clinically infected fish. This 'Myxo-LAMP' assay has a detection limit similar to that of a polymerase chain reaction assay (10(-6)), but is more rapid and only requires a water bath for amplification and is therefore practical for simple and rapid diagnosis of infected tissue.

[Construction of high-yield strain by optimizing lycopene cyclase for β-carotene production].

PubMed

Jin, Yingfu; Han, Li; Zhang, Shasha; Li, Shizhong; Liu, Weifeng; Tao, Yong

2017-11-25

To optimize key enzymes, such as to explore the gene resources and to modify the expression level, can maximize metabolic pathways of target products. β-carotene is a terpenoid compound with important application value. Lycopene cyclase (CrtY) is the key enzyme in β-carotene biosynthesis pathway, catalyzing flavin adenine dinucleotide (FAD)-dependent cyclization reaction and β-carotene synthesis from lycopene precursor. We optimized lycopene cyclase (CrtY) to improve the synthesis of β-carotene and determined the effect of CrtY expression on metabolic pathways. Frist, we developed a β-carotene synthesis module by coexpressing the lycopene β-cyclase gene crtY with crtEBI module in Escherichia coli. Then we simultaneously optimized the ribosome-binding site (RBS) intensity and the species of crtY using oligo-linker mediated DNA assembly method (OLMA). Five strains with high β-carotene production capacity were screened out from the OLMA library. The β-carotene yields of these strains were up to 15.79-18.90 mg/g DCW (Dry cell weight), 65% higher than that of the original strain at shake flask level. The optimal strain CP12 was further identified and evaluated for β-carotene production at 5 L fermentation level. After process optimization, the final β-carotene yield could reach to 1.9 g/L. The results of RBS strength and metabolic intermediate analysis indicated that an appropriate expression level of CrtY could be beneficial for the function of the β-carotene synthesis module. The results of this study provide important insight into the optimization of β-carotene synthesis pathway in metabolic engineering.

Evaluating Sound Field Amplification Technology in New Brunswick Schools

ERIC Educational Resources Information Center

Rubin, Rhonda; Aquino-Russell, Catherine; Flagg-Williams, Joan

2007-01-01

(Purpose) The purpose of this study was to investigate the effects of classroom sound field amplification on communication in kindergarten through grade 3 classrooms. (Methodology) Sixty classrooms were involved in the study; half of the classrooms were provided with sound field amplification. The flow of communication was measured through…

Primer Extension Mutagenesis Powered by Selective Rolling Circle Amplification

PubMed Central

Huovinen, Tuomas; Brockmann, Eeva-Christine; Akter, Sultana; Perez-Gamarra, Susan; Ylä-Pelto, Jani; Liu, Yuan; Lamminmäki, Urpo

2012-01-01

Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material. PMID:22355397

Increasing water productivity, nitrogen economy, and grain yield of rice by water saving irrigation and fertilizer-N management.

PubMed

Aziz, Omar; Hussain, Saddam; Rizwan, Muhammad; Riaz, Muhammad; Bashir, Saqib; Lin, Lirong; Mehmood, Sajid; Imran, Muhammad; Yaseen, Rizwan; Lu, Guoan

2018-06-01

The looming water resources worldwide necessitate the development of water-saving technologies in rice production. An open greenhouse experiment was conducted on rice during the summer season of 2016 at Huazhong Agricultural University, Wuhan, China, in order to study the influence of irrigation methods and nitrogen (N) inputs on water productivity, N economy, and grain yield of rice. Two irrigation methods, viz. conventional irrigation (CI) and "thin-shallow-moist-dry" irrigation (TSMDI), and three levels of nitrogen, viz. 0 kg N ha -1 (N 0 ), 90 kg N ha -1 (N 1 ), and 180 kg N ha -1 (N 2 ), were examined with three replications. Study data indicated that no significant water by nitrogen interaction on grain yield, biomass, water productivity, N uptake, NUE, and fertilizer N balance was observed. Results revealed that TSMDI method showed significantly higher water productivity and irrigation water applications were reduced by 17.49% in TSMDI compared to CI. Thus, TSMDI enhanced root growth and offered significantly greater water saving along with getting more grain yield compared to CI. Nitrogen tracer ( 15 N) technique accurately assessed the absorption and distribution of added N in the soil crop environment and divulge higher nitrogen use efficiency (NUE) influenced by TSMDI. At the same N inputs, the TSMDI was the optimal method to minimize nitrogen leaching loss by decreasing water leakage about 18.63%, which are beneficial for the ecological environment.

Non-structural carbohydrate partitioning in grass stems: a target to increase yield stability, stress tolerance, and biofuel production.

PubMed

Slewinski, Thomas L

2012-08-01

A dramatic change in agricultural crops is needed in order to keep pace with the demands of an increasing human population, exponential need for renewable fuels, and uncertain climatic changes. Grasses make up the vast majority of agricultural commodities. How these grasses capture, transport, and store carbohydrates underpins all aspects of crop productivity. Sink-source dynamics within the plant direct how much, where, and when carbohydrates are allocated, as well as determine the harvestable tissue. Carbohydrate partitioning can limit the yield capacity of these plants, thus offering a potential target for crop improvement. Grasses have the ability to buffer this sink-source interaction by transiently storing carbohydrates in stem tissue when production from the source is greater than whole-plant demand. These reserves improve yield stability in grain crops by providing an alternative source when photosynthetic capacity is reduced during the later phases of grain filling, or during periods of environmental and biotic stresses. Domesticated grasses such as sugarcane and sweet sorghum have undergone selection for high accumulation of stem carbohydrates, which serve as the primary sources of sugars for human and animal consumption, as well as ethanol production for fuel. With the enormous expectations placed on agricultural production in the near future, research into carbohydrate partitioning in grasses is essential for maintaining and increasing yields in grass crops. This review highlights the current knowledge of non-structural carbohydrate dynamics in grass stems and discusses the impacts of stem reserves in essential agronomic grasses.

Surface-mode-assisted amplification of radiative heat transfer between nanoparticles

NASA Astrophysics Data System (ADS)

Messina, Riccardo; Biehs, Svend-Age; Ben-Abdallah, Philippe

2018-04-01

We show that the radiative heat flux between two nanoparticles can be significantly amplified when they are placed in proximity of a planar substrate supporting a surface resonance. The amplification factor goes beyond two orders of magnitude in the case of dielectric nanoparticles, whereas it is lower in the case of metallic nanoparticles. We analyze how this effect depends on the frequency and on the particle-surface distance by clearly identifying the signature of the surface mode producing the amplification. Finally, we show how the presence of a graphene sheet on top of the substrate can modify the effect by making an amplification of two orders of magnitude possible also in the case of metallic nanoparticles. This long-range amplification effect should play an important role in the thermal relaxation dynamics of nanoparticle networks.

Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection

PubMed Central

Roskos, Kristina; Hickerson, Anna I.; Lu, Hsiang-Wei; Ferguson, Tanya M.; Shinde, Deepali N.; Klaue, Yvonne; Niemz, Angelika

2013-01-01

Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden. PMID:23922706

Frequent amplification of receptor tyrosine kinase genes in welldifferentiated/ dedifferentiated liposarcoma.

PubMed

Asano, Naofumi; Yoshida, Akihiko; Mitani, Sachiyo; Kobayashi, Eisuke; Shiotani, Bunsyo; Komiyama, Motokiyo; Fujimoto, Hiroyuki; Chuman, Hirokazu; Morioka, Hideo; Matsumoto, Morio; Nakamura, Masaya; Kubo, Takashi; Kato, Mamoru; Kohno, Takashi; Kawai, Akira; Kondo, Tadashi; Ichikawa, Hitoshi

2017-02-21

Well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are closely related tumors commonly characterized by MDM2/CDK4 gene amplification, and lack clinically effective treatment options when inoperable. To identify novel therapeutic targets, we performed targeted genomic sequencing analysis of 19 WDLPS and 37 DDLPS tumor samples using a panel of 104 cancer-related genes (NCC oncopanel v3) developed specifically for genomic testing to select suitable molecular targeted therapies. The results of this analysis indicated that these sarcomas had very few gene mutations and a high frequency of amplifications of not only MDM2 and CDK4 but also other genes. Potential driver mutations were found in only six (11%) samples; however, gene amplification events (other than MDM2 and CDK4 amplification) were identified in 30 (54%) samples. Receptor tyrosine kinase (RTK) genes in particular were amplified in 18 (32%) samples. In addition, growth of a WDLPS cell line with IGF1R amplification was suppressed by simultaneous inhibition of CDK4 and IGF1R, using palbociclib and NVP-AEW541, respectively. Combination therapy with CDK4 and RTK inhibitors may be an effective therapeutic option for WDLPS/DDLPS patients with RTK gene amplification.

Anomalous amplification of a homodyne signal via almost-balanced weak values.

PubMed

Liu, Wei-Tao; Martínez-Rincón, Julián; Viza, Gerardo I; Howell, John C

2017-03-01

We propose precision measurements of ultra-small angular velocities of a mirror within a modified Sagnac interferometer, where the counter-propagating beams are spatially separated, using the recently proposed technique of almost-balanced weak values amplification (ABWV) [Phys. Rev. Lett.116, 100803 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.100803]. The separation between the two beams provides additional amplification with respect to using collinear beams in a Sagnac interferometer. Within the same setup, the weak-value amplification technique is also performed for comparison. Much higher amplification factors can be obtained using the almost-balanced weak values technique, with the best one achieved in our experiments being as high as 1.2×10⁷. In addition, the amplification factor monotonically increases with decreasing of the post-selection phase for the ABWV case in our experiments, which is not the case for weak-value amplification (WVA) at small post-selection phases. Both techniques consist of measuring the angular velocity. The sensitivity of the ABWV technique is ∼38  nrad/s per averaged pulse for a repetition rate of 1 Hz and ∼33  nrad/s per averaged pulse for the WVA technique.

Direct PCR amplification of forensic touch and other challenging DNA samples: A review.

