A mariner transposon vector adapted for mutagenesis in oral streptococci

DEFF Research Database (Denmark)

Nilsson, Martin; Christiansen, Natalia; Høiby, Niels

2014-01-01

This article describes the construction and characterization of a mariner-based transposon vector designed for use in oral streptococci, but with a potential use in other Gram-positive bacteria. The new transposon vector, termed pMN100, contains the temperature-sensitive origin of replication rep...... 5000 mutants was used in a screen to identify genes involved in the production of sucrose-dependent extracellular matrix components. Mutants with transposon inserts in genes encoding glycosyltransferases and the competence-related secretory locus were predominantly found in this screen....

Transposons As Tools for Functional Genomics in Vertebrate Models.

Science.gov (United States)

Kawakami, Koichi; Largaespada, David A; Ivics, Zoltán

2017-11-01

Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats. Copyright © 2017 Elsevier Ltd. All rights reserved.

TcA, the putative transposase of the C. elegans Tc1 transposon, has an N-terminal DNA binding domain.

OpenAIRE

Schukkink, R F; Plasterk, R H

1990-01-01

Tc1 is a transposon present in several copies in the genome of all natural isolates of the nematode C.elegans; it is actively transposing in many strains. In those strains Tc1 insertion is the main cause of spontaneous mutations. The transposon contains one large ORF that we call TcA; we assume that the TcA protein is the transposase of Tc1. We expressed TcA in E.coli, purified the protein and showed that it has a strong affinity for DNA (both single stranded and double stranded). A fusion pr...

Stochastic Predator-Prey Dynamics of Transposons in the Human Genome

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Xue, Chi; Goldenfeld, Nigel

2016-11-01

Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations. Our work demonstrates the important role of the number fluctuations in the expression of mobile genetic elements, and shows explicitly how ecological concepts can be applied to the dynamics and fluctuations of living genomes.

Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.

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Filée, Jonathan; Rouault, Jacques-Deric; Harry, Myriam; Hua-Van, Aurélie

2015-12-15

The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species. Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable

Enzymatic engineering of the porcine genome with transposons and recombinases

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Carlson Daniel F

2007-07-01

Full Text Available Abstract Background Swine is an important agricultural commodity and biomedical model. Manipulation of the pig genome provides opportunity to improve production efficiency, enhance disease resistance, and add value to swine products. Genetic engineering can also expand the utility of pigs for modeling human disease, developing clinical treatment methodologies, or donating tissues for xenotransplantation. Realizing the full potential of pig genetic engineering requires translation of the complete repertoire of genetic tools currently employed in smaller model organisms to practical use in pigs. Results Application of transposon and recombinase technologies for manipulation of the swine genome requires characterization of their activity in pig cells. We tested four transposon systems- Sleeping Beauty, Tol2, piggyBac, and Passport in cultured porcine cells. Transposons increased the efficiency of DNA integration up to 28-fold above background and provided for precise delivery of 1 to 15 transgenes per cell. Both Cre and Flp recombinase were functional in pig cells as measured by their ability to remove a positive-negative selection cassette from 16 independent clones and over 20 independent genomic locations. We also demonstrated a Cre-dependent genetic switch capable of eliminating an intervening positive-negative selection cassette and activating GFP expression from episomal and genome-resident transposons. Conclusion We have demonstrated for the first time that transposons and recombinases are capable of mobilizing DNA into and out of the porcine genome in a precise and efficient manner. This study provides the basis for developing transposon and recombinase based tools for genetic engineering of the swine genome.

Transposon mutagenesis in Mycoplasma hyopneumoniae using a novel mariner-based system for generating random mutations.

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Maglennon, Gareth A; Cook, Beth S; Deeney, Alannah S; Bossé, Janine T; Peters, Sarah E; Langford, Paul R; Maskell, Duncan J; Tucker, Alexander W; Wren, Brendan W; Rycroft, Andrew N

2013-12-21

Mycoplasma hyopneumoniae is the cause of enzootic pneumonia in pigs, a chronic respiratory disease associated with significant economic losses to swine producers worldwide. The molecular pathogenesis of infection is poorly understood due to the lack of genetic tools to allow manipulation of the organism and more generally for the Mycoplasma genus. The objective of this study was to develop a system for generating random transposon insertion mutants in M. hyopneumoniae that could prove a powerful tool in enabling the pathogenesis of infection to be unraveled. A novel delivery vector was constructed containing a hyperactive C9 mutant of the Himar1 transposase along with a mini transposon containing the tetracycline resistance cassette, tetM. M. hyopneumoniae strain 232 was electroporated with the construct and tetM-expressing transformants selected on agar containing tetracycline. Individual transformants contained single transposon insertions that were stable upon serial passages in broth medium. The insertion sites of 44 individual transformants were determined and confirmed disruption of several M. hyopneumoniae genes. A large pool of over 10 000 mutants was generated that should allow saturation of the M. hyopneumoniae strain 232 genome. This is the first time that transposon mutagenesis has been demonstrated in this important pathogen and could be generally applied for other Mycoplasma species that are intractable to genetic manipulation. The ability to generate random mutant libraries is a powerful tool in the further study of the pathogenesis of this important swine pathogen.

Construction of a large-scale Burkholderia cenocepacia J2315 transposon mutant library

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Wong, Yee-Chin; Pain, Arnab; Nathan, Sheila

2014-09-01

Burkholderia cenocepacia, a pathogenic member of the Burkholderia cepacia complex (Bcc), has emerged as a significant threat towards cystic fibrosis patients, where infection often leads to the fatal clinical manifestation known as cepacia syndrome. Many studies have investigated the pathogenicity of B. cenocepacia as well as its ability to become highly resistant towards many of the antibiotics currently in use. In addition, studies have also been undertaken to understand the pathogen's capacity to adapt and survive in a broad range of environments. Transposon based mutagenesis has been widely used in creating insertional knock-out mutants and coupled with recent advances in sequencing technology, robust tools to study gene function in a genome-wide manner have been developed based on the assembly of saturated transposon mutant libraries. In this study, we describe the construction of a large-scale library of B. cenocepacia transposon mutants. To create transposon mutants of B. cenocepacia strain J2315, electrocompetent bacteria were electrotransformed with the EZ-Tn5 transposome. Tetracyline resistant colonies were harvested off selective agar and pooled. Mutants were generated in multiple batches with each batch consisting of ˜20,000 to 40,000 mutants. Transposon insertion was validated by PCR amplification of the transposon region. In conclusion, a saturated B. cenocepacia J2315 transposon mutant library with an estimated total number of 500,000 mutants was successfully constructed. This mutant library can now be further exploited as a genetic tool to assess the function of every gene in the genome, facilitating the discovery of genes important for bacterial survival and adaptation, as well as virulence.

Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster.

Science.gov (United States)

Venken, Koen J T; Bellen, Hugo J

2014-06-15

The study of genetics, genes, and chromosomal inheritance was initiated by Thomas Morgan in 1910, when the first visible mutations were identified in fruit flies. The field expanded upon the work initiated by Herman Muller in 1926 when he used X-rays to develop the first balancer chromosomes. Today, balancers are still invaluable to maintain mutations and transgenes but the arsenal of tools has expanded vastly and numerous new methods have been developed, many relying on the availability of the genome sequence and transposable elements. Forward genetic screens based on chemical mutagenesis or transposable elements have resulted in the unbiased identification of many novel players involved in processes probed by specific phenotypic assays. Reverse genetic approaches have relied on the availability of a carefully selected set of transposon insertions spread throughout the genome to allow the manipulation of the region in the vicinity of each insertion. Lastly, the ability to transform Drosophila with single copy transgenes using transposons or site-specific integration using the ΦC31 integrase has allowed numerous manipulations, including the ability to create and integrate genomic rescue constructs, generate duplications, RNAi knock-out technology, binary expression systems like the GAL4/UAS system as well as other methods. Here, we will discuss the most useful methodologies to interrogate the fruit fly genome in vivo focusing on chemical mutagenesis, transposons and transgenes. Genome engineering approaches based on nucleases and RNAi technology are discussed in following chapters. Copyright © 2014 Elsevier Inc. All rights reserved.

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

Science.gov (United States)

Hu, Bingjie; Zhou, Mingbing

2018-02-25

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Evaluating Risks of Insertional Mutagenesis by DNA Transposons in Gene Therapy

Science.gov (United States)

Hackett, Perry B.; Largaespada, David A.; Switzer, Kirsten C.; Cooper, Laurence J.N.

2013-01-01

Investigational therapy can be successfully undertaken using viral- and non-viral-mediated ex vivo gene transfer. Indeed, recent clinical trials have established the potential for genetically modified T cells to improve and restore health. Recently the Sleeping Beauty (SB) transposon/transposase system has been applied in clinical trials to stably insert a chimeric antigen receptor (CAR) to redirect T-cell specificity. We discuss the context in which the SB system can be harnessed for gene therapy and describe the human application of SB-modified CAR+ T cells. We have focused on theoretical issues relating to insertional mutagenesis in the context of human genomes that are naturally subjected to remobilization of transposons and the experimental evidence over the last decade of employing SB transposons for defining genes that induce cancer. These findings are put into the context of the use of SB transposons in the treatment of human disease. PMID:23313630

A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases

Institute of Scientific and Technical Information of China (English)

Qingshu Meng; Kaifu Chen; Lina Ma; Songnian Hu; Jun Yu

2011-01-01

Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent model system for transposon study since its genome ( ～ 160 Mb) has been sequenced and is composed of ～65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.

Epigenetics and Evolution: Transposons and the Stochastic Epigenetic Modification Model

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Sergio Branciamore

2015-04-01

Full Text Available In addition to genetic variation, epigenetic variation and transposons can greatly affect the evolutionary fitnesses landscape and gene expression. Previously we proposed a mathematical treatment of a general epigenetic variation model that we called Stochastic Epigenetic Modification (SEM model. In this study we follow up with a special case, the Transposon Silencing Model (TSM, with, once again, emphasis on quantitative treatment. We have investigated the evolutionary effects of epigenetic changes due to transposon (T insertions; in particular, we have considered a typical gene locus A and postulated that (i the expression level of gene A depends on the epigenetic state (active or inactive of a cis- located transposon element T, (ii stochastic variability in the epigenetic silencing of T occurs only in a short window of opportunity during development, (iii the epigenetic state is then stable during further development, and (iv the epigenetic memory is fully reset at each generation. We develop the model using two complementary approaches: a standard analytical population genetics framework (di usion equations and Monte-Carlo simulations. Both approaches led to similar estimates for the probability of fixation and time of fixation of locus TA with initial frequency P in a randomly mating diploid population of effective size Ne. We have ascertained the e ect that ρ, the probability of transposon Modification during the developmental window, has on the population (species. One of our principal conclusions is that as ρ increases, the pattern of fixation of the combined TA locus goes from "neutral" to "dominant" to "over-dominant". We observe that, under realistic values of ρ, epigenetic Modifications can provide an e cient mechanism for more rapid fixation of transposons and cis-located gene alleles. The results obtained suggest that epigenetic silencing, even if strictly transient (being reset at each generation, can still have signi cant

Himar1 Transposon for Efficient Random Mutagenesis in Aggregatibacter actinomycetemcomitans

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Qinfeng Ding

2017-09-01

Full Text Available Aggregatibacter actinomycetemcomitans is the primary etiological agent of aggressive periodontal disease. Identification of novel virulence factors at the genome-wide level is hindered by lack of efficient genetic tools to perform mutagenesis in this organism. The Himar1 mariner transposon is known to yield a random distribution of insertions in an organism’s genome with requirement for only a TA dinucleotide target and is independent of host-specific factors. However, the utility of this system in A. actinomycetemcomitans is unknown. In this study, we found that Himar1 transposon mutagenesis occurs at a high frequency (×10-4, and can be universally applied to wild-type A. actinomycetemcomitans strains of serotypes a, b, and c. The Himar1 transposon inserts were stably inherited in A. actinomycetemcomitans transconjugants in the absence of antibiotics. A library of 16,000 mutant colonies of A. actinomycetemcomitans was screened for reduced biofilm formation. Mutants with transposon inserts in genes encoding pilus, putative ion transporters, multidrug resistant proteins, transcription regulators and enzymes involved in the synthesis of extracellular polymeric substance, bacterial metabolism and stress response were discovered in this screen. Our results demonstrated the utility of the Himar1 mutagenesis system as a novel genetic tool for functional genomic analysis in A. actinomycetemcomitans.

Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics

International Nuclear Information System (INIS)

Chen, Li; Schmidt, Emmett V; Stuart, Lynda; Ohsumi, Toshiro K; Burgess, Shawn; Varshney, Gaurav K; Dastur, Anahita; Borowsky, Mark; Benes, Cyril; Lacy-Hulbert, Adam

2013-01-01

The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Here we describe a gain-of-function forward genetic approach for identifying mechanisms of resistance. This approach uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activate nearby gene expression. Genes of interest are identified using next-gen high-throughput sequencing and barcode multiplexing is used to reduce experimental cost. Using this approach we successfully identify genes involved in paclitaxel resistance in a variety of cancer cell lines, including the multidrug transporter ABCB1, a previously identified major paclitaxel resistance gene. Analysis of co-occurring transposons integration sites in single cell clone allows for the identification of genes that might act cooperatively to produce drug resistance a level of information not accessible using RNAi or ORF expression screening approaches. We have developed a powerful pipeline to systematically discover drug resistance in mammalian cells in vitro. This cost-effective approach can be readily applied to different cell lines, to identify canonical or context specific resistance mechanisms. Its ability to probe complex genetic context and non-coding genomic elements as well as cooperative resistance events makes it a good complement to RNAi or ORF expression based screens

The expanding universe of transposon technologies for gene and cell engineering

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Ivics Zoltán

2010-12-01

Full Text Available Abstract Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion. The mobility of class II transposable elements (DNA transposons can be controlled by conditionally providing the transposase component of the transposition reaction. Thus, a DNA of interest (be it a fluorescent marker, a small hairpin (shRNA expression cassette, a mutagenic gene trap or a therapeutic gene construct cloned between the inverted repeat sequences of a transposon-based vector can be used for stable genomic insertion in a regulated and highly efficient manner. This methodological paradigm opened up a number of avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture, the production of germline transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species, and therapy of genetic disorders in humans. Sleeping Beauty (SB was the first transposon shown to be capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering including transgenesis, insertional mutagenesis, and therapeutic somatic gene transfer both ex vivo and in vivo. The first clinical application of the SB system will help to validate both the safety and efficacy of this approach. In this review, we describe the major transposon systems currently available (with special emphasis on SB, discuss the various parameters and considerations pertinent to their experimental use, and highlight the state of the art in transposon technology in diverse genetic applications.

The expanding universe of transposon technologies for gene and cell engineering.

Science.gov (United States)

Ivics, Zoltán; Izsvák, Zsuzsanna

2010-12-07

Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion. The mobility of class II transposable elements (DNA transposons) can be controlled by conditionally providing the transposase component of the transposition reaction. Thus, a DNA of interest (be it a fluorescent marker, a small hairpin (sh)RNA expression cassette, a mutagenic gene trap or a therapeutic gene construct) cloned between the inverted repeat sequences of a transposon-based vector can be used for stable genomic insertion in a regulated and highly efficient manner. This methodological paradigm opened up a number of avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture, the production of germline transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species, and therapy of genetic disorders in humans. Sleeping Beauty (SB) was the first transposon shown to be capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering including transgenesis, insertional mutagenesis, and therapeutic somatic gene transfer both ex vivo and in vivo. The first clinical application of the SB system will help to validate both the safety and efficacy of this approach. In this review, we describe the major transposon systems currently available (with special emphasis on SB), discuss the various parameters and considerations pertinent to their experimental use, and highlight the state of the art in transposon technology in diverse genetic applications.

TED, an autonomous and rare maize transposon of the mutator superfamily with a high gametophytic excision frequency.

Science.gov (United States)

Li, Yubin; Harris, Linda; Dooner, Hugo K

2013-09-01

Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.

A highly efficient transposon mutagenesis system for the tomato pathogen Clavibacter michiganensis subsp. michiganensis.

Science.gov (United States)

Kirchner, O; Gartemann, K H; Zellermann, E M; Eichenlaub, R; Burger, A

2001-11-01

A transposon mutagenesis system for Clavibacter michiganensis subsp. michiganensis was developed based on antibiotic resistance transposons that were derived from the insertion element IS1409 from Arthrobacter sp. strain TM1 NCIB12013. As a prerequisite, the electroporation efficiency was optimized by using unmethylated DNA and treatment of the cells with glycine such that about 5 x 10(6) transformants per microg of DNA were generally obtained. Electroporation of C. michiganensis subsp. michiganensis with a suicide vector carrying transposon Tn1409C resulted in approximately 1 x 10(3) transposon mutants per pg of DNA and thus is suitable for saturation mutagenesis. Analysis of Tn1409C insertion sites suggests a random mode of transposition. Transposition of Tn1409C was also demonstrated for other subspecies of C. michiganensis.

Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.

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Hong Yang

2014-09-01

Full Text Available Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA. TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1 previous genome-wide direct gene-essentiality assignments; and, 2 flux balance analysis (FBA predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.

[Differential expression of DTSsa4 Tc1-like transposons in closely related populations of Baikal ciscoes].

Science.gov (United States)

Bychenko, O S; Sukhanova, L V; Azhikina, T L; Sverdlov, E D

2009-01-01

Two representatives of Baikal ciscoes - lake cisco and omul - diverged from a common ancestor as recently as 10-20 thousand years ago. We have found an increasing expression level of DTSsa4 Tc1-like DNA transposons in cisco and omul brains. The mapping of the sequences of these transposons from Salmo salar and Danio rerio genomes has shown that in some cases, these transposons are located in the 5' and 3' regions, as well as in the promoter regions of various genes. Probably, Tc1-like transposons affect the activity of neighboring genes, providing the adaptive divergence of the cisco population.

Towards controlled mutagenesis with transposons Ac and Tam3

Energy Technology Data Exchange (ETDEWEB)

Haring, M; Veken, J; Windrich, R; Kneppers, T; Rommens, C; Nijkamp, H J.J.; Hille, J [Department of Genetics, Free University, Amsterdam (Netherlands)

1990-01-01

Full text: The discovery of mobile genetic elements in plants has permitted the use of these transposons for insertional mutagenesis. This applies so far only to Zea mays and Antirrhinum majus, because other plant transposable elements have not been characterised so thoroughly at the genetic and the molecular level. To establish whether transposons (Ac from maize and Tam3 from Antirrhinum) remain mobile in heterologous hosts, either in somatic tissue or after meiosis, a phenotypic assay system for transposition was developed. The separation of the two transposition functions will allow controlled mutagenesis of plant genes. Our results indicate that both transposable elements remain active in heterologous hosts. (author)

TED, an Autonomous and Rare Maize Transposon of the Mutator Superfamily with a High Gametophytic Excision Frequency[W

Science.gov (United States)

Li, Yubin; Harris, Linda; Dooner, Hugo K.

2013-01-01

Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor. PMID:24038653

Identification and evolutionary dynamics of cacta DNA transposons in brassica

International Nuclear Information System (INIS)

Nouroz, F.; Noreen, S.; Harrison, J.S.H.

2017-01-01

Transposable elements are the major drivers of genome evolution and plasticity. Due to their transposition mode, they are classified into two major classes as Retrotransposons and DNA transposons. The En/Spm or CACTA elements are diverse group of DNA transposons proliferating in plant genomes. Various bioinformatics and molecular approaches were used for identification and distribution of CACTA transposons in Brassica genome. A combination of dot plot analysis and BLASTN searches yielded 35 autonomous and 7 non-autonomous CACTA elements in Brassica. The elements ranged in sizes from 1.2 kb non-autonomous elements to 11kb autonomous elements, terminated by 3 bp Target Site Duplication (TSD) and ~15 bp conserved Terminal Inverted Repeat (TIR) motifs (5'-CACTACAAGAAAACA-3'), with heterogeneous internal regions. The transposase (TNP) was identified from autonomous CACTA elements, while other protein domains from Brassica and other plants CACTA revealed similar organizations with minor differences. Both transposases (TNPD, TNPA) are present in most CACTA, while a few CACTA harboured an additional ATHILA ORF1-like domain. The PCR analysis amplified the CACTA transposases from 40 Brassica accessions (A, B, and C-genome) suggesting their distribution among various Brassica crops. A detailed characterization and evolutionary analysis of the identified CACTA elements allowed some to be placed in genome-specific groups, while most of them (Brassica-Arabidopsis elements) have followed the same evolutionary line. The distribution of CACTA in Brassica concluded that 3 bp TSDs generating CACTA transposons contributed significantly to genome size and evolution of Brassica genome. (author)

piggyBac transposon somatic mutagenesis with an activated reporter and tracker (PB-SMART for genetic screens in mice.

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Sean F Landrette

Full Text Available Somatic forward genetic screens have the power to interrogate thousands of genes in a single animal. Retroviral and transposon mutagenesis systems in mice have been designed and deployed in somatic tissues for surveying hematopoietic and solid tumor formation. In the context of cancer, the ability to visually mark mutant cells would present tremendous advantages for identifying tumor formation, monitoring tumor growth over time, and tracking tumor infiltrations and metastases into wild-type tissues. Furthermore, locating mutant clones is a prerequisite for screening and analyzing most other somatic phenotypes. For this purpose, we developed a system using the piggyBac (PB transposon for somatic mutagenesis with an activated reporter and tracker, called PB-SMART. The PB-SMART mouse genetic screening system can simultaneously induce somatic mutations and mark mutated cells using bioluminescence or fluorescence. The marking of mutant cells enable analyses that are not possible with current somatic mutagenesis systems, such as tracking cell proliferation and tumor growth, detecting tumor cell infiltrations, and reporting tissue mutagenesis levels by a simple ex vivo visual readout. We demonstrate that PB-SMART is highly mutagenic, capable of tumor induction with low copy transposons, which facilitates the mapping and identification of causative insertions. We further integrated a conditional transposase with the PB-SMART system, permitting tissue-specific mutagenesis with a single cross to any available Cre line. Targeting the germline, the system could also be used to conduct F1 screens. With these features, PB-SMART provides an integrated platform for individual investigators to harness the power of somatic mutagenesis and phenotypic screens to decipher the genetic basis of mammalian biology and disease.

The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes

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Satoshi Kimura

2016-08-01

Full Text Available Transposon insertion sequencing (TIS; also known as TnSeq is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness. Here, we investigated whether the histone-like nucleoid structuring (H-NS protein, which preferentially associates with AT-rich sequences, modulates the frequency of Mariner transposon insertion in the Vibrio cholerae genome, using comparative analysis of TIS results from wild-type (wt and Δhns V. cholerae strains. These analyses were overlaid on gene classification based on GC content as well as on extant genome-wide identification of H-NS binding loci. Our analyses revealed a significant dearth of insertions within AT-rich loci in wt V. cholerae that was not apparent in the Δhns insertion library. Additionally, we observed a striking correlation between genetic loci that are overrepresented in the Δhns insertion library relative to their insertion frequency in wt V. cholerae and loci previously found to physically interact with H-NS. Collectively, our findings reveal that factors other than genetic fitness can systematically modulate the frequency of transposon insertions in TIS studies and add a cautionary note to interpretation of TIS data, particularly for AT-rich sequences.

Mos1 transposon-based transformation of fish cell lines using baculoviral vectors

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Yokoo, Masako [Laboratory of Applied Molecular Entomology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589 (Japan); Fujita, Ryosuke [Laboratory of Applied Molecular Entomology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589 (Japan); Innate Immunity Laboratory, Graduate School of Life Science and Creative Research Institution, Hokkaido University, Sapporo 001-0021 (Japan); Nakajima, Yumiko [Functional Genomics Group, COMB, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213 (Japan); Yoshimizu, Mamoru; Kasai, Hisae [Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611 (Japan); Asano, Shin-ichiro [Laboratory of Applied Molecular Entomology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589 (Japan); Bando, Hisanori, E-mail: hban@abs.agr.hokudai.ac.jp [Laboratory of Applied Molecular Entomology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589 (Japan)

2013-09-13

Highlights: •The baculovirus vector infiltrates the cells of economic important fishes. •Drosophila Mos1 transposase expressed in fish cells maintains its ability to localize to the nucleus. •The baculoviral vector carrying Mos1 is a useful tool to stably transform fish cells. -- Abstract: Drosophila Mos1 belongs to the mariner family of transposons, which are one of the most ubiquitous transposons among eukaryotes. We first determined nuclear transportation of the Drosophila Mos1-EGFP fusion protein in fish cell lines because it is required for a function of transposons. We next constructed recombinant baculoviral vectors harboring the Drosophila Mos1 transposon or marker genes located between Mos1 inverted repeats. The infectivity of the recombinant virus to fish cells was assessed by monitoring the expression of a fluorescent protein encoded in the viral genome. We detected transgene expression in CHSE-214, HINAE, and EPC cells, but not in GF or RTG-2 cells. In the co-infection assay of the Mos1-expressing virus and reporter gene-expressing virus, we successfully transformed CHSE-214 and HINAE cells. These results suggest that the combination of a baculovirus and Mos1 transposable element may be a tool for transgenesis in fish cells.

Mos1 transposon-based transformation of fish cell lines using baculoviral vectors

International Nuclear Information System (INIS)

Yokoo, Masako; Fujita, Ryosuke; Nakajima, Yumiko; Yoshimizu, Mamoru; Kasai, Hisae; Asano, Shin-ichiro; Bando, Hisanori

2013-01-01

Highlights: •The baculovirus vector infiltrates the cells of economic important fishes. •Drosophila Mos1 transposase expressed in fish cells maintains its ability to localize to the nucleus. •The baculoviral vector carrying Mos1 is a useful tool to stably transform fish cells. -- Abstract: Drosophila Mos1 belongs to the mariner family of transposons, which are one of the most ubiquitous transposons among eukaryotes. We first determined nuclear transportation of the Drosophila Mos1-EGFP fusion protein in fish cell lines because it is required for a function of transposons. We next constructed recombinant baculoviral vectors harboring the Drosophila Mos1 transposon or marker genes located between Mos1 inverted repeats. The infectivity of the recombinant virus to fish cells was assessed by monitoring the expression of a fluorescent protein encoded in the viral genome. We detected transgene expression in CHSE-214, HINAE, and EPC cells, but not in GF or RTG-2 cells. In the co-infection assay of the Mos1-expressing virus and reporter gene-expressing virus, we successfully transformed CHSE-214 and HINAE cells. These results suggest that the combination of a baculovirus and Mos1 transposable element may be a tool for transgenesis in fish cells

Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility.

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Vrljicak, Pavle; Tao, Shijie; Varshney, Gaurav K; Quach, Helen Ngoc Bao; Joshi, Adita; LaFave, Matthew C; Burgess, Shawn M; Sampath, Karuna

2016-04-07

DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germ-line transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence the integration of heterologous DNA in genomes, and have implications for targeted genome engineering. Copyright © 2016 Vrljicak et al.

Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica.

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Hickman, Alison B; Ewis, Hosam E; Li, Xianghong; Knapp, Joshua A; Laver, Thomas; Doss, Anna-Louise; Tolun, Gökhan; Steven, Alasdair C; Grishaev, Alexander; Bax, Ad; Atkinson, Peter W; Craig, Nancy L; Dyda, Fred

2014-07-17

Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. Although isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple nonspecific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA. Copyright © 2014 Elsevier Inc. All rights reserved.

Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids

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Davidson William S

2007-11-01

Full Text Available Abstract Background Several genome duplications have occurred in the evolutionary history of teleost fish. In returning to a stable diploid state, the polyploid genome reorganized, and large portions are lost, while the fish lines evolved to numerous species. Large scale transposon movement has been postulated to play an important role in the genome reorganization process. We analyzed the DNA sequence of several large loci in Salmo salar and other species for the presence of DNA transposon families. Results We have identified bursts of activity of 14 families of DNA transposons (12 Tc1-like and 2 piggyBac-like families, including 11 novel ones in genome sequences of Salmo salar. Several of these families have similar sequences in a number of closely and distantly related fish, lamprey, and frog species as well as in the parasite Schistosoma japonicum. Analysis of sequence similarities between copies within the families of these bursts demonstrates several waves of transposition activities coinciding with salmonid species divergence. Tc1-like families show a master gene-like copying process, illustrated by extensive but short burst of copying activity, while the piggyBac-like families show a more random copying pattern. Recent families may include copies with an open reading frame for an active transposase enzyme. Conclusion We have identified defined bursts of transposon activity that make use of master-slave and random mechanisms. The bursts occur well after hypothesized polyploidy events and coincide with speciation events. Parasite-mediated lateral transfer of transposons are implicated.

TCUP: A novel hAT transposon active in maize tissue culture

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Alan eSmith

2012-01-01

Full Text Available Transposable elements are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced transposable elements that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP, which is transcribed at high levels in long-term maize Black Mexican Sweet (BMS tissue culture and up-regulated in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected movement of TCUP in two long-term tissue cultured cell lines of the genotype Hi-II AxB and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.

Transposon display supports transpositional activity of P elements in ...

Indian Academy of Sciences (India)

. Abstract. Mobilization of two P element subfamilies (canonical and O-type) from Drosophila sturtevanti and D. saltans was evaluated for copy number and transposition activity using the transposon display (TD) technique. Pairwise distances ...

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH

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Burgis Timothy A

2009-07-01

Full Text Available Abstract Background In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth. Results We have developed a robust microarray and PCR-based method, Transposon-Mediated Differential Hybridisation (TMDH, that uses novel bioinformatics to identify transposon inserts in genome-wide libraries. Following a microarray-based screen, genes lacking transposon inserts are re-tested using a PCR and sequencing-based approach. We carried out a TMDH analysis of the S. aureus genome using a large random mariner transposon library of around a million mutants, and identified a total of 351 S. aureus genes important for survival and growth in culture. A comparison with the essential gene list experimentally derived for Bacillus subtilis highlighted interesting differences in both pathways and individual genes. Conclusion We have determined the first comprehensive list of S. aureus essential genes. This should act as a useful starting point for the identification of potential targets for novel antimicrobial compounds. The TMDH methodology we have developed is generic and could be applied to identify essential genes in other bacterial pathogens.

Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements

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Smith, Sara N.; Zhao, Lili; Wu, Weisheng

2017-01-01

The Gram-negative bacterium Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs), which are often polymicrobial. Numerous prior studies have uncovered virulence factors for P. mirabilis pathogenicity in a murine model of ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. In this study, we utilized five pools of 10,000 transposon mutants each and transposon insertion-site sequencing (Tn-Seq) to identify the full arsenal of P. mirabilis HI4320 fitness factors for single-species versus polymicrobial CAUTI with Providencia stuartii BE2467. 436 genes in the input pools lacked transposon insertions and were therefore concluded to be essential for P. mirabilis growth in rich medium. 629 genes were identified as P. mirabilis fitness factors during single-species CAUTI. Tn-Seq from coinfection with P. stuartii revealed 217/629 (35%) of the same genes as identified by single-species Tn-Seq, and 1353 additional factors that specifically contribute to colonization during coinfection. Mutants were constructed in eight genes of interest to validate the initial screen: 7/8 (88%) mutants exhibited the expected phenotypes for single-species CAUTI, and 3/3 (100%) validated the expected phenotypes for polymicrobial CAUTI. This approach provided validation of numerous previously described P. mirabilis fitness determinants from an ascending model of UTI, the discovery of novel fitness determinants specifically for CAUTI, and a stringent assessment of how polymicrobial infection influences fitness requirements. For instance, we describe a requirement for branched-chain amino acid biosynthesis by P. mirabilis during coinfection due to high-affinity import of leucine by P. stuartii. Further investigation of genes and pathways that provide a competitive advantage during both single-species and polymicrobial CAUTI will likely provide robust targets for therapeutic intervention to reduce P. mirabilis

Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements.

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Armbruster, Chelsie E; Forsyth-DeOrnellas, Valerie; Johnson, Alexandra O; Smith, Sara N; Zhao, Lili; Wu, Weisheng; Mobley, Harry L T

2017-06-01

The Gram-negative bacterium Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs), which are often polymicrobial. Numerous prior studies have uncovered virulence factors for P. mirabilis pathogenicity in a murine model of ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. In this study, we utilized five pools of 10,000 transposon mutants each and transposon insertion-site sequencing (Tn-Seq) to identify the full arsenal of P. mirabilis HI4320 fitness factors for single-species versus polymicrobial CAUTI with Providencia stuartii BE2467. 436 genes in the input pools lacked transposon insertions and were therefore concluded to be essential for P. mirabilis growth in rich medium. 629 genes were identified as P. mirabilis fitness factors during single-species CAUTI. Tn-Seq from coinfection with P. stuartii revealed 217/629 (35%) of the same genes as identified by single-species Tn-Seq, and 1353 additional factors that specifically contribute to colonization during coinfection. Mutants were constructed in eight genes of interest to validate the initial screen: 7/8 (88%) mutants exhibited the expected phenotypes for single-species CAUTI, and 3/3 (100%) validated the expected phenotypes for polymicrobial CAUTI. This approach provided validation of numerous previously described P. mirabilis fitness determinants from an ascending model of UTI, the discovery of novel fitness determinants specifically for CAUTI, and a stringent assessment of how polymicrobial infection influences fitness requirements. For instance, we describe a requirement for branched-chain amino acid biosynthesis by P. mirabilis during coinfection due to high-affinity import of leucine by P. stuartii. Further investigation of genes and pathways that provide a competitive advantage during both single-species and polymicrobial CAUTI will likely provide robust targets for therapeutic intervention to reduce P. mirabilis

An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation.

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Carter, Jared D; Pereira, Andy; Dickerman, Allan W; Veilleux, Richard E

2013-05-01

Tomato (Solanum lycopersicum) is a model organism for Solanaceae in both molecular and agronomic research. This project utilized Agrobacterium tumefaciens transformation and the transposon-tagging construct Activator (Ac)/Dissociator (Ds)-ATag-Bar_gosGFP to produce activation-tagged and knockout mutants in the processing tomato cultivar M82. The construct carried hygromycin resistance (hyg), green fluorescent protein (GFP), and the transposase (TPase) of maize (Zea mays) Activator major transcript X054214.1 on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds-ATag element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 11,000 selfed and cv M82 backcrossed progeny was produced from the functional T0 line. This population was screened using glufosinate herbicide, hygromycin leaf painting, and multiplex polymerase chain reaction (PCR). Insertion sites of transposed Ds-ATag elements were identified through thermal asymmetric interlaced PCR, and resulting product sequences were aligned to the recently published tomato genome. A population of 509 independent, Ds-only transposant lines spanning all 12 tomato chromosomes has been developed. Insertion site analysis demonstrated that more than 80% of these lines harbored Ds insertions conducive to activation tagging. The capacity of the Ds-ATag element to alter transcription was verified by quantitative real-time reverse transcription-PCR in two mutant lines. The transposon-tagged lines have been immortalized in seed stocks and can be accessed through an online database, providing a unique resource for tomato breeding and analysis of gene function in the background of a commercial tomato cultivar.

Induction of transposon TN1 translocation under the action of different mutagens

International Nuclear Information System (INIS)

Kubanejshvili, M.G.; Smirnov, S.P.; Tarasov, V.A.

1983-01-01

Migration of ampicillin transposon Tn1 under normal conditions in Escherichia coli cells proceeds with low frequency (10 -4 transpositions for cell). The low transposition frequency is conditioned by the transposition repression, realized by the gene-repressor in transposon structure and, probably, by other regulating genes of the bacterium-host. E. coli cell treatment by physical and chemical mutagens resulted in induction of translocation of ampicillin transposon Tn1 from plasmid RP4 into other replicons. Mitomycin C and ultraviolet radiation produced stronger inducing effect as compared to nitroso-guanidine (NG). The effect of the given mutagens on transposition Tn1 correlated with their activating capacity with respect to inducible SOS-functions of E coli. The mutation of rec A didn't influence on spontaneous Tn1 transposition, but blocked completely the induction of transposition process under mutagen effect. The relationship of inducible transposition with SOS-functions in E. coli cells, controlled by recA and lexA genes, as well as the possible role of the process in genetic microorganism variability are discussed in the paper

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population

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Baier John

2007-05-01

Full Text Available Abstract Background Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations. Results Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill. Conclusion We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.

The bandit, a new DNA transposon from a hookworm-possible horizontal genetic transfer between host and parasite.

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Thewarach Laha

2007-09-01

Full Text Available An enhanced understanding of the hookworm genome and its resident mobile genetic elements should facilitate understanding of the genome evolution, genome organization, possibly host-parasite co-evolution and horizontal gene transfer, and from a practical perspective, development of transposon-based transgenesis for hookworms and other parasitic nematodes.A novel mariner-like element (MLE was characterized from the genome of the dog hookworm, Ancylostoma caninum, and termed bandit. The consensus sequence of the bandit transposon was 1,285 base pairs (bp in length. The new transposon was flanked by perfect terminal inverted repeats of 32 nucleotides in length with a common target site duplication TA, and it encoded an open reading frame (ORF of 342 deduced amino acid residues. Phylogenetic comparisons confirmed that the ORF encoded a mariner-like transposase, which included conserved catalytic domains, and that the bandit transposon belonged to the cecropia subfamily of MLEs. The phylogenetic analysis also indicated that the Hsmar1 transposon from humans was the closest known relative of bandit, and that bandit and Hsmar1 constituted a clade discrete from the Tc1 subfamily of MLEs from the nematode Caenorhabditis elegans. Moreover, homology models based on the crystal structure of Mos1 from Drosophila mauritiana revealed closer identity in active site residues of the catalytic domain including Ser281, Lys289 and Asp293 between bandit and Hsmar1 than between Mos1 and either bandit or Hsmar1. The entire bandit ORF was amplified from genomic DNA and a fragment of the bandit ORF was amplified from RNA, indicating that this transposon is actively transcribed in hookworms.A mariner-like transposon termed bandit has colonized the genome of the hookworm A. caninum. Although MLEs exhibit a broad host range, and are identified in other nematodes, the closest phylogenetic relative of bandit is the Hsmar1 element of humans. This surprising finding suggests

Induction of rat liver tumor using the Sleeping Beauty transposon and electroporation.

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Park, June-Shine; Kim, Bae-Hwan; Park, Sung Goo; Jung, Sun Young; Lee, Do Hee; Son, Woo-Chan

2013-05-10

The Sleeping Beauty (SB) transposon system has been receiving much attention as a gene transfer method of choice since it allows permanent gene expression after insertion into the host chromosome. However, low transposition frequency in higher eukaryotes limits its use in commonly-used mammalian species. Researchers have therefore attempted to modify gene delivery and expression to overcome this limitation. In mouse liver, tumor induction using SB introduced by the hydrodynamic method has been successfully accomplished. Liver tumor in rat models using SB could also be of great use; however, dose of DNA, injection volume, rate of injection and achieving back pressure limit the use of the hydrodynamics-based gene delivery. In the present study, we combined the electroporation, a relatively simple and easy gene delivery method, with the SB transposon system and as a result successfully induced tumor in rat liver by directly injecting the c-Myc, HRAS and shp53 genes. The tumor phenotype was determined as a sarcomatoid carcinoma. To our knowledge, this is the first demonstration of induction of tumor in the rat liver using the electroporation-enhanced SB transposon system. Copyright © 2013 Elsevier Inc. All rights reserved.

An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader.

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Paun, Linda; Nitsche, Benjamin; Homan, Tim; Ram, Arthur F; Kempken, Frank

2016-07-01

The ascomycete Aspergillus niger is widely used in the biotechnology, for instance in producing most of the world's citric acid. It is also known as a major food and feed contaminant. While generation of gene knockouts for functional genomics has become feasible in ku70 mutants, analyzing gene functions or metabolic pathways remains a laborious task. An unbiased transposon-based mutagenesis approach may aid this process of analyzing gene functions by providing mutant libraries in a short time. The Vader transposon is a non-autonomous DNA-transposon, which is activated by the homologous tan1-transposase. However, in the most commonly used lab strain of A. niger (N400 strain and derivatives), we found that the transposase, encoded by the tan1 gene, is mutated and inactive. To establish a Vader transposon-based mutagenesis system in the N400 background, we expressed the functional transposase of A. niger strain CBS 513.88 under the control of an inducible promoter based on the Tet-on system, which is activated in the presence of the antibiotic doxycycline (DOX). Increasing amounts of doxycycline lead to higher Vader excision frequencies, whereas little to none activity of Vader was observed without addition of doxycycline. Hence, this system appears to be suitable for producing stable mutants in the A. niger N400 background.

Prolonged Expression of Secreted Enzymes in Dogs After Liver-Directed Delivery of Sleeping Beauty Transposons: Implications for Non-Viral Gene Therapy of Systemic Disease.

Science.gov (United States)

Aronovich, Elena L; Hyland, Kendra A; Hall, Bryan C; Bell, Jason B; Olson, Erik R; Rusten, Myra Urness; Hunter, David W; Ellinwood, N Matthew; McIvor, R Scott; Hackett, Perry B

2017-07-01

The non-viral, integrating Sleeping Beauty (SB) transposon system is efficient in treating systemic monogenic disease in mice, including hemophilia A and B caused by deficiency of blood clotting factors and mucopolysaccharidosis types I and VII caused by α-L-iduronidase (IDUA) and β-glucuronidase (GUSB) deficiency, respectively. Modified approaches of the hydrodynamics-based procedure to deliver transposons to the liver in dogs were recently reported. Using the transgenic canine reporter secreted alkaline phosphatase (cSEAP), transgenic protein in the plasma was demonstrated for up to 6 weeks post infusion. This study reports that immunosuppression of dogs with gadolinium chloride (GdCl 3 ) prolonged the presence of cSEAP in the circulation up to 5.5 months after a single vector infusion. Transgene expression declined gradually but appeared to stabilize after about 2 months at approximately fourfold baseline level. Durability of transgenic protein expression in the plasma was inversely associated with transient increase of liver enzymes alanine transaminase and aspartate transaminase in response to the plasmid delivery procedure, which suggests a deleterious effect of hepatocellular toxicity on transgene expression. GdCl 3 treatment was ineffective for repeat vector infusions. In parallel studies, dogs were infused with potentially therapeutic transposons. Activities of transgenic IDUA and GUSB in plasma peaked at 50-350% of wildtype, but in the absence of immunosuppression lasted only a few days. Transposition was detectable by excision assay only when the most efficient transposase, SB100X, was used. Dogs infused with transposons encoding canine clotting factor IX (cFIX) were treated with GdCl 3 and showed expression profiles similar to those in cSEAP-infused dogs, with expression peaking at 40% wt (2 μg/mL). It is concluded that GdCl 3 can support extended transgene expression after hydrodynamic introduction of SB transposons in dogs, but that alternative

Transposon-mediated BAC transgenesis in human ES cells

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Rostovskaya, Maria; Fu, Jun; Obst, Mandy; Baer, Isabell; Weidlich, Stefanie; Wang, Hailong; Smith, Andrew J. H.; Anastassiadis, Konstantinos; Stewart, A. Francis

2012-01-01

Transgenesis is a cornerstone of molecular biology. The ability to integrate a specifically engineered piece of DNA into the genome of a living system is fundamental to our efforts to understand life and exploit its implications for medicine, nanotechnology and bioprospecting. However, transgenesis has been hampered by position effects and multi-copy integration problems, which are mainly due to the use of small, plasmid-based transgenes. Large transgenes based on native genomic regions cloned into bacterial artificial chromosomes (BACs) circumvent these problems but are prone to fragmentation. Herein, we report that contrary to widely held notions, large BAC-sized constructs do not prohibit transposition. We also report the first reliable method for BAC transgenesis in human embryonic stem cells (hESCs). The PiggyBac or Sleeping Beauty transposon inverted repeats were integrated into BAC vectors by recombineering, followed by co-lipofection with the corresponding transposase in hESCs to generate robust fluorescent protein reporter lines for OCT4, NANOG, GATA4 and PAX6. BAC transposition delivers several advantages, including increased frequencies of single-copy, full-length integration, which will be useful in all transgenic systems but especially in difficult venues like hESCs. PMID:22753106

An Enterobacter plasmid as a new genetic background for the transposon Tn1331

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Alavi MR

2011-11-01

Full Text Available Mohammad R Alavi1,2, Vlado Antonic2, Adrien Ravizee1, Peter J Weina3, Mina Izadjoo1,2, Alexander Stojadinovic21Division of Wound Biology and Translational Research, Armed Forces Institute of Pathology and American Registry of Pathology, Washington DC, 2Combat Wound Initiative Program, Walter Reed Army Medical Center, Washington DC, 3The Walter Reed Army Institute of Research, Silver Spring, MD, USABackground: Genus Enterobacter includes important opportunistic nosocomial pathogens that could infect complex wounds. The presence of antibiotic resistance genes in these microorganisms represents a challenging clinical problem in the treatment of these wounds. In the authors’ screening of antibiotic-resistant bacteria from complex wounds, an Enterobacter species was isolated that harbors antibiotic-resistant plasmids conferring resistance to Escherichia coli. The aim of this study was to identify the resistance genes carried by one of these plasmids.Methods: The plasmids from the Enterobacter isolate were propagated in E. coli and one of the plasmids, designated as pR23, was sequenced by the Sanger method using fluorescent dye-terminator chemistry on a genetic analyzer. The assembled sequence was annotated by search of the GenBank database.Results: Plasmid pR23 is composed of the transposon Tn1331 and a backbone plasmid that is identical to the plasmid pPIGDM1 from Enterobacter agglomerans. The multidrug-resistance transposon Tn1331, which confers resistance to aminoglycoside and beta lactam antibiotics, has been previously isolated only from Klebsiella. The Enterobacter plasmid pPIGDM1, which carries a ColE1-like origin of replication and has no apparent selective marker, appears to provide a backbone for propagation of Tn1331 in Enterobacter. The recognition sequence of Tn1331 transposase for insertion into pPIGDM1 is the pentanucleotide TATTA, which occurs only once throughout the length of this plasmid.Conclusion: Transposition of Tn1331 into

Hybrid Lentivirus-transposon Vectors With a Random Integration Profile in Human Cells

DEFF Research Database (Denmark)

Staunstrup, Nicklas H; Moldt, Brian; Mátés, Lajos

2009-01-01

Gene delivery by human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors (LVs) is efficient, but genomic integration of the viral DNA is strongly biased toward transcriptionally active loci resulting in an increased risk of insertional mutagenesis in gene therapy protocols. Nonviral...... Sleeping Beauty (SB) transposon vectors have a significantly safer insertion profile, but efficient delivery into relevant cell/tissue types is a limitation. In an attempt to combine the favorable features of the two vector systems we established a novel hybrid vector technology based on SB transposase......-mediated insertion of lentiviral DNA circles generated during transduction of target cells with integrase (IN)-defective LVs (IDLVs). By construction of a lentivirus-transposon hybrid vector allowing transposition exclusively from circular viral DNA substrates, we demonstrate that SB transposase added in trans...

The rde-1 gene, RNA interference, and transposon silencing in C. elegans.

Science.gov (United States)

Tabara, H; Sarkissian, M; Kelly, W G; Fleenor, J; Grishok, A; Timmons, L; Fire, A; Mello, C C

1999-10-15

Double-stranded (ds) RNA can induce sequence-specific inhibition of gene function in several organisms. However, both the mechanism and the physiological role of the interference process remain mysterious. In order to study the interference process, we have selected C. elegans mutants resistant to dsRNA-mediated interference (RNAi). Two loci, rde-1 and rde-4, are defined by mutants strongly resistant to RNAi but with no obvious defects in growth or development. We show that rde-1 is a member of the piwi/sting/argonaute/zwille/eIF2C gene family conserved from plants to vertebrates. Interestingly, several, but not all, RNAi-deficient strains exhibit mobilization of the endogenous transposons. We discuss implications for the mechanism of RNAi and the possibility that one natural function of RNAi is transposon silencing.

Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish.

Directory of Open Access Journals (Sweden)

Maura McGrail

2011-04-01

Full Text Available Large-scale sequencing of human cancer genomes and mouse transposon-induced tumors has identified a vast number of genes mutated in different cancers. One of the outstanding challenges in this field is to determine which genes, when mutated, contribute to cellular transformation and tumor progression. To identify new and conserved genes that drive tumorigenesis we have developed a novel cancer model in a distantly related vertebrate species, the zebrafish, Danio rerio. The Sleeping Beauty (SB T2/Onc transposon system was adapted for somatic mutagenesis in zebrafish. The carp ß-actin promoter was cloned into T2/Onc to create T2/OncZ. Two transgenic zebrafish lines that contain large concatemers of T2/OncZ were isolated by injection of linear DNA into the zebrafish embryo. The T2/OncZ transposons were mobilized throughout the zebrafish genome from the transgene array by injecting SB11 transposase RNA at the 1-cell stage. Alternatively, the T2/OncZ zebrafish were crossed to a transgenic line that constitutively expresses SB11 transposase. T2/OncZ transposon integration sites were cloned by ligation-mediated PCR and sequenced on a Genome Analyzer II. Between 700-6800 unique integration events in individual fish were mapped to the zebrafish genome. The data show that introduction of transposase by transgene expression or RNA injection results in an even distribution of transposon re-integration events across the zebrafish genome. SB11 mRNA injection resulted in neoplasms in 10% of adult fish at ∼10 months of age. T2/OncZ-induced zebrafish tumors contain many mutated genes in common with human and mouse cancer genes. These analyses validate our mutagenesis approach and provide additional support for the involvement of these genes in human cancers. The zebrafish T2/OncZ cancer model will be useful for identifying novel and conserved genetic drivers of human cancers.

Restorer-of-Fertility Mutations Recovered in Transposon-Active Lines of S Male-Sterile Maize

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Susan Gabay-Laughnan

2018-01-01

Full Text Available Mitochondria execute key pathways of central metabolism and serve as cellular sensing and signaling entities, functions that depend upon interactions between mitochondrial and nuclear genetic systems. This is exemplified in cytoplasmic male sterility type S (CMS-S of Zea mays, where novel mitochondrial open reading frames are associated with a pollen collapse phenotype, but nuclear restorer-of-fertility (restorer mutations rescue pollen function. To better understand these genetic interactions, we screened Activator-Dissociation (Ac-Ds, Enhancer/Suppressor-mutator (En/Spm, and Mutator (Mu transposon-active CMS-S stocks to recover new restorer mutants. The frequency of restorer mutations increased in transposon-active stocks compared to transposon-inactive stocks, but most mutants recovered from Ac-Ds and En/Spm stocks were unstable, reverting upon backcrossing to CMS-S inbred lines. However, 10 independent restorer mutations recovered from CMS-S Mu transposon stocks were stable upon backcrossing. Many restorer mutations condition seed-lethal phenotypes that provide a convenient test for allelism. Eight such mutants recovered in this study included one pair of allelic mutations that were also allelic to the previously described rfl2-1 mutant. Targeted analysis of mitochondrial proteins by immunoblot identified two features that consistently distinguished restored CMS-S pollen from comparably staged, normal-cytoplasm, nonmutant pollen: increased abundance of nuclear-encoded alternative oxidase relative to mitochondria-encoded cytochrome oxidase and decreased abundance of mitochondria-encoded ATP synthase subunit 1 compared to nuclear-encoded ATP synthase subunit 2. CMS-S restorer mutants thus revealed a metabolic plasticity in maize pollen, and further study of these mutants will provide new insights into mitochondrial functions that are critical to pollen and seed development.

42 CFR 137.327 - May multiple projects be included in a single construction project agreement?

Science.gov (United States)

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false May multiple projects be included in a single construction project agreement? 137.327 Section 137.327 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF...-GOVERNANCE Construction Project Assumption Process § 137.327 May multiple projects be included in a single...

Multiple levels in the organisation of innovation : project organization in single-firm projects and multi-firm projects

NARCIS (Netherlands)

Jaspers, F.P.H.; Ende, van den J.C.M.; Borgh, van der W.; Yin, Jie

2008-01-01

Studies about how the organization of new product (and new service) development projects (NPD) projects influences project performance typically investigate this in Single-firm projects, i.e. projects with high ownership integration. However, NPD projects are often performed by two or more

Rim 2/Hipa CACTA transposon display ; A new genetic marker technique in Oryza species

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Lee Ju

2005-03-01

Full Text Available Abstract Background Transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. Transposons are generally divided into two classes according to the mechanism underlying their transposition: RNA intermediate class 1 and DNA intermediate class 2. CACTA is a class 2 transposon superfamily, which is found exclusively in plants. As some transposons, including the CACTA superfamily, are highly abundant in plant species, and their nucleotide sequences are highly conserved within a family, they can be utilized as genetic markers, using a slightly modified version of the conventional AFLP protocol. Rim2 /Hipa is a CACTA transposon family having 16 bp consensus TIR sequences to be present in high copy numbers in rice genome. This research was carried out in order to develop a Rim2/Hipa CACTA-AFLP or Rim2/Hipa CACTA-TD (transposon display, hereafter Rim2/Hipa-TD protocol for the study of genetic markers in map construction and the study of genetic diversity in rice. Results Rim2/Hipa-TD generated ample polymorphic profiles among the different rice accessions, and the amplification profiles were highly reproducible between different thermocyclers and Taq polymerases. These amplification profiles allowed for clear distinction between two different ecotypes, Japonica and Indica, of Oryza sativa. In the analysis of RIL populations, the Rim2/Hipa-TD markers were found to be segregated largely in a dominant manner, although in a few cases, non-parental bands were observed in the segregating populations. Upon linkage analysis, the Rim2/Hipa-TD markers were found to be distributed in the regions proximal to the centromeres of the chromosomes. The distribution of the Rim2/Hipa CACTA elements was surveyed in 15 different Oryza species via Rim2/Hipa-TD. While Rim2/Hipa-TD yielded ample amplification profiles between 100 to 700 bp in the AA diploid Oryza species, other species having BB, CC

A large inversion in the linear chromosome of Streptomyces griseus caused by replicative transposition of a new Tn3 family transposon.

