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Sample records for pyrophosphorylase gene final

  1. [Enhancement of photoassimilate utilization by manipulation of ADP-glucose pyrophosphorylase gene]. Final progress report

    SciTech Connect

    Okita, T.W.

    1999-04-01

    Part 1 of this research focuses on patterns of gene expression of ADPG-pyrophosphorylase in native and transgenic potato plants. To elucidate the mechanism controlling AGP expression during plant development, the expression of the potato tuber AGP small subunit (sAGP) gene was analyzed in transgenic potato plants using a promoter-{beta}-glucuronidase expression system. Part II evaluated the structure-function relationships of AGP.

  2. Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica

    DOEpatents

    Jarvis, Eric E.; Roessler, Paul G.

    1999-01-01

    The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities.

  3. Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica

    DOEpatents

    Jarvis, E.E.; Roessler, P.G.

    1999-07-27

    The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities. 8 figs.

  4. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Progress report, [March 15, 1989--April 14, 1990

    SciTech Connect

    Okita, T.W.

    1990-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of the gene that encodes for ADPglucose pyrophosphorylase, a key regulatory enzyme of starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. During the last two years we have obtained information on the structure of this enzyme from both potato tuber and rice endosperm, using a combination of biochemical and molecular biological approaches. Moreover, we present evidence that this enzyme may be localized at discrete regions of the starch grain within the amyloplast, and plays a role in controlling overall starch biosynthesis in potato tubers.

  5. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Summary of progress, [April 15, 1991--April 14, 1992

    SciTech Connect

    Okita, T.W.

    1992-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of genes encoding enzymes that may be rate-limiting in starch biosynthesis. In developing storage tissues such as tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. In view of the regulatory role of ADPglucose pyrophosphorylase in starch biosynthesis at both the genetic and biochemical level, we have focused our attention on the genes that encode for this enzyme in potato tubers. The proposed objectives of the grant were to (1) analyze the structure of the tuber enzyme, (2) isolate and characterize the structure of its genes, and (3) identify the regulatory elements controlling ADPglucose pyrophosphorylase during plant development. During the last two and 1/2 years we have met or have made considerable progress in achieving these objectives as discussed in more detail below.

  6. Overexpression of UDP-glucose pyrophosphorylase gene could increase cellulose content in Jute (Corchorus capsularis L.).

    PubMed

    Zhang, Gaoyang; Qi, Jianmin; Xu, Jiantang; Niu, Xiaoping; Zhang, Yujia; Tao, Aifen; Zhang, Liwu; Fang, Pingping; Lin, Lihui

    2013-12-13

    In this study, the full-length cDNA of the UDP-glucose pyrophosphorylase gene was isolated from jute by homologous cloning (primers were designed according to the sequence of UGPase gene of other plants) and modified RACE techniques; the cloned gene was designated CcUGPase. Using bioinformatic analysis, the gene was identified as a member of the UGPase gene family. Real-time PCR analysis revealed differential spatial and temporal expression of the CcUGPase gene, with the highest expression levels at 40 and 120d. PCR and Southern hybridization results indicate that the gene was integrated into the jute genome. Overexpression of CcUGPase gene in jute revealed increased height and cellulose content compared with control lines, although the lignin content remained unchanged. The results indicate that the jute UGPase gene participates in cellulose biosynthesis. These data provide an important basis for the application of the CcUGPase gene in the improvement of jute fiber quality.

  7. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene. Progress report, [April 15, 1988--April 14, 1989

    SciTech Connect

    Okita, T.W.

    1989-12-31

    During this period researchers have been successful in determining the structure of the rice pyrophosphorylase gene. Potato tuber ADPglucose pyrophosphorylse purification and structure studies were carried out as well as recombinant DNA studies. Evidence suggests that the tuber form is made up of subunits with similar molecular weights and immunological relatedness. In contrast, the spinach leaf enzyme and presumably the maize endosperm species is composed of two dissimilar sununits encoded by different genes.

  8. Sucrose regulation of ADP-glucose pyrophosphorylase subunit genes transcript levels in leaves and fruits

    NASA Technical Reports Server (NTRS)

    Li, Xiangyang; Xing, Jinpeng; Gianfagna, Thomas J.; Janes, Harry W.

    2002-01-01

    ADP-glucose pyrophosphorylase (AGPase, EC2.7.7.27) is a key regulatory enzyme in starch biosynthesis. The enzyme is a heterotetramer with two S and two B subunits. In tomato, there are three multiple forms of the S subunit gene. Agp S1, S2 and B are highly expressed in fruit from 10 to 25 days after anthesis. Agp S3 is only weakly expressed in fruit. Sucrose significantly elevates expression of Agp S1, S2 and B in both leaves and fruits. Agp S1 exhibits the highest degree of regulation by sucrose. In fact, sucrose may be required for Agp S1 expression. For excised leaves incubated in water, no transcripts for Agp S1 could be detected in the absence of sucrose, whereas it took up to 16 h in water before transcripts were no longer detectable for Agp S2 and B. Neither Agp S3 nor the tubulin gene is affected by sucrose, demonstrating that this response is specifically regulated by a carbohydrate metabolic signal, and is not due to a general increase in metabolism caused by sucrose treatment. Truncated versions of the promoter for Agp S1 indicate that a specific region 1.3-3.0 kb upstream from the transcription site is responsible for sucrose sensitivity. This region of the S1 promoter contains several cis-acting elements present in the promoters of other genes that are also regulated by sucrose. c2002 Elsevier Science Ireland Ltd. All rights reserved.

  9. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene. Progress report, [April 15, 1987--April 14, 1988

    SciTech Connect

    Okita, T.W.

    1988-12-31

    Many agronomically important crops are viewed as significant resources of renewable energy. Overall crop productivity could be increased if the efficiency of photoassimilate conversion into dry matter such as starch were improved in storage tissues. Starch production is controlled by the catalytic activity of ADPglucose pyrophosphorylase in the first step of starch biosynthesis. This research focuses on the genetic structure and molecular mechanisms by which it is controlled during plant development and how it is affected by environmental and hormonal conditions. The current goal is to isolate the genes for this enzyme present in both cereal endosperm and potato tuber tissues, and to elucidate its structure and the controlling sequences responsible for gene expression. The long term goal is the improvement of starch production in storage organs by manipulating this gene so that it encodes an enzyme refractive to inorganic phosphate inhibition.

  10. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase genes. Progress report, [April 15, 1990--April 14, 1991

    SciTech Connect

    Okita, T.W.

    1990-12-31

    The long term goal of this project is to assess the feasibility of increasing the conversion of photosynthate a key regulatory enzyme in starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is primarily regulated by the gene activation, expression, and allosteric regulation of ADPglucose pyrophosphorylase, as well as starch synthase, and branching enzyme. During the last year we have elucidated the structure of both subunits which compose this tetrameric enzyme and determined the temporal and spatial expression of the genes encoding each subunit as well as their correlation to starch biosynthesis. Genomic clones to both subunits have also been isolated and the gene structure of the small subunit determined. Transgenic potato plants have been produced containing deletions of the small subunit promoter. Currently, cis acting elements and their involvement in spatial and temporal expression are under investigation.

  11. A single gene encodes two different transcripts for the ADP-glucose pyrophosphorylase small subunit from barley (Hordeum vulgare).

    PubMed Central

    Thorbjørnsen, T; Villand, P; Kleczkowski, L A; Olsen, O A

    1996-01-01

    ADP-glucose pyrophosphorylase (AGPase), a heterotetrameric enzyme composed of two small and two large subunits, catalyses the first committed step of starch synthesis in plant tissues. In an attempt to learn more about the organization and expression of the small-subunit gene of AGPase, we have studied the small-subunit transcripts as well as the structure of the gene encoding these transcripts in barley (Hordeum vulgare L. cv. Bomi). Two different transcripts (bepsF1 and blps14) were identified: bepF1 was abundantly expressed in the starchy endosperm but not in leaves, whereas blps14 was isolated from leaves but was also found to be present at a moderate level in the starchy endosperm. The sequences for the two transcripts are identical over approx. 90% of the length, with differences being confined solely to their 5' ends. In blps14, the unique 5' end is 259 nt long and encodes a putative plastid transit peptide sequence. For the 178-nt 5' end of bepsF1, on the other hand, no transit peptide sequence could be recognized. A lambda clone that hybridized to the AGPase transcripts was isolated from a barley genomic library and characterized. The restriction map has suggested a complex organization of the gene, with alternative exons encoding the different 5' ends of the two transcripts followed by nine exons coding for the common part of the transcripts. The sequence of a portion of the genomic clone, covering the alternative 5'-end exons as well as upstream regions, has verified that both transcripts are encoded by the gene. The results suggest that the small-subunit gene of barley AGPase transcribes two different mRNAs by a mechanism classified as alternative splicing. PMID:8546676

  12. Enhanced Production of Polysaccharide Through the Overexpression of Homologous Uridine Diphosphate Glucose Pyrophosphorylase Gene in a Submerged Culture of Lingzhi or Reishi Medicinal Mushroom, Ganoderma lucidum (Higher Basidiomycetes).

    PubMed

    Ji, Sen-Lin; Liu, Rui; Ren, Meng-Fei; Li, Huan-Jun; Xu, Jun-Wei

    2015-01-01

    This study aimed to improve polysaccharide production by engineering the biosynthetic pathway in Ganoderma lucidum through the overexpression of the homologous UDP glucose pyrophosphorylase (UGP) gene. The effects of UGP gene overexpression on intracellular polysaccharide (IPS) content, extracellular polysaccharide (EPS) production, and transcription levels of 3 genes encoding the enzymes involved in polysaccharide biosynthesis, including phosphoglucomutase (PGM), UGP, and α-1,3-glucan synthase (GLS), were investigated. The maximum IPS content and EPS production in G. lucidum overexpressing the UGP gene were 24.32 mg/100 mg dry weight and 1.66 g/L, respectively, which were higher by 42% and 36% than those of the wild-type strain. The transcription levels of PGM, UGP, and GLS were up-regulated by 1.6, 2.6, and 2.4-fold, respectively, in the engineered strain, suggesting that increased polysaccharide biosynthesis may result from a higher expression of those genes.

  13. Molecular characterization and sequence diversity of genes encoding the large subunit of the ADP-glucose pyrophosphorylase in wheat (Triticum aestivum L.).

    PubMed

    Rose, Meghan K; Huang, Xiu-Qiang; Brûlé-Babel, Anita

    2016-02-01

    The large subunit of ADP glucose pyrophosphorylase (AGPase), the rate limiting enzyme in starch biosynthesis in Triticum aestivum L., is encoded by the ADP glucose pyrophosphorylase large subunit (AGP-L) gene. This was the first report on the development of three genome-specific primer sets for isolating the complete genomic sequence of all three homoeologous AGP-L genes on group 1 chromosomes. All three AGP-L genes consisted of 15 introns and 15 exons. The lengths of the structural genes from start to stop codon were 3334 bp for AGP-L-A1, 3351 bp for AGP-L-B1, and 3340 bp for AGP-L-D1. The coding region was 1569 bases long in all three genomes. All three AGP-L genes encoded 522 amino acid residues including the transit peptide sequences with 62 amino acid residues and the mature protein with 460 amino acid residues. The mature protein of three AGP-L genes was highly conserved. Three AGP-L genes were sequenced in 47 diverse spring and winter wheat genotypes. One and two haplotypes were found for AGP-L-D1 and AGP-L-A1, respectively. In total, 67 SNPs (single nucleotide polymorphisms) and 13 indels (insertions or deletions) forming five haplotypes were identified for AGP-L-B1. All 13 indels and 58 of the 67 SNPs among the 47 genotypes were located in the non-coding regions, while the remaining nine SNPs were synonymous substitutions in the coding region. Significant LD was found among the 45 SNPs and ten indels located from intron 2 to intron 3. Association analysis indicated that four SNPs were strongly associated with seed number per spike and thousand kernel weight.

  14. The sweet potato ADP-glucose pyrophosphorylase gene (ibAGP1) promoter confers high-level expression of the GUS reporter gene in the potato tuber.

    PubMed

    Kim, Tae-Won; Goo, Young-Min; Lee, Cheol-Ho; Lee, Byung-Hyun; Bae, Jung-Myung; Lee, Shin-Woo

    2009-10-01

    Molecular farming refers to the process of creating bioengineered plants with the capability of producing potentially valuable products, such as drugs, vaccines, and chemicals. We have investigated the potential of the sweet potato ADP-glucose pyrophosphorylase gene (ibAGP1) promoter and its transit peptide (TP) as an expression system for the mass production of foreign proteins in potato. The ibAGP1 promoter and its TP sequence were transformed into potato along with beta-glucuronidase (GUS) as a reporter gene, and GUS activity was subsequently analyzed in the transgenic potato plants. In tuber tissues, GUS activity in transgenic plants carrying only the ibAGP1 promoter (ibAGP1::GUS) increased up to 15.6-fold compared with that of transgenic plants carrying only the CaMV35S promoter (CaMV35S::GUS). GUS activity in transgenic plants was further enhanced by the addition of the sweetpotato TP to the recombinant vector (ibAGP1::TP::GUS), with tuber tissues showing a 26-fold increase in activity compared with that in the CaMV35S::GUS-transgenic lines. In leaf tissues, the levels of GUS activity found in ibAGP1::GUS-transgenic lines were similar to those in CaMV35S::GUS-lines, but they were significantly enhanced in ibAGP1::TP::GUS-lines. GUS activity gradually increased with increasing tuber diameter in ibAGP1::GUS-transgenic plants, reaching a maximum level when the tuber was 35 mm in diameter. In contrast, extremely elevated levels of GUS activity - up to about 10-fold higher than that found in CaMV35S::GUS-lines - were found in ibAGP1::TP::GUS-transgenic lines at a much earlier stage of tuber development (diameter 4 mm), and these higher levels were maintained throughout the entire tuber developmental stage. These results suggest that the sweetpotato ibAGP1 promoter and its TP are a potentially strong foreign gene expression system that can be used for molecular farming in potato plants.

  15. Cloning and expression of GDP-D-mannose pyrophosphorylase gene and ascorbic acid content of acerola (Malpighia glabra L.) fruit at ripening stages.

    PubMed

    Badejo, Adebanjo A; Jeong, Seok T; Goto-Yamamoto, Nami; Esaka, Muneharu

    2007-09-01

    Acerola (Malpighia glabra L.) is one of the richest natural sources of L-ascorbic acid (AsA; vitamin C). GDP-D-mannose pyrophosphorylase (GMP; EC 2.7.7.13) was found to play a major role in the proposed AsA biosynthetic pathway in plants, considering that Arabidopsis vtc1-1 mutant with point mutation in this gene has a highly reduced AsA content. GMP cDNA was isolated from acerola fruits, designated MgGMP, using rapid amplification of cDNA ends (RACE), and its expression was monitored during fruit ripening. The full-length cDNA was found to have an ORF of 1083bp encoding a polypeptide of 361 amino acids. In silico analysis of the predicted amino acid sequence showed a pI of 6.45 and molecular mass of 39.7kD. MgGMP showed over 80% amino acid sequence identity with other plant GMP homologues. The phylogenetic tree shows the close relation of MgGMP to the GMP of other plants as against those from parasite, yeasts and mammals. Southern analysis indicated that M. glabra contains not less than two copies of GMP genes. Northern blot analysis showed the transcript abundance of MgGMP in all the organs of acerola examined, with the fruit having the highest expression. The relative transcript abundance of MgGMP mRNA levels in the fruits changes as the ripening process progresses, with the unripe green fruits having the highest relative mRNA level, and the lowest was found in the fruits at advanced ripening stage. A strong correlation was also observed between the relative MgGMP mRNA levels and the AsA contents of acerola during fruit ripening.

  16. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Progress report, April 1993--January 1994

    SciTech Connect

    Okita, T.W.

    1994-04-01

    Part I of this research concerns patterns of gene expression of ADPG-PP in native and transgenic potato plants. The expression of both potato ADPG-PP subunits were analyzed on the transcript and antigen levels. The small and large subunits were coordinately expressed during tuber development suggesting a role for the temporal regulation of ADPG-PP expression as well as providing further support for earlier work in the heterotetrameric subunit structure of the tuber enzyme. Part II involves studies on the structure-function relationships of ADPG-PP, more specifically the mutagenesis of the large and small subunit DNAs of ADPG-PP.

  17. Localization of the human UGP2 gene encoding the muscle isoform of UDPglucose pyrophosphorylase to 2p13-p14 by fluorescence in situ hybridization

    SciTech Connect

    Cheng, Sou-De; Peng, Hwei-Ling; Chang, Hwan-You

    1997-02-01

    UDPglucose pyrophosphorylase (UGP, EC 2.7.7.9) catalyzes the transfer of a glucose moiety from Glc1P to MgUTP, forming UDPglc and MgPPi. This reaction is necessary in several tissues. In liver and muscle, UDPglc is the direct precursor of glycogen, while in lactating mammary gland it is converted to UDPgalactose and thence lactose. Liver also requires UDPglc for the formation of UDPglucuronate, which then acts as a source for the formation of soluble glucuronides of xenobiotic and endobiotic metabolites destined for excretion. 6 refs., 1 fig.

  18. Reducing AsA leads to leaf lesion and defence response in knock-down of the AsA biosynthetic enzyme GDP-D-mannose pyrophosphorylase gene in tomato plant.

    PubMed

    Zhang, Chanjuan; Ouyang, Bo; Yang, Changxian; Zhang, Xiaohui; Liu, Hui; Zhang, Yuyang; Zhang, Junhong; Li, Hanxia; Ye, Zhibiao

    2013-01-01

    As a vital antioxidant, L-ascorbic acid (AsA) affects diverse biological processes in higher plants. Lack of AsA in cell impairs plant development. In the present study, we manipulated a gene of GDP-mannose pyrophosphorylase which catalyzes the conversion of D-mannose-1-P to GDP-D-mannose in AsA biosynthetic pathway and found out the phenotype alteration of tomato. In the tomato genome, there are four members of GMP gene family and they constitutively expressed in various tissues in distinct expression patterns. As expected, over-expression of SlGMP3 increased total AsA contents and enhanced the tolerance to oxidative stress in tomato. On the contrary, knock-down of SlGMP3 significantly decreased AsA contents below the threshold level and altered the phenotype of tomato plants with lesions and further senescence. Further analysis indicated the causes for this symptom could result from failing to instantly deplete the reactive oxygen species (ROS) as decline of free radical scavenging activity. More ROS accumulated in the leaves and then triggered expressions of defence-related genes and mimic symptom occurred on the leaves similar to hypersensitive responses against pathogens. Consequently, the photosynthesis of leaves was dramatically fallen. These results suggested the vital roles of AsA as an antioxidant in leaf function and defence response of tomato.

  19. Isolation and characterization of a starchless mutant of Arabidopsis thaliana (L. ) Heynh lacking ADPglucose pyrophosphorylase activity

    SciTech Connect

    Lin, Tsanpiao; Caspar, T.; Somerville, C.; Preiss, J. )

    1988-04-01

    A mutant of Arabidopsis thaliana lacking ADPglucose pyrophosphorylase activity (EC 2.7.7.27) was isolated (from a mutagenized population of plants) by screening for the absence of leaf starch. The mutant grows as vigorously as the wild type in continuous light but more slowly than the wild type in a 12 hours light/12 hours dark photoperiod. Genetic analysis showed that the deficiency of both starch and ADPglucose pyrophosphorylase activity were attributable to a single, nuclear, recessive mutation at a locus designated adg1. The absence of starch in the mutant demonstrates that starch synthesis in the chloroplast is entirely dependent on a pathway involving ADPglucose pyrophosphorylase. Analysis of leaf extracts by two-dimensional polyacrylamide gel electrophoresis followed by Western blotting experiments using antibodies specific for spinach ADPglucose pyrophosphorylase showed that two proteins, present in the wild type, were absent from the mutant. The heterozygous F{sub 1} progeny of a cross between the mutant and wild type had a specific activity of ADP-glucose pyrophosphorylase indistinguishable from the wild type. These observations suggest that the mutation in the adg1 gene in TL25 might affect a regulatory locus.

  20. Both UDP N-acetylglucosamine pyrophosphorylases of Tribolium castaneum are critical for molting, survival, and fecundity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A bioinformatics search of the genome of the red flour beetle, Tribolium castaneum, resulted in the identification of two genes encoding proteins closely related to UDP-N-acetylglucosamine pyrophosphorylases (UAP), which provide the activated precursor, UDP-N-acetylglucosamine, for the synthesis of ...

  1. Structure Function Relationships of ADP-Glucose Pyrophosphorylase and Branching Enzyme: Manipulation of Their Genes for Alteration of Starch Quanlity and Quantity

    SciTech Connect

    Jack Preiss

    2006-02-16

    Conversion of the Potato tuber ADP-glucose Pyrophopshorylase Regulatory Subunit into a Catalytic Subunit. ADP-glucose synthesis, a rate-limiting reaction in starch synthesis, is catalyzed by ADP-glucose pyrophosphorylase (ADPGlc PPase). The enzyme in plants is allosterically activated by 3-phosphoglycerate (3PGA) and inhibited by inorganic phosphate (Pi) and is composed of two subunits as a heterotetramer, a2b2. Subunit a is the catalytic subunit and subunit b is designated as the regulatory subunit.The b subunit increases the affinty of the activator for the catalytic subunit. Recent results have shown that the subunits are derived from the same ancestor subunit as the regulatory subunit can be converted to a catalytically subunit via mutation of just two amino acids. Lys44 and Thr54 in the large subunit from potato tuber were converted to the homologous catalytic subunit residues, Arg33 and Lys43. The activity of the large subunit mutants cannot be readily tested with a co-expressed wild-type small (catalytic) subunit because of the intrinsic activity of the latter. We co-expressed the regulatory-subunit mutants with SmallD145N, an inactive S subunit in which the catalytic Asp145 was mutated. The activity of the small (catalytic) subunit was reduced more than three orders of magnitude. Coexpression of the L subunit double mutant LargeK44R/T54K with SmallD145N generated an enzyme with considerable activity, 10% and 18% of the wildtype enzyme, in the ADP-glucose synthetic and pyrophosphorolytic direction, respectively. Replacement of those two residues in the small subunit by the homologous amino acids in the L subunits (mutations R33K and K43T) decreased the activity one and two orders of magnitude. The wild-type enzyme and SmallD145NLargeK44R/T54K had very similar kinetic properties indicating that the substrate site has been conserved. The fact that only two mutations in the L subunit restored enzyme activity is very strong evidence that the large subunit is

  2. Suppression of sorbitol dependence in a strain bearing a mutation in the SRB1/PSA1/VIG9 gene encoding GDP-mannose pyrophosphorylase by PDE2 overexpression suggests a role for the Ras/cAMP signal-transduction pathway in the control of yeast cell-wall biogenesis.

    PubMed

    Tomlin, G C; Hamilton, G E; Gardner, D C; Walmsley, R M; Stateva, L I; Oliver, S G

    2000-09-01

    Complementation studies and allele replacement in Saccharomyces cerevisiae revealed that PSA1/VIG9, an essential gene that encodes GDP-mannose pyrophosphorylase, is the wild-type SRB1 gene. Cloning and sequencing of the srb1-1 allele showed that it determines a single amino acid change from glycine to aspartic acid at residue 276 (srb1(D276)). Genetic evidence is presented showing that at least one further mutation is required for the sorbitol dependence of srb1(D276). A previously reported complementing gene, which this study has now identified as PDE2, is a multi-copy suppressor of sorbitol dependence and is not, as was previously suggested, the SRB1 gene. srb and pde2 mutants share a number of phenotypes, including lysis upon hypotonic shock and enhanced transformability. These data are consistent with the idea that the Ras/cAMP pathway might modulate cell-wall construction.

  3. Immunocytochemical localization of ADPglucose pyrophosphorylase in developing potato tuber cells

    SciTech Connect

    Kim, Woo Taek; Franceschi, V.R.; Okita, T.W. ); Robinson, N.L.; Morell, M.; Preiss, J. )

    1989-09-01

    The subcellular localization of ADPglucose pyrophosphorylase, a key regulatory enzyme in starch biosynthesis, was determined in developing potato tuber cells by immunocytochemical localization techniques at the light microscopy level. Specific labeling of ADPglucose pyrophosphorylase by either immunofluorescence or immunogold followed by silver enhancement was detected only in the amyloplasts and indicates that this enzyme is located exclusively in the amyloplasts in developing potato tuber cells. Labeling occurred on the starch grains and, in some instances, specific labeling patterns were evident which may be related to sites active in starch deposition.

  4. A starch deficient mutant of Arabidopsis thaliana with low ADPglucose pyrophosphorylase activity lacks one of the two subunits of the enzyme

    SciTech Connect

    Lin, Tsanpiao; Caspar, T.; Somerville, C.R.; Preiss, J. )

    1988-12-01

    A starch deficient mutant of Arabidopsis thaliana (L.) Heynh. has been isolated in which leaf extracts contain only about 5% as much activity of ADPglucose pyrophosphorylase (EC 2.7.7.27) as the wild type. A single, nuclear mutation at a previously undescribed locus designated adg2 is responsible for the mutant phenotype. Although the mutant contained only 5% as much ADPglucose pyrophosphorylase activity as the wild type, it accumulated 40% as much starch when grown in a 12 hour photoperiod. The mutant also contained about 40% as much starch as the wild type when grown in continuous light, suggesting that the rate of synthesis regulates its steady state accumulation. Immunological analysis of leaf extracts using antibodies against the spinach 54 and 51 kilodalton (kD) ADPglucose pyrophosphorylase subunits indicated that the mutant is deficient in a cross-reactive 54 kD polypeptide and has only about 4% as much as the wild type of a cross-reactive 51 kD polypeptide. This result and genetic studies suggested that adg2 is a structural gene which codes for the 54 kD polypeptide, and provides the first functional evidence that the 54 kD polypeptide is a required component of the native ADPglucose pyrophosphorylase enzyme.

  5. Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea.

    PubMed

    Machtey, Matías; Kuhn, Misty L; Flasch, Diane A; Aleanzi, Mabel; Ballicora, Miguel A; Iglesias, Alberto A

    2012-11-01

    Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.

  6. Insights into Glycogen Metabolism in Chemolithoautotrophic Bacteria from Distinctive Kinetic and Regulatory Properties of ADP-Glucose Pyrophosphorylase from Nitrosomonas europaea

    PubMed Central

    Machtey, Matías; Kuhn, Misty L.; Flasch, Diane A.; Aleanzi, Mabel; Ballicora, Miguel A.

    2012-01-01

    Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO2 via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms. PMID:22961847

  7. Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica.

    PubMed

    Edwards, Thomas E; Gardberg, Anna S; Phan, Isabelle Q H; Zhang, Yang; Staker, Bart L; Myler, Peter J; Lorimer, Donald D

    2015-05-01

    Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it appears to lack three α-helices at the N-terminus and contains two amino acids in the allosteric pocket that make it appear more like the enzyme from the human host than that from the other parasite T. brucei. Thus, allosteric inhibitors of T. brucei UAP are unlikely to target Entamoeba UAPs.

  8. PCR cloning and characterization of multiple ADP-glucose pyrophosphorylase cDNAs from tomato

    NASA Technical Reports Server (NTRS)

    Chen, B. Y.; Janes, H. W.; Gianfagna, T.

    1998-01-01

    Four ADP-glucose pyrophosphorylase (AGP) cDNAs were cloned from tomato fruit and leaves by the PCR techniques. Three of them (agp S1, agp S2, and agp S3) encode the large subunit of AGP, the fourth one (agp B) encodes the small subunit. The deduced amino acid sequences of the cDNAs show very high identities (96-98%) to the corresponding potato AGP isoforms, although there are major differences in tissue expression profiles. All four tomato AGP transcripts were detected in fruit and leaves; the predominant ones in fruit are agp B and agp S1, whereas in leaves they are agp B and agp S3. Genomic southern analysis suggests that the four AGP transcripts are encoded by distinct genes.

  9. Leishmania major UDP-sugar pyrophosphorylase salvages galactose for glycoconjugate biosynthesis.

    PubMed

    Damerow, Sebastian; Hoppe, Carolin; Bandini, Giulia; Zarnovican, Patricia; Buettner, Falk F R; Ferguson, Michael A J; Routier, Françoise H

    2015-10-01

    Leishmaniases are a set of tropical and sub-tropical diseases caused by protozoan parasites of the genus Leishmania whose severity ranges from self-healing cutaneous lesions to fatal visceral infections. Leishmania parasites synthesise a wide array of cell surface and secreted glycoconjugates that play important roles in infection. These glycoconjugates are particularly abundant in the promastigote form and known to be essential for establishment of infection in the insect midgut and effective transmission to the mammalian host. Since they are rich in galactose, their biosynthesis requires an ample supply of UDP-galactose. This nucleotide-sugar arises from epimerisation of UDP-glucose but also from an uncharacterised galactose salvage pathway. In this study, we evaluated the role of the newly characterised UDP-sugar pyrophosphorylase (USP) of Leishmania major in UDP-galactose biosynthesis. Upon deletion of the USP encoding gene, L. major lost the ability to synthesise UDP-galactose from galactose-1-phosphate but its ability to convert glucose-1-phosphate into UDP-glucose was fully maintained. Thus USP plays a role in UDP-galactose activation but does not significantly contribute to the de novo synthesis of UDP-glucose. Accordingly, USP was shown to be dispensable for growth and glycoconjugate biosynthesis under standard growth conditions. However, in a mutant seriously impaired in the de novo synthesis of UDP-galactose (due to deficiency of the UDP-glucose pyrophosphorylase) addition of extracellular galactose increased biosynthesis of the cell surface lipophosphoglycan. Thus under restrictive conditions, such as those encountered by Leishmania in its natural habitat, galactose salvage by USP may play a substantial role in biosynthesis of the UDP-galactose pool. We hypothesise that USP recycles galactose from the blood meal within the midgut of the insect for synthesis of the promastigote glycocalyx and thereby contributes to successful vector infection.

  10. On the Kinetic and Allosteric Regulatory Properties of the ADP-Glucose Pyrophosphorylase from Rhodococcus jostii: An Approach to Evaluate Glycogen Metabolism in Oleaginous Bacteria

    PubMed Central

    Cereijo, Antonela E.; Asencion Diez, Matías D.; Dávila Costa, José S.; Alvarez, Héctor M.; Iglesias, Alberto A.

    2016-01-01

    Rhodococcus spp. are oleaginous bacteria that accumulate glycogen during exponential growth. Despite the importance of these microorganisms in biotechnology, little is known about the regulation of carbon and energy storage, mainly the relationship between glycogen and triacylglycerols metabolisms. Herein, we report the molecular cloning and heterologous expression of the gene coding for ADP-glucose pyrophosphorylase (EC 2.7.7.27) of Rhodococcus jostii, strain RHA1. The recombinant enzyme was purified to electrophoretic homogeneity to accurately characterize its oligomeric, kinetic, and regulatory properties. The R. jostii ADP-glucose pyrophosphorylase is a homotetramer of 190 kDa exhibiting low basal activity to catalyze synthesis of ADP-glucose, which is markedly influenced by different allosteric effectors. Glucose-6P, mannose-6P, fructose-6P, ribose-5P, and phosphoenolpyruvate were major activators; whereas, NADPH and 6P-gluconate behaved as main inhibitors of the enzyme. The combination of glucose-6P and other effectors (activators or inhibitors) showed a cross-talk effect suggesting that the different metabolites could orchestrate a fine regulation of ADP-glucose pyrophosphorylase in R. jostii. The enzyme exhibited some degree of affinity toward ATP, GTP, CTP, and other sugar-1P substrates. Remarkably, the use of glucosamine-1P was sensitive to allosteric activation. The relevance of the fine regulation of R. jostii ADP-glucose pyrophosphorylase is further analyzed in the framework of proteomic studies already determined for the bacterium. Results support a critical role for glycogen as a temporal reserve that provides a pool of carbon able of be re-routed to produce long-term storage of lipids under certain conditions. PMID:27313571

  11. GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability of Aspergillus fumigatus.

    PubMed

    Jiang, Hechun; Ouyang, Haomiao; Zhou, Hui; Jin, Cheng

    2008-09-01

    GDP-mannose pyrophosphorylase (GMPP) catalyses the synthesis of GDP-mannose, which is the precursor for the mannose residues in glycoconjugates, using mannose 1-phosphate and GTP as substrates. Repression of GMPP in yeast leads to phenotypes including cell lysis, defective cell wall, and failure of polarized growth and cell separation. Although several GMPPs have been isolated and characterized in filamentous fungi, the physiological consequences of their actions are not clear. In this study, Afsrb1, which is a homologue of yeast SRB1/PSA1/VIG9, was identified in the Aspergillus fumigatus genome. The Afsrb1 gene was expressed in Escherichia coli, and recombinant AfSrb1 was functionally confirmed as a GMPP. By the replacement of the native Afsrb1 promoter with an inducible Aspergillus nidulans alcA promoter, the conditional inactivation mutant strain YJ-gmpp was constructed. The presence of 3 % glucose completely blocked transcription of P(alcA)-Afsrb1, and was lethal to strain YJ-gmpp. Repression of Afsrb1 expression in strain YJ-gmpp led to phenotypes including hyphal lysis, defective cell wall, impaired polarity maintenance, and branching site selection. Also, rapid germination and reduced conidiation were documented. However, in contrast to yeast, strain YJ-gmpp retained the ability to direct polarity establishment and septation. Our results showed that the Afsrb1 gene is essential for cell wall integrity, morphogenesis and viability of Aspergillus fumigatus.

  12. GDP-D-mannose pyrophosphorylase from Pogonatherum paniceum enhances salinity and drought tolerance of transgenic tobacco.

    PubMed

    Ai, Taobo; Liao, Xuehong; Li, Rui; Fan, Linhong; Luo, Fengxue; Xu, Ying; Wang, Shenghua

    Pogonatherum paniceum is a highly drought- and salt-tolerant plant species that is typically used for ecological restoration and the conservation of soil and water in many countries. Understanding the molecular mechanisms underlying plant abiotic stress responses, especially to salinity and drought stresses, in species such as P. paniceum could be important to broader crop improvement efforts. GDP-D-mannose pyrophosphorylase (GMPase) is the limiting enzyme in the synthesis of L-ascorbic acid (AsA), which plays a crucial role in the detoxification of reactive oxygen species (ROS). We have cloned and characterized the cDNA of the PpGMP gene of P. paniceum encoding a GMPase. The full-length cDNA sequence contains 1411 nucleotides encoding a putative protein with 361 amino acid residues and an approximate molecular mass of 39.68 kDa. The GMPase transcript was up-regulated in P. paniceum plants subjected to salinity and drought stress, respectively. Transgenic tobacco expressing PpGMPase exhibited enhanced salinity and drought resistance, a higher seed germination rate, better growth performance, a higher AsA content, a more stable redox state, higher superoxide dismutase (SOD) activity, and lower levels of malonaldehyde (MDA) and H2O2 under drought and salinity stress. Taken together, expression of PpGMPase in tobacco conferred salinity and drought stress tolerance by increasing the content of AsA, thereby enhancing ROS-detoxifying functions. Thus, PpGMP is a potential candidate gene for crop improvement.

  13. Up-regulation of sucrose synthase and UDP-glucose pyrophosphorylase impacts plant growth and metabolism.

    PubMed

    Coleman, Heather D; Ellis, Dave D; Gilbert, Margarita; Mansfield, Shawn D

    2006-01-01

    The effects of the overexpression of sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) on plant growth and metabolism were evaluated in tobacco (Nicotiana tabacum cv. Xanthi). T(1) transgenic plants expressing either gene under the control of a tandem repeat cauliflower mosaic virus 35S promoter (2x35S) or a xylem-localized 4CL promoter (4-coumarate:CoA ligase; 4CL) were generated, and reciprocally crossed to generate plants expressing both genes. Transcript levels, enzyme activity, growth parameters, fibre properties and carbohydrate content of stem tissue were quantified. The expression profiles of both genes confirmed the expression pattern of the promoters: 2x35S expressed more strongly in leaves, while 4CL expression was highest in stem tissue. In-depth plant characterization revealed that the single-transgene lines showed significant increases in the height growth compared with corresponding control lines. The double-transgene plants demonstrated an additive effect, proving to be even taller than the single-transgene parents. Several of these lines had associated increases in soluble sugar content. Although partitioning of storage carbohydrates into starch or cellulose was not observed, the increased height growth and increases in soluble carbohydrates suggest a role for SuSy as a marker in sink strength and lend credit to the function of UGPase in a similar role. The up-regulation of these two genes, although not increasing the percentage cellulose content, was effective in increasing the total biomass, and thus the overall cellulose yield, from a given plant.

  14. Multiple forms of ADP-glucose pyrophosphorylase from tomato fruit

    NASA Technical Reports Server (NTRS)

    Chen, B. Y.; Janes, H. W.

    1997-01-01

    ADP-glucose pyrophosphorylase (AGP) was purified from tomato (Lycopersicon esculentum Mill.) fruit to apparent homogeneity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis the enzyme migrated as two close bands with molecular weights of 50,000 and 51,000. Two-dimensional polyacrylamide gel electrophoresis analysis of the purified enzyme, however, revealed at least five major protein spots that could be distinguished by their slight differences in net charge and molecular weight. Whereas all of the spots were recognized by the antiserum raised against tomato fruit AGP holoenzyme, only three of them reacted strongly with antiserum raised against the potato tuber AGP large subunit, and the other two spots (with lower molecular weights) reacted specifically with antisera raised against spinach leaf AGP holoenzyme and the potato tuber AGP small subunit. The results suggest the existence of at least three isoforms of the AGP large subunit and two isoforms of the small subunit in tomato fruit in vivo. The native molecular mass of the enzyme determined by gel filtration was 220 +/- 10 kD, indicating a tetrameric structure for AGP from tomato fruit. The purified enzyme is very sensitive to 3-phosphoglycerate/inorganic phosphate regulation.

  15. Characterization of Recombinant UDP- and ADP-Glucose Pyrophosphorylases and Glycogen Synthase To Elucidate Glucose-1-Phosphate Partitioning into Oligo- and Polysaccharides in Streptomyces coelicolor

    PubMed Central

    Asención Diez, Matías D.; Peirú, Salvador; Demonte, Ana M.; Gramajo, Hugo

    2012-01-01

    Streptomyces coelicolor exhibits a major secondary metabolism, deriving important amounts of glucose to synthesize pigmented antibiotics. Understanding the pathways occurring in the bacterium with respect to synthesis of oligo- and polysaccharides is of relevance to determine a plausible scenario for the partitioning of glucose-1-phosphate into different metabolic fates. We report the molecular cloning of the genes coding for UDP- and ADP-glucose pyrophosphorylases as well as for glycogen synthase from genomic DNA of S. coelicolor A3(2). Each gene was heterologously expressed in Escherichia coli cells to produce and purify to electrophoretic homogeneity the respective enzymes. UDP-glucose pyrophosphorylase (UDP-Glc PPase) was characterized as a dimer exhibiting a relatively high Vmax in catalyzing UDP-glucose synthesis (270 units/mg) and with respect to dTDP-glucose (94 units/mg). ADP-glucose pyrophosphorylase (ADP-Glc PPase) was found to be tetrameric in structure and specific in utilizing ATP as a substrate, reaching similar activities in the directions of ADP-glucose synthesis or pyrophosphorolysis (Vmax of 0.15 and 0.27 units/mg, respectively). Glycogen synthase was arranged as a dimer and exhibited specificity in the use of ADP-glucose to elongate α-1,4-glucan chains in the polysaccharide. ADP-Glc PPase was the only of the three enzymes exhibiting sensitivity to allosteric regulation by different metabolites. Mannose-6-phosphate, phosphoenolpyruvate, fructose-6-phosphate, and glucose-6-phosphate behaved as major activators, whereas NADPH was a main inhibitor of ADP-Glc PPase. The results support a metabolic picture where glycogen synthesis occurs via ADP-glucose in S. coelicolor, with the pathway being strictly regulated in connection with other routes involved with oligo- and polysaccharides, as well as with antibiotic synthesis in the bacterium. PMID:22210767

  16. Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis.

    PubMed

    Medeot, Daniela B; Romina Rivero, María; Cendoya, Eugenia; Contreras-Moreira, Bruno; Rossi, Fernando A; Fischer, Sonia E; Becker, Anke; Jofré, Edgardo

    2016-03-01

    In Gram-negative bacteria, tyrosine phosphorylation has been shown to play a role in the control of exopolysaccharide (EPS) production. This study demonstrated that the chromosomal ORF SMc02309 from Sinorhizobium meliloti 2011 encodes a protein with significant sequence similarity to low molecular mass protein-tyrosine phosphatases (LMW-PTPs), such as the Escherichia coli Wzb. Unlike other well-characterized EPS biosynthesis gene clusters, which contain neighbouring LMW-PTPs and kinase, the S. meliloti succinoglycan (EPS I) gene cluster located on megaplasmid pSymB does not encode a phosphatase. Biochemical assays revealed that the SMc02309 protein hydrolyses p-nitrophenyl phosphate (p-NPP) with kinetic parameters similar to other bacterial LMW-PTPs. Furthermore, we show evidence that SMc02309 is not the LMW-PTP of the bacterial tyrosine-kinase (BY-kinase) ExoP. Nevertheless, ExoN, a UDP-glucose pyrophosphorylase involved in the first stages of EPS I biosynthesis, is phosphorylated at tyrosine residues and constitutes an endogenous substrate of the SMc02309 protein. Additionally, we show that the UDP-glucose pyrophosphorylase activity is modulated by SMc02309-mediated tyrosine dephosphorylation. Moreover, a mutation in the SMc02309 gene decreases EPS I production and delays nodulation on Medicago sativa roots.

  17. Improving starch yield in cereals by over-expression of ADPglucose pyrophosphorylase: expectations and unanticipated outcomes.

    PubMed

    Tuncel, Aytug; Okita, Thomas W

    2013-10-01

    Significant improvements in crop productivity are required to meet the nutritional requirements of a growing world population. This challenge is magnified by an increased demand for bioenergy as a means to mitigate carbon inputs into the environment. Starch is a major component of the harvestable organs of many crop plants, and various endeavors have been taken to improve the yields of starchy organs through the manipulation of starch synthesis. Substantial efforts have centered on the starch regulatory enzyme ADPglucose pyrophosphorylase (AGPase) due to its pivotal role in starch biosynthesis. These efforts include over-expression of this enzyme in cereal plants such as maize, rice and wheat as well as potato and cassava, as they supply the bulk of the staple food worldwide. In this perspective, we describe efforts to increase starch yields in cereal grains by first providing an introduction about the importance of source-sink relationship and the motives behind the efforts to alter starch biosynthesis and turnover in leaves. We then discuss the catalytic and regulatory properties of AGPase and the molecular approaches used to enhance starch synthesis by manipulation of this process during grain filling using seed-specific promoters. Several studies have demonstrated increases in starch content per seed using endosperm-specific promoters, but other studies have demonstrated an increase in seed number with only marginal impact on seed weight. Potential mechanisms that may be responsible for this paradoxical increase in seed number will also be discussed. Finally, we describe current efforts and future prospects to improve starch yield in cereals. These efforts include further enhancement of starch yield in rice by augmenting the process of ADPglucose transport into amyloplast as well as other enzymes involved in photoassimilate partitioning in seeds.