PubMed

Cavanaugh, Sarah E; Bathrick, Abigail S

2018-01-01

DNA evidence sample processing typically involves DNA extraction, quantification, and STR amplification; however, DNA loss can occur at both the DNA extraction and quantification steps, which is not ideal for forensic evidence containing low levels of DNA. Direct PCR amplification of forensic unknown samples has been suggested as a means to circumvent extraction and quantification, thereby retaining the DNA typically lost during those procedures. Direct PCR amplification is a method in which a sample is added directly to an amplification reaction without being subjected to prior DNA extraction, purification, or quantification. It allows for maximum quantities of DNA to be targeted, minimizes opportunities for error and contamination, and reduces the time and monetary resources required to process samples, although data analysis may take longer as the increased DNA detection sensitivity of direct PCR may lead to more instances of complex mixtures. ISO 17025 accredited laboratories have successfully implemented direct PCR for limited purposes (e.g., high-throughput databanking analysis), and recent studies indicate that direct PCR can be an effective method for processing low-yield evidence samples. Despite its benefits, direct PCR has yet to be widely implemented across laboratories for the processing of evidentiary items. While forensic DNA laboratories are always interested in new methods that will maximize the quantity and quality of genetic information obtained from evidentiary items, there is often a lag between the advent of useful methodologies and their integration into laboratories. Delayed implementation of direct PCR of evidentiary items can be attributed to a variety of factors, including regulatory guidelines that prevent laboratories from omitting the quantification step when processing forensic unknown samples, as is the case in the United States, and, more broadly, a reluctance to validate a technique that is not widely used for evidence samples. The

Integrated microfluidic systems for cell lysis, mixing/pumping and DNA amplification

NASA Astrophysics Data System (ADS)

Lee, Chia-Yen; Lee, Gwo-Bin; Lin, Jr-Lung; Huang, Fu-Chun; Liao, Chia-Sheng

2005-06-01

The present paper reports a fully automated microfluidic system for the DNA amplification process by integrating an electroosmotic pump, an active micromixer and an on-chip temperature control system. In this DNA amplification process, the cell lysis is initially performed in a micro cell lysis reactor. Extracted DNA samples, primers and reagents are then driven electroosmotically into a mixing region where they are mixed by the active micromixer. The homogeneous mixture is then thermally cycled in a micro-PCR (polymerase chain reaction) chamber to perform DNA amplification. Experimental results show that the proposed device can successfully automate the sample pretreatment operation for DNA amplification, thereby delivering significant time and effort savings. The new microfluidic system, which facilitates cell lysis, sample driving/mixing and DNA amplification, could provide a significant contribution to ongoing efforts to miniaturize bio-analysis systems by utilizing a simple fabrication process and cheap materials.

Fast implementation of length-adaptive privacy amplification in quantum key distribution

NASA Astrophysics Data System (ADS)

Zhang, Chun-Mei; Li, Mo; Huang, Jing-Zheng; Patcharapong, Treeviriyanupab; Li, Hong-Wei; Li, Fang-Yi; Wang, Chuan; Yin, Zhen-Qiang; Chen, Wei; Keattisak, Sripimanwat; Han, Zhen-Fu

2014-09-01

Post-processing is indispensable in quantum key distribution (QKD), which is aimed at sharing secret keys between two distant parties. It mainly consists of key reconciliation and privacy amplification, which is used for sharing the same keys and for distilling unconditional secret keys. In this paper, we focus on speeding up the privacy amplification process by choosing a simple multiplicative universal class of hash functions. By constructing an optimal multiplication algorithm based on four basic multiplication algorithms, we give a fast software implementation of length-adaptive privacy amplification. “Length-adaptive” indicates that the implementation of privacy amplification automatically adapts to different lengths of input blocks. When the lengths of the input blocks are 1 Mbit and 10 Mbit, the speed of privacy amplification can be as fast as 14.86 Mbps and 10.88 Mbps, respectively. Thus, it is practical for GHz or even higher repetition frequency QKD systems.

Estimation of empirical site amplification factors in Taiwan

NASA Astrophysics Data System (ADS)

Chung, Chi-Hsuan; Wen, Kuo-Liang; Kuo, Chun-Hsiang

2017-04-01

Lots of infrastructures are under construction in metropolises in Taiwan in recent years and thus leads to increasement of population density and urbanization in those area. Taiwan island is located in plate boundaries in which the high seismicity is caused by active tectonic plates. The Chi-Chi earthquake (Mw 7.6) in 1999 caused a fatality of more than 2000, and the Meinong earthquake (Mw 6.5) in 2016 caused a fatality of 117 in Tainan city as well as damages on hundreds of buildings. The cases imply seismic vulnerability of urban area. During the improvements for seismic hazard analysis and seismic design, consideration of seismic site amplifications in different site conditions is one of important issues. This study used selected and processed strong motion records observed by the TSMIP network. The site conditions considered as Vs30 used in this study were investigated at most stations (Kuo et al. 2012; Kuo et al. 2016). Since strong motion records and site conditions are both available, we are able to use the data to analyze site amplifications of seismic waves at different periods. The result may be a reference for future modification of seismic design codes to decrease potential seismic hazards and losses. We adopted the strong motion and site database of the SSHAC (Senior Seismic Hazard Analysis Committee) Level 3 project in Taiwan. The selected significant crustal and subduction events of magnitude larger than six for analysis. The amplification factors of PGA, PGV, PGD, and spectra acceleration at 0.3, 1.0, and 3.0 seconds were evaluated using the processed strong motions. According to the recommendation of SSHAC Level 3 project, the site condition of Vs30 = 760 m/s is considered as the reference rock site in this study. The stations with Vs30 between 600 m/s and 900 m/s and used as the reference rock sites in reality. For each event, we find a reference rock site and other site within a certain distance (region dependent) to calculate site amplifications

Rate and yield relationships in the production of xanthan gum by batch fermentations using complex and chemically defined growth media

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

Pinches, A.; Pallent, L.J.

1986-10-01

Rate and yield information relating to biomass and product formation and to nitrogen, glucose and oxygen consumption are described for xanthan gum batch fermentations in which both chemically defined (glutamate nitrogen) and complex (peptone nitrogen) media are employed. Simple growth and product models are used for data interpretation. For both nitrogen sources, rate and yield parameter estimates are shown to be independent of initial nitrogen concentrations. For stationary phases, specific rates of gum production are shown to be independent of nitrogen source but dependent on initial nitrogen concentration. The latter is modeled empirically and suggests caution in applying simple productmore » models to xanthan gum fermentations. 13 references.« less

Control of Brillouin short-pulse seed amplification by chirping the pump pulse

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

Lehmann, G.; Spatschek, K. H.

Seed amplification via Brillouin backscattering of a long pump pulse is considered. Similar to Raman amplification, several obstructive effects may occur during short-pulse Brillouin amplification. One is the spontaneous Raman backscattering of the pump before interacting with the seed. Preforming the plasma and/or chirping the pump will reduce unwanted pump backscattering. Optimized regions for low-loss pump propagation were proposed already in conjunction with Raman seed amplification. Hence, the influence of the chirp of the pump during Brillouin interaction with the seed becomes important and will be considered here. Both, the linear as well as the nonlinear evolution phases of themore » seed caused by Brillouin amplification under the action of a chirped pump are investigated. The amplification rate as well as the seed profiles are presented as function of the chirping rate. Also the dependence of superradiant scaling rates on the chirp parameter is discussed.« less

Noiseless amplification of weak coherent fields exploiting energy fluctuations of the field

NASA Astrophysics Data System (ADS)

Partanen, Mikko; Häyrynen, Teppo; Oksanen, Jani; Tulkki, Jukka

2012-12-01

Quantum optics dictates that amplification of a pure state by any linear deterministic amplifier always introduces noise in the signal and results in a mixed output state. However, it has recently been shown that noiseless amplification becomes possible if the requirement of a deterministic operation is relaxed. Here we propose and analyze a noiseless amplification scheme where the energy required to amplify the signal originates from the stochastic fluctuations in the field itself. In contrast to previous amplification setups, our setup shows that a signal can be amplified even if no energy is added to the signal from external sources. We investigate the relation between the amplification and its success rate as well as the statistics of the output states after successful and failed amplification processes. Furthermore, we also optimize the setup to find the maximum success rates in terms of the reflectivities of the beam splitters used in the setup and discuss the relation of our setup with the previous setups.

Weak-value amplification as an optimal metrological protocol

NASA Astrophysics Data System (ADS)

Alves, G. Bié; Escher, B. M.; de Matos Filho, R. L.; Zagury, N.; Davidovich, L.

2015-06-01

The implementation of weak-value amplification requires the pre- and postselection of states of a quantum system, followed by the observation of the response of the meter, which interacts weakly with the system. Data acquisition from the meter is conditioned to successful postselection events. Here we derive an optimal postselection procedure for estimating the coupling constant between system and meter and show that it leads both to weak-value amplification and to the saturation of the quantum Fisher information, under conditions fulfilled by all previously reported experiments on the amplification of weak signals. For most of the preselected states, full information on the coupling constant can be extracted from the meter data set alone, while for a small fraction of the space of preselected states, it must be obtained from the postselection statistics.

Climate driven crop planting date in the ACME Land Model (ALM): Impacts on productivity and yield

NASA Astrophysics Data System (ADS)

Drewniak, B.

2017-12-01

Climate is one of the key drivers of crop suitability and productivity in a region. The influence of climate and weather on the growing season determine the amount of time crops spend in each growth phase, which in turn impacts productivity and, more importantly, yields. Planting date can have a strong influence on yields with earlier planting generally resulting in higher yields, a sensitivity that is also present in some crop models. Furthermore, planting date is already changing and may continue, especially if longer growing seasons caused by future climate change drive early (or late) planting decisions. Crop models need an accurate method to predict plant date to allow these models to: 1) capture changes in crop management to adapt to climate change, 2) accurately model the timing of crop phenology, and 3) improve crop simulated influences on carbon, nutrient, energy, and water cycles. Previous studies have used climate as a predictor for planting date. Climate as a plant date predictor has more advantages than fixed plant dates. For example, crop expansion and other changes in land use (e.g., due to changing temperature conditions), can be accommodated without additional model inputs. As such, a new methodology to implement a predictive planting date based on climate inputs is added to the Accelerated Climate Model for Energy (ACME) Land Model (ALM). The model considers two main sources of climate data important for planting: precipitation and temperature. This method expands the current temperature threshold planting trigger and improves the estimated plant date in ALM. Furthermore, the precipitation metric for planting, which synchronizes the crop growing season with the wettest months, allows tropical crops to be introduced to the model. This presentation will demonstrate how the improved model enhances the ability of ALM to capture planting date compared with observations. More importantly, the impact of changing the planting date and introducing tropical

Amplification and chromosomal dispersion of human endogenous retroviral sequences

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

Steele, P.E.; Martin, M.A.; Rabson, A.B.