Science.gov (United States)

Murata, M; Uchida, T; Yang, Y; Lezhava, A; Kinashi, H

2011-04-01

We have comprehensively analyzed the linear chromosomes of Streptomyces griseus mutants constructed and kept in our laboratory. During this study, macrorestriction analysis of AseI and DraI fragments of mutant 402-2 suggested a large chromosomal inversion. The junctions of chromosomal inversion were cloned and sequenced and compared with the corresponding target sequences in the parent strain 2247. Consequently, a transposon-involved mechanism was revealed. Namely, a transposon originally located at the left target site was replicatively transposed to the right target site in an inverted direction, which generated a second copy and at the same time caused a 2.5-Mb chromosomal inversion. The involved transposon named TnSGR was grouped into a new subfamily of the resolvase-encoding Tn3 family transposons based on its gene organization. At the end, terminal diversity of S. griseus chromosomes is discussed by comparing the sequences of strains 2247 and IFO13350.

Identification of novel genes responsible for ethanol and/or thermotolerance by transposon mutagenesis in Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyun-Soo [Ewha Womans Univ., Seoul (Korea, Republic of). Dept. of Life Sciences; Kim, Na-Rae [Ewha Womans Univ., Seoul (Korea, Republic of). Div. of Life and Pharmaceutical Sciences; Yang, Jungwoo [Ewha Womans Univ., Seoul (Korea, Republic of). Microbial Resources Research Center; Choi, Wonja [Ewha Womans Univ., Seoul (Korea, Republic of). Dept. of Life Sciences; Ewha Womans Univ., Seoul (Korea, Republic of). Div. of Life and Pharmaceutical Sciences; Ewha Womans Univ., Seoul (Korea, Republic of). Microbial Resources Research Center

2011-08-15

Saccharomyces cerevisiae strains tolerant to ethanol and heat stresses are important for industrial ethanol production. In this study, five strains (Tn 1-5) tolerant to up to 15% ethanol were isolated by screening a transposon-mediated mutant library. Two of them displayed tolerance to heat (42 C). The determination of transposon insertion sites and Northern blot analysis identified seven putative genes (CMP2, IMD4, SSK2, PPG1, DLD3, PAM1, and MSN2) and revealed simultaneous down-regulations of CMP2 and IMD4, and SSK2 and PPG1, down-regulation of DLD3, and disruptions of the open reading frame of PAM1 and MSN2, indicating that ethanol and/or heat tolerance can be conferred. Knockout mutants of these seven individual genes were ethanol tolerant and three of them (SSK2, PPG1, and PAM1) were tolerant to heat. Such tolerant phenotypes reverted to sensitive phenotypes by the autologous or overexpression of each gene. Five transposon mutants showed higher ethanol production and grew faster than the control strain when cultured in rich media containing 30% glucose and initial 6% ethanol at 30 C. Of those, two thermotolerant transposon mutants (Tn 2 and Tn 3) exhibited significantly enhanced growth and ethanol production compared to the control at 42 C. The genes identified in this study may provide a basis for the application in developing industrial yeast strains. (orig.)

Molecular characterization of Vulmar1, a complete mariner transposon of sugar beet and diversity of mariner- and En/Spm-like sequences in the genus Beta.

Science.gov (United States)

Jacobs, Gunnar; Dechyeva, Daryna; Menzel, Gerhard; Dombrowski, Cora; Schmidt, Thomas

2004-12-01

Transposons of the Tc1-mariner superfamily are widespread in eukaryotic genomes. We have isolated the mariner element Vulmar1 from Beta vulgaris L., which is 3909 bp long and bordered by perfect terminal inverted repeats of 32 bp with homology to terminal inverted repeats of transposons from soybean and rice. According to a characteristic amino acid signature, Vulmar1 can be assigned to the DD39D group of mariner transposons. Vulmar1 is flanked by a 5'-TA-3' target site duplication that is typical for mariner transposons. Southern hybridization revealed that mariner-like copies are highly abundant in Beta species, and sequence analysis of 10 transposase fragments from representative species of the four Beta sections revealed an identity between 34% and 100% after conceptual translation. By fluorescent in situ hybridization, Vulmar1 was detected in distal euchromatin as well as in some intercalary and pericentromeric regions of all B. vulgaris chromosomes. In addition, using PCR, we were able to amplify fragments of the transposase gene of En/Spm-like transposons in the genus Beta. En/Spm-like transposase sequences are highly amplified in four Beta sections and showed a considerable degree of conservation (88.5-100%) at the protein level, while the homology to corresponding regions of En/Spm transposons of other plant species ranges from 49.5% to 62.5%. By fluorescent in situ hybridization, En/Spm-like transposon signals of strong intensity were detected on all chromosomes of B. vulgaris.

The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination.

Science.gov (United States)

Delprat, Alejandra; Negre, Bàrbara; Puig, Marta; Ruiz, Alfredo

2009-11-18

Transposable elements (TEs) are responsible for the generation of chromosomal inversions in several groups of organisms. However, in Drosophila and other Dipterans, where inversions are abundant both as intraspecific polymorphisms and interspecific fixed differences, the evidence for a role of TEs is scarce. Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii. To assess the impact of TEs in Drosophila chromosomal evolution and shed light on the mechanism involved, we isolated and sequenced the two breakpoints of another widespread polymorphic inversion from D. buzzatii, 2z(3). In the non inverted chromosome, the 2z(3) distal breakpoint was located between genes CG2046 and CG10326 whereas the proximal breakpoint lies between two novel genes that we have named Dlh and Mdp. In the inverted chromosome, the analysis of the breakpoint sequences revealed relatively large insertions (2,870-bp and 4,786-bp long) including two copies of the transposon Galileo (subfamily Newton), one at each breakpoint, plus several other TEs. The two Galileo copies: (i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric. Our observations provide the best evidence gathered so far for the role of TEs in the generation of Drosophila inversions. In addition, they show unequivocally that ectopic recombination is the causative mechanism. The fact that the three polymorphic D. buzzatii inversions investigated so far were generated by the same transposon family is remarkable and is conceivably due to Galileo's unusual structure and current (or recent) transpositional activity.

Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

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Gaigalat Lars

2006-08-01

Full Text Available Abstract Background Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium. Results A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4-monophosphatases (EC 3.1.3.25. Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown

Characterization and Diversity of Novel PIF/Harbinger DNA Transposons in Brassica Genomes

International Nuclear Information System (INIS)

Nouroz, F.; Noreen, S.; Harrison, H.

2016-01-01

Among DNA transposons, PIF/Harbinger is most recently identified superfamily characterized by 3 bp target site duplications (TSDs), flanked by 14-45 bp terminal inverted repeats (TIRs) and displaying DDD or DDE domain displaying transposase. Their autonomous elements contain two open reading frames, ORF1 and ORF2 encoding superfamily specific transposase and DNA-binding domain. Harbinger DNA transposons are recently identified in few plants. In present study, computational and molecular approaches were used for the identification of 8 Harbinger transposons, of which only 2 were complete with putative trans posase, while rest 6 lack transposase and are considered as defective or non-autonomous elements. They ranged in size from 0.5-4 kb with 3 bp TSDs, 15-42 bp TIRs and internal AT richregions. The PCR amplification of Brassica Harbinger transposase revealed diversity and ancient nature of these elements. The amplification polymorphism of some non-autonomous Harbingers showed species specific distribution. Phylogenetic analyses of transposase clustered them into two clades (monocot and dicot) and five sub-clades. The Brassica, Arabidopsis and Malustransposase clustered into genera specific sub-clades; although a lot of homology in transposase was observed. The multiple sequence alignment of Brassica and related transposase showed homology in five conserved blocks. The DD/Sub 35/E triad and sequences showed similarity to already known Pong-like or Arabidopsis ATIS12 Harbinger transposase in contrast to other transposase having DD/Sub 47/E or DD/Sub 48/E motifs. The present study will be helpful in the characterization of Harbingers, their structural diversity in related genera and Harbinger based molecular markers for varietal/lines identifications. (author)

Single-shell tank interim stabilization project plan

Energy Technology Data Exchange (ETDEWEB)

Ross, W.E.

1998-05-11

This project plan establishes the management framework for conduct of the TWRS Single-Shell Tank Interim Stabilization completion program. Specifically, this plan defines the mission needs and requirements; technical objectives and approach; organizational structure, roles, responsibilities, and interfaces; and operational methods. This plan serves as the project executional baseline.

Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon

Directory of Open Access Journals (Sweden)

Hackett Perry B

2006-06-01

Full Text Available Abstract Background Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. Results Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA system that is capable of activating the expression of genes under control of a Tet response element (TRE promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. Conclusion Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene

Derivation and characterization of sleeping beauty transposon-mediated porcine induced pluripotent stem cells

DEFF Research Database (Denmark)

Kues, Wilfried A.; Herrmann, Doris; Barg-Kues, Brigitte

2013-01-01

the nonviral Sleeping Beauty transposon system to deliver the reprogramming factors Oct4, Sox2, Klf4, and cMyc. Successful reprogramming to a pluripotent state was indicated by changes in cell morphology and reactivation of the Oct4-EGFP reporter. The transposon-reprogrammed induced pluripotent stem (i......PS) cells showed long-term proliferation in vitro over >40 passages, expressed transcription factors typical of embryonic stem cells, including OCT4, NANOG, SOX2, REX1, ESRRB, DPPA5, and UTF1 and surface markers of pluripotency, including SSEA-1 and TRA-1-60. In vitro differentiation resulted in derivatives......The domestic pig is an important large animal model for preclinical testing of novel cell therapies. Recently, we produced pluripotency reporter pigs in which the Oct4 promoter drives expression of the enhanced green fluorescent protein (EGFP). Here, we reprogrammed Oct4-EGFP fibroblasts employing...

Improvement of DNA transfer frequency and transposon mutagenesis of Erwinia carotovora subsp. betavasculorum.

Science.gov (United States)

Rella, M; Axelrood, P E; Weinhold, A R; Schroth, M N

1989-01-01

The production of antibiotics and their role in microbial competition under natural conditions can be readily studied by the use of transposon mutants. Several antibiotic-producing strains of Erwinia carotovora subsp. betavasculorum were unable to accept foreign DNA. A plasmid delivery system was developed, using ethyl methanesulfonate mutagenesis, which entailed isolating E. carotovora subsp. betavasculorum mutants able to accept foreign DNA and transfer it to other strains. This enabled transposon mutagenesis of a wild-type antibiotic-producing strain of E. carotovora subsp. betavasculorum. Twelve antibiotic-negative mutants were isolated, and one of these showed a reduction in antibiotic production in vitro. Many of these mutants also showed a reduction in their ability to macerate potato tissue. The mutants were classified into four genetic groups on the basis of their genetic and phenotypic characteristics, indicating that several genes are involved in antibiotic biosynthesis by E. carotovora subsp. betavasculorum. PMID:2543291

Using PATIMDB to create bacterial transposon insertion mutant libraries.

Science.gov (United States)

Urbach, Jonathan M; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M

2009-04-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software.

Single-shell tank interim stabilization project plan

Energy Technology Data Exchange (ETDEWEB)

Ross, W.E.

1998-03-27

Solid and liquid radioactive waste continues to be stored in 149 single-shell tanks at the Hanford Site. To date, 119 tanks have had most of the pumpable liquid removed by interim stabilization. Thirty tanks remain to be stabilized. One of these tanks (C-106) will be stabilized by retrieval of the tank contents. The remaining 29 tanks will be interim stabilized by saltwell pumping. In the summer of 1997, the US Department of Energy (DOE) placed a moratorium on the startup of additional saltwell pumping systems because of funding constraints and proposed modifications to the Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) milestones to the Washington State Department of Ecology (Ecology). In a letter dated February 10, 1998, Final Determination Pursuant to Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) in the Matter of the Disapproval of the DOE`s Change Control Form M-41-97-01 (Fitzsimmons 1998), Ecology disapproved the DOE Change Control Form M-41-97-01. In response, Fluor Daniel Hanford, Inc. (FDH) directed Lockheed Martin Hanford Corporation (LNMC) to initiate development of a project plan in a letter dated February 25, 1998, Direction for Development of an Aggressive Single-Shell Tank (SST) Interim Stabilization Completion Project Plan in Support of Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement). In a letter dated March 2, 1998, Request for an Aggressive Single-Shell Tank (SST) Interim Stabilization Completion Project Plan, the DOE reaffirmed the need for an aggressive SST interim stabilization completion project plan to support a finalized Tri-Party Agreement Milestone M-41 recovery plan. This project plan establishes the management framework for conduct of the TWRS Single-Shell Tank Interim Stabilization completion program. Specifically, this plan defines the mission needs and requirements; technical objectives and approach; organizational structure, roles, responsibilities

Single-shell tank interim stabilization project plan

International Nuclear Information System (INIS)

Ross, W.E.

1998-01-01

Solid and liquid radioactive waste continues to be stored in 149 single-shell tanks at the Hanford Site. To date, 119 tanks have had most of the pumpable liquid removed by interim stabilization. Thirty tanks remain to be stabilized. One of these tanks (C-106) will be stabilized by retrieval of the tank contents. The remaining 29 tanks will be interim stabilized by saltwell pumping. In the summer of 1997, the US Department of Energy (DOE) placed a moratorium on the startup of additional saltwell pumping systems because of funding constraints and proposed modifications to the Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) milestones to the Washington State Department of Ecology (Ecology). In a letter dated February 10, 1998, Final Determination Pursuant to Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) in the Matter of the Disapproval of the DOE's Change Control Form M-41-97-01 (Fitzsimmons 1998), Ecology disapproved the DOE Change Control Form M-41-97-01. In response, Fluor Daniel Hanford, Inc. (FDH) directed Lockheed Martin Hanford Corporation (LNMC) to initiate development of a project plan in a letter dated February 25, 1998, Direction for Development of an Aggressive Single-Shell Tank (SST) Interim Stabilization Completion Project Plan in Support of Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement). In a letter dated March 2, 1998, Request for an Aggressive Single-Shell Tank (SST) Interim Stabilization Completion Project Plan, the DOE reaffirmed the need for an aggressive SST interim stabilization completion project plan to support a finalized Tri-Party Agreement Milestone M-41 recovery plan. This project plan establishes the management framework for conduct of the TWRS Single-Shell Tank Interim Stabilization completion program. Specifically, this plan defines the mission needs and requirements; technical objectives and approach; organizational structure, roles, responsibilities

The Tol2 transposon system mediates the genetic engineering of T-cells with CD19-specific chimeric antigen receptors for B-cell malignancies.

Science.gov (United States)

Tsukahara, T; Iwase, N; Kawakami, K; Iwasaki, M; Yamamoto, C; Ohmine, K; Uchibori, R; Teruya, T; Ido, H; Saga, Y; Urabe, M; Mizukami, H; Kume, A; Nakamura, M; Brentjens, R; Ozawa, K

2015-02-01

Engineered T-cell therapy using a CD19-specific chimeric antigen receptor (CD19-CAR) is a promising strategy for the treatment of advanced B-cell malignancies. Gene transfer of CARs to T-cells has widely relied on retroviral vectors, but transposon-based gene transfer has recently emerged as a suitable nonviral method to mediate stable transgene expression. The advantages of transposon vectors compared with viral vectors include their simplicity and cost-effectiveness. We used the Tol2 transposon system to stably transfer CD19-CAR into human T-cells. Normal human peripheral blood lymphocytes were co-nucleofected with the Tol2 transposon donor plasmid carrying CD19-CAR and the transposase expression plasmid and were selectively propagated on NIH3T3 cells expressing human CD19. Expanded CD3(+) T-cells with stable and high-level transgene expression (~95%) produced interferon-γ upon stimulation with CD19 and specifically lysed Raji cells, a CD19(+) human B-cell lymphoma cell line. Adoptive transfer of these T-cells suppressed tumor progression in Raji tumor-bearing Rag2(-/-)γc(-/-) immunodeficient mice compared with control mice. These results demonstrate that the Tol2 transposon system could be used to express CD19-CAR in genetically engineered T-cells for the treatment of refractory B-cell malignancies.

MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes

Science.gov (United States)

Venken, Koen J. T.; Schulze, Karen L.; Haelterman, Nele A.; Pan, Hongling; He, Yuchun; Evans-Holm, Martha; Carlson, Joseph W.; Levis, Robert W.; Spradling, Allan C.; Hoskins, Roger A.; Bellen, Hugo J.

2011-01-01

We demonstrate the versatility of a collection of insertions of the transposon Minos mediated integration cassette (MiMIC), in Drosophila melanogaster. MiMIC contains a gene-trap cassette and the yellow+ marker flanked by two inverted bacteriophage ΦC31 attP sites. MiMIC integrates almost at random in the genome to create sites for DNA manipulation. The attP sites allow the replacement of the intervening sequence of the transposon with any other sequence through recombinase mediated cassette exchange (RMCE). We can revert insertions that function as gene traps and cause mutant phenotypes to wild type by RMCE and modify insertions to control GAL4 or QF overexpression systems or perform lineage analysis using the Flp system. Insertions within coding introns can be exchanged with protein-tag cassettes to create fusion proteins to follow protein expression and perform biochemical experiments. The applications of MiMIC vastly extend the Drosophila melanogaster toolkit. PMID:21985007

High definition TV projection via single crystal faceplate technology

Science.gov (United States)

Kindl, H. J.; St. John, Thomas

1993-03-01

Single crystal phosphor faceplates are epitaxial phosphors grown on crystalline substrates with the advantages of high light output, resolution, and extended operational life. Single crystal phosphor faceplate industrial technology in the United States is capable of providing a faceplate appropriate to the projection industry of up to four (4) inches in diameter. Projection systems incorporating cathode ray tubes utilizing single crystal phosphor faceplates will produce 1500 lumens of white light with 1000 lines of resolution, non-interlaced. This 1500 lumen projection system will meet all of the currently specified luminance and resolution requirements of Visual Display systems for flight simulators. Significant logistic advantages accrue from the introduction of single crystal phosphor faceplate CRT's. Specifically, the full performance life of a CRT is expected to increase by a factor of five (5); ie, from 2000 to 10,000 hours of operation. There will be attendant reductions in maintenance time, spare CRT requirements, system down time, etc. The increased brightness of the projection system will allow use of lower gain, lower cost simulator screen material. Further, picture performance characteristics will be more balanced across the full simulator.

Transposon mutations in the flagella biosynthetic pathway of the solvent-tolerant Pseudomonas putida S12 result in a decreased expression of solvent efflux genes

NARCIS (Netherlands)

Kieboom, J; Bruinenberg, R; Keizer-Gunnink, [No Value; de Bont, JAM

2001-01-01

Fourteen solvent-sensitive transposon mutants were generated from the solvent-tolerant Pseudomonas putida strain S12 by applying the TnMOD-KmO mutagenesis system. These mutants were unable to grow in the presence of octanol and toluene. By cloning the region flanking the transposon insertion point a

Single-copy insertion of transgenes in Caenorhabditis elegans

DEFF Research Database (Denmark)

Frøkjaer-Jensen, Christian; Davis, M Wayne; Hopkins, Christopher E

2008-01-01

developed a method that inserts a single copy of a transgene into a defined site. Mobilization of a Mos1 transposon generates a double-strand break in noncoding DNA. The break is repaired by copying DNA from an extrachromosomal template into the chromosomal site. Homozygous single-copy insertions can...... be obtained in less than 2 weeks by injecting approximately 20 worms. We have successfully inserted transgenes as long as 9 kb and verified that single copies are inserted at the targeted site. Single-copy transgenes are expressed at endogenous levels and can be expressed in the female and male germlines....

Transcription and somatic transposition of the maize En/Spm transposon system in rice

NARCIS (Netherlands)

Greco, R.; Ouwerkerk, P.B.F.; Taal, A.J.C.; Sallaud, C.; Guiderdoni, E.; Meijer, A.H.; Hoge, J.H.C.; Pereira, A.B.

2004-01-01

Transposition of the maize En/Spm system in rice was investigated using a two-component construct consisting of an immobilised transposase source driven by the CaMV 35S-promoter, and a modified I/dSpm transposon. Mobilization of I/dSpm in somatic sectors was demonstrated by sequencing of excision

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.

Science.gov (United States)

Lorenzen, Marcé D; Gnirke, Andreas; Margolis, Jonathan; Garnes, Jeffrey; Campbell, Margie; Stuart, Jeffrey J; Aggarwal, Rajat; Richards, Stephen; Park, Yoonseong; Beeman, Richard W

2008-07-22

Maternal-Effect Dominant Embryonic Arrest ("Medea") factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We show that Medea(1) activity in Tribolium castaneum is associated with a composite Tc1 transposon inserted just downstream of the neurotransmitter reuptake symporter bloated tubules (blot), whose Drosophila ortholog has both maternal and zygotic functions. The 21.5-kb insertion contains defective copies of elongation initiation factor-3, ATP synthase subunit C, and an RNaseD-related gene, as well as a potentially intact copy of a prokaryotic DUF1703 gene. Sequence comparisons suggest that the current distribution of Medea(1) reflects global emanation after a single transpositional event in recent evolutionary time. The Medea system in Tribolium represents an unusual type of intragenomic conflict and could provide a useful vehicle for driving desirable genes into populations.

Microbial Fe (III) reduction and hydrogen production by a transposon-mutagenized strain of Pantoea agglomerans BH18

International Nuclear Information System (INIS)

Liu, Hongyan; Wang, Guangce

2015-01-01

Based on the transposon-mutagenized library of Pantoea agglomerans BH18, mutant screens were conducted to obtain the strain with the highest Fe (III) reduction and hydrogen production. Of these transposon-mutagenized mutants, the mutant strain TB230 was screened for high Fe (III)-reducing efficiency and hydrogen production. The PCR amplification and kanamycin resistance selection results indicated that the transposon insertion of the mutant strain TB230 was stable. Hydrogen production of the mutant strain TB230 was (2.21 ± 0.34) mol H 2 /mol glucose, which increased hydrogen production by over 40% compared with that of the wild type strain. The accumulation concentration of Fe (II) in the medium of the mutant strain TB230 with Fe (OH) 3 as the sole electron acceptor was (7.39 ± 0.49) mmol/l, which was approximately 3-fold greater than that of the wild type strain. The mutant strain TB230 showed high Fe (III)-reducing activity and hydrogen production by adopting glucose and pyruvate as the carbon source. In addition, the mutant strain TB230 was capable of Fe (III) reduction and hydrogen production under fresh or marine conditions. This result indicates that the mutant strain with high microbial Fe (III) reduction and hydrogen production is beneficial for the improvement of anaerobic performance. - Highlights: • The mutant strain TB230 was a transposon-mutagenized strain of Pantoea agglomerans BH18. • Strain TB230 was screened for high Fe (III)-reducing efficiency and hydrogen production. • H 2 yield and Fe (III)-reducing activity were 2.21 ± 0.34 and 7.39 ± 0.49 in marine condition. • Strain TB230 was capable of Fe (III) reduction and hydrogen production in fresh or marine condition

Single-Shell Tank (SST) Interim Stabilization Project Plan

International Nuclear Information System (INIS)

VLADIMIROFF, D.T.; BOYLES, V.C.

2000-01-01

This project plan establishes the management framework for the conduct of the CHG Single-Shell Tank Interim Stabilization completion program. Specifically, this plan defines the mission needs and requirements; technical objectives and approach; organization structure, roles, responsibilities, and interfaces; and operational methods. This plan serves as the project executional baseline

Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery

Directory of Open Access Journals (Sweden)

Edith eCoronado

2014-11-01

Full Text Available The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested, which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.

Transposon mutagenesis reveals differential pathogenesis of Ralstonia solanacearum on tomato and Arabidopsis.

Science.gov (United States)

Lin, Yu-Mei; Chou, I-Chun; Wang, Jaw-Fen; Ho, Fang-I; Chu, Yu-Ju; Huang, Pei-Cheng; Lu, Der-Kang; Shen, Hwei-Ling; Elbaz, Mounira; Huang, Shu-Mei; Cheng, Chiu-Ping

2008-09-01

Ralstonia solanacearum causes a deadly wilting disease on a wide range of crops. To elucidate pathogenesis of this bacterium in different host plants, we set out to identify R. solanacearum genes involved in pathogenesis by screening random transposon insertion mutants of a highly virulent strain, Pss190, on tomato and Arabidopsis thaliana. Mutants exhibiting various decreased virulence levels on these two hosts were identified. Sequence analysis showed that most, but not all, of the identified pathogenesis genes are conserved among distinct R. solanacearum strains. A few of the disrupted loci were not reported previously as being involved in R. solanacearum pathogenesis. Notably, a group of mutants exhibited differential pathogenesis on tomato and Arabidopsis. These results were confirmed by characterizing allelic mutants in one other R. solanacearum strain of the same phylotype. The significantly decreased mutants' colonization in Arabidopsis was found to be correlated with differential pathogenesis on these two plants. Differential requirement of virulence genes suggests adaptation of this bacterium in different host environments. Together, this study reveals commonalities and differences of R. solanacearum pathogenesis on single solanaceous and nonsolanaceous hosts, and provides important new insights into interactions between R. solanacearum and different host plants.

Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation

Science.gov (United States)

2012-01-01

Background In the silkworm, Bombyx mori, femaleness is strongly controlled by the female-specific W chromosome. Originally, it was presumed that the W chromosome encodes female-determining gene(s), accordingly called Fem. However, to date, neither Fem nor any protein-coding gene has been identified from the W chromosome. Instead, the W chromosome is occupied with numerous transposon-related sequences. Interestingly, the silkworm W chromosome is a source of female-enriched PIWI-interacting RNAs (piRNAs). piRNAs are small RNAs of 23-30 nucleotides in length, which are required for controlling transposon activity in animal gonads. A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet. Results Here we molecularly characterize the KG line. Genomic PCR analyses using currently available W chromosome-specific PCR markers indicated that no large deletion existed in the KG W chromosome. Genetic analyses demonstrated that sib-crosses within the KG line suppressed masculinization. Masculinization reactivated when crossing KG females with wild type males. Importantly, the KG ovaries exhibited a significantly abnormal transcriptome. First, the KG ovaries misexpressed testis-specific genes. Second, a set of female-enriched piRNAs was downregulated in the KG ovaries. Third, several transposons were overexpressed in the KG ovaries. Conclusions Collectively, the mutation in the KG W chromosome causes broadly altered expression of testis-specific genes, piRNAs, and transposons. To our knowledge, this is the first study that describes a W chromosome mutant with such an intriguing phenotype. PMID:22452797

PLE-wu, a new member of piggyBac transposon family from insect, is active in mammalian cells.

Science.gov (United States)

Wu, Chunxiao; Wang, Shu

2014-10-01

piggyBac, a highly active transposon in insect and mammalian cells, is a very useful tool in genome manipulation. A new piggyBac-like element (PLE), named PLE-wu, was identified from a mutant baculovirus cultured in sf9 insect cells. This new transposon is 2931 bp in length and encodes two active forms of transposase, a 708-amino acid-long transposase and a short 576-residue-long transposase translated from a downstream in-frame initiation codon. PLE-wu has asymmetric terminal structures, containing 6-bp inverted terminal repeats, 32-bp imperfect inverted and direct sub-terminal repeats. Similar to piggyBac, PLE-wu exhibits traceless excision activity in both insect and mammalian cells, restoring the original TTAA target sequence upon excision. It also retains the insertion activity in mammalian cells with a plasmid to chromosome transposition rate about 10-fold higher than random integration. Plasmid rescue assays revealed that the TTAA target sequence was duplicated at the junctions of the insertion site. Deletion of the terminal sequences including the sub-terminal repeats decreased the transposition activity of the 708-residue-long transposase, while the transposition activity of the short form of transposase was not affected. With its low sequence similarity to piggyBac, PLE-wu will contribute to the understanding the mechanism of PLE transposition, as well as design of new transposon systems with higher activity. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans.

OpenAIRE

Rezsohazy, R; van Luenen, H G; Durbin, R M; Plasterk, R H

1997-01-01

We have found a novel transposon in the genome of Caenorhabditis elegans. Tc7 is a 921 bp element, made up of two 345 bp inverted repeats separated by a unique, internal sequence. Tc7 does not contain an open reading frame. The outer 38 bp of the inverted repeat show 36 matches with the outer 38 bp of Tc1. This region of Tc1 contains the Tc1-transposase binding site. Furthermore, Tc7 is flanked by TA dinucleotides, just like Tc1, which presumably correspond to the target duplication generated...

Improvement of DNA transfer frequency and transposon mutagenesis of Erwinia carotovora subsp. betavasculorum.

OpenAIRE

Rella, M; Axelrood, P E; Weinhold, A R; Schroth, M N

1989-01-01

The production of antibiotics and their role in microbial competition under natural conditions can be readily studied by the use of transposon mutants. Several antibiotic-producing strains of Erwinia carotovora subsp. betavasculorum were unable to accept foreign DNA. A plasmid delivery system was developed, using ethyl methanesulfonate mutagenesis, which entailed isolating E. carotovora subsp. betavasculorum mutants able to accept foreign DNA and transfer it to other strains. This enabled tra...

Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection.

Science.gov (United States)

Yang, Guanhua; Billings, Gabriel; Hubbard, Troy P; Park, Joseph S; Yin Leung, Ka; Liu, Qin; Davis, Brigid M; Zhang, Yuanxing; Wang, Qiyao; Waldor, Matthew K

2017-10-03

Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant's fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affect E. piscicida 's fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses. IMPORTANCE Transposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogen

Fast and efficient Drosophila melanogaster gene knock-ins using MiMIC transposons.

Science.gov (United States)

Vilain, Sven; Vanhauwaert, Roeland; Maes, Ine; Schoovaerts, Nils; Zhou, Lujia; Soukup, Sandra; da Cunha, Raquel; Lauwers, Elsa; Fiers, Mark; Verstreken, Patrik

2014-10-08

Modern molecular genetics studies necessitate the manipulation of genes in their endogenous locus, but most of the current methodologies require an inefficient donor-dependent homologous recombination step to locally modify the genome. Here we describe a methodology to efficiently generate Drosophila knock-in alleles by capitalizing on the availability of numerous genomic MiMIC transposon insertions carrying recombinogenic attP sites. Our methodology entails the efficient PhiC31-mediated integration of a recombination cassette flanked by unique I-SceI and/or I-CreI restriction enzyme sites into an attP-site. These restriction enzyme sites allow for double-strand break-mediated removal of unwanted flanking transposon sequences, while leaving the desired genomic modifications or recombination cassettes. As a proof-of-principle, we mutated LRRK, tau, and sky by using different MiMIC elements. We replaced 6 kb of genomic DNA encompassing the tau locus and 35 kb encompassing the sky locus with a recombination cassette that permits easy integration of DNA at these loci and we also generated a functional LRRK(HA) knock in allele. Given that ~92% of the Drosophila genes are located within the vicinity (MiMIC element, our methodology enables the efficient manipulation of nearly every locus in the fruit fly genome without the need for inefficient donor-dependent homologous recombination events. Copyright © 2014 Vilain et al.

Facile construction of a random protein domain insertion library using an engineered transposon.

Science.gov (United States)

Shah, Vandan; Pierre, Brennal; Kim, Jin Ryoun

2013-01-15

Insertional fusion between multiple protein domains represents a novel means of creating integrated functionalities. Currently, there is no robust guideline for selection of insertion sites ensuring the desired functional outcome of insertional fusion. Therefore, construction and testing of random domain insertion libraries, in which a host protein domain is randomly inserted into a guest protein domain, significantly benefit extensive exploration of sequence spaces for insertion sites. Short peptide residues are usually introduced between protein domains to alleviate structural conflicts, and the interdomain linker residues may affect the functional outcome of protein insertion complexes. Unfortunately, optimal control of interdomain linker residues is not always available in conventional methods used to construct random domain insertion libraries. Moreover, most conventional methods employ blunt-end rather than sticky-end ligation between host and guest DNA fragments, thus lowering library construction efficiency. Here, we report the facile construction of random domain insertion libraries using an engineered transposon. We show that random domain insertion with optimal control of interdomain linker residues was possible with our engineered transposon-based method. In addition, our method employs sticky-end rather than blunt-end ligation between host and guest DNA fragments, thus allowing for facile construction of relatively large sized libraries. Copyright © 2012 Elsevier Inc. All rights reserved.

Projection operator treatment of single particle resonances

International Nuclear Information System (INIS)

Lev, A.; Beres, W.P.

1976-01-01

A projection operator method is used to obtain the energy and width of a single particle resonance. The resonance energy is found without scanning. An example of the first g/sub 9/2/ neutron resonance in 40 Ca is given and compared with the traditional phase shift method. The results of both approaches are quite similar. 4 figures

Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library.

Science.gov (United States)

Oumeraci, Tonio; Jensen, Vanessa; Talbot, Steven R; Hofmann, Winfried; Kostrzewa, Markus; Schlegelberger, Brigitte; von Neuhoff, Nils; Häussler, Susanne

2015-01-01

Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments. In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed. Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions. The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.

Stable, Nonviral Expression of Mutated Tumor Neoantigen-specific T-cell Receptors Using the Sleeping Beauty Transposon/Transposase System

Science.gov (United States)

Deniger, Drew C; Pasetto, Anna; Tran, Eric; Parkhurst, Maria R; Cohen, Cyrille J; Robbins, Paul F; Cooper, Laurence JN; Rosenberg, Steven A

2016-01-01

Neoantigens unique to each patient's tumor can be recognized by autologous T cells through their T-cell receptor (TCR) but the low frequency and/or terminal differentiation of mutation-specific T cells in tumors can limit their utility as adoptive T-cell therapies. Transfer of TCR genes into younger T cells from peripheral blood with a high proliferative potential could obviate this problem. We generated a rapid, cost-effective strategy to genetically engineer cancer patient T cells with TCRs using the clinical Sleeping Beauty transposon/transposase system. Patient-specific TCRs reactive against HLA-A*0201-restriced neoantigens AHNAKS2580F or ERBB2H473Y or the HLA-DQB*0601-restricted neoantigen ERBB2IPE805G were assembled with murine constant chains and cloned into Sleeping Beauty transposons. Patient peripheral blood lymphocytes were coelectroporated with SB11 transposase and Sleeping Beauty transposon, and transposed T cells were enriched by sorting on murine TCRβ (mTCRβ) expression. Rapid expansion of mTCRβ+ T cells with irradiated allogeneic peripheral blood lymphocytes feeders, OKT3, interleukin-2 (IL-2), IL-15, and IL-21 resulted in a preponderance of effector (CD27−CD45RA−) and less-differentiated (CD27+CD45RA+) T cells. Transposed T cells specifically mounted a polyfunctional response against cognate mutated neoantigens and tumor cell lines. Thus, Sleeping Beauty transposition of mutation-specific TCRs can facilitate the use of personalized T-cell therapy targeting unique neoantigens. PMID:26945006

Gene Therapy with the Sleeping Beauty Transposon System.

Science.gov (United States)

Kebriaei, Partow; Izsvák, Zsuzsanna; Narayanavari, Suneel A; Singh, Harjeet; Ivics, Zoltán

2017-11-01

The widespread clinical implementation of gene therapy requires the ability to stably integrate genetic information through gene transfer vectors in a safe, effective, and economical manner. The latest generation of Sleeping Beauty (SB) transposon vectors fulfills these requirements, and may overcome limitations associated with viral gene transfer vectors and transient nonviral gene delivery approaches that are prevalent in ongoing clinical trials. The SB system enables high-level stable gene transfer and sustained transgene expression in multiple primary human somatic cell types, thereby representing a highly attractive gene transfer strategy for clinical use. Here, we review the most important aspects of using SB for gene therapy, including vectorization as well as genomic integration features. We also illustrate the path to successful clinical implementation by highlighting the application of chimeric antigen receptor (CAR)-modified T cells in cancer immunotherapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Transposon-mediated random gene disruption with moderate halophilic bacteria and its application for halophilic bacterial siderophore analysis.

Science.gov (United States)

Matsui, Toru; Nishino, Tomohiko

2016-12-01

Analytical conditions using chromo azurol S was validated for quantification of siderophore in aqueous samples, followed by the characterization of siderophore derived from newly isolated moderately halophilic bacteria. Conditions with good linearity between the absorbance and the siderophore concentration were obtained at a siderophore concentration less than 20 µM, in the wavelength range between 630 and 660 nm with developing time for at least 2 h. Of the halophilic bacteria isolated from Tunisian soil, Halomonas sp., namely strain 21a was selected as siderophore producing halophiles. The strain produced siderophore significantly in the absence of iron in minimal medium. Siderophore-deficient mutant, namely IIa10, of the strain 21a was obtained from gene disruptant library constructed using transposon complex by electroporation. Genomic sequence analysis of the mutant IIa10 revealed that the transposon-inserted gene was TonB-dependent receptor. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced Expression of Anti-CD19 Chimeric Antigen Receptor in piggyBac Transposon-Engineered T Cells

Directory of Open Access Journals (Sweden)

Daisuke Morita

2018-03-01

Full Text Available Adoptive T cell therapy using chimeric antigen receptor (CAR-modified T cells is a promising cancer immunotherapy. We previously developed a non-viral method of gene transfer into T cells using a piggyBac transposon system to improve the cost-effectiveness of CAR-T cell therapy. Here, we have further improved our technology by a novel culture strategy to increase the transfection efficiency and to reduce the time of T cell manufacturing. Using a CH2CH3-free CD19-specific CAR transposon vector and combining irradiated activated T cells (ATCs as feeder cells and virus-specific T cell receptor (TCR stimulation, we achieved 51.4% ± 14% CAR+ T cells and 2.8-fold expansion after 14 culture days. Expanded CD19.CAR-T cells maintained a significant fraction of CD45RA+CCR7+ T cells and demonstrated potent antitumor activity against CD19+ leukemic cells both in vitro and in vivo. Therefore, piggyBac-based gene transfer may provide an alternative to viral gene transfer for CAR-T cell therapy.

High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer.

Science.gov (United States)

Garcia-Fernàndez, J; Bayascas-Ramírez, J R; Marfany, G; Muñoz-Mármol, A M; Casali, A; Baguñà, J; Saló, E

1995-05-01

Several DNA sequences similar to the mariner element were isolated and characterized in the platyhelminthe Dugesia (Girardia) tigrina. They were 1,288 bp long, flanked by two 32 bp-inverted repeats, and contained a single 339 amino acid open-reading frame (ORF) encoding the transposase. The number of copies of this element is approximately 8,000 per haploid genome, constituting a member of the middle-repetitive DNA of Dugesia tigrina. Sequence analysis of several elements showed a high percentage of conservation between the different copies. Most of them presented an intact ORF and the standard signals of actively expressed genes, which suggests that some of them are or have recently been functional transposons. The high degree of similarity shared with other mariner elements from some arthropods, together with the fact that this element is undetectable in other planarian species, strongly suggests a case of horizontal transfer between these two distant phyla.

nanos-Driven expression of piggyBac transposase induces mobilization of a synthetic autonomous transposon in the malaria vector mosquito, Anopheles stephensi.

Science.gov (United States)

Macias, Vanessa M; Jimenez, Alyssa J; Burini-Kojin, Bianca; Pledger, David; Jasinskiene, Nijole; Phong, Celine Hien; Chu, Karen; Fazekas, Aniko; Martin, Kelcie; Marinotti, Osvaldo; James, Anthony A

2017-08-01

Transposons are a class of selfish DNA elements that can mobilize within a genome. If mobilization is accompanied by an increase in copy number (replicative transposition), the transposon may sweep through a population until it is fixed in all of its interbreeding members. This introgression has been proposed as the basis for drive systems to move genes with desirable phenotypes into target species. One such application would be to use them to move a gene conferring resistance to malaria parasites throughout a population of vector mosquitos. We assessed the feasibility of using the piggyBac transposon as a gene-drive mechanism to distribute anti-malarial transgenes in populations of the malaria vector, Anopheles stephensi. We designed synthetic gene constructs that express the piggyBac transposase in the female germline using the control DNA of the An. stephensi nanos orthologous gene linked to marker genes to monitor inheritance. Two remobilization events were observed with a frequency of one every 23 generations, a rate far below what would be useful to drive anti-pathogen transgenes into wild mosquito populations. We discuss the possibility of optimizing this system and the impetus to do so. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Tn5051-like mer-containing transposon identified in a heavy metal tolerant strain Achromobacter sp. AO22

Directory of Open Access Journals (Sweden)

Bhave Mrinal

2009-03-01

Full Text Available Abstract Background Achromobacter sp. AO22 (formerly Alcaligenes sp. AO22, a bacterial strain isolated from a lead-contaminated industrial site in Australia, was previously found to be resistant to moderate to high levels of mercury, copper and other heavy metals. However, the nature and location of the genetic basis for mercuric ion resistance in this strain, had not been previously identified. Findings Achromobacter sp. AO22 contains a functional mer operon with all four essential genes (merRTPA and shows >99% DNA sequence identity to that of Tn501. The mer operon was present on a transposon, designated TnAO22, captured by introducing a broad-host-range IncP plasmid into Achromobacter sp. AO22 and subsequently transferring it to E. coli recipients. The transposition frequency of TnAO22 was 10-2 to 10-3 per target plasmid transferred. Analysis of TnAO22 sequence revealed it belonged to the Tn21 subgroup of the Tn3 superfamily of transposons, with the transposition module having >99% identity with Tn5051 of a Pseudomonas putida strain isolated from a water sample in New York. Conclusion TnAO22 is thus a new variant of Tn5051 of the Tn3 superfamily and the transposon and its associated mercury resistance system are among the few such systems reported in a soil bacterium. Achromobacter sp. AO22 can thus be exploited for applications such as in situ mercury bioremediation of contaminated sites, or the mobile unit and mer operon could be mobilized to other bacteria for similar purposes.

IS30-related transposon mediated insertional inactivation of bile salt hydrolase (bsh1) gene of Lactobacillus plantarum strain Lp20.

Science.gov (United States)

Kumar, Rajesh; Grover, Sunita; Kaushik, Jai K; Batish, Virender Kumar

2014-01-01

Lactobacillus plantarum is a flexible and versatile microorganism that inhabits a variety of niches, and its genome may express up to four bsh genes to maximize its survival in the mammalian gut. However, the ecological significance of multiple bsh genes in L. plantarum is still not clearly understood. Hence, this study demonstrated the disruption of bile salt hydrolase (bsh1) gene due to the insertion of a transposable element in L. plantarum Lp20 - a wild strain of human fecal origin. Surprisingly, L. plantarum strain Lp20 produced a ∼2.0 kb bsh1 amplicon against the normal size (∼1.0 kb) bsh1 amplicon of Bsh(+)L. plantarum Lp21. Strain Lp20 exhibited minimal Bsh activity in spite of having intact bsh2, bsh3 and bsh4 genes in its genome and hence had a Bsh(-) phenotype. Cloning and sequence characterization of Lp20 bsh1 gene predicted four individual open reading frames (ORFs) within this region. BLAST analysis of ORF1 and ORF2 revealed significant sequence similarity to the L. plantarum bsh1 gene while ORF3 and ORF4 showed high sequence homology to IS30-family transposases. Since, IS30-related transposon element was inserted within Lp20 bsh1 gene in reverse orientation (3'-5'), it introduced several stop codons and disrupted the protein reading frames of both Bsh1 and transposase. Inverted terminal repeats (GGCAGATTG) of transposon, mediated its insertion at 255-263 nt and 1301-1309 nt positions of Lp20 bsh1 gene. In conclusion, insertion of IS30 related-transposon within the bsh1 gene sequence of L. plantarum strain Lp20 demolished the integrity and functionality of Bsh1 enzyme. Additionally, this transposon DNA sequence remains active among various Lactobacillus spp. and hence harbors the potential to be explored in the development of efficient insertion mutagenesis system. Copyright © 2013 Elsevier GmbH. All rights reserved.

TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

Directory of Open Access Journals (Sweden)

Sarver Aaron L

2012-06-01

Full Text Available Abstract Background Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1 map junction fragments within the genome and 2 identify Common Insertion Sites (CISs within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. Results We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. Conclusions The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches

The logic of single-cell projections from visual cortex.

Science.gov (United States)

Han, Yunyun; Kebschull, Justus M; Campbell, Robert A A; Cowan, Devon; Imhof, Fabia; Zador, Anthony M; Mrsic-Flogel, Thomas D

2018-04-05

Neocortical areas communicate through extensive axonal projections, but the logic of information transfer remains poorly understood, because the projections of individual neurons have not been systematically characterized. It is not known whether individual neurons send projections only to single cortical areas or distribute signals across multiple targets. Here we determine the projection patterns of 591 individual neurons in the mouse primary visual cortex using whole-brain fluorescence-based axonal tracing and high-throughput DNA sequencing of genetically barcoded neurons (MAPseq). Projections were highly diverse and divergent, collectively targeting at least 18 cortical and subcortical areas. Most neurons targeted multiple cortical areas, often in non-random combinations, suggesting that sub-classes of intracortical projection neurons exist. Our results indicate that the dominant mode of intracortical information transfer is not based on 'one neuron-one target area' mapping. Instead, signals carried by individual cortical neurons are shared across subsets of target areas, and thus concurrently contribute to multiple functional pathways.

Analysis of Installed Measures and Energy Savings for Single-Family Residential Better Buildings Projects

Energy Technology Data Exchange (ETDEWEB)

Heaney, M. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Polly, B. [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2015-04-30

This report presents an analysis of data for residential single-family projects reported by 37 organizations that were awarded federal financial assistance (cooperative agreements or grants) by the U.S. Department of Energy’s Better Buildings Neighborhood Program.1 The report characterizes the energy-efficiency measures installed for single-family residential projects and analyzes energy savings and savings prediction accuracy for measures installed in a subset of those projects.

Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon

Directory of Open Access Journals (Sweden)

de Koning-Ward Tania F

2011-03-01

Full Text Available Abstract The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism. See research article: http://www.biomedcentral.com/1471-2164/12/155

High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.

Science.gov (United States)

Kebschull, Justus M; Garcia da Silva, Pedro; Reid, Ashlan P; Peikon, Ian D; Albeanu, Dinu F; Zador, Anthony M

2016-09-07

Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of Tn3000, a Transposon Responsible for blaNDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India.

Science.gov (United States)

Campos, Juliana Coutinho; da Silva, Maria José Félix; dos Santos, Paulo Roberto Nascimento; Barros, Elaine Menezes; Pereira, Mayne de Oliveira; Seco, Bruna Mara Silva; Magagnin, Cibele Massotti; Leiroz, Leonardo Kalab; de Oliveira, Théo Gremen Mimary; de Faria-Júnior, Célio; Cerdeira, Louise Teixeira; Barth, Afonso Luís; Sampaio, Suely Carlos Ferreira; Zavascki, Alexandre Prehn; Poirel, Laurent; Sampaio, Jorge Luiz Mello

2015-12-01

In Enterobacteriaceae, the blaNDM genes have been found in many different genetic contexts, and a wide diversity of plasmid scaffolds bearing those genes has been found. In August 2013, we identified NDM-1-producing Escherichia coli and Enterobacter hormaechei strains from a single rectal swab sample from a patient hospitalized in Rio de Janeiro, Brazil, who had no history of travel abroad. Complete DNA sequencing using the Illumina platform and annotation of the two plasmids harboring the blaNDM-1 gene, one from each strain, showed that they belonged to incompatibility groups IncFIIK and IncX3 and harbored a novel transposon named Tn3000. Similar genetic structures have been identified among other isolates in Brazil but also on plasmids from other continents. Our findings suggest that the blaNDM-1 gene may be transmitted by Tn3000 in different parts of the world. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Increased encapsulated cell biodelivery of nerve growth factor in the brain by transposon-mediated gene transfer

DEFF Research Database (Denmark)

Fjord-Larsen, L; Kusk, Poul Henrik; Emerich, D F

2012-01-01

transposon expression technology to establish a new clinical grade cell line, NGC0211, with at least 10 times higher NGF production than that of NGC-0295. To test whether encapsulation of this cell line provides a relevant dose escalation step in delivering NGF for treatment of the cognitive decline in AD...... cases correlate with highly improved potency.Gene Therapy advance online publication, 24 November 2011; doi:10.1038/gt.2011.178....

Transgenerational changes in plant physiology and in transposon expression in response to UV-C stress in Arabidopsis thaliana.

Science.gov (United States)

Migicovsky, Zoe; Kovalchuk, Igor

2014-01-01

Stress has a negative impact on crop yield by altering a gain in biomass and affecting seed set. Recent reports suggest that exposure to stress also influences the response of the progeny. In this paper, we analyzed seed size, leaf size, bolting time and transposon expression in 2 consecutive generations of Arabidopsis thaliana plants exposed to moderate UV-C stress. Since previous reports suggested a potential role of Dicer-like (DCL) proteins in the establishment of transgenerational response, we used dcl2, dcl3 and dcl4 mutants in parallel with wild-type plants. These studies revealed that leaf number decreased in the progeny of UV-C stressed plants, and bolting occurred later. Transposons were also re-activated in the progeny of stressed plants. Changes in the dcl mutants were less prominent than in wild-type plants. DCL2 and DCL3 appeared to be more important in the transgenerational stress memory than DCL4 because transgenerational changes were less profound in the dcl2 and dcl3 mutants.

Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients

Science.gov (United States)

Sun, Ting; Renner, Susanne S.; Xu, Yuxing; Qin, Yan; Wu, Jianqiang; Sun, Guiling

2016-01-01

A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca. PMID:27452947

Progress of the Enhanced Hanford Single Shell Tank (SST) Integrity Project

Energy Technology Data Exchange (ETDEWEB)

Venetz, Theodore J. [Washington River Protection Solutions, Richland, WA (United States); Washenfelder, Dennis J. [Washington River Protection Solutions, Richland, WA (United States); Boomer, Kayle D. [Washington River Protection Solutions, Richland, WA (United States); Johnson, Jeremy M. [USDOE Office of River Protection, Richland, WA (United States); Castleberry, Jim L. [Washington River Protection Solutions, Richland, WA (United States)

2015-01-07

To improve the understanding of the single-shell tanks (SSTs) integrity, Washington River Protection Solutions, LLC (WRPS), the USDOE Hanford Site tank contractor, developed an enhanced Single-Shell Tank Integrity Project (SSTIP) in 2009. An expert panel on SST integrity, consisting of various subject matters experts in industry and academia, was created to provide recommendations supporting the development of the project. This panel developed 33 recommendations in four main areas of interest: structural integrity, liner degradation, leak integrity and prevention, and mitigation of contamination migration. In late 2010, seventeen of these recommendations were used to develop the basis for the M-45-10-1 Change Package for the Hanford Federal Agreement and Compliance Order, which is also known as the Tri-Party Agreement.

Novel Aminoglycoside Resistance Transposons and Transposon-Derived Circular Forms Detected in Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates

Science.gov (United States)

Dwibedi, Chinmay Kumar; Sjöström, Karin; Edquist, Petra; Wai, Sun Nyunt; Uhlin, Bernt Eric

2016-01-01

Acinetobacter baumannii has emerged as an important opportunistic pathogen equipped with a growing number of antibiotic resistance genes. Our study investigated the molecular epidemiology and antibiotic resistance features of 28 consecutive carbapenem-resistant clinical isolates of A. baumannii collected throughout Sweden in 2012 and 2013. The isolates mainly belonged to clonal complexes (CCs) with an extensive international distribution, such as CC2 (n = 16) and CC25 (n = 7). Resistance to carbapenems was related to blaOXA-23 (20 isolates), blaOXA-24/40-like (6 isolates), blaOXA-467 (1 isolate), and ISAba1-blaOXA-69 (1 isolate). Ceftazidime resistance was associated with blaPER-7 in the CC25 isolates. Two classical point mutations were responsible for resistance to quinolones in all the isolates. Isolates with high levels of resistance to aminoglycosides carried the 16S rRNA methylase armA gene. The isolates also carried a variety of genes encoding aminoglycoside-modifying enzymes. Several novel structures involved in aminoglycoside resistance were identified, including Tn6279, ΔTn6279, Ab-ST3-aadB, and different assemblies of Tn6020 and TnaphA6. Importantly, a number of circular forms related to the IS26 or ISAba125 composite transposons were detected. The frequent occurrence of these circular forms in the populations of several isolates indicates a potential role of these circular forms in the dissemination of antibiotic resistance genes. PMID:26824943

R-prime site-directed transposon Tn7 mutagenesis of the photosynthetic apparatus in Rhodopseudomonas capsulata

Energy Technology Data Exchange (ETDEWEB)

Youvan, D C [Univ. of California, Berkeley; Elder, J T; Sandlin, D E; Zsebo, K; Alder, D P; Panopoulos, N J; Marrs, B L; Hearst, J E

1982-01-01

Site-directed mutagenesis of the photosynthetic apparatus (PSA) genes in Rhodopseudomonas capsulata is presented utilizing a transposon Tn7 mutagenized R-prime. The R-prime, pRPS404, bears most of the genes necessary for the differentiation of the photosynthetic apparatus. Mutagenesis of the R-prime with Tn7 in Escherichia coli, conjugation into R. capsulata, and homologous recombination with the wild-type alleles efficiently generates photosynthetic apparatus lesions. Wild-type alleles are lost spontaneously and the Tn7-induced lesions are revealed by subsequent intramolecular recombination between IS21 insertion elements that bracket the prime sequences in direct repeat. The molecular nature of the intermediates involved in the transposition, recombination and deletion have been investigated by Southern hybridization analysis. The spontaneous loss of wild-type alleles after homologous recombination with the chromosome may be of general use to other prokaryotic site-directed transposon mutagenesis schemes. The IS21-mediated deletion of the prime DNA is dependent on the RecA protein in E. coli, generating the parental R-factor bearing one IS21 element. A genetic-physical map exists for a portion of the prime photosynthetic apparatus DNA. When Tn7 is inserted into a bacteriochlorophyll gene in the R-prime and then crossed into R. capsulata, mutants are produced that accumulate a bacteriochlorophyll precursor, which is in excellent agreement with the existing genetic-physical map. This corroborates the mutagenesis scheme.