  18. Aspartic acid 413 is important for the normal allosteric functioning of ADP-glucose pyrophosphorylase.

    PubMed Central

    Greene, T W; Woodbury, R L; Okita, T W

    1996-01-01

    As part of a structure-function analysis of the higher-plant ADP-glucose pyrophosphorylase (AGP), we used a random mutagenesis approach in combination with a novel bacterial complementation system to isolate over 100 mutants that were defective in glycogen production (T.W. Greene, S.E. Chantler, M.L. Khan, G.F. Barry, J. Preiss, T.W. Okita [1996] Proc Natl Acad Sci USA 93: 1509-1513). One mutant of the large subunit M27 was identified by its capacity to only partially complement a mutation in the structural gene for the bacterial AGP (glg C), as determined by its light-staining phenotype when cells were exposed to l3 vapors. Enzyme-linked immunosorbent assay and enzymatic pyrophosphorylysis assays of M27 cell extracts showed that the level of expression and AGP activity was comparable to those of cells that expressed the wild-type recombinant enzyme. Kinetic analysis indicated that the M27 AGP displays normal Michaelis constant values for the substrates glucose-1-phosphate and ATP but requires 6- to 10-fold greater levels of 3-phosphoglycerate (3-PGA) than the wild-type recombinant enzyme for maximum activation. DNA sequence analysis showed that M27 contains a single point mutation that resulted in the replacement of aspartic acid 413 to alanine. Substitution of a lysine residue at this site almost completely abolished activation by 3-PGA. Aspartic acid 413 is adjacent to a lysine residue that was previously identified by chemical modification studies to be important in the binding of 3-PGA (K. Ball, J. Preiss [1994] J Biol Chem 269: 24706-24711). The kinetic properties of M27 corroborate the importance of this region in the allosteric regulation of a higher-plant AGP. PMID:8938421

  19. Functional inactivation of UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) induces early leaf senescence and defence responses in rice.

    PubMed

    Wang, Zhaohai; Wang, Ya; Hong, Xiao; Hu, Daoheng; Liu, Caixiang; Yang, Jing; Li, Yang; Huang, Yunqing; Feng, Yuqi; Gong, Hanyu; Li, Yang; Fang, Gen; Tang, Huiru; Li, Yangsheng

    2015-02-01

    Plant leaf senescence and defence responses are important biological processes, but the molecular mechanisms involved are not well understood. This study identified a new rice mutant, spotted leaf 29 (spl29). The SPL29 gene was identified by map-based cloning, and SPL29 was confirmed as UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) by enzymatic analysis. The mutant spl29 lacks UAP activity. The biological phenotypes for which UAP is responsible have not previously been reported in plants. The spl29 mutant displayed early leaf senescence, confirmed by chlorophyll loss and photosystem II decline as physiological indicators, chloroplast degradation as a cellular characteristic, and both upregulation of senescence transcription factors and senescence-associated genes, and downregulation of photosynthesis-related genes, as molecular evidence. Defence responses were induced in the spl29 mutant, shown by enhanced resistance to bacterial blight inoculation and upregulation of defence response genes. Reactive oxygen species, including O2 (-) and H2O2, accumulated in spl29 plants; there was also increased malondialdehyde content. Enhanced superoxide dismutase activity combined with normal catalase activity in spl29 could be responsible for H2O2 accumulation. The plant hormones jasmonic acid and abscisic acid also accumulated in spl29 plants. ROS and plant hormones probably play important roles in early leaf senescence and defence responses in the spl29 mutant. Based on these findings, it is suggested that UAP1 is involved in regulating leaf senescence and defence responses in rice.

  20. Functional inactivation of UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) induces early leaf senescence and defence responses in rice

    PubMed Central

    Wang, Zhaohai; Wang, Ya; Hong, Xiao; Hu, Daoheng; Liu, Caixiang; Yang, Jing; Li, Yang; Huang, Yunqing; Feng, Yuqi; Gong, Hanyu; Li, Yang; Fang, Gen; Tang, Huiru; Li, Yangsheng

    2015-01-01

    Plant leaf senescence and defence responses are important biological processes, but the molecular mechanisms involved are not well understood. This study identified a new rice mutant, spotted leaf 29 (spl29). The SPL29 gene was identified by map-based cloning, and SPL29 was confirmed as UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) by enzymatic analysis. The mutant spl29 lacks UAP activity. The biological phenotypes for which UAP is responsible have not previously been reported in plants. The spl29 mutant displayed early leaf senescence, confirmed by chlorophyll loss and photosystem II decline as physiological indicators, chloroplast degradation as a cellular characteristic, and both upregulation of senescence transcription factors and senescence-associated genes, and downregulation of photosynthesis-related genes, as molecular evidence. Defence responses were induced in the spl29 mutant, shown by enhanced resistance to bacterial blight inoculation and upregulation of defence response genes. Reactive oxygen species, including O2 – and H2O2, accumulated in spl29 plants; there was also increased malondialdehyde content. Enhanced superoxide dismutase activity combined with normal catalase activity in spl29 could be responsible for H2O2 accumulation. The plant hormones jasmonic acid and abscisic acid also accumulated in spl29 plants. ROS and plant hormones probably play important roles in early leaf senescence and defence responses in the spl29 mutant. Based on these findings, it is suggested that UAP1 is involved in regulating leaf senescence and defence responses in rice. PMID:25399020

  1. Molecular and functional analysis of UDP-N-acetylglucosamine Pyrophosphorylases from the Migratory Locust, Locusta migratoria.

    PubMed

    Liu, Xiaojian; Li, Feng; Li, Daqi; Ma, Enbo; Zhang, Wenqing; Zhu, Kun Yan; Zhang, Jianzhen

    2013-01-01

    UDP-N-acetylglucosamine pyrophosphorylases (UAP) function in the formation of extracellular matrix by producing N-acetylglucosamine (GlcNAc) residues needed for chitin biosynthesis and protein glycosylation. Herein, we report two UAP cDNA's derived from two different genes (LmUAP1 and LmUAP2) in the migratory locust Locusta migratoria. Both the cDNA and their deduced amino acid sequences showed about 70% identities between the two genes. Phylogenetic analysis suggests that LmUAP1 and LmUAP2 derive from a relatively recent gene duplication event. Both LmUAP1 and LmUAP2 were widely expressed in all the major tissues besides chitin-containing tissues. However, the two genes exhibited different developmental expression patterns. High expression of LmUAP1 was detected during early embryogenesis, then decreased greatly, and slowly increased before egg hatch. During nymphal development, the highest expression of LmUAP1 appeared just after molting but declined in each inter-molting period and then increased before molting to the next stage, whereas LmUAP2 was more consistently expressed throughout all these stages. When the early second- and fifth-instar nymphs (1-day-old) were injected with LmUAP1 double-stranded RNA (dsRNA), 100% mortality was observed 2 days after the injection. When the middle second- and fifth-instar nymphs (3- to 4-day-old) were injected with LmUAP1 dsRNA, 100% mortality was observed during their next molting process. In contrast, when the insects at the same stages were injected with LmUAP2 dsRNA, these insects were able to develop normally and molt to the next stage successfully. It is presumed that the lethality caused by RNAi of LmUAP1 is due to reduced chitin biosynthesis of the integument and midgut, whereas LmUAP2 is not essential for locust development at least in nymph stage. This study is expected to help better understand different functions of UAP1 and UAP2 in the locust and other insect species.

  2. Molecular and Functional Analysis of UDP-N-Acetylglucosamine Pyrophosphorylases from the Migratory Locust, Locusta migratoria

    PubMed Central

    Li, Daqi; Ma, Enbo; Zhang, Wenqing; Zhu, Kun Yan; Zhang, Jianzhen

    2013-01-01

    UDP-N-acetylglucosamine pyrophosphorylases (UAP) function in the formation of extracellular matrix by producing N-acetylglucosamine (GlcNAc) residues needed for chitin biosynthesis and protein glycosylation. Herein, we report two UAP cDNA’s derived from two different genes (LmUAP1 and LmUAP2) in the migratory locust Locusta migratoria. Both the cDNA and their deduced amino acid sequences showed about 70% identities between the two genes. Phylogenetic analysis suggests that LmUAP1 and LmUAP2 derive from a relatively recent gene duplication event. Both LmUAP1 and LmUAP2 were widely expressed in all the major tissues besides chitin-containing tissues. However, the two genes exhibited different developmental expression patterns. High expression of LmUAP1 was detected during early embryogenesis, then decreased greatly, and slowly increased before egg hatch. During nymphal development, the highest expression of LmUAP1 appeared just after molting but declined in each inter-molting period and then increased before molting to the next stage, whereas LmUAP2 was more consistently expressed throughout all these stages. When the early second- and fifth-instar nymphs (1-day-old) were injected with LmUAP1 double-stranded RNA (dsRNA), 100% mortality was observed 2 days after the injection. When the middle second- and fifth-instar nymphs (3- to 4-day-old) were injected with LmUAP1 dsRNA, 100% mortality was observed during their next molting process. In contrast, when the insects at the same stages were injected with LmUAP2 dsRNA, these insects were able to develop normally and molt to the next stage successfully. It is presumed that the lethality caused by RNAi of LmUAP1 is due to reduced chitin biosynthesis of the integument and midgut, whereas LmUAP2 is not essential for locust development at least in nymph stage. This study is expected to help better understand different functions of UAP1 and UAP2 in the locust and other insect species. PMID:23977188

  3. Plastidic phosphoglucomutase and ADP-glucose pyrophosphorylase mutants impair starch synthesis in rice pollen grains and cause male sterility

    PubMed Central

    Lee, Sang-Kyu; Eom, Joon-Seob; Hwang, Seon-Kap; Shin, Dongjin; An, Gynheung; Okita, Thomas W.; Jeon, Jong-Seong

    2016-01-01

    To elucidate the starch synthesis pathway and the role of this reserve in rice pollen, we characterized mutations in the plastidic phosphoglucomutase, OspPGM, and the plastidic large subunit of ADP-glucose (ADP-Glc) pyrophosphorylase, OsAGPL4. Both genes were up-regulated in maturing pollen, a stage when starch begins to accumulate. Progeny analysis of self-pollinated heterozygous lines carrying the OspPGM mutant alleles, osppgm-1 and osppgm-2, or the OsAGPL4 mutant allele, osagpl4-1, as well as reciprocal crosses between the wild type (WT) and heterozygotes revealed that loss of OspPGM or OsAGPL4 caused male sterility, with the former condition rescued by the introduction of the WT OspPGM gene. While iodine staining and transmission electron microscopy analyses of pollen grains from homozygous osppgm-1 lines produced by anther culture confirmed the starch null phenotype, pollen from homozygous osagpl4 mutant lines, osagpl4-2 and osagpl4-3, generated by the CRISPR/Cas system, accumulated small amounts of starch which were sufficient to produce viable seed. Such osagpl4 mutant pollen, however, was unable to compete against WT pollen successfully, validating the important role of this reserve in fertilization. Our results demonstrate that starch is mainly polymerized from ADP-Glc synthesized from plastidic hexose phosphates in rice pollen and that starch is an essential requirement for successful fertilization in rice. PMID:27588462

  4. Plastidic phosphoglucomutase and ADP-glucose pyrophosphorylase mutants impair starch synthesis in rice pollen grains and cause male sterility.

    PubMed

    Lee, Sang-Kyu; Eom, Joon-Seob; Hwang, Seon-Kap; Shin, Dongjin; An, Gynheung; Okita, Thomas W; Jeon, Jong-Seong

    2016-10-01

    To elucidate the starch synthesis pathway and the role of this reserve in rice pollen, we characterized mutations in the plastidic phosphoglucomutase, OspPGM, and the plastidic large subunit of ADP-glucose (ADP-Glc) pyrophosphorylase, OsAGPL4 Both genes were up-regulated in maturing pollen, a stage when starch begins to accumulate. Progeny analysis of self-pollinated heterozygous lines carrying the OspPGM mutant alleles, osppgm-1 and osppgm-2, or the OsAGPL4 mutant allele, osagpl4-1, as well as reciprocal crosses between the wild type (WT) and heterozygotes revealed that loss of OspPGM or OsAGPL4 caused male sterility, with the former condition rescued by the introduction of the WT OspPGM gene. While iodine staining and transmission electron microscopy analyses of pollen grains from homozygous osppgm-1 lines produced by anther culture confirmed the starch null phenotype, pollen from homozygous osagpl4 mutant lines, osagpl4-2 and osagpl4-3, generated by the CRISPR/Cas system, accumulated small amounts of starch which were sufficient to produce viable seed. Such osagpl4 mutant pollen, however, was unable to compete against WT pollen successfully, validating the important role of this reserve in fertilization. Our results demonstrate that starch is mainly polymerized from ADP-Glc synthesized from plastidic hexose phosphates in rice pollen and that starch is an essential requirement for successful fertilization in rice.

  5. Impact of Heterologous Expression of Escherichia coli UDP-Glucose Pyrophosphorylase on Trehalose and Glycogen Synthesis in Corynebacterium glutamicum

    PubMed Central

    Padilla, Leandro; Morbach, Susanne; Krämer, Reinhard; Agosin, Eduardo

    2004-01-01

    Trehalose is a disaccharide with a wide range of applications in the food industry. We recently proposed a strategy for trehalose production based on improved strains of the gram-positive bacterium Corynebacterium glutamicum. This microorganism synthesizes trehalose through two major pathways, OtsBA and TreYZ, by using UDP-glucose and ADP-glucose, respectively, as the glucosyl donors. In this paper we describe improvement of the UDP-glucose supply through heterologous expression in C. glutamicum of the UDP-glucose pyrophosphorylase gene from Escherichia coli, either expressed alone or coexpressed with the E. coli ots genes (galU otsBA synthetic operon). The impact of such expression on trehalose accumulation and excretion, glycogen accumulation, and the growth pattern of new recombinant strains is described. Expression of the galU otsBA synthetic operon resulted in a sixfold increase in the accumulated and excreted trehalose relative to that in a wild-type strain. Surprisingly, single expression of galU also resulted in an increase in the accumulated trehalose. This increase in trehalose synthesis was abolished upon deletion of the TreYZ pathway. These results proved that UDP-glucose has an important role not only in the OtsBA pathway but also in the TreYZ pathway. PMID:15240254

  6. Enhanced UDP-glucose and UDP-galactose by homologous overexpression of UDP-glucose pyrophosphorylase in Lactobacillus casei.

    PubMed

    Rodríguez-Díaz, Jesús; Yebra, María J

    2011-07-20

    UDP-sugars are widely used as substrates in the synthesis of oligosaccharides catalyzed by glycosyltransferases. In the present work a metabolic engineering strategy aimed to direct the carbon flux towards UDP-glucose and UDP-galactose biosynthesis was successfully applied in Lactobacillus casei. The galU gene coding for UDP-glucose pyrophosphorylase (GalU) enzyme in L. casei BL23 was cloned under control of the inducible nisA promoter and it was shown to be functional by homologous overexpression. Notably, about an 80-fold increase in GalU activity resulted in approximately a 9-fold increase of UDP-glucose and a 4-fold increase of UDP-galactose. This suggested that the endogenous UDP-galactose 4-epimerase (GalE) activity, which inter-converts both UDP-sugars, is not sufficient to maintain the UDP-glucose/UDP-galactose ratio. The L. casei galE gene coding for GalE was cloned downstream of galU and the resulting plasmid was transformed in L. casei. The new recombinant strain showed about a 4-fold increase of GalE activity, however this increment did not affect that ratio, suggesting that GalE has higher affinity for UDP-galactose than for UDP-glucose. The L. casei strains constructed here that accumulate high intracellular levels of UDP-sugars would be adequate hosts for the production of oligosaccharides.

  7. The subunit structure of potato tuber ADPglucose pyrophosphorylase. [Solanum tuberosum L

    SciTech Connect

    Okita, T.W.; Nakata, P.A.; Anderson, J.M. ); Sowokinos, J. ); Morell, M.; Preiss, J. )

    1990-06-01

    ADPglucose pyrophosphorylase has been extensively purified from potato (Solanum tuberosum L.) tuber tissue to study its structure. By employing a modified published procedure together with Mono Q chromatography, a near homogeneous enzyme preparation was obtained with substantial improvement in enzyme yield and specific activity. In single dimensional sodium dodecyl sulfate polyacrylamide gels, the enzyme migrated as a single polypeptide band with a mobility of about 50,000 daltons. Analysis by two-dimensional polyacrylamide gel electrophoresis, however, revealed the presence of two types of subunits which could be distinguished by their slight differences in net charge and molecular weight. The smaller potato tuber subunit was recognized by antiserum prepared against the smaller spinach leaf 51 kilodalton ADPglucose pyrophosphorylase subunit. In contrast, the anti-54 kilodalton raised against the spinach leaf subunit did not significantly react to the tuber enzyme subunits. The results are consistent with the hypothesis that the potato tuber ADPglucose pyrophosphorylase is not composed of a simple homotetramer as previously suggested, but is a product of two separate and distinct subunits as observed for the spinach leaf and maize enzymes.

  8. Mutagenesis of the potato ADPglucose pyrophosphorylase and characterization of an allosteric mutant defective in 3-phosphoglycerate activation

    SciTech Connect

    Greene, T.W.; Chantler, S.E.; Kahn, M.L.

    1996-02-20

    ADPglucose pyrophosphorylase (glucose-1-phosphate adenylytransferase; AD P:{alpha}-D-glucose-1-phosphate adenylyltransferase, EC 2.7.7.27) catalyzes a key regulatory step in {alpha}-glucan synthesis in bacteria and higher plants. We have previously shown that the expression of the cDNA sequences of the potato tuber large (LS) and small (SS) subunits yielded a functional heterotetrameric enzyme capable of complementing a mutation in the single AGP (glgC) structural gene of Escherichia coli. This heterologous complementation provides a powerful genetic approach to obtain biochemical information on the specific roles of LS and SS in enzyme function. By mutagenizing the LS cDNA with hydroxylamine and then coexpressing with wild-type SS in an E. coli glgC{sup {minus}} strain, >350 mutant colonies were identified that were impaired in glycogen production. One mutant exhibited enzymatic and antigen levels comparable to the wild-type recombinant enzyme but required 45-fold greater levels of the activator 3-phosphoglycerate for maximum activity. Sequence analysis identified a single nucleotide change that resulted in the change of Pro-52 to Leu. This heterologous genetic system provides and efficient means to identify residues important for catalysis and allosteric functioning and should lead to novel approaches to increase plant productivity. 31 refs., 4 figs., 1 tab.

  9. Enhanced heat stability and kinetic parameters of maize endosperm ADPglucose pyrophosphorylase by alteration of phylogenetically identified amino acids.

    PubMed

    Boehlein, Susan K; Shaw, Janine R; Georgelis, Nikolaos; Hannah, L Curtis

    2014-02-01

    ADP-glucose pyrophosphorylase (AGPase) controls the rate-limiting step in starch biosynthesis and is regulated at various levels. Cereal endosperm enzymes, in contrast to other plant AGPases, are particularly heat labile and transgenic studies highlight the importance of temperature for cereal yield. Previously, a phylogenetic approach identified Type II and positively selected amino acid positions in the large subunit of maize endosperm AGPase. Glycogen content, kinetic parameters and heat stability were measured in AGPases having mutations in these sites and interesting differences were observed. This study expands on our earlier evolutionary work by determining how all Type II and positively selected sites affect kinetic constants, heat stability and catalytic rates at increased temperatures. Variants with enhanced properties were identified and combined into one gene, designated Sh2-E. Enhanced properties include: heat stability, enhanced activity at 37 °C, activity at 55 °C, reduced Ka and activity in the absence of activator. The resulting enzyme exhibited all improved properties of the various individual changes. Additionally, Sh2-E was expressed with a small subunit variant with enhanced enzyme properties resulting in an enzyme that has exceptional heat stability, a high catalytic rate at increased temperatures and significantly decreased Km values for both substrates in the absence of the activator.

  10. Transcriptional and Metabolic Adjustments in ADP-Glucose Pyrophosphorylase-Deficient bt2 Maize Kernels1[W

    PubMed Central

    Cossegal, Magalie; Chambrier, Pierre; Mbelo, Sylvie; Balzergue, Sandrine; Martin-Magniette, Marie-Laure; Moing, Annick; Deborde, Catherine; Guyon, Virginie; Perez, Pascual; Rogowsky, Peter

    2008-01-01

    During the cloning of monogenic recessive mutations responsible for a defective kernel phenotype in a Mutator-induced Zea mays mutant collection, we isolated a new mutant allele in Brittle2 (Bt2), which codes for the small subunit of ADP-glucose pyrophosphorylase (AGPase), a key enzyme in starch synthesis. Reverse transcription-polymerase chain reaction experiments with gene-specific primers confirmed a predominant expression of Bt2 in endosperm, of Agpsemzm in embryo, and of Agpslzm in leaf, but also revealed considerable additional expression in various tissues for all three genes. Bt2a, the classical transcript coding for a cytoplasmic isoform, was almost exclusively expressed in the developing endosperm, whereas Bt2b, an alternative transcript coding for a plastidial isoform, was expressed in almost all tissues tested with a pattern very similar to that of Agpslzm. The phenotypic analysis showed that, at 30 d after pollination (DAP), mutant kernels were plumper than wild-type kernels, that the onset of kernel collapse took place between 31 and 35 DAP, and that the number of starch grains was greatly reduced in the mutant endosperm but not the mutant embryo. A comparative transcriptome analysis of wild-type and bt2-H2328 kernels at middevelopment (35 DAP) with the 18K GeneChip Maize Genome Array led to the conclusion that the lack of Bt2-encoded AGPase triggers large-scale changes on the transcriptional level that concern mainly genes involved in carbohydrate or amino acid metabolic pathways. Principal component analysis of 1H nuclear magnetic resonance metabolic profiles confirmed the impact of the bt2-H2328 mutation on these pathways and revealed that the bt2-H2328 mutation did not only affect the endosperm, but also the embryo at the metabolic level. These data suggest that, in the bt2-H2328 endosperms, regulatory networks are activated that redirect excess carbon into alternative biosynthetic pathways (amino acid synthesis) or into other tissues (embryo

  11. Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity

    PubMed Central

    Dong, Suomeng; Yin, Weixiao; Kong, Guanghui; Yang, Xinyu; Qutob, Dinah; Chen, Qinghe; Kale, Shiv D.; Sui, Yangyang; Zhang, Zhengguang; Dou, Daolong; Zheng, Xiaobo; Gijzen, Mark; M. Tyler, Brett; Wang, Yuanchao

    2011-01-01

    Plants have evolved pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) to protect themselves from infection by diverse pathogens. Avirulence (Avr) effectors that trigger plant ETI as a result of recognition by plant resistance (R) gene products have been identified in many plant pathogenic oomycetes and fungi. However, the virulence functions of oomycete and fungal Avr effectors remain largely unknown. Here, we combined bioinformatics and genetics to identify Avr3b, a new Avr gene from Phytophthora sojae, an oomycete pathogen that causes soybean root rot. Avr3b encodes a secreted protein with the RXLR host-targeting motif and C-terminal W and Nudix hydrolase motifs. Some isolates of P. sojae evade perception by the soybean R gene Rps3b through sequence mutation in Avr3b and lowered transcript accumulation. Transient expression of Avr3b in Nicotiana benthamiana increased susceptibility to P. capsici and P. parasitica, with significantly reduced accumulation of reactive oxygen species (ROS) around invasion sites. Biochemical assays confirmed that Avr3b is an ADP-ribose/NADH pyrophosphorylase, as predicted from the Nudix motif. Deletion of the Nudix motif of Avr3b abolished enzyme activity. Mutation of key residues in Nudix motif significantly impaired Avr3b virulence function but not the avirulence activity. Some Nudix hydrolases act as negative regulators of plant immunity, and thus Avr3b might be delivered into host cells as a Nudix hydrolase to impair host immunity. Avr3b homologues are present in several sequenced Phytophthora genomes, suggesting that Phytophthora pathogens might share similar strategies to suppress plant immunity. PMID:22102810

  12. Screening assay for inhibitors of a recombinant Streptococcus pneumoniae UDP-glucose pyrophosphorylase.

    PubMed

    Zavala, Agustín; Kovacec, Verónica; Levín, Gustavo; Moglioni, Albertina; Miranda, María Victoria; García, Ernesto; Bonofiglio, Laura; Mollerach, Marta

    2017-12-01

    The UDP-glucose pyrophosphorylase of Streptococcus pneumoniae (GalUSpn) is absolutely required for the biosynthesis of capsular polysaccharide, the sine qua non virulence factor of pneumococcus. Since the eukaryotic enzymes are completely unrelated to their prokaryotic counterparts, we propose that the GalU enzyme is a critical target to fight the pneumococcal disease. A recombinant GalUSpn was overexpressed and purified. An enzymatic assay that is rapid, sensitive and easy to perform was developed. This assay was appropriate for screening chemical libraries for searching GalU inhibitors. This work represents a fundamental step in the exploration of novel antipneumococcal drugs.

  13. Comparison of Starch and ADP-Glucose Pyrophosphorylase Levels in Nonembryogenic Cells and Developing Embryos from Induced Carrot Cultures

    PubMed Central

    Keller, Gregory L.; Nikolau, Basil J.; Ulrich, Thomas H.; Wurtele, Eve Syrkin

    1988-01-01

    Cultures of carrot (Daucus carota L.) in a medium without added 2,4-dichlorophenoxyacetic acid were separated into fractions of embryos at different stages of development (large globular and heart, torpedo, and germinating) and nonembryogenic cells. The average starch content per cell in these fractions was similar. However, due to the smaller sizes of the cells of the embryos relative to the nonembryogenic cells, starch content per weight of tissue was higher in the embryos. The ADP-glucose pyrophosphorylase activity per cell in the nonembryogenic cells was double that of the embryo cells. Furthermore, the ratio of ADP-glucose pyrophosphorylase to starch was over 2-fold higher in the nonembryogenic cells, indicating that starch content is not simply determined by ADP-glucose pyrophosphorylase levels. ADP-glucose pyrophosphorylase activity of all culture fractions was directly proportional to the level of a single 50 kilodalton polypeptide detected by immunoblot analysis, using antiserum raised to the purified spinach leaf enzyme. In the same immunoblot analysis, novel polypeptides of 63 and 100 kilodalton were detected in embryos but were absent from nonembryogenic cells. This is one of the few reported examples of specific proteins which differentially accumulate in embryos and nonembryogenic cells. Images Fig. 2 PMID:16665929

  14. Substrate binding properties of potato tuber ADP-glucose pyrophosphorylase as determined by isothermal titration calorimetry.

    PubMed

    Cakir, Bilal; Tuncel, Aytug; Green, Abigail R; Koper, Kaan; Hwang, Seon-Kap; Okita, Thomas W; Kang, ChulHee

    2015-06-04

    Substrate binding properties of the large (LS) and small (SS) subunits of potato tuber ADP-glucose pyrophosphorylase were investigated by using isothermal titration calorimetry. Our results clearly show that the wild type heterotetramer (S(WT)L(WT)) possesses two distinct types of ATP binding sites, whereas the homotetrameric LS and SS variant forms only exhibited properties of one of the two binding sites. The wild type enzyme also exhibited significantly increased affinity to this substrate compared to the homotetrameric enzyme forms. No stable binding was evident for the second substrate, glucose-1-phosphate, in the presence or absence of ATPγS suggesting that interaction of glucose-1-phosphate is dependent on hydrolysis of ATP and supports the Theorell-Chance bi bi reaction mechanism.

  15. PCR amplification and sequences of cDNA clones for the small and large subunits of ADP-glucose pyrophosphorylase from barley tissues.

    PubMed

    Villand, P; Aalen, R; Olsen, O A; Lüthi, E; Lönneborg, A; Kleczkowski, L A

    1992-06-01

    Several cDNAs encoding the small and large subunit of ADP-glucose pyrophosphorylase (AGP) were isolated from total RNA of the starchy endosperm, roots and leaves of barley by polymerase chain reaction (PCR). Sets of degenerate oligonucleotide primers, based on previously published conserved amino acid sequences of plant AGP, were used for synthesis and amplification of the cDNAs. For either the endosperm, roots and leaves, the restriction analysis of PCR products (ca. 550 nucleotides each) has revealed heterogeneity, suggesting presence of three transcripts for AGP in the endosperm and roots, and up to two AGP transcripts in the leaf tissue. Based on the derived amino acid sequences, two clones from the endosperm, beps and bepl, were identified as coding for the small and large subunit of AGP, respectively, while a leaf transcript (blpl) encoded the putative large subunit of AGP. There was about 50% identity between the endosperm clones, and both of them were about 60% identical to the leaf cDNA. Northern blot analysis has indicated that beps and bepl are expressed in both the endosperm and roots, while blpl is detectable only in leaves. Application of the PCR technique in studies on gene structure and gene expression of plant AGP is discussed.

  16. Mutations in GDP-Mannose Pyrophosphorylase B Cause Congenital and Limb-Girdle Muscular Dystrophies Associated with Hypoglycosylation of α-Dystroglycan

    PubMed Central

    Carss, Keren J.; Stevens, Elizabeth; Foley, A. Reghan; Cirak, Sebahattin; Riemersma, Moniek; Torelli, Silvia; Hoischen, Alexander; Willer, Tobias; van Scherpenzeel, Monique; Moore, Steven A.; Messina, Sonia; Bertini, Enrico; Bönnemann, Carsten G.; Abdenur, Jose E.; Grosmann, Carla M.; Kesari, Akanchha; Punetha, Jaya; Quinlivan, Ros; Waddell, Leigh B.; Young, Helen K.; Wraige, Elizabeth; Yau, Shu; Brodd, Lina; Feng, Lucy; Sewry, Caroline; MacArthur, Daniel G.; North, Kathryn N.; Hoffman, Eric; Stemple, Derek L.; Hurles, Matthew E.; van Bokhoven, Hans; Campbell, Kevin P.; Lefeber, Dirk J.; Lin, Yung-Yao; Muntoni, Francesco

    2013-01-01

    Congenital muscular dystrophies with hypoglycosylation of α-dystroglycan (α-DG) are a heterogeneous group of disorders often associated with brain and eye defects in addition to muscular dystrophy. Causative variants in 14 genes thought to be involved in the glycosylation of α-DG have been identified thus far. Allelic mutations in these genes might also cause milder limb-girdle muscular dystrophy phenotypes. Using a combination of exome and Sanger sequencing in eight unrelated individuals, we present evidence that mutations in guanosine diphosphate mannose (GDP-mannose) pyrophosphorylase B (GMPPB) can result in muscular dystrophy variants with hypoglycosylated α-DG. GMPPB catalyzes the formation of GDP-mannose from GTP and mannose-1-phosphate. GDP-mannose is required for O-mannosylation of proteins, including α-DG, and it is the substrate of cytosolic mannosyltransferases. We found reduced α-DG glycosylation in the muscle biopsies of affected individuals and in available fibroblasts. Overexpression of wild-type GMPPB in fibroblasts from an affected individual partially restored glycosylation of α-DG. Whereas wild-type GMPPB localized to the cytoplasm, five of the identified missense mutations caused formation of aggregates in the cytoplasm or near membrane protrusions. Additionally, knockdown of the GMPPB ortholog in zebrafish caused structural muscle defects with decreased motility, eye abnormalities, and reduced glycosylation of α-DG. Together, these data indicate that GMPPB mutations are responsible for congenital and limb-girdle muscular dystrophies with hypoglycosylation of α-DG. PMID:23768512

  17. Analysis of Gene Targeting & Nonhomologous End-joining. Final Report

    SciTech Connect

    Haber, J. E.

    2002-11-30

    Overall, we identified a number of new proteins that participate in nonhomologous end-joining and also in telomere addition to the ends of broken chromosomes. We showed that NHEJ is severely reduced in cells expressing both yeast mating-type genes and then went on to identify the NEJ1 gene that was under this control. We showed the epistasis relations among a set of mutations that impair telomere addition and we showed that there are in fact two pathways to repair broken chromosomes in the absence of telomerase. We characterized the DNA damage checkpoint pathway in response to a single broken chromosome and characterized especially the adaptation of cells arrested by an unrepaired DSB. We demonstrated that the DNA damage response is nuclear-limited. We showed adaptation defects for Tid1and Srs2 proteins and showed that Srs2 was also recovery-defective, even when DNA was repaired.

  18. Proposed Consent Agreement and Final Order: Gene R. Cheeseman and GR Cheeseman Construction LLC

    EPA Pesticide Factsheets

    EPA's proposed Consent Agreement and Final Order in the matter of Gene R. Cheeseman and GR Cheeseman Construction LLC for violations of the Clean Water Act at their 5230 Shaune Drive property located in Juneau, Alaska.

  19. Two Leptinotarsa uridine diphosphate N-acetylglucosamine pyrophosphorylases are specialized for chitin synthesis in larval epidermal cuticle and midgut peritrophic matrix.

    PubMed

    Shi, Ji-Feng; Fu, Jia; Mu, Li-Li; Guo, Wen-Chao; Li, Guo-Qing

    2016-01-01

    Uridine diphosphate-N-acetylglucosamine-pyrophosphorylase (UAP) is involved in the biosynthesis of chitin, an essential component of the epidermal cuticle and midgut peritrophic matrix (PM) in insects. In the present paper, two putative LdUAP genes were cloned in Leptinotarsa decemlineata. In vivo bioassay revealed that 20-hydroxyecdysone (20E) and an ecdysteroid agonist halofenozide activated the expression of the two LdUAPs, whereas a decrease in 20E by RNA interference (RNAi) of an ecdysteroidogenesis gene LdSHD and a 20E signaling gene LdFTZ-F1 repressed the expression. Juvenile hormone (JH), a JH analog pyriproxyfen and an increase in JH by RNAi of an allatostatin gene LdAS-C downregulated LdUAP1 but upregulated LdUAP2, whereas a decrease in JH by silencing of a JH biosynthesis gene LdJHAMT had converse effects. Thus, expression of LdUAPs responded to both 20E and JH. Moreover, knockdown of LdUAP1 reduced chitin contents in whole larvae and integument samples, thinned tracheal taenidia, impaired larval-larval molt, larval-pupal ecdysis and adult emergence. In contrast, silencing of LdUAP2 significantly reduced foliage consumption, decreased chitin content in midgut samples, damaged PM, and retarded larval growth. The resulting larvae had lighter fresh weights, smaller body sizes and depleted fat body. As a result, the development was arrested. Combined knockdown of LdUAP1 and LdUAP2 caused an additive negative effect. Our data suggest that LdUAP1 and LdUAP2 have specialized functions in biosynthesizing chitin in the epidermal cuticle and PM respectively in L. decemlineata.

  20. Identification of Regions Critically Affecting Kinetics and Allosteric Regulation of the Escherichia coli ADP-Glucose Pyrophosphorylase by Modeling and Pentapeptide-Scanning Mutagenesis▿

    PubMed Central

    Ballicora, Miguel A.; Erben, Esteban D.; Yazaki, Terutaka; Bertolo, Ana L.; Demonte, Ana M.; Schmidt, Jennifer R.; Aleanzi, Mabel; Bejar, Clarisa M.; Figueroa, Carlos M.; Fusari, Corina M.; Iglesias, Alberto A.; Preiss, Jack

    2007-01-01

    ADP-glucose pyrophosphorylase (ADP-Glc PPase) is the enzyme responsible for the regulation of bacterial glycogen synthesis. To perform a structure-function relationship study of the Escherichia coli ADP-Glc PPase enzyme, we studied the effects of pentapeptide insertions at different positions in the enzyme and analyzed the results with a homology model. We randomly inserted 15 bp in a plasmid with the ADP-Glc PPase gene. We obtained 140 modified plasmids with single insertions of which 21 were in the coding region of the enzyme. Fourteen of them generated insertions of five amino acids, whereas the other seven created a stop codon and produced truncations. Correlation of ADP-Glc PPase activity to these modifications validated the enzyme model. Six of the insertions and one truncation produced enzymes with sufficient activity for the E. coli cells to synthesize glycogen and stain in the presence of iodine vapor. These were in regions away from the substrate site, whereas the mutants that did not stain had alterations in critical areas of the protein. The enzyme with a pentapeptide insertion between Leu102 and Pro103 was catalytically competent but insensitive to activation. We postulate this region as critical for the allosteric regulation of the enzyme, participating in the communication between the catalytic and regulatory domains. PMID:17496097

  1. UDP-sugar pyrophosphorylase is essential for arabinose and xylose recycling, and is required during vegetative and reproductive growth in Arabidopsis.

    PubMed

    Geserick, Claudia; Tenhaken, Raimund

    2013-04-01

    Numerous nucleotide sugars are needed in plants to synthesize cell wall polymers and glycoproteins. The de novo synthesis of nucleotide sugars is of major importance. During growth, however, some polymers are broken down to monosaccharides. Reactivation of these sugars into nucleotide sugars occurs in two steps: first, by a substrate-specific sugar-1-kinase and, second, by UDP-sugar-pyrophosphorylase (USP), which has broad substrate specificity. A knock-out of the USP gene results in non-fertile pollen. By using various genetic complementation approaches we obtained a strong (>95%) knock-down line in USP that allowed us to investigate the physiological role of the enzyme during the life cycle. Mutant plants show an arabinose reduction in the cell wall, and accumulate mainly two sugars, arabinose and xylose, in the cytoplasm. The arabinogalactanproteins in usp mutants show no significant reduction in size. USP is also part of the myo-inositol oxygenation pathway to UDP-glucuronic acid; however, free glucuronic acid does not accumulate in cells, suggesting alternative conversion pathways of this monosaccharide. The knock-down plants are mostly sterile because of the improper formation of anthers and pollen sacks.

  2. Inactivation of thioredoxin f1 leads to decreased light activation of ADP-glucose pyrophosphorylase and altered diurnal starch turnover in leaves of Arabidopsis plants.

    PubMed

    Thormählen, Ina; Ruber, Joachim; von Roepenack-Lahaye, Edda; Ehrlich, Sven-Matthias; Massot, Vincent; Hümmer, Christine; Tezycka, Justyna; Issakidis-Bourguet, Emmanuelle; Geigenberger, Peter

    2013-01-01

    Chloroplast thioredoxin f (Trx f) is an important regulator of primary metabolic enzymes. However, genetic evidence for its physiological importance is largely lacking. To test the functional significance of Trx f in vivo, Arabidopsis mutants with insertions in the trx f1 gene were studied, showing a drastic decrease in Trx f leaf content. Knockout of Trx f1 led to strong attenuation in reductive light activation of ADP-glucose pyrophosphorylase (AGPase), the key enzyme of starch synthesis, in leaves during the day and in isolated chloroplasts, while sucrose-dependent redox activation of AGPase in darkened leaves was not affected. The decrease in light-activation of AGPase in leaves was accompanied by a decrease in starch accumulation, an increase in sucrose levels and a decrease in starch-to-sucrose ratio. Analysis of metabolite levels at the end of day shows that inhibition of starch synthesis was unlikely due to shortage of substrates or changes in allosteric effectors. Metabolite profiling by gas chromatography-mass spectrometry pinpoints only a small number of metabolites affected, including sugars, organic acids and ethanolamine. Interestingly, metabolite data indicate carbon shortage in trx f1 mutant leaves at the end of night. Overall, results provide in planta evidence for the role played by Trx f in the light activation of AGPase and photosynthetic carbon partitioning in plants.

  3. Two decades of clinical gene therapy--success is finally mounting.

    PubMed

    Herzog, Roland W; Cao, Ou; Srivastava, Arun

    2010-02-01

    Human gene therapy has made substantial progress since the initiation of the first clinical trials 20 years ago. Here, we summarized important applications of gene transfer protocols in the treatment of various human diseases using different viral vectors. Recent successful trials on the treatment of ocular diseases and inherited immune deficiencies are particularly encouraging and have raised hopes that human gene therapy as a standard treatment option will finally become a reality. While immune responses and insertional mutagenesis pose obstacles for this novel form of molecular medicine, continuous progress suggests that a wider range of diseases can be treated with gene therapy in the future.

  4. Toward the mechanism of NH(4) (+) sensitivity mediated by Arabidopsis GDP-mannose pyrophosphorylase.

    PubMed

    Kempinski, Chase F; Haffar, Rawaa; Barth, Carina

    2011-05-01

    The ascorbic acid (AA)-deficient Arabidopsis thaliana mutant vtc1-1, which is defective in GDP-mannose pyrophosphorylase (GMPase), exhibits conditional hypersensitivity to ammonium (NH(4) (+) ), a phenomenon that is independent of AA deficiency. As GMPase is important for GDP-mannose biosynthesis, a nucleotide sugar necessary for protein N-glycosylation, it has been thought that GDP-mannose deficiency is responsible for the growth defect in vtc1-1 in the presence of NH(4) (+) . Therefore, the motivation for this work was to elucidate the growth and developmental processes that are affected in vtc1-1 in the presence of NH(4) (+) and to determine whether GDP-mannose deficiency generally causes NH(4) (+) sensitivity. Furthermore, as NH(4) (+) may alter cytosolic pH, we investigated the responses of vtc1-1 to pH changes in the presence and absence of NH(4) (+) . Using qRT-PCR and staining procedures, we demonstrate that defective N-glycosylation in vtc1-1 contributes to cell wall, membrane and cell cycle defects, resulting in root growth inhibition in the presence of NH(4) (+) . However, by using mutants acting upstream of vtc1-1 and contributing to GDP-mannose biosynthesis, we show that GDP-mannose deficiency does not generally lead to and is not the primary cause of NH(4) (+) sensitivity. Instead, our data suggest that GMPase responds to pH alterations in the presence of NH(4) (+) .

  5. Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase

    SciTech Connect

    Quirk, Stephen; Seley-Radtke, Katherine L.

    2006-04-01

    The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution. The human nucleotide-sugar metabolizing enzyme GTP fucose pyrophosphorylase (GFPP) has been purified to homogeneity by an affinity chromatographic procedure that utilizes a novel nucleoside analog. This new purification regime results in a protein preparation that produces significantly better crystals than traditional purification methods. The purified 66.6 kDa monomeric protein has been crystallized via hanging-drop vapor diffusion at 293 K. Crystals of the native enzyme diffract to 2.8 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. There is a single GFPP monomer in the asymmetric unit, giving a Matthews coefficient of 2.38 Å{sup 3} Da{sup −1} and a solvent content of 48.2%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme.

  6. Oligomerization, membrane association, and in vivo phosphorylation of sugarcane UDP-glucose pyrophosphorylase.

    PubMed

    Soares, Jose Sergio M; Gentile, Agustina; Scorsato, Valeria; Lima, Aline da C; Kiyota, Eduardo; Dos Santos, Marcelo Leite; Piattoni, Claudia V; Huber, Steven C; Aparicio, Ricardo; Menossi, Marcelo

    2014-11-28

    Sugarcane is a monocot plant that accumulates sucrose to levels of up to 50% of dry weight in the stalk. The mechanisms that are involved in sucrose accumulation in sugarcane are not well understood, and little is known with regard to factors that control the extent of sucrose storage in the stalks. UDP-glucose pyrophosphorylase (UGPase; EC 2.7.7.9) is an enzyme that produces UDP-glucose, a key precursor for sucrose metabolism and cell wall biosynthesis. The objective of this work was to gain insights into the ScUGPase-1 expression pattern and regulatory mechanisms that control protein activity. ScUGPase-1 expression was negatively correlated with the sucrose content in the internodes during development, and only slight differences in the expression patterns were observed between two cultivars that differ in sucrose content. The intracellular localization of ScUGPase-1 indicated partial membrane association of this soluble protein in both the leaves and internodes. Using a phospho-specific antibody, we observed that ScUGPase-1 was phosphorylated in vivo at the Ser-419 site in the soluble and membrane fractions from the leaves but not from the internodes. The purified recombinant enzyme was kinetically characterized in the direction of UDP-glucose formation, and the enzyme activity was affected by redox modification. Preincubation with H2O2 strongly inhibited this activity, which could be reversed by DTT. Small angle x-ray scattering analysis indicated that the dimer interface is located at the C terminus and provided the first structural model of the dimer of sugarcane UGPase in solution.