1986-09-01

Endogenous retroviral sequences have undergone amplification events involving both viral and flanking cellular sequences. The authors cloned members of an amplified family of full-length endogenous retroviral sequences. Genomic blotting, employing a flanking cellular DNA probe derived from a member of this family, revealed a similar array of reactive bands in both humans and chimpanzees, indicating that an amplification event involving retroviral and associated cellular DNA sequences occurred before the evolutionary separation of these two primates. Southern analyses of restricted somatic cell hybrid DNA preparations suggested that endogenous retroviral segments are widely dispersed in the human genome and that amplification andmore » dispersion events may be linked.« less

Post-Fragmentation Whole Genome Amplification-Based Method

NASA Technical Reports Server (NTRS)

Benardini, James; LaDuc, Myron T.; Langmore, John

2011-01-01

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have

Ethiopian Wheat Yield and Yield Gap Estimation: A Spatial Small Area Integrated Data Approach

NASA Astrophysics Data System (ADS)

Mann, M.; Warner, J.

2015-12-01

Despite the collection of routine annual agricultural surveys and significant advances in GIS and remote sensing products, little econometric research has been undertaken in predicting developing nation's agricultural yields. In this paper, we explore the determinants of wheat output per hectare in Ethiopia during the 2011-2013 Meher crop seasons aggregated to the woreda administrative area. Using a panel data approach, combining national agricultural field surveys with relevant GIS and remote sensing products, the model explains nearly 40% of the total variation in wheat output per hectare across the country. The model also identifies specific contributors to wheat yields that include farm management techniques (eg. area planted, improved seed, fertilizer, irrigation), weather (eg. rainfall), water availability (vegetation and moisture deficit indexes) and policy intervention. Our findings suggest that woredas produce between 9.8 and 86.5% of their potential wheat output per hectare given their altitude, weather conditions, terrain, and plant health. At the median, Amhara, Oromiya, SNNP, and Tigray produce 48.6, 51.5, 49.7, and 61.3% of their local attainable yields, respectively. This research has a broad range of applications, especially from a public policy perspective: identifying causes of yield fluctuations, remotely evaluating larger agricultural intervention packages, and analyzing relative yield potential. Overall, the combination of field surveys with spatial data can be used to identify management priorities for improving production at a variety of administrative levels.

Short-pulse amplification by strongly coupled stimulated Brillouin scattering

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

Edwards, Matthew R., E-mail: mredward@princeton.edu; Mikhailova, Julia M.; Jia, Qing

2016-08-15

We examine the feasibility of strongly coupled stimulated Brillouin scattering as a mechanism for the plasma-based amplification of sub-picosecond pulses. In particular, we use fluid theory and particle-in-cell simulations to compare the relative advantages of Raman and Brillouin amplification over a broad range of achievable parameters.

Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay.

PubMed

Zhou, Dinggang; Wang, Chunfeng; Li, Zhu; Chen, Yun; Gao, Shiwu; Guo, Jinlong; Lu, Wenying; Su, Yachun; Xu, Liping; Que, Youxiong

2016-01-01

Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg(2+), 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane.

Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

PubMed Central

Zhou, Dinggang; Wang, Chunfeng; Li, Zhu; Chen, Yun; Gao, Shiwu; Guo, Jinlong; Lu, Wenying; Su, Yachun; Xu, Liping; Que, Youxiong

2016-01-01

Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg2+, 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane. PMID:27014303

Rapid sex identification of papaya (Carica papaya) using multiplex loop-mediated isothermal amplification (mLAMP).

PubMed

Hsu, Te-Hua; Gwo, Jin-Chywan; Lin, Kuan-Hung

2012-10-01

Papaya (Carica papaya L.) is established as a cash crop throughout the tropical and subtropical regions due to its easy adaptation to diverse agricultural conditions, high yields, and prompt returns. The sex types of papaya plants are hermaphrodite, male, and female. Among them, hermaphroditic plants are the major type in papaya production, because the fruit has commercial advantages over that of the other sexes. Sex inheritance in papaya is determined by the M and M(h) dominant alleles in males and hermaphrodites, respectively, and a recessive m allele in females. Currently, all hermaphrodite seeds are not available due to the lethality of dominant homozygosity. Therefore, in this study, six male-hermaphrodite-specific markers were developed for a rapid sex identification using multiplex loop-mediated isothermal amplification (mLAMP) to efficiently and precisely select hermaphroditic individuals in the seedling or early growth stage. The LM1-LAMP assay consisted of two sex-LAMP reactions for amplifying two male-specific markers (T12 and Cpsm90) in one reaction, and showed several advantages in terms of a rapid reaction time (<1 h), isothermal conditions (less equipment required), a high efficiency (0.5 ng of DNA required in the reaction mixture), and an economical reaction system (5 μl in volume). The established method can be easily performed in the field by visual inspection and facilitates the selection of all hermaphroditic individuals in papaya production.

DNA sequence responsible for the amplification of adjacent genes.

PubMed

Pasion, S G; Hartigan, J A; Kumar, V; Biswas, D K

1987-10-01

A 10.3-kb DNA fragment in the 5'-flanking region of the rat prolactin (rPRL) gene was isolated from F1BGH(1)2C1, a strain of rat pituitary tumor cells (GH cells) that produces prolactin in response to 5-bromodeoxyuridine (BrdU). Following transfection and integration into genomic DNA of recipient mouse L cells, this DNA induced amplification of the adjacent thymidine kinase gene from Herpes simplex virus type 1 (HSV1TK). We confirmed the ability of this "Amplicon" sequence to induce amplification of other linked or unlinked genes in DNA-mediated gene transfer studies. When transferred into the mouse L cells with the 10.3-5'rPRL gene sequence of BrdU-responsive cells, both the human growth hormone and the HSV1TK genes are amplified in response to 5-bromodeoxyuridine. This observation is substantiated by BrdU-induced amplification of the cotransferred bacterial Neo gene. Cotransfection studies reveal that the BrdU-induced amplification capability is associated with a 4-kb DNA sequence in the 5'-flanking region of the rPRL gene of BrdU-responsive cells. These results demonstrate that genes of heterologous origin, linked or unlinked, and selected or unselected, can be coamplified when located within the amplification boundary of the Amplicon sequence.

Freshly excavated fossil bones are best for amplification of ancient DNA.

PubMed

Pruvost, Mélanie; Schwarz, Reinhard; Correia, Virginia Bessa; Champlot, Sophie; Braguier, Séverine; Morel, Nicolas; Fernandez-Jalvo, Yolanda; Grange, Thierry; Geigl, Eva-Maria

2007-01-16

Despite the enormous potential of analyses of ancient DNA for phylogeographic studies of past populations, the impact these analyses, most of which are performed with fossil samples from natural history museum collections, has been limited to some extent by the inefficient recovery of ancient genetic material. Here we show that the standard storage conditions and/or treatments of fossil bones in these collections can be detrimental to DNA survival. Using a quantitative paleogenetic analysis of 247 herbivore fossil bones up to 50,000 years old and originating from 60 different archeological and paleontological contexts, we demonstrate that freshly excavated and nontreated unwashed bones contain six times more DNA and yield twice as many authentic DNA sequences as bones treated with standard procedures. This effect was even more pronounced with bones from one Neolithic site, where only freshly excavated bones yielded results. Finally, we compared the DNA content in the fossil bones of one animal, a approximately 3,200-year-old aurochs, excavated in two separate seasons 57 years apart. Whereas the washed museum-stored fossil bones did not permit any DNA amplification, all recently excavated bones yielded authentic aurochs sequences. We established that during the 57 years when the aurochs bones were stored in a collection, at least as much amplifiable DNA was lost as during the previous 3,200 years of burial. This result calls for a revision of the postexcavation treatment of fossil bones to better preserve the genetic heritage of past life forms.

Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum

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

Biswas, Ranjita; Prabhu, Sandeep; Lynd, Lee R

2014-01-01

Large-scale production of lignocellulosic biofuel is a potential solution to sustainably meet global energy needs. One-step consolidated bioprocessing (CBP) is a potentially advantageous approach for the production of biofuels, but requires an organism capable of hydrolyzing biomass to sugars and fermenting the sugars to ethanol at commercially viable titers and yields. Clostridium thermocellum, a thermophilic anaerobe, can ferment cellulosic biomass to ethanol and organic acids, but low yield, low titer, and ethanol sensitivity remain barriers to industrial production. Here, we deleted the hypoxanthine phosphoribosyltransferase gene in ethanol tolerant strain of C. thermocellum adhE*(EA) in order to allow use of previouslymore » developed gene deletion tools, then deleted lactate dehydrogenase (ldh) to redirect carbon flux towards ethanol. Upon deletion of ldh, the adhE*(EA) ldh strain produced 30% more ethanol than wild type on minimal medium. The adhE*(EA) ldh strain retained tolerance to 5% v/v ethanol, resulting in an ethanol tolerant platform strain of C. thermocellum for future metabolic engineering efforts.« less

Role of Atmospheric Transport on the Arctic Amplification: Adjusting Role

NASA Astrophysics Data System (ADS)

KUG, J.; Yim, B.; Jin, F.