Genetic Transformation of Hordeum vulgare ssp. spontaneum for the Development of a Transposon-Based Insertional Mutagenesis System.

Science.gov (United States)

Cardinal, Marie-Josée; Kaur, Rajvinder; Singh, Jaswinder

2016-10-01

Domestication and intensive selective breeding of plants has triggered erosion of genetic diversity of important stress-related alleles. Researchers highlight the potential of using wild accessions as a gene source for improvement of cereals such as barley, which has major economic and social importance worldwide. Previously, we have successfully introduced the maize Ac/Ds transposon system for gene identification in cultivated barley. The objective of current research was to investigate the response of Hordeum vulgare ssp. spontaneum wild barley accessions in tissue culture to standardize parameters for introduction of Ac/Ds transposons through genetic transformation. We investigated the response of ten wild barley genotypes for callus induction, regenerative green callus induction and regeneration of fertile plants. The activity of exogenous Ac/Ds elements was observed through a transient assay on immature wild barley embryos/callus whereby transformed embryos/calli were identified by the expression of GUS. Transient Ds expression bombardment experiments were performed on 352 pieces of callus (3-5 mm each) or immature embryos in 4 genotypes of wild barley. The transformation frequency of putative transgenic callus lines based on transient GUS expression ranged between 72 and100 % in wild barley genotypes. This is the first report of a transformation system in H. vulgare ssp. spontaneum.

High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn1546 Transposon

Science.gov (United States)

Berendsen, Erwin M.; Koning, Rosella A.; Boekhorst, Jos; de Jong, Anne; Kuipers, Oscar P.; Wells-Bennik, Marjon H. J.

2016-01-01

Bacterial endospore formers can produce spores that are resistant to many food processing conditions, including heat. Some spores may survive heating processes aimed at production of commercially sterile foods. Recently, it was shown that a spoVA operon, designated spoVA2mob, present on a Tn1546 transposon in Bacillus subtilis, leads to profoundly increased wet heat resistance of B. subtilis spores. Such Tn1546 transposon elements including the spoVA2mob operon were also found in several strains of Bacillus amyloliquefaciens and Bacillus licheniformis, and these strains were shown to produce spores with significantly higher resistances to wet heat than their counterparts lacking this transposon. In this study, the locations and compositions of Tn1546 transposons encompassing the spoVA2mob operons in B. amyloliquefaciens and B. licheniformis were analyzed. Introduction of these spoVA2mob operons into B. subtilis 168 (producing spores that are not highly heat resistant) rendered mutant 168 strains that produced high-level heat resistant spores, demonstrating that these elements in B. amyloliquefaciens and B. licheniformis are responsible for high level heat resistance of spores. Assessment of growth of the nine strains of each species between 5.2°C and 57.7°C showed some differences between strains, especially at lower temperatures, but all strains were able to grow at 57.7°C. Strains of B. amyloliquefaciens and B. licheniformis that contain the Tn1546 elements (and produce high-level heat resistant spores) grew at temperatures similar to those of their Tn1546-negative counterparts that produce low-level heat resistant spores. The findings presented in this study allow for detection of B. amyloliquefaciens and B. licheniformis strains that produce highly heat resistant spores in the food chain. PMID:27994575

Horizontal transfers of Mariner transposons between mammals and insects.

Science.gov (United States)

Oliveira, Sarah G; Bao, Weidong; Martins, Cesar; Jurka, Jerzy

2012-09-26

Active transposable elements (TEs) can be passed between genomes of different species by horizontal transfer (HT). This may help them to avoid vertical extinction due to elimination by natural selection or silencing. HT is relatively frequent within eukaryotic taxa, but rare between distant species. Closely related Mariner-type DNA transposon families, collectively named as Mariner-1_Tbel families, are present in the genomes of two ants and two mammalian genomes. Consensus sequences of the four families show pairwise identities greater than 95%. In addition, mammalian Mariner1_BT family shows a close evolutionary relationship with some insect Mariner families. Mammalian Mariner1_BT type sequences are present only in species from three groups including ruminants, tooth whales (Odontoceti), and New World leaf-nosed bats (Phyllostomidae). Horizontal transfer accounts for the presence of Mariner_Tbel and Mariner1_BT families in mammals. Mariner_Tbel family was introduced into hedgehog and tree shrew genomes approximately 100 to 69 million years ago (MYA). Most likely, these TE families were transferred from insects to mammals, but details of the transfer remain unknown.

Nanopatterning of magnetic disks by single-step Ar+ Ion projection

NARCIS (Netherlands)

Dietzel, A.H.; Berger, R.; Loeschner, H.; Platzgummer, E.; Stengl, G.; Bruenger, W.H.; Letzkus, F.

2003-01-01

Large-area Ar+ projection has been used to generate planar magnetic nanostructures on a 1¿-format hard disk in a single step (see Figure). The recording pattern was transferred to a Co/Pt multilayer without resist processes or any other contact to the delicate media surface. It is conceivable that

Chick derived induced pluripotent stem cells by the poly-cistronic transposon with enhanced transcriptional activity.

Science.gov (United States)

Katayama, Masafumi; Hirayama, Takashi; Tani, Tetsuya; Nishimori, Katsuhiko; Onuma, Manabu; Fukuda, Tomokazu

2018-02-01

Induced pluripotent stem (iPS) cell technology lead terminally differentiated cells into the pluripotent stem cells through the expression of defined reprogramming factors. Although, iPS cells have been established in a number of mammalian species, including mouse, human, and monkey, studies on iPS cells in avian species are still very limited. To establish chick iPS cells, six factors were used within the poly-cistronic reprogramming vector (PB-R6F), containing M3O (MyoD derived transactivation domain fused with Oct3/4), Sox2, Klf4, c-Myc, Lin28, and Nanog. The PB-R6F derived iPS cells were alkaline-phosphatase and SSEA-1 positive, which are markers of pluripotency. Elevated levels of endogenous Oct3/4 and Nanog genes were detected in the established iPS cells, suggesting the activation of the FGF signaling pathway is critical for the pluripotent status. Histological analysis of teratoma revealed that the established chick iPS cells have differentiation ability into three-germ-layer derived tissues. This is the first report of establishment of avian derived iPS cells with a single poly-cistronic transposon based expression system. The establishment of avian derived iPS cells could contribute to the genetic conservation and modification of avian species. © 2017 Wiley Periodicals, Inc.

A LTR copia retrotransposon and Mutator transposons interrupt Pgip genes in cultivated and wild wheats.

Science.gov (United States)

Di Giovanni, Michela; Cenci, Alberto; Janni, Michela; D'Ovidio, Renato

2008-04-01

Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. Wheat pgip genes have been isolated from the B (Tapgip1) and D (Tapgip2) genomes, and now we report the identification of pgip genes from the A genomes of wild and cultivated wheats. By Southern blots and sequence analysis of BAC clones we demonstrated that wheat contains a single copy pgip gene per genome and the one from the A genome, pgip3, is inactivated by the insertion of a long terminal repeat copia retrotranspon within the fourth LRR. We demonstrated also that this retrotransposon insertion is present in Triticum urartu and all the polyploidy wheats assayed, but is absent in T. monococcum (Tmpgip3), suggesting that this insertion took place after the divergence between T. monococcum and T. urartu, but before the formation of the polyploid wheats. We identified also two independent insertion events of new Class II transposable elements, Vacuna, belonging to the Mutator superfamily, that interrupted the Tdipgip1 gene of T. turgidum ssp. dicoccoides. The occurrence of these transposons within the coding region of Tdipgip1 facilitated the mapping of the Pgip locus in the pericentric region of the short arm of chromosome group 7. We speculate that the inactivation of pgip genes are tolerated because of redundancy of PGIP activities in the wheat genome.

Development of a high-frequency in vivo transposon mutagenesis system for Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942.

Science.gov (United States)

Watabe, Kazuyuki; Mimuro, Mamoru; Tsuchiya, Tohru

2014-11-01

Synechocystis sp. PCC 6803 (Synechocystis) is the first sequenced photosynthetic organism and has two advantages: natural transformation and light-activated heterotrophic growth. Such characteristics have mainly promoted reverse genetic analysis in this organism, however, to date approximately 50% of genes are still annotated as 'unknown protein' or 'hypothetical protein'. Therefore, forward genetic analysis is required for the identification of significant genes responsible for photosynthesis and other physiological phenomena among the genes of unknown function. The in vivo transposon mutagenesis system is one of the major methods for random mutagenesis. However, present in vivo transposon mutagenesis systems for cyanobacteria face problems such as relatively low frequency of transposition and repeated transposition in the host cells. In this study, we constructed vectors based on a mini-Tn5-derived vector that was designed to prevent repeated transposition. Our vectors carry a hyperactive transposase and optimized recognition sequence of transposase, which were reported to enhance frequency of transposition. Using the vector, we succeeded in highly frequent transposition (9×10(-3) per recipient cell) in Synechocystis. Transposon insertion sites of 10 randomly selected mutants indicated that the insertion sites spread throughout the genome with low sequence dependency. Furthermore, one of the 10 mutants exhibited the slow-growing phenotype, and the mutant was functionally complemented by using our expression vector. Our system also worked with another model cyanobacterium, Synechococcus elongatus PCC 7942, with high frequency. These results indicate that the developed system can be applied to the forward genetic analysis of a broad range of cyanobacteria. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

Science.gov (United States)

Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

2010-02-01

A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12.

Science.gov (United States)

Miki, Takeyoshi; Yamamoto, Yoshihiro; Matsuda, Hideo

2008-01-01

We developed a novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12. The basic idea of the method is to randomly disrupt the genes on the DNA fragments cloned on the Kohara library by inserting a mini-transposon first, and then transfer the disrupted genes from the lambda vector to the E. coli chromosome by homologous recombination. Using this method, we constructed a set of 8402 Km(r) cis-diploid mutants harboring a mini-Tn10 insertion mutation and the corresponding wild-type gene on a chromosome, as well as a set of 6954 haploid mutants derived from the cis-diploid mutants. The major advantage of the strategy used is that the indispensable genes or sites for growth can be identified. Preliminary results suggest that 415 open reading frames are indispensable for growth in E. coli cells. A total of 6404 haploid mutants were deposited to Genetic Strains Research Center, National Institute of Genetics, Japan (Chapter 26) and are available for public distribution upon request (http://shigen.lab.nig.ac.jp/ecoli/strain/nbrp/resource.jsp).

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

Science.gov (United States)

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.

Transcriptome-wide Identification and Expression Analysis of Brachypodium distachyon Transposons in Response to Viral Infection

Directory of Open Access Journals (Sweden)

Tuğba Gürkök

2017-10-01

Full Text Available Transposable elements (TEs are the most abundant group of genomic elements in plants that can be found in genic or intergenic regions of their host genomes. Several stimuli such as biotic or abiotic stress have roles in either activating their transcription or transposition. Here the effect of the Panicum mosaic virus (PMV and its satellite virus (SPMV infection on the transposon transcription of the Brachypodium distachyon model plant was investigated. To evaluate the transcription activity of TEs, transcriptomic data of mock and virus inoculated plants were compared. Our results indicate that major components of TEs are retroelements in all RNA-seq libraries. The number of transcribed TEs detected in mock inoculated plants is higher than virus inoculated plants. In comparison with mock inoculated plants 13% of the TEs showed at least two folds alteration upon PMV infection and 21% upon PMV+SPMV infection. Rather than inoculation with PMV alone inoculation with PMV+SPMV together also increased various TE encoding transcripts expressions. MuDR-N78C_OS encoding transcript was strongly up-regulated against both PMV and PMV+SPMV infection. The synergism generated by PMV and SPMV together enhanced TE transcripts expressions than PMV alone. It was observed that viral infection induced the transcriptional activity of several transposons. The results suggest that increased expressions of TEs might have a role in response to biotic stress in B. distachyon. Identification of TEs which are taking part in stress can serve useful information for functional genomics and designing novel breeding strategies in developing stress resistance crops.

Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway

Science.gov (United States)

Dubois, Emeline; Bischerour, Julien; Marmignon, Antoine; Mathy, Nathalie; Régnier, Vinciane; Bétermier, Mireille

2012-01-01

Sequences related to transposons constitute a large fraction of extant genomes, but insertions within coding sequences have generally not been tolerated during evolution. Thanks to their unique nuclear dimorphism and to their original mechanism of programmed DNA elimination from their somatic nucleus (macronucleus), ciliates are emerging model organisms for the study of the impact of transposable elements on genomes. The germline genome of the ciliate Paramecium, located in its micronucleus, contains thousands of short intervening sequences, the IESs, which interrupt 47% of genes. Recent data provided support to the hypothesis that an evolutionary link exists between Paramecium IESs and Tc1/mariner transposons. During development of the macronucleus, IESs are excised precisely thanks to the coordinated action of PiggyMac, a domesticated piggyBac transposase, and of the NHEJ double-strand break repair pathway. A PiggyMac homolog is also required for developmentally programmed DNA elimination in another ciliate, Tetrahymena. Here, we present an overview of the life cycle of these unicellular eukaryotes and of the developmentally programmed genome rearrangements that take place at each sexual cycle. We discuss how ancient domestication of a piggyBac transposase might have allowed Tc1/mariner elements to spread throughout the germline genome of Paramecium, without strong counterselection against insertion within genes. PMID:22888464

Transposon defense by endo-siRNAs, piRNAs and somatic pilRNAs in Drosophila: contributions of Loqs-PD and R2D2.

Directory of Open Access Journals (Sweden)

Milijana Mirkovic-Hösle

Full Text Available Transposable elements are a serious threat for genome integrity and their control via small RNA mediated silencing pathways is an ancient strategy. The fruit fly Drosophila melanogaster has two silencing activities that target transposons: endogenous siRNAs (esiRNAs or endo-siRNAs and Piwi-interacting small RNAs (piRNAs. The biogenesis of endo-siRNAs involves the Dicer-2 co-factors Loqs-PD, which acts predominantly during processing of dsRNA by Dcr-2, and R2D2, which primarily helps to direct siRNAs into the RNA interference effector Ago2. Nonetheless, loss of either protein is not sufficient to produce a phenotype comparable with a dcr-2 mutation. We provide further deep sequencing evidence supporting the notion that R2D2 and Loqs-PD have partially overlapping function. Certain transposons display a preference for either dsRBD-protein during production or loading; this appeared to correlate neither with overall abundance, classification of the transposon or a specific site of genomic origin. The endo-siRNA biogenesis pathway in germline operates according to the same principles as the existing model for the soma, and its impairment does not significantly affect piRNAs. Expanding the analysis, we confirmed the occurrence of somatic piRNA-like RNAs (pilRNAs that show a ping-pong signature. We detected expression of the Piwi-family protein mRNAs only barely above background, indicating that the somatic pilRNAs may arise from a small sub-population of somatic cells that express a functional piRNA pathway.

Tumor-directed gene therapy in mice using a composite nonviral gene delivery system consisting of the piggyBac transposon and polyethylenimine

International Nuclear Information System (INIS)

Kang, Yu; Zhang, Xiaoyan; Jiang, Wei; Wu, Chaoqun; Chen, Chunmei; Zheng, Yufang; Gu, Jianren; Xu, Congjian

2009-01-01

Compared with viral vectors, nonviral vectors are less immunogenic, more stable, safer and easier to replication for application in cancer gene therapy. However, nonviral gene delivery system has not been extensively used because of the low transfection efficiency and the short transgene expression, especially in vivo. It is desirable to develop a nonviral gene delivery system that can support stable genomic integration and persistent gene expression in vivo. Here, we used a composite nonviral gene delivery system consisting of the piggyBac (PB) transposon and polyethylenimine (PEI) for long-term transgene expression in mouse ovarian tumors. A recombinant plasmid PB [Act-RFP, HSV-tk] encoding both the herpes simplex thymidine kinase (HSV-tk) and the monomeric red fluorescent protein (mRFP1) under PB transposon elements was constructed. This plasmid and the PBase plasmid were injected into ovarian cancer tumor xenografts in mice by in vivo PEI system. The antitumor effects of HSV-tk/ganciclovir (GCV) system were observed after intraperitoneal injection of GCV. Histological analysis and TUNEL assay were performed on the cryostat sections of the tumor tissue. Plasmid construction was confirmed by PCR analysis combined with restrictive enzyme digestion. mRFP1 expression could be visualized three weeks after the last transfection of pPB/TK under fluorescence microscopy. After GCV admission, the tumor volume of PB/TK group was significantly reduced and the tumor inhibitory rate was 81.96% contrasted against the 43.07% in the TK group. Histological analysis showed that there were extensive necrosis and lymphocytes infiltration in the tumor tissue of the PB/TK group but limited in the tissue of control group. TUNEL assays suggested that the transfected cells were undergoing apoptosis after GCV admission in vivo. Our results show that the nonviral gene delivery system coupling PB transposon with PEI can be used as an efficient tool for gene therapy in ovarian cancer

A TALE of transposition: Tn3-like transposons play a major role in the spread of pathogenicity determinants of Xanthomonas citri and other xanthomonads.

Science.gov (United States)

Ferreira, Rafael Marini; de Oliveira, Amanda Carolina P; Moreira, Leandro M; Belasque, José; Gourbeyre, Edith; Siguier, Patricia; Ferro, Maria Inês T; Ferro, Jesus A; Chandler, Michael; Varani, Alessandro M

2015-02-17

Members of the genus Xanthomonas are among the most important phytopathogens. A key feature of Xanthomonas pathogenesis is the translocation of type III secretion system (T3SS) effector proteins (T3SEs) into the plant target cells via a T3SS. Several T3SEs and a murein lytic transglycosylase gene (mlt, required for citrus canker symptoms) are found associated with three transposition-related genes in Xanthomonas citri plasmid pXAC64. These are flanked by short inverted repeats (IRs). The region was identified as a transposon, TnXax1, with typical Tn3 family features, including a transposase and two recombination genes. Two 14-bp palindromic sequences within a 193-bp potential resolution site occur between the recombination genes. Additional derivatives carrying different T3SEs and other passenger genes occur in different Xanthomonas species. The T3SEs include transcription activator-like effectors (TALEs). Certain TALEs are flanked by the same IRs as found in TnXax1 to form mobile insertion cassettes (MICs), suggesting that they may be transmitted horizontally. A significant number of MICs carrying other passenger genes (including a number of TALE genes) were also identified, flanked by the same TnXax1 IRs and delimited by 5-bp target site duplications. We conclude that a large fraction of T3SEs, including individual TALEs and potential pathogenicity determinants, have spread by transposition and that TnXax1, which exhibits all of the essential characteristics of a functional transposon, may be involved in driving MIC transposition. We also propose that TALE genes may diversify by fork slippage during the replicative Tn3 family transposition. These mechanisms may play a crucial role in the emergence of Xanthomonas pathogenicity. Xanthomonas genomes carry many insertion sequences (IS) and transposons, which play an important role in their evolution and architecture. This study reveals a key relationship between transposons and pathogenicity determinants in

Horizontal transfers of Mariner transposons between mammals and insects

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Oliveira Sarah G

2012-09-01

Full Text Available Abstract Background Active transposable elements (TEs can be passed between genomes of different species by horizontal transfer (HT. This may help them to avoid vertical extinction due to elimination by natural selection or silencing. HT is relatively frequent within eukaryotic taxa, but rare between distant species. Findings Closely related Mariner-type DNA transposon families, collectively named as Mariner-1_Tbel families, are present in the genomes of two ants and two mammalian genomes. Consensus sequences of the four families show pairwise identities greater than 95%. In addition, mammalian Mariner1_BT family shows a close evolutionary relationship with some insect Mariner families. Mammalian Mariner1_BT type sequences are present only in species from three groups including ruminants, tooth whales (Odontoceti, and New World leaf-nosed bats (Phyllostomidae. Conclusions Horizontal transfer accounts for the presence of Mariner_Tbel and Mariner1_BT families in mammals. Mariner_Tbel family was introduced into hedgehog and tree shrew genomes approximately 100 to 69 million years ago (MYA. Most likely, these TE families were transferred from insects to mammals, but details of the transfer remain unknown.

Single-photon sources for quantum technologies - Results of the joint research project SIQUTE

DEFF Research Database (Denmark)

Kück, S.; López, M.; Rodiek, B.

2017-01-01

In this presentation, the results of the joint research project “Single-Photon Sources for Quantum Technologies” (SIQUTE) [1] will be presented. The focus will be on the development of absolutely characterized single-photon sources, on the realization of an efficient waveguide-based single-photon......-photon source at the telecom wavelengths of 1.3 µm and 1.55 µm, on the implementation of the quantum-enhanced resolution in confocal fluorescence microscopy and on the development of a detector for very low photon fluxes...

Moving through the stressed genome: Emerging regulatory roles for transposons in plant stress tolerance

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Negi Pooja

2016-10-01

Full Text Available The recognition of a positive correlation between organism genome size with its transposable element (TE content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock’s original ’Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences which project TEs as distributed genomic control modules. According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution and function, and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response.

Science.gov (United States)

Negi, Pooja; Rai, Archana N; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

Science.gov (United States)

Negi, Pooja; Rai, Archana N.; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement. PMID:27777577

Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH, an asparagine synthetase gene involved in its immune-activating capacity.

Science.gov (United States)

Ito, Masahiro; Kim, Yun-Gi; Tsuji, Hirokazu; Takahashi, Takuya; Kiwaki, Mayumi; Nomoto, Koji; Danbara, Hirofumi; Okada, Nobuhiko

2014-01-01

Lactobacillus casei ATCC 27139 enhances host innate immunity, and the J1 phage-resistant mutants of this strain lose the activity. A transposon insertion mutant library of L. casei ATCC 27139 was constructed, and nine J1 phage-resistant mutants out of them were obtained. Cloning and sequencing analyses identified three independent genes that were disrupted by insertion of the transposon element: asnH, encoding asparagine synthetase, and dnaJ and dnaK, encoding the molecular chaperones DnaJ and DnaK, respectively. Using an in vivo mouse model of Listeria infection, only asnH mutant showed deficiency in their ability to enhance host innate immunity, and complementation of the mutation by introduction of the wild-type asnH in the mutant strain recovered the immuno-augmenting activity. AsnH protein exhibited asparagine synthetase activity when the lysozyme-treated cell wall extracts of L. casei ATCC 27139 was added as substrate. The asnH mutants lost the thick and rigid peptidoglycan features that are characteristic to the wild-type cells, indicating that AsnH of L. casei is involved in peptidoglycan biosynthesis. These results indicate that asnH is required for the construction of the peptidoglycan composition involved in the immune-activating capacity of L. casei ATCC 27139.

Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH, an asparagine synthetase gene involved in its immune-activating capacity.

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Masahiro Ito

Full Text Available Lactobacillus casei ATCC 27139 enhances host innate immunity, and the J1 phage-resistant mutants of this strain lose the activity. A transposon insertion mutant library of L. casei ATCC 27139 was constructed, and nine J1 phage-resistant mutants out of them were obtained. Cloning and sequencing analyses identified three independent genes that were disrupted by insertion of the transposon element: asnH, encoding asparagine synthetase, and dnaJ and dnaK, encoding the molecular chaperones DnaJ and DnaK, respectively. Using an in vivo mouse model of Listeria infection, only asnH mutant showed deficiency in their ability to enhance host innate immunity, and complementation of the mutation by introduction of the wild-type asnH in the mutant strain recovered the immuno-augmenting activity. AsnH protein exhibited asparagine synthetase activity when the lysozyme-treated cell wall extracts of L. casei ATCC 27139 was added as substrate. The asnH mutants lost the thick and rigid peptidoglycan features that are characteristic to the wild-type cells, indicating that AsnH of L. casei is involved in peptidoglycan biosynthesis. These results indicate that asnH is required for the construction of the peptidoglycan composition involved in the immune-activating capacity of L. casei ATCC 27139.

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome.

Science.gov (United States)

Gonçalves, Juliana W; Valiati, Victor Hugo; Delprat, Alejandra; Valente, Vera L S; Ruiz, Alfredo

2014-09-13

Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral

The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing.

Science.gov (United States)

Basquin, Denis; Spierer, Anne; Begeot, Flora; Koryakov, Dmitry E; Todeschini, Anne-Laure; Ronsseray, Stéphane; Vieira, Cristina; Spierer, Pierre; Delattre, Marion

2014-01-01

Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3-7 protein in Drosophila ovaries. We present evidences that Su(var)3-7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3-7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3-7 is required for genome integrity. Females homozygous for Su(var)3-7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3-7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3-7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3-7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3-7 and piwi or aubergine controls important developmental processes independently of transposon silencing.

Heuristic algorithm for single resource constrained project scheduling problem based on the dynamic programming

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Stanimirović Ivan

2009-01-01

Full Text Available We introduce a heuristic method for the single resource constrained project scheduling problem, based on the dynamic programming solution of the knapsack problem. This method schedules projects with one type of resources, in the non-preemptive case: once started an activity is not interrupted and runs to completion. We compare the implementation of this method with well-known heuristic scheduling method, called Minimum Slack First (known also as Gray-Kidd algorithm, as well as with Microsoft Project.

Transposons and integrons in colistin-resistant clones of Klebsiella pneumoniae and Acinetobacter baumannii with epidemic or sporadic behaviour.

Science.gov (United States)

Arduino, Sonia M; Quiroga, María Paula; Ramírez, María Soledad; Merkier, Andrea Karina; Errecalde, Laura; Di Martino, Ana; Smayevsky, Jorgelina; Kaufman, Sara; Centrón, Daniela

2012-10-01

Multiple transposons, integrons and carbapenemases were found in Klebsiella pneumoniae colistin-resistant isolates as well as a genomic resistance island of the AbaR type in Acinetobacter baumannii colistin-resistant isolates from different hospitals from Buenos Aires City. PFGE analysis showed a polyclonal dissemination of antimicrobial resistance mechanisms among K. pneumoniae isolates, while in A. baumannii isolates the epidemic clone 1 from South America was found. Resistance determinants associated with horizontal gene transfer are contributing to the evolution to pandrug resistance in both epidemic and sporadic clones.

Fifth Single-Shell Tank Integrity Project Expert Panel Meeting August 28-29, 2014

Energy Technology Data Exchange (ETDEWEB)

Martin, Todd M. [Washington River Protection Solutions, LLC, Richland, WA (United States; Gunter, Jason R. [Washington River Protection Solutions, LLC, Richland, WA (United States); Boomer, Kayle D. [Washington River Protection Solutions, LLC, Richland, WA (United States)

2015-01-07

On August 28th and 29th, 2014 the Single-Shell Tank Integrity Project (SSTIP) Expert Panel (Panel) convened in Richland, Washington. This was the Panel’s first meeting since 2011 and, as a result, was focused primarily on updating the Panel on progress in response to the past recommendations (Single-Shell Tank Integrity Expert Panel Report, RPP-RPT-45921, Rev 0, May 2010). This letter documents the Panel’s discussions and feedback on Phase I activities and results.

Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA).

Science.gov (United States)

Warburton, Philip J; Allan, Elaine; Hunter, Stephanie; Ward, John; Booth, Veronica; Wade, William G; Mullany, Peter

2011-11-01

The human oral cavity is host to a complex microbial community estimated to comprise >700 bacterial species, of which at least half are thought to be not yet cultivable in vitro. To investigate the plasmids present in this community, we used a transposon-aided capture system, which allowed the isolation of plasmids from human oral supra- and subgingival plaque samples. Thirty-two novel plasmids and a circular molecule that could be an integrase-generated circular intermediate were isolated. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet.

Science.gov (United States)

Hirano, Ryoko; Naito, Ken; Fukunaga, Kenji; Watanabe, Kazuo N; Ohsawa, Ryo; Kawase, Makoto

2011-06-01

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles.

Science.gov (United States)

Muszewska, Anna; Steczkiewicz, Kamil; Stepniewska-Dziubinska, Marta; Ginalski, Krzysztof

2017-12-01

Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut-and-paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species' lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Spin-flip configuration interaction singles with exact spin-projection: Theory and applications to strongly correlated systems.

Science.gov (United States)

Tsuchimochi, Takashi

2015-10-14

Spin-flip approaches capture static correlation with the same computational scaling as the ordinary single reference methods. Here, we extend spin-flip configuration interaction singles (SFCIS) by projecting out intrinsic spin-contamination to make it spin-complete, rather than by explicitly complementing it with spin-coupled configurations. We give a general formalism of spin-projection for SFCIS, applicable to any spin states. The proposed method is viewed as a natural unification of SFCIS and spin-projected CIS to achieve a better qualitative accuracy at a low computational cost. While our wave function ansatz is more compact than previously proposed spin-complete SF approaches, it successfully offers more general static correlation beyond biradicals without sacrificing good quantum numbers. It is also shown that our method is invariant with respect to open-shell orbital rotations, due to the uniqueness of spin-projection. We will report benchmark calculations to demonstrate its qualitative performance on strongly correlated systems, including conical intersections that appear both in ground-excited and excited-excited degeneracies.

The Drosophila Su(var)3–7 Gene Is Required for Oogenesis and Female Fertility, Genetically Interacts with piwi and aubergine, but Impacts Only Weakly Transposon Silencing

Science.gov (United States)

Begeot, Flora; Koryakov, Dmitry E.; Todeschini, Anne-Laure; Ronsseray, Stéphane; Vieira, Cristina; Spierer, Pierre; Delattre, Marion

2014-01-01

Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3–7 protein in Drosophila ovaries. We present evidences that Su(var)3–7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3–7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3–7 is required for genome integrity. Females homozygous for Su(var)3–7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3–7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3–7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3–7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3–7 and piwi or aubergine controls important developmental processes independently of transposon silencing. PMID:24820312

The Foldback-like element Galileo belongs to the P superfamily of DNA transposons and is widespread within the Drosophila genus.

Science.gov (United States)

Marzo, Mar; Puig, Marta; Ruiz, Alfredo

2008-02-26

Galileo is the only transposable element (TE) known to have generated natural chromosomal inversions in the genus Drosophila. It was discovered in Drosophila buzzatii and classified as a Foldback-like element because of its long, internally repetitive, terminal inverted repeats (TIRs) and lack of coding capacity. Here, we characterized a seemingly complete copy of Galileo from the D. buzzatii genome. It is 5,406 bp long, possesses 1,229-bp TIRs, and encodes a 912-aa transposase similar to those of the Drosophila melanogaster 1360 (Hoppel) and P elements. We also searched the recently available genome sequences of 12 Drosophila species for elements similar to Dbuz\\Galileo by using bioinformatic tools. Galileo was found in six species (ananassae, willistoni, peudoobscura, persimilis, virilis, and mojavensis) from the two main lineages within the Drosophila genus. Our observations place Galileo within the P superfamily of cut-and-paste transposons and extend considerably its phylogenetic distribution. The interspecific distribution of Galileo indicates an ancient presence in the genus, but the phylogenetic tree built with the transposase amino acid sequences contrasts significantly with that of the species, indicating lineage sorting and/or horizontal transfer events. Our results also suggest that Foldback-like elements such as Galileo may evolve from DNA-based transposon ancestors by loss of the transposase gene and disproportionate elongation of TIRs.

WE-G-BRF-04: Robust Real-Time Volumetric Imaging Based On One Single Projection

International Nuclear Information System (INIS)

Xu, Y; Yan, H; Ouyang, L; Wang, J; Jiang, S; Jia, X; Zhou, L

2014-01-01

Purpose: Real-time volumetric imaging is highly desirable to provide instantaneous image guidance for lung radiation therapy. This study proposes a scheme to achieve this goal using one single projection by utilizing sparse learning and a principal component analysis (PCA) based lung motion model. Methods: A patient-specific PCA-based lung motion model is first constructed by analyzing deformable vector fields (DVFs) between a reference image and 4DCT images at each phase. At the training stage, we “learn” the relationship between the DVFs and the projection using sparse learning. Specifically, we first partition the projections into patches, and then apply sparse learning to automatically identify patches that best correlate with the principal components of the DVFs. Once the relationship is established, at the application stage, we first employ a patchbased intensity correction method to overcome the problem of different intensity scale between the calculated projection in the training stage and the measured projection in the application stage. The corrected projection image is then fed to the trained model to derive a DVF, which is applied to the reference image, yielding a volumetric image corresponding to the projection. We have validated our method through a NCAT phantom simulation case and one experiment case. Results: Sparse learning can automatically select those patches containing motion information, such as those around diaphragm. For the simulation case, over 98% of the lung region pass the generalized gamma test (10HU/1mm), indicating combined accuracy in both intensity and spatial domain. For the experimental case, the average tumor localization errors projected to the imager are 0.68 mm and 0.4 mm on the axial and tangential direction, respectively. Conclusion: The proposed method is capable of accurately generating a volumetric image using one single projection. It will potentially offer real-time volumetric image guidance to facilitate lung

WE-G-BRF-04: Robust Real-Time Volumetric Imaging Based On One Single Projection

Energy Technology Data Exchange (ETDEWEB)

Xu, Y [UT Southwestern Medical Center, Dallas, TX (United States); Southern Medical University, Guangzhou (China); Yan, H; Ouyang, L; Wang, J; Jiang, S; Jia, X [UT Southwestern Medical Center, Dallas, TX (United States); Zhou, L [Southern Medical University, Guangzhou (China)

2014-06-15

Purpose: Real-time volumetric imaging is highly desirable to provide instantaneous image guidance for lung radiation therapy. This study proposes a scheme to achieve this goal using one single projection by utilizing sparse learning and a principal component analysis (PCA) based lung motion model. Methods: A patient-specific PCA-based lung motion model is first constructed by analyzing deformable vector fields (DVFs) between a reference image and 4DCT images at each phase. At the training stage, we “learn” the relationship between the DVFs and the projection using sparse learning. Specifically, we first partition the projections into patches, and then apply sparse learning to automatically identify patches that best correlate with the principal components of the DVFs. Once the relationship is established, at the application stage, we first employ a patchbased intensity correction method to overcome the problem of different intensity scale between the calculated projection in the training stage and the measured projection in the application stage. The corrected projection image is then fed to the trained model to derive a DVF, which is applied to the reference image, yielding a volumetric image corresponding to the projection. We have validated our method through a NCAT phantom simulation case and one experiment case. Results: Sparse learning can automatically select those patches containing motion information, such as those around diaphragm. For the simulation case, over 98% of the lung region pass the generalized gamma test (10HU/1mm), indicating combined accuracy in both intensity and spatial domain. For the experimental case, the average tumor localization errors projected to the imager are 0.68 mm and 0.4 mm on the axial and tangential direction, respectively. Conclusion: The proposed method is capable of accurately generating a volumetric image using one single projection. It will potentially offer real-time volumetric image guidance to facilitate lung

Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides

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Bogumil Jacek Karas

2014-07-01

Full Text Available With only hundreds of genes contained within their genomes, mycoplasmas have become model organisms for precise understanding of cellular processes, as well as platform organisms for predictable engineering of microbial functions for mission-critical applications. Despite the availability of whole genome writing in Mycoplasma mycoides, some traditional methods for genetic engineering are underdeveloped in mycoplasmas. Here we demonstrate two facile transposon-mediated approaches for introducing genes into the synthetic cell based on M. mycoides. The marker-less approach involves preparing a fragment containing only a small genomic region of interest with flanking transposase-binding sites, followed by in vitro transposase loading and introduction into the cells. The marker-driven approach involves cloning an open reading frame (ORF of interest into a vector containing a marker for mycoplasma transformation, as well as sites for transposase loading and random genomic integration. An innovative feature of this construct is to use a single promoter to express the transformation marker and the introduced ORF. The marker-driven approach can be conveniently applied to any exogenous or synthetic gene without any information on the effect of the gene on the strain, whereas the marker-less approach requires that the fragment has a recognizable effect. Using the marker-less method, we found that a region containing the nusG gene rescues a slow growth phenotype of a strain containing a larger deletion encompassing this gene. Using the marker-driven approach, we better defined this finding, thereby establishing that nusG is required for a normal growth rate in synthetic M. mycoides. These methods are suitable for complementation tests to identify genes responsible for assorted functions lacking in deletion mutants. These approaches are also expected to facilitate rapid testing of various natural and engineered genes or gene clusters from numerous sources in

Mobile clusters of single board computers: an option for providing resources to student projects and researchers.

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Baun, Christian

2016-01-01

Clusters usually consist of servers, workstations or personal computers as nodes. But especially for academic purposes like student projects or scientific projects, the cost for purchase and operation can be a challenge. Single board computers cannot compete with the performance or energy-efficiency of higher-value systems, but they are an option to build inexpensive cluster systems. Because of the compact design and modest energy consumption, it is possible to build clusters of single board computers in a way that they are mobile and can be easily transported by the users. This paper describes the construction of such a cluster, useful applications and the performance of the single nodes. Furthermore, the clusters' performance and energy-efficiency is analyzed by executing the High Performance Linpack benchmark with a different number of nodes and different proportion of the systems total main memory utilized.

Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- and Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals

DEFF Research Database (Denmark)

de Vries, Lisbeth Elvira; Christensen, H.; Skov, R. L.

2009-01-01

To analyse the sequence diversity of the tetracycline resistance gene tet(M) in Staphylococcus aureus from humans and animals and to determine mobile elements associated with tet(M) in S. aureus. In total, 205 tetracycline-resistant isolates were screened for tet(M) by PCR. tet(M) genes were...... sequenced and compared with tet(M) deposited in GenBank. Based on phylogenetic analysis isolates were screened for Tn916- and Tn5801-like xis/int genes, and transposons were confirmed by linking PCR. spa typing was performed and selected isolates were used as donors in a filter mating experiment. Forty......-one isolates (21.3%, 60.7%, 2.6% and 4.4% of the human, pig, poultry and cattle isolates, respectively) were tet(M) positive. tet(M) was located on Tn5801-like and Tn916-like transposons in humans and on a specific Tn916-like element in animals. Human isolates were of different spa types (t034, t008, t037, t...

Tracking single dynamic MEG dipole sources using the projected Extended Kalman Filter.

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Yao, Yuchen; Swindlehurst, A Lee

2011-01-01

This paper presents two new algorithms based on the Extended Kalman Filter (EKF) for tracking the parameters of single dynamic magnetoencephalography (MEG) dipole sources. We assume a dynamic MEG dipole source with possibly both time-varying location and dipole orientation. The standard EKF-based tracking algorithm performs well under the assumption that the dipole source components vary in time as a Gauss-Markov process, provided that the background noise is temporally stationary. We propose a Projected-EKF algorithm that is adapted to a more forgiving condition where the background noise is temporally nonstationary, as well as a Projected-GLS-EKF algorithm that works even more universally, when the dipole components vary arbitrarily from one sample to the next.

Radiation and transposon-induced genetic damage in Drosophila melanogaster

International Nuclear Information System (INIS)

Balter, H.; Griffith, C.S.; American Museum of Natural History, New York; Margulies, L.

1992-01-01

The interaction of X-ray-induced and transposon-induced damage was investigated in P-M hybrid dysgenesis in Drosophila melanogaster. X-ray dose-response of 330-1320 rad was monitored for sterility, fecundicity and partial X/Y chromosome loss among F 2 progeny derived from dysgenic cross of M strain females xP strain males (cross A) and its reciprocal (cross B), using a weaker and the standard Harwich P strain subline. The synergistic effect of P element activity and X-rays on sterility was observed only in cross A hybrids and the dose-response was nonlinear in hybrids derived from the strong standard reference Harwich subline, H W . This finding suggests that lesions induced by both mutator systems which produce the synergistic effects are 2-break events. Effect of increasing dose on the decline of fecundicity was synergistic, but linear, in hybrids of either subline. There was no interaction evident and thus no synergism in X/Y nondisjunction and partial Y chromosome loss measured by the loss of the B s marker alone or together with the y + marker. Interaction was detected in the loss of the y + marker alone from the X and Y chromosomes. The possible three-way interaction of X-rays (660 rad), post-replication repair deficiency and P elements mobility was assessed by measuring transmission distortion in dysgenic males derived from the Π 2 P strain. (author). 38 refs.; 5 tabs

Results of single borehole hydraulic tests in the Mizunami Underground Research Laboratory project. FY 2012 - FY 2015

International Nuclear Information System (INIS)

Onoe, Hironori; Takeuchi, Ryuji

2016-11-01

This report summarize the results of the single borehole hydraulic tests of 151 sections carried out at the -300 m Stage and the -500 m Stage of the Mizunami Underground Research Laboratory from FY 2012 to FY 2015. The details of each test (test interval depth, geology, etc.) as well as the interpreted hydraulic parameters and analytical methods used are presented in this report. Furthermore, the previous results of the single borehole hydraulic tests carried out in the Regional Hydrogeological Study Project and the Mizunami Underground Research Laboratory Project before FY 2012 are also summarized in this report. (author)

Identification of Genes Involved in Biofilm Formation and Respiration via Mini-Himar Transposon Mutagenesis of Geobacter sulfurreducens▿ †

Science.gov (United States)

Rollefson, Janet B.; Levar, Caleb E.; Bond, Daniel R.

2009-01-01

Electron transfer from cells to metals and electrodes by the Fe(III)-reducing anaerobe Geobacter sulfurreducens requires proper expression of redox proteins and attachment mechanisms to interface bacteria with surfaces and neighboring cells. We hypothesized that transposon mutagenesis would complement targeted knockout studies in Geobacter spp. and identify novel genes involved in this process. Escherichia coli mating strains and plasmids were used to develop a conjugation protocol and deliver mini-Himar transposons, creating a library of over 8,000 mutants that was anaerobically arrayed and screened for a range of phenotypes, including auxotrophy for amino acids, inability to reduce Fe(III) citrate, and attachment to surfaces. Following protocol validation, mutants with strong phenotypes were further characterized in a three-electrode system to simultaneously quantify attachment, biofilm development, and respiratory parameters, revealing mutants defective in Fe(III) reduction but unaffected in electron transfer to electrodes (such as an insertion in GSU1330, a putative metal export protein) or defective in electrode reduction but demonstrating wild-type biofilm formation (due to an insertion upstream of the NHL domain protein GSU2505). An insertion in a putative ATP-dependent transporter (GSU1501) eliminated electrode colonization but not Fe(III) citrate reduction. A more complex phenotype was demonstrated by a mutant containing an insertion in a transglutaminase domain protein (GSU3361), which suddenly ceased to respire when biofilms reached approximately 50% of the wild-type levels. As most insertions were not in cytochromes but rather in transporters, two-component signaling proteins, and proteins of unknown function, this collection illustrates how biofilm formation and electron transfer are separate but complementary phenotypes, controlled by multiple loci not commonly studied in Geobacter spp. PMID:19395486

Generation of mariner-based transposon insertion mutant library of Bacillus sphaericus 2297 and investigation of genes involved in sporulation and mosquito-larvicidal crystal protein synthesis.

Science.gov (United States)

Wu, Yiming; Hu, Xiaomin; Ge, Yong; Zheng, Dasheng; Yuan, Zhiming

2012-05-01

Bacillus sphaericus has been used with great success in mosquito control programs worldwide. Under conditions of nutrient limitation, it undergoes sporulation via a series of well defined morphological stages. However, only a small number of genes involved in sporulation have been identified. To identify genes associated with sporulation, and to understand the relationship between sporulation and crystal protein synthesis, a random mariner-based transposon insertion mutant library of B. sphaericus strain 2297 was constructed and seven sporulation-defective mutants were selected. Sequencing of the DNA flanking of the transposon insertion identified several genes involved in sporulation. The morphologies of mutants were determined by electron microscopy and synthesis of crystal proteins was analyzed by SDS-PAGE and Western blot. Four mutants blocked at early stages of sporulation failed to produce crystal proteins and had lower larvicidal activity. However, the other three mutants were blocked at later stages and were able to form crystal proteins, and the larvicidal activity was similar to wild type. These results indicated that crystal protein synthesis in B. sphaericus is dependent on sporulation initiation. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice.

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Misuzu Nosaka

2012-09-01

Full Text Available RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE, which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs and are processed into small RNAs (small interfering RNAs, siRNAs that suppress TEs by RNA-directed DNA methylation. Thus, the majority of TEs are epigenetically silenced. On the other hand, most of the eukaryotic genome is composed of TEs and their remnants, suggesting that TEs have evolved countermeasures against host-mediated silencing. Under some circumstances, TEs can become active and increase in copy number. Knowledge is accumulating on the mechanisms of TE silencing by the host; however, the mechanisms by which TEs counteract silencing are poorly understood. Here, we show that a class of TEs in rice produces a microRNA (miRNA to suppress host silencing. Members of the microRNA820 (miR820 gene family are located within CACTA DNA transposons in rice and target a de novo DNA methyltransferase gene, OsDRM2, one of the components of epigenetic silencing. We confirmed that miR820 negatively regulates the expression of OsDRM2. In addition, we found that expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci. Furthermore, we found that the nucleotide sequence of miR820 and its recognition site within the target gene in some Oryza species have co-evolved to maintain their base-pairing ability. The co-evolution of these sequences provides evidence for the functionality of this regulation. Our results demonstrate how parasitic elements in the genome escape the host's defense machinery. Furthermore, our analysis of the regulation of OsDRM2 by miR820 sheds light on the action of transposon-derived small RNAs, not only as a defense mechanism for host genomes but also as a regulator of interactions between hosts and their parasitic elements.

Stable gene transfer of CCR5 and CXCR4 siRNAs by sleeping beauty transposon system to confer HIV-1 resistance

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Akkina Ramesh

2008-07-01

Full Text Available Abstract Background Thus far gene therapy strategies for HIV/AIDS have used either conventional retroviral vectors or lentiviral vectors for gene transfer. Although highly efficient, their use poses a certain degree of risk in terms of viral mediated oncogenesis. Sleeping Beauty (SB transposon system offers a non-viral method of gene transfer to avoid this possible risk. With respect to conferring HIV resistance, stable knock down of HIV-1 coreceptors CCR5 and CXCR4 by the use of lentiviral vector delivered siRNAs has proved to be a promising strategy to protect cells from HIV-1 infection. In the current studies our aim is to evaluate the utility of SB system for stable gene transfer of CCR5 and CXCR4 siRNA genes to derive HIV resistant cells as a first step towards using this system for gene therapy. Results Two well characterized siRNAs against the HIV-1 coreceptors CCR5 and CXCR4 were chosen based on their previous efficacy for the SB transposon gene delivery. The siRNA transgenes were incorporated individually into a modified SB transfer plasmid containing a FACS sortable red fluorescence protein (RFP reporter and a drug selectable neomycin resistance gene. Gene transfer was achieved by co-delivery with a construct expressing a hyperactive transposase (HSB5 into the GHOST-R3/X4/R5 cell line, which expresses the major HIV receptor CD4 and and the co-receptors CCR5 and CXCR4. SB constructs expressing CCR5 or CXCR4 siRNAs were also transfected into MAGI-CCR5 or MAGI-CXCR4 cell lines, respectively. Near complete downregulation of CCR5 and CXCR4 surface expression was observed in transfected cells. During viral challenge with X4-tropic (NL4.3 or R5-tropic (BaL HIV-1 strains, the respective transposed cells showed marked viral resistance. Conclusion SB transposon system can be used to deliver siRNA genes for stable gene transfer. The siRNA genes against HIV-1 coreceptors CCR5 and CXCR4 are able to downregulate the respective cell surface proteins

Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation.

Science.gov (United States)

Rep, Martijn; van der Does, H Charlotte; Cornelissen, Ben J C

2005-06-01

The facultative pathogenic fungus Fusarium oxysporum is known to harbour many different transposable and/or repetitive elements. We have identified Drifter, a novel DNA transposon of the hAT family in F. oxysporum. It was found adjoining SIX1-H, a truncated homolog of the SIX1 avirulence gene in F. oxysporum f. sp. lycopersici. Absence of a target site duplication as well as the 5' part of SIX1-H suggests that transposition of Drifter into the ancestor of SIX1-H was followed by loss of a chromosomal segment through recombination between Drifters. F. oxysporum isolates belonging to various formae speciales harbour between 0 and 5 full-length copies of Drifter and/or one or more copies with an internal deletion. Transcription of Drifter is activated during starvation for carbon or nitrogen.

Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis

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Abdjad Asih Nawangsih

2011-04-01

Full Text Available Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis. X. oryzae pv. oryzae (Xoo causes bacterial leaf blight (BLB of rice (Oryza sativa L., a major disease that constrains production of the staple crop in many countries of the world. Identification of X. oryzae pv. oryzae (Xoo was conducted based on the disease symptoms, pathogenicity, morphological, physiological, and genetic characteristics of bacterial cultures isolated from the infected plants. Fifty bacterial isolates predicted as Xoo have been successfully isolated. They are aerobic, rod shaped, and Gram negative bacteria. The isolates were evaluated for their hypersensitivity in tobacco and pathogenicity in rice plant. Fifty isolates induced hypersensitive reaction in tobacco and showed pathogenicity symptom in rice in different length. Based on physiological test, hypersensitivity and pathogenicity reactions, three bacterial isolates strongly predicted as Xoo, i.e. STG21, STG42, and STG46, were non indole formation, non pigment fluorescent, hydrolyzed casein, catalase activity positive, but negative oxidase. Partial sequencing of 16S rRNA genes of STG21 and STG42 showed 80% and 82% homology with X. oryzae, respectively, while STG46 showed 84% homology with X. campestris. Mini-Tn5 transposon mutagenesis of STG21 generated one of the mutants (M5 lossed it’s ability to induce hypersensitive reaction in tobacco plant and deficient in pathogenicity on rice. The lesion length of rice leaf caused by the mutant M5 decreased up to 80%.

ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth

DEFF Research Database (Denmark)

Markljung, Ellen; Jiang, Lin; Jaffe, Jacob D

2009-01-01

and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (Ch......, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6...... is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth....

The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis.

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Silje V Veiseth

2011-03-01

Full Text Available Chromatin structure and gene expression are regulated by posttranslational modifications (PTMs on the N-terminal tails of histones. Mono-, di-, or trimethylation of lysine residues by histone lysine methyltransferases (HKMTases can have activating or repressive functions depending on the position and context of the modified lysine. In Arabidopsis, trimethylation of lysine 9 on histone H3 (H3K9me3 is mainly associated with euchromatin and transcribed genes, although low levels of this mark are also detected at transposons and repeat sequences. Besides the evolutionarily conserved SET domain which is responsible for enzyme activity, most HKMTases also contain additional domains which enable them to respond to other PTMs or cellular signals. Here we show that the N-terminal WIYLD domain of the Arabidopsis SUVR4 HKMTase binds ubiquitin and that the SUVR4 product specificity shifts from di- to trimethylation in the presence of free ubiquitin, enabling conversion of H3K9me1 to H3K9me3 in vitro. Chromatin immunoprecipitation and immunocytological analysis showed that SUVR4 in vivo specifically converts H3K9me1 to H3K9me3 at transposons and pseudogenes and has a locus-specific repressive effect on the expression of such elements. Bisulfite sequencing indicates that this repression involves both DNA methylation-dependent and -independent mechanisms. Transcribed genes with high endogenous levels of H3K4me3, H3K9me3, and H2Bub1, but low H3K9me1, are generally unaffected by SUVR4 activity. Our results imply that SUVR4 is involved in the epigenetic defense mechanism by trimethylating H3K9 to suppress potentially harmful transposon activity.

A quality improvement project to reduce the intraoperative use of single-dose fentanyl vials across multiple patients in a pediatric institution.

Science.gov (United States)

Buck, David; Subramanyam, Rajeev; Varughese, Anna

2016-01-01

The use of a single-dose vial across multiple patients presents a risk to sterility and is against CDC guidelines. We initiated a quality improvement (QI) project to reduce the intraoperative use of single-dose vials of fentanyl across multiple patients at Cincinnati Children's Hospital Medical Center (CCHMC). The initial step of the improvement project was the development of a Key Driver Diagram. The diagram has the SMART aim of the project, key drivers inherent to the process we are trying to improve, and specific interventions targeting the key drivers. The number of patients each week receiving an IV dose of fentanyl, from a vial previously accessed for another patient was tracked in a high turnover operating room (OR). The improvement model used was based on the concept of building Plan-Do-Study-Act (PDSA) cycles. Tests of change included provider education, provision of an increased number of fentanyl vials, alternate wasting processes, and provision of single-use fentanyl syringes by the pharmacy. Prior to initiation of this project, it was common for a single fentanyl vial to be accessed for multiple patients. Our data showed an average percentage of failures of just over 50%. During the end of the project, after 7 months, the mean percentage failures had dropped to 5%. Preparation of 20 mcg single-use fentanyl syringes by pharmacy, combined with education of providers on appropriate use, was successful in reducing failures to below our goal of 25%. Appropriately sized fentanyl syringes prepared by pharmacy, education on correct use of single-dose vials, and reminders in the OR, reduced the percentage of patients receiving a dose of fentanyl from a vial previously accessed for another patient in a high-volume otolaryngology room. © 2015 John Wiley & Sons Ltd.

Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample.

Science.gov (United States)

Leclercq, Sébastien Olivier; Wang, Chao; Zhu, Yaxin; Wu, Hai; Du, Xiaochen; Liu, Zhipei; Feng, Jie

2016-11-01

Tetracycline antibiotics are widely used in livestock, and tetracycline resistance genes (TRG) are frequently reported in the manure of farmed animals. However, the diversity of TRG-carrying transposons in manure has still been rarely investigated. Using a culture-free functional metagenomic procedure, combined with large-insert library construction and sequencing, bioinformatic analyses, and functional experiments, we identified 17 distinct TRGs in a single pig manure sample, including two new tet genes: tet(59), encoding a tetracycline efflux pump, and tet(W/N/W), encoding mosaic ribosomal protection. Our study also revealed six new TRG-carrying putative nonconjugative transposons: Tn5706-like transposon Tn6298, IS200/605-related transposon Tn6303, Tn3 family transposon Tn6299, and three ISCR2-related transposons, Tn62300, Tn62301, and Tn62302 IMPORTANCE: Fertilization of agricultural fields with animal manure is believed to play a major role in antibiotic resistance dissemination in the environment. There is growing concern for the possible spread of antibiotic resistance from the environment to humans since genetic resistance determinants may be located in transposons and other mobile genetic elements potentially transferable to pathogens. Among the various antibiotic resistance genes found in manure, tetracycline resistance genes (TRGs) are some of the most common. The present study provides a detailed snapshot of the tetracycline mobilome in a single pig manure sample, revealing an unappreciated diversity of TRGs and potential TRG mobility vectors. Our precise identification of the TRG-carrying units will enable us to investigate in more details their mobility effectiveness. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing.

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Shota Teramoto

2014-06-01

Full Text Available Miniature inverted-repeat transposable elements (MITEs are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu, mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP, and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP. Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution.

Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion.

Science.gov (United States)

Younger, Andrew K D; Su, Peter Y; Shepard, Andrea J; Udani, Shreya V; Cybulski, Thaddeus R; Tyo, Keith E J; Leonard, Joshua N

2018-02-01

Naturally evolved metabolite-responsive biosensors enable applications in metabolic engineering, ranging from screening large genetic libraries to dynamically regulating biosynthetic pathways. However, there are many metabolites for which a natural biosensor does not exist. To address this need, we developed a general method for converting metabolite-binding proteins into metabolite-responsive transcription factors-Biosensor Engineering by Random Domain Insertion (BERDI). This approach takes advantage of an in vitro transposon insertion reaction to generate all possible insertions of a DNA-binding domain into a metabolite-binding protein, followed by fluorescence activated cell sorting to isolate functional biosensors. To develop and evaluate the BERDI method, we generated a library of candidate biosensors in which a zinc finger DNA-binding domain was inserted into maltose binding protein, which served as a model well-studied metabolite-binding protein. Library diversity was characterized by several methods, a selection scheme was deployed, and ultimately several distinct and functional maltose-responsive transcriptional biosensors were identified. We hypothesize that the BERDI method comprises a generalizable strategy that may ultimately be applied to convert a wide range of metabolite-binding proteins into novel biosensors for applications in metabolic engineering and synthetic biology. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Synthetic Biology Project - Developing a single-molecule device for screening drug-target interactions.

Science.gov (United States)

Firman, Keith; Evans, Luke; Youell, James

2012-07-16

This review describes a European-funded project in the area of Synthetic Biology. The project seeks to demonstrate the application of engineering techniques and methodologies to the design and construction of a biosensor for detecting drug-target interactions at the single-molecule level. Production of the proteins required for the system followed the principle of previously described "bioparts" concepts (a system where a database of biological parts - promoters, genes, terminators, linking tags and cleavage sequences - is used to construct novel gene assemblies) and cassette-type assembly of gene expression systems (the concept of linking different "bioparts" to produce functional "cassettes"), but problems were quickly identified with these approaches. DNA substrates for the device were also constructed using a cassette-system. Finally, micro-engineering was used to build a magnetoresistive Magnetic Tweezer device for detection of single molecule DNA modifying enzymes (motors), while the possibility of constructing a Hall Effect version of this device was explored. The device is currently being used to study helicases from Plasmodium as potential targets for anti-malarial drugs, but we also suggest other potential uses for the device. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery.

Science.gov (United States)

Kiljunen, Saija; Pajunen, Maria I; Dilks, Kieran; Storf, Stefanie; Pohlschroder, Mechthild; Savilahti, Harri

2014-12-09

Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea.

Finite state projection based bounds to compare chemical master equation models using single-cell data

Energy Technology Data Exchange (ETDEWEB)

Fox, Zachary [School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523 (United States); Neuert, Gregor [Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 (United States); Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232 (United States); Department of Biomedical Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee 37232 (United States); Munsky, Brian [School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523 (United States); Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523 (United States)

2016-08-21

Emerging techniques now allow for precise quantification of distributions of biological molecules in single cells. These rapidly advancing experimental methods have created a need for more rigorous and efficient modeling tools. Here, we derive new bounds on the likelihood that observations of single-cell, single-molecule responses come from a discrete stochastic model, posed in the form of the chemical master equation. These strict upper and lower bounds are based on a finite state projection approach, and they converge monotonically to the exact likelihood value. These bounds allow one to discriminate rigorously between models and with a minimum level of computational effort. In practice, these bounds can be incorporated into stochastic model identification and parameter inference routines, which improve the accuracy and efficiency of endeavors to analyze and predict single-cell behavior. We demonstrate the applicability of our approach using simulated data for three example models as well as for experimental measurements of a time-varying stochastic transcriptional response in yeast.

Results of single borehole hydraulic testing in the Mizunami Underground Research Laboratory project. Phase 2

International Nuclear Information System (INIS)

Daimaru, Shuji; Takeuchi, Ryuji; Onoe, Hironori; Saegusa, Hiromitsu

2012-09-01

This report summarize the results of the single borehole hydraulic tests of 79 sections conducted as part of the Construction phase (Phase 2) in the Mizunami Underground Research Laboratory (MIU) Project. The details of each test (test interval depth, geology, etc.) as well as the interpreted hydraulic parameters and analytical method used are presented in this report. (author)

Spherical Projection Based Straight Line Segment Extraction for Single Station Terrestrial Laser Point Cloud

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ZHANG Fan

2015-06-01

Full Text Available Due to the discrete distribution computing errors and lack of adaptability are ubiquitous in the current straight line extraction for TLS data methods. A 3D straight line segment extraction method is proposed based on spherical projection for single station terrestrial laser point clouds. Firstly, horizontal and vertical angles of each laser point are calculated by means of spherical coordinates, intensity panoramic image according to the two angles is generated. Secondly, edges which include straight line features are detected from intensity panoramic image by using of edge detection algorithm. Thirdly, great circles are detected from edges of panoramic image using spherical Hough transform. According to the axiom that a straight line segment in 3D space is a spherical great circle after spherical projection, detecting great circles from spherical projected data sets is essentially detecting straight line segments from 3D data sets without spherical projection. Finally, a robust 3D straight line fitting method is employed to fitting the straight lines and calculating parameters of the straight line segments. Experiments using different data sets and comparison with other methods show the accuracy and applicability of the proposed method.

[Restoration filtering based on projection power spectrum for single-photon emission computed tomography].

Science.gov (United States)

Kubo, N

1995-04-01

To improve the quality of single-photon emission computed tomographic (SPECT) images, a restoration filter has been developed. This filter was designed according to practical "least squares filter" theory. It is necessary to know the object power spectrum and the noise power spectrum. The power spectrum is estimated from the power spectrum of a projection, when the high-frequency power spectrum of a projection is adequately approximated as a polynomial exponential expression. A study of the restoration with the filter based on a projection power spectrum was conducted, and compared with that of the "Butterworth" filtering method (cut-off frequency of 0.15 cycles/pixel), and "Wiener" filtering (signal-to-noise power spectrum ratio was a constant). Normalized mean-squared errors (NMSE) of the phantom, two line sources located in a 99mTc filled cylinder, were used. NMSE of the "Butterworth" filter, "Wiener" filter, and filtering based on a power spectrum were 0.77, 0.83, and 0.76 respectively. Clinically, brain SPECT images utilizing this new restoration filter improved the contrast. Thus, this filter may be useful in diagnosis of SPECT images.

Restoration filtering based on projection power spectrum for single-photon emission computed tomography

International Nuclear Information System (INIS)

Kubo, Naoki

1995-01-01

To improve the quality of single-photon emission computed tomographic (SPECT) images, a restoration filter has been developed. This filter was designed according to practical 'least squares filter' theory. It is necessary to know the object power spectrum and the noise power spectrum. The power spectrum is estimated from the power spectrum of a projection, when the high-frequency power spectrum of a projection is adequately approximated as a polynomial exponential expression. A study of the restoration with the filter based on a projection power spectrum was conducted, and compared with that of the 'Butterworth' filtering method (cut-off frequency of 0.15 cycles/pixel), and 'Wiener' filtering (signal-to-noise power spectrum ratio was a constant). Normalized mean-squared errors (NMSE) of the phantom, two line sources located in a 99m Tc filled cylinder, were used. NMSE of the 'Butterworth' filter, 'Wiener' filter, and filtering based on a power spectrum were 0.77, 0.83, and 0.76 respectively. Clinically, brain SPECT images utilizing this new restoration filter improved the contrast. Thus, this filter may be useful in diagnosis of SPECT images. (author)

Individual mediodorsal thalamic neurons project to multiple areas of the rat prefrontal cortex: A single neuron-tracing study using virus vectors.

Science.gov (United States)

Kuramoto, Eriko; Pan, Shixiu; Furuta, Takahiro; Tanaka, Yasuhiro R; Iwai, Haruki; Yamanaka, Atsushi; Ohno, Sachi; Kaneko, Takeshi; Goto, Tetsuya; Hioki, Hiroyuki

2017-01-01

The prefrontal cortex has an important role in a variety of cognitive and executive processes, and is generally defined by its reciprocal connections with the mediodorsal thalamic nucleus (MD). The rat MD is mainly subdivided into three segments, the medial (MDm), central (MDc), and lateral (MDl) divisions, on the basis of the cytoarchitecture and chemoarchitecture. The MD segments are known to topographically project to multiple prefrontal areas at the population level: the MDm mainly to the prelimbic, infralimbic, and agranular insular areas; the MDc to the orbital and agranular insular areas; and the MDl to the prelimbic and anterior cingulate areas. However, it is unknown whether individual MD neurons project to single or multiple prefrontal cortical areas. In the present study, we visualized individual MD neurons with Sindbis virus vectors, and reconstructed whole structures of MD neurons. While the main cortical projection targets of MDm, MDc, and MDl neurons were generally consistent with those of previous results, it was found that individual MD neurons sent their axon fibers to multiple prefrontal areas, and displayed various projection patterns in the target areas. Furthermore, the axons of single MD neurons were not homogeneously spread, but were rather distributed to form patchy axon arbors approximately 1 mm in diameter. The multiple-area projections and patchy axon arbors of single MD neurons might be able to coactivate cortical neuron groups in distant prefrontal areas simultaneously. Furthermore, considerable heterogeneity of the projection patterns is likely, to recruit the different sets of cortical neurons, and thus contributes to a variety of prefrontal functions. J. Comp. Neurol. 525:166-185, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection

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Guanhua Yang

2017-10-01

Full Text Available Transposon insertion sequencing (TIS is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection. Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE. From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen collected over a 2-week infection period from a natural host (the flatfish turbot. PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses.

A Traceless Selection: Counter-selection System That Allows Efficient Generation of Transposon and CRISPR-modified T-cell Products

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Riccardo Mezzadra

2016-01-01

Full Text Available Recent years have seen major breakthroughs in genome-engineering systems, such as transposon-mediated gene delivery systems and CRISPR-Cas9-mediated genome-editing tools. In these systems, transient expression of auxiliary genes is responsible for permanent genomic modification. For both systems, it would be valuable to select for cells that are likely to undergo stable genome modification. Importantly, in particular for clinical applications of genome-engineered cell products, it will also be of importance to remove those cells that, due to random vector integration, display an unwanted stable expression of the auxiliary gene. Here, we develop a traceless selection system that on the one hand allows efficient enrichment of modified cells, and on the other hand can be used to select against cells that retain expression of the auxiliary gene. The value of this system to produce highly enriched-auxiliary gene-free cell products is demonstrated.

A Research Project on Successful Single-Parent Families.

Science.gov (United States)

Barry, Ann

1979-01-01

Studies variables associated with successful single-parent families. Single parents volunteered to share their positive family experiences. Information was sought on ages of family members and length of single-parent family status, education level and income, relations with absent parent, and relations with children. A hypothesis and counseling…

Transposon mutagenesis identifies novel genes associated with Staphylococcus aureus persister formation

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Wang ewenjie

2015-12-01

Full Text Available Pathogenic bacterial persisters are responsible for the recalcitrance of chronic and persistent infections to antimicrobial therapy. Although the mechanisms of persister formation and survival have been widely studied in Escherichia coli, persistence mechanisms in S. aureus remain largely unknown. Here, we screened a transposon mutant library of a clinical methicillin-resistant Staphylococcus aureus（MRSA）strain, USA500 (ST8, under antibiotic pressure and identified 13 genes whose insertion mutations resulted in a defect in persistence. These candidate genes were further confirmed by evaluating the survival of the mutants upon exposure to levofloxacin and several other stress conditions. We found 13 insertion mutants with significantly lower persister numbers under several stress conditions, including sdhA, sdhB, ureG, mnhG1, fbaA, ctaB, clpX, parE, HOU_0223, HOU_0587, HOU_2091, HOU_2315 and HOU_2346, which mapped into pathways of oxidative phosphorylation, TCA cycle, glycolysis, cell cycle and ABC transporters, suggesting that these genes and pathways may play an important role in persister formation and survival. The newly constructed knockout strains of ureG, sdhA and sdhB and their complemented strains were also tested for defect in persisters following exposure to levofloxacin and several other stress conditions. The results from these experiments were consistent with the screening results, which indicated that deletion of these genes in MRSA USA500 leads to persister defect. These findings provide novel insights into the mechanisms of persister formation and survival in S. aureus and offer new targets for the development of persister-directed antibiotics for the improved treatment of chronic and persistent infections.

Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.

Science.gov (United States)

Luo, Wentian; Galvan, Daniel L; Woodard, Lauren E; Dorset, Dan; Levy, Shawn; Wilson, Matthew H

2017-08-21

Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X. Chimeric transposases were evaluated for expression, transposition activity, chromatin immunoprecipitation at the target loci, and targeted knockout of the HPRT gene in human cells. One ZFP-PB and one TALE-PB chimera demonstrated notable HPRT gene targeting. In contrast, Cas9/dCas9-PB chimeras did not result in gene targeting. Instead, the HPRT locus appeared to be protected from transposon integration. Supplied separately, PB permitted highly efficient isolation of Cas9-mediated knockout of HPRT, with zero transposon integrations in HPRT by deep sequencing. In summary, these tools may allow isolation of 'targeted-only' cells, be utilized to protect a genomic locus from transposon integration, and enrich for Cas9-mutated cells. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1990-01-01

The status of our project on single-electron tunneling is at this point excellent. As outlined in our original proposal, a key goal in the development of this project was the demonstration and exploration of the microwave properties of single-electron systems. As discussed here, such work has to date been carried out

Salmonella Persistence in Tomatoes Requires a Distinct Set of Metabolic Functions Identified by Transposon Insertion Sequencing

Science.gov (United States)

Desai, Prerak; Porwollik, Steffen; Canals, Rocio; Perez, Daniel R.; Chu, Weiping; McClelland, Michael; Teplitski, Max

2016-01-01

ABSTRACT Human enteric pathogens, such as Salmonella spp. and verotoxigenic Escherichia coli, are increasingly recognized as causes of gastroenteritis outbreaks associated with the consumption of fruits and vegetables. Persistence in plants represents an important part of the life cycle of these pathogens. The identification of the full complement of Salmonella genes involved in the colonization of the model plant (tomato) was carried out using transposon insertion sequencing analysis. With this approach, 230,000 transposon insertions were screened in tomato pericarps to identify loci with reduction in fitness, followed by validation of the screen results using competition assays of the isogenic mutants against the wild type. A comparison with studies in animals revealed a distinct plant-associated set of genes, which only partially overlaps with the genes required to elicit disease in animals. De novo biosynthesis of amino acids was critical to persistence within tomatoes, while amino acid scavenging was prevalent in animal infections. Fitness reduction of the Salmonella amino acid synthesis mutants was generally more severe in the tomato rin mutant, which hyperaccumulates certain amino acids, suggesting that these nutrients remain unavailable to Salmonella spp. within plants. Salmonella lipopolysaccharide (LPS) was required for persistence in both animals and plants, exemplifying some shared pathogenesis-related mechanisms in animal and plant hosts. Similarly to phytopathogens, Salmonella spp. required biosynthesis of amino acids, LPS, and nucleotides to colonize tomatoes. Overall, however, it appears that while Salmonella shares some strategies with phytopathogens and taps into its animal virulence-related functions, colonization of tomatoes represents a distinct strategy, highlighting this pathogen's flexible metabolism. IMPORTANCE Outbreaks of gastroenteritis caused by human pathogens have been increasingly associated with foods of plant origin, with tomatoes

Overview Of Enhanced Hanford Single-Shell Tank (SST) Integrity Project - 12128

International Nuclear Information System (INIS)

Venetz, T.J.; Boomer, K.D.; Washenfelder, D.J.; Johnson, J.B.

2012-01-01

To improve the understanding of the single-shell tanks integrity, Washington River Protection Solutions, LLC, the USDOE Hanford Site tank contractor, developed an enhanced Single-Shell Tank (SST) Integrity Project in 2009. An expert panel on SST integrity, consisting of various subject matters experts in industry and academia, was created to provide recommendations supporting the development of the project. This panel developed 33 recommendations in four main areas of interest: structural integrity, liner degradation, leak integrity and prevention, and mitigation of contamination migration, Seventeen of these recommendations were used to develop the basis for the M-45-10-1 Change Package for the Hanford Federal Agreement and Compliance Order, which is also known as the Tri-Party Agreement. The change package identified two phases of work for SST integrity. The initial phase has been focused on efforts to envelope the integrity of the tanks. The initial phase was divided into two primary areas of investigation: structural integrity and leak integrity. If necessary based on the outcome from the initial work, a second phase would be focused on further definition of the integrity of the concrete and liners. Combined these two phases are designed to support the formal integrity assessment of the Hanford SSTs in 2018 by Independent Qualified Registered Engineer. The work to further define the DOE's understanding of the structural integrity SSTs involves preparing a modern Analysis of Record using a finite element analysis program. Structural analyses of the SSTs have been conducted since 1957, but these analyses used analog calculation, less rigorous models, or focused on individual structures. As such, an integrated understanding of all of the SSTs has not been developed to modern expectations. In support of this effort, other milestones will address the visual inspection of the tank concrete and the collection of concrete core samples from the tanks for analysis of

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1991-01-01

The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal in the development of this project was the demonstration and exploration of the microwave properties of single-electron system. As discussed in this paper such work has to data been carried out. Also as discussed in our previous progress report, the next step in the experimental evolution of the project will be to use lithographically-defined small dots as capacitors as outlined in our proposal. At this point we have made such microdotsdots as will be discussed. We have also continued our work with metal droplets to form single-electron tunnel systems

Copy number of the transposon, Pokey, in rDNA is positively correlated with rDNA copy number in Daphnia obtuse [corrected].

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Kaitlynn LeRiche

Full Text Available Pokey is a class II DNA transposon that inserts into 28S ribosomal RNA (rRNA genes and other genomic regions of species in the subgenus, Daphnia. Two divergent lineages, PokeyA and PokeyB have been identified. Recombination between misaligned rRNA genes changes their number and the number of Pokey elements. We used quantitative PCR (qPCR to estimate rRNA gene and Pokey number in isolates from natural populations of Daphnia obtusa, and in clonally-propagated mutation accumulation lines (MAL initiated from a single D. obtusa female. The change in direction and magnitude of Pokey and rRNA gene number did not show a consistent pattern across ∼ 87 generations in the MAL; however, Pokey and rRNA gene number changed in concert. PokeyA and 28S gene number were positively correlated in the isolates from both natural populations and the MAL. PokeyB number was much lower than PokeyA in both MAL and natural population isolates, and showed no correlation with 28S gene number. Preliminary analysis did not detect PokeyB outside rDNA in any isolates and detected only 0 to 4 copies of PokeyA outside rDNA indicating that Pokey may be primarily an rDNA element in D. obtusa. The recombination rate in this species is high and the average size of the rDNA locus is about twice as large as that in other Daphnia species such as D. pulicaria and D. pulex, which may have facilitated expansion of PokeyA to much higher numbers in D. obtusa rDNA than these other species.

Accuracy of Dual-Energy Virtual Monochromatic CT Numbers: Comparison between the Single-Source Projection-Based and Dual-Source Image-Based Methods.

Science.gov (United States)

Ueguchi, Takashi; Ogihara, Ryota; Yamada, Sachiko

2018-03-21

To investigate the accuracy of dual-energy virtual monochromatic computed tomography (CT) numbers obtained by two typical hardware and software implementations: the single-source projection-based method and the dual-source image-based method. A phantom with different tissue equivalent inserts was scanned with both single-source and dual-source scanners. A fast kVp-switching feature was used on the single-source scanner, whereas a tin filter was used on the dual-source scanner. Virtual monochromatic CT images of the phantom at energy levels of 60, 100, and 140 keV were obtained by both projection-based (on the single-source scanner) and image-based (on the dual-source scanner) methods. The accuracy of virtual monochromatic CT numbers for all inserts was assessed by comparing measured values to their corresponding true values. Linear regression analysis was performed to evaluate the dependency of measured CT numbers on tissue attenuation, method, and their interaction. Root mean square values of systematic error over all inserts at 60, 100, and 140 keV were approximately 53, 21, and 29 Hounsfield unit (HU) with the single-source projection-based method, and 46, 7, and 6 HU with the dual-source image-based method, respectively. Linear regression analysis revealed that the interaction between the attenuation and the method had a statistically significant effect on the measured CT numbers at 100 and 140 keV. There were attenuation-, method-, and energy level-dependent systematic errors in the measured virtual monochromatic CT numbers. CT number reproducibility was comparable between the two scanners, and CT numbers had better accuracy with the dual-source image-based method at 100 and 140 keV. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Projected interaction picture of field operators and memory superoperators. A master equation for the single-particle Green's function in a Liouville space

International Nuclear Information System (INIS)

Grinberg, H.

1983-11-01

The projection operator method of Zwanzig and Feshbach is used to construct the time-dependent field operators in the interaction picture. The formula developed to describe the time dependence involves time-ordered cosine and sine projected evolution (memory) superoperators, from which a master equation for the interaction-picture single-particle Green's function in a Liouville space is derived. (author)

One to rule them all

Science.gov (United States)

Bouuaert, Corentin Claeys; Tellier, Michael; Chalmers, Ronald

2014-01-01

The development of transposon-based genome manipulation tools can benefit greatly from understanding transposons’ inherent regulatory mechanisms. The Tc1-mariner transposons, which are being widely used in biotechnological applications, are subject to a self-inhibitory mechanism whereby increasing transposase expression beyond a certain point decreases the rate of transposition. In a recent paper, Liu and Chalmers performed saturating mutagenesis on the highly conserved WVPHEL motif in the mariner-family transposase from the Hsmar1 element. Curiously, they found that the majority of all possible single mutations were hyperactive. Biochemical characterizations of the mutants revealed that the hyperactivity is due to a defect in communication between transposase subunits, which normally regulates transposition by reducing the rate of synapsis. This provides important clues for improving transposon-based tools. However, some WVPHEL mutants also showed features that would be undesirable for most biotechnological applications: they showed uncontrolled DNA cleavage activities and defects in the coordination of cleavage between the two transposon ends. The study illustrates how the knowledge of inhibitory mechanisms can help improve transposon tools but also highlights an important challenge, which is to specifically target a regulatory mechanism without affecting other important functions of the transposase. PMID:24812590

Autoantigen La promotes efficient RNAi, antiviral response, and transposon silencing by facilitating multiple-turnover RISC catalysis.

Science.gov (United States)

Liu, Ying; Tan, Huiling; Tian, Hui; Liang, Chunyang; Chen, She; Liu, Qinghua

2011-11-04

The effector of RNA interference (RNAi) is the RNA-induced silencing complex (RISC). C3PO promotes the activation of RISC by degrading the Argonaute2 (Ago2)-nicked passenger strand of duplex siRNA. Active RISC is a multiple-turnover enzyme that uses the guide strand of siRNA to direct the Ago2-mediated sequence-specific cleavage of complementary mRNA. How this effector step of RNAi is regulated is currently unknown. Here, we used the human Ago2 minimal RISC system to purify Sjögren's syndrome antigen B (SSB)/autoantigen La as an activator of the RISC-mediated mRNA cleavage activity. Our reconstitution studies showed that La could promote multiple-turnover RISC catalysis by facilitating the release of cleaved mRNA from RISC. Moreover, we demonstrated that La was required for efficient RNAi, antiviral defense, and transposon silencing in vivo. Taken together, the findings of C3PO and La reveal a general concept that regulatory factors are required to remove Ago2-cleaved products to assemble or restore active RISC. Copyright © 2011 Elsevier Inc. All rights reserved.

OVERVIEW OF ENHANCED HANFORD SINGLE-SHELL TANK (SST) INTEGRITY PROJECT - 12128

Energy Technology Data Exchange (ETDEWEB)

VENETZ TJ; BOOMER KD; WASHENFELDER DJ; JOHNSON JB

2012-01-25

To improve the understanding of the single-shell tanks integrity, Washington River Protection Solutions, LLC, the USDOE Hanford Site tank contractor, developed an enhanced Single-Shell Tank (SST) Integrity Project in 2009. An expert panel on SST integrity, consisting of various subject matters experts in industry and academia, was created to provide recommendations supporting the development of the project. This panel developed 33 recommendations in four main areas of interest: structural integrity, liner degradation, leak integrity and prevention, and mitigation of contamination migration, Seventeen of these recommendations were used to develop the basis for the M-45-10-1 Change Package for the Hanford Federal Agreement and Compliance Order, which is also known as the Tri-Party Agreement. The change package identified two phases of work for SST integrity. The initial phase has been focused on efforts to envelope the integrity of the tanks. The initial phase was divided into two primary areas of investigation: structural integrity and leak integrity. If necessary based on the outcome from the initial work, a second phase would be focused on further definition of the integrity of the concrete and liners. Combined these two phases are designed to support the formal integrity assessment of the Hanford SSTs in 2018 by Independent Qualified Registered Engineer. The work to further define the DOE's understanding of the structural integrity SSTs involves preparing a modern Analysis of Record using a finite element analysis program. Structural analyses of the SSTs have been conducted since 1957, but these analyses used analog calculation, less rigorous models, or focused on individual structures. As such, an integrated understanding of all of the SSTs has not been developed to modern expectations. In support of this effort, other milestones will address the visual inspection of the tank concrete and the collection of concrete core samples from the tanks for analysis

Real-time volumetric image reconstruction and 3D tumor localization based on a single x-ray projection image for lung cancer radiotherapy.

Science.gov (United States)

Li, Ruijiang; Jia, Xun; Lewis, John H; Gu, Xuejun; Folkerts, Michael; Men, Chunhua; Jiang, Steve B

2010-06-01

To develop an algorithm for real-time volumetric image reconstruction and 3D tumor localization based on a single x-ray projection image for lung cancer radiotherapy. Given a set of volumetric images of a patient at N breathing phases as the training data, deformable image registration was performed between a reference phase and the other N-1 phases, resulting in N-1 deformation vector fields (DVFs). These DVFs can be represented efficiently by a few eigenvectors and coefficients obtained from principal component analysis (PCA). By varying the PCA coefficients, new DVFs can be generated, which, when applied on the reference image, lead to new volumetric images. A volumetric image can then be reconstructed from a single projection image by optimizing the PCA coefficients such that its computed projection matches the measured one. The 3D location of the tumor can be derived by applying the inverted DVF on its position in the reference image. The algorithm was implemented on graphics processing units (GPUs) to achieve real-time efficiency. The training data were generated using a realistic and dynamic mathematical phantom with ten breathing phases. The testing data were 360 cone beam projections corresponding to one gantry rotation, simulated using the same phantom with a 50% increase in breathing amplitude. The average relative image intensity error of the reconstructed volumetric images is 6.9% +/- 2.4%. The average 3D tumor localization error is 0.8 +/- 0.5 mm. On an NVIDIA Tesla C1060 GPU card, the average computation time for reconstructing a volumetric image from each projection is 0.24 s (range: 0.17 and 0.35 s). The authors have shown the feasibility of reconstructing volumetric images and localizing tumor positions in 3D in near real-time from a single x-ray image.

A transposon mutant library of Bacillus cereus ATCC 10987 reveals novel genes required for biofilm formation and implicates motility as an important factor for pellicle-biofilm formation.

Science.gov (United States)

Okshevsky, Mira; Louw, Matilde Greve; Lamela, Elena Otero; Nilsson, Martin; Tolker-Nielsen, Tim; Meyer, Rikke Louise

2018-04-01

Bacillus cereus is one of the most common opportunistic pathogens causing foodborne illness, as well as a common source of contamination in the dairy industry. B. cereus can form robust biofilms on food processing surfaces, resulting in food contamination due to shedding of cells and spores. Despite the medical and industrial relevance of this species, the genetic basis of biofilm formation in B. cereus is not well studied. In order to identify genes required for biofilm formation in this bacterium, we created a library of 5000 +  transposon mutants of the biofilm-forming strain B. cereusATCC 10987, using an unbiased mariner transposon approach. The mutant library was screened for the ability to form a pellicle biofilm at the air-media interface, as well as a submerged biofilm at the solid-media interface. A total of 91 genes were identified as essential for biofilm formation. These genes encode functions such as chemotaxis, amino acid metabolism and cellular repair mechanisms, and include numerous genes not previously known to be required for biofilm formation. Although the majority of disrupted genes are not directly responsible for motility, further investigations revealed that the vast majority of the biofilm-deficient mutants were also motility impaired. This observation implicates motility as a pivotal factor in the formation of a biofilm by B. cereus. These results expand our knowledge of the fundamental molecular mechanisms of biofilm formation by B. cereus. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Implementation of knowledge management approach in project oriented activities. Experience from simulator upgrade project

International Nuclear Information System (INIS)

Pironkov, L.

2010-01-01

Project specifics: Replacement of analogue process control system with Ovation®based Distributed Control System; Hybrid solution with simulated I&C logic and stimulated Human Machine Interface; Initial design ‐“turn‐key” project based on standard relationship “single customer –single contractor

Long-Term PEDF Release in Rat Iris and Retinal Epithelial Cells after Sleeping Beauty Transposon-Mediated Gene Delivery

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Laura Garcia-Garcia

2017-12-01

Full Text Available Pigment epithelium derived factor (PEDF is a potent antiangiogenic, neurotrophic, and neuroprotective molecule that is the endogenous inhibitor of vascular endothelial growth factor (VEGF in the retina. An ex vivo gene therapy approach based on transgenic overexpression of PEDF in the eye is assumed to rebalance the angiogenic-antiangiogenic milieu of the retina, resulting in growth regression of choroidal blood vessels, the hallmark of neovascular age-related macular degeneration. Here, we show that rat pigment epithelial cells can be efficiently transfected with the PEDF-expressing non-viral hyperactive Sleeping Beauty transposon system delivered in a form free of antibiotic resistance marker miniplasmids. The engineered retinal and iris pigment epithelium cells secrete high (141 ± 13 and 222 ± 14 ng PEDF levels in 72 hr in vitro. In vivo studies showed cell survival and insert expression during at least 4 months. Transplantation of the engineered cells to the subretinal space of a rat model of choroidal neovascularization reduces almost 50% of the development of new vessels.

In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations

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Edenilson Rabello

2005-01-01

Full Text Available This study assessed the abundance of microsatellites, or simple sequence repeats (SSR, in 19 Eucalyptus EST libraries from FORESTs, containing cDNA sequences from five species: E. grandis, E. globulus, E. saligna, E. urophylla and E. camaldulensis. Overall, a total of 11,534 SSRs and 8,447 SSR-containing sequences (25.5% of total ESTs were identified, with an average of 1 SSR/2.5 kb when considering all motifs and 1 SSR/3.1 kb when mononucleotides were not included. Dimeric repeats were the most abundant (41.03%, followed by trimerics (36.11% and monomerics (19.59%. The most frequent motifs were A/T (87.24% for monomerics, AG/CT (94.44% for dimerics, CCG/CGG (37.87% for trimerics, AAGG/CCTT (18.75% for tetramerics, AGAGG/CCTCT (14.04% for pentamerics and ACGGCG/CGCCGT (6.30% for hexamerics. According to sequence length, Class II or potentially variable markers were the most commonly found, followed by Class III. Two sequences presented high similarity to previously published Eucalyptus sequences from the NCBI database, EMBRA_72 and EMBRA_122. Local blastn search for transposons did not reveal the presence of any transposable elements with a cut-off value of 10-50. The large number of microsatellites identified will contribute to the refinement of marker-assisted mapping and to the discovery of novel markers for virtually all genes of economic interest.

Study on single-channel signals of water Cherenkov detector array for the LHAASO project

Energy Technology Data Exchange (ETDEWEB)

Li, H.C., E-mail: lihuicai@ihep.ac.cn [University of Nankai, Tianjin 300071 (China); Yao, Z.G.; Chen, M.J. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Yu, C.X. [University of Nankai, Tianjin 300071 (China); Zha, M.; Wu, H.R.; Gao, B.; Wang, X.J. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Liu, J.Y.; Liao, W.Y. [University of Nankai, Tianjin 300071 (China); Huang, D.Z. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)

2017-05-11

The Large High Altitude Air Shower Observatory (LHAASO) is planned to be built at Daocheng, Sichuan Province, China. The water Cherenkov detector array (WCDA), with an area of 78,000 m{sup 2} and capacity of 350,000 tons of purified water, is one of the major components of the LHAASO project. A 9-cell detector prototype array has been built at the Yangbajing site, Tibet, China to comprehensively understand the water Cherenkov technique and investigate the engineering issues of WCDA. In this paper, the rate and charge distribution of single-channel signals are evaluated using a full detail Monte Carlo simulation. The results are discussed and compared with the results obtained with prototype array.

Femtosecond few- to single-electron point-projection microscopy for nanoscale dynamic imaging

Directory of Open Access Journals (Sweden)

A. R. Bainbridge

2016-03-01

Full Text Available Femtosecond electron microscopy produces real-space images of matter in a series of ultrafast snapshots. Pulses of electrons self-disperse under space-charge broadening, so without compression, the ideal operation mode is a single electron per pulse. Here, we demonstrate femtosecond single-electron point projection microscopy (fs-ePPM in a laser-pump fs-e-probe configuration. The electrons have an energy of only 150 eV and take tens of picoseconds to propagate to the object under study. Nonetheless, we achieve a temporal resolution with a standard deviation of 114 fs (equivalent to a full-width at half-maximum of 269 ± 40 fs combined with a spatial resolution of 100 nm, applied to a localized region of charge at the apex of a nanoscale metal tip induced by 30 fs 800 nm laser pulses at 50 kHz. These observations demonstrate real-space imaging of reversible processes, such as tracking charge distributions, is feasible whilst maintaining femtosecond resolution. Our findings could find application as a characterization method, which, depending on geometry, could resolve tens of femtoseconds and tens of nanometres. Dynamically imaging electric and magnetic fields and charge distributions on sub-micron length scales opens new avenues of ultrafast dynamics. Furthermore, through the use of active compression, such pulses are an ideal seed for few-femtosecond to attosecond imaging applications which will access sub-optical cycle processes in nanoplasmonics.

Drosophila transposon insertions as unknowns for structured inquiry recombination mapping exercises in an undergraduate genetics course.

Science.gov (United States)

Marcus, Jeffrey M; Hughes, Tia M

2009-06-01

Structured inquiry approaches, in which students receive a Drosophila strain of unknown genotype to analyze and map the constituent mutations, are a common feature of many genetics teaching laboratories. The required crosses frustrate many students because they are aware that they are participating in a fundamentally trivial exercise, as the map locations of the genes are already established and have been recalculated thousands of times by generations of students. We modified the traditional structured inquiry approach to include a novel research experience for the students in our undergraduate genetics laboratories. Students conducted crosses with Drosophila strains carrying P[lacW] transposon insertions in genes without documented recombination map positions, representing a large number of unique, but equivalent genetic unknowns. Using the eye color phenotypes associated with the inserts as visible markers, it is straightforward to calculate recombination map positions for the interrupted loci. Collectively, our students mapped 95 genetic loci on chromosomes 2 and 3. In most cases, the calculated 95% confidence interval for meiotic map location overlapped with the predicted map position based on cytology. The research experience evoked positive student responses and helped students better understand the nature of scientific research for little additional cost or instructor effort.

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis.

Science.gov (United States)

Freeling, Michael; Xu, Jie; Woodhouse, Margaret; Lisch, Damon

2015-06-01

The Genome Balance Hypothesis originated from a recent study that provided a mechanism for the phenomenon of genome dominance in ancient polyploids: unique 24nt RNA coverage near genes is greater in genes on the recessive subgenome irrespective of differences in gene expression. 24nt RNAs target transposons. Transposon position effects are now hypothesized to balance the expression of networked genes and provide spring-like tension between pericentromeric heterochromatin and microtubules. The balance (coordination) of gene expression and centromere movement is under selection. Our hypothesis states that this balance can be maintained by many or few transposons about equally well. We explain known balanced distributions of junk DNA within genomes and between subgenomes in allopolyploids (and our hypothesis passes "the onion test" for any so-called solution to the C-value paradox). Importantly, when the allotetraploid maize chromosomes delete redundant genes, their nearby transposons are also lost; this result is explained if transposons near genes function. The Genome Balance Hypothesis is hypothetical because the position effect mechanisms implicated are not proved to apply to all junk DNA, and the continuous nature of the centromeric and gene position effects have not yet been studied as a single phenomenon. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Single-shell tank interim stabilization risk analysis

International Nuclear Information System (INIS)

Basche, A.D.

1998-01-01

The purpose of the Single-Shell Tank (SST) Interim Stabilization Risk Analysis is to provide a cost and schedule risk analysis of HNF-2358, Rev. 1, Single-Shell Tank Interim Stabilization Project Plan (Project Plan) (Ross et al. 1998). The analysis compares the required cost profile by fiscal year (Section 4.2) and revised schedule completion date (Section 4.5) to the Project Plan. The analysis also evaluates the executability of the Project Plan and recommends a path forward for risk mitigation

Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences.

Directory of Open Access Journals (Sweden)

Annemieke Smet

Full Text Available BACKGROUND: CTX-M-producing Escherichia coli strains are regarded as major global pathogens. METHODOLOGY/PRINCIPAL FINDINGS: The nucleotide sequence of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46: 144871-bp from Escherichia coli isolates obtained from patients with urinary tract infections and one plasmid (pEC_Bactec: 92970-bp from an Escherichia coli strain isolated from the joint of a horse with arthritis were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries two resistance genes: bla(TEM-1 and bla(CTX-M-15. It shares more than 90% homology with a previously published bla(CTX-M-plasmid from E. coli of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type FII and FIA. On the pEC_B24 backbone, two resistance genes, bla(TEM-1 and bla(CTX-M-15, were found. Six resistance genes, bla(TEM-1, bla(CTX-M-15, bla(OXA-1, aac6'-lb-cr, tetA and catB4, were detected on the pEC_L8 backbone. The same antimicrobial drug resistance genes, with the exception of tetA, were also identified on the pEC_L46 backbone. Genome analysis of all 4 plasmids studied provides evidence of a seemingly frequent transposition event of the bla(CTX-M-15-ISEcp1 element. This element seems to have a preferred insertion site at the tnpA gene of a bla(TEM-carrying Tn3-like transposon, the latter itself being inserted by a transposition event. The IS26-composite transposon, which contains the bla(OXA-1, aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8 and pEC_L46 by homologous recombination rather than a transposition event. Results obtained for pEC_L46 indicated that IS26 also plays an important role in structural rearrangements of the plasmid backbone and seems to facilitate the mobilisation of fragments from other plasmids. CONCLUSIONS: Collectively, these data suggests that IS26 together with ISEcp1 could play a critical role in the evolution of

Single Shell Tank Waste Characterization Project for Tank B-110, Core 9 - data package and PNL validation summary report

International Nuclear Information System (INIS)

Pool, K.N.; Jones, T.E.; McKinley, S.G.; Tingey, J.M.; Longaker, T.M.; Gibson, J.A.

1990-01-01

This Data Package contains results obtained by Pacific Northwest Laboratory (PNL) staff in the characterization and analyses of Core 9 segments taken from the Single-Shell Tank (SST) 110B. The characterization and analysis of Core 9 segments are outlined in the Waste Characterization Plan for Hanford Site Single-Shell Tanks and in the Pacific Northwest Laboratory (PNL) Single-Shell Tank Waste Characterization Support FY 89/90 Statement of Work (SOW), Rev. 1 dated March, 1990. Specific analyses for each sub-sample taken from a segment are delineated in Test Instructions prepared by the PNL Single-Shell Tank Waste Characterization Project Management Office (SST Project) in accordance with procedures contained in the SST Waste Characterization Procedure Compendium (PNL-MA-599). Analytical procedures used in the characterization activities are also included in PNL-MA-599. Core 9 included five segments although segment 1 did not have sufficient material for characterization. The five samplers were received from Westinghouse Hanford Company (WHC) on 11/21-22/89. Each segment was contained in a sampler and was enclosed in a shipping cask. The shipping cask was butted up to the 325-A hot cell and the sampler moved into the hot cell. The material in the sampler (i.e., the segment) was extruded from the sampler, limited physical characteristics assessed, and photographed. At this point samples were taken for particle size and volatile organic analyses. Each segment was then homogenized. Sub-samples were taken for required analyses as delineated in the appropriate Test Instruction. Table 1 includes sample numbers assigned to Core 9 segment materials being transferred from 325-A Hot Cell. Sample numbers 90-0298, 90-0299, 90-0302, and 90-0303 were included in Table 1 although no analyses were requested for these samples. Table 2 lists Core 9 sub-sample numbers per sample preparation method

Number projection method

International Nuclear Information System (INIS)

Kaneko, K.

1987-01-01

A relationship between the number projection and the shell model methods is investigated in the case of a single-j shell. We can find a one-to-one correspondence between the number projected and the shell model states

The One-Page Project Manager Comunicate and Manage Any Project With a Single Sheet of Paper

CERN Document Server

Campbell, Clark A

2007-01-01

The One-Page Project Manager shows you how to boil down any project into a simple, one-page document that can be used to communicate all essential details to upper management, other departments, suppliers, and audiences. This practical guide will save time and effort, helping you identify the vital parts of a project and communicate those parts and duties to other team members.

Molecular characterization and diversity of a novel non-autonomous mutator-like transposon family in brassica

International Nuclear Information System (INIS)

Nouroz, F.

2015-01-01

Transposable elements (TEs) are capable of mobilizing from one genomic location to other, with changes in their copy numbers. Mutator-like elements (MULEs) are DNA transposons characterized by 9 bp target site duplications (TSDs), with high variability in sequence and length, and include non-conserved terminal inverted repeats (TIRs). We identified and characterized a family of Mutator-like elements designated as Shahroz. The structural and molecular analyses revealed that family had a small number of mostly defective non-autonomous MULEs and has shown limited activity in the evolutionary history of the Brassica A-genome. The Shahroz elements range in size from 2734 to 3160 bp including 76 bp imperfect TIRs and 9 bp variable TSDs. The individual copies have shown high homology (52-99%) in their entire lengths. The study revealed that the elements are less in numbers but active in Brassica rapa genomes and PCR amplification revealed their specificity and amplification in A-genome containing diploid and polyploids Brassica. The phylogenetic analysis of Brassica MULEs with other plant Mutator elements revealed that no correlation exists between Brassica MULEs and other elements suggesting a separate line of evolution. Analyzing the regions flanking the insertions revealed that the insertions have showed a preference for AT rich regions. The detailed study of these insertions revealed that although less in number and small sizes, they have played a role in Brassica genome evolution by their mobilization. (author)

Wide Awake and Ready to Move: 20 Years of Non-Viral Therapeutic Genome Engineering with the Sleeping Beauty Transposon System.

Science.gov (United States)

Hodge, Russ; Narayanavari, Suneel A; Izsvák, Zsuzsanna; Ivics, Zoltán

2017-10-01

Gene therapies will only become a widespread tool in the clinical treatment of human diseases with the advent of gene transfer vectors that integrate genetic information stably, safely, effectively, and economically. Two decades after the discovery of the Sleeping Beauty (SB) transposon, it has been transformed into a vector system that is fulfilling these requirements. SB may well overcome some of the limitations associated with viral gene transfer vectors and transient non-viral gene delivery approaches that are being used in the majority of ongoing clinical trials. The SB system has achieved a high level of stable gene transfer and sustained transgene expression in multiple primary human somatic cell types, representing crucial steps that may permit its clinical use in the near future. This article reviews the most important aspects of SB as a tool for gene therapy, including aspects of its vectorization and genomic integration. As an illustration, the clinical development of the SB system toward gene therapy of age-related macular degeneration and cancer immunotherapy is highlighted.

pGLO Mutagenesis: A Laboratory Procedure in Molecular Biology for Biology Students

Science.gov (United States)

Bassiri, Eby A.

2011-01-01

A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with…

Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

Science.gov (United States)

Nagata, Takeshi; Iwata, Suehiro

2004-02-22

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing.

Science.gov (United States)

Rosconi, Federico; de Vries, Stefan P W; Baig, Abiyad; Fabiano, Elena; Grant, Andrew J

2016-11-15

The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we

Functional genomics strategies with transposons in rice

NARCIS (Netherlands)

Greco, R.

2003-01-01

Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

Preparation and tomographic reconstruction of an arbitrary single-photon path qubit

International Nuclear Information System (INIS)

Baek, So-Young; Kim, Yoon-Ho

2011-01-01

We report methods for preparation and tomographic reconstruction of an arbitrary single-photon path qubit. The arbitrary single-photon path qubit is prepared losslessly by passing the heralded single-photon state from spontaneous parametric down-conversion through variable beam splitter. Quantum state tomography of the single-photon path qubit is implemented by introducing path-projection measurements based on the first-order single-photon quantum interference. Using the state preparation and path-projection measurements methods for the single-photon path qubit, we demonstrate preparation and complete tomographic reconstruction of the single-photon path qubit with arbitrary purity. -- Highlights: → We report methods for preparation and tomographic reconstruction of an arbitrary single-photon path qubit. → We implement path-projection measurements based on the first-order single-photon quantum interference. → We demonstrate preparation and complete tomographic reconstruction of the single-photon path qubit with arbitrary purity.

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1991-01-01

The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal for this project has been the development of a scanning tunneling instrument for the purpose of imaging individual particles and tunneling into these particles at high magnetic fields. Further progress is discussed in this report

Identifying Issues in Applying Integrated Project Delivery to Domestic Nuclear Power Plant Construction Projects

Energy Technology Data Exchange (ETDEWEB)

Kim, Young Joo [Korean Nuclear Society, Daejeon (Korea, Republic of)

2016-05-15

Integrated Project Delivery (IPD) is defined as that people, systems, business structures, and practices of key stakeholders are incorporated into a single-team, with a single process, which executes a project in a way of optimizing the project's outcome, increasing values delivered to the end user, reducing waste, and maximizing efficiency throughout the phases of engineering to construction. The researcher had carried out literature review in terms of IPD to identify major characteristics of IPD which are presented in the following section and had compared such characteristics against peculiarities of nuclear power plant (NPP) construction projects in order to shed light on obstacles in possible application of IPD method to domestic NPP construction projects in the coming days. In this research, three (3) major characteristics of IPD were identified: 1) key stakeholders signing one balanced contract, forming de facto one body, sharing risk and reward 2) an integrated project team being formed in the early stage of a project and providing input to minimize time and cost loss from rework downstream 3) team members co-locating, having open and direct communication, making decisions on time, and pursuing the success of the project itself.

Ambidextrous Leadership and Sustainability-Based Project Performance: The Role of Project Culture

Directory of Open Access Journals (Sweden)

Junwei Zheng

2017-12-01

Full Text Available Most studies in the project management field emphasized the effects of leaders or managers, but these effects have rarely been examined at the project level. To cover this research gap, this study applies organizational ambidexterity theory to examine the effects among ambidextrous leadership, ambidextrous culture and sustainability-based project performance. Using a valid sample of 217 project leaders and members from Chinese construction projects, the method of multiple linear regression was adopted to assess the direct relationship among ambidextrous leadership, ambidextrous culture and project performance. Moreover, the bootstrapping technique through structural equation modeling, has been used to analyze the mediating effect of ambidextrous culture. Additionally, the sample data was divided into different groups according to the median value of the variables to conduct the ANOVA and to assess the within-group differences. The results indicated a positive and direct relationship that ambidextrous leadership has on project performance and ambidextrous culture. In addition, there was also a mediating impact of ambidextrous leadership on project performance via ambidextrous culture. Thus, ambidextrous leadership combined with transformational leadership as well as transactional leadership likely has a stronger positive impact on project performance through fostering the adaptive culture and consistent culture. Our findings contribute to an in-depth understanding of the role of the leader and culture for project outcomes. The project-based organization in construction projects could train project leaders’ ambidextrous leadership behavior to facilitate the formation of an ambidextrous culture and to increase project performance. Moreover, this study enriches the existing literature on leadership and project management by highlighting the important path of ambidextrous leadership and ambidextrous culture on the performance at the project level

Prediction of single-component NAPL behavior for the TEVES Project using T2VOC

International Nuclear Information System (INIS)

Webb, S.W.; Phelan, J.M.

1995-01-01

Detailed simulations have been performed for the TEVES (Thermal Enhanced Vapor Extraction System) Project using the TOUGH2 code considering air, water, and a single-component NAPL. A critical parameter varied in the simulations is the borehole vacuum which directly affects air flow through the system and indirectly influences soil temperatures and water and NAPL fluid masses. Contaminant migration from the heated zone into the unheated soil can occur if the borehole vacuum, or borehole flow rate, is not sufficient. Under these conditions, evaporation of liquids (water and NAPL) due to the heating can cause flow from the heated zone into the unheated soil. Insufficient air sweep may be indicated by a vapor dominated mass flow rate into the borehole, at least for the present configuration. Sufficient air flow through the heated zone must be provided to contain the contaminants within the heated zone

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis

Science.gov (United States)

Chakraborty, Syandan; Ji, HaYeun; Chen, Jack; Gersbach, Charles A.; Leong, Kam W.

2014-01-01

Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells. PMID:25492703

Single Electron Tunneling

International Nuclear Information System (INIS)

Ruggiero, Steven T.

2005-01-01

Financial support for this project has led to advances in the science of single-electron phenomena. Our group reported the first observation of the so-called ''Coulomb Staircase'', which was produced by tunneling into ultra-small metal particles. This work showed well-defined tunneling voltage steps of width e/C and height e/RC, demonstrating tunneling quantized on the single-electron level. This work was published in a now well-cited Physical Review Letter. Single-electron physics is now a major sub-field of condensed-matter physics, and fundamental work in the area continues to be conducted by tunneling in ultra-small metal particles. In addition, there are now single-electron transistors that add a controlling gate to modulate the charge on ultra-small photolithographically defined capacitive elements. Single-electron transistors are now at the heart of at least one experimental quantum-computer element, and single-electron transistor pumps may soon be used to define fundamental quantities such as the farad (capacitance) and the ampere (current). Novel computer technology based on single-electron quantum dots is also being developed. In related work, our group played the leading role in the explanation of experimental results observed during the initial phases of tunneling experiments with the high-temperature superconductors. When so-called ''multiple-gap'' tunneling was reported, the phenomenon was correctly identified by our group as single-electron tunneling in small grains in the material. The main focus throughout this project has been to explore single electron phenomena both in traditional tunneling formats of the type metal/insulator/particles/insulator/metal and using scanning tunneling microscopy to probe few-particle systems. This has been done under varying conditions of temperature, applied magnetic field, and with different materials systems. These have included metals, semi-metals, and superconductors. Amongst a number of results, we have

Distributed Project Work

DEFF Research Database (Denmark)

Borch, Ole; Kirkegaard, B.; Knudsen, Morten

1998-01-01

Project work has been used for many years at Aalborg University to improve learning of theory and methods given in courses. In a closed environment where the students are forming a group in a single room, the interaction behaviour is more or less given from the natural life. Group work in a distr......Project work has been used for many years at Aalborg University to improve learning of theory and methods given in courses. In a closed environment where the students are forming a group in a single room, the interaction behaviour is more or less given from the natural life. Group work...... in a distributed fashion over the Internet needs more attention to the interaction protocol since the physical group room is not existing. The purpose in this paper is to develop a method for online project work by using the product: Basic Support for Cooperative Work (BSCV). An analysis of a well-proven protocol...... for information exchange in the traditional project environment is performed. A group of teachers and a student group using small project examples test the method. The first test group used a prototype for testing and found the new activity synchronization difficult to adapt, so the method was finally adjusted...