  7. Oligomerization, Membrane Association, and in Vivo Phosphorylation of Sugarcane UDP-glucose Pyrophosphorylase*

    PubMed Central

    Soares, Jose Sergio M.; Gentile, Agustina; Scorsato, Valeria; Lima, Aline da C.; Kiyota, Eduardo; dos Santos, Marcelo Leite; Piattoni, Claudia V.; Huber, Steven C.; Aparicio, Ricardo; Menossi, Marcelo

    2014-01-01

    Sugarcane is a monocot plant that accumulates sucrose to levels of up to 50% of dry weight in the stalk. The mechanisms that are involved in sucrose accumulation in sugarcane are not well understood, and little is known with regard to factors that control the extent of sucrose storage in the stalks. UDP-glucose pyrophosphorylase (UGPase; EC 2.7.7.9) is an enzyme that produces UDP-glucose, a key precursor for sucrose metabolism and cell wall biosynthesis. The objective of this work was to gain insights into the ScUGPase-1 expression pattern and regulatory mechanisms that control protein activity. ScUGPase-1 expression was negatively correlated with the sucrose content in the internodes during development, and only slight differences in the expression patterns were observed between two cultivars that differ in sucrose content. The intracellular localization of ScUGPase-1 indicated partial membrane association of this soluble protein in both the leaves and internodes. Using a phospho-specific antibody, we observed that ScUGPase-1 was phosphorylated in vivo at the Ser-419 site in the soluble and membrane fractions from the leaves but not from the internodes. The purified recombinant enzyme was kinetically characterized in the direction of UDP-glucose formation, and the enzyme activity was affected by redox modification. Preincubation with H2O2 strongly inhibited this activity, which could be reversed by DTT. Small angle x-ray scattering analysis indicated that the dimer interface is located at the C terminus and provided the first structural model of the dimer of sugarcane UGPase in solution. PMID:25320091

  8. Octamerization is essential for enzymatic function of human UDP-glucose pyrophosphorylase.

    PubMed

    Führing, Jana; Damerow, Sebastian; Fedorov, Roman; Schneider, Julia; Münster-Kühnel, Anja-Katharina; Gerardy-Schahn, Rita

    2013-04-01

    Uridine diphosphate-glucose pyrophosphorylase (UGP) occupies a central position in carbohydrate metabolism in all kingdoms of life, since its product uridine diphosphate-glucose (UDP-glucose) is essential in a number of anabolic and catabolic pathways and is a precursor for other sugar nucleotides. Its significance as a virulence factor in protists and bacteria has given momentum to the search for species-specific inhibitors. These attempts are, however, hampered by high structural conservation of the active site architecture. A feature that discriminates UGPs of different species is the quaternary organization. While UGPs in protists are monomers, di- and tetrameric forms exist in bacteria, and crystal structures obtained for the enzyme from yeast and human identified octameric UGPs. These octamers are formed by contacts between highly conserved amino acids in the C-terminal β-helix. Still under debate is the question whether octamerization is required for the functionality of the human enzyme. Here, we used single amino acid replacements in the C-terminal β-helix to interrogate the impact of highly conserved residues on octamer formation and functional activity of human UGP (hUGP). Replacements were guided by the sequence of Arabidopsis thaliana UGP, known to be active as a monomer. Correlating the data obtained in blue native PAGE, size exclusion chromatography and enzymatic activity testing, we prove that the octamer is the active enzyme form. This new insight into structure-function relationships in hUGP does not only improve the understanding of the catalysis of this important enzyme, but in addition broadens the basis for studies aimed at designing drugs that selectively inhibit UGPs from pathogens.

  9. Purification, crystallization and preliminary X-ray diffraction studies of UDP-N-acetylglucosamine pyrophosphorylase from Candida albicans

    SciTech Connect

    Maruyama, Daisuke; Nishitani, Yuichi; Nonaka, Tsuyoshi; Kita, Akiko; Fukami, Takaaki A.; Mio, Toshiyuki; Yamada-Okabe, Hisafumi; Yamada-Okabe, Toshiko; Miki, Kunio

    2006-12-01

    UDP-N-acetylglucosamine pyrophosphorylase was purified and crystallized and X-ray diffraction data were collected to 2.3 Å resolution. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine. UAP from Candida albicans was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals of the substrate and product complexes both diffract X-rays to beyond 2.3 Å resolution using synchrotron radiation. The crystals of the substrate complex belong to the triclinic space group P1, with unit-cell parameters a = 47.77, b = 62.89, c = 90.60 Å, α = 90.01, β = 97.72, γ = 92.88°, whereas those of the product complex belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.95, b = 90.87, c = 94.88 Å.

  10. ADP-glucose pyrophosphorylase-deficient pea embryos reveal specific transcriptional and metabolic changes of carbon-nitrogen metabolism and stress responses.

    PubMed

    Weigelt, Kathleen; Küster, Helge; Rutten, Twan; Fait, Aaron; Fernie, Alisdair R; Miersch, Otto; Wasternack, Claus; Emery, R J Neil; Desel, Christine; Hosein, Felicia; Müller, Martin; Saalbach, Isolde; Weber, Hans

    2009-01-01

    We present a comprehensive analysis of ADP-glucose pyrophosphorylase (AGP)-repressed pea (Pisum sativum) seeds using transcript and metabolite profiling to monitor the effects that reduced carbon flow into starch has on carbon-nitrogen metabolism and related pathways. Changed patterns of transcripts and metabolites suggest that AGP repression causes sugar accumulation and stimulates carbohydrate oxidation via glycolysis, tricarboxylic acid cycle, and mitochondrial respiration. Enhanced provision of precursors such as acetyl-coenzyme A and organic acids apparently support other pathways and activate amino acid and storage protein biosynthesis as well as pathways fed by cytosolic acetyl-coenzyme A, such as cysteine biosynthesis and fatty acid elongation/metabolism. As a consequence, the resulting higher nitrogen (N) demand depletes transient N storage pools, specifically asparagine and arginine, and leads to N limitation. Moreover, increased sugar accumulation appears to stimulate cytokinin-mediated cell proliferation pathways. In addition, the deregulation of starch biosynthesis resulted in indirect changes, such as increased mitochondrial metabolism and osmotic stress. The combined effect of these changes is an enhanced generation of reactive oxygen species coupled with an up-regulation of energy-dissipating, reactive oxygen species protection, and defense genes. Transcriptional activation of mitogen-activated protein kinase pathways and oxylipin synthesis indicates an additional activation of stress signaling pathways. AGP-repressed embryos contain higher levels of jasmonate derivatives; however, this increase is preferentially in nonactive forms. The results suggest that, although metabolic/osmotic alterations in iAGP pea seeds result in multiple stress responses, pea seeds have effective mechanisms to circumvent stress signaling under conditions in which excessive stress responses and/or cellular damage could prematurely initiate senescence or apoptosis.

  11. Mutagenesis of cysteine 81 prevents dimerization of the APS1 subunit of ADP-glucose pyrophosphorylase and alters diurnal starch turnover in Arabidopsis thaliana leaves.

    PubMed

    Hädrich, Nadja; Hendriks, Janneke H M; Kötting, Oliver; Arrivault, Stéphanie; Feil, Regina; Zeeman, Samuel C; Gibon, Yves; Schulze, Waltraud X; Stitt, Mark; Lunn, John E

    2012-04-01

    Many plants, including Arabidopsis thaliana, retain a substantial portion of their photosynthate in leaves in the form of starch, which is remobilized to support metabolism and growth at night. ADP-glucose pyrophosphorylase (AGPase) catalyses the first committed step in the pathway of starch synthesis, the production of ADP-glucose. The enzyme is redox-activated in the light and in response to sucrose accumulation, via reversible breakage of an intermolecular cysteine bridge between the two small (APS1) subunits. The biological function of this regulatory mechanism was investigated by complementing an aps1 null mutant (adg1) with a series of constructs containing a full-length APS1 gene encoding either the wild-type APS1 protein or mutated forms in which one of the five cysteine residues was replaced by serine. Substitution of Cys81 by serine prevented APS1 dimerization, whereas mutation of the other cysteines had no effect. Thus, Cys81 is both necessary and sufficient for dimerization of APS1. Compared to control plants, the adg1/APS1(C81S) lines had higher levels of ADP-glucose and maltose, and either increased rates of starch synthesis or a starch-excess phenotype, depending on the daylength. APS1 protein levels were five- to tenfold lower in adg1/APS1(C81S) lines than in control plants. These results show that redox modulation of AGPase contributes to the diurnal regulation of starch turnover, with inappropriate regulation of the enzyme having an unexpected impact on starch breakdown, and that Cys81 may play an important role in the regulation of AGPase turnover.

  12. The rice endosperm ADP-glucose pyrophosphorylase large subunit is essential for optimal catalysis and allosteric regulation of the heterotetrameric enzyme.

    PubMed

    Tuncel, Aytug; Kawaguchi, Joe; Ihara, Yasuharu; Matsusaka, Hiroaki; Nishi, Aiko; Nakamura, Tetsuhiro; Kuhara, Satoru; Hirakawa, Hideki; Nakamura, Yasunori; Cakir, Bilal; Nagamine, Ai; Okita, Thomas W; Hwang, Seon-Kap; Satoh, Hikaru

    2014-06-01

    Although an alternative pathway has been suggested, the prevailing view is that starch synthesis in cereal endosperm is controlled by the activity of the cytosolic isoform of ADPglucose pyrophosphorylase (AGPase). In rice, the cytosolic AGPase isoform is encoded by the OsAGPS2b and OsAGPL2 genes, which code for the small (S2b) and large (L2) subunits of the heterotetrameric enzyme, respectively. In this study, we isolated several allelic missense and nonsense OsAGPL2 mutants by N-methyl-N-nitrosourea (MNU) treatment of fertilized egg cells and by TILLING (Targeting Induced Local Lesions in Genomes). Interestingly, seeds from three of the missense mutants (two containing T139I and A171V) were severely shriveled and had seed weight and starch content comparable with the shriveled seeds from OsAGPL2 null mutants. Results from kinetic analysis of the purified recombinant enzymes revealed that the catalytic and allosteric regulatory properties of these mutant enzymes were significantly impaired. The missense heterotetramer enzymes and the S2b homotetramer had lower specific (catalytic) activities and affinities for the activator 3-phosphoglycerate (3-PGA). The missense heterotetramer enzymes showed more sensitivity to inhibition by the inhibitor inorganic phosphate (Pi) than the wild-type AGPase, while the S2b homotetramer was profoundly tolerant to Pi inhibition. Thus, our results provide definitive evidence that starch biosynthesis during rice endosperm development is controlled predominantly by the catalytic activity of the cytoplasmic AGPase and its allosteric regulation by the effectors. Moreover, our results show that the L2 subunit is essential for both catalysis and allosteric regulatory properties of the heterotetramer enzyme.

  13. ADP-glucose pyrophosphorylase is localized to both the cytoplasm and plastids in developing pericarp of tomato fruit

    NASA Technical Reports Server (NTRS)

    Chen, B. Y.; Wang, Y.; Janes, H. W.

    1998-01-01

    The intracellular location of ADP-glucose pyrophosphorylase (AGP) in developing pericarp of tomato (Lycopersicon esculentum Mill) has been investigated by immunolocalization. With the use of a highly specific anti-tomato fruit AGP antibody, the enzyme was localized in cytoplasm as well as plastids at both the light and electron microscope levels. The immunogold particles in plastids were localized in the stroma and at the surface of the starch granule, whereas those in the cytoplasm occurred in cluster-like patterns. Contrary to the fruit, the labeling in tomato leaf cells occurred exclusively in the chloroplasts. These data demonstrate that AGP is localized to both the cytoplasm and plastids in developing pericarp cells of tomato.

  14. Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.).

    PubMed

    Danishuddin, Mohd; Chatrath, Ravish; Singh, Rajender

    2011-05-07

    Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGPSGln113- AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78Å. The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.

  15. A glgC gene essential only for the first of two spatially distinct phases of glycogen synthesis in Streptomyces coelicolor A3(2).

    PubMed Central

    Martin, M C; Schneider, D; Bruton, C J; Chater, K F; Hardisson, C

    1997-01-01

    By using a PCR approach based on conserved regions of ADP-glucose pyrophosphorylases, a glgC gene was cloned from Streptomyces coelicolor A3(2). The deduced glgC gene product showed end-to-end relatedness to other bacterial ADP-glucose pyrophosphorylases. The glgC gene is about 1,000 kb from the leftmost chromosome end and is not closely linked to either of the two glgB genes of S. coelicolor, which encode glycogen branching enzymes active in different locations in differentiated colonies. Disruption of glgC eliminated only the first of two temporal peaks of ADP-glucose pyrophosphorylase activity and glycogen accumulation and prevented cytologically observable glycogen accumulation in the substrate mycelium of colonies (phase I), while glycogen deposition in young spore chains (phase II) remained readily detectable. The cloned glgC gene therefore encodes an ADP-glucose pyrophosphorylase essential only for phase I (and it is therefore named glgCI). A second, phase II-specific, glgC gene should also exist in S. coelicolor, though it was not detected by hybridization analysis. PMID:9401038

  16. Identification, subcellular localization, biochemical properties, and high-resolution crystal structure of Trypanosoma brucei UDP-glucose pyrophosphorylase

    PubMed Central

    Mariño, Karina; Güther, Maria Lucia Sampaio; Wernimont, Amy K; Amani, Mernhaz; Hui, Raymond; Ferguson, Michael AJ

    2010-01-01

    The protozoan parasite Trypanosoma brucei is the causative agent of the cattle disease Nagana and human African sleeping sickness. Glycoproteins play key roles in the parasite’s survival and infectivity, and the de novo biosyntheses of the sugar nucleotides UDP-galactose (UDP-Gal), UDP-N-acetylglucosamine, and GDP-fucose have been shown to be essential for their growth. The only route to UDP-Gal in T. brucei is through the epimerization of UDP-glucose (UDP-Glc) by UDP-Glc 4′-epimerase. UDP-Glc is also the glucosyl donor for the unfolded glycoprotein glucosyltransferase (UGGT) involved in glycoprotein quality control in the endoplasmic reticulum and is the presumed donor for the synthesis of base J (β-d-glucosylhydroxymethyluracil), a rare deoxynucleotide found in telomere-proximal DNA in the bloodstream form of T. brucei. Considering that UDP-Glc plays such a central role in carbohydrate metabolism, we decided to characterize UDP-Glc biosynthesis in T. brucei. We identified and characterized the parasite UDP-glucose pyrophosphorylase (TbUGP), responsible for the formation of UDP-Glc from glucose-1-phosphate and UTP, and localized the enzyme to the peroxisome-like glycosome organelles of the parasite. Recombinant TbUGP was shown to be enzymatically active and specific for glucose-1-phosphate. The high-resolution crystal structure was also solved, providing a framework for the design of potential inhibitors against the parasite enzyme. PMID:20724435

  17. Enhanced activity of ADP glucose pyrophosphorylase and formation of starch induced by Azospirillum brasilense in Chlorella vulgaris.

    PubMed

    Choix, Francisco J; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E

    2014-05-10

    ADP-glucose pyrophosphorylase (AGPase) regulates starch biosynthesis in higher plants and microalgae. This study measured the effect of the bacterium Azospirillum brasilense on AGPase activity in the freshwater microalga Chlorella vulgaris and formation of starch. This was done by immobilizing both microorganisms in alginate beads, either replete with or deprived of nitrogen or phosphorus and all under heterotrophic conditions, using d-glucose or Na-acetate as the carbon source. AGPase activity during the first 72h of incubation was higher in C. vulgaris when immobilized with A. brasilense. This happened simultaneously with higher starch accumulation and higher carbon uptake by the microalgae. Either carbon source had similar effects on enzyme activity and starch accumulation. Starvation either by N or P had the same pattern on AGPase activity and starch accumulation. Under replete conditions, the population of C. vulgaris immobilized alone was higher than when immobilized together, but under starvation conditions A. brasilense induced a larger population of C. vulgaris. In summary, adding A. brasilense enhanced AGPase activity, starch formation, and mitigation of stress in C. vulgaris.

  18. Phytoalexin detoxification genes and gene products: Implication for the evolution of host specific traits for pathogenicity. Final report

    SciTech Connect

    VanEtten, H.

    1997-06-01

    The overall objectives of this research were to determine which differences among PDA genes were associated with different levels of virulence on pea and to clone and characterize a MAK gene. The authors also proposed to characterize the pisatin detoxifying system in pea pathogens in addition to N. haematococca to assess whether pathogens of a common host had evolved similar pathogenicity genes.

  19. Regulatory properties of ADP glucose pyrophosphorylase are required for adjustment of leaf starch synthesis in different photoperiods.

    PubMed

    Mugford, Sam T; Fernandez, Olivier; Brinton, Jemima; Flis, Anna; Krohn, Nicole; Encke, Beatrice; Feil, Regina; Sulpice, Ronan; Lunn, John E; Stitt, Mark; Smith, Alison M

    2014-12-01

    Arabidopsis (Arabidopsis thaliana) leaves synthesize starch faster in short days than in long days, but the mechanism that adjusts the rate of starch synthesis to daylength is unknown. To understand this mechanism, we first investigated whether adjustment occurs in mutants lacking components of the circadian clock or clock output pathways. Most mutants adjusted starch synthesis to daylength, but adjustment was compromised in plants lacking the GIGANTEA or FLAVIN-BINDING, KELCH REPEAT, F BOX1 components of the photoperiod-signaling pathway involved in flowering. We then examined whether the properties of the starch synthesis enzyme adenosine 5'-diphosphate-glucose pyrophosphorylase (AGPase) are important for adjustment of starch synthesis to daylength. Modulation of AGPase activity is known to bring about short-term adjustments of photosynthate partitioning between starch and sucrose (Suc) synthesis. We found that adjustment of starch synthesis to daylength was compromised in plants expressing a deregulated bacterial AGPase in place of the endogenous AGPase and in plants containing mutant forms of the endogenous AGPase with altered allosteric regulatory properties. We suggest that the rate of starch synthesis is in part determined by growth rate at the end of the preceding night. If growth at night is low, as in short days, there is a delay before growth recovers during the next day, leading to accumulation of Suc and stimulation of starch synthesis via activation of AGPase. If growth at night is fast, photosynthate is used for growth at the start of the day, Suc does not accumulate, and starch synthesis is not up-regulated.

  20. Pine Gene Discovery Project - Final Report - 08/31/1997 - 02/28/2001

    SciTech Connect

    Whetten, R. W.; Sederoff, R. R.; Kinlaw, C.; Retzel, E.

    2001-04-30

    Integration of pines into the large scope of plant biology research depends on study of pines in parallel with study of annual plants, and on availability of research materials from pine to plant biologists interested in comparing pine with annual plant systems. The objectives of the Pine Gene Discovery Project were to obtain 10,000 partial DNA sequences of genes expressed in loblolly pine, to determine which of those pine genes were similar to known genes from other organisms, and to make the DNA sequences and isolated pine genes available to plant researchers to stimulate integration of pines into the wider scope of plant biology research. Those objectives have been completed, and the results are available to the public. Requests for pine genes have been received from a number of laboratories that would otherwise not have included pine in their research, indicating that progress is being made toward the goal of integrating pine research into the larger molecular biology research community.

  1. Role of starvation genes in the survival of deep subsurface bacterial communities. Final report

    SciTech Connect

    Matin, A.; Schmidt, T.; Caldwell, D.

    1998-11-01

    The investigation dealt with several aspects of subsurface bacterial survival and their nature. Mutants of Pseudomonas putida, a common environmental bacterium with counterparts in the subsurface, were isolated by transposon mutagenesis. These mutants were highly sensitive to starvation stress. Reporter gene fusions also showed that these genes were starvation genes since they were induced several fold when the cultures were started. Since the regulatory religions (promoters) of starvation genes are of interest in bioremediation and in experiments designed to understand the roles of starvation genes in the maintenance of microbial community structure, the promoter of one of these genes (pstarv1, contained in strain MK107) was characterized in detail. As a preliminary to these studies, the growth characteristics of Pseudomonas putida MK1 and MK107 were compared for cells growing in batch cultures or as an attached monolayer in microstat cultures.

  2. Transposon tagging of disease resistance genes. Final report, May 1, 1988--April 30, 1993

    SciTech Connect

    Michelmore, R.

    1994-09-01

    The goal of this project was to develop a transposon mutagenesis system for lettuce and to clone and characterize disease resistance genes by transposon tagging. The majority of studies were conducted with the Ac/Ds System. Researchers made and tested several constructs as well as utilized constructions shown to be functional in other plant species. Researchers demonstrated movement of Ac and DS in lettuce; however, they transposed at much lower frequencies in lettuce than in other plant species. Therefore, further manipulation of the system, particularly for flower specific expression of transposase, is required before a routine transposon system is available for lettuce. Populations of lettuce were generated and screened to test for the stability of resistance genes and several spontaneous mutations were isolated. Researchers also identified a resistance gene mutant in plants transformed with a Ds element and chimeric transposase gene. This is currently being characterized in detail.

  3. Structure and expression of nuclear genes encoding rubisco activase. Final technical report

    SciTech Connect

    Zielinski, R.E.

    1994-06-01

    Rubisco activase (Rca) is a soluble chloroplast protein that catalyzes the activation of rubisco, the enzyme that initiates the photosynthetic carbon reduction cycle, to catalytic competency. Rca in barley consists of three polypeptides, one of 46- and two of 42-kDa, but the quaternary structure of the protein is not known. The authors have isolated and completely sequenced 8.8 kb of barley genomic DNA containing two, tandemly oriented activase genes (RcaA and RcaB) and three different cDNAs encoding the 42- and 46-kDa Rca polypeptide isoforms. Genomic Southern blot assays indicate that these sequences represent the entire Rca gene family in barley. Pre-mRNAs transcribed from the RcaA gene are alternatively spliced to give mRNAs encoding both 46- (RcaA1) and 42-kDa (RcaA2) Rca isoforms. The RcaB gene encodes a single polypeptide of 42 kDa. Primer extension and northern blot assays indicate that RcaB mRNA is expressed at a level that is 10- to 100-fold lower than RcaA mRNA. Analyses at the mRNA and protein level showed that Rca gene expression is coordinated by that of the rubisco subunits during barley leaf development.

  4. Characterization of embryo-specific genes. Final report, April 1, 1987--March 31, 1992

    SciTech Connect

    Sung, R.

    1992-06-12

    The objective of the proposed research is to characterize the function and regulation of a set of embryonic genes which are expressed in the embryos, not in the plants. 22 cDNA clones were isolated from a cDNA library we constructed using mRNAS of -carrot somatic embryos. These cDNA clones identified mRNA species that are present in the somatic and zygotic embryos, but not in adult plants. The sequence of all 22cDNA clones were determined; genomic clones for three cDNA clones, DC8, DC59, and DC49 were isolated and gene sequences determined. DC8, DC49, and several other genes identified by the cDNA sequences belong to the category of late embryogenesis abundant protein genes, Lea. The function of these gens have not yet been determined, but they share common structural features, are regulated by ABA and are speculated to play a role in seed desiccation.

  5. A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism

    PubMed Central

    Führing, Jana Indra; Cramer, Johannes Thomas; Schneider, Julia; Baruch, Petra; Gerardy-Schahn, Rita; Fedorov, Roman

    2015-01-01

    In mammals, UDP-glucose pyrophosphorylase (UGP) is the only enzyme capable of activating glucose-1-phosphate (Glc-1-P) to UDP-glucose (UDP-Glc), a metabolite located at the intersection of virtually all metabolic pathways in the mammalian cell. Despite the essential role of its product, the molecular basis of UGP function is poorly understood. Here we report the crystal structure of human UGP in complex with its product UDP-Glc. Beyond providing first insight into the active site architecture, we describe the substrate binding mode and intermolecular interactions in the octameric enzyme that are crucial to its activity. Importantly, the quaternary mechanism identified for human UGP in this study may be common for oligomeric sugar-activating nucleotidyltransferases. Elucidating such mechanisms is essential for understanding nucleotide sugar metabolism and opens the perspective for the development of drugs that specifically inhibit simpler organized nucleotidyltransferases in pathogens. PMID:25860585

  6. An HPLC method for the assay of UDP-glucose pyrophosphorylase and UDP-glucose-4-epimerase in Solieria chordalis (Rhodophyceae).

    PubMed

    Goulard, F; Diouris, M; Deslandes, E; Floc'h, J Y

    2001-01-01

    An efficient method to assay both UDP-glucose pyrophosphorylase and UDP-glucose-4-epimerase in a crude extract of the red seaweed, Solieria chordalis is described. The method is based on the direct quantification by reverse-phase high-performance liquid chromatography of the UDP-sugars generated in the reaction mixture. UDP-glucose, UDP-galactose and UTP were detected by spectrophotometry at 254 nm and their recoveries ranged from 97 to 100%. In the course of the reaction, a correlation was observed between the reduction in the area of the substrate peak and the occurrence of product peak(s). This highly reproducible method for enzyme assay is fast since no intermediate reaction mixture is required.

  7. Genetic analysis of the regulation of TCH gene expression, Final Report

    SciTech Connect

    Braam, Janet

    2008-10-28

    The Arabidopsis TCH genes, originally isolated as a consequence of their upregulation in response to the mechanical stimulus of touch, are also upregulated by a variety of seemingly disparate environmental and hormonal stimuli. To gain insight into the complexities of TCH gene regulation, a number of approaches were taken. Regulatory elements responsible for regulation were identified and characteristics of the regulation were evaluated. Reporter genes were used to monitor expression localization and dynamics. Microarray analyses of genome-wide expression behavior indicated that touch-inducible gene expression is more widespread than generally appreciated. Identification of all touch-regulated genes shed light on the types of cellular processes that may be altered in response to mechanical stress perturbations. Expression of the TCH2 gene, also called CML24, encoding a calmodulin (CaM)-like (CML) protein, was evaluated. CML24 shares over 40% amino acid sequence identity with CaM, has 4 EF hands and undergoes a Ca2+-dependent change in migration rate through denaturing gel electrophoresis, indicating that CML24 binds Ca2+ and, as a consequence, undergoes conformational changes. CML24 expression occurs in all major organs and is induced from 2- to 15-fold in plants subjected to touch, darkness, heat, cold, hydrogen peroxide, abscisic acid (ABA) and indole-3-acetic acid. The putative CML24 regulatory region confers reporter expression at sites of predicted mechanical stress, in regions undergoing growth, in vascular tissues and various floral organs and in stomata, trichomes and hydathodes. CML24 underexpressing transgenics are resistant to ABA inhibition of germination and seedling growth, defective in long-day induction of flowering, and have enhanced tolerance to CoCl2, molybdic acid, ZnSO4 and MgCl2. These data present evidence that CML24 encodes a potential Ca2+ sensor that may function to enable responses to ABA, day length and presence of various salts. Further

  8. Final Report [Function of the Arabidopsis TIR1 gene in auxin response

    SciTech Connect

    Estelle, Mark

    2000-12-18

    During this grant period substantial progress was made in the characterization of the TIR1 gene in Arabidopsis. Studies showed that the TIR1 protein is part of a protein complex that includes AtCUL1, ASK1 and RBX1. This complex, called SCF-TIR1, functions in the ubiquitin-mediated protein degradation pathway. Our work is the first report of an SCF complex in a plant system. The results of our studies are described in more detail in the report together with a publication resulting from this study.

  9. Expression profiling of genes involved in ascorbate biosynthesis and recycling during fleshy root development in radish.

    PubMed

    Xu, Yao; Zhu, Xianwen; Chen, Yinglong; Gong, Yiqin; Liu, Liwang

    2013-09-01

    Ascorbate is a primary antioxidant and an essential enzyme cofactor in plants, which has an important effect on the development of plant root system. To investigate the molecular mechanisms of ascorbate accumulation during root development and reveal the key genes of the ascorbate biosynthesis and recycling pathways, the expression of 16 related genes together with ascorbate abundance were analyzed in the flesh and skin of radish (Raphanus sativus L.) fleshy root. The content of ascorbate decreased with root growth in both the flesh and skin. Expression of GDP-d-mannose pyrophosphorylase, GDP-d-mannose-3',5'-epimerase and d-galacturonate reductase were also decreased and correlated with ascorbate levels in the flesh. In the skin, the expression of GDP-d-mannose pyrophosphorylase and l-galactose dehydrogenase was correlated with ascorbate levels. These results suggested that ascorbate accumulation is affected mainly by biosynthesis rather than recycling in radish root, and the l-galactose pathway may be the major biosynthetic route of ascorbate, and moreover, the salvage pathway may also contribute to ascorbate accumulation. The data suggested that GDP-d-mannose pyrophosphorylase could play an important role in the regulation of ascorbate accumulation during radish fleshy taproot development.

  10. Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

    SciTech Connect

    Jirtle, Randy L.

    2012-10-11

    The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (<10 cGy) during early gestation. This information is particularly important to ascertain given the increased use of CT scans in disease diagnosis, increased number of people predicted to live and work in space, and the present concern about radiological terrorism. We showed for the first time that LDIR significantly increased DNA methylation at the A{sup vy} locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in

  11. A Novel, Photosynthesis-Associated Thioredoxin-Like Gene: Final Technical Report

    SciTech Connect

    Collier, Jackie, L

    2005-09-13

    ''. These results are consistent with a role for TxlA in the synthesis of the cytochrome b6f complex, which is required for both photosynthetic and respiratory electron transport in cyanobacteria. In contrast, our PCC 7942 mutants in which the C-terminal domain of TxlA was removed are viable and appear to have normal cytochrome content, but have a subtle pigmentation phenotype (increased content of phycocyanin relative to chlorophyll) that depends on both light and CO2 availability. We have also found that PCC 6803 Sll1980 inactivation mutant merodiploids have a similar pigmentation phenotype to the PCC 7942 C-terminal truncation mutants when grown photoautotrophically. In addition, when grown heterotrophically the PCC 6803 Sll1980 inactivation mutant merodiploids remain green instead of turning a golden color like the wild-type, and they are more sensitive to the b6f complex inhibitor DBMIB than is wild type PCC 6803. That the PCC 6803 Sll1980 inactivation mutant merodiploids have these phenotypes despite the fact that they still contain normal copies of the sll1980 gene suggests that the presence of truncated Sll1980 protein interferes with the function of normal Sll1980 protein. Together, these physiological data suggest that TxlA has an essential redox role in cyanobacteria, perhaps a biosynthetic one, and may also have a nonessential regulatory role reflected in the phenotypes of the PCC 7942 C-terminal truncation mutants and the PCC 6803 Sll1980 inactivation mutant merodiploids.

  12. Decreasing the mitochondrial synthesis of malate in potato tubers does not affect plastidial starch synthesis, suggesting that the physiological regulation of ADPglucose pyrophosphorylase is context dependent.

    PubMed

    Szecowka, Marek; Osorio, Sonia; Obata, Toshihiro; Araújo, Wagner L; Rohrmann, Johannes; Nunes-Nesi, Adriano; Fernie, Alisdair R

    2012-12-01

    Modulation of the malate content of tomato (Solanum lycopersicum) fruit by altering the expression of mitochondrially localized enzymes of the tricarboxylic acid cycle resulted in enhanced transitory starch accumulation and subsequent effects on postharvest fruit physiology. In this study, we assessed whether such a manipulation would similarly affect starch biosynthesis in an organ that displays a linear, as opposed to a transient, kinetic of starch accumulation. For this purpose, we used RNA interference to down-regulate the expression of fumarase in potato (Solanum tuberosum) under the control of the tuber-specific B33 promoter. Despite displaying similar reductions in both fumarase activity and malate content as observed in tomato fruit expressing the same construct, the resultant transformants were neither characterized by an increased flux to, or accumulation of, starch, nor by alteration in yield parameters. Since the effect in tomato was mechanistically linked to derepression of the reaction catalyzed by ADP-glucose pyrophosphorylase, we evaluated whether the lack of effect on starch biosynthesis was due to differences in enzymatic properties of the enzyme from potato and tomato or rather due to differential subcellular compartmentation of reductant in the different organs. The results are discussed in the context both of current models of metabolic compartmentation and engineering.

  13. Dithiothreitol decreases in vitro activity of ADP-glucose pyrophosphorylase from leaves of apple (Malus domestica Borkh.) and many other plant species.

    PubMed

    Chen, Li-Song; Qi, Yi-Ping

    2007-01-01

    Inclusion of dithiothreitol (DTT) in the extraction buffer and pre-incubation of apple leaf ADP-glucose pyrophosphorylase (AGPase) with DTT resulted in a decrease in AGPase activity whether the assay was performed in the presence or absence of 3-phosphoglycerate (PGA). When PGA was included in the pre-incubation mixture or when pre-incubation of AGPase with PGA was followed by DTT, the latter did not cause any decrease in AGPase activity. However, once AGPase was decreased by DTT, subsequent incubation of the enzyme with PGA did not reverse the decrease. Pre-incubation of AGPase from leaves of Arabidopsis thaliana, sorghum, soybean, tobacco, spinach, wheat, barley, tomato and potato, and tubers of potato with DTT, generally caused a decrease in AGPase activity when assayed in the presence of PGA. When assayed in the absence of PGA, however, a diverse response of AGPase was observed among species to pre-incubation with DTT. The activity of AGPase from potato tubers was increased by DTT; the activity of AGPase from both potato and tomato leaves was not affected by DTT; the activity of AGPase from leaves of other species was decreased by DTT. It is concluded that DTT decreases in vitro activity of AGPase from leaves of apple and many other plant species such that DTT should not be routinely included in the extraction or assay mixture of leaf AGPase.

  14. A mutation in GDP-mannose pyrophosphorylase causes conditional hypersensitivity to ammonium, resulting in Arabidopsis root growth inhibition, altered ammonium metabolism, and hormone homeostasis.

    PubMed

    Barth, Carina; Gouzd, Zachary A; Steele, Hilary P; Imperio, Ryan M

    2010-01-01

    Ascorbic acid (AA) is an antioxidant fulfilling a multitude of cellular functions. Given its pivotal role in maintaining the rate of cell growth and division in the quiescent centre of the root, it was hypothesized that the AA-deficient Arabidopsis thaliana mutants vtc1-1, vtc2-1, vtc3-1, and vtc4-1 have altered root growth. To test this hypothesis, root development was studied in the wild type and vtc mutants grown on Murashige and Skoog medium. It was discovered, however, that only the vtc1-1 mutant has strongly retarded root growth, while the other vtc mutants exhibit a wild-type root phenotype. It is demonstrated that the short-root phenotype in vtc1-1 is independent of AA deficiency and oxidative stress. Instead, vtc1-1 is conditionally hypersensitive to ammonium (NH(4)(+)). To provide new insights into the mechanism of NH(4)(+) sensitivity in vtc1-1, root development, NH(4)(+) content, glutamine synthetase (GS) activity, glutamate dehydrogenase activity, and glutamine content were assessed in wild-type and vtc1-1 mutant plants grown in the presence and absence of high NH(4)(+) and the GS inhibitor MSO. Since VTC1 encodes a GDP-mannose pyrophosphorylase, an enzyme generating GDP-mannose for AA biosynthesis and protein N-glycosylation, it was also tested whether protein N-glycosylation is affected in vtc1-1. Furthermore, since root development requires the action of a variety of hormones, it was investigated whether hormone homeostasis is linked to NH(4)(+) sensitivity in vtc1-1. Our data suggest that NH(4)(+) hypersensitivity in vtc1-1 is caused by disturbed N-glycosylation and that it is associated with auxin and ethylene homeostasis and/or nitric oxide signalling.

  15. A mutation in GDP-mannose pyrophosphorylase causes conditional hypersensitivity to ammonium, resulting in Arabidopsis root growth inhibition, altered ammonium metabolism, and hormone homeostasis

    PubMed Central

    Barth, Carina; Gouzd, Zachary A.; Steele, Hilary P.; Imperio, Ryan M.

    2010-01-01

    Ascorbic acid (AA) is an antioxidant fulfilling a multitude of cellular functions. Given its pivotal role in maintaining the rate of cell growth and division in the quiescent centre of the root, it was hypothesized that the AA-deficient Arabidopsis thaliana mutants vtc1-1, vtc2-1, vtc3-1, and vtc4-1 have altered root growth. To test this hypothesis, root development was studied in the wild type and vtc mutants grown on Murashige and Skoog medium. It was discovered, however, that only the vtc1-1 mutant has strongly retarded root growth, while the other vtc mutants exhibit a wild-type root phenotype. It is demonstrated that the short-root phenotype in vtc1-1 is independent of AA deficiency and oxidative stress. Instead, vtc1-1 is conditionally hypersensitive to ammonium (NH4+). To provide new insights into the mechanism of NH4+ sensitivity in vtc1-1, root development, NH4+ content, glutamine synthetase (GS) activity, glutamate dehydrogenase activity, and glutamine content were assessed in wild-type and vtc1-1 mutant plants grown in the presence and absence of high NH4+ and the GS inhibitor MSO. Since VTC1 encodes a GDP-mannose pyrophosphorylase, an enzyme generating GDP-mannose for AA biosynthesis and protein N-glycosylation, it was also tested whether protein N-glycosylation is affected in vtc1-1. Furthermore, since root development requires the action of a variety of hormones, it was investigated whether hormone homeostasis is linked to NH4+ sensitivity in vtc1-1. Our data suggest that NH4+ hypersensitivity in vtc1-1 is caused by disturbed N-glycosylation and that it is associated with auxin and ethylene homeostasis and/or nitric oxide signalling. PMID:20007685

  16. Identification of genes in anonymous DNA sequences. Final report: Report period, 15 April 1993--15 April 1994

    SciTech Connect

    Fields, C.A.

    1994-09-01

    This Report concludes the DOE Human Genome Program project, ``Identification of Genes in Anonymous DNA Sequence.`` The central goals of this project have been (1) understanding the problem of identifying genes in anonymous sequences, and (2) development of tools, primarily the automated identification system gm, for identifying genes. The activities supported under the previous award are summarized here to provide a single complete report on the activities supported as part of the project from its inception to its completion.

  17. Organ-specific gene expression in maize: The P-wr allele. Final report, August 15, 1993--August 14, 1996

    SciTech Connect

    Peterson, T.A.

    1997-06-01

    The ultimate aim of our work is to understand how a regulatory gene produces a specific pattern of gene expression during plant development. Our model is the P-wr gene of maize, which produces a distinctive pattern of pigmentation of maize floral organs. We are investigating this system using a combination of classical genetic and molecular approaches. Mechanisms of organ-specific gene expression are a subject of intense research interest, as it is the operation of these mechanisms during eukaryotic development which determine the characteristics of each organism Allele-specific expression has been characterized in only a few other plant genes. In maize, organ-specific pigmentation regulated by the R, B, and Pl genes is achieved by differential transcription of functionally conserved protein coding sequences. Our studies point to a strikingly different mechanism of organ-specific gene expression, involving post-transcriptional regulation of the regulatory P gene. The novel pigmentation pattern of the P-wr allele is associated with differences in the encoded protein. Furthermore, the P-wr gene itself is present as a unique tandemly amplified structure, which may affect its transcriptional regulation.

  18. Bayesian Computational Approaches for Gene Regulation Studies of Bioethanol and Biohydrogen Production. Final Scientific/Technical Report

    SciTech Connect

    Newberg, Lee; McCue, Lee Anne; Van Roey, Patrick

    2014-04-17

    The project developed mathematical models and first-version software tools for the understanding of gene regulation across multiple related species. The project lays the foundation for understanding how certain alpha-proteobacterial species control their own genes for bioethanol and biohydrogen production, and sets the stage for exploiting bacteria for the production of fuels. Enabling such alternative sources of fuel is a high priority for the Department of Energy and the public.

  19. Medical Devices; Immunology and Microbiology Devices; Classification of Autosomal Recessive Carrier Screening Gene Mutation Detection System. Final order.

    PubMed

    2015-10-27

    The Food and Drug Administration (FDA) has classified an autosomal recessive carrier screening gene mutation detection system into class II (special controls). The special controls that apply to this device are identified in this order and will be part of the codified language for the autosomal recessive carrier screening gene mutation detection system classification. The Agency has classified the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device.

  20. Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall.

    PubMed

    Malhotra, Nikhil; Sood, Hemant; Chauhan, Rajinder Singh

    2016-12-01

    Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13-171 folds) compared to shoots. Comparative expression analysis of those genes between tuberous root developmental stages showed 11-97 folds increase in transcripts in fully developed roots compared to young rootlets, thereby implying their association in biosynthesis, accumulation and storage of primary metabolites towards root biomass. Cluster analysis revealed a positive correlation with the gene expression data for different stages of tuberous root formation in A. heterophyllum. The outcome of this study can be useful in genetic improvement of A. heterophyllum for root biomass yield.

  1. Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana.

    PubMed

    Jost, R; Berkowitz, O; Wirtz, M; Hopkins, L; Hawkesford, M J; Hell, R

    2000-08-08

    The final step of cysteine biosynthesis in plants is catalyzed by O-acetylserine (thiol) lyase (OAS-TL), which occurs as several isoforms found in the cytosol, the plastids and the mitochondria. Genomic DNA blot hybridization and isolation of genomic clones indicate single copy genes (oasA1, oasA2, oasB and oasC) that encode the activities of OAS-TL A, B and C found in separate subcellular compartments in the model plant Arabidopsis thaliana. Sequence analysis reveals that the newly discovered oasA2 gene represents a pseudogene that is still transcribed, but is not functionally translated. The comparison of gene structures suggests that oasA1/oasA2 and oasB/oasC are closely related and may be derived from a common ancestor by subsequent duplications. OAS-TL A, B and C were overexpressed in an Escherichia coli mutant lacking cysteine synthesis and exhibited bifunctional OAS-TL and beta-cyanoalanine synthase (CAS) activities. However, all three proteins represent true OAS-TLs according to kinetic analysis and are unlikely to function in cyanide detoxification or secondary metabolism. In addition, it was demonstrated that the mitochondrial OAS-TL C exhibits in vivo protein-protein interaction capabilities with respect to cysteine synthase complex formation similar to cytosolic OAS-TL A and plastid OAS-TL B. Multiple database accessions for each of the A. thaliana OAS-TL isoforms can thus be attributed to a specified number of oas genes to which functionally defined gene products are assigned, and which are responsible for compartment-specific cysteine synthesis.

  2. Identification of key genes involved in polysaccharide bioflocculant synthesis in Bacillus licheniformis.

    PubMed

    Chen, Zhen; Liu, Peize; Li, Zhipeng; Yu, Wencheng; Wang, Zhi; Yao, Haosheng; Wang, Yuanpeng; Li, Qingbiao; Deng, Xu; He, Ning

    2017-03-01

    The present study reports the sequenced genome of Bacillus licheniformis CGMCC 2876, which is composed of a 4,284,461 bp chromosome that contains 4,188 protein-coding genes, 72 tRNA genes, and 21 rRNA genes. Additional analysis revealed an eps gene cluster with 16 open reading frames. Conserved Domains Database analysis combined with qPCR experiments indicated that all genes in this cluster were involved in polysaccharide bioflocculant synthesis. Phosphoglucomutase and UDP-glucose pyrophosphorylase were supposed to be key enzymes in polysaccharide secretion in B. licheniformis. A biosynthesis pathway for the production of polysaccharide bioflocculant involving the integration of individual genes was proposed based on functional analysis. Overexpression of epsDEF from the eps gene cluster in B. licheniformis CGMCC 2876 increased the flocculating activity of the recombinant strain by 90% compared to the original strain. Similarly, the crude yield of polysaccharide bioflocculant was enhanced by 27.8%. Overexpression of the UDP-glucose pyrophosphorylase gene not only increased the flocculating activity by 71% but also increased bioflocculant yield by 13.3%. Independent of UDP-N-acetyl-D-mannosamine dehydrogenase gene, flocculating activity, and polysaccharide yield were negatively impacted by overexpression of the UDP-N-acetylglucosamine 2-epimerase gene. Overall, epsDEF and gtaB2 were identified as key genes for polysaccharide bioflocculant synthesis in B. licheniformis. These results will be useful for further engineering of B. licheniformis for industrial bioflocculant production. Biotechnol. Bioeng. 2017;114: 645-655. © 2016 Wiley Periodicals, Inc.

  3. Genes

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Genes URL of this page: //medlineplus.gov/ency/article/ ...

  4. Exploration of new perspectives and limitations in Agrobacterium-mediated gene transfer technology. Final report, June 1, 1992--May 31, 1995

    SciTech Connect

    Marton, L.