2013-12-01

It is controversial whether the atmospheric transport plays a role in arctic amplification. Recently, Hwang et al. (2011) showed that the magnitude of the arctic amplification is negatively correlated with anomalous poleward atmospheric transport. That is, when the arctic amplification is strong (weak), the atmospheric transport plays a negative (positive) role in the arctic amplification. In this study, it is discussed what is a physical mechanism to determine the role of atmospheric transport and relation with the arctic amplification. Here, we suggest adjusting roles of atmospheric transport. The strength of local feedback over the Arctic determines zonal wind changes. The zonal wind changes are determined by two factors. The first one is polar cap cooling, and second is surface warming. They play opposite roles. So, there will be two different zonal wind responses in high-latitude to the greenhouse warming. Depending on the zonal wind response, the atmospheric transport can play a different role because the zonal wind changes can organize synoptic eddy feedbacks including heat flux, which largely contributes to poleward energy transport. We show here that when polar cap cooling is strong, and surface warming over Arctic is relatively weak, the Jet stream tends to be shifted poleward, so it leads to poleward atmospheric transport. On the other hand, when the surface warming is too strong, it lead to southward shift of Jet stream and equatorward atmospheric transport, which paly a negative role in the Arctic amplification.

HPV-18 E6 mutants reveal p53 modulation of viral DNA amplification in organotypic cultures

PubMed Central

Kho, Eun-Young; Wang, Hsu-Kun; Banerjee, N. Sanjib; Broker, Thomas R.; Chow, Louise T.

2013-01-01

Human papillomaviruses (HPVs) amplify in differentiated strata of a squamous epithelium. The HPV E7 protein destabilizes the p130/retinoblastoma susceptibility protein family of tumor suppressors and reactivates S-phase reentry, thereby facilitating viral DNA amplification. The high-risk HPV E6 protein destabilizes the p53 tumor suppressor and many other host proteins. However, the critical E6 targets relevant to viral DNA amplification have not been identified, because functionally significant E6 mutants are not stably maintained in transfected cells. Using Cre-loxP recombination, which efficiently generates HPV genomic plasmids in transfected primary human keratinocytes, we have recapitulated a highly productive infection of HPV-18 in organotypic epithelial cultures. By using this system, we now report the characterization of four HPV-18 E6 mutations. An E6 null mutant accumulated high levels of p53 and amplified very poorly. p53 siRNA or ectopic WT E6 partially restored amplification, whereas three missense E6 mutations that did not effectively destabilize p53 complemented the null mutant poorly. Unexpectedly, in cis, two of the missense mutants amplified, albeit to a lower extent than the WT and only in cells with undetectable p53. These observations and others implicate p53 and additional host proteins in regulating viral DNA amplification and also suggest an inhibitory effect of E6 overexpression. We show that high levels of viral DNA amplification are critical for late protein expression and report several previously undescribed viral RNAs, including bicistronic transcripts predicted to encode E5 and L2 or an alternative form of E1^E4 and L1. PMID:23572574

Design of nuclease-based target recycling signal amplification in aptasensors.

PubMed

Yan, Mengmeng; Bai, Wenhui; Zhu, Chao; Huang, Yafei; Yan, Jiao; Chen, Ailiang

2016-03-15

Compared with conventional antibody-based immunoassay methods, aptasensors based on nucleic acid aptamer have made at least two significant breakthroughs. One is that aptamers are more easily used for developing various simple and rapid homogeneous detection methods by "sample in signal out" without multi-step washing. The other is that aptamers are more easily employed for developing highly sensitive detection methods by using various nucleic acid-based signal amplification approaches. As many substances playing regulatory roles in physiology or pathology exist at an extremely low concentration and many chemical contaminants occur in trace amounts in food or environment, aptasensors for signal amplification contribute greatly to detection of such targets. Among the signal amplification approaches in highly sensitive aptasensors, the nuclease-based target recycling signal amplification has recently become a research focus because it shows easy design, simple operation, and rapid reaction and can be easily developed for homogenous assay. In this review, we summarized recent advances in the development of various nuclease-based target recycling signal amplification with the aim to provide a general guide for the design of aptamer-based ultrasensitive biosensing assays. Copyright © 2015 Elsevier B.V. All rights reserved.

What is the Best Model Specification and Earth Observation Product for Predicting Regional Grain Yields in Food Insecure Countries?

NASA Astrophysics Data System (ADS)

Davenport, F., IV; Harrison, L.; Shukla, S.; Husak, G. J.; Funk, C. C.

2017-12-01

We evaluate the predictive accuracy of an ensemble of empirical model specifications that use earth observation data to predict sub-national grain yields in Mexico and East Africa. Products that are actively used for seasonal drought monitoring are tested as yield predictors. Our research is driven by the fact that East Africa is a region where decisions regarding agricultural production are critical to preventing the loss of economic livelihoods and human life. Regional grain yield forecasts can be used to anticipate availability and prices of key staples, which can turn can inform decisions about targeting humanitarian response such as food aid. Our objective is to identify-for a given region, grain, and time year- what type of model and/or earth observation can most accurately predict end of season yields. We fit a set of models to county level panel data from Mexico, Kenya, Sudan, South Sudan, and Somalia. We then examine out of sample predicative accuracy using various linear and non-linear models that incorporate spatial and time varying coefficients. We compare accuracy within and across models that use predictor variables from remotely sensed measures of precipitation, temperature, soil moisture, and other land surface processes. We also examine at what point in the season a given model or product is most useful for determining predictive accuracy. Finally we compare predictive accuracy across a variety of agricultural regimes including high intensity irrigated commercial agricultural and rain fed subsistence level farms.

A polymorphism in the bovine gamma-S-crystallin gene revealed by allele-specific amplification.

PubMed

Kemp, S J; Maillard, J C; Teale, A J

1993-04-01

A polymorphism was detected in the 3' untranslated region of the bovine gamma-S-crystallin gene by direct sequencing of polymerase chain reaction (PCR) products from genomic DNA of an N'Dama bull and a Boran cow. A set of three PCR primers was designed to detect this difference and thus give allele-specific amplification. The two allele-specific primers differ in length by 20 nucleotides so that the allelic products may be distinguished by simple agarose gel electrophoresis following a single PCR reaction. This provides a simple and rapid assay for this polymorphism.

Amplification in Double Heterostructure GaAs Lasers.

DTIC Science & Technology

1981-03-15

done, for example, in the book by Siegman . When the laser signal which is to be amplified is a single mode, it is important to include the possibility...k A’AD-A097 862 AEROSPACE CORP EL SEGUNDO CA ELECTRONICS RESEARCH LAP) P 5 20/5 I AMPLIFICATION IN DOUBLE HETEROSTRUCTURE GAAS LASERS .(U IMAR al E...GARMIRE, M CHANG F04701-80-C-0081I UNCLASSIFIED TR GO81(6930 03)-2 SD-TA8-30 NL Amplification in Double Heterostructure GaAs Lasers E. GARMIRE nd M

Modified telomeric repeat amplification protocol: a quantitative radioactive assay for telomerase without using electrophoresis.

PubMed

Szatmari, I; Tókés, S; Dunn, C B; Bardos, T J; Aradi, J

2000-06-15

A polymerase chain reaction (PCR)-based radioactive telomerase assay was developed in our laboratory which is quantitative and does not require electrophoretic evaluation (designated as TP-TRAP; it utilizes two reverse primers). The main steps of the assay include (1) extension of a 20-mer oligonucleotide substrate (MTS) by telomerase, (2) amplification of the telomerase products in the presence of [(3)H]dTTP using the substrate oligonucleotide and two reverse primers (RPC3, 38 mer; RP, 20 mer), (3) isolation of the amplified radioactive dsDNA by precipitation and filtration, (4) determination of the radioactivity of the acid-insoluble DNA. The length of the telomerase products does not increase on amplification. This valuable feature of the assay is achieved by utilization of the two reverse primers and a highly specific PCR protocol. The assay is linear, accurate, and suitable for cell-biological studies where slight quantitative differences in telomerase activity must be detected. The assay is also suitable for screening and characterization of telomerase inhibitors, as shown with a chemically modified oligonucleotide reverse transcriptase inhibitor [(s(4)dU)(35)]. Copyright 2000 Academic Press.

Femtosecond optical parametric amplification in BBO and KTA driven by a Ti:sapphire laser for LIDT testing and diagnostic development

NASA Astrophysics Data System (ADS)

Meadows, Alexander R.; Cupal, Josef; Hříbek, Petr; Durák, Michal; Kramer, Daniel; Rus, Bedřich

2017-05-01

We present the design of a collinear femtosecond optical parametric amplification (OPA) system producing a tunable output at wavelengths between 1030 nm and 1080 nm from a Ti:Sapphire pump laser at a wavelength of 795 nm. Generation of a supercontinuum seed pulse is followed by one stage of amplification in Beta Barium Borate (BBO) and two stages of amplification in Potassium Titanyle Arsenate (KTA), resulting in a 225 μJ output pulse with a duration of 90 fs. The output of the system has been measured by self-referenced spectral interferometry to yield the complete spectrum and spectral phase of the pulse. When compared to KTP, the greater transparency of KTA in the spectral range from 3 - 4 μm allows for reduced idler absorption and enhanced gain from the OPA process when it is pumped by the fundamental frequency of a Ti:sapphire laser. In turn, the use of the Ti:sapphire fundamental at 795 nm as a pump improves the efficiency with which light can be converted to wavelengths between 1030 nm and 1080 nm and subsequently used to test components for Nd-based laser systems. This OPA system is operated at 1 kHz for diagnostic development and laser-induced damage threshold testing of optical components for the ELI-Beamlines project.

Towards in vivo amplification: Overcoming hurdles in the use of hematopoietic stem cells in transplantation and gene therapy

PubMed Central

Nagree, Murtaza S; López-Vásquez, Lucía; Medin, Jeffrey A

2015-01-01

With the advent of safer and more efficient gene transfer methods, gene therapy has become a viable solution for many inherited and acquired disorders. Hematopoietic stem cells (HSCs) are a prime cell compartment for gene therapy aimed at correcting blood-based disorders, as well as those amenable to metabolic outcomes that can effect cross-correction. While some resounding clinical successes have recently been demonstrated, ample room remains to increase the therapeutic output from HSC-directed gene therapy. In vivo amplification of therapeutic cells is one avenue to achieve enhanced gene product delivery. To date, attempts have been made to provide HSCs with resistance to cytotoxic drugs, to include drug-inducible growth modules specific to HSCs, and to increase the engraftment potential of transduced HSCs. This review aims to summarize amplification strategies that have been developed and tested and to discuss their advantages along with barriers faced towards their clinical adaptation. In addition, next-generation strategies to circumvent current limitations of specific amplification schemas are discussed. PMID:26730268

Exploratory study of fission product yields of neutron-induced fission of U 235 ,   U 238 , and Pu 239 at 8.9 MeV

DOE PAGES

Bhatia, C.; Fallin, B. F.; Gooden, M. E.; ...