Bioreactor scale up and protein product quality characterization of piggyBac transposon derived CHO pools.

Science.gov (United States)

Rajendra, Yashas; Balasubramanian, Sowmya; Peery, Robert B; Swartling, James R; McCracken, Neil A; Norris, Dawn L; Frye, Christopher C; Barnard, Gavin C

2017-03-01

Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies, and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7.6 g/L in a 16 day bioprocess using piggyBac transposon-mediated gene integration. In this study, we wanted to understand why the piggyBac pool titers were significantly higher (2-10 fold) than the control CHO pools. Higher titers were the result of a combination of increased average gene copy number, significantly higher messenger RNA levels and the homogeneity (i.e. less diverse population distribution) of the piggyBac pools, relative to the control pools. In order to validate the use of piggyBac pools to support preclinical drug development, we then performed an in-depth product quality analysis of purified protein. The product quality of protein obtained from the piggyBac pools was very similar to the product quality profile of protein obtained from the control pools. Finally, we demonstrated the scalability of these pools from shake flasks to 36L bioreactors. Overall, these results suggest that gram quantities of therapeutic protein can be rapidly obtained from piggyBac CHO pools without significantly changing product quality attributes. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:534-540, 2017. © 2017 American Institute of Chemical Engineers.

Genome-Wide Transposon Mutagenesis Indicates that Mycobacterium marinum Customizes Its Virulence Mechanisms for Survival and Replication in Different Hosts

KAUST Repository

Weerdenburg, Eveline M.

2015-02-17

The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogen Mycobacterium marinum whether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show that M. marinum contains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore, M. marinum contains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.

78 FR 33755 - Project Financing Loans

Science.gov (United States)

2013-06-05

... CFR Part 1710 [0572-AC21] Project Financing Loans AGENCY: Rural Utilities Service, USDA. ACTION... also considering regulations to clarify the agency's procedures for single asset/project financing... parameters necessary to more effectively and prudently use project financing in the RUS electric loan program...

Expression of phage-transposons of Pseudomonas aeruginosa in cells of Pseudomonas putida PpGl. II. Zygotic induction, an essential condition for the emergence of defective lysogens

Energy Technology Data Exchange (ETDEWEB)

Gorbunova, S.A.; Akhverdyan, V.Z.; Krylov, V.N.

1986-06-01

The presence of a large number of clones, which have lost the ability to produce phase, is a feature of PpGl exconjugants, which have acquired markers of the hybrid plasmid containing the genome of the PAO1 phage transposon. Analysis of these clones indicates that they contain plasmids with different defects in the phage genome (point mutations and different deletion lengths which may have an effect on both the phage genome and also plasmid RP4). Mutations of a particular region are selected, the region of early prophage genes. The process of zygotic induction is an essential condition for the arisal of mutants (including deletion mutants). The results of the experiment, which was based on the Luria-Delbruik test, showed that a significant proportion of the mutations, including deletion mutations, arise in the recipient cells PpGl.

Project Soar.

Science.gov (United States)

Austin, Marion

1982-01-01

Project Soar, a Saturday enrichment program for gifted students (6-14 years old), allows students to work intensively in a single area of interest. Examples are cited of students' work in crewel embroidery, creative writing, and biochemistry. (CL)

Project governance: "Schools of thought"

Directory of Open Access Journals (Sweden)

Michiel Christiaan Bekker

2014-02-01

Full Text Available The terminology, definition and context of project governance have become a focal subject for research and discussions in project management literature. This article reviews literature on the subject of project governance and categorise the arguments into three schools of thought namely the single-firm school, multi-firm school and large capital school. The single-firm school is concerned with governance principles related to internal organisational projects and practice these principles at a technical level. The multi-firm school address the governance principles concerned with two of more organisations participating on a contractual basis on the same project and focus their governance efforts at the technical and strategic level. The large capital school consider projects as temporary organisations, forming their own entity and establishing governance principles at an institutional level. From these schools of thought it can be concluded that the definition of project governance is dependent on the type of project and hierarchical positioning in the organisation. It is also evident that further research is required to incorporate other governance variables and mechanisms such as transaction theory, social networks and agency theory. The development of project governance frameworks should also consider the complexity of projects spanning across international companies, across country borders and incorporating different value systems, legal systems, corporate governance guidelines, religions and business practices.

The Single And Multi Project Approach To Planning And Scheduling

DEFF Research Database (Denmark)

Andersson, Niclas

2008-01-01

The fragmentation of the construction industry in Denmark is reflected in the organisation of construction projects, which typically involves a large number of subcontractors. The main contractor, being responsible for the planning and scheduling of construction work, is thus faced with the chall......The fragmentation of the construction industry in Denmark is reflected in the organisation of construction projects, which typically involves a large number of subcontractors. The main contractor, being responsible for the planning and scheduling of construction work, is thus faced...

An optimum condition for attainment of a single currency project in West Africa

Directory of Open Access Journals (Sweden)

Moses Abanyam Chiawa

2014-01-01

Full Text Available The paper examines the primary and secondary convergence conditions for a monetary union in the second monetary zone for West Africa. The focus of the paper is on the primary conditions as they provide the basis for the secondary conditions. The annual panel data used for the research are obtained from the West African Monetary Agency website: www.wami.imao.org. The panel variables are first tested for unit root and stationarity. The panel unit root test results show that all the variables are integrated of order one. The stationarity test confirms the result, as the variables are non-stationarity in level but stationarity after first difference. The Long-run co integration equation is obtained using the pooled group mean estimator. Linear programming is then applied on the result of the long-run equationto obtain the optimal conditions for attainment of single currency project for West Africa. The result shows that the objective value of 0.0462 is obtained with inflation contributing more to the variation in the government external reserves. The Central Banks in West Africa should be cautious in implementing inflation targeting as a way of tackling their economic problem.

Genome-Wide Mutagenesis in Borrelia burgdorferi.

Science.gov (United States)

Lin, Tao; Gao, Lihui

2018-01-01

Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector. STM procedure combined with Luminex Flex ® Map™ technology and next-generation sequencing (e.g., Tn-seq) are the powerful high-throughput tools for the determination of Borrelia burgdorferi virulence determinants. The assessment of multiple tissue sites and two DNA resources at two different time points using Luminex Flex ® Map™ technology provides a robust data set. B. burgdorferi transposon mutant screening indicates that a high proportion of genes are the novel virulence determinants that are required for mouse and tick infection. In this protocol, an effective signature-tagged Himar1-based transposon suicide vector was developed and used to generate a sequence-defined library of nearly 4800 mutants in the infectious B. burgdorferi B31 clone. In STM, signature-tagged suicide vectors are constructed by inserting unique DNA sequences (tags) into the transposable elements. The signature-tagged transposon mutants are generated when transposon suicide vectors are transformed into an infectious B. burgdorferi clone, and the transposable element is transposed into the 5'-TA-3' sequence in the B. burgdorferi genome with the signature tag. The transposon library is created and consists of many sub-libraries, each sub-library has several hundreds of mutants with same tags. A group of mice or ticks are infected with a mixed

Kinematic Measurement of Knee Prosthesis from Single-Plane Projection Images

Science.gov (United States)

Hirokawa, Shunji; Ariyoshi, Shogo; Takahashi, Kenji; Maruyama, Koichi

In this paper, the measurement of 3D motion from 2D perspective projections of knee prosthesis is described. The technique reported by Banks and Hodge was further developed in this study. The estimation was performed in two steps. The first-step estimation was performed on the assumption of orthogonal projection. Then, the second-step estimation was subsequently carried out based upon the perspective projection to accomplish more accurate estimation. The simulation results have demonstrated that the technique archived sufficient accuracies of position/orientation estimation for prosthetic kinematics. Then we applied our algorithm to the CCD images, thereby examining the influences of various artifacts, possibly incorporated through an imaging process, on the estimation accuracies. We found that accuracies in the experiment were influenced mainly by the geometric discrepancies between the prosthesis component and computer generated model and by the spacial inconsistencies between the coordinate axes of the positioner and that of the computer model. However, we verified that our algorithm could achieve proper and consistent estimation even for the CCD images.

Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development.

Science.gov (United States)

Takeda, Haruna; Rust, Alistair G; Ward, Jerrold M; Yew, Christopher Chin Kuan; Jenkins, Nancy A; Copeland, Neal G

2016-04-05

Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC.

Development of stable reporter system cloning luxCDABE genes into chromosome of Salmonella enterica serotypes using Tn7 transposon

Directory of Open Access Journals (Sweden)

Lawrence Mark L

2010-07-01

Full Text Available Abstract Background Salmonellosis may be a food safety problem when raw food products are mishandled and not fully cooked. In previous work, we developed bioluminescent Salmonella enterica serotypes using a plasmid-based reporting system that can be used for real-time monitoring of the pathogen's growth on food products in short term studies. In this study, we report the use of a Tn7-based transposon system for subcloning of luxCDABE genes into the chromosome of eleven Salmonella enterica serotypes isolated from the broiler production continuum. Results We found that the lux operon is constitutively expressed from the chromosome post-transposition and the lux cassette is stable without external pressure, i.e. antibiotic selection, for all Salmonella enterica serotypes used. Bioluminescence expression is based on an active electron transport chain and is directly related with metabolic activity. This relationship was quantified by measuring bioluminescence against a temperature gradient in aqueous solution using a luminometer. In addition, bioluminescent monitoring of two serotypes confirmed that our chicken skin model has the potential to be used to evaluate pathogen mitigation strategies. Conclusions This study demonstrated that our new stable reporting system eliminates bioluminescence variation due to plasmid instability and provides a reliable real-time experimental system to study application of preventive measures for Salmonella on food products in real-time for both short and long term studies.

Environmental impact assessment of Kachchh tidal power project

International Nuclear Information System (INIS)

Yadav, Ramanand; Lal, B.B.

1995-01-01

The Kachchh tidal power development project is a single-basin, single -effect and ebb generation development by construction of a tidal power barrage of about 3.25 km length across Hansthal creek. The project may disturb the ecosystem of the region. The paper deals in detail the environmental impacts of the project on climate, water velocity, flow and sedimentation pattern, water quality, flora and fauna, fishery, tourism and recreation, wild life, public health and socio-economic conditions. (author). 4 refs., 1 fig., 2 tabs

Heat-inducible transgenic expression in the silkmoth Bombyx mori

Czech Academy of Sciences Publication Activity Database

Uhlířová, Miroslava; Asahina, Masako; Riddiford, L. M.; Jindra, Marek

2002-01-01

Roč. 212, - (2002), s. 145-151 ISSN 0949-944X R&D Projects: GA AV ČR IAB5007002 Institutional research plan: CEZ:AV0Z5007907 Keywords : Germline transformation * piggyBac transposon Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.339, year: 2002

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae DNA transposon: a phylogenetic perspective

Directory of Open Access Journals (Sweden)

Mason-Gamer Roberta J

2007-06-01

Full Text Available Abstract Background Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs. The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss. Results A Stowaway-like element resides within the fourth intron of a β-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the β-amylase gene tree topology, and in light of sequence comparisons of the β-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages and two flanking deletions. The sequences that do contain elements are polyphyletic on the β-amylase tree, and their elements are divergent at the sequence level. The β-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another. Conclusion Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into the same site in β-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide

A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia.

Science.gov (United States)

Barry, Elizabeth G; Witherspoon, David J; Lampe, David J

2004-02-01

Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences.

Distributed Project Work

DEFF Research Database (Denmark)

Borch, Ole; Kirkegaard, B.; Knudsen, Morten

1998-01-01

for information exchange in the traditional project environment is performed. A group of teachers and a student group using small project examples test the method. The first test group used a prototype for testing and found the new activity synchronization difficult to adapt, so the method was finally adjusted...... to be very precises and with success used on the second test group. Distributed project work is coming pretty soon and with little improvement in server tools, projects in different topics with a large and inhomogeneous profile of users are realistic.......Project work has been used for many years at Aalborg University to improve learning of theory and methods given in courses. In a closed environment where the students are forming a group in a single room, the interaction behaviour is more or less given from the natural life. Group work...

Single well techniques

International Nuclear Information System (INIS)

Drost, W.

1983-01-01

The single well technique method includes measurement of parameters of groundwater flow in saturated rock. For determination of filtration velocity the dilution of radioactive tracer is measured, for direction logging the collimeter is rotated in the probe linked with the compass. The limiting factor for measurement of high filtration velocities is the occurrence of turbulent flow. The single well technique is used in civil engineering projects, water works and subsurface drainage of liquid waste from disposal sites. The radioactive tracer method for logging the vertical fluid movement in bore-holes is broadly used in groundwater survey and exploitation. (author)

Anti-spoof touchless 3D fingerprint recognition system using single shot fringe projection and biospeckle analysis

Science.gov (United States)

Chatterjee, Amit; Bhatia, Vimal; Prakash, Shashi

2017-08-01

Fingerprint is a unique, un-alterable and easily collected biometric of a human being. Although it is a 3D biological characteristic, traditional methods are designed to provide only a 2D image. This touch based mapping of 3D shape to 2D image losses information and leads to nonlinear distortions. Moreover, as only topographic details are captured, conventional systems are potentially vulnerable to spoofing materials (e.g. artificial fingers, dead fingers, false prints, etc.). In this work, we demonstrate an anti-spoof touchless 3D fingerprint detection system using a combination of single shot fringe projection and biospeckle analysis. For fingerprint detection using fringe projection, light from a low power LED source illuminates a finger through a sinusoidal grating. The fringe pattern modulated because of features on the fingertip is captured using a CCD camera. Fourier transform method based frequency filtering is used for the reconstruction of 3D fingerprint from the captured fringe pattern. In the next step, for spoof detection using biospeckle analysis a visuo-numeric algorithm based on modified structural function and non-normalized histogram is proposed. High activity biospeckle patterns are generated because of interaction of collimated laser light with internal fluid flow of the real finger sample. This activity reduces abruptly in case of layered fake prints, and is almost absent in dead or fake fingers. Furthermore, the proposed setup is fast, low-cost, involves non-mechanical scanning and is highly stable.

The Employment Retention and Advancement Project: Paths to Advancement for Single Parents

Science.gov (United States)

Miller, Cynthia; Deitch, Victoria; Hill, Aaron

2010-01-01

Between 2000 and 2003, the Employment Retention and Advancement (ERA) project identified and implemented a diverse set of innovative models designed to promote employment stability and wage or earnings progression among low-income individuals, mostly current or former welfare recipients. The project's goal was to determine which strategies could…

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis.

Science.gov (United States)

Marzo, Mar; Bello, Xabier; Puig, Marta; Maside, Xulio; Ruiz, Alfredo

2013-02-04

Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome.

Assessing the Nonequilibrium Thermodynamics in a Quenched Quantum Many-Body System via Single Projective Measurements

Directory of Open Access Journals (Sweden)

L. Fusco

2014-08-01

Full Text Available We analyze the nature of the statistics of the work done on or by a quantum many-body system brought out of equilibrium. We show that, for the sudden quench and for an initial state that commutes with the initial Hamiltonian, it is possible to retrieve the whole nonequilibrium thermodynamics via single projective measurements of observables. We highlight, in a physically clear way, the qualitative implications for the statistics of work coming from considering processes described by operators that either commute or do not commute with the unperturbed Hamiltonian of a given system. We consider a quantum many-body system and derive an expression that allows us to give a physical interpretation, for a thermal initial state, to all of the cumulants of the work in the case of quenched operators commuting with the unperturbed Hamiltonian. In the commuting case, the observables that we need to measure have an intuitive physical meaning. Conversely, in the noncommuting case, we show that, although it is possible to operate fully within the single-measurement framework irrespectively of the size of the quench, some difficulties are faced in providing a clear-cut physical interpretation to the cumulants. This circumstance makes the study of the physics of the system nontrivial and highlights the nonintuitive phenomenology of the emergence of thermodynamics from the fully quantum microscopic description. We illustrate our ideas with the example of the Ising model in a transverse field showing the interesting behavior of the high-order statistical moments of the work distribution for a generic thermal state and linking them to the critical nature of the model itself.

The Identification of Genes Important in Pseudomonas syringae pv. phaseolicola Plant Colonisation Using In Vitro Screening of Transposon Libraries.

Directory of Open Access Journals (Sweden)

Bharani Manoharan

Full Text Available The bacterial plant pathogen Pseudomonas syringae pv. phaseolicola (Pph colonises the surface of common bean plants before moving into the interior of plant tissue, via wounds and stomata. In the intercellular spaces the pathogen proliferates in the apoplastic fluid and forms microcolonies (biofilms around plant cells. If the pathogen can suppress the plant's natural resistance response, it will cause halo blight disease. The process of resistance suppression is fairly well understood, but the mechanisms used by the pathogen in colonisation are less clear. We hypothesised that we could apply in vitro genetic screens to look for changes in motility, colony formation, and adhesion, which are proxies for infection, microcolony formation and cell adhesion. We made transposon (Tn mutant libraries of Pph strains 1448A and 1302A and found 106/1920 mutants exhibited alterations in colony morphology, motility and biofilm formation. Identification of the insertion point of the Tn identified within the genome highlighted, as expected, a number of altered motility mutants bearing mutations in genes encoding various parts of the flagellum. Genes involved in nutrient biosynthesis, membrane associated proteins, and a number of conserved hypothetical protein (CHP genes were also identified. A mutation of one CHP gene caused a positive increase in in planta bacterial growth. This rapid and inexpensive screening method allows the discovery of genes important for in vitro traits that can be correlated to roles in the plant interaction.

Single-Shell Tank (SST) Retrieval Project Plan for Tank 241-C-104 Retrieval

International Nuclear Information System (INIS)

DEFIGH PRICE, C.

2000-01-01

In support of the SST Interim Closure Project, Project W-523 ''Tank 241-C-104 Waste Retrieval System'' will provide systems for retrieval and transfer of radioactive waste from tank 241-C-104 (C-104) to the DST staging tank 241-AY-101 (AY-101). At the conclusion of Project W-523, a retrieval system will have been designed and tested to meet the requirements for Acceptance of Beneficial Use and been turned over to operations. Completion of construction and operations of the C-104 retrieval system will meet the recently proposed near-term Tri-Party Agreement milestone, M-45-03F (Proposed Tri-Party Agreement change request M-45-00-01A, August, 30 2000) for demonstrating limits of retrieval technologies on sludge and hard heels in SSTs, reduce near-term storage risks associated with aging SSTs, and provide feed for the tank waste treatment plant. This Project Plan documents the methodology for managing Project W-523; formalizes responsibilities; identifies key interfaces required to complete the retrieval action; establishes the technical, cost, and schedule baselines; and identifies project organizational requirements pertaining to the engineering process such as environmental, safety, quality assurance, change control, design verification, testing, and operational turnover

Distributed Processing Using Single-chip Microcomputers

National Research Council Canada - National Science Library

Pritchett, William

1996-01-01

This project investigates the use of single-chip microprocessors as nodes in a token ring control network and explores the implementation of a protocol to manage communication across such a network...

Single-Family Houses That Meet The Future Energy Demands

DEFF Research Database (Denmark)

Rose, Jørgen; Svendsen, Svend

2002-01-01

). Before any further tightening of the regulations are introduced, however, it is necessary to illustrate the consequences of such actions with regard to finance, building technology, indoor climate and comfort. Therefore a series of investigations and experimental projects are being launched, in order...... to examine these consequences thoroughly. The department is presently contributing to this end by participating in quite a few investigative projects, where single-family houses are designed to meet the proposed future energy demands. This paper describes the results obtained from one such project where...... the department, in co-operation with a major building entrepreneur, has developed a single-family house that shows that there are no evident problems in meeting the future energy demands....

Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at "Evolution Canyon", Mount Carmel, Israel.

Science.gov (United States)

Beiles, Avigdor; Raz, Shmuel; Ben-Abu, Yuval; Nevo, Eviatar

2015-10-14

The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (D. melanogaster) from the ecologically tropic, hot, and dry south-facing slope (SFS) or "African" slope (AS) of EC and compared it with the TE frequencies on the temperate-cool and humid north-facing slope (NFS) or "European" slope (ES), separated, on average, by 250 m. The flies were sampled from two stations on each slope. We received their results, including the frequencies of each TE on each slope, and the probabilities of the statistical analyses (G-tests) of each TE separately. We continued the analysis of the inter-slope differences of the frequencies of the TEs, and based our different conclusions on that analysis and on the difference between micro (=EC) and macro (2000 km.) comparisons [Gonzalez et al. 2015 doi: 10.1186/s13062-015-0075-4 ]. Our collaborators based all their conclusions on the non-significant results of each of the individual tests of the 28 TEs. We analysed also the distribution of the TE differences between the slopes, based on their results. Thirteen TEs were more frequent on the SFS, 11 were more frequent on the NFS, and four had equal frequencies. Because of the equalizing effect of the ongoing migration, only small and temporary differences between the slopes (0 - 0.06) were regarded by us as random fluctuations (drift). Three TEs were intermediate (0.08-0.09) and await additional research. The 11 TEs with large frequency differences (0.12 - 0.22) were regarded by us as putative adaptive TEs, because the equalizing power of ongoing migration will eliminate random large differences. Five of them were higher on the SFS and six were higher on the NFS. Gaps in the distribution of the differences distinguished between the large and

Project Politics, Priorities and Participation in Rural Water Schemes

Directory of Open Access Journals (Sweden)

Barbara van Koppen

2012-02-01

Full Text Available Governments, NGOs and financers invest considerable resources in rural domestic water supplies and irrigation development. However, elite capture and underuse, if not complete abandonment, are frequent. While the blame is often put on 'corrupt, lazy and indisciplined' communities, this article explores the question of how the public water sector itself contributes to this state of affairs. Four case studies, which are part of the research project Cooperation and Conflict in Local Water Governance, are examined: two domestic water supply projects (Mali, Vietnam; one participatory multiple use project (Zambia; and one large-scale irrigation project (Bolivia. It was found that accountability of water projects was upward and tended to lie in construction targets for single uses with already allocated funding. This rendered project implementers dependent upon the village elite for timely spending. Yet, the elite appeared hardly motivated to maintain communal schemes, unless they themselves benefited. The dependency of projects on the elite can be reduced by ensuring participatory and inclusive planning that meets the project’s conditions before budget allocation. Although such approaches are common outside the water sector, a barrier in the water sector is that central public funds are negotiated by each sector by profiling unique expertise and single livelihood goals, which trickle down as single use silos. The article concludes with reflections on plausible benefits of participatory multiple use services for equity and sustainability.

Scheduling of resource-constrained projects

CERN Document Server

Klein, Robert

2000-01-01

Project management has become a widespread instrument enabling organizations to efficiently master the challenges of steadily shortening product life cycles, global markets and decreasing profit margins. With projects increasing in size and complexity, their planning and control represents one of the most crucial management tasks. This is especially true for scheduling, which is concerned with establishing execution dates for the sub-activities to be performed in order to complete the project. The ability to manage projects where resources must be allocated between concurrent projects or even sub-activities of a single project requires the use of commercial project management software packages. However, the results yielded by the solution procedures included are often rather unsatisfactory. Scheduling of Resource-Constrained Projects develops more efficient procedures, which can easily be integrated into software packages by incorporated programming languages, and thus should be of great interest for practiti...

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

Energy Technology Data Exchange (ETDEWEB)

McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; Adams, C.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; Gómez-Cadenas, J. J.; González-Díaz, D.; Gutiérrez, R. M.; Guenette, R.; Hafidi, K.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Johnston, S.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Monrabal, F.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Repond, J.; Renner, J.; Riordan, S.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Simón, A.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.

2018-03-01

A new method to tag the barium daughter in the double beta decay of $^{136}$Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba$^{++}$) resolution at a transparent scanning surface has been demonstrated. A single-step photo-bleach confirms the single ion interpretation. Individual ions are localized with super-resolution ($\\sim$2~nm), and detected with a statistical significance of 12.9~$\\sigma$ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

Science.gov (United States)

McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; Adams, C.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; Gómez-Cadenas, J. J.; González-Díaz, D.; Gutiérrez, R. M.; Guenette, R.; Hafidi, K.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Johnston, S.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Monrabal, F.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Repond, J.; Renner, J.; Riordan, S.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Simón, A.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.; NEXT Collaboration

2018-03-01

A new method to tag the barium daughter in the double-beta decay of Xe 136 is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba++ ) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (˜2 nm ), and detected with a statistical significance of 12.9 σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

Basic objects of marketing in project activities

OpenAIRE

Онищенко, Світлана Петрівна; Берневек, Тетяна Іванівна

2013-01-01

The article identified the main types of a project product from the point of view of a business level that is necessary to determine the specificity of the project marketing. As such objects of marketing - variants of the project product we have singled out: a product, a combination "product-market segment," a commodity group, a strategic business unit, a company. We have analyzed the relation "product life cycle - project-organization" and received a generalized representation of this relati...

A method for volumetric imaging in radiotherapy using single x-ray projection

International Nuclear Information System (INIS)

Xu, Yuan; Yan, Hao; Ouyang, Luo; Wang, Jing; Jiang, Steve B.; Jia, Xun; Zhou, Linghong; Cervino, Laura

2015-01-01

Purpose: It is an intriguing problem to generate an instantaneous volumetric image based on the corresponding x-ray projection. The purpose of this study is to develop a new method to achieve this goal via a sparse learning approach. Methods: To extract motion information hidden in projection images, the authors partitioned a projection image into small rectangular patches. The authors utilized a sparse learning method to automatically select patches that have a high correlation with principal component analysis (PCA) coefficients of a lung motion model. A model that maps the patch intensity to the PCA coefficients was built along with the patch selection process. Based on this model, a measured projection can be used to predict the PCA coefficients, which are then further used to generate a motion vector field and hence a volumetric image. The authors have also proposed an intensity baseline correction method based on the partitioned projection, in which the first and the second moments of pixel intensities at a patch in a simulated projection image are matched with those in a measured one via a linear transformation. The proposed method has been validated in both simulated data and real phantom data. Results: The algorithm is able to identify patches that contain relevant motion information such as the diaphragm region. It is found that an intensity baseline correction step is important to remove the systematic error in the motion prediction. For the simulation case, the sparse learning model reduced the prediction error for the first PCA coefficient to 5%, compared to the 10% error when sparse learning was not used, and the 95th percentile error for the predicted motion vector was reduced from 2.40 to 0.92 mm. In the phantom case with a regular tumor motion, the predicted tumor trajectory was successfully reconstructed with a 0.82 mm error for tumor center localization compared to a 1.66 mm error without using the sparse learning method. When the tumor motion

Office of River Protection: Simplifying Project management tools

International Nuclear Information System (INIS)

TAYLOR, D.G.

2000-01-01

The primary approach to the effort was to form a multi-organizational team comprised of federal and contractor staff to develop and implement the necessary tools and systems to manage the project. In late 1999 the DOE Manager of the Office of River Protection formed the Project Integration Office to achieve the objective of managing the efforts as a single project. The first major task, and the foundation upon which to base the development of all other tools, was the establishment of a single baseline of activities. However, defining a single scope schedule and cost was a difficult matter indeed. Work scopes were available throughout the project, but the level of detail and the integration of the activities existed primarily between working groups and individuals and not on a project-wide basis. This creates a situation where technical needs, logic flaws, resource balancing, and other similar integration needs are not elevated for management attention and resolution. It should be noted that probably 90% of the interface issues were known and being addressed. The key is simplifying the process and providing tangible assurance that the other 10% does not contain issues that can delay the project. Fortunately all of the contractors employed a common scheduling tool, which served as the basis for first communicating and then integrating baseline activities. Utilizing a powerful computer-based scheduling tool, it was soon possible to integrate the various schedules after the following was accomplished: Establishment of a scheduling specification (standardized input, coding, and approach to logic); and Clearly defined project assumptions

Optic issues in ongoing ERL projects

International Nuclear Information System (INIS)

Smith, S.L.; Muratori, B.D.; Owen, H.L.; Hoffstaetter, G.H.; Litvinenko, V.N.; Ben-Zvi, I.; Bai, M.; Beebe-Wang, J.; Blaskiewicz, M.; Calaga, R.; Fischer, W.; Chang, X.Y.; Kayran, D.; Kewisch, J.; MacKay, W.W.; Montag, C.; Parker, B.; Ptitsyn, V.; Roser, T.; Ruggiero, A.; Satogata, T.; Surrow, B.; Tepikian, S.; Trbojevic, D.; Yakimenko, V.; Zhang, S.Y.; Piot, Ph.

2006-01-01

A wide range of optics issues for energy recovery linac (ERL)-based projects are illustrated through the presentation of ongoing projects covering both light sources, at Cornell and Daresbury and high energy and nuclear physics accelerators at the Brookhaven National Laboratory. This presented range of projects demonstrates how the different designs teams see the challenges of studying and solving optics issues for their particular project's ERLs, with studies appropriate to the stage of maturity of the project. Finally, as an illustration of the complexity and detail behind a single aspect of ERL optics design we present an overview of the highly important generic topic of longitudinal phase space evolution in ERLs

Insertion of transposon in the vicinity of SSK2 confers enhanced tolerance to furfural in Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyun-Soo [Ewha Womans Univ., Seoul (Korea, Republic of). Dept. of Life Science; Kim, Na-Rae [Ewha Womans Univ., Seoul (Korea, Republic of). Div. of Life and Pharmaceutical Sciences; Kim, Wankee [Ewha Womans Univ., Seoul (Korea, Republic of). Dept. of Life Science; Ajou Univ., Suwon (Korea, Republic of). Inst. for Medical Sciences; Choi, Wonja [Ewha Womans Univ., Seoul (Korea, Republic of). Dept. of Life Science; Ewha Womans Univ., Seoul (Korea, Republic of). Microbial Resources Research Center

2012-07-15

Furfural is one of the major inhibitors generated during sugar production from cellulosic materials and, as an aldehyde, inhibits various cellular activities of microorganisms used, leading to prolonged lag time during ethanologenic fermentation. Since Saccharomyces cerevisiae strains tolerant to furfural are of great economic benefit in producing bioethanol, much effort to obtain more efficient strains continues to be made. In this study, we examined the furfural tolerance of transposon mutant strains (Tn 1-5) with enhanced ethanol tolerance and found that one of them (Tn 2), in which SSK2 is downregulated at the transcriptional level, displayed improved furfural tolerance. Such phenotype was abolished by complementation of the entire open reading frame of SSK2, which encodes a mitogen-activated protein (MAP) kinase kinase kinase of the high osmolarity glycerol (HOG) signaling pathway, suggesting an inhibitory effect of SSK2 in coping with furfural stress. Tn 2 showed a significant decrease in the intracellular level of reactive oxygen species (ROS) and early and high activation of Hog1p, a MAP kinase integral to the HOG pathway in response to furfural. The transcriptional levels of CTT1 and GLR1, two of known Hog1p downstream target genes whose protein products are involved in reducing ROS, were increased by 43 % and 56 % respectively compared with a control strain, probably resulting in the ROS decrease. Tn 2 also showed a shortened lag time during fermentation in the presence of furfural, resulting from efficient conversion of furfural to non-toxic (or less toxic) furfuryl alcohol. Taken together, the enhanced furfural tolerance of Tn 2 is suggested to be conferred by the combined effect of an early event of less ROS accumulation and a late event of efficient detoxification of furfural. (orig.)

Insertion of transposon in the vicinity of SSK2 confers enhanced tolerance to furfural in Saccharomyces cerevisiae.

Science.gov (United States)

Kim, Hyun-Soo; Kim, Na-Rae; Kim, Wankee; Choi, Wonja

2012-07-01

Furfural is one of the major inhibitors generated during sugar production from cellulosic materials and, as an aldehyde, inhibits various cellular activities of microorganisms used, leading to prolonged lag time during ethanologenic fermentation. Since Saccharomyces cerevisiae strains tolerant to furfural are of great economic benefit in producing bioethanol, much effort to obtain more efficient strains continues to be made. In this study, we examined the furfural tolerance of transposon mutant strains (Tn 1-5) with enhanced ethanol tolerance and found that one of them (Tn 2), in which SSK2 is downregulated at the transcriptional level, displayed improved furfural tolerance. Such phenotype was abolished by complementation of the entire open reading frame of SSK2, which encodes a mitogen-activated protein (MAP) kinase kinase kinase of the high osmolarity glycerol (HOG) signaling pathway, suggesting an inhibitory effect of SSK2 in coping with furfural stress. Tn 2 showed a significant decrease in the intracellular level of reactive oxygen species (ROS) and early and high activation of Hog1p, a MAP kinase integral to the HOG pathway in response to furfural. The transcriptional levels of CTT1 and GLR1, two of known Hog1p downstream target genes whose protein products are involved in reducing ROS, were increased by 43 % and 56 % respectively compared with a control strain, probably resulting in the ROS decrease. Tn 2 also showed a shortened lag time during fermentation in the presence of furfural, resulting from efficient conversion of furfural to non-toxic (or less toxic) furfuryl alcohol. Taken together, the enhanced furfural tolerance of Tn 2 is suggested to be conferred by the combined effect of an early event of less ROS accumulation and a late event of efficient detoxification of furfural.

Identification and Characterization of Non-Cellulose-Producing Mutants of Gluconacetobacter hansenii Generated by Tn5 Transposon Mutagenesis

Science.gov (United States)

Deng, Ying; Nagachar, Nivedita; Xiao, Chaowen; Tien, Ming

2013-01-01

The acs operon of Gluconacetobacter is thought to encode AcsA, AcsB, AcsC, and AcsD proteins that constitute the cellulose synthase complex, required for the synthesis and secretion of crystalline cellulose microfibrils. A few other genes have been shown to be involved in this process, but their precise role is unclear. We report here the use of Tn5 transposon insertion mutagenesis to identify and characterize six non-cellulose-producing (Cel−) mutants of Gluconacetobacter hansenii ATCC 23769. The genes disrupted were acsA, acsC, ccpAx (encoding cellulose-complementing protein [the subscript “Ax” indicates genes from organisms formerly classified as Acetobacter xylinum]), dgc1 (encoding guanylate dicyclase), and crp-fnr (encoding a cyclic AMP receptor protein/fumarate nitrate reductase transcriptional regulator). Protein blot analysis revealed that (i) AcsB and AcsC were absent in the acsA mutant, (ii) the levels of AcsB and AcsC were significantly reduced in the ccpAx mutant, and (iii) the level of AcsD was not affected in any of the Cel− mutants. Promoter analysis showed that the acs operon does not include acsD, unlike the organization of the acs operon of several strains of closely related Gluconacetobacter xylinus. Complementation experiments confirmed that the gene disrupted in each Cel− mutant was responsible for the phenotype. Quantitative real-time PCR and protein blotting results suggest that the transcription of bglAx (encoding β-glucosidase and located immediately downstream from acsD) was strongly dependent on Crp/Fnr. A bglAx knockout mutant, generated via homologous recombination, produced only ∼16% of the wild-type cellulose level. Since the crp-fnr mutant did not produce any cellulose, Crp/Fnr may regulate the expression of other gene(s) involved in cellulose biosynthesis. PMID:24013627

Electronic Resources Management Project Presentation 2012

KAUST Repository

Ramli, Rindra M.

2012-11-05

This presentation describes the electronic resources management project undertaken by the KAUST library. The objectives of this project is to migrate information from MS Sharepoint to Millennium ERM module. One of the advantages of this migration is to consolidate all electronic resources into a single and centralized location. This would allow for better information sharing among library staff.

Quantitative reconstruction from a single diffraction-enhanced image

International Nuclear Information System (INIS)

Paganin, D.M.; Lewis, R.A.; Kitchen, M.

2003-01-01

Full text: We develop an algorithm for using a single diffraction-enhanced image (DEI) to obtain a quantitative reconstruction of the projected thickness of a single-material sample which is embedded within a substrate of approximately constant thickness. This algorithm is used to quantitatively map inclusions in a breast phantom, from a single synchrotron DEI image. In particular, the reconstructed images quantitatively represent the projected thickness in the bulk of the sample, in contrast to DEI images which greatly emphasise sharp edges (high spatial frequencies). In the context of an ultimate aim of improved methods for breast cancer detection, the reconstructions are potentially of greater diagnostic value compared to the DEI data. Lastly, we point out that the methods of analysis presented here are also applicable to the quantitative analysis of differential interference contrast (DIC) images

Controlled ecological life support system breadboard project, 1988

Science.gov (United States)

Knott, W. M.

1990-01-01

The Closed Ecological Life Support System (CELSS) Breadboard Project, NASA's effort to develop the technology required to produce a functioning bioregenerative system, is discussed. The different phases of the project and its current status are described. The relationship between the project components are shown, and major project activities for fiscal years 1989 to 1993 are listed. The Biomass Production Chamber (BPC) became operational and tests of wheat as a single crop are nearing completion.

Leveraging Text Content for Management of Construction Project Documents

Science.gov (United States)

Alqady, Mohammed

2012-01-01

The construction industry is a knowledge intensive industry. Thousands of documents are generated by construction projects. Documents, as information carriers, must be managed effectively to ensure successful project management. The fact that a single project can produce thousands of documents and that a lot of the documents are generated in a…

Systems Engineering Implementation Plan for Single-Shell Tanks (SST) Retrieval Projects

International Nuclear Information System (INIS)

LEONARD, M.W.; HOFFERBER, G.A.

2000-01-01

This document communicates the planned implementation of the Systems Engineering processes and products for the SST retrieval projects as defined in the Systems Engineering Management Plan for the Tank Farm Contractor

Systems Engineering Implementation Plan for Single Shell Tanks (SST) Retrieval Projects

Energy Technology Data Exchange (ETDEWEB)

LEONARD, M.W.; HOFFERBER, G.A.

2000-11-30

This document communicates the planned implementation of the Systems Engineering processes and products for the SST retrieval projects as defined in the Systems Engineering Management Plan for the Tank Farm Contractor.

Decommissioning project management unit started its activities

International Nuclear Information System (INIS)

Medeliene, D.

2002-01-01

The Decommissioning Project Management Unit team comprises western experts as well as experts from INPP Decommissioning Service who all work as a single team. The DPMU will develop the Final Decommissioning Plan and a more detailed Decommissioning Project, which will describe how the plant will be removed from service and safely decommissioned

A new biotype of Fusarium oxysporum f. sp. lycopersici race 2 emerged by a transposon-driven mutation of avirulence gene AVR1.

Science.gov (United States)

Kashiwa, Takeshi; Suzuki, Tatsuya; Sato, Akira; Akai, Kotaro; Teraoka, Tohru; Komatsu, Ken; Arie, Tsutomu

2016-07-01

Emergence of races in Fusarium oxysporum f. sp. lycopersici (Fol) is caused by loss or mutation of at least one avirulence (AVR) gene. The product of AVR1 is a small protein (Avr1) secreted by Fol in tomato xylem sap during infection. This protein triggers Fol race 1 specific resistance (I) in tomato, indicating that AVR1 is an AVR gene. Deletion of AVR1 in race 1 resulted in the emergence of race 2, and an additional mutation in AVR2 generated race 3. Previously, we reported a new biotype of race 3, KoChi-1, in which AVR1 was truncated by a transposon Hormin, which suggested a new route to evolution of races in Fol However, to date no race 2 isolate carrying Hormin-truncated AVR1 has been reported. In this report, we describe such isolates, represented by Chiba-5, in which Hormin insertion occurred in AVR1 at a position different from that in KoChi-1. AVR1 truncation in both isolates resulted in production of defective Avr1 proteins. Chiba-5 and KoChi-1 belong to different phylogenetic clades, A1 and A2, respectively, suggesting that insertion of Hormin in AVR1 in Chiba-5 and KoChi-1 occurred as independent evolutionary events. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular genetics and epigenetics of CACTA elements

KAUST Repository

Fedoroff, Nina V.

2013-01-01

The CACTA transposons, so named for a highly conserved motif at element ends, comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) plant transposons. CACTA transposons characteristically include subterminal sequences of several

MULTIPLE PROJECT MANAGEMENT IN THE CONSTRUCTION INDSUTRY

Directory of Open Access Journals (Sweden)

Luciana Hazin Alencar

2010-06-01

Full Text Available The field of project management has historically focused on the administration of one project at a time, a focus that is insufficient given the growing need for organizations to manage multiple projects simultaneously. The requirements of Multiple Project Management (MPM involves demands and practices that are different from those of single projects. MPM poses a special need for coordination of shared resources across multiple projects in a way that can maintain the firm’s strategic focus and facilitate effective decision making. The construction industry is noteworthy for its frequent need for the management of multiple projects. This paper offers a review of the last five years of indexed literature related to multiple project management in the construction industry, identifies gaps and suggests promising new avenues of inquiry.

Key performance indicators for successful simulation projects

OpenAIRE

Jahangirian, M; Taylor, SJE; Young, T; Robinson, S

2016-01-01

There are many factors that may contribute to the successful delivery of a simulation project. To provide a structured approach to assessing the impact various factors have on project success, we propose a top-down framework whereby 15 Key Performance Indicators (KPI) are developed that represent the level of successfulness of simulation projects from various perspectives. They are linked to a set of Critical Success Factors (CSF) as reported in the simulation literature. A single measure cal...

Reconfigurable Boolean logic using magnetic single-electron transistors

Czech Academy of Sciences Publication Activity Database

Gonzalez-Zalba, M.F.; Ciccarelli, C.; Zarbo, Liviu; Irvine, A.C.; Campion, R.C.; Gallagher, B. L.; Jungwirth, Tomáš; Ferguson, A.J.; Wunderlich, Joerg

2015-01-01

Roč. 10, č. 4 (2015), e0125142 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) LM2011026; GA ČR GB14-37427G EU Projects: European Commission(XE) 268066 - 0MSPIN Institutional support: RVO:68378271 Keywords : single-electron transitor * reconfigurable logic * ferromagnetic semiconductor Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.057, year: 2015

High-quality single crystals for neutron experiments

Indian Academy of Sciences (India)

studies and our collaborative research projects with other UK and international groups will be discussed. Keywords. Crystal growth; floating zone method; neutron scattering. ... of single crystals of new materials is a highly competitive business.

A model validation framework for climate change projection and impact assessment

DEFF Research Database (Denmark)

Madsen, Henrik; Refsgaard, Jens C.; Andréassian, Vazken

2014-01-01

methods for projection of climate change (single and ensemble model projections and space‐timesubstitution) and use of different data sources as proxy for future climate conditions (long historical records comprising non‐ stationarity, paleo data, and controlled experiments). The basic guiding principles...... proxy data, reflecting future conditions. This test can be used with both single and ensemble model projections as well as with space‐time‐substitutions. It is generally expected to be more powerful when applied to a model ensemble than to a single model. Since space‐timesubstitutions include...... a differential split‐sample test using best available proxy data that reflect the expected future conditions at the site being considered. Such proxy data may be obtained from long historical records comprising nonstationarity, paleo data, or controlled experiments. The test can be applied with different...

Universal platform for quantitative analysis of DNA transposition

Directory of Open Access Journals (Sweden)

Pajunen Maria I

2010-11-01

Full Text Available Abstract Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a

Overview of quasi single helicity experiments in reversed field pinches

International Nuclear Information System (INIS)

Martin, P.; Marrelli, L.; Spizzo, G.

2003-01-01

We report the results of an experimental and theoretical project dedicated to the study of Quasi Single Helicity Reversed Field Pinch plasmas. The project has involved several RFP devices and numerical codes. It appears that QSH spectra are a feature common to all the experiments. (author)

Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro mariner transposition and natural transformation.

Science.gov (United States)

Guschinskaya, Natalia; Brunel, Romain; Tourte, Maxime; Lipscomb, Gina L; Adams, Michael W W; Oger, Philippe; Charpentier, Xavier

2016-11-08

Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes.

Costs Associated With Single-Use and Conventional Sets for Distal Radius Plating.

Science.gov (United States)

Fugarino, Bryce; Fox, Mary Patricia; Terhoeve, Cristina; Pappas, Nicholas

2017-11-01

Volar plating of distal radius fractures is an increasingly common procedure. Presterilized, single-use volar plate fixation sets have been purported to increase operating room efficiency and decrease cost. The purpose of this study was to compare the actual cost of using a conventional set compared with the projected cost of using its single-use counterpart. We retrospectively analyzed 30 consecutive cases of volar plate fixation in which conventional instrument sets were used. Hardware and processing costs were calculated for the conventional sets and compared with the projected cost of using single-use sets. The mean total cost of hardware and processing for the conventional sets was $2,728, whereas the projected cost for the single-use sets was slightly higher at $2,868. Twenty-three of the 30 cases would have required additional screws not available in the single-use set. The cost of the additional screws needed to supplement the single-use set would have added an average of $282/case. Overall, the combined hardware and processing cost was lower for conventional sets in 25 of the 30 cases. Although the price of the single-use set is less than the mean charge for use of a conventional set, additional screws not available in the single-use set were required in 77% of cases and consequently rendered the conventional set cheaper in 83% of cases. Stocking the single-use sets with additional screws to reflect the most commonly used screw lengths could make these sets more cost effective in the future. Economic and decision analysis IV. Copyright © 2017 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

2017-11-28

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO₂ and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO₂ nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO₂ nanoparticle surfaces by using ultrafast single

Chemical and UV Mutagenesis.

Science.gov (United States)

Bose, Jeffrey L

2016-01-01

The ability to create mutations is an important step towards understanding bacterial physiology and virulence. While targeted approaches are invaluable, the ability to produce genome-wide random mutations can lead to crucial discoveries. Transposon mutagenesis is a useful approach, but many interesting mutations can be missed by these insertions that interrupt coding and noncoding sequences due to the integration of an entire transposon. Chemical mutagenesis and UV-based random mutagenesis are alternate approaches to isolate mutations of interest with the potential of only single nucleotide changes. Once a standard method, difficulty in identifying mutation sites had decreased the popularity of this technique. However, thanks to the recent emergence of economical whole-genome sequencing, this approach to making mutations can once again become a viable option. Therefore, this chapter provides an overview protocol for random mutagenesis using UV light or DNA-damaging chemicals.

GT-MHR project

International Nuclear Information System (INIS)

Kiryushin, A.; Kodochigov, N.

2002-01-01

The paper presents new generation reactor - modular helium reactor with gas turbine (GT-MHR), which satisfies the requirements of the developing nuclear power. The paper describes the reactor plant and peculiarities of GT-MHR technical concept, such as high efficiency (about 48%) of electric power generation, increased safety of the plant, etc. The technologies, which are the innovative essence of GT-MHR project, are: (1) fuel in the form of fuel particles with multi-layer ceramic coatings which confine fission products at high temperatures (of about 1600 deg.); (2) large gas turbines; (3) single-shaft vertical turbomachine design; (4) electromagnetic bearings; (5) high-effective compact heat exchangers. Main technical and economical indices of GT-MHR project are presented. (author)

Classification of human- and automated resource allocation approaches in multi-project management

NARCIS (Netherlands)

Ponsteen, A.; Kusters, R.J.; Pasian, B.; Storm, P.

2015-01-01

Managing a multi-project environment requires a different method than managing a single project. The main challenge of managing a multi-project environment is the allocation of scarce human resources over the projects in execution. As part of a broader research on this topic, the aim of this paper

High Energy Single Frequency Resonant Amplifier, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This SBIR phase I project proposes a single frequency high energy resonant amplifier for remote sensing. Current state-of-art technologies can not provide all...

Analysis of critical paths for schedule control of nuclear power projects

International Nuclear Information System (INIS)

Shi Liangmin; Ma Limin; Fan Kai

2005-01-01

Study on the critical paths for the schedule control of nuclear power projects has been performed for reactor M310, based on the experiences from Daya Bay project and Ling Ao project. The study shows that the critical paths for the nuclear power project are from NI civil work, NI erection, commissioning of single systems directly serving the CFT to the joint-test. For NI civil work, the critical path is the main civil work of the reactor building, pre-stressing, handover of rooms for important areas, and key CW-erection interfaces; there are four critical paths for NI erection; For startup, two stages can be identified: commissioning of 16 single systems directly serving the CFT and joint-test. (authors)

Integrated project management type contracts

International Nuclear Information System (INIS)

Heisler, S.I.

1975-01-01

The concept of integrated project management represents a single source to which the owner can turn for all project management functions excepting for those relating to outside parties such as site purchase, personnel selection etc. Other functions such as design, procurement, construction management, schedule and cost control, quality assurance/quality control are usually handled by the integrated project manager as the agent of the owner. The arrangement is flexible and the responsibilities can be varied to suit the size and experience of the owner. Past experience in the United States indicates an increase in the trend toward IPM work and it appears that overseas this trend is developing also. (orig./RW) [de

EpiCollect+: linking smartphones to web applications for complex data collection projects.

Science.gov (United States)

Aanensen, David M; Huntley, Derek M; Menegazzo, Mirko; Powell, Chris I; Spratt, Brian G

2014-01-01

Previously, we have described the development of the generic mobile phone data gathering tool, EpiCollect, and an associated web application, providing two-way communication between multiple data gatherers and a project database. This software only allows data collection on the phone using a single questionnaire form that is tailored to the needs of the user (including a single GPS point and photo per entry), whereas many applications require a more complex structure, allowing users to link a series of forms in a linear or branching hierarchy, along with the addition of any number of media types accessible from smartphones and/or tablet devices (e.g., GPS, photos, videos, sound clips and barcode scanning). A much enhanced version of EpiCollect has been developed (EpiCollect+). The individual data collection forms in EpiCollect+ provide more design complexity than the single form used in EpiCollect, and the software allows the generation of complex data collection projects through the ability to link many forms together in a linear (or branching) hierarchy. Furthermore, EpiCollect+ allows the collection of multiple media types as well as standard text fields, increased data validation and form logic. The entire process of setting up a complex mobile phone data collection project to the specification of a user (project and form definitions) can be undertaken at the EpiCollect+ website using a simple 'drag and drop' procedure, with visualisation of the data gathered using Google Maps and charts at the project website. EpiCollect+ is suitable for situations where multiple users transmit complex data by mobile phone (or other Android devices) to a single project web database and is already being used for a range of field projects, particularly public health projects in sub-Saharan Africa. However, many uses can be envisaged from education, ecology and epidemiology to citizen science.

Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.

Directory of Open Access Journals (Sweden)

Laurel D Wright

2015-10-01

Full Text Available We identified a functional single strand origin of replication (sso in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA. In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1 maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2 stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements.

Reduction of artefacts due to missing projections using OSEM

International Nuclear Information System (INIS)

Hutton, B.F.; Kyme, A.; Choong, K.

2002-01-01

Full text: It is well recognised that missing or corrupted projections can result in artefacts. This occasionally occurs due to errors in data transfer from acquisition memory to disk. A possible approach for reducing these artefacts was investigated, Using ordered subsets expectation maximization (OSEM) the iterative reconstruction proceeds by progressively including additional projections until a single iteration is complete. Clinically useful results can be obtained using a small subset size in a single iteration. Stopping prior to the complete iteration so as to avoid inclusion of missing or corrupted data should provide a 'partial' reconstruction with minimal artefacts. To test this hypothesis projections were selectively removed from a complete data set (2, 4, 8, 12 adjacent projections) and reconstructions were performed using both filtered back projection (FBP) and OSEM. To maintain a constant number of sub-iterations in OSEM an equal number of duplicate projections were substituted for the missing projections. Both 180 and 360 degrees reconstructions with missing data were compared with reconstruction for the complete data using sum of absolute differences. Results indicate that missing data causes artefacts for both FBP and OSEM however the severity of artefacts is significantly reduced using OSEM. The effect of missing data is generally greater for 180 degrees acquisition. OSEM is recommended for minimising reconstruction artefacts due to missing projections. Copyright (2002) The Australian and New Zealand Society of Nuclear Medicine Inc

Twinning processes in Cu-Al-Ni martensite single crystals investigated by neutron single crystal diffraction method

Czech Academy of Sciences Publication Activity Database

Molnar, P.; Šittner, P.; Novák, V.; Lukáš, Petr

2008-01-01

Roč. 481, Sp.Iss.SI (2008), s. 513-517 ISSN 0921-5093 R&D Projects: GA AV ČR IAA100480704 Institutional research plan: CEZ:AV0Z10480505 Keywords : Cu-Al-Ni * single crystals * neutron diffraction Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.806, year: 2008

Decision models in explorative and exploitative innovation projects: a case study

NARCIS (Netherlands)

Wolbers, Michiel; Hofman, Erwin; Halman, Johannes I.M.

2013-01-01

Innovation processes are seen as collections of decisions that are made in the context of a single innovation project. Those decisions determine the course and the final success of an innovation project. There is, however, a lack of literature on how decisions are made in innovation projects. In

Forestry and biomass energy projects

DEFF Research Database (Denmark)

Swisher, J.N.