    1996-02-01

    Genetic manipulation of plants often involves the introduction of homologous or partly homologous genes. Ectropic introduction of homologous sequences into plant genomes may trigger epigenetic changes, making expression of the genes unpredictable. The main project objective was to examine the feasibility of using Agrobacterium-mediated gene transfer for homologous gene targeting in plants.

  5. Sucrose metabolism gene families and their biological functions

    PubMed Central

    Jiang, Shu-Ye; Chi, Yun-Hua; Wang, Ji-Zhou; Zhou, Jun-Xia; Cheng, Yan-Song; Zhang, Bao-Lan; Ma, Ali; Vanitha, Jeevanandam; Ramachandran, Srinivasan

    2015-01-01

    Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions. PMID:26616172

  6. Final Report

    SciTech Connect

    Gurney, Kevin R.

    2015-01-12

    This document constitutes the final report under DOE grant DE-FG-08ER64649. The organization of this document is as follows: first, I will review the original scope of the proposed research. Second, I will present the current draft of a paper nearing submission to Nature Climate Change on the initial results of this funded effort. Finally, I will present the last phase of the research under this grant which has supported a Ph.D. student. To that end, I will present the graduate student’s proposed research, a portion of which is completed and reflected in the paper nearing submission. This final work phase will be completed in the next 12 months. This final workphase will likely result in 1-2 additional publications and we consider the results (as exemplified by the current paper) high quality. The continuing results will acknowledge the funding provided by DOE grant DE-FG-08ER64649.

  7. Final Report

    SciTech Connect

    DeTar, Carleton

    2012-12-10

    This document constitutes the Final Report for award DE-FC02-06ER41446 as required by the Office of Science. It summarizes accomplishments and provides copies of scientific publications with significant contribution from this award.

  8. Final Report

    SciTech Connect

    Balmain, Allan

    2007-03-28

    The specific aims of this project were as follows: Aim 1: Identify mouse genetic loci that affect the survival time of mice post radiation Aim 2: Identify somatic genetic alterations that are indicative of tumor suppressor and oncogene loci involved in radiation-induced cancers. Aim 3: Identify candidate radiation susceptibility genes by gene expression microarray analysis of the radiation response in normal tissues or in tumors from the strains used for aims 1 and 2.

  9. Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots.

    PubMed

    Li, Chun; Li, Qi-Gang; Dunwell, Jim M; Zhang, Yuan-Ming

    2012-10-01

    Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. In regard to the starch content in the seeds of crop plants, there is a distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare evolutionary rate, gene duplication, and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed 1) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred before the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots, 2) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed, and 3) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, for example, ADP-glucose pyrophosphorylase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

  10. Final Scientific/Technical Report for DOE Award No. DE-FG02-03ER15426: Role of Arabidopsis PINHEAD gene in meristem function

    SciTech Connect

    Dr. M. Kathryn Barton

    2011-11-29

    The shoot apical meristems of land plants are small mounds of hundreds of cells located at the tips of branches. It is from these small clusters of cells that essentially all above ground plant biomass and therefore much of our energy supply originates. Several key genes have been discovered that are necessary for cells in the shoot apical meristem to take on stem cell properties. The goal of this project is to understand how the synthesis and accumulation of the mRNAs and proteins encoded by these genes is controlled. A thorough understanding of the molecules that control the growth of shoot apical meristems in plants will help us to manipulate food, fiber and biofuel crops to better feed, clothe and provide energy for humans.

  11. Horizontal gene transfer as adaptive response to heavy metal stress in subsurface microbial communities. Final report for period October 15, 1997 - October 15, 2000

    SciTech Connect

    Smets, B. F.

    2001-12-21

    Horizontal gene transfer as adaptive response to heavy metal stress in the presence of heavy metal stress was evaluated in oligotrophic subsurface soil laboratory scale microcosms. Increasing levels of cadmium (10, 100 and 1000 mM) were applied and an E. coli donor was used to deliver the target plasmids, pMOL187 and pMOL222, which contained the czc and ncc operons, and the helper plasmid RP4. Plasmid transfer was evaluated through monitoring of the heavy metal resistance and presence of the genes. The interactive, clearly revealed, effect of biological and chemical external factors on the extent of plasmid-DNA propagation in microbial communities in contaminated soil environments was observed in this study. Additionally, P.putida LBJ 415 carrying a suicide construct was used to evaluate selective elimination of a plasmid donor.

  12. Final Report

    SciTech Connect

    Normanly, J.

    1999-11-29

    The primary goal was the characterization of tryptophan (Trp)-independent biosynthesis of the auxin indole-3-acetic acid (IAA). Our work and that of others indicates that indole is a precursor to IAA in a Trp-independent pathway and the objectives of this grant have been the isolation of indole-metabolizing genes from Arabidopsis.

  13. Final report

    SciTech Connect

    Susan S. Golden

    2005-03-31

    The originally funded project was geared to pursue research on regulation of photosystem II (PSII) in the cyanobacterium Synechococcus elongatus PCC 7942. We characterized a locus, psfR, (psbA stimulating factor) that affects expression of the psbAI gene, which encodes the PSII protein D1. Over-expression of psfR, which encodes a protein with receiver and pseudo-receiver domains, acts at the promoter region to elevate expression of psbAI and a subset of other loci. We reoriented the remainder of the funding to make a greater impact through completion of a functional genomics project that had been initiated with funding from another agency. The goal is inactivation of each gene individually in the S. elongatus genome, and completion of the entire genome sequence. At the end of the project we will have screened all loci for involvement in circadian rhythms of gene expression and assembled an archived set of clones that can be used to create the mutations to screen for any other phenotype. During the project period we: (1) prepared a functional genomics website for S. elongatus PCC 7942 that posts sequences prior to GenBank release, and presents the strategy and progress for the genomics project (http://www.bio.tamu.edu/synecho/); (2) determined the sequence of and annotated the S. elongatus 46 kb plasmid, pANL; (3) submitted assembled sequences with annotation of 8 cosmid inserts to GenBank (313 kb), with sites of transposon insertions indicated; (4) mutagenized approximately an additional 600 kb of the genome (16 cosmids) and identified sequences flanking the mutations; (5) recombined mutagenesis substrates into the S. elongatus genome to produce gene inactivations (at the sites of transposon insertions) for approximately 415 kb of mutagenized sequence (85% of these have already been screened for circadian phenotypes) (6) identified the clpPIIclpX locus as important in determining circadian period; and (7) demonstrated effectiveness of antisense RNA for decreasing

  14. Prognostic role of KiSS-1 and possibility of therapeutic modality of metastin, the final peptide of the KiSS-1 gene, in urothelial carcinoma.

    PubMed

    Takeda, Toshikazu; Kikuchi, Eiji; Mikami, Shuji; Suzuki, Eriko; Matsumoto, Kazuhiro; Miyajima, Akira; Okada, Yasunori; Oya, Mototsugu

    2012-04-01

    The KiSS-1 gene has been reported to be a metastasis suppressor gene in human melanoma. The gene product was isolated from human placenta as the ligand of GPR54, a G protein-coupled receptor, and the C-terminally amidated peptide of 54 amino acids is called metastin. The binding of metastin to GPR54 has been shown to inhibit tumor metastasis in some tumor cells; however, its function remains unclear in urothelial carcinoma. We first evaluated KiSS-1 expression and GPR54 expression in 151 patients with upper urinary tract urothelial carcinoma to determine their prognostic significance. Next, we examined the role of metastin in the invasiveness and lung metastasis of MBT-2 variant (MBT-2V), which is a highly metastatic murine bladder cancer cell. Multivariate analysis revealed that KiSS-1 expression was an independent predictor of metastasis and overall survival. However, GPR54 expression was not selected. Hematogeneous metastasis had a significantly lower level of KiSS-1 expression compared with lymph node metastasis. Metastin treatment significantly reduced the invasiveness of MBT-2V cells and inhibited the DNA-binding activity of NF-κB by blocking its nuclear translocation, leading to a reduction in the expression and activity of matrix metalloproteinase-9. Metastin treatment dramatically prevented the occurrence of lung metastatic nodules (6.3 ± 2.3, n = 15) compared with controls (30.4 ± 5.1, n = 15; P < 0.01), as well as had survival benefit. KiSS-1 plays an important role in the prognosis of upper tract urothelial carcinoma and metastin may be an effective inhibitor of metastasis in urothelial carcinoma through its blockade of NF-κB function.

  15. Final Report

    SciTech Connect

    Marchant, Gary E.

    2013-04-23

    This is the final report of a two year project entitled "Governing Nanotechnology Risks and Benefits in the Transition to Regulation: Innovative Public and Private Approaches." This project examined the role of new governance or "soft law" mechanisms such as codes of conduct, voluntary programs and partnership agreements to manage the risks of emerging technologies such as nanotechnology. A series of published or in publication papers and book chapters are attached.

  16. Final Report

    SciTech Connect

    R. Paul Drake

    2001-11-30

    This final report describes work involving 22 investigators from 11 institutions to explore the dynamics present in supernova explosions by means of experiments on the Omega laser. The specific experiments emphasized involved the unstable expansion of a spherical capsule and the coupling of perturbations at a first interface to a second interface by means of a strong shock. Both effects are present in supernovae. The experiments were performed at Omega and the computer simulations were undertaken at several institutions. B139

  17. Final Report

    SciTech Connect

    Stinis, Panos

    2016-08-07

    This is the final report for the work conducted at the University of Minnesota (during the period 12/01/12-09/18/14) by PI Panos Stinis as part of the "Collaboratory on Mathematics for Mesoscopic Modeling of Materials" (CM4). CM4 is a multi-institution DOE-funded project whose aim is to conduct basic and applied research in the emerging field of mesoscopic modeling of materials.

  18. Final report: FASEB Summer Research Conference on ''Post-transcriptional control of gene expression: Effectors of mRNA decay'' [agenda and attendees list

    SciTech Connect

    Maquat, Lynne

    2002-12-01

    The goal of this meeting was to provide an interactive forum for scientists working on prokaryotic and eukaryotic mRNA decay. A special seminar presented by a leader in the field of mRNA decay in S. cerevisiae focused on what is known and what needs to be determined, not only for yeast but for other organisms. The large attendance (110 participants) reflects the awareness that mRNA decay is a key player in gene regulation in a way that is affected by the many steps that precede mRNA formation. Sessions were held on the following topics: mRNA transport and mRNP; multicomponent eukaryotic nucleases; nonsense-mediated mRNA decay and nonsense-associated altered splicing; Cis-acting sequences/Trans-acting factors of mRNA decay; translational accuracy; multicomponent bacterial nucleases; interplay between mRNA polyadenylation, translation and decay in prokaryotes and prokaryotic organelles; and RNA interference and other RNA mediators of gene expression. In addition to the talks and two poster sessions, there were three round tables: (1) Does translation occur in the nucleus? (2) Differences and similarities in the mechanisms of mRNA decay in different eukaryotes, and (3) RNA surveillance in bacteria?

  19. Influence of crop load on the expression patterns of starch metabolism genes in alternate-bearing citrus trees.

    PubMed

    Nebauer, Sergio G; Renau-Morata, Begoña; Lluch, Yolanda; Baroja-Fernández, Edurne; Pozueta-Romero, Javier; Molina, Rosa-Victoria

    2014-07-01

    The fruit is the main sink organ in Citrus and captures almost all available photoassimilates during its development. Consequently, carbohydrate partitioning and starch content depend on the crop load of Citrus trees. Nevertheless, little is known about the mechanisms controlling the starch metabolism at the tree level in relation to presence of fruit. The aim of this study was to find the relation between the seasonal variation of expression and activity of the genes involved in carbon metabolism and the partition and allocation of carbohydrates in 'Salustiana' sweet orange trees with different crop loads. Metabolisable carbohydrates, and the expression and activity of the enzymes involved in sucrose and starch metabolism, including sucrose transport, were determined during the year in the roots and leaves of 40-year-old trees bearing heavy crop loads ('on' trees) and trees with almost no fruits ('off' trees). Fruit altered photoassimilate partitioning in trees. Sucrose content tended to be constant in roots and leaves, and surplus fixed carbon is channeled to starch production. Differences between 'on' and 'off' trees in starch content can be explained by differences in ADP-glucose pyrophosphorylase (AGPP) expression/activity and α-amylase activity which varies depending on crop load. The observed relation of AGPP and UGPP (UDP-glucose pyrophosphorylase) is noteworthy and indicates a direct link between sucrose and starch synthesis. Furthermore, different roles for sucrose transporter SUT1 and SUT2 have been proposed. Variation in soluble sugars content cannot explain the differences in gene expression between the 'on' and 'off' trees. A still unknown signal from fruit should be responsible for this control.

  20. Final Report Grant No. DE-FG02-98ER20307 Lipopolysaccharide Structures and Genes Required for Root Nodule Development August 1, 2004 to July 31, 2008

    SciTech Connect

    Noel, K. Dale

    2008-12-07

    the roles of other important bacterial factors at multiple stages of nodule development. The project also investigated the biosynthesis of this bacterial factor. It has a complex structure and the first accomplishment was the determination of the sequences of genetic regions known to be important. Next the discovered genes were mutated to identify the 26 that are required for its synthesis. In addition, six others were discovered that are believed to change its structure under various environmental conditions. By studying mutants affected in specific genes, genes were associated with each of the predicted steps in the biosynthesis. Current work is testing the predicted biosynthetic model with studies conducted in vitro with bacterial extracts. Overall, the work funded by this grant establishes this system as a model for host-bacterial interactions based on specific polysaccharide structure. All areas that are needed for a comprehensive model have been significantly advanced: the biological function, the structural features that are crucial, the complete set of bacterial genes involved, and a model for the biosynthesis.

  1. The anti-metastatic nm23-1 gene is needed for the final step of mammary duct maturation of the mouse nipple.

    PubMed

    Deplagne, Camille; Peuchant, Evelyne; Moranvillier, Isabelle; Dubus, Pierre; Dabernat, Sandrine

    2011-04-07

    Nm23/NDP kinases are multifunctional enzymes involved in the general homeostasis of triphosphate nucleosides. Numerous studies have shown that NDPKs also serve as regulatory factors of various cell activities, not always connected to nucleotide phosphorylation. In particular, the nme-1 gene, encoding the NM23-1/NDPKA protein, has been reported as a metastasis suppressor gene. This activity was validated in hepatocellular tumors induced in nm23-1 deficient mice. Yet, data describing the primary physiological functions of nm23-1/NDPKA is still scarce. We have characterized in depth the phenotype of nm23-1 deletion in the mammary gland in mice carrying whole body nm23-M1 invalidation. We also asked why the nm23-M1⁻/⁻ mutant females displayed severe nursing disability. We found that the growth retardation of mutant virgin glands was due to reduced proliferation and apoptosis of the epithelial cells within the terminal end buds. The balance of pro/anti-apoptotic factors was impaired in comparison with wild type glands. In the lactating glands, the reduced proliferation rate persisted, but the apoptotic factors were unchanged. However, those defects did not seem to affect the gland maturation since the glands lacking nm23-1/NDPKA appeared morphologically normal. Thorough examination of all the functional aspects of the mammary glands revealed that lack of nm23-1/NDPKA does not impact the production or the ejection of milk in the lumen of lobuloalveolae. Interestingly, an epithelial plug was found to obstruct the extremity of the unique lactiferous duct delivering the milk out of the nipple. These cells, normally disappearing after lactation takes place, persisted in the mutant nipples. This work provides a rare instance of nm23-1/NDPKA physiological functions in the mammary glands and reveals its implication as a modulator factor of proliferation and apoptosis in this tissue.

  2. Final Report

    SciTech Connect

    R Paul Drake

    2004-01-12

    OAK-B135 This is the final report from the project Hydrodynamics by High-Energy-Density Plasma Flow and Hydrodynamics and Radiation Hydrodynamics with Astrophysical Applications. This project supported a group at the University of Michigan in the invention, design, performance, and analysis of experiments using high-energy-density research facilities. The experiments explored compressible nonlinear hydrodynamics, in particular at decelerating interfaces, and the radiation hydrodynamics of strong shock waves. It has application to supernovae, astrophysical jets, shock-cloud interactions, and radiative shock waves.

  3. Final Report

    SciTech Connect

    Freeling, Michael

    2002-07-01

    OAK-B135 Well-studied maize gene Adh1 has been shown to carry tissue-specific, anaerobic induction-specific and pollen-specific information in the sequences near protein-coding sequences.-- The grass ligule network of function proves to be one of the simplest systems of organogenesis known in plants, requiring two specific transcription factors. -- Programmed cell death happens at the maize ligule, and kernels situated ''backwards'' in the ear occur due to timed identity transformations caused during a dosage-sensitive regulatory step. B263

  4. Comparative evolution of the recA gene of surface and deep subsurface microorganisms (an evolutionary clock of intermediate rate). Final report

    SciTech Connect

    Miller, R.V.

    1998-04-01

    Because of the ability of the recA protein product to maintain both DNA integrity and increase genetic diversity, this gene may be essential to the survival of microorganisms following the damaging effects of numerous environmental stresses such as exposure to solar UV radiation, exposure to gamma radiation, starvation, and changing environments. While the various activities and amino-acid sequence of recA have been highly conserved among the eubacteria and archaea, little is known as to whether a strict structure-function relationship has been conserved. In other words, are the same regions of this highly plastic, functionally heterogeneous protein involved in the same catalytic capacities throughout the bacterial kingdom? While it is reasonable to assume that this type of conservation has also occurred, we felt it necessary to test the assumption by demonstrating that mutations in different genera of bacteria which eliminate similar functions (i.e., lead to similar phenotypes) are caused by changes in the amino-acid sequence in the same regions of their recA proteins. Therefore, we located the changes in nucleotide sequence in two recA mutants of P. aeruginosa which displayed mutant phenotypes in recombination and UV resistance. Our assumption was that if structure-function relationships held, these mutations would be found in areas already identified as essential for the function of the E. coli recA protein.

  5. Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

    PubMed Central

    Jourda, Cyril; Cardi, Céline; Gibert, Olivier; Giraldo Toro, Andrès; Ricci, Julien; Mbéguié-A-Mbéguié, Didier; Yahiaoui, Nabila

    2016-01-01

    Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage. PMID:27994606

  6. Final Report

    SciTech Connect

    Webb, Robert C.; Kamon, Teruki; Toback, David; Safonov, Alexei; Dutta, Bhaskar; Dimitri, Nanopoulos; Pope, Christopher; White, James

    2013-11-18

    Overview The High Energy Physics Group at Texas A&M University is submitting this final report for our grant number DE-FG02-95ER40917. This grant has supported our wide range of research activities for over a decade. The reports contained here summarize the latest work done by our research team. Task A (Collider Physics Program): CMS & CDF Profs. T. Kamon, A. Safonov, and D. Toback co-lead the Texas A&M (TAMU) collider program focusing on CDF and CMS experiments. Task D: Particle Physics Theory Our particle physics theory task is the combined effort of Profs. B. Dutta, D. Nanopoulos, and C. Pope. Task E (Underground Physics): LUX & NEXT Profs. R. Webb and J. White(deceased) lead the Xenon-based underground research program consisting of two main thrusts: the first, participation in the LUX two-phase xenon dark matter search experiment and the second, detector R&D primarily aimed at developing future detectors for underground physics (e.g. NEXT and LZ).

  7. Over-expression of AGPase genes enhances seed weight and starch content in transgenic maize.

    PubMed

    Li, Ning; Zhang, Shujuan; Zhao, Yajie; Li, Bei; Zhang, Juren

    2011-02-01

    Cereal crops accumulate starch in the seed endosperm as an energy reserve. ADP-glucose pyrophosphorylase (AGPase) plays a key role in regulating starch biosynthesis in cereal seeds. The AGPase in the maize endosperm is a heterotetramer of two small subunits, encoded by Brittle2 (Bt2) gene, and two large subunits, encoded by the Shrunken2 (Sh2) gene. The two genes (Bt2, Sh2) from maize were introduced into two elite maize inbred lines, solely and in tandem, and under the control of endosperm-specific promoters for over-expression. PCR, Southern blotting, and real-time RT-PCR analysis indicated that the transgenes were integrated into the genome of transgenic plants and were over-expressed in their progeny. The over-expression of either gene enhanced AGPase activity, seed weight and starch content compared with the WT, but the amounts were lower than plants with over-expression of both Bt2 and Sh2. Developing seeds from co-expression transgenic maize plants had higher cytoplasmic AGPase activity: the 100-grain weight increased 15% over the wild type (WT), and the starch content increased to over 74% compared with the WT of 65%. These results indicate that over-expression of the genes in transgenic maize plants could improve kernel traits. This report provides a feasible approach for increasing starch content and seed weight in maize.

  8. Final report

    SciTech Connect

    Dobbs, Fred C.

    2003-01-15

    species of flagellates, Spumella sp. and Bodo sp. (identifications are tentative) were isolated from South Oyster sediments by repetitive serial dilution/extinction method. Protistan cells were cultured with Cereal leaf Prescott medium and pelleted by centrifugation. Protistan DNAs were extracted with a DNA extraction kit (Sigma Co.) and the sequencing of their SSrDNA is underway. Finally, to follow up on our collaboration of Dr. Bill Johnson (Univ. of Utah), one of the co-PIs under the same NABIR umbrella, we are pleased to report we have successfully tested antibody-ferrographic capture of protists (See previous year's report for more background). Polyclonal FITC-conjugated antibody specific for a flagellate, Spumella sp., was produced by Rockland Inc., and we now are able to enumerate that species using ferrographic capture. There are, however, some issues of non-specific staining that remain to be resolved.

  9. D-galactose catabolism in Penicillium chrysogenum: Expression analysis of the structural genes of the Leloir pathway.

    PubMed

    Jónás, Ágota; Fekete, Erzsébet; Németh, Zoltán; Flipphi, Michel; Karaffa, Levente

    2016-09-01

    In this study, we analyzed the expression of the structural genes encoding the five enzymes comprising the Leloir pathway of D-galactose catabolism in the industrial cell factory Penicillium chrysogenum on various carbon sources. The genome of P. chrysogenum contains a putative galactokinase gene at the annotated locus Pc13g10140, the product of which shows strong structural similarity to yeast galactokinase that was expressed on lactose and D-galactose only. The expression profile of the galactose-1-phosphate uridylyl transferase gene at annotated locus Pc15g00140 was essentially similar to that of galactokinase. This is in contrast to the results from other fungi such as Aspergillus nidulans, Trichoderma reesei and A. niger, where the ortholog galactokinase and galactose-1-phosphate uridylyl transferase genes were constitutively expressed. As for the UDP-galactose-4-epimerase encoding gene, five candidates were identified. We could not detect Pc16g12790, Pc21g12170 and Pc20g06140 expression on any of the carbon sources tested, while for the other two loci (Pc21g10370 and Pc18g01080) transcripts were clearly observed under all tested conditions. Like the 4-epimerase specified at locus Pc21g10370, the other two structural Leloir pathway genes - UDP-glucose pyrophosphorylase (Pc21g12790) and phosphoglucomutase (Pc18g01390) - were expressed constitutively at high levels as can be expected from their indispensable function in fungal cell wall formation.

  10. Identification of a signal transduction response sequence element necessary for induction of a Dictyostelium discoideum gene by extracellular cyclic AMP.

    PubMed Central

    Pavlovic, J; Haribabu, B; Dottin, R P

    1989-01-01

    The signal transduction pathways that lead to gene induction are being intensively investigated in Dictyostelium discoideum. We have identified by deletion and transformation analysis a sequence element necessary for induction of a gene coding for uridine diphosphoglucose pyrophosphorylase (UDPGP1) of D. discoideum in response to extracellular cyclic AMP (cAMP). This regulatory element is located 380 base pairs upstream of the transcription start site and contains a G+C-rich partially palindromic sequence. It is not required for transcription per se but is required for induction of the gene in response to the stimulus of extracellular cAMP. The cAMP response sequence is also required for induction of the gene during normal development. A second A+T-rich cis-acting region located immediately downstream of the cAMP response sequence appears to be essential for the basal level of expression of the UDPGP1 gene. The position of the cAMP response element coincides with a DNase I-hypersensitive site that is observed when the UDPGP1 gene is actively transcribed. Images PMID:2557538

  11. Maize Sh2 gene is constrained by natural selection but escaped domestication.

    PubMed

    Manicacci, D; Falque, M; Le Guillou, S; Piégu, B; Henry, A-M; Le Guilloux, M; Damerval, C; De Vienne, D

    2007-03-01

    In Zea mays L., we studied the molecular evolution of Shrunken2 (Sh2), a gene that encodes the large subunits of a major enzyme in endosperm starch biosynthesis, ADP-glucose pyrophosphorylase. We compared 4669 bp of the Sh2 coding region on 50 accessions of maize and teosinte. Very few nucleotide polymorphisms were found when compared with other genes in Z. mays, revealing an effect of purifying selection in the whole species that predates domestication. Additionally, the comparison of Sh2 sequences in all Z. mays subspecies and outgroups Z. diploperennis and Tripsacum dactyloides suggests the occurrence of an ancient selective sweep in the Sh2 3' region. The amount and nature of nucleotide diversity are similar in both maize and teosinte, confirming previous results that suggested that Sh2 has not been involved in maize domestication. The very low level of nucleotide diversity as well as the highly conserved protein sequence suggest that natural selection retained effective Sh2 allele(s) long before agriculture started, making human selection inefficient on this gene.

  12. Improved polysaccharide production in a submerged culture of Ganoderma lucidum by the heterologous expression of Vitreoscilla hemoglobin gene.

    PubMed

    Li, Huan-Jun; Zhang, De-Huai; Yue, Tong-Hui; Jiang, Lu-Xi; Yu, Xuya; Zhao, Peng; Li, Tao; Xu, Jun-Wei

    2016-01-10

    Expression of Vitreoscilla hemoglobin (VHb) gene was used to improve polysaccharide production in Ganoderma lucidum. The VHb gene, vgb, under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase gene promoter was introduced into G. lucidum. The activity of expressed VHb was confirmed by the observation of VHb specific CO-difference spectrum with a maximal absorption at 419 nm for the transformant. The effects of VHb expression on intracellular polysaccharide (IPS) content, extracellular polysaccharide (EPS) production and transcription levels of three genes encoding the enzymes involved in polysaccharide biosynthesis, including phosphoglucomutase (PGM), uridine diphosphate glucose pyrophosphorylase (UGP), and β-1,3-glucan synthase (GLS), were investigated. The maximum IPS content and EPS production in the vgb-bearing G. lucidum were 26.4 mg/100mg dry weight and 0.83 g/L, respectively, which were higher by 30.5% and 88.2% than those of the wild-type strain. The transcription levels of PGM, UGP and GLS were up-regulated by 1.51-, 1.55- and 3.83-fold, respectively, in the vgb-bearing G. lucidum. This work highlights the potential of VHb to enhance G. lucidum polysaccharide production by large scale fermentation.

  13. A single gene mutation that increases maize seed weight

    SciTech Connect

    Giroux, M.J.; Shaw, J.; Hannah, L.C. |

    1996-06-11

    The maize endosperm-specific gene shrunken2 (Sh2) encodes the large subunit of the heterotetrameric starch synthetic enzyme adenosine diphosphoglucose pyrophosphorylase (AGP; EC 2.7.7.27). Here we exploit an in vivo, site-specific mutagenesis system to create short insertion mutations in a region of the gene known to be involved in the allosteric regulation of AGP. The site-specific mutagen is the transposable element dissociation (Ds). Approximately one-third (8 of 23) of the germinal revertants sequenced restored the wild-type sequence, whereas the remaining revertants contained insertions of 3 or 6 bp. All revertants retained the original reading frame 3 feet to the insertion site and involved the addition of tyrosine and/or serine. Each insertion revertant reduced total AGP activity and the amount of the SH2 protein. The revertant containing additional tyrosine and serine residues increased seed weight 11-18% without increasing or decreasing the percentage of starch. Other insertion revertants lacking an additional serine reduced seed weight. Reduced sensitivity to phosphate, a long-known inhibitor of AGP, was found in the high seed-weight revertant. This alteration is likely universally important since insertion of tyrosine and serine in the potato large subunit of AGP at the comparable position and expression in Escherichia coli also led to a phosphate-insensitive enzyme. These results show that single gene mutations giving rise to increased seed weight, and therefore perhaps yield, are clearly possible in a plant with a long history of intensive and successful breeding efforts. 20 refs., 5 figs., 5 tabs.

  14. Genes and Gene Therapy

    MedlinePlus

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  15. Identification of LmUAP1 as a 20-hydroxyecdysone response gene in the chitin biosynthesis pathway from the migratory locust, Locusta migratoria.

    PubMed

    Liu, Xiao-Jian; Sun, Ya-Wen; Li, Da-Qi; Li, Sheng; Ma, En-Bo; Zhang, Jian-Zhen

    2016-10-03

    In Locusta migratoria, we found that two chitin biosynthesis genes, UDP N-acetylglucosamine pyrophosphorylase gene LmUAP1 and chitin synthase gene LmCHS1, are expressed mainly in the integument and are responsible for cuticle formation. However, whether these genes are regulated by 20-hydroxyecdysone (20E) is still largely unclear. Here, we showed the developmental expression pattern of LmUAP1, LmCHS1 and the corresponding 20E titer during the last instar nymph stage of locust. RNA interference (RNAi) directed toward a common region of the two isoforms of LmEcR (LmEcRcom) reduced the expression level of LmUAP1, while there was no difference in the expression of LmCHS1. Meantime, injection of 20E in vivo induced the expression of LmUAP1 but not LmCHS1. Further, we found injection-based RNAi of LmEcRcom resulted in 100% mortality. The locusts failed to molt with no apolysis, and maintained in the nymph stage until death. In conclusion, our preliminary results indicated that LmUAP1 in the chitin biosynthesis pathway is a 20E late-response gene and LmEcR plays an essential role in locust growth and development, which could be a good potential target for RNAi-based pest control.

  16. Effects of starch- vs. fiber-based energy supplements during winter grazing on partitioning of fat among depots and adipose tissue gene expression in growing cattle and final carcass characteristics.

    PubMed

    Sharman, E D; Lancaster, P A; Krehbiel, C R; Hilton, G G; Stein, D R; Desilva, U; Horn, G W

    2013-05-01

    Fifty-five normal-weaned Angus steers (268 ± 22 kg; 265 ± 16 d of age) were used to evaluate the effects of starch- vs. fiber-based energy supplements for stocker cattle grazing low-quality dormant native range on growth performance, body composition, and adipose tissue development of different fat depots. Steers were randomly allotted to 4 treatments: 1.02 kg·steer(-1)·d(-1) of a 40% CP cottonseed meal-based supplement (CON), corn/soybean meal-based supplement fed at 1% of BW (CORN), soybean hull/soybean meal-based supplement fed at 1% of BW (SBH), or dried distillers grains with solubles fed at 1% of BW (DDGS). All supplements were individually fed 5 d/wk during the 121-d winter grazing phase. After winter grazing, 3 steers per treatment were harvested to determine body composition and carcass characteristics, and collect subcutaneous (SC) and perirenal (PR) adipose tissue samples. The remaining steers grazed cool-season grass pastures for 74 d without supplementation before finishing. Steers were fed a common finishing diet for 113 d before harvest, at which time carcass characteristics were collected at a commercial abattoir. Energy supplementation increased (P < 0.01) winter grazing ADG compared with CON steers, and CORN steers had greater (P < 0.01) ADG than SBH and DDGS steers. Energy supplementation increased (P < 0.04) mesenteric/omental fat mass but did not influence (P > 0.13) 12th rib fat thickness or marbling score at intermediate harvest compared with CON steers. The mRNA expression of genes involved in lipogenesis and markers of adipogenesis were greater (P < 0.05) in PR adipose tissue of energy-supplemented steers compared with CON steers but not in SC adipose tissue. Fiber-supplemented steers had greater (P < 0.01) mRNA expression of fatty acid synthase and fatty acid binding protein 4 compared with CORN steers in PR adipose tissue but not SC adipose tissue. At final harvest, energy-supplemented steers had greater (P < 0.05) KPH and yield grade

  17. Transcriptional Profiles of Hybrid Eucalyptus Genotypes with Contrasting Lignin Content Reveal That Monolignol Biosynthesis-related Genes Regulate Wood Composition

    PubMed Central

    Shinya, Tomotaka; Iwata, Eiji; Nakahama, Katsuhiko; Fukuda, Yujiroh; Hayashi, Kazunori; Nanto, Kazuya; Rosa, Antonio C.; Kawaoka, Akiyoshi

    2016-01-01

    Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected 3-year old hybrid Eucalyptus (Eucalyptus urophylla × Eucalyptus grandis) genotypes (AM063 and AM380) that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0 and 48.2%, α-cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA) and sucrose synthase (SUSY) were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase and xyloglucan endotransglucoxylase than those in AM380. Most monolignol biosynthesis-related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase, cinnamate-4-hydroxylase (C4H) and 4-coumarate-CoA ligase (4CL). Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF, and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents in Eucalyptus plants. PMID

  18. [Chinese waxy elites SW70 and SW22 are revealed to be new multimutants of starch-synthesis enzyme coding genes].

    PubMed

    Ding, Xiang Zhen; Yang, Ming Ming; Wang, Bei Guo; Yan, Gui Qin; Duan, Ke; Huang, Jian Hua

    2008-10-01

    Waxy maize (wx) is a type of spontaneous starch mutant as compared to wild type foodstuff maize (Wx). The mechanisms underlying waxy maize kernel development are intricate and diversified. Here we characterized the expression of 21 genes belonging to four families, i.e., ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch debranching enzyme (DBE) in the developing kernels of waxy maize inbred SW22, SW70 and relative wild type inbred 5003 at 1, 2 and 4 weeks after pollination. Dynamic expression pattern of a number of genes in developing kernels of SW22 were different from that in 5003 and SW70. Besides, obvious presence of wx transcripts in SW22 and SW70 were observed, though at the level lower than that in wild type 5003. Unexpectedly, the transcripts of Gbssllb and isoamylase-type DBE coding gene Iso2 were completely absent in SW22 and SW70. The above observation prompted the hypothesis that partial or complete loss-of-function of Wx, and/or there exist lose-of-function of uncharacterized gene (s) important for amylose synthesis in SW22 such as GbssIIb and Iso2, which may account for the absence of amylose accumulation in SW22.

  19. Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme.

    PubMed

    Corbi, J; Debieu, M; Rousselet, A; Montalent, P; Le Guilloux, M; Manicacci, D; Tenaillon, M I

    2011-03-01

    Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU(leaf) through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU(end), LSU(emb)) or breeding (LSU(leaf)), two exhibit patterns consistent with diversifying (SSU(leaf)) and balancing selection (SSU(emb)) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.

  20. Final Technical Report

    SciTech Connect

    Schuur, Edward; Luo, Yiqi

    2016-12-01

    This final grant report is a continuation of the final grant report submitted for DE-SC0006982 as the Principle Investigator (Schuur) relocated from the University of Florida to Northern Arizona University. This report summarizes the original project goals, as well as includes new project activities that were completed in the final period of the project.

  1. Vet Centers. Final rule.

    PubMed

    2016-03-02

    The Department of Veterans Affairs (VA) adopts as final an interim final rule that amends its medical regulation that governs Vet Center services. The National Defense Authorization Act for Fiscal Year 2013 (the 2013 Act) requires Vet Centers to provide readjustment counseling services to broader groups of veterans, members of the Armed Forces, including a member of a reserve component of the Armed Forces, and family members of such veterans and members. This final rule adopts as final the regulatory criteria to conform to the 2013 Act, to include new and revised definitions.

  2. Progress Report for DOE DE-FG03-98ER20317 ''Regulation of the floral homeotic gene AGAMOUS'' Current and Final Funding Period: September 1, 2002, to December 31, 2002

    SciTech Connect

    Weigel, D.

    2003-03-11

    OAK-B135 Results obtained during this funding period: (1) Phylogenetic footprinting of AG regulatory sequences Sequences necessary and sufficient for AGAMOUS (AG) expression in the center of Arabidopsis flowers are located in the second intron, which is about 3 kb in size. This intron contains binding sites for two transcription factors, LEAFY (LFY) and WUSCHEL (WUS), which are direct activators of AG. We used the new method of phylogenetic shadowing to identify new regulatory elements. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. (2) Repression of AG by MADS box genes A candidate for repressing AG in the shoot apical meristem has been the MADS box gene FUL, since it is expressed in the shoot apical meristem and since an activated version (FUL:VP16) leads to ectopic AG expression in the shoot apical meristem. However, there is no ectopic AG expression in full single mutants. We therefore started to generate VP16 fusions of several other MADS box genes expressed in the shoot apical meristem, to determine which of these might be candidates for FUL redundant genes. We found that AGL6:VP16 has a similar phenotype as FUL:VP16, suggesting that AGL6 and FUL interact. We are now testing this hypothesis. (3) Two candidate AG regulators, WOW and ULA Because the phylogenetic footprinting project has identified several new candidate regulatory motifs, of which at least one (the CCAATCA motif) has rather strong effects, we had decided to put the analysis of WOW and ULA on hold, and to focus on using the newly identified motifs as tools. We conduct ed yeast one-hybrid screen with two of the conserved motifs, and identified several classes of transcription factors that can interact with them. One of these is encoded by the PAN gene

  3. Cassini's Grand Finale: The Final Orbits

    NASA Astrophysics Data System (ADS)

    Spilker, Linda; Edgington, Scott

    2016-04-01

    The Cassini-Huygens mission, a joint collaboration between NASA, ESA and the Italian Space Agency, is approaching its last year of operations after nearly 12 years in orbit around Saturn. Cassini will send back its final bits of unique data on September 15th, 2017 as it plunges into Saturn's atmosphere, vaporizing and satisfying planetary protection requirements. Before that time Cassini will continue its legacy of exploration and discovery with 12 close flybys of Titan in 2016 and 2017 that will return new science data as well as sculpt the inclinations and periods of the final orbits. Even though all of our close icy satellite flybys, including those of Enceladus, are now completed, numerous Voyager-class flybys (<100,000 km) of Mimas and Enceladus remain as well as some of our best flybys of the tiny ring moons. Cassini will also continue to study seasonal and temporal changes in the system as northern summer solstice approaches. In November 2016 Cassini will transition to a series of orbits with peripases just outside Saturn's F ring. These 20 orbits will include close flybys of some tiny ring moons and excellent views of the F ring and outer A ring. The 126th and final close flyby of Titan will propel Cassini across Saturn's main rings and into its final orbits. Cassini's Grand Finale, starting in April 2017, is comprised of 22 orbits at an inclination of 63 degrees. Cassini will repeatedly dive between the innermost rings and the upper atmosphere of the planet providing insights into fundamental questions unattainable during the rest of the mission. Cassini will be the first spacecraft to explore this region. These close orbits provide the highest resolution observations of both the rings and Saturn, and direct in situ sampling of the ring particles, composition, plasma, Saturn's exosphere and the innermost radiation belts. Saturn's gravitational field will be measured to unprecedented accuracy, providing information on the interior structure of the planet

  4. Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat

    PubMed Central

    Batra, Ritu; Saripalli, Gautam; Mohan, Amita; Gupta, Saurabh; Gill, Kulvinder S.; Varadwaj, Pritish K.; Balyan, Harindra S.; Gupta, Pushpendra K.

    2017-01-01

    ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. “True” orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) “QTCL” motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T. urartu, rice and sorghum, while “LGGG” motif in LS was present in all species except T. urartu and chickpea; SS provides thermostability to AGPase, while LS is involved in regulation of AGPase activity; (iv) heterotetrameric structure of AGPase was predicted and analyzed in real time environment through molecular dynamics simulation for all the species; (v) several cis-acting regulatory elements were identified in the AGPase promoters with their possible role in regulating spatial and temporal expression (endosperm and leaf tissue) and also the expression, in response to abiotic stresses; and (vi) expression analysis revealed downregulation of both subunits under conditions of heat and drought stress. The results of the present study have allowed better understanding of structure and evolution of the genes and the encoded proteins and provided clues for exploitation of variability in these genes for engineering thermostable AGPase. PMID:28174576

  5. Final Technical Report

    SciTech Connect

    Stuart B. Levy, M.D.

    2008-07-07

    P. fluorescens PfO-1 is a soil bacterium isolated by this laboratory from sandy loam soil (4). Because of the importance of adhesion for persistence in natural environments, we utilized adherence to sand as an assay to screen a library of PfO-1 mutants for defects in adhesion. Three adhesion defective mutants, PfO-5, PfO-10, and PfO-15 were recovered. PfO-5 and PfO-10 had different insertions in the same gene, which we called adnA, and also showed motility defects (3). PfO-15 was motile, but was hyper-flagellated. The insertion was in a different gene, adnB, which shows similarity to mot genes involved in flagella functions (Strain and Levy, unpublished). These early studies demonstrated the important but separable requirements for flagella and motility in adherence. In a field study, the adnA mutant PfO-5 was less able to persist than the wildtype PfO-1 and did not spread as fast or as far from the point of inoculation as did PfO-1 (7), linking adhesion and soil fitness. DNA sequencing revealed that AdnA shares 82% identity with the flagella regulator FleQ from P. aeruginosa (3). FleQ is required for adhesion of P. aeruginosa to respiratory mucin, which is important for pathogenesis (1, 2). Using a gene fusion approach, seven loci that are expressed in an AdnA-dependent manner were identified (8). The loci were called ''aba'', for affected by AdnA. We uncovered genes involved in motility, chemotaxis, LPS synthesis, and two genes of no known function. Four of the aba genes were not reported to be in the FleQ regulon (5). We recently began using the IVET (in vivo expression technology) promoter-trap to identify genes whose expression is upregulated in soil. We identified 22 sequences (termed iiv for induced in vivo) that are upregulated in sterile soil (9). Ten of these genes are similar to sequences present in genbank, and two sequences are classed as ''hypothetical''. We also found ten iiv genes that are antisense to known genes, providing new insight into genome

  6. Final technical report

    SciTech Connect

    Edward DeLong

    2011-10-07

    Our overarching goals in this project were to: Develop and improve high-throughput sequencing methods and analytical approaches for quantitative analyses of microbial gene expression at the Hawaii Ocean Time Series Station and the Bermuda Atlantic Time Series Station; Conduct field analyses following gene expression patterns in picoplankton microbial communities in general, and Prochlorococcus flow sorted from that community, as they respond to different environmental variables (light, macronutrients, dissolved organic carbon), that are predicted to influence activity, productivity, and carbon cycling; Use the expression analyses of flow sorted Prochlorococcus to identify horizontally transferred genes and gene products, in particular those that are located in genomic islands and likely to confer habitat-specific fitness advantages; Use the microbial community gene expression data that we generate to gain insights, and test hypotheses, about the variability, genomic context, activity and function of as yet uncharacterized gene products, that appear highly expressed in the environment. We achieved the above goals, and even more over the course of the project. This includes a number of novel methodological developments, as well as the standardization of microbial community gene expression analyses in both field surveys, and experimental modalities. The availability of these methods, tools and approaches is changing current practice in microbial community analyses.

  7. Final Technical Report

    SciTech Connect

    Simon Silver

    2009-05-28

    The work done with DOE support during this 15 year period was extensive and successful. It is best summarized by the list of 58 publications (below) which reported progress made with DOE support. These are from the grant period and a few more recent reporting on grant research. Mostly these are primary research reports in reviewed journals. There are also, however, many summary reviews in review journals and in scientific monographs, as they also are key places for reporting research progress. What we did during this grant period (and much longer) was to characterize genetic determinants for bacterial resistances to additional toxic heavy metals of DOE concern, through starting with phenotypic properties of the resistant bacteria to DNA sequence determination and characterization of the genes involved. Over the years (and as shown in the list of publications), the toxic metal-forming elements we have studied included Ag, As, Cd, Cr, and Hg. In each case, we started with basically nothing (or very little) known, progressed through quite detailed understanding, until other laboratory groups also became strongly involved in related studies. More recently, with DOE support, we were the first laboratory group in the world to identify genes for bacterial resistance to silver salts (sil genes) and the closely related silver-and-copper resistance genes cus. This was initially reported in detail in Gupta et al. (1999; see publications list below). We also identified the first toxic metal 'gene island' (multiple transcripts and perhaps 25 genes each in need of detailed study) which encodes the subunits of arsenite oxidase (which we called aso; Silver and Phung, 2005; but most other researchers have subsequently settled on aox for the gene mnemonic). Both of these systems were firsts. Now a few years later, a search on GenBank shows that each is now represented by gene families with more than a dozen examples that have been identified and sequenced. Most of the additional

  8. Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network.