2015-06-05

Using dual-fission chambers each loaded with a thick (200–400–mg/cm 2) actinide target of 235,238U or 239Pu and two thin (~10–100–μg/cm 2) reference foils of the same actinide, the cumulative yields of fission products ranging from 92Sr to 147Nd have been measured at E n = 8.9MeV. The 2H(d,n) 3He reaction provided the quasimonoenergetic neutron beam. Here, the experimental setup and methods used to determine the fission product yield (FPY) are described, and results for typically eight high-yield fission products are presented.

New perspectives on microbial community distortion after whole-genome amplification

EPA Science Inventory

Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the e...

Culture medium pH influence on Gluconacetobacter physiology: Cellulose production rate and yield enhancement in presence of multiple carbon sources.

PubMed

Yassine, Fatima; Bassil, Nathalie; Flouty, Roula; Chokr, Ali; Samrani, Antoine El; Boiteux, Gisèle; Tahchi, Mario El

2016-08-01

Gluconacetobacter genera are valued for bacterial cellulose (BC) and acetic acid production. BC is produced at optimal yields in classical microbiological media that are expensive for a large scale of production. In addition, BC usage for industrial purposes is limited due to low conversion rate into cellulose and to long incubation duration. In this paper, Gluconacetobacter isolated from apple vinegar was kinetically studied to evaluate cellulose production in presence of different carbon sources. Acetic and citric acid effect on Gluconacetobacter metabolism is clarified. It was shown that Gluconacetobacter uses glucose as a primary carbon source for cells growth and products formation. Acetic acid employment as a co-carbon source in Hestrin Schramm medium showed an increase of 17% in BC yield with a moderate decrease in the crystallite size of the resulting polymer. Copyright © 2016 Elsevier Ltd. All rights reserved.

CCNE1 amplification is associated with aggressive potential in endometrioid endometrial carcinomas.

PubMed

Nakayama, Kentaro; Rahman, Mohammed Tanjimur; Rahman, Munmun; Nakamura, Kohei; Ishikawa, Masako; Katagiri, Hiroshi; Sato, Emi; Ishibashi, Tomoka; Iida, Kouji; Ishikawa, Noriyuki; Kyo, Satoru

2016-02-01

The clinicopathological significance of amplification was investigated of the gene encoding cyclin E (CCNE1) and we assessed whether CCNE1 was a potential target in endometrioid endometrial carcinomas. CCNE1 amplification and CCNE1 or F-box and WD repeat domain-containing 7 (FBXW7) expression in endometrial endometrioid carcinoma was assessed by immunohistochemistry and fluorescence in situ hybridization. CCNE1 knockdown by small interfering RNA (siRNA) was used to assess the CCNE1 function. The results showed that CCNE1 amplification was present in 9 (8.3%) of 108 endometrial carcinomas. CCNE1 amplification was correlated with high histological grade (Grade 3; p=0.0087) and lymphovascular space invasion (p=0.0258). No significant association was observed between CCNE1 amplification and FIGO stage (p=0.851), lymph node metastasis (p=0.078), body mass index (p=0.265), deep myometrial invasion (p=0.256), menopausal status (p=0.289) or patient age (p=0.0817). CCNE1 amplification was significantly correlated with shorter progression-free and overall survival (p=0.0081 and 0.0073, respectively). CCNE1 protein expression or loss of FBXW7 expression in endometrial endometrioid carcinoma tended to be correlated with shorter progression-free and overall survival; however, this difference was not statistically significant. Multivariate analysis showed that CCNE1 amplification was an independent prognostic factor for overall survival but not for progression-free survival (P=0.0454 and 0.2175, respectively). Profound growth inhibition was observed in siRNA-transfected cancer cells with endogenous CCNE1 overexpression compared with that in cancer cells having low CCNE1 expression. CCNE1 amplification was independent of p53, HER2, MLH1 and ARID1A expression but dependent on PTEN expression in endometrial carcinomas. These findings indicated that CCNE1 amplification was critical for the survival of endometrial endometrioid carcinomas. Furthermore, the effects of CCNE1 knockdown

CCNE1 amplification is associated with aggressive potential in endometrioid endometrial carcinomas

PubMed Central

NAKAYAMA, KENTARO; RAHMAN, MOHAMMED TANJIMUR; RAHMAN, MUNMUN; NAKAMURA, KOHEI; ISHIKAWA, MASAKO; KATAGIRI, HIROSHI; SATO, EMI; ISHIBASHI, TOMOKA; IIDA, KOUJI; ISHIKAWA, NORIYUKI; KYO, SATORU

2016-01-01

The clinicopathological significance of amplification was investigated of the gene encoding cyclin E (CCNE1) and we assessed whether CCNE1 was a potential target in endometrioid endometrial carcinomas. CCNE1 amplification and CCNE1 or F-box and WD repeat domain-containing 7 (FBXW7) expression in endometrial endometrioid carcinoma was assessed by immunohistochemistry and fluorescence in situ hybridization. CCNE1 knockdown by small interfering RNA (siRNA) was used to assess the CCNE1 function. The results showed that CCNE1 amplification was present in 9 (8.3%) of 108 endometrial carcinomas. CCNE1 amplification was correlated with high histological grade (Grade 3; P=0.0087) and lymphovascular space invasion (P=0.0258). No significant association was observed between CCNE1 amplification and FIGO stage (P=0.851), lymph node metastasis (P=0.078), body mass index (P=0.265), deep myometrial invasion (P=0.256), menopausal status (P=0.289) or patient age (P=0.0817). CCNE1 amplification was significantly correlated with shorter progression-free and overall survival (P=0.0081 and 0.0073, respectively). CCNE1 protein expression or loss of FBXW7 expression in endometrial endometrioid carcinoma tended to be correlated with shorter progression-free and overall survival; however, this difference was not statistically significant. Multivariate analysis showed that CCNE1 amplification was an independent prognostic factor for overall survival but not for progression-free survival (P=0.0454 and 0.2175, respectively). Profound growth inhibition was observed in siRNA-transfected cancer cells with endogenous CCNE1 overexpression compared with that in cancer cells having low CCNE1 expression. CCNE1 amplification was independent of p53, HER2, MLH1 and ARID1A expression but dependent on PTEN expression in endometrial carcinomas. These findings indicated that CCNE1 amplification was critical for the survival of endometrial endometrioid carcinomas. Furthermore, the effects of CCNE1 knockdown

Mass-yield distributions of fission products from 20, 32, and 45 MeV proton-induced fission of 232Th

NASA Astrophysics Data System (ADS)

Naik, H.; Goswami, A.; Kim, G. N.; Kim, K.; Suryanarayana, S. V.

2013-10-01

The yields of various fission products in the 19.6, 32.2, and 44.8 MeV proton-induced fission of 232Th have been determined by recoil catcher and an off-line γ-ray spectrometric technique using the BARC-TIFR Pelletron in India and MC-50 cyclotron in Korea. The mass-yield distributions were obtained from the fission product yield using the charge distribution corrections. The peak-to-valley (P/V) ratio of the present work and that of literature data for 232Th(p,f) and 238U(p,f) were obtained from the mass yield distribution. The present and the existing literature data for 232Th(p,f), 232Th(n,f), and 232Th( γ,f) at various energies were compared with those for 238U(p,f), 238U(n,f), and 238U( γ,f) to examine the probable nuclear structure effect. The role of Th-anomaly on the peak-to-valley ratio in proton-, neutron-, and photon-induced fission of 232Th was discussed with the similar data in 238U. On the other hand, the fine structure in the mass yield distributions of the fissioning systems at various excitation energies has been explained from the point of standard I and II asymmetric mode of fission besides the probable role of even-odd effect, A/ Z ratio, and fissility parameter.

Modeling magnetic field amplification in nonlinear diffusive shock acceleration

NASA Astrophysics Data System (ADS)

Vladimirov, Andrey

2009-02-01

This research was motivated by the recent observations indicating very strong magnetic fields at some supernova remnant shocks, which suggests in-situ generation of magnetic turbulence. The dissertation presents a numerical model of collisionless shocks with strong amplification of stochastic magnetic fields, self-consistently coupled to efficient shock acceleration of charged particles. Based on a Monte Carlo simulation of particle transport and acceleration in nonlinear shocks, the model describes magnetic field amplification using the state-of-the-art analytic models of instabilities in magnetized plasmas in the presence of non-thermal particle streaming. The results help one understand the complex nonlinear connections between the thermal plasma, the accelerated particles and the stochastic magnetic fields in strong collisionless shocks. Also, predictions regarding the efficiency of particle acceleration and magnetic field amplification, the impact of magnetic field amplification on the maximum energy of accelerated particles, and the compression and heating of the thermal plasma by the shocks are presented. Particle distribution functions and turbulence spectra derived with this model can be used to calculate the emission of observable nonthermal radiation.

An Intrinsically Digital Amplification Scheme for Hearing Aids

NASA Astrophysics Data System (ADS)

Blamey, Peter J.; Macfarlane, David S.; Steele, Brenton R.

2005-12-01

Results for linear and wide-dynamic range compression were compared with a new 64-channel digital amplification strategy in three separate studies. The new strategy addresses the requirements of the hearing aid user with efficient computations on an open-platform digital signal processor (DSP). The new amplification strategy is not modeled on prior analog strategies like compression and linear amplification, but uses statistical analysis of the signal to optimize the output dynamic range in each frequency band independently. Using the open-platform DSP processor also provided the opportunity for blind trial comparisons of the different processing schemes in BTE and ITE devices of a high commercial standard. The speech perception scores and questionnaire results show that it is possible to provide improved audibility for sound in many narrow frequency bands while simultaneously improving comfort, speech intelligibility in noise, and sound quality.