1994-01-01

This paper presents a comprehensive and consistent methodology to account for the costs and net carbon flows of different categories of forestry and biomass energy projects and describes the application of the methodology to several sets of projects in Latin America. The results suggest that both...... biomass energy development and forestry measures including reforestation and forest protection can contribute significantly to the reduction of global CO2 emissions, and that local land-use capacity must determine the type of project that is appropriate in specific cases. No single approach alone...... is sufficient as either a national or global strategy for sustainable land use or carbon emission reduction. The methodology allows consistent comparisons of the costs and quantities of carbon stored in different types of projects and/or national programs, facilitating the inclusion of forestry and biomass...

Programmed Rearrangement in Ciliates: Paramecium.

Science.gov (United States)

Betermier, Mireille; Duharcourt, Sandra

2014-12-01

Programmed genome rearrangements in the ciliate Paramecium provide a nice illustration of the impact of transposons on genome evolution and plasticity. During the sexual cycle, development of the somatic macronucleus involves elimination of ∼30% of the germline genome, including repeated DNA (e.g., transposons) and ∼45,000 single-copy internal eliminated sequences (IES). IES excision is a precise cut-and-close process, in which double-stranded DNA cleavage at IES ends depends on PiggyMac, a domesticated piggyBac transposase. Genome-wide analysis has revealed that at least a fraction of IESs originate from Tc/mariner transposons unrelated to piggyBac. Moreover, genomic sequences with no transposon origin, such as gene promoters, can be excised reproducibly as IESs, indicating that genome rearrangements contribute to the control of gene expression. How the system has evolved to allow elimination of DNA sequences with no recognizable conserved motif has been the subject of extensive research during the past two decades. Increasing evidence has accumulated for the participation of noncoding RNAs in epigenetic control of elimination for a subset of IESs, and in trans-generational inheritance of alternative rearrangement patterns. This chapter summarizes our current knowledge of the structure of the germline and somatic genomes for the model species Paramecium tetraurelia, and describes the DNA cleavage and repair factors that constitute the IES excision machinery. We present an overview of the role of specialized RNA interference machineries and their associated noncoding RNAs in the control of DNA elimination. Finally, we discuss how RNA-dependent modification and/or remodeling of chromatin may guide PiggyMac to its cognate cleavage sites.

Advances of Single-Cell Sequencing Technique in Tumors

Directory of Open Access Journals (Sweden)

Ji-feng FENG

2017-03-01

Full Text Available With the completion of human genome project (HGP and the international HapMap project as well as rapid development of high-throughput biochip technology, whole genomic sequencing-targeted analysis of genomic structures has been primarily finished. Application of single cell for the analysis of the whole genomics is not only economical in material collection, but more importantly, the cell will be more purified, and the laboratory results will be more accurate and reliable. Therefore, exploration and analysis of hereditary information of single tumor cells has become the dream of all researchers in the field of basic research of tumors. At present, single-cell sequencing (SCS on malignancies has been widely used in the studies of pathogeneses of multiple malignancies, such as glioma, renal cancer and hematologic neoplasms, and in the studies of the metastatic mechanism of breast cancer by some researchers. This study mainly reviewed the SCS, the mechanisms and the methods of SCS in isolating tumor cells, and application of SCS technique in tumor-related basic research and clinical treatment.

Electric field imaging of single atoms

Science.gov (United States)

Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

THE LICK AGN MONITORING PROJECT: RECALIBRATING SINGLE-EPOCH VIRIAL BLACK HOLE MASS ESTIMATES

Energy Technology Data Exchange (ETDEWEB)

Park, Daeseong; Woo, Jong-Hak [Astronomy Program, Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Treu, Tommaso; Bennert, Vardha N. [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Barth, Aaron J.; Walsh, Jonelle [Department of Physics and Astronomy, 4129 Frederick Reines Hall, University of California, Irvine, CA 92697-4575 (United States); Bentz, Misty C. [Department of Physics and Astronomy, Georgia State University Atlanta, GA 30303 (United States); Canalizo, Gabriela [Department of Physics and Astronomy, University of California, Riverside, 900 University Ave., Riverside, CA 92521 (United States); Filippenko, Alexei V. [Department of Astronomy, University of California, Berkeley, CA 94720-3411 (United States); Gates, Elinor [Lick Observatory, P.O. Box 85, Mount Hamilton, CA 95140 (United States); Greene, Jenny E. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States); Malkan, Matthew A., E-mail: woo@astro.snu.ac.kr [Department of Physics and Astronomy, University of California, Los Angeles, CA 90024 (United States)

2012-03-01

We investigate the calibration and uncertainties of black hole (BH) mass estimates based on the single-epoch (SE) method, using homogeneous and high-quality multi-epoch spectra obtained by the Lick Active Galactic Nucleus (AGN) Monitoring Project for nine local Seyfert 1 galaxies with BH masses <10{sup 8} M{sub Sun }. By decomposing the spectra into their AGNs and stellar components, we study the variability of the SE H{beta} line width (full width at half-maximum intensity, FWHM{sub H{beta}} or dispersion, {sigma}{sub H{beta}}) and of the AGN continuum luminosity at 5100 A (L{sub 5100}). From the distribution of the 'virial products' ({proportional_to} FWHM{sub H{beta}}{sup 2} L{sup 0.5}{sub 5100} or {sigma}{sub H{beta}}{sup 2} L{sup 0.5}{sub 5100}) measured from SE spectra, we estimate the uncertainty due to the combined variability as {approx}0.05 dex (12%). This is subdominant with respect to the total uncertainty in SE mass estimates, which is dominated by uncertainties in the size-luminosity relation and virial coefficient, and is estimated to be {approx}0.46 dex (factor of {approx}3). By comparing the H{beta} line profile of the SE, mean, and root-mean-square (rms) spectra, we find that the H{beta} line is broader in the mean (and SE) spectra than in the rms spectra by {approx}0.1 dex (25%) for our sample with FWHM{sub H{beta}} <3000 km s{sup -1}. This result is at variance with larger mass BHs where the difference is typically found to be much less than 0.1 dex. To correct for this systematic difference of the H{beta} line profile, we introduce a line-width dependent virial factor, resulting in a recalibration of SE BH mass estimators for low-mass AGNs.

Open Crowdsourcing: Leveraging Community Software Developers for IT Projects

Science.gov (United States)

Phair, Derek

2012-01-01

This qualitative exploratory single-case study was designed to examine and understand the use of volunteer community participants as software developers and other project related roles, such as testers, in completing a web-based application project by a non-profit organization. This study analyzed the strategic decision to engage crowd…

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

Ho, Wilson [Univ. of California, Irvine, CA (United States)

2018-02-03

Interfacial electron transfer (ET) plays an important role in many chemical and biological processes. Specifically, interfacial ET in TiO₂-based systems is important to solar energy technology, catalysis, and environmental remediation technology. However, the microscopic mechanism of interfacial ET is not well understood with regard to atomic surface structure, molecular structure, bonding, orientation, and motion. In this project, we used two complementary methodologies; single-molecule fluorescence spectroscopy, and scanning-tunneling microscopy and spectroscopy (STM and STS) to address this scientific need. The goal of this project was to integrate these techniques and measure the molecular dependence of ET between adsorbed molecules and TiO₂ semiconductor surfaces and the ET induced reactions such as the splitting of water. The scanning probe techniques, STM and STS, are capable of providing the highest spatial resolution but not easily time-resolved data. Single-molecule fluorescence spectroscopy is capable of good time resolution but requires further development to match the spatial resolution of the STM. The integrated approach involving Peter Lu at Bowling Green State University (BGSU) and Wilson Ho at the University of California, Irvine (UC Irvine) produced methods for time and spatially resolved chemical imaging of interfacial electron transfer dynamics and photocatalytic reactions. An integral aspect of the joint research was a significant exchange of graduate students to work at the two institutions. This project bridged complementary approaches to investigate a set of common problems by working with the same molecules on a variety of solid surfaces, but using appropriate techniques to probe under ambient (BGSU) and ultrahigh vacuum (UCI) conditions. The molecular level understanding of the fundamental interfacial electron transfer processes obtained in this joint project will be important for developing efficient light harvesting

Half Moon Cove Tidal Project. Feasibility report

Energy Technology Data Exchange (ETDEWEB)

1980-11-01

The proposed Half Moon Cove Tidal Power Project would be located in a small cove in the northern part of Cobscook Bay in the vicinity of Eastport, Maine. The project would be the first tidal electric power generating plant in the United States of America. The basin impounded by the barrier when full will approximate 1.2 square miles. The average tidal range at Eastport is 18.2 feet. The maximum spring tidal range will be 26.2 feet and the neap tidal range 12.8 feet. The project will be of the single pool-type single effect in which generation takes place on the ebb tide only. Utilizing an average mean tidal range of 18.2 feet the mode of operation enables generation for approximately ten and one-half (10-1/2) hours per day or slightly in excess of five (5) hours per tide. The installed capacity will be 12 MW utilizing 2 to 6 MW units. An axial flow, or Bulb type of turbine was selected for this study.

Modeling and Development of Superconducting Nanowire Single Photon Detectors

Data.gov (United States)

National Aeronautics and Space Administration — This proposal outlines a research project as the central component of a Ph.D. program focused on the device physics of superconducting nanowire single photon...

Uses of Single Photon Lidar (SPL) in the Monitoring Reporting and Verification of afforestation and carbon offset projects

Science.gov (United States)

Dolan, K. A.; DeCola, P.; Dubayah, R.; Huang, W.; Hurtt, G. C.; Tang, H.; Whitehurst, A.

2017-12-01

As societies move towards increased valuation of carbon through markets, regulations, and voluntary agreements the need to develop comprehensive, traceable and continuous, carbon monitoring, reporting and verification (MRV) systems has risen in priority locally to globally. Future landuse decisions, to conserve, develop or reforest, rests on the perceived valuation of anthropogenic and ecological benefits, as well as our ability to measure, report, verify, and "project" those benefits. Two carbon markets in the US, the Regional Green House Gas Initiative (RGGI) and the California Cap and Trade, accept carbon credits or offsets from the forestry sector from avoided emissions through forest conservation, by the enhancement land carbon sequestration through improved forest management and through reforestation projects. These investments often go beyond state, and national boundaries. For example, Blue Source a leading investment firm in forest carbon credits invested in over 20,000 acres of Pennsylvania forests in collaboration with The Nature Conservatory (TNC) Forest Conservation Program. Further local to national governments are writing their own climate policies and regulations and are setting targets for forest carbon storage and sequestration as part of their climate action portfolios. Yet, often little resources or effort is left for monitoring the success of projects such as afforestation initiatives once they have been completed. While field data is critical to monitoring efforts, covering the vast areas needed and getting accurate structural information from field campaigns alone can be difficult and costly. The use of Lidar as a supplement to other developed forest monitoring techniques has advanced significantly over the last decade. Here we evaluate the use of single photon lidar (SPL) collected in the summer of 2015, developed for rapidly collecting high-density, three-dimensional data over a variety of terrain targets, to aid in carbon offset MRV on an

User's operating procedures. Volume 1: Scout project information programs

Science.gov (United States)

Harris, C. G.; Harris, D. K.

1985-01-01

A review of the user's operating procedures for the Scout Project Automatic Data System, called SPADS is given. SPADS is the result of the past seven years of software development on a Prime minicomputer located at the Scout Project Office. SPADS was developed as a single entry, multiple cross reference data management and information retrieval system for the automation of Project office tasks, including engineering, financial, managerial, and clerical support. The instructions to operate the Scout Project Information programs in data retrieval and file maintenance via the user friendly menu drivers is presented.

Review of technologies for the pretreatment of retrieved single-shell tank waste at Hanford

International Nuclear Information System (INIS)

Gerber, M.A.

1992-08-01

The purpose of the study reported here was to identify and evaluate innovative processes that could be used to pretreat mixed waste retrieved from the 149 single-shell tanks (SSTs) on the US Department of Energy's (DOE) Hanford site. The information was collected as part of the Single Shell Tank Waste Treatment project at Pacific Northwest Laboratory (PNL). The project is being conducted for Westinghouse Hanford Company under their SST Disposal Program

Scatter measurement and correction method for cone-beam CT based on single grating scan

Science.gov (United States)

Huang, Kuidong; Shi, Wenlong; Wang, Xinyu; Dong, Yin; Chang, Taoqi; Zhang, Hua; Zhang, Dinghua

2017-06-01

In cone-beam computed tomography (CBCT) systems based on flat-panel detector imaging, the presence of scatter significantly reduces the quality of slices. Based on the concept of collimation, this paper presents a scatter measurement and correction method based on single grating scan. First, according to the characteristics of CBCT imaging, the scan method using single grating and the design requirements of the grating are analyzed and figured out. Second, by analyzing the composition of object projection images and object-and-grating projection images, the processing method for the scatter image at single projection angle is proposed. In addition, to avoid additional scan, this paper proposes an angle interpolation method of scatter images to reduce scan cost. Finally, the experimental results show that the scatter images obtained by this method are accurate and reliable, and the effect of scatter correction is obvious. When the additional object-and-grating projection images are collected and interpolated at intervals of 30 deg, the scatter correction error of slices can still be controlled within 3%.

Molecular genetics and epigenetics of CACTA elements

KAUST Repository

Fedoroff, Nina V.

2013-08-21

The CACTA transposons, so named for a highly conserved motif at element ends, comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) plant transposons. CACTA transposons characteristically include subterminal sequences of several hundred nucleotides containing closely spaced direct and inverted repeats of a short, conserved sequence of 14-15 bp. The Supressor-mutator (Spm) transposon, identified and subjected to detailed genetic analysis by Barbara McClintock, remains the paradigmatic element of the CACTA family. The Spm transposon encodes two proteins required for transposition, the transposase (TnpD) and a regulatory protein (TnpA) that binds to the subterminal repeats. Spm expression is subject to both genetic and epigenetic regulation. The Spm-encoded TnpA serves as an activator of the epigenetically inactivated, methylated Spm, stimulating both transient and heritable activation of the transposon. TnpA also serves as a negative regulator of the demethylated active element promoter and is required, in addition to the TnpD, for transposition. © Springer Science+Business Media, New York 2013.

Genetic analysis of attTn7, the transposon Tn7 attachment site in Escherichia coli, using a novel M13-based transduction assay.

Science.gov (United States)

Qadri, M I; Flores, C C; Davis, A J; Lichtenstein, C P

1989-05-05

The large (14 kb; kb = 10(3) bases) bacterial transposon, Tn7 (encoding resistance to trimethoprim and streptomycin/spectinomycin), has unusual properties. Like other elements, Tn7 transposes with low efficiency and low target-site specificity, but Tn7 also transposes, with high frequency in a unique orientation, to a preferred "attachment" site, called attTn7, in the Escherichia coli chromosome and similarly into plasmids containing attTn7. We developed a novel bacteriophage M13-based assay system to measure the transposition frequency of Tn7 to M13mp phage vectors containing attTn7 on a cloned 1 kb fragment of chromosomal DNA. Phage harvested from a Tn7 donor strain were used to infect recipient bacteria with selection for trimethoprim resistance. Transposition frequency, expressed as the number of trimethoprim-resistant colonies per plaque-forming unit, was found to be approximately 10(-4) to M13mp::attTn7, in contrast to 10(-10) to M13mp recombinants with approximately 1 kb insertions of other, "generic brand", DNA. By deletion analysis of M13mp::attTn7, we show that attTn7 is contained within a 64 base-pair region; sequences adjacent to the actual insertion site and encoding the carboxy terminus of the glmS gene are required. This assay also provided evidence for transposition immunity conferred by the right end of Tn7.

The MPPC project

International Nuclear Information System (INIS)

Rohrbach, F.

1993-01-01

We report on the work done in massively parallel processing with a view to studying possible solutions for extracting interesting high-energy physics particle events at future high-luminosity hadronic colliders operating in the TeV energy domain. We concentrate on a special Single Instruction Multiple Data (SIMD) architecture: the Associative String Processor (ASP). The Massively Parallel Processing Collaboration (MPPC) Project, grouping nine European institutes, was launched by CERN to carry out this RandD programme. This report, written by partners of the MPPC collaboration, describes the main results achieved at the end of the project: construction of ASP machines, parallel software development and application studies in high-energy physics and in other fields of science. A final, positive assessment of the ASP concept has been made by the Collaboration. (orig.)

Room-Temperature Single-Photon Source for Secure Quantum Communication

Data.gov (United States)

National Aeronautics and Space Administration — We are asking for four years of support for PhD student Justin Winkler's work on a research project entitled "Room temperature single photon source for secure...

Statistical Methods for Single-Particle Electron Cryomicroscopy

DEFF Research Database (Denmark)

Jensen, Katrine Hommelhoff

Electron cryomicroscopy (cryo-EM) is a form of transmission electron microscopy, aimed at reconstructing the 3D structure of a macromolecular complex from a large set of 2D projection images, as they exhibit a very low signal-to-noise ratio (SNR). In the single-particle reconstruction (SPR) probl...

Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark

DEFF Research Database (Denmark)

Pinholt, Mette; Gumpert, Heidi; Bayliss, Sion

2017-01-01

. The majority of the isolates were located in three groups (n = 44, 100 and 218) and clonal spread of VREfm between wards and hospitals was identified. Five Tn1546-like transposon types were identified. A dominant truncated transposon (type 4, 92%) was spread across all but one VREfm group. The closed van......A plasmid was highly covered by reads from isolates containing the type 4 transposon. CONCLUSIONS: This study suggests that it was the dissemination of the type 4 Tn1546-like transposon and plasmid via horizontal transfer to multiple populations of E. faecium, followed by clonal spread of new VREfm clones...

Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons

Czech Academy of Sciences Publication Activity Database

Ivics, Z.; Mátés, L.; Yau, T. Y.; Landa, Vladimír; Zídek, Václav; Bashir, S.; Hoffmann, O. I.; Hiripi, L.; Garrels, W.; Kues, W. A.; Bösze, Z.; Geurts, A.; Pravenec, Michal; Rülicke, T.; Izsvák, Z.

2014-01-01

Roč. 9, č. 4 (2014), s. 773-793 ISSN 1754-2189 R&D Projects: GA TA ČR(CZ) TA02010013; GA MŠk(CZ) LH12061; GA MŠk(CZ) LL1204 Institutional support: RVO:67985823 Keywords : mouse * rat * transgenesis * Sleeping Beauty * protocol Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.673, year: 2014

Science operations management. [with Infrared Astronomy Satellite project

Science.gov (United States)

Squibb, G. F.

1984-01-01

The operation teams engaged in the IR Astronomical Satellite (IRAS) project included scientists from the IRAS International Science Team. The detailed involvement of these scientists in the design, testing, validation, and operations phases of the IRAS mission contributed to the success of this project. The Project Management Group spent a substantial amount of time discussing science-related issues, because science team coleaders were members from the outset. A single scientific point-of-contact for the Management Group enhanced the depth and continuity of agreement reached in decision-making.

South Texas Maquiladora Suppliers Project.

Science.gov (United States)

Patrick, J. Michael

This project was undertaken to assist South Texas industries in improving export to nearby Mexican maquiladoras (factories). The maquiladora program is based on co-production by two plants under a single management, one on each side of the border. Activities addressed four objectives: (1) to determine the dollar value, quantity, and source of the…

Project finance and international energy development

International Nuclear Information System (INIS)

Pollio, G.

1998-01-01

This paper explores the preference for and the features unique to project finance, one of the favoured vehicles for funding energy development. Our main focus is on the interests of project sponsors, commercial banks and host governments. Inclusion of the latter reflects the fact host governments are often leading participants in primary energy and energy-related projects; more recently, they have come to use limited recourse structures to finance local infrastructure development. Traditional analyses, whilst providing useful insights into the interests of leading project participants, are incapable of isolation a single motive or set of motives that can comprehensively account for all of the features common to this form of debt. Within an options-theoretic framework, most of these ambiguities are resolved. Risk management, long recognised as one of the primary reasons for choosing project finance over rival debt structures, is affirmed as a key explanatory factor. One the other hand, options pricing theory provides a radically different perspective on how to project finance contributes to the realisation of these objectives. (author)

Managing trade-offs in landscape restoration and revegetation projects.

Science.gov (United States)

Maron, Martine; Cockfield, Geoff

2008-12-01

Landscape restoration projects often have multiple and disparate conservation, resource enhancement, and sometimes economic objectives, since projects that seek to meet more than one objective tend to be viewed more positively by funding agencies and the community. The degree to which there are trade-offs among desired objectives is an important variable for decision makers, yet this is rarely explicitly considered. In particular, the existence of ecological thresholds has important implications for decision-making at both the project level and the regional level. We develop a model of the possibilities and choices for an agency seeking to achieve two environmental objectives in a region through revegetation of a number of sites. A graphical model of the production possibilities sets for a single revegetation project is developed, and different trade-off relationships are discussed and illustrated. Then the model is used to demonstrate the possibilities for managing all such projects within a region. We show that, where there are thresholds in the trade-off relationship between two objectives, specialization (single- or dominant-objective projects) should be considered. This is illustrated using a case study in which revegetation is used to meet avian biodiversity and salinity mitigation objectives. We conclude that where there are sufficient scientific data, explicit consideration of different types of trade-offs can assist in making decisions about the most efficient mix and type of projects to better achieve a range of objectives within a region.

A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements

Directory of Open Access Journals (Sweden)

Astrid D. Haase

2016-01-01

Full Text Available Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1 the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2 a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.

Assessing Tn5 and Sleeping Beauty for transpositional transgenesis by cytoplasmic injection into bovine and ovine zygotes

Science.gov (United States)

Bevacqua, R. J.; Fernandez-Martin, R.; Canel, N. G.; Gibbons, A.; Texeira, D.; Lange, F.; Vans Landschoot, G.; Savy, V.; Briski, O.; Hiriart, M. I.; Grueso, E.; Ivics, Z.; Taboga, O.; Kues, W. A.; Ferraris, S.

2017-01-01

Transgenic domestic animals represent an alternative to bioreactors for large-scale production of biopharmaceuticals and could also provide more accurate biomedical models than rodents. However, their generation remains inefficient. Recently, DNA transposons allowed improved transgenesis efficiencies in mice and pigs. In this work, Tn5 and Sleeping Beauty (SB) transposon systems were evaluated for transgenesis by simple cytoplasmic injection in livestock zygotes. In the case of Tn5, the transposome complex of transposon nucleic acid and Tn5 protein was injected. In the case of SB, the supercoiled plasmids encoding a transposon and the SB transposase were co-injected. In vitro produced bovine zygotes were used to establish the cytoplasmic injection conditions. The in vitro cultured blastocysts were evaluated for reporter gene expression and genotyped. Subsequently, both transposon systems were injected in seasonally available ovine zygotes, employing transposons carrying the recombinant human factor IX driven by the beta-lactoglobulin promoter. The Tn5 approach did not result in transgenic lambs. In contrast, the Sleeping Beauty injection resulted in 2 lambs (29%) carrying the transgene. Both animals exhibited cellular mosaicism of the transgene. The extraembryonic tissues (placenta or umbilical cord) of three additional animals were also transgenic. These results show that transpositional transgenesis by cytoplasmic injection of SB transposon components can be applied for the production of transgenic lambs of pharmaceutical interest. PMID:28301581

Kernel Function Tuning for Single-Layer Neural Networks

Czech Academy of Sciences Publication Activity Database

Vidnerová, Petra; Neruda, Roman

-, accepted 28.11. 2017 (2018) ISSN 2278-0149 R&D Projects: GA ČR GA15-18108S Institutional support: RVO:67985807 Keywords : single-layer neural networks * kernel methods * kernel function * optimisation Subject RIV: IN - Informatics, Computer Science http://www.ijmerr.com/

Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications.

Science.gov (United States)

Kolacsek, Orsolya; Pergel, Enikő; Varga, Nóra; Apáti, Ágota; Orbán, Tamás I

2017-01-20

There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the ΔΔCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Risk Assessment of Engineering Project Financing Based on PPP Model

Directory of Open Access Journals (Sweden)

Ma Qiuli

2017-01-01

Full Text Available At present, the project financing channel is single, and the urban facilities are in short supply, and the risk assessment and prevention mechanism of financing should be further improved to reduce the risk of project financing. In view of this, the fuzzy comprehensive evaluation model of project financing risk which combined the method of fuzzy comprehensive evaluation and analytic hierarchy process is established. The scientificalness and effectiveness of the model are verified by the example of the world port project in Luohe city, and it provides basis and reference for engineering project financing based on PPP mode.

Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

Science.gov (United States)

Sveinsson, Saemundur; Gill, Navdeep; Kane, Nolan C; Cronk, Quentin

2013-07-24

Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating

SERDP CU-1129 Biological Assessment for Characterizing Contamination Risk at the Genetic-, Individual-, and Population-Level

Science.gov (United States)

2004-04-14

albimanus Quetzal : a Tc1 transposon (Sum P(2) = 8.3e-07) Transposase_5, E = 5.9e-08 Topo 6-2L3 LpTc1.1 A. albimanus Quetzal : a Tc1 transposon (Sum P(2...transposon LpTc1, A. albimanus Quetzal = Anopheles albimanus Quetzal transposase (AAB02109). The clones tank and tank.1 did not have sufficient

Tetracoordinate Co(II) complexes containing bathocuproine and single molecule magnetism

Czech Academy of Sciences Publication Activity Database

Smolko, L.; Černák, J.; Dušek, Michal; Titiš, J.; Boča, R.

2016-01-01

Roč. 40, č. 8 (2016), s. 6593-6598 ISSN 1144-0546 R&D Projects: GA MŠk LO1603; GA ČR(CZ) GA15-12653S EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : crystal structure * single molecule magnetism * Cu(II) complexes Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.269, year: 2016

Dual-mode optical microscope based on single-pixel imaging

OpenAIRE

Rodríguez Jiménez, Angel David; Clemente Pesudo, Pedro Javier; Tajahuerce, Enrique; Lancis Sáez, Jesús

2016-01-01

We demonstrate an inverted microscope that can image specimens in both reflection and transmission modes simultaneously with a single light source. The microscope utilizes a digital micromirror device (DMD) for patterned illumination altogether with two single-pixel photosensors for efficient light detection. The system, a scan-less device with no moving parts, works by sequential projection of a set of binary intensity patterns onto the sample that are codified onto a modified commercial DMD...

In silico reversal of repeat-induced point mutation (RIP identifies the origins of repeat families and uncovers obscured duplicated genes

Directory of Open Access Journals (Sweden)

Hane James K

2010-11-01

Full Text Available Abstract Background Repeat-induced point mutation (RIP is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST. Results DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorum SN15 and predict the origin of several previously uncharacterised classes of repetitive DNA. Conclusions Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal.

RT-qPCR work-flow for single-cell data analysis

Czech Academy of Sciences Publication Activity Database

Stahlberg, A.; Rusňáková, Vendula; Forootan, A.; Anděrová, Miroslava; Kubista, Mikael

2013-01-01

Roč. 59, č. 1 (2013), s. 80-88 ISSN 1046-2023 R&D Projects: GA MŠk(CZ) ME10052; GA ČR GAP303/10/1338 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:68378041 Keywords : RT-qPCR * Single-cell biology * Single-cell data analysis Subject RIV: EB - Genetics ; Molecular Biology; FH - Neurology (UEM-P) Impact factor: 3.221, year: 2013

Experimental investigations on solar heating/heat pump systems for single family houses

DEFF Research Database (Denmark)

Andersen, Elsa; Perers, Bengt

In the period 2013-2017 the project “Experimental investigations on solar heat pump systems for single family houses” is carried out at Department of Civil Engineering, Technical University of Denmark. The aim of this project is to increase the knowledge of the heat and mass transfer in the combi...

Metabolite Profiling to Characterize Disease-related Bacteria GLUCONATE EXCRETION BY PSEUDOMONAS AERUGINOSA MUTANTS AND CLINICAL ISOLATES FROM CYSTIC FIBROSIS PATIENTS

OpenAIRE

Behrends, V; Bell, TJ; Liebeke, M; Cordes-Blauert, A; Ashraf, SN; Nair, C; Zlosnik, JEA; Williams, HD; Bundy, JG

2013-01-01

Metabolic footprinting of supernatants has been proposed as a tool for assigning gene function. We used NMR spectroscopy to measure the exometabolome of 86 single-gene transposon insertion mutant strains (mutants from central carbon metabolism and regulatory mutants) of the opportunistic pathogen Pseudomonas aeruginosa, grown on a medium designed to represent the nutritional content of cystic fibrosis sputum. Functionally related genes had similar metabolic profiles. E.g. for two-component sy...

Magnetic structure of URhSi single crystal

Czech Academy of Sciences Publication Activity Database

Prokeš, K.; Andreev, Alexander V.; Honda, F.; Sechovský, V.

2003-01-01

Roč. 261, - (2003), s. 131-138 ISSN 0304-8853 R&D Projects: GA ČR GA202/02/0739 Institutional research plan: CEZ:AV0Z1010914 Keywords : URhSi single crystal * magnetization * neutron diffraction * magnetic structure determination Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.910, year: 2003

Angular momentum projected semiclassics

International Nuclear Information System (INIS)

Hasse, R.W.

1986-10-01

By using angular momentum projected plane waves as wave functions, we derive semiclassical expressions for the single-particle propagator, the partition function, the nonlocal density matrix, the single-particle density and the one particle- one hole level density for fixed angular momentum and fixed z-component or summed over the z-components. Other quantities can be deduced from the propagator. In coordinate space (r, r') the relevant quantities depend on vertical stroker - r 3 vertical stroke instead of vertical stroker - r'vertical stroke and in Wigner space (R, P) they become proportional to the angular momentum constraints δ(vertical strokeRxPvertical stroke/ℎ - l) and δ((RxP) z /ℎ - m). As applications we calculate the single-particle and one particle- one hole level densities for harmonic oscillator and Hill-Wheeler box potentials and the imaginary part of the optical potential and its volume integral with an underlying harmonic oscillator potential and a zero range two-body interaction. (orig.)

Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris

Directory of Open Access Journals (Sweden)

Scott eJackson

2014-07-01

Full Text Available Common bean (Phaseolus vulgaris is an important legume crop grown and consumed worldwide. With the availability of the common bean genome sequence, the next challenge is to annotate the genome and characterize functional DNA elements. Transposable elements (TEs are the most abundant component of plant genomes and can dramatically affect genome evolution and genetic variation. Thus, it is pivotal to identify TEs in the common bean genome. In this study, we performed a genome-wide transposon annotation in common bean using a combination of homology and sequence structure-based methods. We developed a 2.12-Mb transposon database which includes 791 representative transposon sequences and is available upon request or from www.phytozome.org. Of note, nearly all transposons in the database are previously unrecognized TEs. More than 5,000 transposon-related expressed sequence tags (ESTs were detected which indicates that some transposons may be transcriptionally active. Two Ty1-copia retrotransposon families were found to encode the envelope-like protein which has rarely been identified in plant genomes. Also, we identified an extra open reading frame (ORF termed ORF2 from 15 Ty3-gypsy families that was located between the ORF encoding the retrotransposase and the 3’LTR. The ORF2 was in opposite transcriptional orientation to retrotransposase. Sequence homology searches and phylogenetic analysis suggested that the ORF2 may have an ancient origin, but its function is not clear. This transposon data provides a useful resource for understanding the genome organization and evolution and may be used to identify active TEs for developing transposon-tagging system in common bean and other related genomes.

Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice.

Directory of Open Access Journals (Sweden)

Roy R Chaudhuri

2009-07-01

Full Text Available Genes required for infection of mice by Salmonella Typhimurium can be identified by the interrogation of random transposon mutant libraries for mutants that cannot survive in vivo. Inactivation of such genes produces attenuated S. Typhimurium strains that have potential for use as live attenuated vaccines. A quantitative screen, Transposon Mediated Differential Hybridisation (TMDH, has been developed that identifies those members of a large library of transposon mutants that are attenuated. TMDH employs custom transposons with outward-facing T7 and SP6 promoters. Fluorescently-labelled transcripts from the promoters are hybridised to whole-genome tiling microarrays, to allow the position of the transposon insertions to be determined. Comparison of microarray data from the mutant library grown in vitro (input with equivalent data produced after passage of the library through mice (output enables an attenuation score to be determined for each transposon mutant. These scores are significantly correlated with bacterial counts obtained during infection of mice using mutants with individual defined deletions of the same genes. Defined deletion mutants of several novel targets identified in the TMDH screen are effective live vaccines.

European accelerator facilities for single event effects testing

Energy Technology Data Exchange (ETDEWEB)

Adams, L; Nickson, R; Harboe-Sorensen, R [ESA-ESTEC, Noordwijk (Netherlands); Hajdas, W; Berger, G

1997-03-01

Single event effects are an important hazard to spacecraft and payloads. The advances in component technology, with shrinking dimensions and increasing complexity will give even more importance to single event effects in the future. The ground test facilities are complex and expensive and the complexities of installing a facility are compounded by the requirement that maximum control is to be exercised by users largely unfamiliar with accelerator technology. The PIF and the HIF are the result of experience gained in the field of single event effects testing and represent a unique collaboration between space technology and accelerator experts. Both facilities form an essential part of the European infrastructure supporting space projects. (J.P.N.)

Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

Science.gov (United States)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

Non Invasive Instrumentation For Single Event Effects (NIISEE), Phase I

Data.gov (United States)

National Aeronautics and Space Administration — On this Phase 1 project, Adventium will identify and address key hurdles to achieve Radiation Hardening by Software (RHS) for Single Event Effects (SEEs) for modern...

Limited angle STIM and PIXE tomography of single cells

International Nuclear Information System (INIS)

Andrea, T.; Rothermel, M.; Werner, R.; Butz, T.; Reinert, T.

2010-01-01

STIM (scanning transmission ion microscopy) tomography has been shown to be a valuable method for the three-dimensional characterization of microsamples. It has, however, rarely been employed for the study of single cells, since a free-standing sample is needed for an ordinary tomography experiment. This requirement places high demands on sample preparation techniques. In this study cells fixated on a substrate rather than free-standing were used for tomography. Since the substrate prevented a full rotation of the sample an algorithm for limited-angle tomography was devised. STIM projections covering only a limited angular range of ca. 120 o were supplemented with simulated projections generated from a back and forth iteration between real space and Radon space. The energy loss caused by the substrate was subtracted from each projection. The cells were reconstructed using filtered backprojection. The surface of the cells as well as some interior structures could be reconstructed. Following the STIM projections a lesser number of PIXE (particle induced X-ray emission) projections were taken in order to obtain information about the elemental distribution of the sample. From the PIXE projections the three-dimensional phosphorus distribution within the cell was reconstructed using limited-angle tomography. Superimposition of the STIM and PIXE tomograms revealed the location of intracellular structures. Whereas STIM tomography is sensitive to density contrast, which are greatest at the surface, PIXE tomography is sensitive to changes in elemental concentration. Hence, the combination of the two methods can be very fruitful, while the limited angle approach can compensate some of the difficulties associated with tomography of single cells, namely preparation difficulties and excessive sample damage.

EV car sharing/rental pilot project in Kyoto : an outline of the project

Energy Technology Data Exchange (ETDEWEB)

Kitamura, R. [Kyoto Univ., (Japan). Dept. of Civil Engineering Systems; Masunaga, K. [Japan Electric Vehicle Association, Minato, Tokyo (Japan)

2000-07-01

This paper presented a demonstration project in the City of Kyoto, Japan, which is aimed at determining if a Public Car System is an economically viable option for the twenty first century. The Kyoto electric vehicle (EV) car sharing project comprises advanced systems for EV reservation, check-out and return, and fleet operation and management. The most unique feature of this project is that it utilizes the ever expanding Internet and advanced mobile phones with Internet capabilities. Initially, 35 two-seater EVs will be shared by employees and visitors for business-related trips on weekdays and by tourists on weekends. The car sharing will be only short-term for only a single trip. The EV can be checked out and returned to any service depot located at railroad stations, major business centers and tourist attractions for user convenience. The ultimate goal of the project is to promote energy and resource conservation while providing adequate levels of mobility for people. Converting existing fleets to EVs which produce no exhaust gases is considered to be a viable solution to the problem of air pollution caused by traffic jams. tabs., figs.

Miniature Biometric Sensor Project

Science.gov (United States)

Falker, John; Terrier, Douglas; Clayton, Ronald; Hanson, Andrea; Cooper, Tommy; Downs, Meghan; Flint, Stephanie; Reyna, Baraquiel; Simon, Cory; Wilt, Grier

2015-01-01

Heart rate monitoring (HRM) is a critical need during exploration missions. Unlike the four separate systems used on ISS today, the single HRM system should perform as a diagnostic tool, perform well during exercise or high level activity, and be suitable for use during EVA. Currently available HRM technologies are dependent on uninterrupted contact with the skin and are prone to data drop-out and motion artifact when worn in the spacesuit or during exercise. Here, we seek an alternative to the chest strap and electrode based sensors currently in use on ISS today. This project aims to develop a single, high performance, robust biosensor with focused efforts on improved heart rate data quality collection during high intensity activity such as exercise or EVA.

Single-particle spectral density of the Hubbard model

NARCIS (Netherlands)

Mehlig, B.; Eskes, H.; Hayn, R.; Meinders, M.B.J.

1995-01-01

We calculate the single-particle spectral function for the Hubbard model within the framework of a projection technique equivalent to the two-pole approximation. We show that the two-pole approximation can be well understood as an average characterization of the upper and the lower Hubbard bands,

SINGLE-PARTICLE SPECTRAL DENSITY OF THE HUBBARD-MODEL

NARCIS (Netherlands)

MEHLIG, B; ESKES, H; HAYN, R; MEINDERS, MBJ

1995-01-01

We calculate the single-particle spectral function for the Hubbard model within the framework of a projection technique equivalent to the two-pole approximation. We show that the two-pole approximation can be well understood as an average characterization of the upper and the lower Hubbard bands,

Extending the applicability of an open-ring trap to perform experiments with a single laser-cooled ion

Energy Technology Data Exchange (ETDEWEB)

Cornejo, J. M.; Colombano, M.; Doménech, J.; Rodríguez, D., E-mail: danielrodriguez@ugr.es [Departamento de Física Atómica, Molecular y Nuclear, Universidad de Granada, 18071 Granada (Spain); Block, M. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt (Germany); Helmholtz-Institut Mainz, 55099 Mainz (Germany); Institut für Kernchemie, University of Mainz, 55099 Mainz (Germany); Delahaye, P. [Grand Accélérateur National d’Ions Lourds, 14000 Caen (France)

2015-10-15

A special ion trap was initially built up to perform β-ν correlation experiments with radioactive ions. The trap geometry is also well suited to perform experiments with laser-cooled ions, serving for the development of a new type of Penning trap, in the framework of the project TRAPSENSOR at the University of Granada. The goal of this project is to use a single {sup 40}Ca{sup +} ion as detector for single-ion mass spectrometry. Within this project and without any modification to the initial electrode configuration, it was possible to perform Doppler cooling on {sup 40}Ca{sup +} ions, starting from large clouds and reaching single ion sensitivity. This new feature of the trap might be important also for other experiments with ions produced at radioactive ion beam facilities. In this publication, the trap and the laser system will be described, together with their performance with respect to laser cooling applied to large ion clouds down to a single ion.

IMPROVEMENT OF KEY PROCESSES THROUGH THE ANALYSIS OF VALUE ADDED IN TECHNOLOGY- BASED COMPANIES A SINGLE PROJECT PRODUCTIONS OF THE WATER SECTOR IN CUBA

Directory of Open Access Journals (Sweden)

Reina Maylín, Hernández Oro

2012-01-01

Full Text Available In this paper, we present the main results of research designed to improve key business processes, using a procedure designed for this purpose, and which includes among its main stages, the analysis of value added by activity, adapting to technology based companies’ productions by one of the water sector project in Cuba. The procedure consistently combines different techniques such as multi-criteria decision analysis for selection of the key processes and analysis of value added by activity to identify key processes to improve and identify opportunities for improvement. The main results are able to identify, classify and relate the processes taking place in the organization, and represent them in a process map, and then determine the key processes for improvement, based on the analysis of value added at each process of each of the activities in it. Derived from the results obtained are proposed and implemented a set of organizational improvements had a positive economic impact for the company under study, allowing a positive conclusion on the feasibility of implementation, flexibility and robustness of the procedure developed in technology-based companies single project productions of the water sector in Cuba to support their business management.

User's operating procedures. Volume 3: Projects directorate information programs

Science.gov (United States)

Haris, C. G.; Harris, D. K.

1985-01-01

A review of the user's operating procedures for the scout project automatic data system, called SPADS is presented. SPADS is the results of the past seven years of software development on a prime mini-computer. SPADS was developed as a single entry, multiple cross-reference data management and information retrieval system for the automation of Project office tasks, including engineering, financial, managerial, and clerical support. This volume, three of three, provides the instructions to operate the projects directorate information programs in data retrieval and file maintenance via the user friendly menu drivers.

In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

Directory of Open Access Journals (Sweden)

Shirasawa Kenta

2012-06-01

Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp.

The International intraval project. Phase 1 case 2. Radionuclide migration in single natural fractures in granite

International Nuclear Information System (INIS)

Skagius, K.

1992-01-01

The INTRAVAL study addresses validation of geosphere transport models for use in repository performance assessment by examining various test cases relevant to radioactive waste disposal. This report describes the results from INTRAVAL test case 2 which is based on a set of laboratory experiments studying migration of non-sorbing as well as sorbing tracers in a single fracture in granitic cores. Three project teams have investigated this test case. Models including advection, dispersion, sorption to the fracture surface, matrix diffusion and sorption within the rock matrix were calibrated against the experimental breakthrough curves. Obtained best-fit values of the parameters determining the interaction between tracer and rock were in fair agreement with independently measured data. Models neglecting matrix diffusion and sorption within the rock matrix gave poor fits to the experimental data. These results suggest the need to include matrix diffusion and matrix sorption in the model to represent data for this test case. Furthermore, it was not possible to distinguish between hydrodynamic dispersion and channelling dispersion since equally good fits were obtained with both models. Equally good fits were also obtained with models assuming constant fracture aperture and variable fracture aperture. In the context of performance assessment of repositories in fractured rock, the major outcome from this test case is additional support for the inclusion of matrix diffusion and matrix sorption in the transport models. 17 refs., 14 figs., 3 tabs

WIPP Project Records Management Handbook

International Nuclear Information System (INIS)

1991-01-01

The Waste Isolation Pilot Plant (WIPP) Records Management Handbook provides the WIPP Project Records Management personnel with a tool to use to fulfill the requirements of the WIPP Records Program and direct their actions in the important area of records management. The handbook describes the various project areas involved in records management, and how they function. The handbook provides the requirements for Record Coordinators and Master Record Center (MRC) personnel to follow in the normal course of file management, records scheduling, records turnover, records disposition, and records retrieval. More importantly, the handbook provides a single reference which encompasses the procedures set fourth in DOE Order 1324.2A, ''Records Disposition'' ASME NQA-1, ''Quality Assurance Program Requirements for Nuclear Facilities'' and DOE-AL 5700.6B, ''General Operations Quality Assurance.'' These documents dictate how an efficient system of records management will be achieved on the WIPP Project

The biology and potential for genetic research of transposable elements in filamentous fungi

OpenAIRE

Fávaro,Léia Cecilia de Lima; Araújo,Welington Luiz de; Azevedo,João Lúcio de; Paccola-Meirelles,Luzia Doretto

2005-01-01

Recently many transposable elements have been identified and characterized in filamentous fungi, especially in species of agricultural, biotechnological and medical interest. Similar to the elements found in other eukaryotes, fungal transposons can be classified as class I elements (retrotransposons) that use RNA and reverse transcriptase and class II elements (DNA transposons) that use DNA. The changes (transposition and recombination) caused by transposons can supply wide-ranging genetic va...

CDF End Plug calorimeter Upgrade Project

International Nuclear Information System (INIS)

Apollinari, G.; de Barbaro, P.; Mishina, M.

1994-01-01

We report on the status of the CDF End Plug Upgrade Project. In this project, the CDF calorimeters in the end plug and the forward regions will be replaced by a single scintillator based calorimeter. After an extensive R ampersand D effort on the tile/fiber calorimetry, we have now advanced to a construction phase. We review the results of the R ampersand D leading to the final design of the calorimeters and the development of tooling devised for this project. The quality control program of the production of the electromagnetic and hadronic calorimeters is described. A shower maximum detector for the measurement of the shower centroid and the shower profile of electrons, γ and π 0 has been designed. Its performance requirements, R ampersand D results and mechanical design are discussed

Projection display technologies for the new millennium

Science.gov (United States)

Kahn, Frederic J.

2000-04-01

Although analog CRTs continue to enable most of the world's electronic projection displays such as US consumer rear projection televisions, discrete pixel (digital) active matrix LCD and DLP reflective mirror array projectors have rapidly created large nonconsumer markets--primarily for business. Recent advances in image quality, compactness and cost effectiveness of digital projectors have the potential to revolutionize major consumer and entertainment markets as well. Digital penetration of the mainstream consumer projection TV market will begin in the hear 2000. By 2005 digital projection HDTVs could take the major share of the consumer HDTV projection market. Digital projection is expected to dominate both the consumer HDTV and the cinema market by 2010, resulting in potential shipments for all projection markets exceeding 10 M units per year. Digital projection is improving at a rate 10X faster than analog CRT projectors and 5X faster than PDP flat panels. Continued rapid improvement of digital projection is expected due to its relative immaturity and due to the wide diversity of technological improvements being pursued. Key technology enablers are the imaging panels, light sources and micro-optics. Market shares of single panel projectors, MEMs panels, LCOS panels and low T p-Si TFT LCD panel variants are expected to increase.

Structural science using single crystal and pulse neutron scattering

International Nuclear Information System (INIS)

Noda, Yukio; Kimura, Hiroyuki; Watanabe, Masashi; Ishikawa, Yoshihisa; Tamura, Itaru; Arai, Masatoshi; Takahashi, Miwako; Ohshima, Ken-ichi; Abe, Hiroshi; Kamiyama, Takashi

2008-01-01

The application to single crystal neutron structural analysis is overviewed. Special attention is paid to the pulse neutron method, which will be available soon under J-PARC project in Japan. New proposal and preliminary experiment using Sirius at KENS are described. (author)

Bulk study of a DyNiAl single crystal

Czech Academy of Sciences Publication Activity Database

Prchal, J.; Andreev, Alexander V.; Javorský, P.; Honda, F.; Jurek, Karel

272-276, - (2004), e419-e420 ISSN 0304-8853 R&D Projects: GA ČR GA106/02/0943 Keywords : rare-earth * DyNiAl * magnetic anisotropy * single crystal Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.031, year: 2004

Using Web-Based Peer Benchmarking to Manage the Client-Based Project

Science.gov (United States)

Raska, David; Keller, Eileen Weisenbach; Shaw, Doris

2013-01-01

The complexities of integrating client-based projects into marketing courses provide challenges for the instructor but produce richness of context and active learning for the student. This paper explains the integration of Web-based peer benchmarking as a means of improving student performance on client-based projects within a single semester in…

[Thoughts on the Witnessed Audit in Medical Device Single Audit Program].

Science.gov (United States)

Wen, Jing; Xiao, Jiangyi; Wang, Aijun

2018-02-08

Medical Device Single Audit Program is one of the key projects in International Medical Device Regulators Forum, which has much experience to be used for reference. This paper briefly describes the procedures and contents of the Witnessed Audit in Medical Device Single Audit Program. Some revelations about the work of Witnessed Audit have been discussed, for reference by the Regulatory Authorities and the Auditing Organizations.

Welding and Weldability of Directionally Solidified Single Crystal Nickel-Base Superalloys

Energy Technology Data Exchange (ETDEWEB)

Vitek, J M; David, S A; Reed, R W; Burke, M A; Fitzgerald, T J

1997-09-01

Nickel-base superalloys are used extensively in high-temperature service applications, and in particular, in components of turbine engines. To improve high-temperature creep properties, these alloys are often used in the directionally-solidified or single-crystal form. The objective of this CRADA project was to investigate the weldability of both experimental and commercial nickel-base superalloys in polycrystalline, directionally-solidified, and single-crystal forms.

Project management for economical nuclear energy

International Nuclear Information System (INIS)

Majerle, P.P.

2005-01-01

The price of electricity is significantly influenced by the cost of the initial generation asset. The cost of the initial nuclear generation asset is significantly influenced by the design and construction duration. Negative variations in the cost and duration of actual design and construction have historically impacted the early relative economics of nuclear power generation. Successful management of plant design information will mitigate the risks of the design and construction of future nuclear plants. Information management tools that can model the integrated delivery of large complex projects enable the project owners to accurately evaluate project progress, as well as the economic impact of regulatory, political, or market activities not anticipated in the project execution plan. Significant differences exist in the electrical energy markets, project delivery models, and fuel availability between continents and countries. However, each market and project delivery model is challenged by the need to produce economical electrical energy. The information management system presented in this paper provides a means to capture in a single integrated computerized database the design information developed during plant design, procurement, and construction and to allow this information to be updated and retrieved in real time by all project participants. Utilization of the information management system described herein will enable diverse project teams to rapidly and reliably input, share, and retrieve power plant information, thereby supporting project management's goal to make good on its commitment to the economic promise of tomorrow's nuclear electrical power generation by achieving cost-effective construction. (authors)

Advances in DNA methylation: 5-hydroxymethylcytosine revisited

DEFF Research Database (Denmark)

Dahl, Christina; Grønbæk, Kirsten; Guldberg, Per

2011-01-01

modification involved in gene regulation, X-chromosome inactivation, genomic imprinting, long-term silencing of transposons and cancer development is well described. 5hmC, on the other hand, has only recently entered center stage when it was shown that the Ten-Eleven-Translocation (TET) family of oxygenases...... in cancer development, and developing sequencing methodologies that can accurately distinguish among cytosine, 5mC and 5hmC at single-base-pair resolution....

Implementing a Zero Energy Ready Home Multifamily Project

Energy Technology Data Exchange (ETDEWEB)

Springer, David [Alliance for Residential Building Innovation, Davis, CA (United States); German, Alea [Alliance for Residential Building Innovation, Davis, CA (United States)

2015-08-01

An objective of this project was to gain a highly visible foothold for residential buildings built to the U.S. Department of Energy's Zero Energy Ready Home (ZERH) specification that can be used to encourage participation by other California builders. This report briefly describes two single family homes that were ZERH-certified, and focuses on the experience of working with developer Mutual Housing on a 62 unit multi-family community at the Spring Lake subdivision in Woodland, CA. The Spring Lake project is expected to be the first ZERH certified multi-family project nationwide. This report discusses challenges encountered, lessons learned, and how obstacles were overcome.

Minotaur is critical for primary piRNA biogenesis.

Science.gov (United States)

Vagin, Vasily V; Yu, Yang; Jankowska, Anna; Luo, Yicheng; Wasik, Kaja A; Malone, Colin D; Harrison, Emily; Rosebrock, Adam; Wakimoto, Barbara T; Fagegaltier, Delphine; Muerdter, Felix; Hannon, Gregory J

2013-08-01

Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to silence transposon targets and, as such, form a molecular code that discriminates transposons from endogenous genes. Information ultimately carried by piRNAs is encoded within genomic loci, termed piRNA clusters. These give rise to long, single-stranded, primary transcripts that are processed into piRNAs. Despite the biological importance of this pathway, neither the characteristics that define a locus as a source of piRNAs nor the mechanisms that catalyze primary piRNA biogenesis are well understood. We searched an EMS-mutant collection annotated for fertility phenotypes for genes involved in the piRNA pathway. Twenty-seven homozygous sterile strains showed transposon-silencing defects. One of these, which strongly impacted primary piRNA biogenesis, harbored a causal mutation in CG5508, a member of the Drosophila glycerol-3-phosphate O-acetyltransferase (GPAT) family. These enzymes catalyze the first acylation step on the path to the production of phosphatidic acid (PA). Though this pointed strongly to a function for phospholipid signaling in the piRNA pathway, a mutant form of CG5508, which lacks the GPAT active site, still functions in piRNA biogenesis. We have named this new biogenesis factor Minotaur.

Minotaur is critical for primary piRNA biogenesis

Science.gov (United States)

Vagin, Vasily V.; Yu, Yang; Jankowska, Anna; Luo, Yicheng; Wasik, Kaja A.; Malone, Colin D.; Harrison, Emily; Rosebrock, Adam; Wakimoto, Barbara T.; Fagegaltier, Delphine; Muerdter, Felix; Hannon, Gregory J.

2013-01-01

Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to silence transposon targets and, as such, form a molecular code that discriminates transposons from endogenous genes. Information ultimately carried by piRNAs is encoded within genomic loci, termed piRNA clusters. These give rise to long, single-stranded, primary transcripts that are processed into piRNAs. Despite the biological importance of this pathway, neither the characteristics that define a locus as a source of piRNAs nor the mechanisms that catalyze primary piRNA biogenesis are well understood. We searched an EMS-mutant collection annotated for fertility phenotypes for genes involved in the piRNA pathway. Twenty-seven homozygous sterile strains showed transposon-silencing defects. One of these, which strongly impacted primary piRNA biogenesis, harbored a causal mutation in CG5508, a member of the Drosophila glycerol-3-phosphate O-acetyltransferase (GPAT) family. These enzymes catalyze the first acylation step on the path to the production of phosphatidic acid (PA). Though this pointed strongly to a function for phospholipid signaling in the piRNA pathway, a mutant form of CG5508, which lacks the GPAT active site, still functions in piRNA biogenesis. We have named this new biogenesis factor Minotaur. PMID:23788724

Time-constrained project scheduling with adjacent resources

NARCIS (Netherlands)

Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with adjacent resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

Time-constrained project scheduling with adjacent resources

NARCIS (Netherlands)

Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

2008-01-01

We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with Adjacent Resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

POD-Galerkin Model for Incompressible Single-Phase Flow in Porous Media

KAUST Repository

Wang, Yi; Yu, Bo; Sun, Shuyu

2017-01-01

Fast prediction modeling via proper orthogonal decomposition method combined with Galerkin projection is applied to incompressible single-phase fluid flow in porous media. Cases for different configurations of porous media, boundary conditions

PREFACE TO SPECIAL SECTION: SOUTHERN OXIDANTS STUDY 1999 ATLANTA SUPERSITE PROJECT (SOS3)

Science.gov (United States)

The Atlanta Supersites Project consisted of a one-month intensive field program to compare advanced methods for measurement of PM2.5 mass, chemical composition, including single particle composition in real-time, and aerosol precursor species. The project was the first of EPA's ...