    PubMed

    Jiang, Xue; Zhang, Han; Quan, Xiongwen

    2016-01-01

    Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets.

  9. Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network

    PubMed Central

    Quan, Xiongwen

    2016-01-01

    Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets. PMID:28042568

  10. Endeavour's Final Voyage

    NASA Video Gallery

    After nearly two decades of achievements in space, Endeavour makes one last reach for the stars on its 25th and final mission, STS-134. This webcast examines the mission to come and explores the st...

  11. Final focus nomenclature

    SciTech Connect

    Erickson, R.

    1986-08-08

    The formal names and common names for all devices in the final focus system of the SLC are listed. The formal names consist of a device type designator, microprocessor designator, and a four-digit unit number. (LEW)

  12. Final focus test beam

    SciTech Connect

    Not Available

    1991-03-01

    This report discusses the following: the Final Focus Test Beam Project; optical design; magnets; instrumentation; magnetic measurement and BPM calibration; mechanical alignment and stabilization; vacuum system; power supplies; control system; radiation shielding and personnel protection; infrastructure; and administration.

  13. Expedition 34 Final Training

    NASA Video Gallery

    The Expedition 34 crew members conduct final training at the Gagarin Cosmonaut Training Center before their Dec. 19 launch to the International Space Station. Flight Engineers Chris Hadfield, Roman...

  14. New NLC Final Focus

    SciTech Connect

    Raimondi, P.

    2004-10-11

    A novel design of the Final Focus has recently been proposed [1] and has been adopted now for the Next Linear Collider [2]. This new design has fewer optical elements and is much shorter, nonetheless achieving better chromatic properties. In this paper, the new final focus system is briefly discussed stressing one particular characteristic of the new design--its multi TeV energy reach.

  15. Data breaches. Final rule.

    PubMed

    2008-04-11

    This document adopts, without change, the interim final rule that was published in the Federal Register on June 22, 2007, addressing data breaches of sensitive personal information that is processed or maintained by the Department of Veterans Affairs (VA). This final rule implements certain provisions of the Veterans Benefits, Health Care, and Information Technology Act of 2006. The regulations prescribe the mechanisms for taking action in response to a data breach of sensitive personal information.

  16. Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales

    PubMed Central

    Almagro, Goizeder; Viale, Alejandro M.; Montero, Manuel; Rahimpour, Mehdi; Muñoz, Francisco José; Baroja-Fernández, Edurne; Bahaji, Abdellatif; Zúñiga, Manuel; González-Candelas, Fernando; Pozueta-Romero, Javier

    2015-01-01

    Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria. PMID:25607991

  17. UDP-glucose is a potential intracellular signal molecule in the control of expression of sigma S and sigma S-dependent genes in Escherichia coli.

    PubMed Central

    Böhringer, J; Fischer, D; Mosler, G; Hengge-Aronis, R

    1995-01-01

    The sigma S subunit of RNA polymerase is the master regulator of a regulatory network that controls stationary-phase induction as well as osmotic regulation of many genes in Escherichia coli. In an attempt to identify additional regulatory components in this network, we have isolated Tn10 insertion mutations that in trans alter the expression of osmY and other sigma S-dependent genes. One of these mutations conferred glucose sensitivity and was localized in pgi (encoding phosphoglucose isomerase). pgi::Tn10 strains exhibit increased basal levels of expression of osmY and otsBA in exponentially growing cells and reduced osmotic inducibility of these genes. A similar phenotype was also observed for pgm and galU mutants, which are deficient in phosphoglucomutase and UDP-glucose pyrophosphorylase, respectively. This indicates that the observed effects on gene expression are related to the lack of UDP-glucose (or a derivative thereof), which is common to all three mutants. Mutants deficient in UDP-galactose epimerase (galE mutants) and trehalose-6-phosphate synthase (otsA mutants) do not exhibit such an effect on gene expression, and an mdoA mutant that is deficient in the first step of the synthesis of membrane-derived oligosaccharides, shows only a partial increase in the expression of osmY. We therefore propose that the cellular content of UDP-glucose serves as an internal signal that controls expression of osmY and other sigma S-dependent genes. In addition, we demonstrate that pgi, pgm, and galU mutants contain increased levels of sigma S during steady-state growth, indicating that UDP-glucose interferes with the expression of sigma S itself. PMID:7814331

  18. Studying Genes

    MedlinePlus

    ... Area What are genes? Genes are sections of DNA that contain instructions for making the molecules—many ... material in an organism. This includes genes and DNA elements that control the activity of genes. Does ...

  19. Harnessing gene expression networks to prioritize candidate epileptic encephalopathy genes.

    PubMed

    Oliver, Karen L; Lukic, Vesna; Thorne, Natalie P; Berkovic, Samuel F; Scheffer, Ingrid E; Bahlo, Melanie

    2014-01-01

    We apply a novel gene expression network analysis to a cohort of 182 recently reported candidate Epileptic Encephalopathy genes to identify those most likely to be true Epileptic Encephalopathy genes. These candidate genes were identified as having single variants of likely pathogenic significance discovered in a large-scale massively parallel sequencing study. Candidate Epileptic Encephalopathy genes were prioritized according to their co-expression with 29 known Epileptic Encephalopathy genes. We utilized developing brain and adult brain gene expression data from the Allen Human Brain Atlas (AHBA) and compared this to data from Celsius: a large, heterogeneous gene expression data warehouse. We show replicable prioritization results using these three independent gene expression resources, two of which are brain-specific, with small sample size, and the third derived from a heterogeneous collection of tissues with large sample size. Of the nineteen genes that we predicted with the highest likelihood to be true Epileptic Encephalopathy genes, two (GNAO1 and GRIN2B) have recently been independently reported and confirmed. We compare our results to those produced by an established in silico prioritization approach called Endeavour, and finally present gene expression networks for the known and candidate Epileptic Encephalopathy genes. This highlights sub-networks of gene expression, particularly in the network derived from the adult AHBA gene expression dataset. These networks give clues to the likely biological interactions between Epileptic Encephalopathy genes, potentially highlighting underlying mechanisms and avenues for therapeutic targets.

  20. Final Prep on SSME

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Alvin Pittman Sr., lead electronics technician with Pratt & Whitney Rocketdyne, and Janine Cuevas, a mechanical technician with PWR, perform final preparations on the space shuttle main engine tested Oct. 25, 2005, at NASA's Stennis Space Center. It was the first main engine test since Hurricane Katrina hit the Gulf Coast on Aug. 29.

  1. Final Technical Report

    SciTech Connect

    Gilbert, Chris

    2014-11-13

    The project, Capital Investment to Fund Equipment Purchases and Facility Modifications to Create a Sustainable Future for EnergyXchange served to replace landfill gas energy with alternative energy resources, primarily solar and wood waste. This is the final project closeout report.

  2. GENIE final state interactions

    SciTech Connect

    Dytman, Steven

    2015-10-15

    Final state interactions are an important component of any neutrino-nucleus Monte Carlo program. GENIE has 2 FSI programs which serve different purposes. Each has fair-good agreement with a wide range of hadron-nucleus data. Recent improvements and planned advancements are described.

  3. Rosetta: The Final Furlong

    NASA Astrophysics Data System (ADS)

    Wright, I. P.; Andrews, D. J.; Barber, S. J.; Sheridan, S.; Morgan, G. H.; Morse, A. D.

    2014-09-01

    By the time of the meeting, the Rosetta spacecraft will have formally arrived at its target comet, and final landing site selection will be in progress. One of the instruments that will be sent down to the surface of the comet is Ptolemy (a GC-MS).

  4. Final Technical Report

    SciTech Connect

    Church, Bruce W

    2008-10-15

    Most prokaryotes of interest to DOE are poorly understood. Even when full genomic sequences are available, the function of only a small number of gene products are clear. The critical question is how to best infer the most probable network architectures in cells that are poorly characterized. The project goal is to create a computational hypothesis testing (CHT) framework that combines large-scale dynamical simulation, a database of bioinformatics-derived probable interactions, and numerical parallel architecture data-fitting routines to explore many “what if ?” hypotheses about the functions of genes and proteins within pathways and their downstream effects on molecular concentration profiles and corresponding phenotypes. From this framework we expect to infer signal transduction pathways and gene expression networks in prokaryotes. Detailed mechanistic models of E. Coli have been developed that directly incorporate DNA sequence information. The CHT framework is implemented in the NIEngine network inference software. NIEngine has been applied to recover gene regulatory networks in E. coli to assess performance. Application to Shewanel la oneidensi and other organism of interest DOE will be conducted in partnership with Jim Collin's Lab at Boston University and other academic partners. The CHT framework has also found broad application in the automated learning of biology for purposes of improving human health.

  5. Changes in gravity affect gene expression, protein modulation and metabolite pools of arabidopsis

    NASA Astrophysics Data System (ADS)

    Hampp, R.; Martzivanou, M.; Maier, R. M.; Magel, E.

    Callus cultures of Arabidopsis thaliana (cv. Columbia) in Petri dishes / suspension cultures were exposed to altered g-forces by centrifugation (1 to 10 g), klinorotation, and μ g (sounding rocket flights). Using semi-quantitative RT-PCR, transcripts of genes coding for metabolic key enzymes (ADP-glucose pyrophosphorylase, ADPG-PP; ß-amylase, fructose-1,6-bisphosphatase, FBPase; glyceraldehyde-P dehydrogenase, GAPDH; hydroxymethylglutaryl-CoA reductase, HMG; phenylalanine-ammonium-lyase, PAL; PEP carboxylase, PEPC) were used to monitor threshold conditions for g-number (all) and time of exposure (ß-amylase) which led to altered amounts of the gene product. Exposure to approx. 5 g and higher for 1h resulted in altered transcript levels: transcripts of ß-amylase, PAL, and PEPC were increased, those of ADPG-PP decreased, while those of FBPase, GAPDH, and HMG were not affected. This probably indicates a shift from starch synthesis to starch degradation and increased rates of anaplerosis (PEPC: supply of ketoacids for amino acid synthesis). In order to get more information about g-related effects on gene expression, we used a 1h-exposure to 7 g for a microarray analysis. Transcripts of more than 200 genes were significantly increased in amount (ratio 7g / 1g control; 21.6 and larger). They fall into several categories. Transcripts coding for enzymes of major pathways form the largest group (25%), followed by gene products involved in cellular organisation and cell wall formation / rearrangement (17%), signalling, phosphorylation/dephosphorylation (12%), proteolysis and transport (10% each), hormone synthesis plus related events (8%), defense (4%), stress-response (2%), and gravisensing (2%). Many of the alterations are part of a general stress response, but some changes related to the synthesis / rearrangement of cell wall components could be more hyper-g-specific. Using macroarrays with selected genes according to our hypergravity study (metabolism / signalling

  6. Final Technical Report

    SciTech Connect

    Maxwell, Mike, J., P.E.

    2012-08-30

    The STI product is the Final Technical Report from ReliOn, Inc. for contract award DE-EE0000487: Recovery Act PEM Fuel Cell Systems Providing Emergency Reserve and Backup Power. The program covered the turnkey deployment of 431 ReliOn fuel cell systems at 189 individual sites for AT&T and PG&E with ReliOn functioning as the primary equipment supplier and the project manager. The Final Technical Report provides an executive level summary, a comparison of the actual accomplishments vs. the goals and objectives of the project, as well as a summary of the project activity from the contract award date of August 1, 2009 through the contract expiration date of December 31, 2011. Two photos are included in the body of the report which show hydrogen storage and bulk hydrogen refueling technologies developed as a result of this program.

  7. Geolocation Technologies Final Report

    SciTech Connect

    Magnoli, D E

    2003-06-02

    This paper is the final report for LL998 In Situ Sensing Subtask 7 (Geo-location) undertaken for NNSA NA-22 enabling technologies R&D for Counterproliferation Detection. A few state-of-the-art resolution parameters are presented for accelerometers, indoor and outdoor GPS (Global Positioning Satellite) systems, and INSs (Inertial Navigation Systems). New technologies are described, including one which has demonstrated the ability to track within a building to a resolution of under a foot.

  8. DHS Internship Final Report

    SciTech Connect

    Tew, Karen

    2014-09-01

    I spent the last ten weeks working in the Systems Biology department at Sandia National Laboratories in Livermore, CA. Under the direction of Zachary Bent, I helped do preliminary testing/optimization of a vacuum-driven, capture-based system for pathogen RNA transcript enrichment. I also worked on a project to create mutant Yersinia enterocolitica strains in order to test which genes are involved in intracellular pathogen virulence, as well as sequencing several Klebsiella pneumoniae samples for use by a bioinformaticist.

  9. GeneCards Version 3: the human gene integrator.

    PubMed

    Safran, Marilyn; Dalah, Irina; Alexander, Justin; Rosen, Naomi; Iny Stein, Tsippi; Shmoish, Michael; Nativ, Noam; Bahir, Iris; Doniger, Tirza; Krug, Hagit; Sirota-Madi, Alexandra; Olender, Tsviya; Golan, Yaron; Stelzer, Gil; Harel, Arye; Lancet, Doron

    2010-08-05

    GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73,000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards' unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene's functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database

  10. Gene network biological validity based on gene-gene interaction relevance.

    PubMed

    Gómez-Vela, Francisco; Díaz-Díaz, Norberto

    2014-01-01

    In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown.

  11. Genes and functions controlled by floral organ identity genes.

    PubMed

    Sablowski, Robert

    2010-02-01

    Floral organ identity genes specify the identity of floral organs in a manner analogous to the specification of body segments by Hox genes in animals. Different combinations of organ identity genes co-ordinate the expression of genes required for the development of each type of floral organ, from organ initiation until final differentiation. Here, I review what is known about the genes and functions subordinate to the organ identity genes. The sets of target genes change as organ development progresses and ultimately organ identity genes modify the expression of thousands of genes with a multitude of predicted functions, particularly in reproductive organs. However, genes involved in transcriptional control and hormone functions feature prominently among the early and direct targets. Functional analysis showed that control of organ-specific tissues and structures can be delegated to specialised intermediate regulators, but organ identity genes also fine-tune genes with general roles in shoot organ development, consistent with the notion that organ identity genes modify a core leaf-like developmental program. Future challenges include obtaining data with cellular resolution, predictive modelling of the regulatory network, and quantitative analysis of how organ identity genes and their targets control cell behaviour and ultimately organ shape.

  12. Final Technical Report

    SciTech Connect

    Sobecky, Patricia A; Taillefert, Martial

    2013-03-29

    This final technical report describes results and findings from a research project to examine the role of microbial phosphohydrolase enzymes in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of the radionuclide uranium through the production of insoluble uranium phosphate minerals. The research project investigated the microbial mechanisms and the physical and chemical processes promoting uranium biomineralization and sequestration in oxygenated subsurface soils. Uranium biomineralization under aerobic conditions can provide a secondary biobarrier strategy to immobilize radionuclides should the metal precipitates formed by microbial dissimilatory mechanisms remobilize due to a change in redox state.

  13. Prometheus Project final report

    NASA Technical Reports Server (NTRS)

    Taylor, Randall

    2005-01-01

    This Final Report serves as an executive summary of the Prometheus Project's activities and deliverables from November 2002 through September 2005. It focuses on the challenges from a technical and management perspective, what was different and innovative about this project, and identifies the major options, decisions, and accomplishments of the Project team as a whole. However, the details of the activities performed by DOE NR and its contractors will be documented separately in accordance with closeout requirements of the DOE NR and consistent with agreements between NASA and NR.

  14. Service dogs. Final rule.

    PubMed

    2012-09-05

    The Department of Veterans Affairs (VA) amends its regulations concerning veterans in need of service dogs. Under this final rule, VA will provide to veterans with visual, hearing, or mobility impairments benefits to support the use of a service dog as part of the management of such impairments. The benefits include assistance with veterinary care, travel benefits associated with obtaining and training a dog, and the provision, maintenance, and replacement of hardware required for the dog to perform the tasks necessary to assist such veterans.

  15. STS 65 Final Report

    NASA Technical Reports Server (NTRS)

    Rice, James E.

    1996-01-01

    The report is organized into sections representing the phases of work performed in analyzing the STS 65 results and preparing the instrument for STS 73. Section 1 briefly outlines the Orbital Acceleration Research Experiment (OARE) system features, coordinates, and measurement parameters. Section 2 describes the results from STS 65. The mission description, data calibration, and representative data obtained on STS 65 are presented. Also, the anomalous performance of OARE on STS 65 is discussed. Finally, Section 3 presents a discussion of accuracy achieved and achievable with OARE.

  16. GenePANDA—a novel network-based gene prioritizing tool for complex diseases

    PubMed Central

    Yin, Tianshu; Chen, Shu; Wu, Xiaohui; Tian, Weidong

    2017-01-01

    Here we describe GenePANDA, a novel network-based tool for prioritizing candidate disease genes. GenePANDA assesses whether a gene is likely a candidate disease gene based on its relative distance to known disease genes in a functional association network. A unique feature of GenePANDA is the introduction of adjusted network distance derived by normalizing the raw network distance between two genes with their respective mean raw network distance to all other genes in the network. The use of adjusted network distance significantly improves GenePANDA’s performance on prioritizing complex disease genes. GenePANDA achieves superior performance over five previously published algorithms for prioritizing disease genes. Finally, GenePANDA can assist in prioritizing functionally important SNPs identified by GWAS. PMID:28252032

  17. Cosmology Without Finality

    NASA Astrophysics Data System (ADS)

    Mahootian, F.

    2009-12-01

    The rapid convergence of advancing sensor technology, computational power, and knowledge discovery techniques over the past decade has brought unprecedented volumes of astronomical data together with unprecedented capabilities of data assimilation and analysis. A key result is that a new, data-driven "observational-inductive'' framework for scientific inquiry is taking shape and proving viable. The anticipated rise in data flow and processing power will have profound effects, e.g., confirmations and disconfirmations of existing theoretical claims both for and against the big bang model. But beyond enabling new discoveries can new data-driven frameworks of scientific inquiry reshape the epistemic ideals of science? The history of physics offers a comparison. The Bohr-Einstein debate over the "completeness'' of quantum mechanics centered on a question of ideals: what counts as science? We briefly examine lessons from that episode and pose questions about their applicability to cosmology. If the history of 20th century physics is any indication, the abandonment of absolutes (e.g., space, time, simultaneity, continuity, determinacy) can produce fundamental changes in understanding. The classical ideal of science, operative in both physics and cosmology, descends from the European Enlightenment. This ideal has for over 200 years guided science to seek the ultimate order of nature, to pursue the absolute theory, the "theory of everything.'' But now that we have new models of scientific inquiry powered by new technologies and driven more by data than by theory, it is time, finally, to relinquish dreams of a "final'' theory.

  18. Final Technical Report

    SciTech Connect

    John Tanis

    2005-11-25

    This document comprises the final technical report for atomic collisions research supported by DOE grant No. DE-FG02-87ER13778 from September 1, 2001 through August 31, 2004. The research involved the experimental investigation of excitation and charge-changing processes occurring in ion-atom and ion-molecule collisions. Major emphases of the study were: (1) interference effects resulting from coherent electron emission in H2, (2) production of doubly vacant K-shell (hollow ion) states due to electron correlation, and (3) formation of long-lived metastable states in electron transfer processes. During the period of the grant, this research resulted in 23 publications, 12 invited presentations, and 39 contributed presentations at national and international meetings and other institutions. Brief summaries of the completed research are presented below.

  19. Final reduction gear apparatus

    SciTech Connect

    Yasui, Y.; Hori, H.

    1987-04-21

    A final reduction gear apparatus is described comprising: a differential carrier which houses a gear assembly; an oil seal attached to a side gear shaft opening in the differential carrier, the oil seal having a main lip which may contact a periphery of a side gear shaft; and a guide member located outside of the oil seal at the side gear shaft opening, the guide member being formed as a member separate from the oil seal, the guide member having a slightly larger inner diameter than that of the main lip of the oil seal, and having guide surface concentric to the main lip, wherein 1/2 of the difference between the inner diameter of the guide member and the inner diameter of the main lip of the oil seal is within the limit of the elastic deformability of the main lip.

  20. FINAL/ SCIENTIFIC TECHNICAL REPORT

    SciTech Connect

    McDonald, Henry; Singh, Suminderpal

    2006-08-28

    The overall objective of the Chattanooga fuel cell demonstrations project was to develop and demonstrate a prototype 5-kW grid-parallel, solid oxide fuel cell (SOFC) system that co-produces hydrogen, based on Ion America’s technology. The commercial viability of the 5kW SOFC system was tested by transporting, installing and commissioning the SOFC system at the Alternative Energy Laboratory at the University of Tennessee – Chattanooga. The system also demonstrated the efficiency and the reliability of the system running on natural gas. This project successfully contributed to the achievement of DOE technology validation milestones from the Technology Validation section of the Hydrogen, Fuel Cells and Infrastructure Technologies Program Multi-Year Research, Development and Demonstration Plan. Results of the project can be found in the final technical report.

  1. Final Technical Report

    SciTech Connect

    Klein, Stephen A.

    2003-06-23

    In this final technical report, a summary of work is provided. Concepts were developed for a new statistical cloud parameterization suitable for inclusion into global climate models. These concepts were evaluated by comparison to ARM data and data from cloud resolving models driven by ARM data. The purpose of this grant was to develop a new cloud parameterization for the global climate model of the Geophysical Fluid Dynamics Laboratory (GFDL) of the National Oceanic and Atmospheric Administration (NOAA). Note that uncertainties in cloud parameterizations are a key reason why prediction of climate change from climate models remain unacceptably uncertain. To develop the parameterizations, the observations and models provided by the Department of Energy's Atmospheric Radiation Measurement (ARM) program were analyzed and used.

  2. Final Scientific EFNUDAT Workshop

    ScienceCinema

    None

    2016-07-12

    The Final Scientific EFNUDAT Workshop - organized by the CERN/EN-STI group on behalf of n_TOF Collaboration - will be held at CERN, Geneva (Switzerland) from 30 August to 2 September 2010 inclusive.EFNUDAT website: http://www.efnudat.euTopics of interest include: Data evaluationCross section measurementsExperimental techniquesUncertainties and covariancesFission propertiesCurrent and future facilities  International Advisory Committee: C. Barreau (CENBG, France)T. Belgya (IKI KFKI, Hungary)E. Gonzalez (CIEMAT, Spain)F. Gunsing (CEA, France)F.-J. Hambsch (IRMM, Belgium)A. Junghans (FZD, Germany)R. Nolte (PTB, Germany)S. Pomp (TSL UU, Sweden) Workshop Organizing Committee: Enrico Chiaveri (Chairman)Marco CalvianiSamuel AndriamonjeEric BerthoumieuxCarlos GuerreroRoberto LositoVasilis Vlachoudis Workshop Assistant: Géraldine Jean

  3. Final Progress Report

    SciTech Connect

    Josef Michl

    2011-10-31

    In this project we have established guidelines for the design on organic chromophores suitable for producing high triplet yields via singlet fission. We have proven their utility by identifying a chromophore of a structural class that had never been examined for singlet fission before, 1,3-diphenylisobenzofuran, and demonstrating in two independent ways that a thin layer of this material produces a triplet yield of 200% within experimental error. We have also designed a second chromophore of a very different type, again of a structural class that had not been examined for singlet fission before, and found that in a thin layer it produces a 70% triplet yield. Finally, we have enhanced the theoretical understanding of the quantum mechanical nature of the singlet fission process.

  4. Final cook temperature monitoring

    NASA Astrophysics Data System (ADS)

    Stewart, John; Matthews, Michael; Glasco, Marc

    2006-04-01

    Fully cooked, ready-to-eat products represent one of the fastest growing markets in the meat and poultry industries. Modern meat cooking facilities typically cook chicken strips and nuggets at rates of 6000 lbs per hour, and it is a critical food safety issue to ensure the products on these lines are indeed fully cooked. Common practice now employs oven technicians to constantly measure final cook temperature with insertion-type thermocouple probes. Prior research has demonstrated that thermal imagery of chicken breasts and other products can be used to predict core temperature of products leaving an oven. In practice, implementation of a system to monitor core temperature can be difficult for several reasons. First, a wide variety of products are typically produced on the same production line and the system must adapt to all products. Second, the products can be often hard to find because they often leave the process in random order and may be touching or even overlapping. Another issue is finite measurement time which is typically only a few seconds. Finally, the system is subjected to a rigorous sanitation cycle and must hold up under wash down conditions. To address these problems, a calibrated 320x240 micro-bolometer camera was used to monitor the temperature of formed, breaded poultry products on a fully cooked production line for a period of one year. The study addressed the installation and operation of the system as well as the development of algorithms used to identify the product on a cluttered conveyor belt. It also compared the oven tech insertion probe measurements to the non-contact monitoring system performance.

  5. Final Technical Report

    SciTech Connect

    John M. Davis

    2005-03-31

    The forest products industry consumes large amounts of energy. Understanding how genetic variation in trees actually controls the characteristics of wood, the major raw material utilized by the industry, is an opportunity for energy savings. For companies that are vertically integrated (i.e., have both tree production and processing operations), energy savings can accrue for both production and processing. Tree production demands nitrogen fertilizers, the manufacture of which is highly energy intensive. Wood processing for paper product manufacturing requires digestion and bleaching, both of which are more efficient when the lignin content of wood is reduced. This project identified genes involved in utilization of nitrogen from fertilizer, and the coupling of nitrogen demand to lignin content, establishing a framework for reducing tree nitrogen demand per unit carbon gained. This creates opportunities for genetic manipulation of trees for greater energy efficiency.

  6. State-of-the-art human gene therapy: part I. Gene delivery technologies.

    PubMed

    Wang, Dan; Gao, Guangping

    2014-01-01

    Safe and effective gene delivery is a prerequisite for successful gene therapy. In the early age of human gene therapy, setbacks due to problematic gene delivery vehicles plagued the exciting therapeutic outcome. However, gene delivery technologies rapidly evolved ever since. With the advancement of gene delivery techniques, gene therapy clinical trials surged during the past decade. As the first gene therapy product (Glybera) has obtained regulatory approval and reached clinic, human gene therapy finally realized the promise that genes can be medicines. The diverse gene delivery techniques available today have laid the foundation for gene therapy applications in treating a wide range of human diseases. Some of the most urgent unmet medical needs, such as cancer and pandemic infectious diseases, have been tackled by gene therapy strategies with promising results. Furthermore, combining gene transfer with other breakthroughs in biomedical research and novel biotechnologies opened new avenues for gene therapy. Such innovative therapeutic strategies are unthinkable until now, and are expected to be revolutionary. In part I of this review, we introduced recent development of non-viral and viral gene delivery technology platforms. As cell-based gene therapy blossomed, we also summarized the diverse types of cells and vectors employed in ex vivo gene transfer. Finally, challenges in current gene delivery technologies for human use were discussed.

  7. Gene Therapy

    MedlinePlus

    ... cells in an effort to treat or stop disease. Genes contain your DNA — the code that controls much of your body's form and function, from making you grow taller to regulating your body systems. Genes that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds ...

  8. Final Technical Report

    SciTech Connect

    Aristos Aristidou Natureworks); Robert Kean; Tom Schechinger; Stuart Birrell; Jill Euken

    2007-10-01

    The two main objectives of this project were: 1) to develop and test technologies to harvest, transport, store, and separate corn stover to supply a clean raw material to the bioproducts industry, and 2) engineer fermentation systems to meet performance targets for lactic acid and ethanol manufacturers. Significant progress was made in testing methods to harvest corn stover in a “single pass” harvest mode (collect corn grain and stover at the same time). This is technically feasible on small scale, but additional equipment refinements will be needed to facilitate cost effective harvest on a larger scale. Transportation models were developed, which indicate that at a corn stover yield of 2.8 tons/acre and purchase price of $35/ton stover, it would be unprofitable to transport stover more than about 25 miles; thus suggesting the development of many regional collection centers. Therefore, collection centers should be located within about 30 miles of the farm, to keep transportation costs to an acceptable level. These collection centers could then potentially do some preprocessing (to fractionate or increase bulk density) and/or ship the biomass by rail or barge to the final customers. Wet storage of stover via ensilage was tested, but no clear economic advantages were evident. Wet storage eliminates fire risk, but increases the complexity of component separation and may result in a small loss of carbohydrate content (fermentation potential). A study of possible supplier-producer relationships, concluded that a “quasi-vertical” integration model would be best suited for new bioproducts industries based on stover. In this model, the relationship would involve a multiyear supply contract (processor with purchase guarantees, producer group with supply guarantees). Price will likely be fixed or calculated based on some formula (possibly a cost plus). Initial quality requirements will be specified (but subject to refinement).Producers would invest in harvest

  9. Genetics and molecular biology of methanogen genes. Final report

    SciTech Connect

    Konisky, J.

    1997-10-07

    Adenylate kinase has been isolated from four related methanogenic members of the Archaea. For each the optimum temperature for enzyme activity was similar to the temperature for optimal microbial growth and was approximately 30 C for Methanococcus voltage, 70 C for Methanococcus thermolithotrophicus, 80 C for Methanococcus igneus and 80--90 C for Methanococcus jannaschii. The enzymes were sensitive to the adenylate kinase inhibitor, Ap{sub 5}A [P{sup 1}, P{sup 5}-di(adenosine-5{prime}) pentaphosphate], a property that was exploited to purify the enzymes by CIBACRON Blue affinity chromatography. The enzymes had an estimated molecular weight (approximately 23--25 kDa) in the range common for adenylate kinases. Each of the enzymes had a region of amino acid sequence close to its N-terminus that was similar to the canonical P-loop sequence reported for all adenylate kinases. However, the methanogen sequences lacked a lysine residue that has previously been found to be invariant in adenylate kinases including an enzyme isolated from the Archeon, Sulfolobus acidocaldarius. If verified as a nucleotide binding domain, the methanogen sequence would represent a novel nucleotide binding motif. There was no correlation between amino acid abundance and the optimal temperature for enzyme activity.

  10. Gene transcription and electromagnetic fields. Final progress report

    SciTech Connect

    Henderson, A.S.

    1992-12-31

    Our overall aim is to obtain sufficient information to allow us to ultimately determine whether ELF EM field exposure is an initiating factor in neoplastic transformation and/or if exposure can mimic characteristics of the second-step counterpart in neoplastic disease. This aim is based on our previous findings that levels of some transcripts are increased in cells exposed to EM fields. While the research is basic in nature, the ramifications have bearing on the general safety of exposure to EM fields in industrial and everyday life. A large array of diverse biological effects are reported to occur as the result of exposure to elf EM fields, suggesting that the cell response to EM fields is at a basic level, presumably initiated by molecular and/or biophysical events at the cell membrane. The hypothesized route is a signal transduction pathway involving membrane calcium fluxes. Information flow resulting from signal transduction can mediate the induction of regulatory factors in the cell, and directly affect how transcription is regulated.

  11. Final Technical Report

    SciTech Connect

    Alexander Fridman

    2005-06-01

    This DOE project DE-FC36-04GO14052 ''Plasma Pilot Plant Test for Treating VOC Emissions from Wood Products Plants'' was conducted by Drexel University in cooperation with Georgia-Pacific (G-P) and Kurchatov Institute (KI). The objective of this project was to test the Plasma Pilot Plant capabilities in wood industry. The final goal of the project was to replace the current state-of-the-art, regenerative thermal oxidation (RTO) technology by Low-Temperature Plasma Technology (LTPT) in paper and wood industry for Volatile Organic Components (VOC) destruction in High Volume Low Concentration (HVLC) vent emissions. MetPro Corporation joined the team as an industrial partner from the environmental control business and a potential leader for commercialization. Concurrent Technology Corporation (CTC) has a separate contract with DOE for this technology evaluation. They prepared questionnaires for comparison of this technology and RTO, and made this comparison. These data are presented in this report along with the description of the technology itself. Experiments with the pilot plant were performed with average plasma power up to 3.6 kW. Different design of the laboratory and pilot plant pulsed coronas, as well as different analytical methods revealed many new peculiarities of the VOC abatement process. The work reported herein describes the experimental results for the VOCs removal efficiency with respect to energy consumption, residence time, water effect and initial concentration.

  12. Final Technical Report

    SciTech Connect

    Dmitriy Y. Anistratov; Marvin L. Adams; Todd S. Palmer; Kord S. Smith; Kevin Clarno; Hikaru Hiruta; Razvan Nes

    2003-08-04

    OAK B202 Final Technical Report. The present generation of reactor analysis methods uses few-group nodal diffusion approximations to calculate full-core eigenvalues and power distributions. The cross sections, diffusion coefficients, and discontinuity factors (collectively called ''group constants'') in the nodal diffusion equations are parameterized as functions of many variables, ranging from the obvious (temperature, boron concentration, etc.) to the more obscure (spectral index, moderator temperature history, etc.). These group constants, and their variations as functions of the many variables, are calculated by assembly-level transport codes. The current methodology has two main weaknesses that this project addressed. The first weakness is the diffusion approximation in the full-core calculation; this can be significantly inaccurate at interfaces between different assemblies. This project used the nodal diffusion framework to implement nodal quasidiffusion equations, which can capture transport effects to an arbitrary degree of accuracy. The second weakness is in the parameterization of the group constants; current models do not always perform well, especially at interfaces between unlike assemblies. The project developed a theoretical foundation for parameterization and homogenization models and used that theory to devise improved models. The new models were extended to tabulate information that the nodal quasidiffusion equations can use to capture transport effects in full-core calculations.

  13. Final Technical Report

    SciTech Connect

    Held, Isaac; V. Balaji; Fueglistaler, Stephan

    2016-09-19

    We have constructed and analyzed a series of idealized models of tropical convection interacting with large-scale circulations, with 25-50km resolution and with 1-2km cloud resolving resolution to set the stage for rigorous tests of convection closure schemes in high resolution global climate models. Much of the focus has been on the climatology of tropical cyclogenesis in rotating systems and the related problem of the spontaneous aggregation of convection in non-rotating systems. The PI (Held) will be delivering the honorary Bjerknes lecture at the Fall 2016 AGU meeting in December on this work. We have also provided new analyses of long-standing issues related to the interaction between convection and the large-scale circulation: Kelvin waves in the upper troposphere and lower stratosphere, water vapor transport into the stratosphere, and upper tropospheric temperature trends. The results of these analyses help to improve our understanding of processes, and provide tests for future high resolution global modeling. Our final goal of testing new convections schemes in next-generation global atmospheric models at GFDL has been left for future work due to the complexity of the idealized model results meant as tests for these models uncovered in this work and to computational resource limitations. 11 papers have been published with support from this grant, 2 are in review, and another major summary paper is in preparation.

  14. Omega, the final multiplier

    NASA Astrophysics Data System (ADS)

    Buckley, T. N.

    2008-12-01

    The application of optimisation theory to vegetation processes has rarely extended beyond the context of diurnal to intra-annual gas exchange of individual leaves and crowns. One reason is that the Lagrange multipliers in the leaf-scale solutions, which are marginal products for allocatable photosynthetic resource inputs (water and nitrogen), are mysterious in origin, and their numerical values are difficult to measure -- let alone to predict or interpret in concrete physiological or ecological terms. These difficulties disappear, however, when the optimisation paradigm itself is extended to encompass carbon allocation and growth at the lifespan scale. The trajectories of leaf (and canopy) level marginal products are then implicit in the trajectory of plant and stand structure predicted by optimal carbon allocation. Furthermore, because the input and product are the same resource -- carbon -- in the whole plant optimisation, the product in one time step defines the input constraint, and hence implicitly the marginal product for carbon, in the next time step. This effectively converts the problem from a constrained optimisation of a definite integral, in which the multipliers are undetermined, to an unconstrained maximisation of a state, in which the multipliers are all implicit. This talk will explore how the marginal products for photosynthetic inputs as well as the marginal product for carbon -- i.e., the 'final multiplier,' omega -- are predicted to vary over time and in relation to environmental change during tree growth.

  15. Final Report to DOE

    SciTech Connect

    Ismail Gultepe

    2012-05-15

    This final report summarizes the accomplished goals and provide a list of the publications and presentations made during the project. The goals of the project were accomplished through the various publications submitted to Journals and presentations done at the DOE and international meetings and conferences. The 8 journal articles related to the goals of this project were accepted or submitted. The 23 presentations related to goals of the project were presented at the meetings. There were some minor changes regarding to project goals because of issues encountered during the analysis of the data. For example, a total water probe sensor mounted on the Convair-580 that can be used for defining mixed phase conditions and parameterization, had some problems to estimate magnitude of total water mass, and this resulted in issues providing an accurate parameterization for cloud fraction. Variability related aerosol number concentrations and their composition for direct and indirect effects were studied and published. Results were given to explain aerosol and ice microphysical effects on climate change studies. It is suggested that developed parameterizations should consider the variability in aerosol and ice parameters over the Arctic regions.

  16. Final Technical Report

    SciTech Connect

    Alexander Pigarov

    2012-06-05

    This is the final report for the Research Grant DE-FG02-08ER54989 'Edge Plasma Simulations in NSTX and CTF: Synergy of Lithium Coating, Non-Diffusive Anomalous Transport and Drifts'. The UCSD group including: A.Yu. Pigarov (PI), S.I. Krasheninnikov and R.D. Smirnov, was working on modeling of the impact of lithium coatings on edge plasma parameters in NSTX with the multi-species multi-fluid code UEDGE. The work was conducted in the following main areas: (i) improvements of UEDGE model for plasma-lithium interactions, (ii) understanding the physics of low-recycling divertor regime in NSTX caused by lithium pumping, (iii) study of synergistic effects with lithium coatings and non-diffusive ballooning-like cross-field transport, (iv) simulation of experimental multi-diagnostic data on edge plasma with lithium pumping in NSTX via self-consistent modeling of D-Li-C plasma with UEDGE, and (v) working-gas balance analysis. The accomplishments in these areas are given in the corresponding subsections in Section 2. Publications and presentations made under the Grant are listed in Section 3.

  17. Final Technical Report

    SciTech Connect

    Velasco, Mayda

    2013-11-01

    This work is focused on the design and construction of novel beam diagnostic and instrumentation for charged particle accelerators required for the next generation of linear colliders. Our main interest is in non-invasive techniques. The Northwestern group of Velasco has been a member of the CLIC Test Facility 3 (CTF3) collaboration since 2003, and the beam instrumentation work is developed mostly at this facility1. This 4 kW electron beam facility has a 25-170 MeV electron LINAC. CTF3 performed a set of dedicated measurements to finalize the development of our RF-Pickup bunch length detectors. The RF-pickup based on mixers was fully commissioned in 2009 and the RF-pickup based on diodes was finished in time for the 2010-11 data taking. The analysis of all the data taken in by the summer of 2010 was finish in time and presented at the main conference of the year, LINAC 2010 in Japan.

  18. Tiger LDRD final report

    SciTech Connect

    Steich, D J; Brugger, S T; Kallman, J S; White, D A

    2000-02-01

    This final report describes our efforts on the Three-Dimensional Massively Parallel CEM Technologies LDRD project (97-ERD-009). Significant need exists for more advanced time domain computational electromagnetics modeling. Bookkeeping details and modifying inflexible software constitute a vast majority of the effort required to address such needs. The required effort escalates rapidly as problem complexity increases. For example, hybrid meshes requiring hybrid numerics on massively parallel platforms (MPPs). This project attempts to alleviate the above limitations by investigating flexible abstractions for these numerical algorithms on MPPs using object-oriented methods, providing a programming environment insulating physics from bookkeeping. The three major design iterations during the project, known as TIGER-I to TIGER-III, are discussed. Each version of TIGER is briefly discussed along with lessons learned during the development and implementation. An Application Programming Interface (API) of the object-oriented interface for Tiger-III is included in three appendices. The three appendices contain the Utilities, Entity-Attribute, and Mesh libraries developed during the project. The API libraries represent a snapshot of our latest attempt at insulated the physics from the bookkeeping.

  19. Electrocatalytic hydrocracking. Final report

    SciTech Connect

    Vaart, D.R. van der

    1992-06-01

    This report describes an electrocatalytic method for the chemical addition of hydrogen to a model hydrocarbon compound. In the method, hydrogen formed by water electrolysis at the counter electrode of an electrochemical cell is delivered via conduction through a proton-conducting solid electrolyte. The working electrode of the cell is, at the same time, a hydrocracking catalyst and therefore promotes the reaction of the hydrogen with the hydrocarbon. This process would have clear and distinct advantages over conventional hydroprocessing technologies in that the hydrogen concentration at the catalyst surface could be controlled and maintained by the applied electromotive force. This control would allow operation of the electrocatalytic reactor at ambient pressures instead of the extremely high hydrogen partial pressures required of conventional reactors. In addition, the direct delivery of hydrogen to the catalyst surface should inhibit coke formation and thus prolong the life of the catalyst. Finally, hydrogen utilization efficiencies should be greatly improved since the hydrogen is delivered directly to the reaction site thereby eliminating hydrogen solubility loss in the effluent stream. This report details the demonstration of (a) the ability of a solid electrolyte to perform as a catalyst, (b) the conduction of hydrogen through a solid electrolyte and (c) the simultaneous exploitation of these two properties. Hence, the essential concept of electrocatalytic hydrocracking has been demonstrated. An objective of future work in this area should be to determine whether the hydrocracking or hydrogenation reactions are actually enhanced during the electrocatalytic process when compared to the conventional catalytic process.

  20. Final Technical Report

    SciTech Connect

    Judy D. Wall

    2009-02-27

    Bioremediation of radionuclides and metals in the subsurface necessitate an understanding of the metabolic capacities and interactions of the anaerobic microorganisms that are found there, including members of the sulfate-reducing bacteria (SRB). Genetic investigation into the pathway of reductant flow to U(VI) in the SRB belonging to the genus Desulfovibrio has been the focus of this project. In Dv. desulfuricans strain G20, we confirmed the importance of the tetraheme cytochrome c3 by disruption of the gene encoding that cytochrome, cycA, and demonstrated a decrease in the ability of the mutant (I2) to reduce U(VI). We found that the cytochrome c3 was necessary for electrons from pyruvate to reach sulfate or fumarate as terminal electron acceptors. It was not needed for electrons from lactate to reach sulfate, from which we infer that a different pathway is used for the electrons from these two substrates. Cyrstal structure of the tetraheme cytochrome c3 was obtained and site-directed mutations of the protein indicated a binding site for metals at heme 4 of the structure. Kinetic studies for oxidation of reduced cytochrome c3 with U(VI) or molybdate revealed a preference for U(VI) as a substrate. Evidence for a role for sodium gradients in the energetic scheme for this soil organism was obtained.

  1. Final project report

    SciTech Connect

    Nitin S. Baliga and Leroy Hood

    2008-11-12

    The proposed overarching goal for this project was the following: Data integration, simulation and visualization will facilitate metabolic and regulatory network prediction, exploration, and formulation of hypotheses. We stated three specific aims to achieve the overarching goal of this project: (1) Integration of multiple levels of information such as mRNA and protein levels, predicted protein-protein interactions/associations and gene function will enable construction of models describing environmental response and dynamic behavior. (2) Flexible tools for network inference will accelerate our understanding of biological systems. (3) Flexible exploration and queries of model hypotheses will provide focus and reveal novel dependencies. The underlying philosophy of these proposed aims is that an iterative cycle of experiments, experimental design, and verification will lead to a comprehensive and predictive model that will shed light on systems level mechanisms involved in responses elicited by living systems upon sensing a change in their environment. In the previous years report we demonstrated considerable progress in development of data standards, regulatory network inference and data visualization and exploration. We are pleased to report that several manuscripts describing these procedures have been published in top international peer reviewed journals including Genome Biology, PNAS, and Cell. The abstracts of these manuscripts are given and they summarize our accomplishments in this project.