Does switching to a tobacco-free waterpipe product reduce toxicant intake? A crossover study comparing CO, NO, PAH, volatile aldehydes, tar and nicotine yields

PubMed Central

Shihadeh, Alan; Salman, Rola; Jaroudi, Ezzat; Saliba, Najat; Sepetdjian, Elizabeth; Blank, Melissa D.; Cobb, Caroline O.; Eissenberg, Thomas

2012-01-01

Waterpipe (hookah, narghile, shisha) use has become a global phenomenon, with numerous product variations. One variation is a class of products marketed as “tobacco-free” alternatives for the “health conscious user”. In this study toxicant yields from waterpipes smoked using conventional tobacco-based and tobacco-free preparations were compared. A human-mimic waterpipe smoking machine was used to replicate the puffing sequences of 31 human participants who completed two double-blind ad libitum smoking sessions in a controlled clinical setting: once with a tobacco-based product of their choosing and once with a flavor-matched tobacco-free product. Outcome measures included yields of carbon monoxide, nitric oxide, volatile aldehydes, nicotine, tar, and polycyclic aromatic hydrocarbons. Smoke from both waterpipe preparations contained substantial quantities of toxicants. Nicotine yield was the only outcome that differed significantly between preparations. These findings contradict advertising messages that “herbal” waterpipe products are a healthy alternative to tobacco products. PMID:22406330

Rare decay of the top quark t{yields}cll and single top quark production at the ILC

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

Frank, Mariana; Turan, Ismail

We perform a complete and detailed analysis of the flavor changing neutral current rare top quark decays t{yields}cl{sup +}l{sup -} and t{yields}c{nu}{sub i}{nu}{sub i} at one-loop level in the standard model, two Higgs doublet models (I and II), and in minimal supersymmetric standard model (MSSM). The branching ratios are very small in all models, O(10{sup -14}), except for the case of the unconstrained MSSM, where they can reach O(10{sup -6}) for e{sup +}e{sup -}, {mu}{sup +}{mu}{sup -}, and {nu}{sub i}{nu}{sub i}, and O(10{sup -5}) for {tau}{sup +}{tau}{sup -}. This branching ratio is comparable to the ones for t{yields}cV, cH. Wemore » also study the production rates of single top and the forward-backward asymmetry in e{sup +}e{sup -}{yields}tc and comment on the observability of such a signal at the International Linear Collider.« less

Sequencing of the large dsDNA genome of Oryctes rhinoceros nudivirus using multiple displacement amplification of nanogram amounts of virus DNA.

PubMed

Wang, Yongjie; Kleespies, Regina G; Ramle, Moslim B; Jehle, Johannes A

2008-09-01

The genomic sequence analysis of many large dsDNA viruses is hampered by the lack of enough sample materials. Here, we report a whole genome amplification of the Oryctes rhinoceros nudivirus (OrNV) isolate Ma07 starting from as few as about 10 ng of purified viral DNA by application of phi29 DNA polymerase- and exonuclease-resistant random hexamer-based multiple displacement amplification (MDA) method. About 60 microg of high molecular weight DNA with fragment sizes of up to 25 kbp was amplified. A genomic DNA clone library was generated using the product DNA. After 8-fold sequencing coverage, the 127,615 bp of OrNV whole genome was sequenced successfully. The results demonstrate that the MDA-based whole genome amplification enables rapid access to genomic information from exiguous virus samples.

Statistical Optimization of 1,3-Propanediol (1,3-PD) Production from Crude Glycerol by Considering Four Objectives: 1,3-PD Concentration, Yield, Selectivity, and Productivity.

PubMed

Supaporn, Pansuwan; Yeom, Sung Ho

2018-04-30

This study investigated the biological conversion of crude glycerol generated from a commercial biodiesel production plant as a by-product to 1,3-propanediol (1,3-PD). Statistical analysis was employed to derive a statistical model for the individual and interactive effects of glycerol, (NH 4 ) 2 SO 4 , trace elements, pH, and cultivation time on the four objectives: 1,3-PD concentration, yield, selectivity, and productivity. Optimum conditions for each objective with its maximum value were predicted by statistical optimization, and experiments under the optimum conditions verified the predictions. In addition, by systematic analysis of the values of four objectives, optimum conditions for 1,3-PD concentration (49.8 g/L initial glycerol, 4.0 g/L of (NH 4 ) 2 SO 4 , 2.0 mL/L of trace element, pH 7.5, and 11.2 h of cultivation time) were determined to be the global optimum culture conditions for 1,3-PD production. Under these conditions, we could achieve high 1,3-PD yield (47.4%), 1,3-PD selectivity (88.8%), and 1,3-PD productivity (2.1/g/L/h) as well as high 1,3-PD concentration (23.6 g/L).

A Remote Sensing-Derived Corn Yield Assessment Model

NASA Astrophysics Data System (ADS)

Shrestha, Ranjay Man

Agricultural studies and food security have become critical research topics due to continuous growth in human population and simultaneous shrinkage in agricultural land. In spite of modern technological advancements to improve agricultural productivity, more studies on crop yield assessments and food productivities are still necessary to fulfill the constantly increasing food demands. Besides human activities, natural disasters such as flood and drought, along with rapid climate changes, also inflect an adverse effect on food productivities. Understanding the impact of these disasters on crop yield and making early impact estimations could help planning for any national or international food crisis. Similarly, the United States Department of Agriculture (USDA) Risk Management Agency (RMA) insurance management utilizes appropriately estimated crop yield and damage assessment information to sustain farmers' practice through timely and proper compensations. Through County Agricultural Production Survey (CAPS), the USDA National Agricultural Statistical Service (NASS) uses traditional methods of field interviews and farmer-reported survey data to perform annual crop condition monitoring and production estimations at the regional and state levels. As these manual approaches of yield estimations are highly inefficient and produce very limited samples to represent the entire area, NASS requires supplemental spatial data that provides continuous and timely information on crop production and annual yield. Compared to traditional methods, remote sensing data and products offer wider spatial extent, more accurate location information, higher temporal resolution and data distribution, and lower data cost--thus providing a complementary option for estimation of crop yield information. Remote sensing derived vegetation indices such as Normalized Difference Vegetation Index (NDVI) provide measurable statistics of potential crop growth based on the spectral reflectance and could

Single molecule sequencing of the M13 virus genome without amplification.

PubMed

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X; Yan, Qin; Deem, Michael W; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Word Recognition and Learning: Effects of Hearing Loss and Amplification Feature

PubMed Central

Stewart, Elizabeth C.; Willman, Amanda P.; Odgear, Ian S.

2017-01-01

Two amplification features were examined using auditory tasks that varied in stimulus familiarity. It was expected that the benefits of certain amplification features would increase as the familiarity with the stimuli decreased. A total of 20 children and 15 adults with normal hearing as well as 21 children and 17 adults with mild to severe hearing loss participated. Three models of ear-level devices were selected based on the quality of the high-frequency amplification or the digital noise reduction (DNR) they provided. The devices were fitted to each participant and used during testing only. Participants completed three tasks: (a) word recognition, (b) repetition and lexical decision of real and nonsense words, and (c) novel word learning. Performance improved significantly with amplification for both the children and the adults with hearing loss. Performance improved further with wideband amplification for the children more than for the adults. In steady-state noise and multitalker babble, performance decreased for both groups with little to no benefit from amplification or from the use of DNR. When compared with the listeners with normal hearing, significantly poorer performance was observed for both the children and adults with hearing loss on all tasks with few exceptions. Finally, analysis of across-task performance confirmed the hypothesis that benefit increased as the familiarity of the stimuli decreased for wideband amplification but not for DNR. However, users who prefer DNR for listening comfort are not likely to jeopardize their ability to detect and learn new information when using this feature. PMID:29169314

Increased centrosome amplification in aged stem cells of the Drosophila midgut

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

Park, Joung-Sun; Pyo, Jung-Hoon; Na, Hyun-Jin

Highlights: • Increased centrosome amplification in ISCs of aged Drosophila midguts. • Increased centrosome amplification in ISCs of oxidative stressed Drosophila midguts. • Increased centrosome amplification in ISCs by overexpression of PVR, EGFR, and AKT. • Supernumerary centrosomes can be responsible for abnormal ISC polyploid cells. • Supernumerary centrosomes can be a useful marker for aging stem cells. - Abstract: Age-related changes in long-lived tissue-resident stem cells may be tightly linked to aging and age-related diseases such as cancer. Centrosomes play key roles in cell proliferation, differentiation and migration. Supernumerary centrosomes are known to be an early event in tumorigenesismore » and senescence. However, the age-related changes of centrosome duplication in tissue-resident stem cells in vivo remain unknown. Here, using anti-γ-tubulin and anti-PH3, we analyzed mitotic intestinal stem cells with supernumerary centrosomes in the adult Drosophila midgut, which may be a versatile model system for stem cell biology. The results showed increased centrosome amplification in intestinal stem cells of aged and oxidatively stressed Drosophila midguts. Increased centrosome amplification was detected by overexpression of PVR, EGFR, and AKT in intestinal stem cells/enteroblasts, known to mimic age-related changes including hyperproliferation of intestinal stem cells and hyperplasia in the midgut. Our data show the first direct evidence for the age-related increase of centrosome amplification in intestinal stem cells and suggest that the Drosophila midgut is an excellent model for studying molecular mechanisms underlying centrosome amplification in aging adult stem cells in vivo.« less

Photoactive roadways: Determination of CO, NO and VOC uptake coefficients and photolabile side product yields on TiO2 treated asphalt and concrete

NASA Astrophysics Data System (ADS)

Toro, C.; Jobson, B. T.; Haselbach, L.; Shen, S.; Chung, S. H.

2016-08-01

This work reports uptake coefficients and by-product yields of ozone precursors onto two photocatalytic paving materials (asphalt and concrete) treated with a commercial TiO2 surface application product. The experimental approach used a continuously stirred tank reactor (CSTR) and allowed for testing large samples with the same surface morphology encountered with real urban surfaces. The measured uptake coefficient (γgeo) and surface resistances are useful for parametrizing dry deposition velocities in air quality model evaluation of the impact of photoactive surfaces on urban air chemistry. At 46% relative humidity, the surface resistance to NO uptake was ∼1 s cm-1 for concrete and ∼2 s cm-1 for a freshly coated older roadway asphalt sample. HONO and NO2 were detected as side products from NO uptake to asphalt, with NO2 molar yields on the order of 20% and HONO molar yields ranging between 14 and 33%. For concrete samples, the NO2 molar yields increased with the increase of water vapor, ranging from 1% to 35% and HONO was not detected as a by-product. Uptake of monoaromatic VOCs to the asphalt sample set displayed a dependence on the compound vapor pressure, and was influenced by competitive adsorption from less volatile VOCs. Formaldehyde and acetaldehyde were detected as byproducts, with molar yields ranging from 5 to 32%.