Draft environmental impact statement - BPA/Lower Valley transmission project

International Nuclear Information System (INIS)

1997-06-01

Bonneville Power Administration and Lower Valley Power and Light, Inc., propose to solve a voltage stability problem in the Jackson and Afton, Wyoming areas. For the Agency Proposed Action, BPA and Lower Valley would construct a new 115-kV line from BPA's Swan Valley Substation near Swan Valley in Bonneville County, Idaho about 58 km (36 miles) east to BPA's Teton Substation near Jackson in Teton County, Wyoming. The new line would be next to an existing 115-kV line. Most of the line would be supported by a mix of single-circuit wood pole H-frame structures would be used. The Single-Circuit Line Alternative has all the components of the Agency Proposed Action except that the entire line would be supported by single-circuit structures. The Short Line Alternative has all the components of the Single-Circuit Line Alternative except it would then be removed. For the Static Var Compensation Alternative, BPA would install a Static Var Compensator (SVC) at Teton or Jackson Substation. An SVC is a group of electrical equipment placed at a substation to help control voltage on a transmission system. The No Action Alternative assumes that no new transmission line is built, and no other equipment is added to the transmission system. The USFS (Targhee and Bridger-Teton National Forests) must select al alternative based on their needs and objectives, decide if the project complies with currently approved forest plans, decide if special use permits or easements are needed for construction, operation, and maintenance of project facilities, and decide if they would issue special use permits and letters of consent to grant easements for the project

Project outline of high quality electron beam generation at Waseda University

Energy Technology Data Exchange (ETDEWEB)

Washio, M.; Hama, Y.; Kashiwagi, S.; Kuroda, R.; Kobuki, T. [Waseda Univ., Advanced Research Institute for Science and Engineering, Shinjuku, Tokyo (Japan); Hirose, T. [Tokyo Metropolitan Univ. (Japan). Dept. of Physics

2000-03-01

High quality electron beam generation project has been started at Waseda University under the grant of Ministry of Education, named High-Tech Research Center Project. In the project, we will install a laser photo-cathode RF Gun system with 1.6 accelerating structure cells of s-band and a stabilized RF power source. This RF Gun is expected to produce single electron bunch up to 1 or 2nC with around 10ps pulse duration. (author)

Project outline of high quality electron beam generation at Waseda University

International Nuclear Information System (INIS)

Washio, M.; Hama, Y.; Kashiwagi, S.; Kuroda, R.; Kobuki, T.; Hirose, T.

2000-01-01

High quality electron beam generation project has been started at Waseda University under the grant of Ministry of Education, named High-Tech Research Center Project. In the project, we will install a laser photo-cathode RF Gun system with 1.6 accelerating structure cells of s-band and a stabilized RF power source. This RF Gun is expected to produce single electron bunch up to 1 or 2nC with around 10ps pulse duration. (author)

77 FR 45354 - Notification of Single Source Cooperative Agreement Award for Project Hope

Science.gov (United States)

2012-07-31

... outreach activities that ensured optimal awareness, engagement and discussion by a wide audience of expert...--frequently cited in congressional testimony and the news media--and has a wide-ranging audience that includes... this award, ASPR will capitalize on Project Hope's extensive experience in producing and marketing...

Energy Renovation of Danish Single-Family Houses

DEFF Research Database (Denmark)

Mortensen, Andrea

2015-01-01

. The results show that despite the barriers the owners can in fact be motivated to perform private energy renovations. A sound project economy is all-important for this to happen and it should if possible be supported by improvements in both comfort, indoor environment and architecture to increase......The PhD project is based on requirements from the European Union to reduce the energy consumption and on current renovation needs of and a huge energy saving potential in the Danish single-family houses from the 1960’s and 1970’s. The project focuses on the barriers for energy renovations...... of these houses and on defining motivation factors for the homeowners. The barriers are many and variating in influence and studies show that both professionals and homeowners are affected. The barriers range from lack of interest and knowledge to uncertainties about among others economy and technical solutions...

Combination of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 technique with the piggybac transposon system for mouse in utero electroporation to study cortical development.

Science.gov (United States)

Cheng, Man; Jin, Xubin; Mu, Lili; Wang, Fangyu; Li, Wei; Zhong, Xiaoling; Liu, Xuan; Shen, Wenchen; Liu, Ying; Zhou, Yan

2016-09-01

In utero electroporation (IUE) is commonly used to study cortical development of cerebrum by downregulating or overexpressing genes of interest in neural progenitor cells (NPCs) of small mammals. However, exogenous plasmids are lost or diluted over time. Furthermore, gene knockdown based on short-hairpin RNAs may exert nonspecific effects that lead to aberrant neuronal migration. Genomic engineering by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has great research and therapeutic potentials. Here we integrate the CRISPR/Cas9 components into the piggyBac (PB) transposon system (the CRISPR/Cas9-PB toolkit) for cortical IUEs. The mouse Sry-related HMG box-2 (Sox2) gene was selected as the target for its application. Most transduced cortical NPCs were depleted of SOX2 protein as early as 3 days post-IUE, whereas expressions of SOX1 and PAX6 remained intact. Furthermore, both the WT Cas9 and the D10A nickase mutant Cas9n showed comparable knockout efficiency. Transduced cortical cells were purified with fluorescence-activated cell sorting, and effective gene editing at the Sox2 loci was confirmed. Thus, application of the CRISPR/Cas9-PB toolkit in IUE is a promising strategy to study gene functions in cortical NPCs and their progeny. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Modelling of glass refining kinetics-Part 1. Single bubbles

Czech Academy of Sciences Publication Activity Database

Němec, Lubomír; Kloužek, Jaroslav

2003-01-01

Roč. 47, č. 3 (2003), s. 81-87 ISSN 0862-5468 R&D Projects: GA AV ČR IBS4032103 Institutional research plan: CEZ:AV0Z4032918 Keywords : glass melt * refining * single bubble Subject RIV: CA - Inorganic Chemistry Impact factor: 0.449, year: 2003

User's operating procedures. Volume 2: Scout project financial analysis program

Science.gov (United States)

Harris, C. G.; Haris, D. K.

1985-01-01

A review is presented of the user's operating procedures for the Scout Project Automatic Data system, called SPADS. SPADS is the result of the past seven years of software development on a Prime mini-computer located at the Scout Project Office, NASA Langley Research Center, Hampton, Virginia. SPADS was developed as a single entry, multiple cross-reference data management and information retrieval system for the automation of Project office tasks, including engineering, financial, managerial, and clerical support. This volume, two (2) of three (3), provides the instructions to operate the Scout Project Financial Analysis program in data retrieval and file maintenance via the user friendly menu drivers.

Single-electron transfer living radical copolymerization of SWCNT-g-PMMA via graft from approach

Czech Academy of Sciences Publication Activity Database

Jaisankar, S. N.; Haridharan, N.; Murali, A.; Ponyrko, Sergii; Špírková, Milena; Mandal, A. B.; Matějka, Libor

2014-01-01

Roč. 55, č. 13 (2014), s. 2959-2966 ISSN 0032-3861 R&D Projects: GA ČR GAP108/12/1459 Institutional support: RVO:61389013 Keywords : single electron transfer * single-walled carbon nanotubes * controlled radical polymerization Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.562, year: 2014

Existing sustainable renovation concepts for single-family houses

DEFF Research Database (Denmark)

Tommerup, Henrik M.; Vanhoutteghem, Lies; Svendsen, Svend

2010-01-01

In the Nordic Innovation Centre Project, SuccessFamilies, the main objective is to change the business environment in order to speed up the implementation of sustainable renovation of single-family houses – proposing new service concepts that will combine both the technical solutions, financing...... with individual solutions, traditional warehouses ”do-it-yourself-shops” and some actors marketing single products. To speed up the implementation of sustainable renovation of single-family houses there is a great need for full-service packages. Existing technical renovation concepts, typically focusing...... services as well as other promoting issues to overcome the behavioural, organizational, legal and social barriers that exist in sustainable renovation. A starting point for such a change has been to get an overview of the existing sustainable renovation concepts, i.e. full-service concepts and technical...

Village microgrids: The Chile project

Energy Technology Data Exchange (ETDEWEB)

Baring-Gould, E.I.

1997-12-01

This paper describes a village application in Chile. The objective was to demonstrate the technical, economic and institutional viability of renewable energy for rural electrification, as well as to allow local partners to gain experience with hybrid/renewable technology, resource assessment, system siting and operation. A micro-grid system is viewed as a small village system, up to 1200 kWh/day load with a 50 kW peak load. It can consist of components of wind, photovoltaic, batteries, and conventional generators. It is usually associated with a single generator source, and uses batteries to cover light day time loads. This paper looks at the experiences learned from this project with regard to all of the facets of planning and installing this project.

Optimization of the Geometric Beta for the SSR2 Cavities of the Project X

International Nuclear Information System (INIS)

Solyak, N.; Vostrikov, A.; Yakovlev, V.P.; Awida, M.H.; Berrutti, P.; Gonin, I.V.

2012-01-01

Project X based on the 3 GeV CW superconducting Linac and is currently in the R and D phase. The CW SC Linac starts from a low-energy SCRF section (2.1 - 165 MeV) containing three different types of resonators. HWR f = 162.5 MHz (2.1 - 11 MeV) having beta= 0.11, SSR1 f = 325 MHz (11 - 35 MeV) having beta = 0.21. In this paper we present the analysis that lead to the final design of SSR2 f = 325 MHz cavity (35 - 165 MeV). We present the results of optimization of the geometric beta and the comparison between single, double and triple spoke resonators used in Project X frontend. A β optimization has been carried out for the last spoke cavity section of Project X front end. The optimization process of β opt for a single spoke resonator family SSR2 shown that β opt = 0.47 looks better than the previous choice, which is β opt = 0.4. This change can save some cavities and provide the same final energy for this section, 160 MeV. Single double and triple spoke resonator performances have been compared. The best option is the single spoke resonator SSR2 because the NTTF of a multi-spoke resonator is much narrower than a single one. In the energy range considered (40-160 MeV) the most efficient resonator is the single spoke one.

Why good projects fail anyway.

Science.gov (United States)

Matta, Nadim F; Ashkenas, Ronald N

2003-09-01

Big projects fail at an astonishing rate--more than half the time, by some estimates. It's not hard to understand why. Complicated long-term projects are customarily developed by a series of teams working along parallel tracks. If managers fail to anticipate everything that might fall through the cracks, those tracks will not converge successfully at the end to reach the goal. Take a companywide CRM project. Traditionally, one team might analyze customers, another select the software, a third develop training programs, and so forth. When the project's finally complete, though, it may turn out that the salespeople won't enter in the requisite data because they don't understand why they need to. This very problem has, in fact, derailed many CRM programs at major organizations. There is a way to uncover unanticipated problems while the project is still in development. The key is to inject into the overall plan a series of miniprojects, or "rapid-results initiatives," which each have as their goal a miniature version of the overall goal. In the CRM project, a single team might be charged with increasing the revenues of one sales group in one region by 25% within four months. To reach that goal, team members would have to draw on the work of all the parallel teams. But in just four months, they would discover the salespeople's resistance and probably other unforeseen issues, such as, perhaps, the need to divvy up commissions for joint-selling efforts. The World Bank has used rapid-results initiatives to great effect to keep a sweeping 16-year project on track and deliver visible results years ahead of schedule. In taking an in-depth look at this project, and others, the authors show why this approach is so effective and how the initiatives are managed in conjunction with more traditional project activities.

Relation of project managers' personality and project performance: An approach based on value stream mapping

Directory of Open Access Journals (Sweden)

Maurizio Bevilacqua

2014-09-01

Full Text Available Purpose: This work investigates the influence of project managers’ personality on the success of a project in a Multinational Corporation. The methodology proposed for analyzing the project managers’ personality is based on the Myers-Briggs Type Indicator.Design/methodology/approach: Forty projects carried out in 2012 by multinational corporation, concerning new product development (NPD, have been analyzed, comparing the profile of project managers with results obtained in terms of traditional performance indexes (time delay and over-budget of projects and performance indexes usually used in “Lean Production” sector (waste time and type of “wastes”. A detailed analysis of the most important “wastes” during the project development is carried out using the Value Stream Mapping (VSM technique.Findings and Originality/value: Relying on the Myers–Briggs personality instrument, results show that extroverted managers (as opposed to introverted managers carry out projects that show lower delay and lower waste time. Introverted managers often make “Over-processing” and “Defect” types of waste. Moreover, lower delay and over-budget have been shown by perceiving managers.Research limitations: Regarding the limitations of this work it is necessary to highlight that we collected data from project managers in a retrospective way. While we believe that several aspects of our data collection effort helped enhance the accuracy of the results, future research could conduct real-time case study research to get more detailed insights into the proposed relationships and avoid retrospective bias. Moreover we focused on a single respondent, the project manager. This helped us ensure that their interpretations played an important role in product development. But, we cannot examined the opinion of team members that could be different from project managers opinion regarding some questions.Originality/value: This research provides insight useful

Single molecule SERS: Perspectives of analytical applications

Czech Academy of Sciences Publication Activity Database

Vlčková, B.; Pavel, I.; Sládková, M.; Šišková, K.; Šlouf, Miroslav

834-836, - (2007), s. 42-47 ISSN 0022-2860. [European Congress on Molecular Spectroscopy /28./. Istanbul, 03.09.2006-08.09.2006] R&D Projects: GA ČR GA203/04/0688 Institutional research plan: CEZ:AV0Z40500505 Keywords : surface-enhanced Raman scattering (SERS) * surface-enhanced resonance Raman (SERRS) * single molecule SERS Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.486, year: 2007

Long Short-Term Memory Projection Recurrent Neural Network Architectures for Piano’s Continuous Note Recognition

Directory of Open Access Journals (Sweden)

YuKang Jia

2017-01-01

Full Text Available Long Short-Term Memory (LSTM is a kind of Recurrent Neural Networks (RNN relating to time series, which has achieved good performance in speech recogniton and image recognition. Long Short-Term Memory Projection (LSTMP is a variant of LSTM to further optimize speed and performance of LSTM by adding a projection layer. As LSTM and LSTMP have performed well in pattern recognition, in this paper, we combine them with Connectionist Temporal Classification (CTC to study piano’s continuous note recognition for robotics. Based on the Beijing Forestry University music library, we conduct experiments to show recognition rates and numbers of iterations of LSTM with a single layer, LSTMP with a single layer, and Deep LSTM (DLSTM, LSTM with multilayers. As a result, the single layer LSTMP proves performing much better than the single layer LSTM in both time and the recognition rate; that is, LSTMP has fewer parameters and therefore reduces the training time, and, moreover, benefiting from the projection layer, LSTMP has better performance, too. The best recognition rate of LSTMP is 99.8%. As for DLSTM, the recognition rate can reach 100% because of the effectiveness of the deep structure, but compared with the single layer LSTMP, DLSTM needs more training time.

The e-Learning Conceptual Framework Project. Leaflet

OpenAIRE

Sangrà Morer, Albert

2011-01-01

Aquest projecte es basa en la hipòtesi que en l'actualitat no existeix un concepte únic d'e-learning -acceptat per la majoria de la comunitat científica o, és més, pels professionals. Per tant, l'objectiu és contribuir a la consolidació i l'especificació del concepte d'e-learning tant des del punt de vista científic com des del punt de vista del camp de l'activitat educativa. This project is based on the hypothesis that currently there is no single concept of e-learning -accepted by the ma...

How and Why Do Top Managers Support or Not Support Strategic IS Projects?

NARCIS (Netherlands)

Boonstra, A.; CruzCunha, MM; Varajao, J; Powell, P; Martinho, R

2011-01-01

There is much evidence that top management support is the single most important determinant of IS project success. This is especially the case in complex and large-scale IS projects. Surprisingly however, despite its crucial importance there is only limited knowledge of the types of behaviour

A Guide to Bundling Small-scale CDM Projects

International Nuclear Information System (INIS)

Mariyappan, J.; Bhardwaj, N.; De Coninck, H.; Van der Linden, N.

2005-07-01

Small-scale renewable energy and energy efficiency projects that fit the development needs of many developing countries, can potentially be supported via the Clean Development Mechanism (CDM), one of the Kyoto Protocol's flexible mechanisms for tackling climate change. However, there is concern that due to high transaction costs, as well as many existing barriers, very few investments will be made in small-scale projects, which are often the most suitable development option in countries such as India. In view of this, the 'bundling' together of appropriate small-scale projects on a regional basis has been proposed as a way in which funding can be leveraged from international sources and transaction costs reduced. IT Power, IT Power India and the Energy research Centre of the Netherlands (ECN) are carrying out a 2-year project to establish the capacity within India to enable individual small scale projects to be bundled as a single CDM project. Overall objectives are to develop the necessary institutional capabilities to formulate and implement small scale CDM projects in India; to provide a guide on how to bundle small scale projects under the CDM in developing countries; and to raise the awareness of the potential for investment in small scale energy projects which can gain funding through the CDM

A Large Scale Problem Based Learning inter-European Student Satellite Construction Project

DEFF Research Database (Denmark)

Nielsen, Jens Frederik Dalsgaard; Alminde, Lars; Bisgaard, Morten

2006-01-01

that electronic communication technology was vital within the project. Additionally the SSETI EXPRESS project implied the following problems it didn’t fit to a standard semester - 18 months for the satellite project compared to 5/6 months for a “normal” semester project. difficulties in integrating the tasks......A LARGE SCALE PROBLEM BASED LEARNING INTER-EUROPEAN STUDENT SATELLITE CONSTRUCTION PROJECT This paper describes the pedagogical outcome of a large scale PBL experiment. ESA (European Space Agency) Education Office launched January 2004 an ambitious project: Let students from all over Europe build....... The satellite was successfully launched on October 27th 2005 (http://www.express.space.aau.dk). The project was a student driven project with student project responsibility adding at lot of international experiences and project management skills to the outcome of more traditional one semester, single group...

Energy renovation of an old single-family house

DEFF Research Database (Denmark)

Overgaard, L.L.; Tommerup, Henrik M.; Svendsen, Svend

2005-01-01

After having identified a large potential for profitable energy renovation of the existing building stock, a demonstration project was carried out in practice. This paper deals with the methods and results from the demonstration project concerning a 161 m² poorly insulated single-family house built...... saving improvements carried out in the project are “easy to carry out” and cost-beneficial measures such as cavity wall insulation, loft insulation, insulation of walls under windows and a new second window-frame with energy-saving glass. The work was carried out by professional contractors at a total......). If a conservative way of financing the building work of 157,000 DKK is assumed, the first year’s cost equals DKK 8,500 and the house owner will gain a net saving the first year of DKK 7,500....

Stochastic project networks temporal analysis, scheduling and cost minimization

CERN Document Server

Neumann, Klaus

1990-01-01

Project planning, scheduling, and control are regularly used in business and the service sector of an economy to accomplish outcomes with limited resources under critical time constraints. To aid in solving these problems, network-based planning methods have been developed that now exist in a wide variety of forms, cf. Elmaghraby (1977) and Moder et al. (1983). The so-called "classical" project networks, which are used in the network techniques CPM and PERT and which represent acyclic weighted directed graphs, are able to describe only projects whose evolution in time is uniquely specified in advance. Here every event of the project is realized exactly once during a single project execution and it is not possible to return to activities previously carried out (that is, no feedback is permitted). Many practical projects, however, do not meet those conditions. Consider, for example, a production process where some parts produced by a machine may be poorly manufactured. If an inspection shows that a part does no...

An Action Research Project to Assess Middle School Educators' Professional Development Needs in Single-Sex Classrooms

Science.gov (United States)

Simm, Lynnette Marie Gresham

2010-01-01

According to the National Association of Single-Sex Public Education (NASSPE, 2010), an increase of 540 public schools offering single-sex classrooms in the United States has occurred since 2001. Educators who understand the gender differences between boys and girls can inspire students to learn to the best of their ability; however, the problem…

Double minimum creep of single crystal Ni-base superalloys

Czech Academy of Sciences Publication Activity Database

WU, X.; Wollgramm, P.; Somsen, C.; Dlouhý, Antonín; Kostka, A.; Eggeler, G.

2016-01-01

Roč. 112, JUN (2016), s. 242-260 ISSN 1359-6454 R&D Projects: GA ČR(CZ) GA14-22834S Institutional support: RVO:68081723 Keywords : Single crystal Ni-base superalloys * Primary creep * Transmission electron microscopy * Dislocations * Stacking faults Subject RIV: JG - Metallurgy Impact factor: 5.301, year: 2016

Studsvik`s fuel R and D projects

Energy Technology Data Exchange (ETDEWEB)

Grounes, M [Studsvik Nuclearr AB, Nykoping (Sweden)

1997-08-01

The report reviews some recently performed, ongoing and planned fuel R and D projects, executed by Studsvik Nuclear AB, a subsidiary of Studsvik AB. Data from these projects are used as experimental support for fuel modelling at high burnup. Much of Studsvik Nuclear`s R and D work has been concentrated on fuel testing, which can be made in the R2 test reactor with high precision under realistic water reactor conditions. This type of work started in the early 1960s. The fuel testing projects executed at Studsvik have been organized under three different types of sponsorship: International (multilateral) fuel projects: jointly sponsored internationally on a world-wide basis, with project information remaining restricted to the project participants throughout the project`s duration and for some pre-determined time after project completion; Bilateral fuel projects: sponsored by one single organization, or a few co-operating organizations, with project information remaining restricted to the sponsor, sometimes published later; in-house R and D work: sponsored by Studsvik Nuclear. The fuel testing activities can be divided into a number of well-defined steps as follows: Base irradiation, performed in a power reactor, or in Studsvik`s R2 test reactor; power ramping and/or other in-pile measurements, performed in Studsvik`s R2 test reactor. Non-destructive testing between different phases of an experiment, performed in Studsvik`s R2 reactor pool, or in Studsvik`s Hot Cell Laboratory; destructive post-irradiation examinations, performed in Studsvik`s Hot Cell Laboratory, or in the sponsor`s hot cell laboratory. 47 refs, 2 tabs.

Research project on the thermal pollution of waters

International Nuclear Information System (INIS)

Steinlein; Becker

1977-01-01

The results of essentially completed and current research and development projects - as far as available in a short time - are explained in the present study, compared and their practicle applicability indicated. The number of publications in the literature index is split up into the single specialist fields as follows: 13% hydrodynamics (propagation caculations, models, measurements); 45% biology-chemistry (effects on micro and macro fauna of waters, on water contents, mathematical models of oxygen balance and biocenosis); 31% hydrometeorology including problems on the thermal economy of the waters as well as special thermal load calculations; 5% heat introduction into ground water; 6% others e.g. use of remote sensing for temperature measurement. The current research projects in the FRG are split up into the following single specialist fields: 16% hydromechanics; 42% biology-chemistry; 24% hydrometeorology including thermal economy; 10% use of ground water; 8% others (almost exclusively problems in connection with the use of remote sensing methods). (orig.) [de

A retrospective review of required projects in systems-based practice in a single anesthesiology residency: a 10-year experience.

Science.gov (United States)

Sakai, Tetsuro; Emerick, Trent D; Patel, Rita M

2015-09-01

The Accreditation Council for Graduate Medical Education has emphasized in its core competencies and more recently, in its Milestones Project, that residents understand the importance of systems-based practice (SBP). The objectives of the study are to evaluate the quality of residents' SBP projects and to determine the degrees that were subsequently implemented. A retrospective educational observational study. A university-based anesthesiology training institution. One hundred forty-nine anesthesiology residents in their final (postgraduate year 4) year of training who completed SBP projects for the last 10 years (2004-2013). A structured SBP course was provided for postgraduate year 4 anesthesiology residents with deadlines set such as project identification, data collection, and proposal draft. Each resident's written SBP proposal received inputs by 2 members of the department executive steering committee. The SBP projects concluded with oral presentations by each resident to the department executive steering committee, who provided overall scores. All SBP projects were categorized into 7 categories: safety initiatives, economic analysis, process analysis, policy change recommendations, education initiatives, teamwork/communication, and operating room efficiency. Evaluation scores using a Likert scale (1-9, where 9 is the best) were analyzed. The rate of implementation of project ideas within the department based on the presentations to the executive committee was examined. Of 149 projects, policy change recommendations was the most frequently chosen category (46 projects; 30.9%), followed by process analysis (36 projects; 24.2%). The overall evaluation score was 7.6 ± 0.6 (mean ± SD). A total of 53 projects (35.6%) were implemented in the department. There was no statistical difference between SBPs with implementation vs SBPs without implementation in terms of evaluation scores, year of the presentation, or categories. This SBP project has given residents the

All projects related to | Page 8 | IDRC - International Development ...

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

Improving early childhood development and well-being in refugee and other marginalized countries. Project. Early childhood development research has traditionally focused on single-intervention initiatives and non-refugee populations. Region: Kenya, Bangladesh, India, Canada, South Africa, Pakistan. Program: Maternal ...

A Constitutively Mannose-Sensitive Agglutinating Salmonella enterica subsp. enterica Serovar Typhimurium Strain, Carrying a Transposon in the Fimbrial Usher Gene stbC, Exhibits Multidrug Resistance and Flagellated Phenotypes

Directory of Open Access Journals (Sweden)

Kuan-Hsun Wu

2012-01-01

Full Text Available Static broth culture favors Salmonella enterica subsp. enterica serovar Typhimurium to produce type 1 fimbriae, while solid agar inhibits its expression. A transposon inserted in stbC, which would encode an usher for Stb fimbriae of a non-flagellar Salmonella enterica subsp. enterica serovar Typhimurium LB5010 strain, conferred it to agglutinate yeast cells on both cultures. RT-PCR revealed that the expression of the fimbrial subunit gene fimA, and fimZ, a regulatory gene of fimA, were both increased in the stbC mutant when grown on LB agar; fimW, a repressor gene of fimA, exhibited lower expression. Flagella were observed in the stbC mutant and this phenotype was correlated with the motile phenotype. Microarray data and RT-PCR indicated that the expression of three genes, motA, motB, and cheM, was enhanced in the stbC mutant. The stbC mutant was resistant to several antibiotics, consistent with the finding that expression of yhcQ and ramA was enhanced. A complementation test revealed that transforming a recombinant plasmid possessing the stbC restored the mannose-sensitive agglutination phenotype to the stbC mutant much as that in the parental Salmonella enterica subsp. enterica serovar Typhimurium LB5010 strain, indicating the possibility of an interplay of different fimbrial systems in coordinating their expression.

Superiority of triple-detector single-photon emission tomography over single- and dual-detector systems in the minimization of motion artefacts

International Nuclear Information System (INIS)

Nakajima, Kenichi; Taki, Junichi; Michigishi, Takatoshi; Tonami, Norihisa

1998-01-01

A patient motion-related artefact is one of the most important artefacts in single-photon emission tomography (SPET) imaging. This study evaluated the effect of the number and configuration of SPET detectors on motion artefacts. The following acquisition conditions were simulated based on original 360 projection images: (1) single-detector 180 rotation (S180), (2) a dual-detector rectangular (L-shaped) 180 acquisition (D180L), (3) dual-detector cameras mounted opposite each other with 360 acquisition (D360) and (4) triple-detector 360 acquisition (T360). The motion artefacts were introduced using a syringe and a myocardial phantom. Clinical cases with technetium-99m methoxyisobutylisonitrile and thallium-201 studies were analysed to confirm the validity of this phantom simulation. The effect of continuous alternate rotation acquisition and summing the projections on the reduction of motion artefacts was investigated in each model. The effect of motion depended on the number and the configuration of the SPET detectors. A 1-pixel (6.4 mm) motion in the S180, D180L and D360 models generated only slight artefacts, and a 2-pixel motion led to an apparent decrease in activity or created hot areas in the myocardium. On the other hand, a T360 rotation created few artefacts even with a 2-pixel motion of the last quarter of the projections. Despite the difference in attenuation with 201 Tl and 99m Tc, similar artefact patterns were observed with both radionuclides in selected patient model studies. Continuous alternate rotation could reduce artefacts caused by less than a 2-pixel motion. In conclusion, calculating the average of the sum of the projections of triple-detector 360 rotations with alternate rotation is the best method to minimize motion artefacts. This ''averaging'' effect of motion artefacts is a key to this simulation. (orig.)

Two-dimensional beam profiles and one-dimensional projections

Science.gov (United States)

Findlay, D. J. S.; Jones, B.; Adams, D. J.

2018-05-01

One-dimensional projections of improved two-dimensional representations of transverse profiles of particle beams are proposed for fitting to data from harp-type monitors measuring beam profiles on particle accelerators. Composite distributions, with tails smoothly matched on to a central (inverted) parabola, are shown to give noticeably better fits than single gaussian and single parabolic distributions to data from harp-type beam profile monitors all along the proton beam transport lines to the two target stations on the ISIS Spallation Neutron Source. Some implications for inferring beam current densities on the beam axis are noted.

New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library.

Science.gov (United States)

Laia, Marcelo L; Moreira, Leandro M; Dezajacomo, Juliana; Brigati, Joice B; Ferreira, Cristiano B; Ferro, Maria I T; Silva, Ana C R; Ferro, Jesus A; Oliveira, Julio C F

2009-01-16

Citrus canker is a disease caused by the phytopathogens Xanthomonas citri subsp. citri, Xanthomonas fuscans subsp. aurantifolli and Xanthomonas alfalfae subsp. citrumelonis. The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis. Through transposon insertion mutagenesis, 10,000 mutants of Xanthomonas citri subsp. citri strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime (Citrus limonia) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with Xanthomonas pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the hrpB4 and hrpX genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the htrA gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the

Fourier phase retrieval with a single mask by Douglas-Rachford algorithms.

Science.gov (United States)

Chen, Pengwen; Fannjiang, Albert

2018-05-01

The Fourier-domain Douglas-Rachford (FDR) algorithm is analyzed for phase retrieval with a single random mask. Since the uniqueness of phase retrieval solution requires more than a single oversampled coded diffraction pattern, the extra information is imposed in either of the following forms: 1) the sector condition on the object; 2) another oversampled diffraction pattern, coded or uncoded. For both settings, the uniqueness of projected fixed point is proved and for setting 2) the local, geometric convergence is derived with a rate given by a spectral gap condition. Numerical experiments demonstrate global, power-law convergence of FDR from arbitrary initialization for both settings as well as for 3 or more coded diffraction patterns without oversampling. In practice, the geometric convergence can be recovered from the power-law regime by a simple projection trick, resulting in highly accurate reconstruction from generic initialization.

The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome.

Science.gov (United States)

Cook, R Kimberley; Christensen, Stacey J; Deal, Jennifer A; Coburn, Rachel A; Deal, Megan E; Gresens, Jill M; Kaufman, Thomas C; Cook, Kevin R

2012-01-01

Chromosomal deletions are used extensively in Drosophila melanogaster genetics research. Deletion mapping is the primary method used for fine-scale gene localization. Effective and efficient deletion mapping requires both extensive genomic coverage and a high density of molecularly defined breakpoints across the genome. A large-scale resource development project at the Bloomington Drosophila Stock Center has improved the choice of deletions beyond that provided by previous projects. FLP-mediated recombination between FRT-bearing transposon insertions was used to generate deletions, because it is efficient and provides single-nucleotide resolution in planning deletion screens. The 793 deletions generated pushed coverage of the euchromatic genome to 98.4%. Gaps in coverage contain haplolethal and haplosterile genes, but the sizes of these gaps were minimized by flanking these genes as closely as possible with deletions. In improving coverage, a complete inventory of haplolethal and haplosterile genes was generated and extensive information on other haploinsufficient genes was compiled. To aid mapping experiments, a subset of deletions was organized into a Deficiency Kit to provide maximal coverage efficiently. To improve the resolution of deletion mapping, screens were planned to distribute deletion breakpoints evenly across the genome. The median chromosomal interval between breakpoints now contains only nine genes and 377 intervals contain only single genes. Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism. The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers.

Stripa Project - Summary of defined programs

International Nuclear Information System (INIS)

Carlsson, L.; Olsson, T.; Pusch, R.

1980-11-01

An international cooperation project, the Stripa Project, in the field of nuclear waste management has been established as an autonomous OECH/NEA project. The management of the project has been entrusted to the Divsion Nuclear Fuel Safety (KBS) of the Swedish Nuclear Fuel Supply Company (SKBF). Technical input and contribution of funds are given by the following countries: Canada, Finland, Japan, Sweden, Switzerland and the United States. The report summarizes the programs for investigations funded at this stage. A number of investigations of a geophysical, geochemical and hydraulic nature will be carried out in the boreholes and the drill cores will be mapped and analysed. Another experiment is with various tracers which represent all important types of radionuclides and will be introduced in the naturally flowing water in a single fissure in granite. The experiment will show how well sorption data from the laboratory can be used to predict radionuclide migration in the field with real surfaces and waters. The third project aims at the verification of the suitability of the buffer materials at real conditions on site. Highly compacted bentonite and mixtures of bentonite and quartz sand are proposed as buffer materials in final repositories for high-level radioactive wastes. (GB)

Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality.

Science.gov (United States)

Liberati, Nicole T; Urbach, Jonathan M; Thurber, Tara K; Wu, Gang; Ausubel, Frederick M

2008-01-01

Putative essential genes can be identified by comparing orthologs not disrupted in multiple near-saturated transposon insertion mutation libraries in related strains of the same bacterial species. Methods for identifying all orthologs between two bacterial strains and putative essential orthologs are described. In addition, protocols detailing near-saturation transposon insertion mutagenesis of bacteria are presented, including (1) conjugation-mediated mutagenesis, (2) automated colony picking and liquid handling of mutant cultures, and (3) arbitrary polymerase chain reaction amplification and sequencing of genomic DNA adjacent to transposon insertion sites.

“REPRESENTATION, PROJECTION AND COCHLEAR IMPLANT: A SINGLE CASE STUDY”

Directory of Open Access Journals (Sweden)

Carmela Mento

2014-06-01

Full Text Available From the psychological point of view hearing is an essential sensory modality for the human species, because it contributes to the formation of the first relational connections and emotions. It is important to make a diagnosis early to intervene and limit negative effects.  Deafness is a particular phenomenon (onset, types,  in this paper we undertake a thorough descriptive analysis on all aspects of deafness, in particular the use of a prosthetic device known as cochlear implant.  We have deepened personality variables in a single case with the use of Rorschach Test and Draw-a-person-Test.  We aimed to study, with the clinical interpretation of instruments, which personality variables could be involved in hearing loss condition and Cochlear Implant (CI.  This observational study highlights the psychological dynamics that should be taken into account by operators team, in order to improve the quality of life of these patients and increase their long-term therapeutic outcome.

Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation.

Science.gov (United States)

Thorne, James H; Girvetz, Evan H; McCoy, Michael C

2009-05-01

This study presents a GIS-based database framework used to assess aggregate terrestrial habitat impacts from multiple highway construction projects in California, USA. Transportation planners need such impact assessment tools to effectively address additive biological mitigation obligations. Such assessments can reduce costly delays due to protracted environmental review. This project incorporated the best available statewide natural resource data into early project planning and preliminary environmental assessments for single and multiple highway construction projects, and provides an assessment of the 10-year state-wide mitigation obligations for the California Department of Transportation. Incorporation of these assessments will facilitate early and more strategic identification of mitigation opportunities, for single-project and regional mitigation efforts. The data architecture format uses eight spatial scales: six nested watersheds, counties, and transportation planning districts, which were intersected. This resulted in 8058 map planning units statewide, which were used to summarize all subsequent analyses. Range maps and georeferenced locations of federally and state-listed plants and animals and a 55-class landcover map were spatially intersected with the planning units and the buffered spatial footprint of 967 funded projects. Projected impacts were summarized and output to the database. Queries written in the database can sum expected impacts and provide summaries by individual construction project, or by watershed, county, transportation district or highway. The data architecture allows easy incorporation of new information and results in a tool usable without GIS by a wide variety of agency biologists and planners. The data architecture format would be useful for other types of regional planning.

Evaluating Aggregate Terrestrial Impacts of Road Construction Projects for Advanced Regional Mitigation

Science.gov (United States)

Thorne, James H.; Girvetz, Evan H.; McCoy, Michael C.

2009-05-01

This study presents a GIS-based database framework used to assess aggregate terrestrial habitat impacts from multiple highway construction projects in California, USA. Transportation planners need such impact assessment tools to effectively address additive biological mitigation obligations. Such assessments can reduce costly delays due to protracted environmental review. This project incorporated the best available statewide natural resource data into early project planning and preliminary environmental assessments for single and multiple highway construction projects, and provides an assessment of the 10-year state-wide mitigation obligations for the California Department of Transportation. Incorporation of these assessments will facilitate early and more strategic identification of mitigation opportunities, for single-project and regional mitigation efforts. The data architecture format uses eight spatial scales: six nested watersheds, counties, and transportation planning districts, which were intersected. This resulted in 8058 map planning units statewide, which were used to summarize all subsequent analyses. Range maps and georeferenced locations of federally and state-listed plants and animals and a 55-class landcover map were spatially intersected with the planning units and the buffered spatial footprint of 967 funded projects. Projected impacts were summarized and output to the database. Queries written in the database can sum expected impacts and provide summaries by individual construction project, or by watershed, county, transportation district or highway. The data architecture allows easy incorporation of new information and results in a tool usable without GIS by a wide variety of agency biologists and planners. The data architecture format would be useful for other types of regional planning.

78 FR 41070 - Notice of Single-Case Deviation from Competition Requirements: Transfer of Grantee Request for...

Science.gov (United States)

2013-07-09

... Single-Case Deviation from Competition Requirements: Transfer of Grantee Request for the Detroit Healthy... Health and Human Services (HHS). ACTION: Notice of Single-Case Deviation from Competition Requirements... pregnancy and interconceptional phases for women and infants residing in the proposed project area. In order...

Temperature-dependent particle-number projected moment of inertia

International Nuclear Information System (INIS)

Allal, N. H.; Fellah, M.; Benhamouda, N.; Oudih, M. R.

2008-01-01

Expressions of the parallel and perpendicular temperature-dependent particle-number projected nuclear moment of inertia have been established by means of a discrete projection method. They generalize that of the FTBCS method and are well adapted to numerical computation. The effects of particle-number fluctuations have been numerically studied for some even-even actinide nuclei by using the single-particle energies and eigenstates of a deformed Woods-Saxon mean field. It has been shown that the parallel moment of inertia is practically not modified by the use of the projection method. In contrast, the discrepancy between the projected and FTBCS perpendicular moment of inertia values may reach 5%. Moreover, the particle-number fluctuation effects vary not only as a function of the temperature but also as a function of the deformation for a given temperature. This is not the case for the system energy

Radiation exposure modeling and project schedule visualization

International Nuclear Information System (INIS)

Jaquish, W.R.; Enderlin, V.R.

1995-10-01

This paper discusses two applications using IGRIP (Interactive Graphical Robot Instruction Program) to assist environmental remediation efforts at the Department of Energy (DOE) Hanford Site. In the first application, IGRIP is used to calculate the estimated radiation exposure to workers conducting tasks in radiation environments. In the second, IGRIP is used as a configuration management tool to detect interferences between equipment and personnel work areas for multiple projects occurring simultaneously in one area. Both of these applications have the capability to reduce environmental remediation costs by reducing personnel radiation exposure and by providing a method to effectively manage multiple projects in a single facility

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

Directory of Open Access Journals (Sweden)

Li Xianchun

2007-03-01

Full Text Available Abstract Background Transposons, i.e. transposable elements (TEs, are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search. Results Twelve novel transposons, including LINEs (long interspersed nuclear elements, SINEs (short interspersed nuclear elements, MITEs (miniature inverted-repeat transposable elements, one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1 implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1 involved in ecdysone biosynthesis and developmental regulation are free of TE insertions. Conclusion These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes.

A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries.

Directory of Open Access Journals (Sweden)

David Skurnik

Full Text Available High-throughput sequencing of transposon (Tn libraries created within entire genomes identifies and quantifies the contribution of individual genes and operons to the fitness of organisms in different environments. We used insertion-sequencing (INSeq to analyze the contribution to fitness of all non-essential genes in the chromosome of Pseudomonas aeruginosa strain PA14 based on a library of ∼300,000 individual Tn insertions. In vitro growth in LB provided a baseline for comparison with the survival of the Tn insertion strains following 6 days of colonization of the murine gastrointestinal tract as well as a comparison with Tn-inserts subsequently able to systemically disseminate to the spleen following induction of neutropenia. Sequencing was performed following DNA extraction from the recovered bacteria, digestion with the MmeI restriction enzyme that hydrolyzes DNA 16 bp away from the end of the Tn insert, and fractionation into oligonucleotides of 1,200-1,500 bp that were prepared for high-throughput sequencing. Changes in frequency of Tn inserts into the P. aeruginosa genome were used to quantify in vivo fitness resulting from loss of a gene. 636 genes had <10 sequencing reads in LB, thus defined as unable to grow in this medium. During in vivo infection there were major losses of strains with Tn inserts in almost all known virulence factors, as well as respiration, energy utilization, ion pumps, nutritional genes and prophages. Many new candidates for virulence factors were also identified. There were consistent changes in the recovery of Tn inserts in genes within most operons and Tn insertions into some genes enhanced in vivo fitness. Strikingly, 90% of the non-essential genes were required for in vivo survival following systemic dissemination during neutropenia. These experiments resulted in the identification of the P. aeruginosa strain PA14 genes necessary for optimal survival in the mucosal and systemic environments of a mammalian

Single-layer Ultralight, Flexible, Shielding Tension Shell System for Extreme Heat and Radiation

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this project is to develop a flexible thermal protection system (FTPS) with a Boron Nitride Nanotube (BNNT)-based single-layer, lightweight,...

RPERT: Repetitive-Projects Evaluation and Review Technique

Directory of Open Access Journals (Sweden)

Remon Fayek Aziz

2014-03-01

Full Text Available Estimating expected completion probability of any repetitive construction project with a specified/certain duration including repetitive identical activities by using program evaluation and review technique is the most essential part in construction areas since the activities were had optimistic, most likely and pessimistic durations. This paper focuses on the calculation of expected completion probability of any repetitive construction project within a specified/certain duration (contract duration by using Line Of Balance technique (LOB in case of single or multiple number of crews integrated with Program Evaluation and Review Technique (PERT. Repetitive-Projects Evaluation and Review Technique (RPERT, which is a simplified software, will generate the expected project completion probability of a specified/certain duration (contract duration. RPERT software is designed by java programming code system to provide a number of new and unique capabilities, including: (1 Viewing the expected project completion probability according to a set of specified durations per each identical activity (optimistic time, most likely time, and pessimistic time in the analyzed project; (2 Providing seamless integration with available project time calculations. In order to provide the aforementioned capabilities of RPERT, the system is implemented and developed in four main modules: (1 A user interface module; (2 A database module; (3 A running module; and (4 A processing module. At the end, an illustrative example will be presented to demonstrate and verify the applications of proposed software (RPERT, by using probabilistic calculations for repetitive construction projects.

Single-Family Energy Auditor Job Task Analysis

Energy Technology Data Exchange (ETDEWEB)

Head, Heather R [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Kurnik, Charles W [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2018-05-02

The National Renewable Energy Laboratory (NREL) is contracted by the U.S. Department of Energy (DOE) Weatherization Assistance Program (WAP) to develop and maintain the resources under the Guidelines for Home Energy Professionals (GHEP) project. As part of the GHEP strategy to increase the quality of work conducted for single-family, residential energy-efficiency retrofits, the Home Energy Professionals Job Task Analysis are used as the foundation for quality training programs and trainers.

76 FR 75543 - Castle Creek Hydroelectric Project; Notice of Preliminary Permit Application Accepted for Filing...

Science.gov (United States)

2011-12-02

... Hydroelectric Project; Notice of Preliminary Permit Application Accepted for Filing and Soliciting Comments... (FPA), proposing to study the feasibility of the Castle Creek Hydroelectric Project to be located on... be located adjacent to the original hydroelectric plant, with a single shaft Pelton turbine...

Magnetic properties of a hydrogenation-extracted UCoSn single crystal

Czech Academy of Sciences Publication Activity Database

Kolomiets, A.; Andreev, Alexander V.; Havela, L.

2009-01-01

Roč. 471, 1-2 (2009), s. 21-23 ISSN 0925-8388 R&D Projects: GA MŠk OC 144 Institutional research plan: CEZ:AV0Z10100520 Keywords : uranium intermetallics * single crystal * ferromagnetism * hydrides Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.135, year: 2009

Expression of the gene cluster associated with the Escherichia coli pilus adhesin K99.

OpenAIRE

Lee, J H; Isaacson, R E

1995-01-01

The biogenesis of the pilus adhesin K99 is dependent on the expression of eight contiguous genes, fanA to fanH. Transposon mutants were prepared by using TnlacZ and TnphoA, and selected transposon mutants were used to measure expression of each K99 gene. Expression of the K99 genes is likely controlled at the transcription level, since in general, there were no differences between the results obtained with the two transposons. fanC was the most highly expressed, and fanD was expressed at very...

Insertional inactivation of a chromosomal locus that modulates expression of potential virulence determinants in Staphylococcus aureus.

OpenAIRE

Cheung, A L; Wolz, C; Yeaman, M R; Bayer, A S

1995-01-01

A single insertion of transposon Tn551 into a unique chromosomal locus of Staphylococcus aureus ISP479C has resulted in a pleiotropic effect on the expression of both extracellular and cell wall proteins. In particular, the expression of cell wall protein A and clumping activity with fibrinogen were rendered undetectable in the mutant 1E3 compared with the parent. The secretion of alpha-hemolysin in mutant 1E3 was modestly increased. Southern blot and phenotypic analyses indicated that this l...

Evaluation of Human Adipose Tissue Stromal Heterogeneity in Metabolic Disease Using Single Cell RNA-Seq

Science.gov (United States)

2017-09-01

AWARD NUMBER: W81XWH-15-1-0251 TITLE: “Evaluation of Human Adipose Tissue Stromal Heterogeneity in Metabolic Disease Using Single Cell RNA...Heterogeneity in Metabolic Disease Using Single- Cell RNA-Seq 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Linus Tzu-Yen...ABSTRACT We have developed a robust protocol to generate single cell transcriptional profiles from subcutaneous adipose tissue samples of both human

Notes on nonlocal projective measurements in relativistic systems

International Nuclear Information System (INIS)

Lin, Shih-Yuin

2014-01-01

In quantum mechanical bipartite systems, naive extensions of von Neumann’s projective measurement to nonlocal variables can produce superluminal signals and thus violate causality. We analyze the projective quantum nondemolition state-verification in a two-spin system and see how the projection introduces nonlocality without entanglement. For the ideal measurements of “R-nonlocal” variables, we argue that causality violation can be resolved by introducing further restrictions on the post-measurement states, which makes the measurement “Q-nonlocal”. After we generalize these ideas to quantum mechanical harmonic oscillators, we look into the projective measurements of the particle number of a single mode or a wave-packet of a relativistic quantum field in Minkowski space. It turns out that the causality-violating terms in the expectation values of the local operators, generated either by the ideal measurement of the “R-nonlocal” variable or the quantum nondemolition verification of a Fock state, are all suppressed by the IR and UV cutoffs of the theory. Thus relativistic quantum field theories with such projective measurements are effectively causal

Single-Event Effects in Silicon Carbide Power Devices

Science.gov (United States)

Lauenstein, Jean-Marie; Casey, Megan C.; LaBel, Kenneth A.; Ikpe, Stanley; Topper, Alyson D.; Wilcox, Edward P.; Kim, Hak; Phan, Anthony M.

2015-01-01

This report summarizes the NASA Electronic Parts and Packaging Program Silicon Carbide Power Device Subtask efforts in FY15. Benefits of SiC are described and example NASA Programs and Projects desiring this technology are given. The current status of the radiation tolerance of silicon carbide power devices is given and paths forward in the effort to develop heavy-ion single-event effect hardened devices indicated.

Optimized image acquisition for breast tomosynthesis in projection and reconstruction space

International Nuclear Information System (INIS)

Chawla, Amarpreet S.; Lo, Joseph Y.; Baker, Jay A.; Samei, Ehsan

2009-01-01

Breast tomosynthesis has been an exciting new development in the field of breast imaging. While the diagnostic improvement via tomosynthesis is notable, the full potential of tomosynthesis has not yet been realized. This may be attributed to the dependency of the diagnostic quality of tomosynthesis on multiple variables, each of which needs to be optimized. Those include dose, number of angular projections, and the total angular span of those projections. In this study, the authors investigated the effects of these acquisition parameters on the overall diagnostic image quality of breast tomosynthesis in both the projection and reconstruction space. Five mastectomy specimens were imaged using a prototype tomosynthesis system. 25 angular projections of each specimen were acquired at 6.2 times typical single-view clinical dose level. Images at lower dose levels were then simulated using a noise modification routine. Each projection image was supplemented with 84 simulated 3 mm 3D lesions embedded at the center of 84 nonoverlapping ROIs. The projection images were then reconstructed using a filtered backprojection algorithm at different combinations of acquisition parameters to investigate which of the many possible combinations maximizes the performance. Performance was evaluated in terms of a Laguerre-Gauss channelized Hotelling observer model-based measure of lesion detectability. The analysis was also performed without reconstruction by combining the model results from projection images using Bayesian decision fusion algorithm. The effect of acquisition parameters on projection images and reconstructed slices were then compared to derive an optimization rule for tomosynthesis. The results indicated that projection images yield comparable but higher performance than reconstructed images. Both modes, however, offered similar trends: Performance improved with an increase in the total acquisition dose level and the angular span. Using a constant dose level and angular

Project management plan for Project W-320, Tank 241-C-106 sluicing. Revision 2

Energy Technology Data Exchange (ETDEWEB)

Phillips, D.R.

1994-07-01

A major mission of the US Department of Energy (DOE) is the permanent disposal of Hanford Site defense wastes by utilizing safe, environmentally acceptable, and cost-effective disposal methods that meet applicable regulations. The Tank Waste Remediation System (TWRS) Program was established at the Hanford Site to manage and control activities specific to the remediation of safety watch list tanks, including high-heat-producing tanks, and for the ultimate characterization, retrieval, pretreatment, and disposal of the low- and high-level fractions of the tank waste. Project W-320, Tank 241-C-106 Sluicing, provides the methodology, equipment, utilities, and facilities necessary for retrieving the high-heat waste from single-shell tank (SST) 24-C-106. Project W-320 is a fiscal year (FY) 1993 expense-funded major project, and has a design life of 2 years. Retrieval of the waste in tank 241-C-106 will be accomplished through mobilization of the sludge into a pumpable slurry using past-practice sluicing. The waste is then transferred directly to a double-shell tank for interim storage, subsequent pretreatment, and eventual disposal. A detailed description of the management organization and responsibilities of all participants is presented in this document.

Project management plan for Project W-320, Tank 241-C-106 sluicing. Revision 2

International Nuclear Information System (INIS)

Phillips, D.R.

1994-07-01

A major mission of the US Department of Energy (DOE) is the permanent disposal of Hanford Site defense wastes by utilizing safe, environmentally acceptable, and cost-effective disposal methods that meet applicable regulations. The Tank Waste Remediation System (TWRS) Program was established at the Hanford Site to manage and control activities specific to the remediation of safety watch list tanks, including high-heat-producing tanks, and for the ultimate characterization, retrieval, pretreatment, and disposal of the low- and high-level fractions of the tank waste. Project W-320, Tank 241-C-106 Sluicing, provides the methodology, equipment, utilities, and facilities necessary for retrieving the high-heat waste from single-shell tank (SST) 24-C-106. Project W-320 is a fiscal year (FY) 1993 expense-funded major project, and has a design life of 2 years. Retrieval of the waste in tank 241-C-106 will be accomplished through mobilization of the sludge into a pumpable slurry using past-practice sluicing. The waste is then transferred directly to a double-shell tank for interim storage, subsequent pretreatment, and eventual disposal. A detailed description of the management organization and responsibilities of all participants is presented in this document

Single-photon emission computed tomography

International Nuclear Information System (INIS)

Budinger, T.F.