  2. Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms.

    PubMed

    Harper, April D; Bar-Peled, Maor

    2002-12-01

    UDP-xylose (Xyl) is an important sugar donor for the synthesis of glycoproteins, polysaccharides, various metabolites, and oligosaccharides in animals, plants, fungi, and bacteria. UDP-Xyl also feedback inhibits upstream enzymes (UDP-glucose [Glc] dehydrogenase, UDP-Glc pyrophosphorylase, and UDP-GlcA decarboxylase) and is involved in its own synthesis and the synthesis of UDP-arabinose. In plants, biosynthesis of UDP-Xyl is catalyzed by different membrane-bound and soluble UDP-GlcA decarboxylase (UDP-GlcA-DC) isozymes, all of which convert UDP-GlcA to UDP-Xyl. Because synthesis of UDP-Xyl occurs both in the cytosol and in membranes, it is not known which source of UDP-Xyl the different Golgi-localized xylosyltransferases are utilizing. Here, we describe the identification of several distinct Arabidopsis genes (named AtUXS for UDP-Xyl synthase) that encode functional UDP-GlcA-DC isoforms. The Arabidopsis genome contains five UXS genes and their protein products can be subdivided into three isozyme classes (A-C), one soluble and two distinct putative membrane bound. AtUxs from each class, when expressed in Escherichia coli, generate active UDP-GlcA-DC that converts UDP-GlcA to UDP-Xyl. Members of this gene family have a large conserved C-terminal catalytic domain (approximately 300 amino acids long) and an N-terminal variable domain differing in sequence and size (30-120 amino acids long). Isoforms of class A and B appear to encode putative type II membrane proteins with their catalytic domains facing the lumen (like Golgi-glycosyltransferases) and their N-terminal variable domain facing the cytosol. Uxs class C is likely a cytosolic isoform. The characteristics of the plant Uxs support the hypothesis that unique UDP-GlcA-DCs with distinct subcellular localizations are required for specific xylosylation events.

  3. MTX final report

    SciTech Connect

    Hooper, E.B.; Allen, S.L.; Brown, M.D.; Byers, J.A.; Casper, T.A.; Cohen, B.I.; Cohen, R.H.; Fenstermacher, M.E.; Foote, J.H.; Hoshino, K.

    1994-01-01

    The MTX experiment was proposed in 1986 to apply high frequency microwaves generated by a free-electron laser (FEL) to electron cyclotron resonance heating (ECRH) in a high field, high density tokamak. As the absorption of microwaves at the electron cyclotron resonance requires high frequencies, the opportunity of applying a free-electron laser has appeal as the device is not limited to frequencies in the microwave or long millimeter wavelength regions, in contrast to many other sources. In addition, the FEL is inherently a high power source of microwaves, which would permit single units of 10 MW or more, optimum for reactors. Finally, it was recognized early in the study of the application of the FEL based on the induction linear accelerator, that the nonlinear effects associated with the intense pulses of microwaves naturally generated would offer several unique opportunities to apply ECRH to current drive, MHD control, and other plasma effects. It was consequently decided to adapt the induction accelerator based FEL to heating and controlling the tokamak, and to conduct experiments on the associated physics. To this end, the Alcator C tokamak was moved from the Massachusetts Institute of Technology (MIT) to the Lawrence Livermore National Laboratory where it was installed in Building 431 and operated from March, 1989, until the conclusion of the experiment in October, 1992. The FEL, based on the ETA-11 accelerator and IMP wiggler was brought into operation by the LLNL Electron Beam Group and power injected into the tokamak during an experimental run in the Fall, 1989. Following an upgrade by the MTX group, a second experimental run was made lasting from the Winter, 1992 through the end of the experiment. Significant contributions to the ECRH experiments were made by the Japan Atomic Energy Research Institute (JAERI).

  4. World Cup Final

    NASA Technical Reports Server (NTRS)

    2006-01-01

    On July 9, hundreds of millions of fans worldwide will be glued to their television sets watching the final match of the 2006 FIFA World Cup, played in Berlin's Olympic stadium (Olympiastadion). The stadium was originally built for the 1936 Summer Olympics. The Olympic Stadium seats 76,000,; its roof rises 68 meters over the seats and is made up of transparent panels that allow sunlight to stream in during the day.

    With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER provides scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

    Size: 12.1 by 15.9 kilometers (7.5 by 9.5 miles) Location: 52.5 degrees North latitude, 13.3 degrees East longitude Orientation: North at top Image Data: ASTER bands 3, 2, and 1 Original Data Resolution: 15 meters (49.2 feet) Dates Acquired: October 15, 2005

  5. 78 FR 44592 - Final General Management Plan, Final Wilderness Study, and Final Environmental Impact Statement...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-24

    ... National Park Service Final General Management Plan, Final Wilderness Study, and Final Environmental Impact Statement, Fort Pulaski National Monument, Georgia AGENCY: National Park Service, Interior. ACTION: Notice... 1969, 42 U.S.C. 4332(2)(C), the National Park Service (NPS) announces the availability of a...

  6. Gene Positioning

    PubMed Central

    Ferrai, Carmelo; de Castro, Inês Jesus; Lavitas, Liron; Chotalia, Mita; Pombo, Ana

    2010-01-01

    Eukaryotic gene expression is an intricate multistep process, regulated within the cell nucleus through the activation or repression of RNA synthesis, processing, cytoplasmic export, and translation into protein. The major regulators of gene expression are chromatin remodeling and transcription machineries that are locally recruited to genes. However, enzymatic activities that act on genes are not ubiquitously distributed throughout the nucleoplasm, but limited to specific and spatially defined foci that promote preferred higher-order chromatin arrangements. The positioning of genes within the nuclear landscape relative to specific functional landmarks plays an important role in gene regulation and disease. PMID:20484389

  7. ASEDRA Evaluation Final Report.

    SciTech Connect

    Mitchell, Dean J; Detwiler, Dr. Rebecca; Sjoden, Dr, Glenn E.

    2008-09-01

    The performance of the Advanced Synthetically Enhanced Detector Resolution Algorithm (ASEDRA) was evaluated by performing a blind test of 29 sets of gamma-ray spectra that were provided by DNDO. ASEDRA is a post-processing algorithm developed at the Florida Institute of Nuclear Detection and Security at the University of Florida (UF/FINDS) that extracts char-acteristic peaks in gamma-ray spectra. The QuickID algorithm, also developed at UF/FINDS, was then used to identify nuclides based on the characteristic peaks generated by ASEDRA that are inferred from the spectra. The ASEDRA/QuickID analysis results were evaluated with respect to the performance of the DHSIsotopeID algorithm, which is a mature analysis tool that is part of the Gamma Detector Response and Analysis Software (GADRAS). Data that were used for the blind test were intended to be challenging, and the radiation sources included thick shields around the radioactive materials as well as cargo containing naturally occurring radio-active materials, which masked emission from special nuclear materials and industrial isotopes. Evaluation of the analysis results with respect to the ground truth information (which was provided after the analyses were finalized) showed that neither ASEDRA/QuickID nor GADRAS could identify all of the radiation sources correctly. Overall, the purpose of this effort was primarily to evaluate ASEDRA, and GADRAS was used as a standard against which ASEDRA was compared. Although GADRAS was somewhat more accurate on average, the performance of ASEDRA exceeded that of GADRAS for some of the unknowns. The fact that GADRAS also failed to identify many of the radiation sources attests to the difficulty of analyzing the blind-test data that were used as a basis for the evaluation. This evaluation identified strengths and weaknesses of the two analysis approaches. The importance of good calibration data was also clear because the performance of both analysis methods was impeded by the

  8. Final Technical Report

    SciTech Connect

    Bohdan W. Oppenheim; Rudolf Marloth

    2007-10-26

    Executive Summary The document contains Final Technical Report on the Industrial Assessment Center Program at Loyola Marymount University in Los Angeles, covering the contract period of 9/1/2002 to 11/30/2006, under the contract DE-FC36-02GO 12073. The Report describes six required program tasks, as follows: TASK 1 is a summary of the assessments performed over the life of the award: 77 assessments were performed, 595 AR were recommended, covering a very broad range of manufacturing plants. TASK 2 is a description of the efforts to promote and increase the adoption of assessment recommendations and employ innovative methods to assist in accomplishing these goals. The LMU IAC has been very successful in accomplishing the program goals, including implemented savings of $5,141,895 in energy, $10,045,411 in productivity and $30,719 in waste, for a total of $15,218,025. This represents 44% of the recommended savings of $34,896,392. TASK 3 is a description of the efforts promoting the IAC Program and enhancing recruitment efforts for new clients and expanded geographic coverage. LMU IAC has been very successful recruiting new clients covering Southern California. Every year, the intended number of clients was recruited. TASK 4 describes the educational opportunities, training, and other related activities for IAC students. A total of 38 students graduated from the program, including 2-3 graduate students every semester, and the remainder undergraduate students, mostly from the Mechanical Engineering Department. The students received formal weekly training in energy (75%) and productivity (25). All students underwent extensive safety training. All students praised the IAC experience very highly. TASK 5 describes the coordination and integration of the Center activities with other Center and IAC Program activities, and DOE programs. LMU IAC worked closely with MIT, and SDSU IAC and SFSU IAC, and enthusiastically supported the SEN activities. TASK 6 describes other tasks

  9. [Nonlinear magnetohydrodynamics]. Final report

    SciTech Connect

    Montgomery, D.C.

    1998-11-01

    This is a final report on the research activities carried out under the above grant at Dartmouth. During the period considered, the grant was identified as being for nonlinear magnetohydrodynamics, considered as the most tractable theoretical framework in which the plasma problems associated with magnetic confinement of fusion plasmas could be studied. During the first part of the grant`s lifetime, the author was associated with Los Alamos National Laboratory as a consultant and the work was motivated by the reversed-field pinch. Later, when that program was killed at Los Alamos, the problems became ones that could be motivated by their relation to tokamaks. Throughout the work, the interest was always on questions that were as fundamental as possible, compatible with those motivations. The intent was always to contribute to plasma physics as a science, as well as to the understanding of mission-oriented confined fusion plasmas. Twelve Ph.D. theses were supervised during this period and a comparable number of postdoctoral research associates were temporarily supported. Many of these have gone on to distinguished careers, though few have done so in the context of the controlled fusion program. Their work was a combination of theory and numerical computation, in gradually less and less idealized settings, moving from rectangular periodic boundary conditions in two dimensions, through periodic straight cylinders and eventually, before the grant was withdrawn, to toroids, with a gradually more prominent role for electrical and mechanical boundary conditions. The author never had access to a situation where he could initiate experiments and relate directly to the laboratory data he wanted. Computers were the laboratory. Most of the work was reported in referred publications in the open literature, copies of which were transmitted one by one to DOE at the time they appeared. The Appendix to this report is a bibliography of published work which was carried out under the

  10. Final Technical Report

    SciTech Connect

    Lewis, Randolph

    2013-11-11

    Spider silks have the potential to provide new bio-inspired materials for numerous applications in bioenergetics and products ranging from protective clothing to artificial ligaments and tendons. A number of spider silk genes have been cloned and sequenced by the Lewis laboratory revealing the basis for understanding the key elements of spider silk proteins with respect to their materials performance. In particular, specific amino acid motifs have been identified which have been conserved for over 125 million years in all spiders that use their silk to physically trap prey. The key element in taking the next step toward generating bio-based materials from spider silks will be to move from the current descriptive data to predictive knowledge. Current efforts are focused on mimicking spider silk through synthetic proteins. In developing synthetic silk fibers, we first need to understand the complete secondary and tertiary structure of natural silk so that we can compare synthetic constructs to the natural material. Being able to compare the structure on a single fiber level is critical to the future of molecular directed mimic development because we can vary mechanical properties by different spinning methods. The new generation of synchrotron x-ray diffraction and neutron beamlines will allow, for the first time, determination of the molecular structure of silk fibers and synthetic mimics. We propose an exciting new collaborative research team working jointly between Argonne National Laboratory, Arizona State U. and the University of Wyoming to address the ?characterization of synthetic and natural spider silk fibers using x-ray and neutron diffraction.? Thus these new methodologies will provide understanding of current fibers and determine changes needed to produce fibers with specific properties. The following specific aims are proposed: ? Synthesize spider silk fibers with molecular structures mimicking that of natural silks. Test the mechanic properties of these

  11. HARE: Final Report

    SciTech Connect

    Mckie, Jim

    2012-01-09

    This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. The HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating

  12. Final Technical Report

    SciTech Connect

    Brizard, Alain J

    2009-12-31

    Final Technical Report for U.S. Department of Energy Grant No. DE-FG02-09ER55005 Nonlinear FLR Effects in Reduced Fluid Models Alain J. Brizard, Saint Michael's College The above-mentioned DoE grant was used to support research activities by the PI during a sabbatical leave from Saint Michael's College in 2009. The major focus of the work was the role played by guiding-center and gyrocenter (linear and nonlinear) polarization and magnetization effects in understanding transport processes in turbulent magnetized plasmas. The theoretical tools used for this work include Lie-transform perturbation methods and Lagrangian (variational) methods developed by the PI in previous work. The present final technical report lists (I) the peer-reviewed publications that were written based on work funded by the Grant; (II) invited and contributed conference presentations during the period funded by the Grant; and (III) seminars presented during the period funded by the Grant. I. Peer-reviewed Publications A.J. Brizard and N. Tronko, 2011, Exact momentum conservation for the gyrokinetic Vlasov- Poisson equations, Physics of Plasmas 18 , 082307:1-14 [http://dx.doi.org/10.1063/1.3625554 ]. J. Decker, Y. Peysson, A.J. Brizard, and F.-X. Duthoit, 2010, Orbit-averaged guiding-center Fokker-Planck operator for numerical applications, Physics of Plasmas 17, 112513:1-12 [http://dx.doi.org/10.1063/1.3519514]. A.J. Brizard, 2010, Noether derivation of exact conservation laws for dissipationless reduced fluid models, Physics of Plasmas 17, 112503:1-8 [http://dx.doi.org/10.1063/1.3515303]. F.-X. Duthoit, A.J. Brizard, Y. Peysson, and J. Decker, 2010, Perturbation analysis of trapped particle dynamics in axisymmetric dipole geometry, Physics of Plasmas 17, 102903:1-9 [http://dx.doi.org/10.1063/1.3486554]. A.J. Brizard, 2010, Exact energy conservation laws for full and truncated nonlinear gyrokinetic equations, Physics of Plasmas 17, 042303:1-11 [http://dx.doi.org/10.1063/1.3374428]. A

  13. Final Performance Progress Report

    SciTech Connect

    Houldin, Joseph; Saboor, Veronica

    2016-03-30

    about assessing a company’s technical assets, broadening our view of the business to go beyond what they make or what NAICS code they have…to better understand their capacity, capability, and expertise, and to learn more about THEIR customers. Knowing more about the markets they serve can often provide insight into their level of technical knowledge and sophistication. Finally, in the spirit of realizing the intent of the Accelerator we strove to align and integrate the work and activities supported by the five funding agencies to leverage each effort. To that end, we include in the Integrated Work Plan a graphic that illustrates that integration. What follows is our summary report of the project, aggregated from prior reports.

  14. Gene doping.

    PubMed

    Azzazy, Hassan M E

    2010-01-01

    Gene doping abuses the legitimate approach of gene therapy. While gene therapy aims to correct genetic disorders by introducing a foreign gene to replace an existing faulty one or by manipulating existing gene(s) to achieve a therapeutic benefit, gene doping employs the same concepts to bestow performance advantages on athletes over their competitors. Recent developments in genetic engineering have contributed significantly to the progress of gene therapy research and currently numerous clinical trials are underway. Some athletes and their staff are probably watching this progress closely. Any gene that plays a role in muscle development, oxygen delivery to tissues, neuromuscular coordination, or even pain control is considered a candidate for gene dopers. Unfortunately, detecting gene doping is technically very difficult because the transgenic proteins expressed by the introduced genes are similar to their endogenous counterparts. Researchers today are racing the clock because assuring the continued integrity of sports competition depends on their ability to develop effective detection strategies in preparation for the 2012 Olympics, which may mark the appearance of genetically modified athletes.

  15. Gene therapy.

    PubMed

    Williamson, B

    1982-07-29

    Gene therapy is not yet possible, but may become feasible soon, particularly for well understood gene defects. Although treatment of a patient raises no ethical problems once it can be done well, changing the genes of an early embryo is more difficult, controversial and unlikely to be required clinically.

  16. Final Technical Report

    SciTech Connect

    Stenzel, Reiner; Urrutia, J. Manuel

    2009-09-08

    emissions are only observed in whistler spheromaks and FRCs but not in mirrors or asymmetric configurations lacking magnetic null lines. The collisionless electron energization in a toroidal null line usually produces non-Maxwellian distributions. Off the null axis electrons gain more perpendicular than parallel energy. Distributions with T{sub {perpendicular}} > T{sub {parallel}} lead to whistler instabilities which have been observed. A whistler spheromak is a source of high-frequency whistler emissions. These are usually small amplitude whistlers propagating in a complicated background magnetic field. The waves are emitted from a moving source. High frequency whistlers propagate faster than the spheromak, thus partly move ahead of it and partly in the reverse direction. In test wave experiments wave growth opposite to the direction of the hot electron flow has been observed, confirming that Doppler-shifted cyclotron resonance instabilities account for the emission process. Propagating whistler mirrors produce no significant instabilities except when they interact with other fields which exhibit null lines. For example, a whistler mirror has been launched against a stationary FRC, resulting in strong FRC heating and whistler instabilities. In the whistler mirror configuration the antenna near-zone field produces a toroidal null line outside the coil which can also become a source for whistler emissions. Finally, nonlinear EMHD research has been extended to initially unmagnetized plasmas where a new nonlinear skin depth has been discovered. When a small-amplitude oscillating magnetic field is applied to a plasma the field penetration is governed by the skin depth, collisional or collisionless depending on frequency, collision frequency and plasma frequency. However, when the magnetic field increases the electrons become magnetized and the field penetration occurs in the whistler mode if the cyclotron frequency exceeds the oscillating frequency. This phenomenon has been

  17. Evolutionary Fingerprinting of Genes

    PubMed Central

    Kosakovsky Pond, Sergei L.; Scheffler, Konrad; Gravenor, Michael B.; Poon, Art F.Y.; Frost, Simon D.W.

    2010-01-01

    Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change—an “evolutionary fingerprint” of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast. To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates. PMID:19864470

  18. Vectors for cancer gene therapy.

    PubMed

    Zhang, J; Russell, S J

    1996-09-01

    Many viral and non-viral vector systems have now been developed for gene therapy applications. In this article, the pros and cons of these vector systems are discussed in relation to the different cancer gene therapy strategies. The protocols used in cancer gene therapy can be broadly divided into six categories including gene transfer to explanted cells for use as cell-based cancer vaccines; gene transfer to a small number of tumour cells in situ to achieve a vaccine effect; gene transfer to vascular endothelial cells (VECs) lining the blood vessels of the tumour to interfere with tumour angiogenesis; gene transfer to T lymphocytes to enhance their antitumour effector capability; gene transfer to haemopoietic stem cells (HSCs) to enhance their resistance to cytotoxic drugs and gene transfer to a large number of tumour cells in situ to achieve nonimmune tumour reduction with or without bystander effect. Each of the six strategies makes unique demands on the vector system and these are discussed with reference to currently available vectors. Aspects of vector biology that are in need of further development are discussed in some detail. The final section points to the potential use of replicating viruses as delivery vehicles for efficient in vivo gene transfer to disseminated cancers.

  19. The Ensembl gene annotation system

    PubMed Central

    Aken, Bronwen L.; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J.; Murphy, Daniel N.; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y. Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. Database URL: http://www.ensembl.org/index.html PMID:27337980

  20. Gene networks controlling petal organogenesis.

    PubMed

    Huang, Tengbo; Irish, Vivian F

    2016-01-01

    One of the biggest unanswered questions in developmental biology is how growth is controlled. Petals are an excellent organ system for investigating growth control in plants: petals are dispensable, have a simple structure, and are largely refractory to environmental perturbations that can alter their size and shape. In recent studies, a number of genes controlling petal growth have been identified. The overall picture of how such genes function in petal organogenesis is beginning to be elucidated. This review will focus on studies using petals as a model system to explore the underlying gene networks that control organ initiation, growth, and final organ morphology.

  1. Gene Delivery to the Airway

    PubMed Central

    Keiser, Nicholas W.; Engelhardt, John F.

    2013-01-01

    This unit describes generation of and gene transfer to several commonly used airway models. Isolation and transduction of primary airway epithelial cells are first described. Next, the preparation of polarized airway epithelial monolayers is outlined. Transduction of these polarized cells is also described. Methods are presented for generation of tracheal xenografts as well as both ex vivo and in vivo gene transfer to these xenografts. Finally, a method for in vivo gene delivery to the lungs of rodents is included. Methods for evaluating transgene expression are given in the support protocols. PMID:23853081

  2. Gene dispensability.

    PubMed

    Korona, Ryszard

    2011-08-01

    Genome-wide mutagenesis studies indicate that up to about 90% of genes in bacteria and 80% in eukaryotes can be inactivated individually leaving an organism viable, often seemingly unaffected. Several strategies are used to learn what these apparently dispensable genes contribute to fitness. Assays of growth under hundreds of physical and chemical stresses are among the most effective experimental approaches. Comparative studies of genomic DNA sequences continue to be valuable in discriminating between the core bacterial genome and the more variable niche-specific genes. The concept of the core genome appears currently unfeasible for eukaryotes but progress has been made in understanding why they contain numerous gene duplicates.

  3. 2-Ethylhexanol; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of 2-ethylhexanol (EH: CAS No. 104-76-7) to conduct a 2-year oncogenicity bioassay.

  4. 2-Mercaptobenzothiazole; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA) requiring manufacturers and processors of 2-mercaptobenzothiazole (MBT, CAS No. 149—30-4) to perform testing.

  5. HINTS Puerto Rico: Final Report

    Cancer.gov

    This final report describes HINTS implementation in Puerto Rico. The report addresses sampling; staffing, training and management of data collection; calling protocol; findings from the CATI Operations, and sample weights.

  6. AXKT Phase 3 Final Report

    DTIC Science & Technology

    1993-07-06

    AD-A275 236 - July 6 1993 AXKT PHASE 3 FINAL REPORT CONTRACT N00014-88-C-6027 CDRL A013 I NE * ,~ 9M SUBMITSED BY W80co 02 SIPPICAN, INC.I...Funding Numbers. AXKT Phase 3 Final Report Contract NOOQI 4-88-C-6027 PrOgram Elemeni No. 0603704N 6. Auw~) Project No. R01i180 Task fo. 300 Accession No

  7. Final Vowel-Consonant-e.

    ERIC Educational Resources Information Center

    Burmeister, Lou E.

    The utility value of the final vowel-consonant-e phonic generalization was examined using 2,715 common English words. When the vowel was defined as a single-vowel, the consonant as a single-consonant, and the final e as a single-e the generalization was found to be highly useful, contrary to other recent findings. Using the total sample of 2,715…

  8. Trichoderma genes

    DOEpatents

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  9. Gene therapy.

    PubMed

    Drugan, A; Miller, O J; Evans, M I

    1987-01-01

    Severe genetic disorders are potentially correctable by the addition of a normal gene into tissues. Although the technical problems involving integration, stable expression, and insertional damage to the treated cell are not yet fully solved, enough scientific progress has already been made to consider somatic cell gene therapy acceptable from both the ethical and scientific viewpoints. The resolutions to problems evolving from somatic cell gene therapy will help to overcome the technical difficulties encountered presently with germ line gene manipulation. This procedure would then become morally permissible as it will cause, in time, a reduction in the pool of abnormal genes in the population. Enhancement genetic engineering is technically feasible but morally unacceptable. Eugenic genetic engineering is not technically possible or ethically permissible in the foreseeable future.

  10. [Gene and gene sequence patenting].

    PubMed

    Bergel, S D

    1998-01-01

    According to the author, the patenting of elements isolated or copied from the human body boils down to the issue of genes and gene sequences. He describes the current situation from the comparative law standpoint (U.S. and Spanish law mainly) and then esamines the biotechnology industry's position.

  11. Unraveling photosystems. Final technical report

    SciTech Connect

    1997-09-01

    This report highlights four main points. (1) A residue substitution in phosphoribulokinase of Synechocystis PCC 6803 renders the mutant light-sensitive. The authors isolated a light-sensitive mutant (BRLS) of the photosynthetic cyanobacterium Synechocystis 6803 that does not survive exposure to bright light; 70% of BRLS cells die upon exposure to light of > 3000 lux for 2 hr. (2) Excitation energy transfer from phycocyanin to chlorophyll in an apcA-defective mutant of Synechocystis sp. PCC 6803. A greenish mutant of the normally bule-green cyanobacterium Synechocystis sp. PC 6803, designated UV6p, was isolated and characterized. UV6p possesses functional photosystems I and II but lacks normal light harvesting phycobilisomes because allophycocyanin is absent and core-specific linker proteins are almost entirely absent. (3) Deletion of the psbG1 gene of the cyanobacterium Synechocystis sp. PCC 6803 leads to the activation of the cryptic psbG2 gene. The genes psbG1 and psbG2 in cyanobacterium Synechocystis sp. PCC 6803 are homologous. The psbG1 gene is located on the chromosome and is part of the ndhC-psbG1-ORF157 operon, while psbG2 is located on a plasmid and is not flanked by equivalent ndhC or ORF157 genes. (4) Deletion of the structural gene for the NADH-dehydrogenase subunit 4 of Synechocystis 6803 alters respiratory properties. Chloroplasts and cyanobacteria contain genes encoding polypeptides homologous to some subunits of the mitochondrial respiratory NADH-ubiquinol oxidoreductase complex (NADH dehydrogenase). Nothing is known of the role of the NADH dehydrogenase complex in photosynthesis, respiration, or other functions in chloroplasts, and little is known about their specific roles in the perhaps 42 subunits of this complex in the mitochondrion.

  12. MPO B593110 - Final Report

    SciTech Connect

    Brooksby, C

    2011-07-25

    National Security Technologies, LLC (NSTec) shall provide one (1) Mechanical Engineer to support the Linear Collider Subsystem Development Program at Lawrence Livermore National Security, LLC (LLNS). The NSTec Mechanical Engineer's efforts will include engineering, design, and drawing support for the Vacuum Seal Test. NSTec will also provide a final report of the setup and input to LLNL's project management on project status. The NSTec Mechanical Engineer's efforts will also include engineering, design, and drawing support to the conceptual design for manufacturing of the Flux Concentrator Magnet. NSTec will also contribute to LLNS's final report on the Flux Concentrator Magnet. The deliverables are drawings, sketches, engineering documents, and final reports delivered to the LLNS Technical Representative.

  13. A New Comprehensive Final Exam

    NASA Astrophysics Data System (ADS)

    Bhavsar, Suketu P.

    2015-01-01

    Instructors aspire for students to master all the material covered. The final exam should assess the breadth and depth of their learning and be a significant basis for the final grade. I insist on a comprehensive final because I want students to review early material in light of later topics. I believe that this helps students create connections, integrate understanding, and retain knowledge for the long term. For non-science majors, reviewing and retaining the large amount of astronomy material is daunting. I experimented with a final exam format that calmed their fears and encouraged thorough review. It is only practical for a class of about twenty students or less. I provided a number of challenging conceptual and problem solving questions (at least as many as there were students), crafted to interconnect and span the entire range of topics. The order of the questions reflected the sequence in which the topics had been discussed. Students received these questions in ample time to prepare prior to the final. A student could bring up to 5 standard sheets of notes to the final. At the final, each student picked a number out of a hat. This was the question they had to answer in a 5-minute presentation. They were allowed 15 minutes for a final preparation during which they could use their 5 pages of notes. The presentations were given in order, 1- 20. Written comments on at least 10 other talks, explaining what was missed or correcting a mistake were required. They were graded both on their talk and on their comments. This format required students to be prepared for any question and encouraged interaction and communication while studying. Knowing the questions beforehand provided a guide to their studying as well as allayed their fears about what could be asked. The students also received guidance to what constituted a good answer, namely accuracy (correct scientific argument, appropriate facts, no irrelevant material), thoroughness (answered the complete questions

  14. Karlson ozone sterilizer. Final report

    SciTech Connect

    Karlson, E.

    1984-05-07

    The authors have a functional sterilization system employing ozone as a sterilization agent. This final report covers the work that led to the first medical sterilizer using ozone as the sterilizing agent. The specifications and the final design were set by hospital operating room personnel and public safety standards. Work on kill tests using bacteria, viruses and fungi determined the necessary time and concentration of ozone necessary for sterilization. These data were used in the Karlson Ozone Sterilizer to determine the length of the steps of the operating cycle and the concentration of ozone to be used. 27 references.

  15. Medical Qualification Determinations. Final rule.

    PubMed

    2017-01-18

    The U.S. Office of Personnel Management (OPM) is issuing a final rule to revise its regulations for medical qualification determinations. The revised regulations update references and language; add and modify definitions; clarify coverage and applicability; address the need for medical documentation and medical examination and/or testing for an applicant or employee whose position may or may not have medical standards and/or physical requirements; and recommend the establishment of agency medical review boards. The final rule provides agencies guidance regarding medical evaluation procedures.

  16. Genes V.

    SciTech Connect

    Lewin, B.

    1994-12-31

    This fifth edition book encompasses a wide range of topics covering 1,272 pages. The book is arranged into nine parts with a total of 36 chapters. These nine parts include Introduction; DNA as a Store of Information; Translation; Constructing Cells; Control of Prokaryotypic Gene Expression; Perpetuation of DNA; Organization of the Eukaryotypic Genome; Eukaryotypic Transcription and RNA Processing; The Dynamic Genome; and Genes in Development.

  17. Bisphenol A; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final rule, under section 4 of the Toxic Substances Control Act (TSCA) requiring manufacturers and processors of bisphenol A, hereinafter BPA, (4.4’-isopropylidenediphenol, CAS No. 80-05—7) to conduct a 90-day inhalation study.

  18. Data breaches. Interim final rule.

    PubMed

    2007-06-22

    This document establishes regulations to address data breaches regarding sensitive personal information that is processed or maintained by the Department of Veterans Affairs (VA). The regulations implement certain provisions of Title IX of the Veterans Benefits, Health Care, and Information Technology Act of 2006, which require promulgation of these regulations as an interim final rule.

  19. Russian Cargo Craft Final Undocking

    NASA Video Gallery

    The ISS Progress 47 resupply vehicle, loaded with trash, undocked from the International Space Station’s Pirs docking compartment for the final time July 30 at 5:19 p.m. EDT. The cargo ship undo...

  20. Tetrabromobisphenol A; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of tetrabromobisphenol A (TBBPA. CAS No. 79—94—7) to perform testing for chemical fate and environmental effects.

  1. TRICARE reimbursement revisions. Final rule.

    PubMed

    2012-06-27

    This final rule provides several necessary revisions to the regulation in order for TRICARE to be consistent with Medicare. These revisions affect: Hospice periods of care; reimbursement of physician assistants and assistant-at-surgery claims; and diagnosis-related group values, removing references to specific numeric diagnosis-related group values and replacing them with their narrative description.

  2. LSCA Final Reports: Third Series.

    ERIC Educational Resources Information Center

    Clark, Collin, Ed.

    This document includes final summary reports from 16 recent federally funded Library Services and Construction Act (LSCA) projects in California. This volume covers generally the period 1984-85, and reports are presented in six subject areas: programs for children, information and referral projects, institutional services, literacy, local history,…

  3. Final OSWER Vapor Intrusion Guidance

    EPA Science Inventory

    EPA is preparing to finalize its guidance on assessing and addressing vapor intrusion, which is defined as migration of volatile constituents from contaminated media in the subsurface (soil or groundwater) into the indoor environment. In November 2002, EPA issued draft guidance o...

  4. Environmental Education Program. Final Report.

    ERIC Educational Resources Information Center

    Edwards, Joan; Batty, Sara O.

    This final report deals with the efforts of the Environmental Action Coalition of New York City to change its network of recycling centers from collection points to educational centers for learning about solid waste and related environmental problems. This change was accomplished by first increasing the efficiency and the stability of the centers…

  5. Reengineering Elementary Accounting. Final Report.

    ERIC Educational Resources Information Center

    California State Univ., Chico.

    This final report describes activities and accomplishments of a 3-year project at California State University Chico (CSUC) to reengineer the 2-semester elementary accounting course. The new model emphasized, first, shifting from the traditional view of the preparer of accounting information to that of the user; second, forcing the student to adopt…

  6. MINIMARS conceptual design: Final report

    SciTech Connect

    Lee, J.D.

    1986-09-01

    This volume contains the following sections: (1) fueling systems; (2) blanket; (3) alternative blanket concepts; (4) halo scraper/direct converter system study and final conceptual design; (5) heat-transport and power-conversion systems; (6) tritium systems; (7) minimars air detritiation system; (8) appropriate radiological safety design criteria; and (9) cost estimate. (MOW)

  7. Deaths: Final Data for 1998.

    ERIC Educational Resources Information Center

    Murphy, Sherry L.

    2000-01-01

    This report presents final 1998 data on U.S. deaths and death rates according to demographic and medical characteristics such as age, sex, race, Hispanic origin, marital status, educational attainment, injury at work, state of residence, and cause of death. Trends and patterns in general mortality, life expectancy, and infant and maternal…

  8. Expedited technology demonstration project final report: final forms

    SciTech Connect

    Hopper, R W

    1999-05-01

    ETDP Final Forms was an attempt to demonstrate the fabrication and performance of a ceramic waste form immobilizing the hazardous and radioactive elements of the MSO/SR mineral residues. The ceramic material had been developed previously. The fabrication system was constructed and functioned as designed except for the granulator. Fabrication of our particular ceramic, however, proved unsatisfactory. The ceramic material design was therefore changed toward the end of the project, replacing nepheline with zircon as the sink for silica. Preliminary results were encouraging, but more development is needed. Fabrication of the new ceramic requires major changes in the processing: Calcination and granulation would be replaced by spray drying; and sintering would be at higher temperature. The main goal of the project--demonstrating the fabrication and performance of the waste form--was not achieved. This report summarizes Final Forms' activities. The problem of immobilizing the MSO/SR mineral residues is discussed.

  9. Simulations of neutralized final focus

    SciTech Connect

    Welch, D.R.; Rose, D.V.; Genoni, T.C.; Yu, S.S.; Barnard, J.J.

    2005-01-18

    In order to drive an inertial fusion target or study high energy density physics with heavy ion beams, the beam radius must be focused to < 3 mm and the pulse length must be compressed to < 10 ns. The conventional scheme for temporal pulse compression makes use of an increasing ion velocity to compress the beam as it drifts and beam space charge to stagnate the compression before final focus. Beam compression in a neutralizing plasma does not require stagnation of the compression, enabling a more robust method. The final pulse shape at the target can be programmed by an applied velocity tilt. In this paper, neutralized drift compression is investigated. The sensitivity of the compression and focusing to beam momentum spread, plasma, and magnetic field conditions is studied with realistic driver examples. Using the 3D particle-in-cell code, we examine issues associated with self-field generation, stability, and vacuum-neutralized transport transition and focusing.

  10. NONLINEAR DYNAMICAL SYSTEMS - Final report

    SciTech Connect

    Philip Holmes

    2005-12-31

    This document is the final report on the work completed on DE-FG02-95ER25238 since the start of the second renewal period: Jan 1, 2001. It supplements the annual reports submitted in 2001 and 2002. In the renewal proposal I envisaged work in three main areas: Analytical and topological tools for studying flows and maps Low dimensional models of fluid flow Models of animal locomotion and I describe the progess made on each project.

  11. Inelastic final-state interaction

    SciTech Connect

    Suzuki, Mahiko

    2008-03-01

    The final-state interaction in multichannel decay processes is systematically studied in the hadronic picture with application to B decay in mind. Since the final-state interaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like ''Watson's theorem'' holds for experimentally observed final states. We first solve exactly the two-channel problem as a toy model in order to clarify the issues. The constraints of the two-channel approximation turns out to be too stringent for most B decay modes, but realistic multichannel problems are too complex for useful quantitative analysis at present. To alleviate the stringent constraints of the two-body problem and to cope with complexity beyond it, we introduce a method of approximation that is applicable to the case where one prominent inelastic channel dominates over all others. We illustrate this approximation method with the amplitude of the decay B{yields}K{pi} fed by the intermediate states of a charmed-meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonetheless we are able to obtain some insight in the issue and draw useful conclusions on general features on the strong phases.

  12. Inelastic final-state interaction

    NASA Astrophysics Data System (ADS)

    Suzuki, Mahiko

    2008-03-01

    The final-state interaction in multichannel decay processes is systematically studied in the hadronic picture with application to B decay in mind. Since the final-state interaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like “Watson’s theorem” holds for experimentally observed final states. We first solve exactly the two-channel problem as a toy model in order to clarify the issues. The constraints of the two-channel approximation turns out to be too stringent for most B decay modes, but realistic multichannel problems are too complex for useful quantitative analysis at present. To alleviate the stringent constraints of the two-body problem and to cope with complexity beyond it, we introduce a method of approximation that is applicable to the case where one prominent inelastic channel dominates over all others. We illustrate this approximation method with the amplitude of the decay B→Kπ fed by the intermediate states of a charmed-meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonetheless we are able to obtain some insight in the issue and draw useful conclusions on general features on the strong phases.

  13. Inelastic final-state interaction

    SciTech Connect

    Suzuki, Mahiko; Suzuki, Mahiko

    2007-10-29

    The final-state interaction in multichannel decay processes is systematically studied with application to B decay in mind. Since the final-state interaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like"Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominent inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonetheless we are able to obtain some insight in the issue and draw useful conclusions on general features on the strong phases.

  14. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.

    PubMed

    Dávila López, Marcela; Martínez Guerra, Juan José; Samuelsson, Tore

    2010-05-14

    The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.

  15. Analysis of Gene Order Conservation in Eukaryotes Identifies Transcriptionally and Functionally Linked Genes

    PubMed Central

    Dávila López, Marcela; Martínez Guerra, Juan José; Samuelsson, Tore

    2010-01-01

    The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control. PMID:20498846

  16. JP-8 Final Risk Assessment

    DTIC Science & Technology

    2001-08-01

    billion gallons per year The study was conducted at multiple Air Force installations. Dyess AFB, TX, served as "the beta test site for participant selection...Glutathione-S-Transferase (G-S-T), a gene-regulated enzyme associated with increased susceptibility to multiple oxidative stressors including jet fuel and...installation? The study was conducted at multiple Air Force installations. Dyess AFB, TX, served as the beta test site for participant selection

  17. 04-ERD-052-Final Report

    SciTech Connect

    Loots, G G; Ovcharenko, I; Collette, N; Babu, P; Chang, J; Stubbs, L; Lu, X; Pennachio, C; Harland, R M

    2007-02-26

    Generating the sequence of the human genome represents a colossal achievement for science and mankind. The technical use for the human genome project information holds great promise to cure disease, prevent bioterror threats, as well as to learn about human origins. Yet converting the sequence data into biological meaningful information has not been immediately obvious, and we are still in the preliminary stages of understanding how the genome is organized, what are the functional building blocks and how do these sequences mediate complex biological processes. The overarching goal of this program was to develop novel methods and high throughput strategies for determining the functions of ''anonymous'' human genes that are evolutionarily deeply conserved in other vertebrates. We coupled analytical tool development and computational predictions regarding gene function with novel high throughput experimental strategies and tested biological predictions in the laboratory. The tools required for comparative genomic data-mining are fundamentally the same whether they are applied to scientific studies of related microbes or the search for functions of novel human genes. For this reason the tools, conceptual framework and the coupled informatics-experimental biology paradigm we developed in this LDRD has many potential scientific applications relevant to LLNL multidisciplinary research in bio-defense, bioengineering, bionanosciences and microbial and environmental genomics.

  18. Network Topology Reveals Key Cardiovascular Disease Genes

    PubMed Central

    Stojković, Neda; Radak, Djordje; Pržulj, Nataša

    2013-01-01

    The structure of protein-protein interaction (PPI) networks has already been successfully used as a source of new biological information. Even though cardiovascular diseases (CVDs) are a major global cause of death, many CVD genes still await discovery. We explore ways to utilize the structure of the human PPI network to find important genes for CVDs that should be targeted by drugs. The hope is to use the properties of such important genes to predict new ones, which would in turn improve a choice of therapy. We propose a methodology that examines the PPI network wiring around genes involved in CVDs. We use the methodology to identify a subset of CVD-related genes that are statistically significantly enriched in drug targets and “driver genes.” We seek such genes, since driver genes have been proposed to drive onset and progression of a disease. Our identified subset of CVD genes has a large overlap with the Core Diseasome, which has been postulated to be the key to disease formation and hence should be the primary object of therapeutic intervention. This indicates that our methodology identifies “key” genes responsible for CVDs. Thus, we use it to predict new CVD genes and we validate over 70% of our predictions in the literature. Finally, we show that our predicted genes are functionally similar to currently known CVD drug targets, which confirms a potential utility of our methodology towards improving therapy for CVDs. PMID:23977067

  19. DOE final report 100608.doc

    SciTech Connect

    Golden, Susan S

    2008-10-16

    The aim of this project was to inactivate each locus of the genome of the cyanobacterium Synechococcus elongatus PCC 7942 and screen resulting mutants for altered circadian phenotypes. The immediate goal was to identify all open reading frames (ORFs) that contribute to circadian timing. An additional result was to create a complete archived set of mutagenesis templates, of great utility for the wider research community, that will allow inactivation of any given locus in the genome of S. elongatus. Clones that carry segments of the S. elongatus genome were saturated with transposon insertions in vitro. We completed saturation mutagenesis of the chromosome (~2800 ORFs). The positions of insertions were sequenced for 17,767 mutagenized clones. Each individual insertion into the S. elongatus DNA in a cosmid or plasmid is a substrate for mutagenesis of the genome via homologous recombination. Because the complete insertion mutation clone set is 5-7 fold redundant, we produced a streamlined set of clones that contains one insertion mutation per locus in the genome, a unigene set. All clones are archived as Escherichia coli stocks frozen in glycerol in 96-well plates at -85ºC and as replicas of these plates on Whatman CloneSaver cards. Each of the mutagenesis substrates from the unigene set has been recombined into the chromosome of wild-type S. elongatus and these cyanobacterial mutants have been archived at -85ºC as well. S. elongatus insertion mutants defective for than 1400 independent genes have screened in luciferase reporter gene backgrounds to evaluate the effect of each mutation on circadian rhythms of gene expression. For the first 700 genes tested, mutagenesis of 71 different ORFs resulted in circadian phenotypes. The mutagenesis project also created insertion mutations in the endogenous large plasmid of S. elongatus, pANL. The sequence of pANL revealed two potential addiction cassettes that appear to account for selection for plasmid persistence. Genetic

  20. State-of-the-art human gene therapy: part II. Gene therapy strategies and clinical applications.

    PubMed

    Wang, Dan; Gao, Guangping

    2014-09-01

    In Part I of this Review (Wang and Gao, 2014), we introduced recent advances in gene delivery technologies and explained how they have powered some of the current human gene therapy applications. In Part II, we expand the discussion on gene therapy applications, focusing on some of the most exciting clinical uses. To help readers to grasp the essence and to better organize the diverse applications, we categorize them under four gene therapy strategies: (1) gene replacement therapy for monogenic diseases, (2) gene addition for complex disorders and infectious diseases, (3) gene expression alteration targeting RNA, and (4) gene editing to introduce targeted changes in host genome. Human gene therapy started with the simple idea that replacing a faulty gene with a functional copy can cure a disease. It has been a long and bumpy road to finally translate this seemingly straightforward concept into reality. As many disease mechanisms unraveled, gene therapists have employed a gene addition strategy backed by a deep knowledge of what goes wrong in diseases and how to harness host cellular machinery to battle against diseases. Breakthroughs in other biotechnologies, such as RNA interference and genome editing by chimeric nucleases, have the potential to be integrated into gene therapy. Although clinical trials utilizing these new technologies are currently sparse, these innovations are expected to greatly broaden the scope of gene therapy in the near future.