Impact of the lignocellulosic material on fast pyrolysis yields and product quality.

PubMed

Carrier, Marion; Joubert, Jan-Erns; Danje, Stephen; Hugo, Thomas; Görgens, Johann; Knoetze, Johannes Hansie

2013-12-01

The paper describes the fast pyrolysis conversion of lignocellulosic materials inside a bubbling fluidized bed. The impact of biopolymers distribution in the biomass feed, namely hemicelluloses, cellulose and lignin, on the yields and properties of pyrolytic bio-oils and chars was investigated. Although it is not possible to deconvoluate chemical phenomena from transfer phenomena using bubbling fluidized bed reactors, the key role of hemicelluloses in biomass feedstocks was illustrated by: (i) its influence on the production of pyrolytic water, (ii) its impact on the production of organics, apparently due to its bonding relationship with the lignin and (iii) its ability to inhibit the development of chars porosity, while the cellulose appeared to be the precursor for the microporous character of the biochars. These results are of interest for the selection of suitable feedstocks aimed at producing bio-oil and char as fuels and soil amendment, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

Optically Controlled Signal Amplification for DNA Computation.

PubMed

Prokup, Alexander; Hemphill, James; Liu, Qingyang; Deiters, Alexander

2015-10-16

The hybridization chain reaction (HCR) and fuel-catalyst cycles have been applied to address the problem of signal amplification in DNA-based computation circuits. While they function efficiently, these signal amplifiers cannot be switched ON or OFF quickly and noninvasively. To overcome these limitations, a light-activated initiator strand for the HCR, which enabled fast optical OFF → ON switching, was developed. Similarly, when a light-activated version of the catalyst strand or the inhibitor strand of a fuel-catalyst cycle was applied, the cycle could be optically switched from OFF → ON or ON → OFF, respectively. To move the capabilities of these devices beyond solution-based operations, the components were embedded in agarose gels. Irradiation with customizable light patterns and at different time points demonstrated both spatial and temporal control. The addition of a translator gate enabled a spatially activated signal to travel along a predefined path, akin to a chemical wire. Overall, the addition of small light-cleavable photocaging groups to DNA signal amplification circuits enabled conditional control as well as fast photocontrol of signal amplification.

Empirical Site Amplification Factors Incorporating Soil Nonlinearity in Taiwan

NASA Astrophysics Data System (ADS)

Kuo, C. H.; Chung, C. H.; Che-Min, L.; Huang, J. Y.; Wen, K. L.

2017-12-01

Characteristics of site amplifications caused by both crustal and subduction earthquakes are important in Taiwan. For example, seismic waves were amplified and led to significant building damages in the Taipei Basin by the 1986 Hualien offshore (subduction interface) and the 1999 Chi-Chi earthquakes (crustal), for which the epicentral distances were about 100 km. To understand local site amplifications in Taiwan, empirical site amplification factors for horizontal ground motions are studied using recently constructed strong motion and site databases for the free-field TSMIP stations in Taiwan. Records of large magnitude earthquakes of ML larger than six from 1994 to 2014 were selected for this study. Site amplification factors at site conditions with Vs30 of 120 m/s to 1500 m/s and base accelerations up to 0.7g were inferred from intensity ratios of station pairs within specific distances. The reference site condition is assumed as Vs30 of 760 m/s (B/C boundary). Preliminary results indicate: 1. Soil nonlinearity is more obviously at short periods (PGA, Sa0.3) than long periods (PGV, Sa1.0). 2. Soil nonlinearity is significant for stations belong to site classes of B, C, D, and E in Taiwan. 3. Effect of station-pair distance is seen at short periods (PGA and Sa0.3). 4. No significant different is found in site amplifications of crustal and subduction earthquakes. The result could be a reference for the Fa and Fv in Taiwan's building code.

The Efficiency of Magnetic Field Amplification at Shocks by Turbulence

NASA Technical Reports Server (NTRS)

Ji, Suoqing; Oh, S. Peng; Ruszkowsi, M.; Markevitch, M.

2016-01-01

Turbulent dynamo field amplification has often been invoked to explain the strong field strengths in thin rims in supernova shocks (approx.100 micrograms) and in radio relics in galaxy clusters (approx. micrograms). We present high-resolution magnetohydrodynamic simulations of the interaction between pre-shock turbulence, clumping and shocks, to quantify the conditions under which turbulent dynamo amplification can be significant. We demonstrate numerically converged field amplification which scales with Alfven Mach number, B/B0 varies as MA, up to MA approx.150.This implies that the post-shock field strength is relatively independent of the seed field. Amplification is dominated by compression at low MA, and stretching (turbulent amplification) at high MA. For high MA, the B-field grows exponentially and saturates at equipartition with turbulence, while the vorticity jumps sharply at the shock and subsequently decays; the resulting field is orientated predominately along the shock normal (an effect only apparent in 3D and not 2D). This agrees with the radial field bias seen in supernova remnants. By contrast, for low MA, field amplification is mostly compressional, relatively modest, and results in a predominantly perpendicular field. The latter is consistent with the polarization seen in radio relics. Our results are relatively robust to the assumed level of gas clumping. Our results imply that the turbulent dynamo may be important for supernovae, but is only consistent with the field strength, and not geometry, for cluster radio relics. For the latter, this implies strong pre-existing B-fields in the ambient cluster outskirts.

Target-induced proximity ligation triggers recombinase polymerase amplification and transcription-mediated amplification to detect tumor-derived exosomes in nasopharyngeal carcinoma with high sensitivity.

PubMed

Liu, Wanli; Li, Jianpei; Wu, Yixian; Xing, Shan; Lai, Yanzhen; Zhang, Ge

2018-04-15

Tumor-derived exosomes (TEXs) are extracellular vesicles that are continuously released into the blood by tumor cells and carry specific surface markers of the original tumor cells. Substantial evidence has implicated TEXs as attractive diagnostic markers for cancer. However, the detection of TEXs in blood at an early tumor stage is challenging due to their very low concentration. Here, we established a method called PLA-RPA-TMA assay that allows TEXs to be detected with high sensitivity and specificity. Based on two proximity ligation assay (PLA) probes that recognize a biomarker on a TEX, we generated a unique surrogate DNA signal for the specific biomarker, which was synchronously amplified twice by recombinase polymerase amplification (RPA) coupled with transcription-mediated amplification (TMA), and then the products of the RPA-TMA reaction were quantitatively detected using a gold nanoparticle-based colorimetric assay. We established proof-of-concept evidence for this approach using TEXs from nasopharyngeal carcinoma (NPC) cells, with a detection limit of 10 2 particles/mL, and reported the measurement of plasma Epstein-Barr virus latent membrane protein 1 (LPM1)-positive (LMP1 + , accuracy: 0.956) and epidermal growth factor receptor (EGFR)-positive (EGFR + , accuracy: 0.906) TEXs as potent early diagnostic biomarkers for NPC. Copyright © 2017 Elsevier B.V. All rights reserved.

Pre-amplification in the context of high-throughput qPCR gene expression experiment.

PubMed

Korenková, Vlasta; Scott, Justin; Novosadová, Vendula; Jindřichová, Marie; Langerová, Lucie; Švec, David; Šídová, Monika; Sjöback, Robert

2015-03-11

With the introduction of the first high-throughput qPCR instrument on the market it became possible to perform thousands of reactions in a single run compared to the previous hundreds. In the high-throughput reaction, only limited volumes of highly concentrated cDNA or DNA samples can be added. This necessity can be solved by pre-amplification, which became a part of the high-throughput experimental workflow. Here, we focused our attention on the limits of the specific target pre-amplification reaction and propose the optimal, general setup for gene expression experiment using BioMark instrument (Fluidigm). For evaluating different pre-amplification factors following conditions were combined: four human blood samples from healthy donors and five transcripts having high to low expression levels; each cDNA sample was pre-amplified at four cycles (15, 18, 21, and 24) and five concentrations (equivalent to 0.078 ng, 0.32 ng, 1.25 ng, 5 ng, and 20 ng of total RNA). Factors identified as critical for a success of cDNA pre-amplification were cycle of pre-amplification, total RNA concentration, and type of gene. The selected pre-amplification reactions were further tested for optimal Cq distribution in a BioMark Array. The following concentrations combined with pre-amplification cycles were optimal for good quality samples: 20 ng of total RNA with 15 cycles of pre-amplification, 20x and 40x diluted; and 5 ng and 20 ng of total RNA with 18 cycles of pre-amplification, both 20x and 40x diluted. We set up upper limits for the bulk gene expression experiment using gene expression Dynamic Array and provided an easy-to-obtain tool for measuring of pre-amplification success. We also showed that variability of the pre-amplification, introduced into the experimental workflow of reverse transcription-qPCR, is lower than variability caused by the reverse transcription step.

Drastic disorder-induced reduction of signal amplification in scale-free networks.

PubMed

Chacón, Ricardo; Martínez, Pedro J

2015-07-01

Understanding information transmission across a network is a fundamental task for controlling and manipulating both biological and manmade information-processing systems. Here we show how topological resonant-like amplification effects in scale-free networks of signaling devices are drastically reduced when phase disorder in the external signals is considered. This is demonstrated theoretically by means of a starlike network of overdamped bistable systems, and confirmed numerically by simulations of scale-free networks of such systems. The taming effect of the phase disorder is found to be sensitive to the amplification's strength, while the topology-induced amplification mechanism is robust against this kind of quenched disorder in the sense that it does not significantly change the values of the coupling strength where amplification is maximum in its absence.

Method for improving product yields in an anionic metalloporphyrin-based artificial photosynthesis system

DOEpatents

Shelnutt, John A.