1986-01-01

Single photon tomography dates from the early 1960's when the idea of emission transverse section tomography was presented by Kuhl and Edwards. They used a rectilinear scanner and analogue back-projection methods to detect emissions from a series of sequential positions transverse to the cephaldcaudad axis of the body. This chapter presents an explanation of emission tomography by describing longitudinal and transverse section tomography. In principle all modes of tomography can be considered under the general topic of coded apertures wherein the code ranges from translation of a pinhole collimator to rotation of a parallel hole or focused collimator array

GenBank blastx search result: AK242295 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastx search result: AK241352 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastn search result: AK241152 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastx search result: AK241749 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastx search result: AK241418 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastx search result: AK241200 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

GenBank blastx search result: AK240882 [KOME

Lifescience Database Archive (English)

Full Text Available e cds; transposons Ophelia2, Angela3s, and XJ3, complete sequence; LRR protein WM1.3 (WM1.3) gene, complete cds; Stowaway... MITE, transposons XJ1, Jody, Angela, and XJ and Stowaway MITE, comp

Single-shot color fringe projection for three-dimensional shape measurement of objects with discontinuities.

Science.gov (United States)

Dai, Meiling; Yang, Fujun; He, Xiaoyuan

2012-04-20

A simple but effective fringe projection profilometry is proposed to measure 3D shape by using one snapshot color sinusoidal fringe pattern. One color fringe pattern encoded with a sinusoidal fringe (as red component) and one uniform intensity pattern (as blue component) is projected by a digital video projector, and the deformed fringe pattern is recorded by a color CCD camera. The captured color fringe pattern is separated into its RGB components and division operation is applied to red and blue channels to reduce the variable reflection intensity. Shape information of the tested object is decoded by applying an arcsine algorithm on the normalized fringe pattern with subpixel resolution. In the case of fringe discontinuities caused by height steps, or spatially isolated surfaces, the separated blue component is binarized and used for correcting the phase demodulation. A simple and robust method is also introduced to compensate for nonlinear intensity response of the digital video projector. The experimental results demonstrate the validity of the proposed method.

Optimization of the crystallizability of a single-chain antibody fragment

Czech Academy of Sciences Publication Activity Database

Škerlová, Jana; Král, Vlastimil; Fábry, Milan; Sedláček, Juraj; Veverka, Václav; Řezáčová, Pavlína

2014-01-01

Roč. 70, č. 12 (2014), s. 1701-1706 ISSN 1744-3091 R&D Projects: GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : single-chain antibody fragment * Thermofluor assay * differential scanning fluorimetry * crystallizability optimization * oligomerization * crystallization Subject RIV: CE - Biochemistry Impact factor: 0.527, year: 2014

Comparing genetic variants detected in the 1000 genomes project ...

Indian Academy of Sciences (India)

Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide ...

Single pin BWR benchmark problem for coupled Monte Carlo - Thermal hydraulics analysis

International Nuclear Information System (INIS)

Ivanov, A.; Sanchez, V.; Hoogenboom, J. E.

2012-01-01

As part of the European NURISP research project, a single pin BWR benchmark problem was defined. The aim of this initiative is to test the coupling strategies between Monte Carlo and subchannel codes developed by different project participants. In this paper the results obtained by the Delft Univ. of Technology and Karlsruhe Inst. of Technology will be presented. The benchmark problem was simulated with the following coupled codes: TRIPOLI-SUBCHANFLOW, MCNP-FLICA, MCNP-SUBCHANFLOW, and KENO-SUBCHANFLOW. (authors)

Single pin BWR benchmark problem for coupled Monte Carlo - Thermal hydraulics analysis

Energy Technology Data Exchange (ETDEWEB)

Ivanov, A.; Sanchez, V. [Karlsruhe Inst. of Technology, Inst. for Neutron Physics and Reactor Technology, Herman-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Hoogenboom, J. E. [Delft Univ. of Technology, Faculty of Applied Sciences, Mekelweg 15, 2629 JB Delft (Netherlands)

2012-07-01

As part of the European NURISP research project, a single pin BWR benchmark problem was defined. The aim of this initiative is to test the coupling strategies between Monte Carlo and subchannel codes developed by different project participants. In this paper the results obtained by the Delft Univ. of Technology and Karlsruhe Inst. of Technology will be presented. The benchmark problem was simulated with the following coupled codes: TRIPOLI-SUBCHANFLOW, MCNP-FLICA, MCNP-SUBCHANFLOW, and KENO-SUBCHANFLOW. (authors)

Overview of Hanford Single Shell Tank (SST) Structural Integrity

Energy Technology Data Exchange (ETDEWEB)

Rast, Richard S.; Washenfelder, Dennis J.; Johnson, Jeremy M.

2013-11-14

To improve the understanding of the single-shell tanks (SSTs) integrity, Washington River Protection Solutions, LLC (WRPS), the USDOE Hanford Site tank contractor, developed an enhanced Single-Shell Tank Integrity Project (SSTIP) in 2009. An expert panel on SST integrity, consisting of various subject matters experts in industry and academia, was created to provide recommendations supporting the development of the project. This panel developed 33 recommendations in four main areas of interest: structural integrity, liner degradation, leak integrity and prevention, and mitigation of contamination migration, Seventeen of these recommendations were used to develop the basis for the M-45-10-1 Change Package for the Hanford Federal Agreement and Compliance Order, which is also known as the Tri-Party Agreement. The structural integrity of the tanks is a key element in completing the cleanup mission at the Hanford Site. There are eight primary recommendations related to the structural integrity of Hanford Single-Shell Tanks. Six recommendations are being implemented through current and planned activities. The structural integrity of the Hanford is being evaluated through analysis, monitoring, inspection, materials testing, and construction document review. Structural evaluation in the form of analysis is performed using modern finite element models generated in ANSYS. The analyses consider in-situ, thermal, operating loads and natural phenomena such as earthquakes. Structural analysis of 108 of 149 Hanford Single-Shell Tanks has concluded that the tanks are structurally sound and meet current industry standards. Analysis of the remaining Hanford Single-Shell Tanks is scheduled for FY2014. Hanford Single-Shell Tanks are monitored through a dome deflection program. The program looks for deflections of the tank dome greater than 1/4 inch. No such deflections have been recorded. The tanks are also subjected to visual inspection. Digital cameras record the interior surface of

Overview of Hanford Single Shell Tank (SST) Structural Integrity

International Nuclear Information System (INIS)

Rast, Richard S.; Washenfelder, Dennis J.; Johnson, Jeremy M.

2013-01-01

To improve the understanding of the single-shell tanks (SSTs) integrity, Washington River Protection Solutions, LLC (WRPS), the USDOE Hanford Site tank contractor, developed an enhanced Single-Shell Tank Integrity Project (SSTIP) in 2009. An expert panel on SST integrity, consisting of various subject matters experts in industry and academia, was created to provide recommendations supporting the development of the project. This panel developed 33 recommendations in four main areas of interest: structural integrity, liner degradation, leak integrity and prevention, and mitigation of contamination migration, Seventeen of these recommendations were used to develop the basis for the M-45-10-1 Change Package for the Hanford Federal Agreement and Compliance Order, which is also known as the Tri-Party Agreement. The structural integrity of the tanks is a key element in completing the cleanup mission at the Hanford Site. There are eight primary recommendations related to the structural integrity of Hanford Single-Shell Tanks. Six recommendations are being implemented through current and planned activities. The structural integrity of the Hanford is being evaluated through analysis, monitoring, inspection, materials testing, and construction document review. Structural evaluation in the form of analysis is performed using modern finite element models generated in ANSYS. The analyses consider in-situ, thermal, operating loads and natural phenomena such as earthquakes. Structural analysis of 108 of 149 Hanford Single-Shell Tanks has concluded that the tanks are structurally sound and meet current industry standards. Analysis of the remaining Hanford Single-Shell Tanks is scheduled for FY2014. Hanford Single-Shell Tanks are monitored through a dome deflection program. The program looks for deflections of the tank dome greater than 1/4 inch. No such deflections have been recorded. The tanks are also subjected to visual inspection. Digital cameras record the interior surface of

The average carbon-stock approach for small-scale CDM AR projects

Energy Technology Data Exchange (ETDEWEB)

Garcia Quijano, J.F.; Muys, B. [Katholieke Universiteit Leuven, Laboratory for Forest, Nature and Landscape Research, Leuven (Belgium); Schlamadinger, B. [Joanneum Research Forschungsgesellschaft mbH, Institute for Energy Research, Graz (Austria); Emmer, I. [Face Foundation, Arnhem (Netherlands); Somogyi, Z. [Forest Research Institute, Budapest (Hungary); Bird, D.N. [Woodrising Consulting Inc., Belfountain, Ontario (Canada)

2004-06-15

In many afforestation and reforestation (AR) projects harvesting with stand regeneration forms an integral part of the silvicultural system and satisfies local timber and/or fuelwood demand. Especially clear-cut harvesting will lead to an abrupt and significant reduction of carbon stocks. The smaller the project, the more significant the fluctuations of the carbon stocks may be. In the extreme case a small-scale project could consist of a single forest stand. In such case, all accounted carbon may be removed during a harvesting operation and the time-path of carbon stocks will typically look as in the hypothetical example presented in the report. For the aggregate of many such small-scale projects there will be a constant benefit to the atmosphere during the projects, due to averaging effects.

Final report on LDRD project : single-photon-sensitive imaging detector arrays at 1600 nm

International Nuclear Information System (INIS)

Childs, Kenton David; Serkland, Darwin Keith; Geib, Kent Martin; Hawkins, Samuel D.; Carroll, Malcolm S.; Klem, John Frederick; Sheng, Josephine Juin-Jye; Patel, Rupal K.; Bolles, Desta; Bauer, Tom M.; Koudelka, Robert

2006-01-01

uncertainty existed about the quantum efficiency at 1550 nm the necessary operating temperature. This project has resulted in several conclusions after fabrication and measurement of the proposed structures. We have successfully demonstrated the Ge/Si proof-of-concept in producing high analog gain in a silicon region while absorbing in a Ge region. This has included significant Ge processing infrastructure development at Sandia. However, sensitivity is limited at low temperatures due to high dark currents that we ascribe to tunneling. This leaves remaining uncertainty about whether this structure can achieve the desired performance with further development. GM detection in InGaAs/InAlAs, Ge/Si, Si and pure Ge devices fabricated at Sandia was shown to overcome gain noise challenges, which represents critical learning that will enable Sandia to respond to future single photon detection needs. However, challenges to the operation of these devices in GM remain. The InAlAs multiplication region was not found to be significantly superior to current InP regions for GM, however, improved multiplication region design of InGaAs/InP APDs has been highlighted. For Ge GM detectors it still remains unclear whether an optimal trade-off of parameters can achieve the necessary sensitivity at 1550 nm. To further examine these remaining questions, as well as other application spaces for these technologies, funding for an Intelligence Community post-doc was awarded this year

Final report on LDRD project : single-photon-sensitive imaging detector arrays at 1600 nm.

Energy Technology Data Exchange (ETDEWEB)

Childs, Kenton David; Serkland, Darwin Keith; Geib, Kent Martin; Hawkins, Samuel D.; Carroll, Malcolm S.; Klem, John Frederick; Sheng, Josephine Juin-Jye; Patel, Rupal K.; Bolles, Desta; Bauer, Tom M.; Koudelka, Robert

2006-11-01

uncertainty existed about the quantum efficiency at 1550 nm the necessary operating temperature. This project has resulted in several conclusions after fabrication and measurement of the proposed structures. We have successfully demonstrated the Ge/Si proof-of-concept in producing high analog gain in a silicon region while absorbing in a Ge region. This has included significant Ge processing infrastructure development at Sandia. However, sensitivity is limited at low temperatures due to high dark currents that we ascribe to tunneling. This leaves remaining uncertainty about whether this structure can achieve the desired performance with further development. GM detection in InGaAs/InAlAs, Ge/Si, Si and pure Ge devices fabricated at Sandia was shown to overcome gain noise challenges, which represents critical learning that will enable Sandia to respond to future single photon detection needs. However, challenges to the operation of these devices in GM remain. The InAlAs multiplication region was not found to be significantly superior to current InP regions for GM, however, improved multiplication region design of InGaAs/InP APDs has been highlighted. For Ge GM detectors it still remains unclear whether an optimal trade-off of parameters can achieve the necessary sensitivity at 1550 nm. To further examine these remaining questions, as well as other application spaces for these technologies, funding for an Intelligence Community post-doc was awarded this year.

Synthesizing R&D Data: Experiences from the Integrated Manufacturing Technology Roadmap (IMTR) Project

Energy Technology Data Exchange (ETDEWEB)

merrell, m.a.

1999-05-05

IMTR is a tremendous undertaking to assess the current state and future needs of Manufacturing Technology R&D. A follow-on project to the roadmaps is the development and populating of a Gap Analysis database containing current R&D abstracts related to the roadmaps' technical elements. Efficiently identifying the R&D projects within scope presents many travails of synthesizing data from across a wide spectrum. Challenges to this project were directly proportional to the lack of single-source data collections.

77 FR 61002 - Announcement of the Award of Single-Source Program Expansion Supplement Grants to Seven Assets...

Science.gov (United States)

2012-10-05

... training on money management and consumer issues. Grant recipients must finance the projects with a....602] Announcement of the Award of Single-Source Program Expansion Supplement Grants to Seven Assets... the award of single-source program expansion supplements to seven FY 2012 grantees under the Assets...

Acousto-optic laser projection systems for displaying TV information

International Nuclear Information System (INIS)

Gulyaev, Yu V; Kazaryan, M A; Mokrushin, Yu M; Shakin, O V

2015-01-01

This review addresses various approaches to television projection imaging on large screens using lasers. Results are presented of theoretical and experimental studies of an acousto-optic projection system operating on the principle of projecting an image of an entire amplitude-modulated television line in a single laser pulse. We consider characteristic features of image formation in such a system and the requirements for its individual components. Particular attention is paid to nonlinear distortions of the image signal, which show up most severely at low modulation signal frequencies. We discuss the feasibility of improving the process efficiency and image quality using acousto-optic modulators and pulsed lasers. Real-time projectors with pulsed line imaging can be used for controlling high-intensity laser radiation. (review)

Acousto-optic laser projection systems for displaying TV information

Science.gov (United States)

Gulyaev, Yu V.; Kazaryan, M. A.; Mokrushin, Yu M.; Shakin, O. V.

2015-04-01

This review addresses various approaches to television projection imaging on large screens using lasers. Results are presented of theoretical and experimental studies of an acousto-optic projection system operating on the principle of projecting an image of an entire amplitude-modulated television line in a single laser pulse. We consider characteristic features of image formation in such a system and the requirements for its individual components. Particular attention is paid to nonlinear distortions of the image signal, which show up most severely at low modulation signal frequencies. We discuss the feasibility of improving the process efficiency and image quality using acousto-optic modulators and pulsed lasers. Real-time projectors with pulsed line imaging can be used for controlling high-intensity laser radiation.

Acousto-optic laser projection systems for displaying TV information

Energy Technology Data Exchange (ETDEWEB)

Gulyaev, Yu V [V.A.Kotel' nikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Moscow (Russian Federation); Kazaryan, M A [P N Lebedev Physics Institute, Russian Academy of Sciences, Moscow (Russian Federation); Mokrushin, Yu M [D.V. Efremov Scientific Research Institute of Electrophysical Apparatus (Russian Federation); Shakin, O V [Ioffe Physical Technical Institute, Russian Academy of Sciences, St. Petersburg (Russian Federation)

2015-04-30

This review addresses various approaches to television projection imaging on large screens using lasers. Results are presented of theoretical and experimental studies of an acousto-optic projection system operating on the principle of projecting an image of an entire amplitude-modulated television line in a single laser pulse. We consider characteristic features of image formation in such a system and the requirements for its individual components. Particular attention is paid to nonlinear distortions of the image signal, which show up most severely at low modulation signal frequencies. We discuss the feasibility of improving the process efficiency and image quality using acousto-optic modulators and pulsed lasers. Real-time projectors with pulsed line imaging can be used for controlling high-intensity laser radiation. (review)

The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

Science.gov (United States)

Kessler, Peter S.; Blank, Carrine; Leigh, John A.

1998-01-01

Nitrogen fixation occurs in two domains, Archaea and Bacteria. We have characterized a nif (nitrogen fixation) gene cluster in the methanogenic archaeon Methanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order, nifH, ORF105 (similar to glnB), ORF121 (similar to glnB), nifD, nifK, nifE, nifN, and nifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of the glnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kb nif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ to nifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens. PMID:9515920

Analytical inversion formula for uniformly attenuated fan-beam projections

International Nuclear Information System (INIS)

Weng, Y.; Zeng, G.L.; Gullberg, G.T.

1997-01-01

In deriving algorithms to reconstruct single photon emission computed tomography (SPECT) projection data, it is important that the algorithm compensates for photon attenuation in order to obtain quantitative reconstruction results. A convolution backprojection algorithm was derived by Tretiak and Metz to reconstruct two-dimensional (2-D) transaxial slices from uniformly attenuated parallel-beam projections. Using transformation of coordinates, this algorithm can be modified to obtain a formulation useful to reconstruct uniformly attenuated fan-beam projections. Unlike that for parallel-beam projections, this formulation does not produce a filtered backprojection reconstruction algorithm but instead has a formulation that is an inverse integral operator with a spatially varying kernel. This algorithm thus requires more computation time than does the filtered backprojection reconstruction algorithm for the uniformly attenuated parallel-beam case. However, the fan-beam reconstructions demonstrate the same image quality as that of parallel-beam reconstructions

Analysis of a MULE-cyanide hydratase gene fusion in Verticillium dahliae

Science.gov (United States)

The genome of the phytopathogenic fungus Verticillium dahliae encodes numerous Class II “cut-and-paste” transposable elements, including those of a small group of MULE transposons. We have previously identified a fusion event between a MULE transposon sequence and sequence encoding a cyanide hydrata...

The Aarhus Ion Micro-Trap Project

DEFF Research Database (Denmark)

Miroshnychenko, Yevhen; Nielsen, Otto; Poulsen, Gregers

As part of our involvement in the EU MICROTRAP project, we have designed, manufactured and assembled a micro-scale ion trap with integrated optical fibers. These prealigned fibers will allow delivering cooling laser light to single ions. Therefore, such a trap will not require any direct optical...... and installed in an ultra high vacuum chamber, which includes an ablation oven for all-optical loading of the trap [2]. The next steps on the project are to demonstrate the operation of the micro-trap and the cooling of ions using fiber delivered light. [1] D. Grant, Development of Micro-Scale Ion traps, Master...... Thesis (2008). [2] R.J. Hendricks, D.M. Grant, P.F. Herskind, A. Dantan and M. Drewsen, An all-optical ion-loading technique for scalable microtrap architectures, Applied Physics B, 88, 507 (2007)....

A High Energy and High Efficiency Spectral Shaping Single Frequency Fiber Laser, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — This SBIR phase II project proposes a single frequency high energy fiber laser system for coherent Lidar systems for remote sensing. Current state-of-art...

Vertical Alignment of Single-Walled Carbon Nanotubes on Nanostructure Fabricated by Atomic Force Microscope

National Research Council Canada - National Science Library

Lee, Haiwon

2007-01-01

This project focused on the behavior of single-wall carbon nanotubes (SWCNTs) in the electrophoresis cells and aligned growth of SWCNTs by thermal chemical vapor deposition on selectively deposited metallic nanoparticle...

SDN Project

Energy Technology Data Exchange (ETDEWEB)

Smith, Rhett [Schweitzer Engineering Laboratories Inc, Pullman, WA (United States)

2016-12-23

The SDN Project completed on time and on budget and successfully accomplished 100% of the scope of work outlined in the original Statement of Project Objective (SOPO). The SDN Project formed an alliance between Ameren Corporation, University of Illinois Urbana- Champaign (UIUC), Pacific Northwest National Laboratories (PNNL), and Schweitzer Engineering Laboratories, Inc. (SEL). The objective of the SDN Project is to address Topic Area of Interest 2: Sustain critical energy delivery functions while responding to a cyber-intrusion under Funding Opportunity Announcement DE-FOA-0000797. The goal of the project is to design and commercially release technology that provides a method to sustain critical energy delivery functions during a cyber intrusion and to do this control system operators need the ability to quickly identify and isolate the affected network areas, and re-route critical information and control flows around. The objective of the SDN Project is to develop a Flow Controller that monitors, configures, and maintains the safe, reliable network traffic flows of all the local area networks (LANs) on a control system in the Energy sector. The SDN team identified the core attributes of a control system and produced an SDN flow controller that has the same core attributes enabling networks to be designed, configured and deployed that maximize the whitelisted, deny-bydefault and purpose built networks. This project researched, developed and commercially released technology that: Enables all field networks be to configured and monitored as if they are a single asset to be protected; Enables greatly improved and even precalculated response actions to reliability and cyber events; Supports pre-configured localized response actions tailored to provide resilience against failures and centralized response to cyber-attacks that improve network reliability and availability; Architecturally enables the right subject matter experts, who are usually the information

Conduction channels at finite bias in single-atom gold contacts

DEFF Research Database (Denmark)

Brandbyge, Mads; Kobayashi, Nobuhiko; Tsukada, Masaru

1999-01-01

We consider the effect of a finite voltage bias on the conductance of single-atom gold contacts. We employ a nonorthogonal spn-tight-binding Hamiltonian combined with a local charge neutrality assumption. The conductance and charge distributions for finite bias are calculated using the nonequilib......We consider the effect of a finite voltage bias on the conductance of single-atom gold contacts. We employ a nonorthogonal spn-tight-binding Hamiltonian combined with a local charge neutrality assumption. The conductance and charge distributions for finite bias are calculated using...... of the eigenchannels projected onto tight-binding orbitals. We find a single almost fully transmitting channel with mainly s character for low bias while for high bias this channel becomes less transmitting and additional channels involving only d orbitals start to conduct....

Defining Investment Additionality for CDM projects - practical approaches

International Nuclear Information System (INIS)

Greiner, Sandra; Michaelowa, Axel

2003-01-01

The environmental integrity of the CDM under the Kyoto Protocol depends on the possibility to avoid giving emission credits to projects that would have happened anyway. Whether and how 'Investment Additionality' of CDM projects has to be determined is currently a part of climate negotiations. We discuss the rationale of companies to invest in projects and analyse possible criteria to determine Investment Additionality from a theoretical point of view. Differences in the type of investment call for the application of different criteria. Although some criteria are better than others, no single criterion can outweigh the others in all respects. We therefore suggest a scheme for additionality testing that aims at matching types of investment and criteria in a sensible way. Criteria are evaluated on the grounds of robustness to manipulation, degree of coverage and appropriateness for testing the investment decision under consideration

3D sound in the telepresence project BEAMING

DEFF Research Database (Denmark)

Olesen, Søren Krarup; Markovic, Milos; Madsen, Esben

2012-01-01

three applications: A general purpose theatrical scene, a teaching situation and a medical patient-visiting-doctor scenario. The March 2012 project review deals with the teaching situation. This involves a single microphone recording followed by signal processing that reconstructs the spatial content......The involvement of Aalborg University in the EU project BEAMING will be presented. BEAMING deals with telepresence including multiple modalities; vision, haptics and audio, of which the latter is of main interest here. The setup consists of two types of locations: The Destination, where the Locals...... for the Visitor, 3D audio is provided through headphones. It is rendered based on the Locals' coordinates via a common Internet database including local positional tracking to ensure that information on the Visitor's head rotation has a minimum delay through the network. The BEAMING project currently addresses...

Multivariate volume visualization through dynamic projections

Energy Technology Data Exchange (ETDEWEB)

Liu, Shusen [Univ. of Utah, Salt Lake City, UT (United States); Wang, Bei [Univ. of Utah, Salt Lake City, UT (United States); Thiagarajan, Jayaraman J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Univ. of Utah, Salt Lake City, UT (United States)

2014-11-01

We propose a multivariate volume visualization framework that tightly couples dynamic projections with a high-dimensional transfer function design for interactive volume visualization. We assume that the complex, high-dimensional data in the attribute space can be well-represented through a collection of low-dimensional linear subspaces, and embed the data points in a variety of 2D views created as projections onto these subspaces. Through dynamic projections, we present animated transitions between different views to help the user navigate and explore the attribute space for effective transfer function design. Our framework not only provides a more intuitive understanding of the attribute space but also allows the design of the transfer function under multiple dynamic views, which is more flexible than being restricted to a single static view of the data. For large volumetric datasets, we maintain interactivity during the transfer function design via intelligent sampling and scalable clustering. As a result, using examples in combustion and climate simulations, we demonstrate how our framework can be used to visualize interesting structures in the volumetric space.

TANK FARM REMEDIATION TECHNOLOGY DEVELOPMENT PROJECT AN EXERCISE IN TECHNICAL & REGULATORY COLLABORATION

Energy Technology Data Exchange (ETDEWEB)

JARAYSI, M.N.

2007-01-08

The Tank Farm Remediation Technology Development Project at the Hanford Site focuses on waste storage tanks, pipelines and associated ancillary equipment that are part of the C-200 single-shell tank (SST) farm system located in the C Tank Farm. The purpose of the project is to obtain information on the implementation of a variety of closure activities and to answer questions on technical, operational and regulatory issues associated with closure.

Social anthropological and interdisciplinary research on the conversion of electrically heated single family houses to heating by combined pellet-solar systems

International Nuclear Information System (INIS)

Henning, Annette

2004-01-01

The social anthropological research presented here is part of the interdisciplinary research project PESTO, which focuses on the (partial or complete) conversion of single family houses from electric heating to heating by combined pellet-solar heating systems. Basic to this research is the assumption that it is more likely that energy conversions are carried through, and that they are successful on a long-term basis, if the new products are designed to fit as well as possible into the everyday lives of people. The anthropological interest in the project can be divided into two parts; motives for or against a conversion among men and women in Swedish households, and product design and placement in (previously) electrically heated single-family houses. Literature studies and semi-structured qualitative interviews are the main methods used in the anthropological part of the project. During the next 3-year project period, these investigations will be used to support information and marketing, and to formulate recommendations for conversion practice of electrically heated single-family houses to combined pellet-solar heating. (Author)

Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

DEFF Research Database (Denmark)

Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

2011-01-01

The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

The single European market - a Schumpeterian event?

OpenAIRE

Siebert, Horst

1989-01-01

It is now four years after the White Paper launched the project on the completion of the internal market [Commission, 1985]. 300 steps were packaged and sold in a manner by Delors and Lord Cockfield that "caught on". The basic strategy is simple: abolish or reduce market segmentations that still exist, facilitate free market access, as well as establish the free movement of people, goods, services, and capital (the so-called four freedoms). Will the single European market prove to be an insti...

Experimental and theoretical analysis for improved microscope design of optical projection tomographic microscopy.

Science.gov (United States)

Coe, Ryan L; Seibel, Eric J

2013-09-01

We present theoretical and experimental results of axial displacement of objects relative to a fixed condenser focal plane (FP) in optical projection tomographic microscopy (OPTM). OPTM produces three-dimensional, reconstructed images of single cells from two-dimensional projections. The cell rotates in a microcapillary to acquire projections from different perspectives where the objective FP is scanned through the cell while the condenser FP remains fixed at the center of the microcapillary. This work uses a combination of experimental and theoretical methods to improve the OPTM instrument design.

Advanced Flue Gas Desulfurization (AFGD) demonstration project: Volume 2, Project performance and economics. Final technical report

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-04-30

The project objective is to demonstrate removal of 90--95% or more of the SO{sub 2} at approximately one-half the cost of conventional scrubbing technology; and to demonstrate significant reduction of space requirements. In this project, Pure Air has built a single SO{sub 2} absorber for a 528-MWe power plant. The absorber performs three functions in a single vessel: prequencher, absorber, and oxidation of sludge to gypsum. Additionally, the absorber is of a co- current design, in which the flue gas and scrubbing slurry move in the same direction and at a relatively high velocity compared to conventional scrubbers. These features all combine to yield a state- of-the-art SO{sub 2} absorber that is more compact and less expensive than conventional scrubbers. The project incorporated a number of technical features including the injection of pulverized limestone directly into the absorber, a device called an air rotary sparger located within the base of the absorber, and a novel wastewater evaporation system. The air rotary sparger combines the functions of agitation and air distribution into one piece of equipment to facilitate the oxidation of calcium sulfite to gypsum. Additionally, wastewater treatment is being demonstrated to minimize water disposal problems inherent in many high-chloride coals. Bituminous coals primarily from the Indiana, Illinois coal basin containing 2--4.5% sulfur were tested during the demonstration. The Advanced Flue Gas Desulfurization (AFGD) process has demonstrated removal of 95% or more of the SO{sub 2} while providing a commercial gypsum by-product in lieu of solid waste. A portion of the commercial gypsum is being agglomerated into a product known as PowerChip{reg_sign} gypsum which exhibits improved physical properties, easier flowability and more user friendly handling characteristics to enhance its transportation and marketability to gypsum end-users.

A High Energy and High Efficiency Spectral Shaping Single Frequency Fiber Laser, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This SBIR phase I project proposes a tunable single frequency high energy fiber laser system for coherent Lidar systems for remote sensing. Current state-of-art...

Mutations in the Histone-Like Nucleoid Structuring Regulatory Gene (hns) Decrease the Adherence of Shiga Toxin-Producing Escherichia coli 091:H21 Strain B2F1 to Human Colonic Epithelial Cells and Increase the Production of Hemolysin

National Research Council Canada - National Science Library

Scott, Maria

1999-01-01

...:H21 to human colonic epithelial cells. Transposon mutagenesis of B2F1 was accomplished with the mini-Tn5phoACm mobile element and a mutant bank of B2F1 colonies that carried putative in-frame PhoA-positive transposon insertions was isolated...

Development of an air heating system for single family housing

DEFF Research Database (Denmark)

Afshari, Alireza; Gunner, Amalie; Nikolaisen, Christian Grønborg

2017-01-01

The initial objective of the project was to break with common thinking about Space heating and to document that air heating can be used as the sole source of heating in a single Family house. The basic idea is that the ventilation must be installed in any case and it may equally well form the heat...

Electrochemical Charging of Individual Single-Walled Carbon Nanotubes

Czech Academy of Sciences Publication Activity Database

Kalbáč, Martin; Farhat, H.; Kavan, Ladislav; Kong, J.; Sasaki, K.; Saito, R.; Dresselhaus, M. S.

2009-01-01

Roč. 3, č. 8 (2009), s. 2320-2328 ISSN 1936-0851 R&D Projects: GA ČR GC203/07/J067; GA AV ČR IAA400400804; GA AV ČR IAA400400911; GA AV ČR KAN200100801; GA MŠk ME09060 Institutional research plan: CEZ:AV0Z40400503 Keywords : single-walled carbon nanotubes * Raman spectroscopy * electrochemical gating * spectroelectrochemistry Subject RIV: CG - Electrochemistry Impact factor: 7.493, year: 2009

The ASEAN Economic Community Project

DEFF Research Database (Denmark)

Juego, Bonn

2014-01-01

In this paper, I attempt to unpack the ASEAN Economic Community (AEC) Blueprint to reveal the project’s neoliberal capitalist strategy of ‘accumulation by dispossession’ whereby the drive for the acquisition of more wealth and power by the economically wealthy and politically powerful necessitated...... the deprivation of the peoples’ collective rights and access to the economic, political, social, and ecological commons. I therefore offer a critical reading of the AEC project in the analysis, specifically its agenda for the establishment of a competitive single market, and conclude with some notes...

PROJECT-DRIVEN SOFTWARE BUSINESS IN TRANSILVANIA - A CASE STUDY

Directory of Open Access Journals (Sweden)

Radu Marius

2015-07-01

Full Text Available The fairly low salaries of the IT workers compared to the Western countries, the skills and the location have supported outsourcing become one of the most competitive Romanian sectors. IT sector in Romania maintains a steady growth favoured by outsourcing companies. Moreover Romania is highly competitive when you take into account the level of technical proficiency and soft skills in the country. Romanian labour force can drive relevant projects even in small teams. This case study explores the realty of Romanian IT companies profiles. It presents in comparison two companies bases on organizational and strategic dimensions: project approach orientation, leadership, project value driven, and social responsibility. The corporate goal of the first company presented in the case study - Fortech - is to achieve the best adaptive organizational structure which can sustain its competitive advantage. This advantage results from combination of three main ingredients: scaled up human resource capital, versatile knowledge management and adaptability to customer needs. Fortech manages and administrates and execute their business activities using project management methodologies and practices in order to achieve the strategic goals. On the other hand Dolphin Kiss Company is a “Python boutique agency” created around a single contract and organized on a single project. The project was contracted with a top company from telecommunication industry. The company is a small team of creative software engineers focused on developing a very innovative software business solution. This case study is an empirical qualitative research intended to depict the main differences between two relevant company profiles present in the actual economic context: small team – results oriented – highly skilled VS large structure of outsourcing teams – matrix organized – customer oriented. The case study constructs a space for debates regarding the potential evolution of the

Digital Display Integration Project Project Online 2.0

International Nuclear Information System (INIS)

Bardsley, J. N.

1999-01-01

The electronic display industry is changing in three important ways. First, the dominance of the cathode ray tube (CRT) is being challenged by the development of flat panel displays (FPDs). This will lead to the availability of displays of higher performance, albeit at greater cost. Secondly, the analog interfaces between displays that show data and the computers that generate the data are being replaced by digital connections. Finally, a high-resolution display is becoming the most expensive component in computer system for homes and small offices. It is therefore desirable that the useful lifetime of the display extend over several years and that the electronics allows the display to be used with many different image sources. Hopefully, the necessity of having three or four large CRTs in one office to accommodate different computer operating systems or communication protocols will soon disappear. Instead, we hope to see a set of flat panels that can be switched to show several independent images from multiple sources or a composite image from a single source. The more rapid rate of technological improvements and the higher cost of flat panel displays raise the incentive for greater planning and guidance in the acquisition and integration of high performance displays into large organizations, such as LLNL. The goal of the Digital Display Integration Project (DDIP) is to provide such support. This will be achieved through collaboration with leading suppliers of displays, communications equipment and image-processing products, and by greater exchange of information within the Laboratory. The project will start in October 1999. During the first two years (FY2000-1), the primary focus of the program will be upon: introducing displays with high information content (over 5M pixels); facilitating the transition from analog to digital interfaces; enabling data transfer from key computer platforms; incorporating optical communications to remove length restrictions on data

A macroscopic model for magnetic shape-memory single crystals

Czech Academy of Sciences Publication Activity Database

Bessoud, A. L.; Kružík, Martin; Stefanelli, U.

2013-01-01

Roč. 64, č. 2 (2013), s. 343-359 ISSN 0044-2275 R&D Projects: GA AV ČR IAA100750802; GA ČR GAP201/10/0357 Institutional support: RVO:67985556 Keywords : magnetostriction * evolution Subject RIV: BA - General Mathematics Impact factor: 1.214, year: 2013 http://library.utia.cas.cz/separaty/2012/MTR/kruzik-a macroscopic model for magnetic shape- memory single crystals.pdf

Value of selective MIP reconstructions of respiratory triggered 3D-TSE-MR cholangiography on a workstation versus standard MIP reconstructions and single-shot MRCP

International Nuclear Information System (INIS)

Schaible, R.; Textor, J.; Kreft, B.; Schild, H.; Neubrand, M.

2001-01-01

Comparison of anatomical visualisation and diagnostic value of selective MIP reconstructions of respiratory triggered 3D-TSE-MRCP versus standard MIP reconstructions and single-shot MRCP. Material and Methods: 50 patients with pancreaticobiliary disease were examined at 1.5 Tesla (ACS NT II, Philips Medical Systems) using a breath-hold single-shot (SS) and a respiratory triggered 3D-TSE-MRCP technique in 12 standard MIP projections. Additional selective MIP reconstructions with different slice thickness (2, 4, 10 cm) and projections were performed on a workstation. Visualization of the pancreaticobiliary system and the diagnostic value of the examinations were analysed. Results: Single-shot and 3D-TSE in standard projections showed comparable anatomical visualisation. On selective MIP reconstructions the biliary system (SS p [de

In Vivo Observation of Structural Changes in Neocortical Catecholaminergic Projections in Response to Drugs of Abuse.

Science.gov (United States)

Morimoto, Mai M; Tanaka, Shinji; Mizutani, Shunsuke; Urata, Shinji; Kobayashi, Kazuto; Okabe, Shigeo

2018-01-01

Catecholaminergic (dopamine and norepinephrine) projections to the cortex play an important role in cognitive functions and dysfunctions including learning, addiction, and mental disorders. While dynamics of glutamatergic synapses have been well studied in such contexts, little is known regarding catecholaminergic projections, owing to lack of robust methods. Here we report a system to monitor catecholaminergic projections in vivo over the timeframes that such events occur. Green fluorescent protein (GFP) expression driven by tyrosine hydroxylase promoter in a transgenic mouse line enabled us to perform two-photon imaging of cortical catecholaminergic projections through a cranial window. Repetitive imaging of the same axons over 24 h revealed the highly dynamic nature of catecholaminergic boutons. Surprisingly, administration of single high dose methamphetamine (MAP) induced a transient increase in bouton volumes. This new method opens avenues for longitudinal in vivo evaluation of structural changes at single release sites of catecholamines in association with physiology and pathology of cortical functions.

High-temperature and low-stress creep anisotropy of single-crystal superalloys

Czech Academy of Sciences Publication Activity Database

Jacome, L. A.; Nortershauser, P.; Heyer, J. K.; Lahni, A.; Frenzel, J.; Dlouhý, Antonín; Somsen, C.; Eggeler, G.

2013-01-01

Roč. 61, č. 8 (2013), s. 2926-2943 ISSN 1359-6454 R&D Projects: GA ČR(CZ) GA202/09/2073 Institutional support: RVO:68081723 Keywords : superalloy single crystals * creep anisotropy * rafting * dislocations * deformation mechanisms Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.940, year: 2013

Improving Climate Projections Using "Intelligent" Ensembles

Science.gov (United States)

Baker, Noel C.; Taylor, Patrick C.

2015-01-01

Recent changes in the climate system have led to growing concern, especially in communities which are highly vulnerable to resource shortages and weather extremes. There is an urgent need for better climate information to develop solutions and strategies for adapting to a changing climate. Climate models provide excellent tools for studying the current state of climate and making future projections. However, these models are subject to biases created by structural uncertainties. Performance metrics-or the systematic determination of model biases-succinctly quantify aspects of climate model behavior. Efforts to standardize climate model experiments and collect simulation data-such as the Coupled Model Intercomparison Project (CMIP)-provide the means to directly compare and assess model performance. Performance metrics have been used to show that some models reproduce present-day climate better than others. Simulation data from multiple models are often used to add value to projections by creating a consensus projection from the model ensemble, in which each model is given an equal weight. It has been shown that the ensemble mean generally outperforms any single model. It is possible to use unequal weights to produce ensemble means, in which models are weighted based on performance (called "intelligent" ensembles). Can performance metrics be used to improve climate projections? Previous work introduced a framework for comparing the utility of model performance metrics, showing that the best metrics are related to the variance of top-of-atmosphere outgoing longwave radiation. These metrics improve present-day climate simulations of Earth's energy budget using the "intelligent" ensemble method. The current project identifies several approaches for testing whether performance metrics can be applied to future simulations to create "intelligent" ensemble-mean climate projections. It is shown that certain performance metrics test key climate processes in the models, and

Single Point Adjustments: A New Definition with Examples. Acquisition Review Quarterly, Fall 2001

National Research Council Canada - National Science Library

Bachman, David

2002-01-01

.... A single point adjustment (SPA) is made when a contract's existing cost and/or schedule variances are set to zero and all the remaining work is replanned with the goal of completing the project on schedule and on budget...

Characterization of the Ecosole HCPV tracker and single module inverter

Science.gov (United States)

Carpanelli, Maurizio; Borelli, Gianni; Verdilio, Daniele; De Nardis, Davide; Migali, Fabrizio; Cancro, Carmine; Graditi, Giorgio

2015-09-01

BECAR, the Beghelli group's R&D company, is leading ECOSOLE (Elevated COncentration SOlar Energy), one of the largest European Demonstration projects in solar photovoltaic. ECOSOLE, started in 2012, is focused on the study, design, and realization of new HCPV generator made of high efficiency PV modules equipped with SoG (Silicone on Glass) fresnel lenses and III-V solar cells, and a low cost matched solar tracker with distributed inverters approach. The project also regards the study and demonstration of new high throughput methods for the industrial large scale productions, at very low manufacturing costs. This work reports the description of the characterization of the tracker and single module.

Solar project description for Zien Mechanical Contractors-I single family residence, Milwaukee, Wisconsin

Science.gov (United States)

Beers, D.

1980-02-01

The Zien Mechanical site is a single family residence located in Milwaukee, Wisconsin. The home has two separate solar energy systems: an air system for space heating and cooling; a liquid system to preheat the potable hot water. The space heating and cooling system design and operation modes are described. The space heating system is designed to apply approximately 44 percent of the space heating requirements for the 1388 square foot residence. Engineering drawings are provided and the performance evaluation instrumentation is described.

Sudha Bhattacharya Jawaharlal Nehru University New Delhi

Indian Academy of Sciences (India)

TSC

Bottom strand. 1. 2. 3. G A T C. 5. 1. 3. 4. 2. *. Nicking profile of EN on the 174 bp substrate. Insertion point. Bottom strand labelled 174bp substrate. Transposon insertion point. Endonuclease nicks at three hot spots. The transposon inserts at hot spot # 3 ...

ORF Alignment: NC_003888 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003888 gi|21218662 >1cxqA 5 133 141 282 2e-06 ... ref|NP_624441.1| putative noncomposite... transposon transposase [Streptomyces ... coelicolor A3(2)] emb|CAB52910.1| putative noncomposite... ... transposon transposase [Streptomyces coelicolor A3(2)] ... pir||T36996 probable noncomposite

Study on electrical defects level in single layer two-dimensional Ta2O5

Science.gov (United States)

Dahai, Li; Xiongfei, Song; Linfeng, Hu; Ziyi, Wang; Rongjun, Zhang; Liangyao, Chen; David, Wei Zhang; Peng, Zhou

2016-04-01

Two-dimensional atomic-layered material is a recent research focus, and single layer Ta2O5 used as gate dielectric in field-effect transistors is obtained via assemblies of Ta2O5 nanosheets. However, the electrical performance is seriously affected by electronic defects existing in Ta2O5. Therefore, spectroscopic ellipsometry is used to calculate the transition energies and corresponding probabilities for two different charged oxygen vacancies, whose existence is revealed by x-ray photoelectron spectroscopy analysis. Spectroscopic ellipsometry fitting also calculates the thickness of single layer Ta2O5, exhibiting good agreement with atomic force microscopy measurement. Nondestructive and noncontact spectroscopic ellipsometry is appropriate for detecting the electrical defects level of single layer Ta2O5. Project supported by the National Natural Science Foundation of China (Grant Nos. 11174058 and 61376093), the Fund from Shanghai Municipal Science and Technology Commission (Grant No. 13QA1400400), the National Science and Technology Major Project, China (Grant No. 2011ZX02707), and the Innovation Program of Shanghai Municipal Education Commission (Grant No. 12ZZ010).

Challenges in thermal design of industrial single-phase power inverter

Directory of Open Access Journals (Sweden)

Ninković Predrag

2016-01-01

Full Text Available This paper presents the influence of thermal aspects in design process of an industrial single-phase inverter, choice of its topology and components. Stringent design inputs like very high overload level, demand for natural cooling and very wide input voltage range have made conventional circuit topology inappropriate therefore asking for alternative solution. Different power losses calculations in semiconductors are performed and compared, outlining the guidelines how to choose the final topology. Some recommendations in power magnetic components design are given. Based on the final project, a 20kVA single-phase inverter for thermal power plant supervisory and control system is designed and commissioned.

City project and public space

CERN Document Server

2013-01-01

The book aims at nurturing theoretic reflection on the city and the territory and working out and applying methods and techniques for improving our physical and social landscapes. The main issue is developed around the projectual dimension, with the objective of visualising both the city and the territory from a particular viewpoint, which singles out the territorial dimension as the city’s space of communication and negotiation. Issues that characterise the dynamics of city development will be faced, such as the new, fresh relations between urban societies and physical space, the right to the city, urban equity, the project for the physical city as a means to reveal civitas, signs of new social cohesiveness, the sense of contemporary public space and the sustainability of urban development. Authors have been invited to explore topics that feature a pluralism of disciplinary contributions studying formal and informal practices on the project for the city and seeking conceptual and operative categories capab...

Project report - an overview of the project and experiences with project management

DEFF Research Database (Denmark)

Jørgensen, Michael Søgaard; Mikkelsen, Bent Egberg

1996-01-01

A collection of the project planning and the experiences with project management from the Catering 2000 project.As appendieces articles etc. from journals, newspapers etc. about the project.......A collection of the project planning and the experiences with project management from the Catering 2000 project.As appendieces articles etc. from journals, newspapers etc. about the project....

A single-neuron tracing study of arkypallidal and prototypic neurons in healthy rats.

Science.gov (United States)

Fujiyama, Fumino; Nakano, Takashi; Matsuda, Wakoto; Furuta, Takahiro; Udagawa, Jun; Kaneko, Takeshi

2016-12-01

The external globus pallidus (GP) is known as a relay nucleus of the indirect pathway of the basal ganglia. Recent studies in dopamine-depleted and healthy rats indicate that the GP comprises two main types of pallidofugal neurons: the so-called "prototypic" and "arkypallidal" neurons. However, the reconstruction of complete arkypallidal neurons in healthy rats has not been reported. Here we visualized the entire axonal arborization of four single arkypallidal neurons and six single prototypic neurons in rat brain using labeling with a viral vector expressing membrane-targeted green fluorescent protein and examined the distribution of axon boutons in the target nuclei. Results revealed that not only the arkypallidal neurons but nearly all of the prototypic neurons projected to the striatum with numerous axon varicosities. Thus, the striatum is a major target nucleus for pallidal neurons. Arkypallidal and prototypic GP neurons located in the calbindin-positive and calbindin-negative regions mainly projected to the corresponding positive and negative regions in the striatum. Because the GP and striatum calbindin staining patterns reflect the topographic organization of the striatopallidal projection, the striatal neurons in the sensorimotor and associative regions constitute the reciprocal connection with the GP neurons in the corresponding regions.

An accurate projection algorithm for array processor based SPECT systems

International Nuclear Information System (INIS)

King, M.A.; Schwinger, R.B.; Cool, S.L.

1985-01-01

A data re-projection algorithm has been developed for use in single photon emission computed tomography (SPECT) on an array processor based computer system. The algorithm makes use of an accurate representation of pixel activity (uniform square pixel model of intensity distribution), and is rapidly performed due to the efficient handling of an array based algorithm and the Fast Fourier Transform (FFT) on parallel processing hardware. The algorithm consists of using a pixel driven nearest neighbour projection operation to an array of subdivided projection bins. This result is then convolved with the projected uniform square pixel distribution before being compressed to original bin size. This distribution varies with projection angle and is explicitly calculated. The FFT combined with a frequency space multiplication is used instead of a spatial convolution for more rapid execution. The new algorithm was tested against other commonly used projection algorithms by comparing the accuracy of projections of a simulated transverse section of the abdomen against analytically determined projections of that transverse section. The new algorithm was found to yield comparable or better standard error and yet result in easier and more efficient implementation on parallel hardware. Applications of the algorithm include iterative reconstruction and attenuation correction schemes and evaluation of regions of interest in dynamic and gated SPECT

The biology and potential for genetic research of transposable elements in filamentous fungi

Directory of Open Access Journals (Sweden)

Léia Cecilia de Lima Fávaro

2005-12-01

Full Text Available Recently many transposable elements have been identified and characterized in filamentous fungi, especially in species of agricultural, biotechnological and medical interest. Similar to the elements found in other eukaryotes, fungal transposons can be classified as class I elements (retrotransposons that use RNA and reverse transcriptase and class II elements (DNA transposons that use DNA. The changes (transposition and recombination caused by transposons can supply wide-ranging genetic variation, especially for species that do not have a sexual phase. The application of transposable elements to gene isolation and population analysis is an important tool for molecular biology and studies of fungal evolution.

Calcium chloride improve ethanol production in recombinant ...

African Journals Online (AJOL)

The T7-expression system has been very useful for protein expression in Escherichia coli. Here, a T7- expression transposon was constructed, which allowed simple construction of T7-expression Zymomonas mobilis. This transposon contained the T7 RNA polymerase being driven by the gap promoter from Z. mobilis.

Single feature polymorphism (SFP-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Stitt Mark

2010-03-01

Full Text Available Abstract Background Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits. Results A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait. Conclusions We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.

Single-Shell Tank (SST) Retrieval Sequence Fiscal Year 2000 Update

International Nuclear Information System (INIS)

GARFIELD, J.S.

2000-01-01

This document describes the baseline single-shell tank (SST) waste retrieval sequence for the River Protection Project (RPP) updated for Fiscal Year 2000. The SST retrieval sequence identifies the proposed retrieval order (sequence), the tank selection and prioritization rationale, and planned retrieval dates for Hanford SSTs. In addition, the tank selection criteria and reference retrieval method for this sequence are discussed

Single-cell gene-expression profiling and its potential diagnostic applications

Czech Academy of Sciences Publication Activity Database

Stahlberg, A.; Kubista, Mikael; Aman, P.

2011-01-01

Roč. 11, č. 7 (2011), s. 735-740 ISSN 1473-7159 R&D Projects: GA ČR(CZ) GAP303/10/1338; GA ČR(CZ) GA301/09/1752 Institutional research plan: CEZ:AV0Z50520701 Keywords : gene-expression profiling * RT-qPCR * single-cell gene-expression profiling Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.859, year: 2011

Valorization of a repository in an added value project

International Nuclear Information System (INIS)

Van Hove, E.

2004-01-01

Professor of Sociology (retired), spoke of the valorization of a repository in an added value project. He pointed out that though local stakeholders may lack technical expertise, they consider their personal interests very carefully and projects affecting such interests are taken quite personally. This provides caution but also opportunity for such projects to be conducted in ways that can help, though not guarantee, better acceptance by local stakeholders. Professor Van Hove mentioned three attributes. First, while engineering projects tend to be thought of as mono-functional (e.g. dispose of waste), building flexibility into the project to reflect the interests of the local stakeholders can measurably improve Stakeholder satisfaction. What the implementer may see as a single-purpose project may indeed provide additional, desirable capabilities to a creative local population. Second, while engineering projects, particularly waste management projects are often designed and built in uninteresting, utilitarian ways, a more creative design and implementation can add a sense of enjoyment and pride on the part of the local stakeholders. And third, while engineering projects are often conducted a manner closed to their environment, a more transparent, inclusive process may draw local stakeholders more intimately into the project. All of these features can help by providing inviting borders, by valuing the beauty and aesthetic dimension of the project and by building the project so that it has an appropriate place in the memory of society. Professor Van Hove emphasised that people show great ingenuity in adapting uses and functions beyond those originally intended. The extent to which local stakeholders can help provide the vision and then the reality of such waste management projects can significantly improve their sense of ownership of the project and their ultimate acceptance. (author)

TANK FARM REMEDIATION TECHNOLOGY DEVELOPMENT PROJECT AN EXERCISE IN TECHNICAL and REGULATORY COLLABORATION

International Nuclear Information System (INIS)

JARAYSI, M.N.

2007-01-01

The Tank Farm Remediation Technology Development Project at the Hanford Site focuses on waste storage tanks, pipelines and associated ancillary equipment that are part of the C-200 single-shell tank (SST) farm system located in the C Tank Farm. The purpose of the project is to obtain information on the implementation of a variety of closure activities and to answer questions on technical, operational and regulatory issues associated with closure

Uncooled Radiation Hard SiC Schottky VUV Detectors Capable of Single Photon Sensing, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This project seeks to design, fabricate, characterize and commercialize very large area, uncooled and radiative hard 4H-SiC VUV detectors capable of near single...

Research projects in family medicine funded by the European Union.

Science.gov (United States)

Pavličević, Ivančica; Barać, Lana

2014-01-01

This study aimed at synthesizing funding opportunities in the field of family medicine by determining the number of family medicine projects, as well as number of project leaderships and/ or participations by each country. This was done in order to encourage inclusion of physicians in countries with underdeveloped research networks in successful research networks or to encourage them to form new ones. We searched the Community Research and Development Information Service project database in February 2013. Study covered the period from years 1992 - 2012, selecting the projects within the field of general/family medicine. The search was conducted in February 2013. First search conducted in the CORDIS database came up with a total of 466 projects. After excluding 241 projects with insufficient data, we analysed 225 remaining projects; out of those, 22 (9.8%) were in the field of family medicine and 203 (90.2%) were from other fields of medicine. Sorted by the number of projects per country, Dutch institutions had the highest involvement in family medicine projects and were partners or coordinators in 18 out of 22 selected projects (81.8%), followed by British institutions with 15 (68.8%), and Spanish with 10 projects (45.5%). Croatia was a partner in a single FP7 Health project. Research projects in family medicine funded by the European Union show significant differences between countries. Constant and high-quality international cooperation in family medicine is the prerequisite for improvement and development of scientific research and the profession. Copyright © 2014 by Academy of Sciences and Arts of Bosnia and Herzegovina.

Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

Directory of Open Access Journals (Sweden)

Nynne Sharma

2013-01-01

Full Text Available DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system.

Recent advances in the development of single cell analysis-A review

Czech Academy of Sciences Publication Activity Database

Klepárník, Karel; Foret, František

2013-01-01

Roč. 800, OCT (2013), s. 12-21 ISSN 0003-2670 R&D Projects: GA MŠk(CZ) EE2.3.20.0182; GA ČR GAP206/11/2377 Institutional support: RVO:68081715 Keywords : single cell analysis * capillary electrophoresis * electrochemistry * microfluidic devices Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.517, year: 2013