  1. Attention Genes

    ERIC Educational Resources Information Center

    Posner, Michael I.; Rothbart, Mary K.; Sheese, Brad E.

    2007-01-01

    A major problem for developmental science is understanding how the cognitive and emotional networks important in carrying out mental processes can be related to individual differences. The last five years have seen major advances in establishing links between alleles of specific genes and the neural networks underlying aspects of attention. These…

  2. Designer Genes.

    ERIC Educational Resources Information Center

    Miller, Judith; Miller, Mark

    1983-01-01

    Genetic technologies may soon help fill some of the most important needs of humanity from food to energy to health care. The research of major designer genes companies and reasons why the initial mad rush for biotechnology has slowed are reviewed. (SR)

  3. Stochastic Fluctuations in Gene Regulation

    DTIC Science & Technology

    2005-04-01

    AFRL-IF- RS -TR-2005-126 Final Technical Report April 2005 STOCHASTIC FLUCTUATIONS IN GENE REGULATION Boston University...be releasable to the general public, including foreign nations. AFRL-IF- RS -TR-2005-126 has been reviewed and is approved for publication...AGENCY REPORT NUMBER AFRL-IF- RS -TR-2005-126 11. SUPPLEMENTARY NOTES AFRL Project Engineer: Peter J. Costianes/IFED/(315) 330-4030

  4. SPIRIT 1 Final Flight Report

    DTIC Science & Technology

    1991-05-15

    If _ PL-TR-91-2226 Environmental Research Papers, No.1094 AD-A257 088" S PI R IT I llll l ii l li l IilI FINAL FLIGHT REPORT Donald R. Smith Michael...24213• :_• ./1111111111 II/ ll/ I111ll /i l ! 1111 I~lll’ "This technical report has been reviewed and is approved for publication" ,’TP" D. PRICE...the 500- to 2000-cm-1 (5- to 20-jim) region. This report provides a detailed overview of the SPIRIT 1 flight and mission and the analysis of the flight

  5. Vet Centers. Interim final rule.

    PubMed

    2015-08-04

    The Department of Veterans Affairs (VA) is amending its medical regulation that governs Vet Center services. The National Defense Authorization Act for Fiscal Year 2013 (the 2013 Act) requires Vet Centers to provide readjustment counseling services to broader groups of veterans, members of the Armed Forces, including a member of a reserve component of the Armed Forces, and family members of such veterans and members. This interim final rule amends regulatory criteria to conform to the 2013 Act, to include new and revised definitions.

  6. It Finally Happened to Me

    PubMed Central

    Kannai, Ruth

    2014-01-01

    It finally happened to me: I was sued for malpractice by the family of a patient who had died suddenly. My inner turmoil in the aftermath of this traumatic event affected me deeply. While I was an experienced family doctor dedicated to patient-centered medicine, the event challenged my customary approach to my patients. I share three vignettes from my practice that describe my inner dialogue both “preprosecution” and “postprosecution” and explain how I acted in each case. PMID:25201743

  7. Field practice internship final report

    SciTech Connect

    Foster, T.

    1994-05-01

    This field practice internship final report gives an overview of the field practice, which was completed at the Oak Ridge Y-12 Plant, Martin Marietta Energy Systems, Inc., Environmental Management Department, Oak Ridge, Tennessee. The field practice focused on the completion of the Superfund Amendments and Reauthorization Act (SARA) Title III, Emergency Planning and Community Right-to-Know Act Section 312, Tier II Report. The field practice internship was conducted on a full-time basis between December 13, 1993 through February 18, 1994. Sheila Poligone, Emergency Planning and Community Right-to-Know Act (EPCRA) Coordinator served as the field practice preceptor.

  8. Virtualized Network Control. Final Report

    SciTech Connect

    Ghani, Nasir

    2013-02-01

    This document is the final report for the Virtualized Network Control (VNC) project, which was funded by the United States Department of Energy (DOE) Office of Science. This project was also informally referred to as Advanced Resource Computation for Hybrid Service and TOpology NEtworks (ARCHSTONE). This report provides a summary of the project's activities, tasks, deliverable, and accomplishments. It also provides a summary of the documents, software, and presentations generated as part of this projects activities. Namely, the Appendix contains an archive of the deliverables, documents, and presentations generated a part of this project.

  9. New Approaches to Final Cooling

    SciTech Connect

    Neuffer, David

    2014-11-10

    A high-energy muon collider scenario require a “final cooling” system that reduces transverse emittances by a factor of ~10 while allowing longitudinal emittance increase. The baseline approach has low-energy transverse cooling within high-field solenoids, with strong longitudinal heating. This approach and its recent simulation are discussed. Alternative approaches which more explicitly include emittance exchange are also presented. Round-to-flat beam transform, transverse slicing, and longitudinal bunch coalescence are possible components of the alternative approach. A more explicit understanding of solenoidal cooling beam dynamics is introduced.

  10. [Experimental nuclear physics]. Final report

    SciTech Connect

    1991-04-01

    This is the final report of the Nuclear Physics Laboratory of the University of Washington on work supported in part by US Department of Energy contract DE-AC06-81ER40048. It contains chapters on giant dipole resonances in excited nuclei, nucleus-nucleus reactions, astrophysics, polarization in nuclear reactions, fundamental symmetries and interactions, accelerator mass spectrometry (AMS), ultra-relativistic heavy ions, medium energy reactions, work by external users, instrumentation, accelerators and ion sources, and computer systems. An appendix lists Laboratory personnel, a Ph. D. degree granted in the 1990-1991 academic year, and publications. Refs., 41 figs., 7 tabs.

  11. Gene therapy for bone regeneration.

    PubMed

    Luo, Jeffrey; Sun, Michael H; Kang, Quan; Peng, Ying; Jiang, Wei; Luu, Hue H; Luo, Qing; Park, Jae Yoon; Li, Yien; Haydon, Rex C; He, Tong-Chuan

    2005-04-01

    Efficacious bone regeneration could revolutionize the clinical management of many bone and musculoskeletal disorders. Bone has the unique ability to regenerate and continuously remodel itself throughout life. However, clinical situations arise when bone is unable to heal itself, as with segmental bone loss, fracture non-union, and failed spinal fusion. This leads to significant morbidity and mortality. Current attempts at improved bone healing have been met with limited success, fueling the development of improved techniques. Gene therapy in many ways represents an ideal approach for augmenting bone regeneration. Gene therapy allows specific gene products to be delivered to a precise anatomic location. In addition, the level of transgene expression as well as the duration of expression can be regulated with current techniques. For bone regeneration, the gene of interest should be delivered to the fracture site, expressed at appropriate levels, and then deactivated once the fracture has healed. Delivery of biological factors, mostly bone morphogenetic proteins (BMPs), has yielded promising results both in animal and clinical studies. There has also been tremendous work on discovering new growth factors and exploring previously defined ones. Finally, significant advances are being made in the delivery systems of the genes, ranging from viral and non-viral vectors to tissue engineering scaffolds. Despite some public hesitation to gene therapy, its use has great potential to expand our ability to treat a variety of human bone and musculoskeletal disorders. It is conceivable that in the near future gene therapy can be utilized to induce bone formation in virtually any region of the body in a minimally invasive manner. As bone biology and gene therapy research progresses, the goal of successful human gene transfer for augmentation of bone regeneration draws nearer.

  12. Production and clinical development of nanoparticles for gene delivery

    PubMed Central

    Chen, Jie; Guo, Zhaopei; Tian, Huayu; Chen, Xuesi

    2016-01-01

    Gene therapy is a promising strategy for specific treatment of numerous gene-associated human diseases by intentionally altering the gene expression in pathological cells. A successful clinical application of gene-based therapy depends on an efficient gene delivery system. Many efforts have been attempted to improve the safety and efficiency of gene-based therapies. Nanoparticles have been proved to be the most promising vehicles for clinical gene therapy due to their tunable size, shape, surface, and biological behaviors. In this review, the clinical development of nanoparticles for gene delivery will be particularly highlighted. Several promising candidates, which are closest to clinical applications, will be briefly reviewed. Then, the recent developments of nanoparticles for clinical gene therapy will be identified and summarized. Finally, the development of nanoparticles for clinical gene delivery in future will be prospected. PMID:27088105

  13. Space tug applications. Final report

    SciTech Connect

    1996-01-01

    This article is the final report of the conceptual design efforts for a `space tug`. It includes preliminary efforts, mission analysis, configuration analysis, impact analysis, and conclusions. Of the several concepts evaluated, the nuclear bimodal tug was one of the top candidates, with the two options being the NEBA-1 and NEBA-3 systems. Several potential tug benefits were identified during the mission analysis. The tug enables delivery of large (>3,500 kg) payloads to the outer planets and it increases the GSO delivery capability by 20% relative to current systems. By providing end of life disposal, the tug can be used to extend the life of existing space assets. It can also be used to reboost satellites which were not delivered to their final orbit by the launch system. A specific mission model is the key to validating the tug concept. Once a mission model can be established, mission analysis can be used to determine more precise propellant quantities and burn times. In addition, the specific payloads can be evaluated for mass and volume capability with the launch systems. Results of the economic analysis will be dependent on the total years of operations and the number of missions in the mission model. The mission applications evaluated during this phase drove the need for large propellant quantities and thus did not allow the payloads to step down to smaller and less expensive launch systems.

  14. Inferring Functional Relationships from Conservation of Gene Order.

    PubMed

    Moreno-Hagelsieb, Gabriel

    2017-01-01

    Predicting functional associations using the Gene Neighbor Method depends on the simple idea that if genes are conserved next to each other in evolutionarily distant prokaryotes they might belong to a polycistronic transcription unit. The procedure presented in this chapter starts with the organization of the genes within genomes into pairs of adjacent genes. Then, the pairs of adjacent genes in a genome of interest are mapped to their corresponding orthologs in other, informative, genomes. The final step is to verify if the mapped orthologs are also pairs of adjacent genes in the informative genomes.

  15. Endothelial Genes

    DTIC Science & Technology

    2005-06-01

    Suppression subtractive hybridization re- Cancer: principles and practice of oncology. Philadelphia: Lippincott- vealed an RNA sequence (GenBank accession...Lau YC, Campbell AP, et al. Suppression subtractive hybridization : A method for generating differentially regulated or tissue-tissues, EG-1 appears to...this gene, we investigated its interaction with Src and members of the called suppression subtractive hybridization (12). In human mitogen-activated

  16. Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes

    PubMed Central

    Wang, Jun; Marowsky, Nicholas C.; Fan, Chuanzhu

    2014-01-01

    It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica) genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences) of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes. PMID:25310342

  17. Metagenomics and novel gene discovery

    PubMed Central

    Culligan, Eamonn P; Sleator, Roy D; Marchesi, Julian R; Hill, Colin

    2014-01-01

    Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics. PMID:24317337

  18. Regulation of photoreceptor gene transcription via a highly conserved transcriptional regulatory element by vsx gene products

    PubMed Central

    Pan, Yi; Comiskey, Daniel F.; Kelly, Lisa E.; Chandler, Dawn S.

    2016-01-01

    Purpose The photoreceptor conserved element-1 (PCE-1) sequence is found in the transcriptional regulatory regions of many genes expressed in photoreceptors. The retinal homeobox (Rx or Rax) gene product functions by binding to PCE-1 sites. However, other transcriptional regulators have also been reported to bind to PCE-1. One of these, vsx2, is expressed in retinal progenitor and bipolar cells. The purpose of this study is to identify Xenopus laevis vsx gene products and characterize vsx gene product expression and function with respect to the PCE-1 site. Methods X. laevis vsx gene products were amplified with PCR. Expression patterns were determined with in situ hybridization using whole or sectioned X. laevis embryos and digoxigenin- or fluorescein-labeled antisense riboprobes. DNA binding characteristics of the vsx gene products were analyzed with electrophoretic mobility shift assays (EMSAs) using in vitro translated proteins and radiolabeled oligonucleotide probes. Gene transactivation assays were performed using luciferase-based reporters and in vitro transcribed effector gene products, injected into X. laevis embryos. Results We identified one vsx1 and two vsx2 gene products. The two vsx2 gene products are generated by alternate mRNA splicing. We verified that these gene products are expressed in the developing retina and that expression resolves into distinct cell types in the mature retina. Finally, we found that vsx gene products can bind the PCE-1 site in vitro and that the two vsx2 isoforms have different gene transactivation activities. Conclusions vsx gene products are expressed in the developing and mature neural retina. vsx gene products can bind the PCE-1 site in vitro and influence the expression of a rhodopsin promoter-luciferase reporter gene. The two isoforms of vsx have different gene transactivation activities in this reporter gene system. PMID:28003732

  19. The final portrait of Christ.

    PubMed

    Fauteux, K

    1989-09-01

    Artistic presentations of Jesus are as numerous and varied as the artists who created them. Whether on canvas or in music, Jesus has been portrayed as a redeemer, revolutionary, teacher, and clown. While some people are inspired by a particular presentation of Jesus, others are angered and incensed at what they perceive to be blasphemous. An example of the latter is Martin Scorsese's film, "The Last Temptation of Christ." This article examines why people responded so negatively to this and other artistic presentations of Jesus. It suggests they have failed to recognize how the portrayal reflects a personal experience of the artist and is not meant to be a final portrait of Christ. And on a more unconscious level, these works of art evoke feelings within people which they fear to acknowledge and which they escape by condemning the work.

  20. Dairy methane generator. Final report

    SciTech Connect

    Williams, T.B.

    1981-09-30

    Details of the work completed under this contract are presented. During the winter of 1979-80 three students enrolled, in the Mechanical Design Engineering Technology program at the Pennsylvania State University's Capitol Campus (Middletown, PA), undertook a feasibility study for the utilization of the manure generated by the dairy cows located on Mr. Thomas B. Williams farm for the generation and use of methane gas. The results of their effort was the design of an Anaerobic Digester/Electric Generation System. This preliminary designed system was later changed and improved by another group of P.S.U. MDET students in the spring of 1980. The final design included working drawings and an economic analysis of the estimated investment necessary to complete the Methane Generator/Electric Power Generation System.

  1. Gravimelt Process development. Final report

    SciTech Connect

    Not Available

    1983-06-01

    This final report contains the results of a bench-scale program to continue the development of the TRW proprietary Gravimelt Process for chemically cleaning coal. This project consisted of two major efforts, a laboratory study aimed at identifying parameters which would influence the operation of a bench unit for desulfurization and demineralization of coal and the design, construction and operation of two types of continuous plug-flow type bench-scale fused caustic leachers. This present bench scale project has demonstrated modes for the continuous operation of fused caustic leaching of coal at coal throughputs of 1 to 5 pounds per hour. The remaining process unit operations of leach solutions regeneration and coal washing and filtration should be tested at bench scale together with fused caustic leaching of coal to demonstrate the complete Gravimelt Process. 22 figures, 11 tables.

  2. The biology of novel animal genes: Mouse APEX gene knockout

    SciTech Connect

    MacInnes, M.; Altherr, M.R.; Ludwig, D.; Pedersen, R.; Mold, C.

    1997-07-01

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The controlled breeding of novel genes into mice, including the gene knockout (KO), or conversely by adding back transgenes provide powerful genetic technologies that together suffice to determine in large part the biological role(s) of novel genes. Inbred mouse remains the best understood and most useful mammalian experimental system available for tackling the biology of novel genes. The major mammalian apurinic/apyrimidinic (AP) endonuclease (APE), is involved in a key step in the repair of spontaneous and induced AP sites in DNA. Efficient repair of these lesions is imperative to prevent the stable incorporation of mutations into the cellular genome which may lead to cell death or transformation. Loss or modulation of base excison repair activity in vivo may elevate the spontaneous mutation rate in cells, and may lead to a substantial increase in the incidence of cancer. Despite extensive biochemical analysis, however, the significance of these individual APE functions in vivo has not been elucidated. Mouse embryonic stem (ES) cells heterozygous for a deletion mutation in APE have been generated and whole animals containing the APE mutation have been derived from these ES cells. Animals homozygous for the APE null mutation die early in gestation, underscoring the biological significance of this DNA repair gene.

  3. 78 FR 5821 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include additions or modifications of Base Flood Elevations (BFEs), base flood depths, Special Flood Hazard...

  4. 78 FR 21143 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-09

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final notice. SUMMARY: Flood hazard determinations, which may include additions or modifications of Base Flood Elevations (BFEs), base flood depths, Special Flood Hazard...

  5. 78 FR 52953 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-27

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include additions or modifications of Base Flood Elevations (BFEs), base flood depths, Special Flood Hazard...

  6. 78 FR 52954 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-27

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final notice. SUMMARY: Flood hazard determinations, which may include additions or modifications of Base Flood Elevations (BFEs), base flood depths, Special Flood Hazard...

  7. 78 FR 5820 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include additions or modifications of Base Flood Elevations (BFEs), base flood depths, Special Flood Hazard...

  8. IRIS Final Technical Progress Report

    SciTech Connect

    M. D. Carelli

    2003-11-03

    OAK-B135 This NERI project, originally started as the Secure Transportable Autonomous Light Water Reactor (STAR-LW) and currently known as the International Reactor Innovative and Secure (IRIS) project, had the objective of investigating a novel type of water-cooled reactor to satisfy the Generation IV goals: fuel cycle sustainability, enhanced reliability and safety, and improved economics. The research objectives over the three-year (1999-2002) program were as follows: First year: Assess various design alternatives and establish main characteristics of a point design; Second year: Perform feasibility and engineering assessment of the selected design solutions; Third year: Complete reactor design and performance evaluation, including cost assessment These objectives were fully attained and actually they served to launch IRIS as a full fledged project for eventual commercial deployment. The program did not terminate in 2002 at the end of the NERI program, and has just entered in its fifth year. This has been made possible by the IRIS project participants which have grown from the original four member, two-countries team to the current twenty members, nine countries consortium. All the consortium members work under their own funding and it is estimated that the value of their in-kind contributions over the life of the project has been of the order of $30M. Currently, approximately 100 people worldwide are involved in the project. A very important constituency of the IRIS project is the academia: 7 universities from four countries are members of the consortium and five more US universities are associated via parallel NERI programs. To date, 97 students have worked or are working on IRIS; 59 IRIS-related graduate theses have been prepared or are in preparation, and 41 of these students have already graduated with M.S. (33) or Ph.D. (8) degrees. This ''final'' report (final only as far as the NERI program is concerned) summarizes the work performed in the first four

  9. Advanced Design Studies. Final report

    SciTech Connect

    Steiner, Don

    2012-12-01

    The ARIES-CS project was a multi-year multi-institutional project to assess the feasibility of a compact stellarator as a fusion power plant. The work herein describes efforts to help design one aspect of the device, the divertor, which is responsible for the removal of particle and heat flux from the system, acting as the first point of contact between the magnetically confined hot plasma and the outside world. Specifically, its location and topology are explored, extending previous work on the sub ject. An optimized design is determined for the thermal particle flux using a suite of 3D stellarator design codes which trace magnetic field lines from just inside the confined plasma edge to their strike points on divertor plates. These divertor plates are specified with a newly developed plate design code. It is found that a satisfactory thermal design exists which maintains the plate temperature and heat load distribution below tolerable engineering limits. The design is unique, including a toroidal taper on the outboard plates which was found to be important to our results. The maximum thermal heat flux for the final design was 3.61 M W/m2 and the maximum peaking factor was 10.3, below prescribed limits of 10 M W/m2 and 15.6, respectively. The median length of field lines reaching the plates is about 250 m and their average angle of inclination to the surface is 2 deg. Finally, an analysis of the fast alphas, resulting from fusion in the core, which escape the plasma was performed. A method is developed for obtaining the mapping from magnetic coordinates to real-space coordinates for the ARIES-CS. This allows the alpha exit locations to be identified in real space for the first time. These were then traced using the field line algorithm as well as a guiding center routine accounting for their mass, charge, and specific direction and energy. Results show that the current design is inadequate for accommodating the alpha heat flux, capturing at most 1/3 of lost alphas

  10. Demand Side Bidding. Final Report

    SciTech Connect

    Spahn, Andrew

    2003-12-31

    This document sets forth the final report for a financial assistance award for the National Association of Regulatory Utility Commissioners (NARUC) to enhance coordination between the building operators and power system operators in terms of demand-side responses to Location Based Marginal Pricing (LBMP). Potential benefits of this project include improved power system reliability, enhanced environmental quality, mitigation of high locational prices within congested areas, and the reduction of market barriers for demand-side market participants. NARUC, led by its Committee on Energy Resources and the Environment (ERE), actively works to promote the development and use of energy efficiency and clean distributive energy policies within the framework of a dynamic regulatory environment. Electric industry restructuring, energy shortages in California, and energy market transformation intensifies the need for reliable information and strategies regarding electric reliability policy and practice. NARUC promotes clean distributive generation and increased energy efficiency in the context of the energy sector restructuring process. NARUC, through ERE's Subcommittee on Energy Efficiency, strives to improve energy efficiency by creating working markets. Market transformation seeks opportunities where small amounts of investment can create sustainable markets for more efficient products, services, and design practices.

  11. The Final Approach Spacing Tool

    NASA Technical Reports Server (NTRS)

    Davis, Thomas J.; Bergh, Christopher; Krzeczowski, Ken J.; Schlickenmaier, H. W. (Technical Monitor)

    1994-01-01

    A system for assisting terminal area air traffic controllers in the management and control of arrival traffic, referred to as the Final Approach Spacing Tool (FAST), is being developed at NASA Ames Research Center. In a cooperative program, NASA and FAA have efforts underway to install and evaluate the system at the Dallas/Fort Worth Terminal Radar Approach Control facility. This paper will review the software architecture, the algorithms components, and the human-machine interface. The system is based on continuous updates of a detailed trajectory analyses of all arrival aircraft. FAST interprets the results of these trajectory analyses to build an efficient and procedurally acceptable plan for the arrival traffic that consists of a sequence, schedule, and runway assignment. The system utilizes a heuristically-based conflict resolution algorithm to build a solution trajectory that satisfies the plan, It extracts a series of speed and heading advisories from the solution trajectory to assist the controller in efficiently managing and controlling the arrival traffic down to the runway. The advisories are displayed in a graphical format to the controller. In addition to the radar tracking data, the system also relies on a series of data bases. These data bases contain aircraft performance models, airline preferred operational procedures, airspace structure, air traffic procedural models, and a three dimensional wind model. Field evaluation of FAST is expected to begin in 1994.

  12. Final Report for OJI grant.

    SciTech Connect

    Todd Averett

    2006-10-13

    This document is a final report for DOE grant DE-FG02-00ER41147. The research described herein was funded in large part by this grant with additional support from the National Science Foundation. The primary focus of Averett's research effort is centered around the polarized {sup 3}He target in Hall A at Jefferson Lab. The close proximity of the College of William and Mary to Jefferson Lab has provided an outstanding opportunity to maintain a very active research program which still satisfying the demands of the college. Our research group includes four faculty, two post-doctoral fellows and eight graduate students. Averett also maintains a fully functional polarized {sup 3}e target lab at William and Mary which allows him to support the research program at Jefferson Lab while also doing research on polarized targets themselves. Since 1998, seven experiments using polarized {sup 3}He have been completed by the Jefferson Lab Hall A Polarized {sup 3}He Collaboration. Ten publications have been produced on this research and analysis of the two most recently completed experiments is underway. A description of the recent experiments and results is given below. In addition to target expertise, Averett has remained one of the most active collaborators in the data analysis of these experiments and maintains the largest on-site user group for this purpose as well.

  13. FINAL SCIENTIFIC/TECHNICAL REPORT

    SciTech Connect

    Satish Mohapatra

    2011-12-21

    Dynalene Inc has developed and patented a fuel cell coolant with the help of DOE SBIR Phase I and Phase II funding (Project DE-FG02-04ER83884). However, this coolant could only be produced in lab scale (500 ml to 2 L) due to problems in the optimization and scale-up of a nanoparticle ingredient. This project optimized the nanoparticle production process in 10 L and 100 L reactors (which translates to about 5000 gallons of coolant), optimized the filtration process for the nanoparticles, and develop a high throughput production as well as quality control method for the final coolant formulation. Scale-up of nanoparticle synthesis (using emulsion polymerization) is an extremely challenging task. Dynalene researchers, in collaboration with a university partner, identified all the parameters affecting the size, charge density and coagulation characteristics of the nanoparticles and then optimized these parameters to achieve the goals and the objectives of this project. Nanoparticle synthesis was demonstrated to be reproducible in the 10 L and 100 L scales.

  14. Final report for DESC0004031

    SciTech Connect

    Kitchin, John

    2016-08-08

    In this project we aim to develop new multicomponent oxide-based electrocatalysts for the oxygen evolution reaction using combined theoretical and experimental approaches. We use density functional theory to compute the electronic structure and reactivity proxies of model oxide materials. From the understanding generated from these calculations, we synthesize materials and characterize their oxygen evolution activity. We use in situ spectroscopic methods to characterize oxide electrodes under reaction conditions. We also develop new data sharing strategies to facilitate the reuse of our data by others. Our work has several potential impacts of interest to DOE. First, the discovery of new oxygen evolution electrocatalysts directly affects the efficiency of many energy-related processes from hydrogen generation to air separation and electrochemical fuel synthesis. Second, we have identified new ways to promote the oxygen evolution reaction for some materials through the electrolyte. This opens new pathways to improving the efficiency of processes involving oxygen evolution. The ability to characterize electrodes under operating conditions enables new insights into the actual structure and composition of the materials, which we are finding are not the same as the as prepared materials. Finally, DOE has significant need and interest in improving the ability to share data among researchers.

  15. 37 CFR 2.64 - Final action.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Final action. (a) On the first or any subsequent reexamination or reconsideration the refusal of the... months after the date of the final action. The Office will enter amendments accompanying requests for reconsideration after final action if the amendments comply with the rules of practice in trademark cases and...

  16. 14 CFR 1214.1105 - Final ranking.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Final ranking. 1214.1105 Section 1214.1105 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION SPACE FLIGHT NASA Astronaut Candidate Recruitment and Selection Program § 1214.1105 Final ranking. Final rankings will be based on a combination...

  17. 14 CFR 1214.1105 - Final ranking.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Final ranking. 1214.1105 Section 1214.1105 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION SPACE FLIGHT NASA Astronaut Candidate Recruitment and Selection Program § 1214.1105 Final ranking. Final rankings will be based on a combination...

  18. 14 CFR 1214.1105 - Final ranking.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Final ranking. 1214.1105 Section 1214.1105 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION SPACE FLIGHT NASA Astronaut Candidate Recruitment and Selection Program § 1214.1105 Final ranking. Final rankings will be based on a combination...

  19. 14 CFR 1214.1105 - Final ranking.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Final ranking. 1214.1105 Section 1214.1105 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION SPACE FLIGHT NASA Astronaut Candidate Recruitment and Selection Program § 1214.1105 Final ranking. Final rankings will be based on a combination...

  20. 31 CFR 92.17 - Final action.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Final action. 92.17 Section 92.17 Money and Finance: Treasury Regulations Relating to Money and Finance UNITED STATES MINT OPERATIONS AND... States Mint § 92.17 Final action. (a) In making a final determination whether to impose a penalty,...

  1. 10 CFR 820.32 - Final order.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Final order. 820.32 Section 820.32 Energy DEPARTMENT OF ENERGY PROCEDURAL RULES FOR DOE NUCLEAR ACTIVITIES Enforcement Process § 820.32 Final order. (a) Effect of Initial Decision. The Initial Decision shall be deemed filed as a Final Order thirty days...

  2. Transcriptomic identification and expression of starch and sucrose metabolism genes in the seeds of Chinese chestnut (Castanea mollissima).

    PubMed

    Zhang, Lin; Lin, Qing; Feng, Yanzhi; Fan, Xiaoming; Zou, Feng; Yuan, De-Yi; Zeng, Xiaochun; Cao, Heping

    2015-01-28

    The Chinese chestnut (Castanea mollissima) seed provides a rich source of carbohydrates as food and feed. However, little is known about starch biosynthesis in the seeds. The objectives of this study were to determine seed composition profiles and identify genes involved in starch and sucrose metabolism. Metabolite analysis showed that starch was the major component and rapidly accumulated during seed endosperm development. Amylopectin was approximately 3-fold of amylose content in chestnut starch. Illumina platform-based transcriptome sequencing generated 56671 unigenes in two cDNA libraries from seed endosperms collected at 45 and 75 days after flowering (DAF). A total of 1537 unigenes showed expression differences ≥2-fold in the two stages of seeds including 570 up-regulated and 967 down-regulated unigenes. One hundred and fifty-two unigenes were identified as involved in starch and sucrose metabolism, including 1 for glycogenin glucosyltransferase, 4 for adenylate transporter (brittle1-type), 3 for ADP-glucose pyrophosphorylase (AGP, not brittle2- or shrunken2-type), 3 for starch synthase (SS), 2 for starch branching enzyme, 5 for starch debranching enzyme, 11 for sucrose synthase, and 3 for sucrose-phosphate synthase. Among them, 58 unigenes showed a ≥2-fold expression difference between the 45 and 75 DAF seeds including 11 up- and 47 down-regulated unigenes. The expression of 21 unigenes putatively coding for major enzymes in starch and sucrose metabolism was validated by qPCR using RNA from five seed stages. Expression profiles and correlation analysis indicated that the mRNA levels of AGP (large and small subunits), granule-bound SS2, and soluble SS1 and SS4 were well-correlated with starch accumulation in the seeds. This study suggests that the starch biosynthesis pathway in Chinese chestnut is similar to that of potato tuber/Arabidopsis leaf and differs from that of maize endosperm. The information provides valuable metabolite and genetic resources

  3. International Ultraviolet Explorer Final Archive

    NASA Technical Reports Server (NTRS)

    1997-01-01

    CSC processed IUE images through the Final Archive Data Processing System. Raw images were obtained from both NDADS and the IUEGTC optical disk platters for processing on the Alpha cluster, and from the IUEGTC optical disk platters for DECstation processing. Input parameters were obtained from the IUE database. Backup tapes of data to send to VILSPA were routinely made on the Alpha cluster. IPC handled more than 263 requests for priority NEWSIPS processing during the contract. Staff members also answered various questions and requests for information and sent copies of IUE documents to requesters. CSC implemented new processing capabilities into the NEWSIPS processing systems as they became available. In addition, steps were taken to improve efficiency and throughput whenever possible. The node TORTE was reconfigured as the I/O server for Alpha processing in May. The number of Alpha nodes used for the NEWSIPS processing queue was increased to a maximum of six in measured fashion in order to understand the dependence of throughput on the number of nodes and to be able to recognize when a point of diminishing returns was reached. With Project approval, generation of the VD FITS files was dropped in July. This action not only saved processing time but, even more significantly, also reduced the archive storage media requirements, and the time required to perform the archiving, drastically. The throughput of images verified through CDIVS and processed through NEWSIPS for the contract period is summarized below. The number of images of a given dispersion type and camera that were processed in any given month reflects several factors, including the availability of the required NEWSIPS software system, the availability of the corresponding required calibrations (e.g., the LWR high-dispersion ripple correction and absolute calibration), and the occurrence of reprocessing efforts such as that conducted to incorporate the updated SWP sensitivity-degradation correction in May.

  4. Inverse Cerenkov experiment. Final report

    SciTech Connect

    Kimura, W.D.

    1993-09-30

    The final report describes work performed to investigate inverse Cherenkov acceleration (ICA) as a promising method for laser particle acceleration. In particular, an improved configuration of ICA is being tested in a experiment presently underway on the Accelerator Test Facility (ATF). In the experiment, the high peak power ({approximately} 10 GW) linearly polarized ATF CO{sub 2} laser beam is converted to a radially polarized beam. This is beam is focused with an axicon at the Cherenkov angle onto the ATF 50-MeV e-beam inside a hydrogen gas cell, where the gas acts as the phase matching medium of the interaction. An energy gain of {approximately}12 MeV is predicted assuming a delivered laser peak power of 5 GW. The experiment is divided into two phases. The Phase I experiments, which were completed in the spring of 1992, were conducted before the ATF e-beam was available and involved several successful tests of the optical systems. Phase II experiments are with the e-beam and laser beam, and are still in progress. The ATF demonstrated delivery of the e-beam to the experiment in Dec. 1992. A preliminary ``debugging`` run with the e-beam and laser beam occurred in May 1993. This revealed the need for some experimental modifications, which have been implemented. The second run is tentatively scheduled for October or November 1993. In parallel to the experimental efforts has been ongoing theoretical work to support the experiment and investigate improvement and/or offshoots. One exciting offshoot has been theoretical work showing that free-space laser acceleration of electrons is possible using a radially-polarized, axicon-focused laser beam, but without any phase-matching gas. The Monte Carlo code used to model the ICA process has been upgraded and expanded to handle different types of laser beam input profiles.

  5. The LSST Dome final design

    NASA Astrophysics Data System (ADS)

    DeVries, J.; Neill, D. R.; Barr, J.; De Lorenzi, Simone; Marchiori, Gianpietro

    2016-07-01

    The Large Synoptic Survey Telescope (LSST) is a large (8.4 meter) wide-field (3.5 degree) survey telescope, which will be located on the Cerro Pachón summit in Chile 1. As a result of the Telescope wide field of view, the optical system is unusually susceptible to stray light 2. In addition, balancing the effect of wind induced telescope vibrations with Dome seeing is crucial. The rotating enclosure system (Dome) includes a moving wind screen and light baffle system. All of the Dome vents include hinged light baffles, which provide exceptional Dome flushing, stray light attenuation, and allows for vent maintenance access from inside the Dome. The wind screen also functions as a light screen, and helps define a clear optical aperture for the Telescope. The Dome must operate continuously without rotational travel limits to accommodate the Telescope cadence and travel. Consequently, the Azimuth drives are located on the fixed lower enclosure to accommodate glycol water cooling without the need for a utility cable wrap. An air duct system aligns when the Dome is in its parked position, and this provides air cooling for temperature conditioning of the Dome during the daytime. A bridge crane and a series of ladders, stairs and platforms provide for the inspection, maintenance and repair of all of the Dome mechanical systems. The contract to build the Dome was awarded to European Industrial Engineering in Mestre, Italy in May 2015. In this paper, we present the final design of this telescope and site sub-system.

  6. Oklahoma seismic network. Final report

    SciTech Connect

    Luza, K.V.; Lawson, J.E. Jr. |

    1993-07-01

    The US Nuclear Regulatory Commission has established rigorous guidelines that must be adhered to before a permit to construct a nuclear-power plant is granted to an applicant. Local as well as regional seismicity and structural relationships play an integral role in the final design criteria for nuclear power plants. The existing historical record of seismicity is inadequate in a number of areas of the Midcontinent region because of the lack of instrumentation and (or) the sensitivity of the instruments deployed to monitor earthquake events. The Nemaha Uplift/Midcontinent Geophysical Anomaly is one of five principal areas east of the Rocky Mountain front that has a moderately high seismic-risk classification. The Nemaha uplift, which is common to the states of Oklahoma, Kansas, and Nebraska, is approximately 415 miles long and 12-14 miles wide. The Midcontinent Geophysical Anomaly extends southward from Minnesota across Iowa and the southeastern corner of Nebraska and probably terminates in central Kansas. A number of moderate-sized earthquakes--magnitude 5 or greater--have occurred along or west of the Nemaha uplift. The Oklahoma Geological Survey, in cooperation with the geological surveys of Kansas, Nebraska, and Iowa, conducted a 5-year investigation of the seismicity and tectonic relationships of the Nemaha uplift and associated geologic features in the Midcontinent. This investigation was intended to provide data to be used to design nuclear-power plants. However, the information is also being used to design better large-scale structures, such as dams and high-use buildings, and to provide the necessary data to evaluate earthquake-insurance rates in the Midcontinent.

  7. Application of multidisciplinary analysis to gene expression.

    SciTech Connect

    Wang, Xuefel; Kang, Huining; Fields, Chris; Cowie, Jim R.; Davidson, George S.; Haaland, David Michael; Sibirtsev, Valeriy; Mosquera-Caro, Monica P.; Xu, Yuexian; Martin, Shawn Bryan; Helman, Paul; Andries, Erik; Ar, Kerem; Potter, Jeffrey; Willman, Cheryl L.; Murphy, Maurice H.

    2004-01-01

    Molecular analysis of cancer, at the genomic level, could lead to individualized patient diagnostics and treatments. The developments to follow will signal a significant paradigm shift in the clinical management of human cancer. Despite our initial hopes, however, it seems that simple analysis of microarray data cannot elucidate clinically significant gene functions and mechanisms. Extracting biological information from microarray data requires a complicated path involving multidisciplinary teams of biomedical researchers, computer scientists, mathematicians, statisticians, and computational linguists. The integration of the diverse outputs of each team is the limiting factor in the progress to discover candidate genes and pathways associated with the molecular biology of cancer. Specifically, one must deal with sets of significant genes identified by each method and extract whatever useful information may be found by comparing these different gene lists. Here we present our experience with such comparisons, and share methods developed in the analysis of an infant leukemia cohort studied on Affymetrix HG-U95A arrays. In particular, spatial gene clustering, hyper-dimensional projections, and computational linguistics were used to compare different gene lists. In spatial gene clustering, different gene lists are grouped together and visualized on a three-dimensional expression map, where genes with similar expressions are co-located. In another approach, projections from gene expression space onto a sphere clarify how groups of genes can jointly have more predictive power than groups of individually selected genes. Finally, online literature is automatically rearranged to present information about genes common to multiple groups, or to contrast the differences between the lists. The combination of these methods has improved our understanding of infant leukemia. While the complicated reality of the biology dashed our initial, optimistic hopes for simple answers from

  8. Compare Gene Profiles

    SciTech Connect

    2014-05-31

    Compare Gene Profiles (CGP) performs pairwise gene content comparisons among a relatively large set of related bacterial genomes. CGP performs pairwise BLAST among gene calls from a set of input genome and associated annotation files, and combines the results to generate lists of common genes, unique genes, homologs, and genes from each genome that differ substantially in length from corresponding genes in the other genomes. CGP is implemented in Python and runs in a Linux environment in serial or parallel mode.

  9. Recent advances in fetal gene therapy.

    PubMed

    Buckley, Suzanne M K; Rahim, Ahad A; Chan, Jerry K Y; David, Anna L; Peebles, Donald M; Coutelle, Charles; Waddingtont, Simon N

    2011-04-01

    Over the first decade of this new millennium gene therapy has demonstrated clear clinical benefits in several diseases for which conventional medicine offers no treatment. Clinical trials of gene therapy for single gene disorders have recruited predominantly young patients since older subjects may have suffered irrevocablepathological changes or may not be available because the disease is lethal relatively early in life. The concept of fetal gene therapy is an extension of this principle in that diseases in which irreversible changes occur at or beforebirth can be prevented by gene supplementation or repair in the fetus or associated maternal tissues. This article ccnsiders the enthusiasm and skepticism held for fetal gene therapy and its potential for clinical application. It coversa spectrum of candidate diseases for fetal gene therapy including Pompe disease, Gaucher disease, thalassemia, congenital protein C deficiency and cystic fibrosis. It outlines successful and not-so-successful examples of fetal gene therapy in animal models. Finally the application and potential of fetal gene transfer as a fundamental research tool for developmental biology and generation of somatic transgenic animals is surveyed.

  10. A formal theory of the selfish gene.

    PubMed

    Gardner, A; Welch, J J

    2011-08-01

    Adaptation is conventionally regarded as occurring at the level of the individual organism. In contrast, the theory of the selfish gene proposes that it is more correct to view adaptation as occurring at the level of the gene. This view has received much popular attention, yet has enjoyed only limited uptake in the primary research literature. Indeed, the idea of ascribing goals and strategies to genes has been highly controversial. Here, we develop a formal theory of the selfish gene, using optimization theory to capture the analogy of 'gene as fitness-maximizing agent' in mathematical terms. We provide formal justification for this view of adaptation by deriving mathematical correspondences that translate the optimization formalism into dynamical population genetics. We show that in the context of social interactions between genes, it is the gene's inclusive fitness that provides the appropriate maximand. Hence, genic selection can drive the evolution of altruistic genes. Finally, we use the formalism to assess the various criticisms that have been levelled at the theory of the selfish gene, dispelling some and strengthening others.

  11. Final Report Package_Winnebago

    SciTech Connect

    Carolyn Stewart, Director, Red Mountain Energy Partners

    2006-10-31

    The Winnebago Tribe of Nebraska energy options study results will be used to advance the Tribe’s near term energy management objectives. The array of energy options identified allows the Tribe to select those activities that best fit its energy strategies, goals and objectives. During the course of the study, Red Mountain analyzed both energy options and energy organizational alternatives suitable for the Tribe, presented findings to the Tribal Council, and made recommendations regarding each. Work products delivered to the Tribe, and provided in the Final Report included: • A matrix of energy management options applicable to the Tribe, which provided descriptions of particular conservation, efficiency, weatherization, and demand management alternatives. The matrix also provided insight about relative costs of the alternatives, cost/benefit efficacy, ease of implementation, resources for implementing, and observations about each. • A matrix of utility service options applicable to the Tribe, describing each of the four alternatives described above. The matrix also provided insight about key benefits of each option, required resources, costs and timeframe for implementation, funding sources and analysis, and key issues for consideration. • Discussion guides prepared for each meeting between the Energy Committee and Council, and the Tribe’s contractor, Red Mountain Energy Partners, which included preliminary analysis and findings. • A Position Description for the Energy Manager position, which was reviewed by the Tribal HR Department, and used by the Tribe to develop a position posting. • A Utility Code designed for Winnebago to use in establishing its Utility Board, and, ultimately, to provide guidance for the Board’s further development. • A project summary book developed to include all key information, deliverables and utility provider data for the project. Winnebago’s growth trends and expansion plans require the Tribe to play a more active

  12. Santa Barbara Final Technical Report

    SciTech Connect

    Hacker, Angela; Hansen, Sherman; Watkins, Ashley

    2013-11-30

    This report serves as the Final Report for Santa Barbara County’s Energy Efficiency and Conservation Block Grant (EECBG) BetterBuildings Neighborhood Program (BBNP) award from the U.S. Department of Energy (DOE). This report explains how DOE BBNP funding was invested to develop robust program infrastructure designed to help property owners complete energy improvements, thereby generating substantial outcomes for the local environment and economy. It provides an overview of program development and design within the grant period, program accomplishments and challenges to date, and a plan for the future sustainability of emPower, the County’s innovative clean energy and building efficiency program. During the grant period, Santa Barbara County’s emPower program primarily targeted 32,000 owner occupied, single family, detached residential homes over 25 years old within the County. In order to help these homeowners and their contractors overcome market barriers to completing residential energy improvements, the program developed and promoted six voluntary, market-based service areas: 1) low cost residential financing (loan loss reserve with two local credit unions), 2) residential rebates, 3) local customer service, 4) expert energy advising, 5) workforce development and training, and 6) marketing, education and outreach. The main goals of the program were to lower building energy use, create jobs and develop a lasting regional building performance market. These services have generated important early outcomes and lessons after the program’s first two years in service. The DOE BBNP funding was extended through October 2014 to enable Santa Barbara County to generate continued outcomes. In fact, funding related to residential financing remains wholly available for the foreseeable future to continue offering Home Upgrade Loans to approximately 1,300 homeowners. The County’s investment of DOE BBNP funding was used to build a lasting, effective, and innovative

  13. Large Block Test Final Report

    SciTech Connect

    Lin, W

    2001-12-01

    . Sections 5 through 9 report the measurements made on the block during the preheating, heating, and cooling phases. These measurements include temperature, thermal conductivity and diffusivity, hydrological measurements (electrical resistivity, neutron logging, gas pressure, and relative humidity), geomechanics, selected chemical analyses, and microbial activity. These sections also include analyses and simulations of the block behavior. Finally, conclusions are presented in Section 10. Complete data sets were submitted during the time the test was conducted. The data tracking numbers (DTNs) of all of the data are presented in Table 1-1.