1986-01-01

A method for improving product yields in an anionic metalloporphyrin-based artificial photosynthesis system for hydrogen generation which comprises forming an aqueous solution comprising an electron donor, methylviologen, and certain metalloporphyrins and metallochlorins, and irradiating said aqueous solution with light in the presence of a catalyst. In the photosynthesis process, solar energy is collected and stored in the form of a gas hydrogen. Ligands attached above and below the metalloporphyrin and metallochlorin plane are capable of sterically blocking photochemically inactive electrostatically bound .pi.--.pi. complexes which can develop.

Method for improving product yields in an anionic metalloporphyrin-based artificial photosynthesis system

DOEpatents

Shelnutt, J.A.

1984-11-29

A method is disclosed improving product yields in an anionic metalloporphyrin-based artificial photosynthesis system for hydrogen generation. The method comprises forming an aqueous solution comprising an electron donor, methylviologen, and certain metalloporphyrins and metallochlorins, and irradiating said aqueous solution with light in the presence of a catalyst. In the photosynthesis process, solar energy is collected and stored in the form of a hydrogen. Ligands attached above and below the metalloporphyrin and metallochlorin plane are capable of sterically blocking photochemically inactive electrostatically bound ..pi..-..pi.. complexes which can develop.

[Application of recombinase polymerase amplification in the detection of Pseudomonas aeruginosa].

PubMed

Jin, X J; Gong, Y L; Yang, L; Mo, B H; Peng, Y Z; He, P; Zhao, J N; Li, X L

2018-04-20

Objective: To establish an optimized method of recombinase polymerase amplification (RPA) to rapidly detect Pseudomonas aeruginosa in clinic. Methods: (1) The DNA templates of one standard Pseudomonas aeruginosa strain was extracted and detected by polymerase chain reaction (PCR), real-time fluorescence quantitative PCR and RPA. Time of sample loading, time of amplification, and time of detection of the three methods were recorded. (2) One standard Pseudomonas aeruginosa strain was diluted in 7 concentrations of 1×10(7,) 1×10(6,) 1×10(5,) 1×10(4,) 1×10(3,) 1×10(2,) and 1×10(1) colony forming unit (CFU)/mL after recovery and cultivation. The DNA templates of Pseudomonas aeruginosa and negative control strain Pseudomonas putida were extracted and detected by PCR, real-time fluorescence quantitative PCR, and RPA separately. The sensitivity of the three methods in detecting Pseudomonas aeruginosa was analyzed. (3) The DNA templates of one standard Pseudomonas aeruginosa strain and four negative control strains ( Staphylococcus aureus, Acinetobacter baumanii, Candida albicans, and Pseudomonas putida ) were extracted separately, and then they were detected by PCR, real-time fluorescence quantitative PCR, and RPA. The specificity of the three methods in detecting Pseudomonas aeruginosa was analyzed. (4) The DNA templates of 28 clinical strains of Pseudomonas aeruginosa preserved in glycerin, 1 clinical strain of which was taken by cotton swab, and negative control strain Pseudomonas putida were extracted separately, and then they were detected by RPA. Positive amplification signals of the clinical strains were observed, and the detection rate was calculated. All experiments were repeated for 3 times. Sensitivity results were analyzed by GraphPad Prism 5.01 statistical software. Results: (1) The loading time of RPA, PCR, and real-time fluorescence quantitative PCR for detecting Pseudomonas aeruginosa were all 20 minutes. In PCR, time of amplification was 98 minutes

Organic field effect transistor with ultra high amplification

NASA Astrophysics Data System (ADS)

Torricelli, Fabrizio

2016-09-01

High-gain transistors are essential for the large-scale circuit integration, high-sensitivity sensors and signal amplification in sensing systems. Unfortunately, organic field-effect transistors show limited gain, usually of the order of tens, because of the large contact resistance and channel-length modulation. Here we show organic transistors fabricated on plastic foils enabling unipolar amplifiers with ultra-gain. The proposed approach is general and opens up new opportunities for ultra-large signal amplification in organic circuits and sensors.

Frequency domain optical parametric amplification

PubMed Central

Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

2014-01-01

Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

Non-biased and efficient global amplification of a single-cell cDNA library

PubMed Central

Huang, Huan; Goto, Mari; Tsunoda, Hiroyuki; Sun, Lizhou; Taniguchi, Kiyomi; Matsunaga, Hiroko; Kambara, Hideki

2014-01-01

Analysis of single-cell gene expression promises a more precise understanding of molecular mechanisms of a living system. Most techniques only allow studies of the expressions for limited numbers of gene species. When amplification of cDNA was carried out for analysing more genes, amplification biases were frequently reported. A non-biased and efficient global-amplification method, which uses a single-cell cDNA library immobilized on beads, was developed for analysing entire gene expressions for single cells. Every step in this analysis from reverse transcription to cDNA amplification was optimized. By removing degrading excess primers, the bias due to the digestion of cDNA was prevented. Since the residual reagents, which affect the efficiency of each subsequent reaction, could be removed by washing beads, the conditions for uniform and maximized amplification of cDNAs were achieved. The differences in the amplification rates for randomly selected eight genes were within 1.5-folds, which could be negligible for most of the applications of single-cell analysis. The global amplification gives a large amount of amplified cDNA (>100 μg) from a single cell (2-pg mRNA), and that amount is enough for downstream analysis. The proposed global-amplification method was used to analyse transcript ratios of multiple cDNA targets (from several copies to several thousand copies) quantitatively. PMID:24141095

The Interplay Between Estrogen and Replication Origins in Breast Cancer DNA Amplification

DTIC Science & Technology

2013-09-01

Replication Origins in Breast Cancer DNA Amplification PRINCIPAL INVESTIGATOR: Cinzia Casella CONTRACTING ORGANIZATION: Brown...Interplay Between Estrogen and Replication Origins in Breast Cancer DNA Amplification 5b. GRANT NUMBER W81XWH-11-1-0599 5c. PROGRAM ELEMENT NUMBER 6... amplification and oncogenes activation in breast cancer cells? This project aims to understand the role of estrogen in inducing re-replication, thus

Coherent Spin Amplification Using a Beam Splitter

NASA Astrophysics Data System (ADS)

Yan, Chengyu; Kumar, Sanjeev; Thomas, Kalarikad; See, Patrick; Farrer, Ian; Ritchie, David; Griffiths, Jonathan; Jones, Geraint; Pepper, Michael

2018-03-01

We report spin amplification using a capacitive beam splitter in n -type GaAs where the spin polarization is monitored via a transverse electron focusing measurement. It is shown that partially spin-polarized current injected by the emitter can be precisely controlled, and the spin polarization associated with it can be amplified by the beam splitter, such that a considerably high spin polarization of around 50% can be obtained. Additionally, the spin remains coherent as shown by the observation of quantum interference. Our results illustrate that spin-polarization amplification can be achieved in materials without strong spin-orbit interaction.

Development of a high yielding E. coli periplasmic expression system for the production of humanized Fab' fragments.

PubMed

Ellis, Mark; Patel, Pareshkumar; Edon, Marjory; Ramage, Walter; Dickinson, Robert; Humphreys, David P

2017-01-01

Humanized Fab' fragments may be produced in the periplasm of Escherichia coli but can be subject to degradation by host cell proteases. In order to increase Fab' yield and reduce proteolysis we developed periplasmic protease deficient strains of E. coli. These strains lacked the protease activity of Tsp, protease III and DegP. High cell density fermentations indicated Tsp deficient strains increased productivity two fold but this increase was accompanied by premature cell lysis soon after the induction of Fab' expression. To overcome the reduction in cell viability we introduced suppressor mutations into the spr gene. The mutations partially restored the wild type phenotype of the cells. Furthermore, we coexpressed a range of periplasmic chaperone proteins with the Fab', DsbC had the most significant impact, increasing humanized Fab' production during high cell density fermentation. When DsbC coexpression was combined with a Tsp deficient spr strain we observed an increase in yield and essentially restored "wild type" cell viability. We achieved a final periplasmic yield of over 2.4g/L (final cell density OD 600 105), 40 h post Fab' induction with minimal cell lysis.The data suggests that proteolysis, periplasm integrity, protein folding and disulphide bond formation are all potential limiting steps in the production of Fab' fragments in the periplasm of E. coli. In this body of work, we have addressed these limiting steps by utilizing stabilized protease deficient strains and chaperone coexpression. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:212-220, 2017. © 2016 American Institute of Chemical Engineers.

Non-normality and classification of amplification mechanisms in stability and resolvent analysis

NASA Astrophysics Data System (ADS)

Symon, Sean; Rosenberg, Kevin; Dawson, Scott T. M.; McKeon, Beverley J.

2018-05-01

Eigenspectra and pseudospectra of the mean-linearized Navier-Stokes operator are used to characterize amplification mechanisms in laminar and turbulent flows in which linear mechanisms are important. Success of mean flow (linear) stability analysis for a particular frequency is shown to depend on whether two scalar measures of non-normality agree: (1) the product between the resolvent norm and the distance from the imaginary axis to the closest eigenvalue and (2) the inverse of the inner product between the most amplified resolvent forcing and response modes. If they agree, the resolvent operator can be rewritten in its dyadic representation to reveal that the adjoint and forward stability modes are proportional to the forcing and response resolvent modes at that frequency. Hence the real parts of the eigenvalues are important since they are responsible for resonant amplification and the resolvent operator is low rank when the eigenvalues are sufficiently separated in the spectrum. If the amplification is pseudoresonant, then resolvent analysis is more suitable to understand the origin of observed flow structures. Two test cases are studied: low Reynolds number cylinder flow and turbulent channel flow. The first deals mainly with resonant mechanisms, hence the success of both classical and mean stability analysis with respect to predicting the critical Reynolds number and global frequency of the saturated flow. Both scalar measures of non-normality agree for the base and mean flows, and the region where the forcing and response modes overlap scales with the length of the recirculation bubble. In the case of turbulent channel flow, structures result from both resonant and pseudoresonant mechanisms, suggesting that both are necessary elements to sustain turbulence. Mean shear is exploited most efficiently by stationary disturbances while bounds on the pseudospectra illustrate how pseudoresonance is responsible for the most amplified disturbances at spatial

Error amplification to promote motor learning and motivation in therapy robotics.