  14. Final report on SNAC 11

    SciTech Connect

    Huber, Patrick

    2013-06-26

    This report details how the $5,000 DOE grant to support the workshop titled “Sterile Neutrinos at the Crossroads” (or SNAC11) was allocated and spent. The SNAC11 workshop covered three days during which there were 28 talks, multiple discussion sessions, a poster session with 9 posters delivered, and an impromptu public lecture on the OPERA superluminal neutrino result by the former project manager of OPERA (this was the first official OPERA talk on the subject in North America). The workshop scientific agenda can be viewed at http://www.cpe.vt.edu/snac/program.html. Emerging out of the workshop discussions, was the idea to write a comprehensive white paper describing the current state of the light sterile neutrino. This effort soon became an international collaboration. The final document, titled “Light Sterile Neutrinos: A White Paper” has nearly 200 authors, is 267 pages long, and cites 730 unique references. It has been posted the preprint archive as arXiv:1204.5379 [hep-ph]. Workshop local organizing committee co-chairs, Patrick Huber and Jonathan Link, are the white paper’s head editors. The white paper’s sections and section editors are as follows: 1. Theory and Motivation (Gabriela Barenboim, Valencia and Werner Rodejohann, MPI Heidelberg) 2. Astrophysical Evidence (Kev Abazajian, UC Irvine and Yvonne Wong, Aachen) 3. Evidence from Oscillation Experiments (Joachim Kopp, FNAL and Bill Louis, LANL) 4. Global Picture (Thierry Lasserre, CEA Saclay and Thomas Schwetz, MPI Heidelberg) 5. Requirements for Future Measurements (Bonnie Fleming, Yale and Joe Formaggio, MIT) 6. Appendix: Possible Future Experiments (Patrick Huber, Virginia Tech and Jon Link, Virginia Tech) In all 56 people participated in the workshop, of these 11 were young scientists. The workshop was covered in a feature article in Science (Science, 334, (2011), 304-306.). The DOE award was spent, as budgeted, as contractual services to VT CPE, which is the unit within the University

  15. Gene and enhancer traps for gene discovery.

    PubMed

    Rojas-Pierce, Marcela; Springer, Patricia S

    2003-01-01

    Gene traps and enhancer traps provide a valuable tool for gene discovery. With this system, genes can be identified based solely on the expression pattern of an inserted reporter gene. The use of a reporter gene, such as beta-glucuoronidase (GUS), provides a very sensitive assay for the identification of tissue- and cell-type specific expression patterns. In this chapter, protocols for examining and documenting GUS reporter gene activity in individual lines are described. Methods for the amplification of sequences flanking transposant insertions and subsequent molecular and genetic characterization of individual insertions are provided.

  16. 76 FR 65746 - Notice of Availability of Joint Final Environmental Impact Statement/Final Environmental Impact...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-24

    ..., LVRWB10B3800] Notice of Availability of Joint Final Environmental Impact Statement/Final Environmental Impact... Utilities Commission (CPUC) have prepared a Final Environmental Impact Statement (EIS) and Final Environmental Impact Report (EIR) as a joint environmental analysis document for Tule Wind, LLC's Tule...

  17. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome.

    PubMed

    Zhang, Yong E; Vibranovski, Maria D; Landback, Patrick; Marais, Gabriel A B; Long, Manyuan

    2010-10-05

    Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI). These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.

  18. PRIMA-X Final Report

    SciTech Connect

    Lorenz, Daniel; Wolf, Felix

    2016-02-17

    Darmstadt) starting February 1st, 2015, the project ended at GRS on January 31st, 2015. This report reflects the work accomplished at GRS until then. The work of GRS is expected to be continued at TU Darmstadt. The first main accomplishment of GRS is the design of different thread-level aggregation techniques. We created a prototype capable of aggregating the thread-level information in performance profiles using these techniques. The next step will be the integration of the most promising techniques into the Score-P measurement system and their evaluation. The second main accomplishment is a substantial increase of Score-P’s scalability, achieved by improving the design of the system-tree representation in Score-P’s profile format. We developed a new representation and a distributed algorithm to create the scalable system tree representation. Finally, we developed a lightweight approach to MPI wait-state profiling. Former algorithms either needed piggy-backing, which can cause significant runtime overhead, or tracing, which comes with its own set of scaling challenges. Our approach works with local data only and, thus, is scalable and has very little overhead.

  19. CHK2, A Candidate Prostate Cancer Susceptibility Gene

    DTIC Science & Technology

    2005-01-01

    confirmation. One pari 2000; Bulavin et al. 2001). Recently, heterozygous o germline mutations in the CHEK2 gene have been iden- family had Hispanic ancestry...AD Award Number: DAMD17-02-1-0093 TITLE: CHK2, A Candidate Prostate Cancer Susceptibility Gene PRINCIPAL INVESTIGATOR: Wanguo Liu, Ph.D. CONTRACTING...blank) January 2005 Final (1 Jan 2002 - 31 Dec 2004) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS CHK2, A Candidate Prostate Cancer Susceptibility Gene DAMD17

  20. Superconducting quadrupoles for the SLC final focus

    SciTech Connect

    Erickson, R.; Fieguth, T.; Murray, J.J.

    1987-01-01

    The final focus system of the SLC will be upgraded by replacing the final quadrupoles with higher gradient superconducting magnets positioned closer to the interaction point. The parameters of the new system have been chosen to be compatible with the experimental detectors with a minimum of changes to other final focus components. These parameter choices are discussed along with the expected improvement in SLC performance.

  1. 78 FR 36098 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-17

    ... CONTACT: Luis Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation... 13132. Executive Order 12988, Civil Justice Reform. This final rule meets the applicable standards...

  2. 45 CFR 150.219 - Final determination.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ENFORCEMENT IN GROUP AND INDIVIDUAL INSURANCE MARKETS CMS Enforcement Processes for Determining Whether States... the State a written notice of its final determination. The notice includes the following:...

  3. 78 FR 32679 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-31

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  4. 78 FR 14316 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-05

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  5. 78 FR 36216 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-17

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  6. 78 FR 36220 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-17

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  7. 78 FR 14318 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-05

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  8. 78 FR 20337 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ... Rodriguez, Chief, Engineering Management Branch, Federal Insurance and Mitigation Administration, FEMA, 500... notification. This final notice is issued in accordance with section 110 of the Flood Disaster Protection...

  9. Identification of feature genes for smoking-related lung adenocarcinoma based on gene expression profile data

    PubMed Central

    Liu, Ying; Ni, Ran; Zhang, Hui; Miao, Lijun; Wang, Jing; Jia, Wenqing; Wang, Yuanyuan

    2016-01-01

    This study aimed to identify the genes and pathways associated with smoking-related lung adenocarcinoma. Three lung adenocarcinoma associated datasets (GSE43458, GSE10072, and GSE50081), the subjects of which included smokers and nonsmokers, were downloaded to screen the differentially expressed feature genes between smokers and nonsmokers. Based on the identified feature genes, we constructed the protein–protein interaction (PPI) network and optimized feature genes using closeness centrality (CC) algorithm. Then, the support vector machine (SVM) classification model was constructed based on the feature genes with higher CC values. Finally, pathway enrichment analysis of the feature genes was performed. A total of 213 down-regulated and 83 up-regulated differentially expressed genes were identified. In the constructed PPI network, the top ten nodes with higher degrees and CC values included ANK3, EPHA4, FGFR2, etc. The SVM classifier was constructed with 27 feature genes, which could accurately identify smokers and nonsmokers. Pathways enrichment analysis for the 27 feature genes revealed that they were significantly enriched in five pathways, including proteoglycans in cancer (EGFR, SDC4, SDC2, etc.), and Ras signaling pathway (FGFR2, PLA2G1B, EGFR, etc.). The 27 feature genes, such as EPHA4, FGFR2, and EGFR for SVM classifier construction and cancer-related pathways of Ras signaling pathway and proteoglycans in cancer may play key roles in the progression and development of smoking-related lung adenocarcinoma. PMID:27994470

  10. Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies

    PubMed Central

    Chen, Guanjie; Yuan, Ao; Zhou, Jie; Bentley, Amy R.; Adeyemo, Adebowale; Rotimi, Charles N.

    2012-01-01

    Missing heritability is still a challenge for Genome Wide Association Studies (GWAS). Gene-gene interactions may partially explain this residual genetic influence and contribute broadly to complex disease. To analyze the gene-gene interactions in case-control studies of complex disease, we propose a simple, non-parametric method that utilizes the F-statistic. This approach consists of three steps. First, we examine the joint distribution of a pair of SNPs in cases and controls separately. Second, an F-test is used to evaluate the ratio of dependence in cases to that of controls. Finally, results are adjusted for multiple tests. This method was used to evaluate gene-gene interactions that are associated with risk of Type 2 Diabetes among African Americans in the Howard University Family Study. We identified 18 gene-gene interactions (P < 0.0001). Compared with the commonly-used logistical regression method, we demonstrate that the F-ratio test is an efficient approach to measuring gene-gene interactions, especially for studies with limited sample size. PMID:22837643

  11. Drosophila X-Linked Genes Have Lower Translation Rates than Autosomal Genes.

    PubMed

    Zhang, Zhenguo; Presgraves, Daven C

    2016-02-01

    In Drosophila, X-linked and autosomal genes achieve comparable expression at the mRNA level. Whether comparable X-autosome gene expression is realized at the translational and, ultimately, the protein levels is, however, unknown. Previous studies suggest the possibility of higher translation rates for X-linked genes owing to stronger usage of preferred codons. In this study, we use public ribosome profiling data from Drosophila melanogaster to infer translation rates on the X chromosome versus the autosomes. We find that X-linked genes have consistently lower ribosome densities than autosomal genes in S2 cells, early embryos, eggs, and mature oocytes. Surprisingly, the lower ribosome densities of X-linked genes are not consistent with faster translation elongation but instead imply slower translation initiation. In particular, X-linked genes have sequence features known to slow translation initiation such as stronger mRNA structure near start codons and longer 5'-UTRs. Comparison to outgroup species suggests that stronger mRNA structure is an evolved feature of Drosophila X chromosomes. Finally, we find that the magnitude of the X-autosome difference in ribosome densities is smaller for genes encoding members of protein complexes, suggesting that stoichiometry constrains the evolution of translation rates. In sum, our analyses suggest that Drosophila X-linked genes have evolved lower translation rates than autosomal genes despite stronger usage of preferred codons.

  12. In Silico Evolution of Gene Cooption in Pattern-Forming Gene Networks

    PubMed Central

    Spirov, Alexander V.; Sabirov, Marat A.; Holloway, David M.

    2012-01-01

    Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability—a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean) approach is necessary for addressing realistic continuous variation in biochemical parameters. PMID:23365523

  13. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants.

    PubMed

    De Smet, Riet; Adams, Keith L; Vandepoele, Klaas; Van Montagu, Marc C E; Maere, Steven; Van de Peer, Yves

    2013-02-19

    The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.

  14. Final Report for Regulation of Embryonic Development in Higher Plants

    SciTech Connect

    Harada, John J.

    2013-10-22

    The overall goal of the project was to define the cellular processes that underlie embryo development in plants at a mechanistic level. Our studies focused on a critical transcriptional regulator, Arabidopsis LEAFY COTYLEDON (LEC1), that is necessary and sufficient to induce processes required for embryo development. Because LEC1 regulates lipid accumulation during the maturation phase of embryo development, information about LEC1 may be useful in designing approaches to enhance biofuel production in plants. During the tenure of this project, we determined the molecular mechanisms by which LEC1 acts as a transcription factor in embryos. We also identified genes directly regulated by LEC1 and showed that many of these genes are involved in maturation processes. This information has been useful in dissecting the gene regulatory networks controlling embryo development. Finally, LEC1 is a novel isoform of a transcription factor that is conserved among eukaryotes, and LEC1 is active primarily in seeds. Therefore, we determined that the LEC1-type transcription factors first appeared in lycophytes during land plant evolution. Together, this study provides basic information that has implications for biofuel production.

  15. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

    PubMed Central

    Huddleston, Jennifer R

    2014-01-01

    Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed. PMID:25018641

  16. A Combinatorial Approach to Detecting Gene-Gene and Gene-Environment Interactions in Family Studies

    PubMed Central

    Lou, Xiang-Yang; Chen, Guo-Bo; Yan, Lei; Ma, Jennie Z.; Mangold, Jamie E.; Zhu, Jun; Elston, Robert C.; Li, Ming D.

    2008-01-01

    Widespread multifactor interactions present a significant challenge in determining risk factors of complex diseases. Several combinatorial approaches, such as the multifactor dimensionality reduction (MDR) method, have emerged as a promising tool for better detecting gene-gene (G × G) and gene-environment (G × E) interactions. We recently developed a general combinatorial approach, namely the generalized multifactor dimensionality reduction (GMDR) method, which can entertain both qualitative and quantitative phenotypes and allows for both discrete and continuous covariates to detect G × G and G × E interactions in a sample of unrelated individuals. In this article, we report the development of an algorithm that can be used to study G × G and G × E interactions for family-based designs, called pedigree-based GMDR (PGMDR). Compared to the available method, our proposed method has several major improvements, including allowing for covariate adjustments and being applicable to arbitrary phenotypes, arbitrary pedigree structures, and arbitrary patterns of missing marker genotypes. Our Monte Carlo simulations provide evidence that the PGMDR method is superior in performance to identify epistatic loci compared to the MDR-pedigree disequilibrium test (PDT). Finally, we applied our proposed approach to a genetic data set on tobacco dependence and found a significant interaction between two taste receptor genes (i.e., TAS2R16 and TAS2R38) in affecting nicotine dependence. PMID:18834969

  17. Freshwater Biological Traits Database (Final Report)

    EPA Science Inventory

    Cover of the Freshwater Biological Traits Database <span class=Final Report"> This final report discusses the development of a database of freshwater biolo...

  18. IRIS Toxicological Review of Hexachloroethane (Final Report)

    EPA Science Inventory

    EPA has finalized the Toxicological Review of Hexachloroethane: in support of the Integrated Risk Information System (IRIS). Now final, this assessment may be used by EPA’s program and regional offices to inform decisions to protect human health.

  19. 33 CFR 20.1101 - Finality.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Finality. 20.1101 Section 20.1101 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL RULES OF PRACTICE... Hearing, and Availability of Orders § 20.1101 Finality. (a) Civil penalty proceedings. (1) Unless...

  20. Tech Prep II: Implementation Final Report.

    ERIC Educational Resources Information Center

    Brown, Jane A.

    This document contains the final progress report on a tech prep implementation project and the Work Force Challenge 2000 Report developed during the project. The final report lists these major accomplishments: approximately 1,500 educators in grades K-12 were provided information concerning future global issues in the work force and the effects in…

  1. 78 FR 14576 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-06

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include... management measures that a community is required either to adopt or to show evidence of having in effect...

  2. 77 FR 46972 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  3. 77 FR 3625 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  4. 75 FR 23608 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-04

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  5. 75 FR 5894 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  6. 75 FR 78926 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  7. 75 FR 59095 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-27

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  8. 77 FR 76929 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-31

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  9. 77 FR 74610 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  10. 75 FR 78617 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-16

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  11. 77 FR 6980 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-10

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  12. 75 FR 77762 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-14

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  13. 78 FR 33991 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-06

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  14. 77 FR 41323 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-13

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  15. 78 FR 6745 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  16. 78 FR 27 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-02

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  17. 75 FR 23600 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-04

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  18. 75 FR 23595 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-04

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  19. 75 FR 34381 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-17

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  20. 78 FR 6743 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  1. 77 FR 46980 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  2. 77 FR 6976 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-10

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  3. 78 FR 5738 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  4. 75 FR 43418 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-26

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the National Flood Insurance Program (NFIP). DATES: The date of issuance of the Flood...

  5. 19 CFR 122.85 - Final airport.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Final airport. 122.85 Section 122.85 Customs... AIR COMMERCE REGULATIONS Procedures for Residue Cargo and Stopover Passengers § 122.85 Final airport. When an aircraft enters at the last domestic airport of discharge, the traveling general...

  6. 19 CFR 122.85 - Final airport.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Final airport. 122.85 Section 122.85 Customs... AIR COMMERCE REGULATIONS Procedures for Residue Cargo and Stopover Passengers § 122.85 Final airport. When an aircraft enters at the last domestic airport of discharge, the traveling general...

  7. 22 CFR 223.10 - Final decision.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Final decision. 223.10 Section 223.10 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ADMINISTRATIVE ENFORCEMENT PROCEDURES OF POST-EMPLOYMENT RESTRICTIONS § 223.10 Final decision. (a) In cases where the former employee failed to request a hearing...

  8. 22 CFR 223.10 - Final decision.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Final decision. 223.10 Section 223.10 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ADMINISTRATIVE ENFORCEMENT PROCEDURES OF POST-EMPLOYMENT RESTRICTIONS § 223.10 Final decision. (a) In cases where the former employee failed to request a hearing...

  9. 22 CFR 223.10 - Final decision.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Final decision. 223.10 Section 223.10 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ADMINISTRATIVE ENFORCEMENT PROCEDURES OF POST-EMPLOYMENT RESTRICTIONS § 223.10 Final decision. (a) In cases where the former employee failed to request a hearing...

  10. 22 CFR 223.10 - Final decision.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Final decision. 223.10 Section 223.10 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ADMINISTRATIVE ENFORCEMENT PROCEDURES OF POST-EMPLOYMENT RESTRICTIONS § 223.10 Final decision. (a) In cases where the former employee failed to request a hearing...

  11. 22 CFR 223.10 - Final decision.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Final decision. 223.10 Section 223.10 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ADMINISTRATIVE ENFORCEMENT PROCEDURES OF POST-EMPLOYMENT RESTRICTIONS § 223.10 Final decision. (a) In cases where the former employee failed to request a hearing...

  12. 33 CFR 20.1101 - Finality.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Finality. 20.1101 Section 20.1101 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL RULES OF PRACTICE, PROCEDURE, AND EVIDENCE FOR FORMAL ADMINISTRATIVE PROCEEDINGS OF THE COAST GUARD Finality, Petitions for Hearing, and Availability of Orders §...

  13. Techniques of Final Preseal Visual Inspection

    NASA Technical Reports Server (NTRS)

    Anstead, R. J.

    1975-01-01

    A dissertation is given on the final preseal visual inspection of microcircuit devices to detect manufacturing defects and reduce failure rates in service. The processes employed in fabricating monolithic integrated circuits and hybrid microcircuits, various failure mechanisms resulting from deficiencies in those processes, and the rudiments of performing final inspection are outlined.

  14. 25 CFR 11.709 - Final account.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Final account. 11.709 Section 11.709 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Probate Proceedings § 11.709 Final account. (a) When the affairs of an estate have been fully...

  15. 25 CFR 11.709 - Final account.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Final account. 11.709 Section 11.709 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Probate Proceedings § 11.709 Final account. (a) When the affairs of an estate have been fully...

  16. 25 CFR 11.709 - Final account.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Final account. 11.709 Section 11.709 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Probate Proceedings § 11.709 Final account. (a) When the affairs of an estate have been fully...

  17. 25 CFR 11.709 - Final account.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Final account. 11.709 Section 11.709 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Probate Proceedings § 11.709 Final account. (a) When the affairs of an estate have been fully...

  18. 25 CFR 11.709 - Final account.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Final account. 11.709 Section 11.709 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Probate Proceedings § 11.709 Final account. (a) When the affairs of an estate have been fully...

  19. 75 FR 29915 - Direct Final Rulemaking Procedures

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-28

    ... specified number of days after the date of publication in the Federal Register, unless FMCSA receives... proposed and final rules. FMCSA will not use the direct final rule procedures for complex or controversial...://www.regulations.gov by searching Docket ID number FMCSA 2009-0354 at any time or to the ground...

  20. 43 CFR 4.1275 - Final decisions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Final decisions. 4.1275 Section 4.1275 Public Lands: Interior Office of the Secretary of the Interior DEPARTMENT HEARINGS AND APPEALS PROCEDURES... Or Orders of Administrative Law Judges § 4.1275 Final decisions. The Board may adopt, affirm,...

  1. 77 FR 49367 - Final Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-16

    ... SECURITY Federal Emergency Management Agency 44 CFR Part 67 Final Flood Elevation Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final rule. SUMMARY: Base (1% annual-chance) Flood... participation in the ] National Flood Insurance Program (NFIP). DATES: The date of issuance of the...

  2. IRIS Toxicological Review of Trimethylbenzenes (Final Report)

    EPA Science Inventory

    EPA has finalized the Integrated Risk Information System (IRIS) Assessment of Trimethylbenzenes (TMBs). This assessment addresses the potential non-cancer and cancer human health effects from long-term exposure to TMBs. Now final, this assessment will be the first IRIS a...

  3. 78 FR 43905 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-22

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include... management measures that a community is required either to adopt or to show evidence of having in effect...

  4. 78 FR 43904 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-22

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final notice. SUMMARY: Flood hazard determinations, which may include... management measures ] that a community is required either to adopt or to show evidence of having in effect...

  5. 78 FR 43904 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-22

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include... management measures that a community is required either to adopt or to show evidence of having in effect...

  6. 78 FR 29763 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-21

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final Notice. SUMMARY: Flood hazard determinations, which may include... management measures that a community is required either to adopt or to show evidence of having in effect...

  7. 78 FR 45938 - Final Flood Hazard Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-30

    ... SECURITY Federal Emergency Management Agency Final Flood Hazard Determinations AGENCY: Federal Emergency Management Agency, DHS. ACTION: Final notice. SUMMARY: Flood hazard determinations, which may include... management measures that a community is required either to adopt or to show evidence of having in effect...

  8. 49 CFR 106.30 - Final rule.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Final rule. 106.30 Section 106.30 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION... effective date. A final rule will also identify issues raised by commenters in response to the notice...

  9. 49 CFR 106.30 - Final rule.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 2 2013-10-01 2013-10-01 false Final rule. 106.30 Section 106.30 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION... effective date. A final rule will also identify issues raised by commenters in response to the notice...

  10. 49 CFR 106.30 - Final rule.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 2 2012-10-01 2012-10-01 false Final rule. 106.30 Section 106.30 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION... effective date. A final rule will also identify issues raised by commenters in response to the notice...

  11. 49 CFR 106.30 - Final rule.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 2 2014-10-01 2014-10-01 false Final rule. 106.30 Section 106.30 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION... effective date. A final rule will also identify issues raised by commenters in response to the notice...

  12. 49 CFR 106.30 - Final rule.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 2 2011-10-01 2011-10-01 false Final rule. 106.30 Section 106.30 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION... effective date. A final rule will also identify issues raised by commenters in response to the notice...

  13. IRIS Toxicological Review of Pentachlorophenol (Final Report)

    EPA Science Inventory

    EPA has finalized the Toxicological Review of Pentachlorophenol: in support of the Integrated Risk Information System (IRIS). Now final, this assessment may be used by EPA’s program and regional offices to inform decisions to protect human health.

  14. 21 CFR 1303.37 - Final order.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 9 2012-04-01 2012-04-01 false Final order. 1303.37 Section 1303.37 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE QUOTAS Hearings § 1303.37 Final order. As... the order is based. The order shall specify the date on which it shall take effect. The...

  15. 21 CFR 1303.37 - Final order.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Final order. 1303.37 Section 1303.37 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE QUOTAS Hearings § 1303.37 Final order. As... the order is based. The order shall specify the date on which it shall take effect. The...

  16. EPA Finalizes Increases in Renewable Fuel Levels

    EPA Pesticide Factsheets

    (12/01/2015 - ATLANTA) - The U.S. Environmental Protection Agency (EPA) announced final volume requirements under the Renewable Fuel Standard (RFS) program today for the years 2014, 2015 and 2016, and final volume requirements for biomass-based dies

  17. 50 CFR 296.11 - Final determination.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Final determination. 296.11 Section 296.11 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE CONTINENTAL SHELF FISHERMEN'S CONTINGENCY FUND § 296.11 Final determination. (a) If...

  18. IRIS Toxicological Review of Biphenyl (Final Report)

    EPA Science Inventory

    EEPA has finalized the Toxicological Review of Biphenyl: in support of the Integrated Risk Information System (IRIS). Now final, this assessment may be used by EPA’s program and regional offices to inform decisions to protect human health.

  19. 21 CFR 1315.62 - Final order.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 9 2013-04-01 2013-04-01 false Final order. 1315.62 Section 1315.62 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE IMPORTATION AND PRODUCTION QUOTAS FOR EPHEDRINE, PSEUDOEPHEDRINE, AND PHENYLPROPANOLAMINE Hearings § 1315.62 Final order. As soon as...

  20. 21 CFR 1315.62 - Final order.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 9 2014-04-01 2014-04-01 false Final order. 1315.62 Section 1315.62 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE IMPORTATION AND PRODUCTION QUOTAS FOR EPHEDRINE, PSEUDOEPHEDRINE, AND PHENYLPROPANOLAMINE Hearings § 1315.62 Final order. As soon as...

  1. 21 CFR 1315.62 - Final order.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 9 2011-04-01 2011-04-01 false Final order. 1315.62 Section 1315.62 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE IMPORTATION AND PRODUCTION QUOTAS FOR EPHEDRINE, PSEUDOEPHEDRINE, AND PHENYLPROPANOLAMINE Hearings § 1315.62 Final order. As soon as...

  2. 11 CFR 9409.9 - Final determination.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 11 Federal Elections 1 2011-01-01 2011-01-01 false Final determination. 9409.9 Section 9409.9 Federal Elections ELECTION ASSISTANCE COMMISSION TESTIMONY BY COMMISSION EMPLOYEES RELATING TO OFFICIAL INFORMATION AND PRODUCTION OF OFFICIAL RECORDS IN LEGAL PROCEEDINGS § 9409.9 Final determination. The...

  3. 11 CFR 9409.9 - Final determination.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 11 Federal Elections 1 2010-01-01 2010-01-01 false Final determination. 9409.9 Section 9409.9 Federal Elections ELECTION ASSISTANCE COMMISSION TESTIMONY BY COMMISSION EMPLOYEES RELATING TO OFFICIAL INFORMATION AND PRODUCTION OF OFFICIAL RECORDS IN LEGAL PROCEEDINGS § 9409.9 Final determination. The...

  4. 11 CFR 9409.9 - Final determination.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 11 Federal Elections 1 2012-01-01 2012-01-01 false Final determination. 9409.9 Section 9409.9 Federal Elections ELECTION ASSISTANCE COMMISSION TESTIMONY BY COMMISSION EMPLOYEES RELATING TO OFFICIAL INFORMATION AND PRODUCTION OF OFFICIAL RECORDS IN LEGAL PROCEEDINGS § 9409.9 Final determination. The...

  5. 11 CFR 9409.9 - Final determination.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 11 Federal Elections 1 2013-01-01 2012-01-01 true Final determination. 9409.9 Section 9409.9 Federal Elections ELECTION ASSISTANCE COMMISSION TESTIMONY BY COMMISSION EMPLOYEES RELATING TO OFFICIAL INFORMATION AND PRODUCTION OF OFFICIAL RECORDS IN LEGAL PROCEEDINGS § 9409.9 Final determination. The...

  6. 11 CFR 9409.9 - Final determination.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 11 Federal Elections 1 2014-01-01 2014-01-01 false Final determination. 9409.9 Section 9409.9 Federal Elections ELECTION ASSISTANCE COMMISSION TESTIMONY BY COMMISSION EMPLOYEES RELATING TO OFFICIAL INFORMATION AND PRODUCTION OF OFFICIAL RECORDS IN LEGAL PROCEEDINGS § 9409.9 Final determination. The...

  7. 24 CFR 2004.25 - Final determination.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... IN RESPONSE TO SUBPOENAS OR DEMANDS OF COURTS OR OTHER AUTHORITIES Requests for Testimony and Production of Documents § 2004.25 Final determination. The Counsel makes the final determination on demands... determination, the reasons for the grant or denial of the demand or request, and any conditions that the...

  8. 32 CFR 989.20 - Final EIS.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ENVIRONMENTAL IMPACT ANALYSIS PROCESS (EIAP) § 989.20 Final EIS. (a) If changes in the draft EIS are minor or... analysis is required. (b) The EPF processes all necessary supplements to EISs (40 CFR 1502.9) in the same way as the original Draft and Final EIS, except that a new scoping process is not required. (c)...

  9. Gene doping: gene delivery for olympic victory.

    PubMed

    Gould, David

    2013-08-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place.

  10. Autism spectrum disorders: from genes to neurobiology.

    PubMed

    Willsey, A Jeremy; State, Matthew W

    2015-02-01

    Advances in genome-wide technology, coupled with the availability of large cohorts, are finally yielding a steady stream of autism spectrum disorder (ASD) genes carrying mutations of large effect. These findings represent important molecular clues, but at the same time present notable challenges to traditional strategies for moving from genes to neurobiology. A remarkable degree of genetic heterogeneity, the biological pleiotropy of ASD genes, and the tremendous complexity of the human brain are prompting the development of new strategies for translating genetic discoveries into therapeutic targets. Recent developments in systems biology approaches that 'contextualize' these genetic findings along spatial, temporal, and cellular axes of human brain development are beginning to bridge the gap between high-throughput gene discovery and testable pathophysiological hypotheses.

  11. Cloning and Sequencing the First HLA Gene

    PubMed Central

    Jordan, Bertrand R.

    2010-01-01

    This Perspectives article recounts the isolation and sequencing of the first human histocompatibility gene (HLA) in 1980–1981. At the time, general knowledge of the molecules of the immune system was already fairly extensive, and gene rearrangements in the immunoglobulin complex (discovered in 1976) had generated much excitement: HLA was quite obviously the next frontier. The author was able to use a homologous murine H-2 cDNA to identify putative human HLA genomic clones in a λ-phage library and thus to isolate and sequence the first human histocompatibility gene. This personal account relates the steps that led to this result, describes the highly competitive international environment, and highlights the role of location, connections, and sheer luck in such an achievement. It also puts this work in perspective with a short description of the current knowledge of histocompatibility genes and, finally, presents some reflections on the meaning of “discovery.” PMID:20457890

  12. Functional and phylogenetic analysis of the Aspergillus ochraceoroseus aflQ (ordA) gene ortholog

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Within the Aspergillus parasiticus and A. flavus aflatoxin (AF) biosynthetic gene cluster the aflQ (ordA) and aflP (omtA) genes encode an oxidoreductase and methyltransferase, respectively. These genes are required for the final steps in the conversion of sterigmatocystin (ST) to aflatoxin B1 (AFB1...

  13. Accelerated evolution of morph-biased genes in pea aphids.

    PubMed

    Purandare, Swapna R; Bickel, Ryan D; Jaquiery, Julie; Rispe, Claude; Brisson, Jennifer A

    2014-08-01

    Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors, results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed selection, the consequence of which is the buildup of slightly deleterious mutations at these genes. Over time, this is expected to result in increased protein divergence at these genes between species and a signature of relaxed purifying selection within species. Here we test these theoretical expectations using morph-biased genes in the pea aphid, a species that produces multiple morphs via polyphenism. We find that morph-biased genes exhibit faster rates of evolution (in terms of dN/dS) relative to unbiased genes and that divergence generally increases with increasing morph bias. Further, genes with expression biased toward rarer morphs (sexual females and males) show faster rates of evolution than genes expressed in the more common morph (asexual females), demonstrating that the amount of time a gene spends being expressed in a morph is associated with its rate of evolution. And finally, we show that genes expressed in the rarer morphs experience decreased purifying selection relative to unbiased genes, suggesting that it is a relaxation of purifying selection that contributes to their faster rates of evolution. Our results provide an important empirical look at the impact of phenotypic plasticity on gene evolution.

  14. Accelerated Evolution of Morph-Biased Genes in Pea Aphids

    PubMed Central

    Purandare, Swapna R.; Bickel, Ryan D.; Jaquiery, Julie; Rispe, Claude; Brisson, Jennifer A.

    2014-01-01

    Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors, results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed selection, the consequence of which is the buildup of slightly deleterious mutations at these genes. Over time, this is expected to result in increased protein divergence at these genes between species and a signature of relaxed purifying selection within species. Here we test these theoretical expectations using morph-biased genes in the pea aphid, a species that produces multiple morphs via polyphenism. We find that morph-biased genes exhibit faster rates of evolution (in terms of dN/dS) relative to unbiased genes and that divergence generally increases with increasing morph bias. Further, genes with expression biased toward rarer morphs (sexual females and males) show faster rates of evolution than genes expressed in the more common morph (asexual females), demonstrating that the amount of time a gene spends being expressed in a morph is associated with its rate of evolution. And finally, we show that genes expressed in the rarer morphs experience decreased purifying selection relative to unbiased genes, suggesting that it is a relaxation of purifying selection that contributes to their faster rates of evolution. Our results provide an important empirical look at the impact of phenotypic plasticity on gene evolution. PMID:24770714

  15. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke...

  16. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke...

  17. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke...

  18. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke...

  19. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke...

  20. 78 FR 14111 - Final Candidate Conservation Agreement With Assurances, Final Environmental Assessment, and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-04

    ... Fish and Wildlife Service Final Candidate Conservation Agreement With Assurances, Final Environmental... Environmental Policy Act of 1969 (NEPA). The Oklahoma Department of Wildlife Conservation (ODWC) applied for an... conservation (e.g., prescribed burning, prescribed grazing, upland wildlife habitat management,...

  1. Efficient exploration of the space of reconciled gene trees.

    PubMed

    Szöllõsi, Gergely J; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

    2013-11-01

    Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source

  2. Mechanisms and dynamics of orphan gene emergence in insect genomes.

    PubMed

    Wissler, Lothar; Gadau, Jürgen; Simola, Daniel F; Helmkampf, Martin; Bornberg-Bauer, Erich

    2013-01-01

    Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome. Several case studies demonstrated that orphans can contribute to lineage-specific adaptation. Here, we study orphan genes by comparing 30 arthropod genomes, focusing in particular on seven recently sequenced ant genomes. This setup allows analyzing a major metazoan taxon and a comparison between social Hymenoptera (ants and bees) and nonsocial Diptera (flies and mosquitoes). First, we find that recently split lineages undergo accelerated genomic reorganization, including the rapid gain of many orphan genes. Second, between the two insect orders Hymenoptera and Diptera, orphan genes are more abundant and emerge more rapidly in Hymenoptera, in particular, in leaf-cutter ants. With respect to intragenomic localization, we find that ant orphan genes show little clustering, which suggests that orphan genes in ants are scattered uniformly over the genome and between nonorphan genes. Finally, our results indicate that the genetic mechanisms creating orphan genes-such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements-act at different rates in insects, primates, and plants. In Formicidae, the majority of orphan genes has their origin in intergenic regions, pointing to a high rate of de novo gene formation or generalized gene loss, and support a recently proposed dynamic model of frequent gene birth and death.

  3. Autism and Genes

    ERIC Educational Resources Information Center

    National Institutes of Health, 2005

    2005-01-01

    This document defines and discusses autism and how genes play a role in the condition. Answers to the following questions are covered: (1) What are genes? (2) What is autism? (3) What causes autism? (4) Why study genes to learn about autism? (5) How do researchers look for the genes involved in autism? (screen the whole genome; conduct cytogenetic…

  4. Compare Gene Calls

    SciTech Connect

    Ecale Zhou, Carol L.

    2016-07-05

    Compare Gene Calls (CGC) is a Python code used for combining and comparing gene calls from any number of gene callers. A gene caller is a computer program that predicts the extends of open reading frames within genomes of biological organisms.

  5. Oligomerization, membrane association and in vivo phosphorylation of sugarcane UDP-glucose pyrophosphorylase

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane is a C4 plant that accumulates sucrose to levels of up to 50% of dry weight in the stalk. The mechanisms involved in sucrose accumulation in sugarcane are not well understood and little is known with regard to factors that control the extent of sucrose storage in stalks. UDP-glucose pyroph...

  6. A comparative analysis of soft computing techniques for gene prediction.

    PubMed

    Goel, Neelam; Singh, Shailendra; Aseri, Trilok Chand

    2013-07-01

    The rapid growth of genomic sequence data for both human and nonhuman species has made analyzing these sequences, especially predicting genes in them, very important and is currently the focus of many research efforts. Beside its scientific interest in the molecular biology and genomics community, gene prediction is of considerable importance in human health and medicine. A variety of gene prediction techniques have been developed for eukaryotes over the past few years. This article reviews and analyzes the application of certain soft computing techniques in gene prediction. First, the problem of gene prediction and its challenges are described. These are followed by different soft computing techniques along with their application to gene prediction. In addition, a comparative analysis of different soft computing techniques for gene prediction is given. Finally some limitations of the current research activities and future research directions are provided.

  7. Single-nucleotide polymorphism-gene intermixed networking reveals co-linkers connected to multiple gene expression phenotypes

    PubMed Central

    Gong, Bin-Sheng; Zhang, Qing-Pu; Zhang, Guang-Mei; Zhang, Shao-Jun; Zhang, Wei; Lv, Hong-Chao; Zhang, Fan; Lv, Sa-Li; Li, Chuan-Xing; Rao, Shao-Qi; Li, Xia

    2007-01-01

    Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by some genetical genomics approaches. In this study, gene expression profiles were used as expression traits. And relationships among the genes, which were co-linked to a common SNP(s), were identified by integrating the two types of information. Further research on the co-expressions among the co-linked genes was carried out after the gene-SNP relationships were established using the Haseman-Elston sib-pair regression. The results showed that the co-expressions among the co-linked genes were significantly higher if the number of connections between the genes and a SNP(s) was more than six. Then, the genes were interconnected via one or more SNP co-linkers to construct a gene-SNP intermixed network. The genes sharing more SNPs tended to have a stronger correlation. Finally, a gene-gene network was constructed with their intensities of relationships (the number of SNP co-linkers shared) as the weights for the edges. PMID:18466544

  8. Gene Therapy and Gene Editing for the Corneal Dystrophies.

    PubMed

    Williams, Keryn A; Irani, Yazad D

    2016-01-01

    Despite ever-increasing understanding of the genetic underpinnings of many corneal dystrophies, gene therapy designed to ameliorate disease has not yet been reported in any human patient. In this review, we explore the likely reasons for this apparent failure of translation. We identify the requirements for success: the genetic defect involved must have been identified and mapped, vision in the affected patient must be significantly impaired or likely to be impaired, no better or equivalently effective treatment must be available, the treatment must be capable of modulating corneal pathology, and delivery of the construct to the appropriate cell must be practicable. We consider which of the corneal dystrophies might be amenable to treatment by genetic manipulations, summarize existing therapeutic options for treatment, and explore gene editing using clustered regularly interspaced short palindromic repeat/Cas and other similar transformative technologies as the way of the future. We then summarize recent laboratory-based advances in gene delivery and the development of in vitro and in vivo models of the corneal dystrophies. Finally, we review recent experimental work that has increased our knowledge of the pathobiology of these conditions.

  9. Inferring gene regression networks with model trees

    PubMed Central

    2010-01-01

    Background Novel strategies are required in order to handle the huge amount of data produced by microarray technologies. To infer gene regulatory networks, the first step is to find direct regulatory relationships between genes building the so-called gene co-expression networks. They are typically generated using correlation statistics as pairwise similarity measures. Correlation-based methods are very useful in order to determine whether two genes have a strong global similarity but do not detect local similarities. Results We propose model trees as a method to identify gene interaction networks. While correlation-based methods analyze each pair of genes, in our approach we generate a single regression tree for each gene from the remaining genes. Finally, a graph from all the relationships among output and input genes is built taking into account whether the pair of genes is statistically significant. For this reason we apply a statistical procedure to control the false discovery rate. The performance of our approach, named REGNET, is experimentally tested on two well-known data sets: Saccharomyces Cerevisiae and E.coli data set. First, the biological coherence of the results are tested. Second the E.coli transcriptional network (in the Regulon database) is used as control to compare the results to that of a correlation-based method. This experiment shows that REGNET performs more accurately at detecting true gene associations than the Pearson and Spearman zeroth and first-order correlation-based methods. Conclusions REGNET generates gene association networks from gene expression data, and differs from correlation-based methods in that the relationship between one gene and others is calculated simultaneously. Model trees are very useful techniques to estimate the numerical values for the target genes by linear regression functions. They are very often more precise than linear regression models because they can add just different linear regressions to separate

  10. Genetics in methylotrophic bacteria: Appendix. Final report

    SciTech Connect

    Lidstrom, M.E.

    1998-09-01

    This research has focused primarily on promoters in Methylobacterium extorquens AM1 and in methanotrophic bacteria. In Methylobacterium extorquens work continued on the moxF promoter. The author constructed chromosomal lacZ fusions of this promoter to avoid the regulation problems of plasmid-borne fragments and has shown that this is regulated normally in the chromosome. She has constructed lacZ fusions to some of the mox genes involved in the synthesis of the cofactor, PQQ, in order to carry out similar analysis of transcription of PQQ genes. The author has continued to isolate mox genes in methanotrophs for the purpose of studying their promoters and transcriptional regulation.

  11. Epilepsy-associated genes.

    PubMed

    Wang, Jie; Lin, Zhi-Jian; Liu, Liu; Xu, Hai-Qing; Shi, Yi-Wu; Yi, Yong-Hong; He, Na; Liao, Wei-Ping

    2017-01-01

    Development in genetic technology has led to the identification of an increasing number of genes associated with epilepsy. These discoveries will both provide the basis for including genetic tests in clinical practice and improve diagnosis and treatment of epilepsy. By searching through several databases (OMIM, HGMD, and EpilepsyGene) and recent publications on PubMed, we found 977 genes that are associated with epilepsy. We classified these genes into 4 categories according to the manifestation of epilepsy in phenotypes. We found 84 genes that are considered as epilepsy genes: genes that cause epilepsies or syndromes with epilepsy as the core symptom. 73 genes were listed as neurodevelopment-associated genes: genes associated with both brain-development malformations and epilepsy. Several genes (536) were epilepsy-related: genes associated with both physical or other systemic abnormalities and epilepsy or seizures. We found 284 additional genes putatively associated with epilepsy; this requires further verification. These integrated data will provide new insights useful for both including genetic tests in the clinical practice and evaluating the results of genetic tests. We also summarized the epilepsy-associated genes according to their function, with the goal to better characterize the association between genes and epilepsies and to further understand the mechanisms underlying epilepsy.

  12. ETS fusion genes in prostate cancer.

    PubMed

    Gasi Tandefelt, Delila; Boormans, Joost; Hermans, Karin; Trapman, Jan

    2014-06-01

    Prostate cancer is very common in elderly men in developed countries. Unravelling the molecular and biological processes that contribute to tumor development and progressive growth, including its heterogeneity, is a challenging task. The fusion of the genes ERG and TMPRSS2 is the most frequent genomic alteration in prostate cancer. ERG is an oncogene that encodes a member of the family of ETS transcription factors. At lower frequency, other members of this gene family are also rearranged and overexpressed in prostate cancer. TMPRSS2 is an androgen-regulated gene that is preferentially expressed in the prostate. Most of the less frequent ETS fusion partners are also androgen-regulated and prostate-specific. During the last few years, novel concepts of the process of gene fusion have emerged, and initial experimental results explaining the function of the ETS genes ERG and ETV1 in prostate cancer have been published. In this review, we focus on the most relevant ETS gene fusions and summarize the current knowledge of the role of ETS transcription factors in prostate cancer. Finally, we discuss the clinical relevance of TMRPSS2-ERG and other ETS gene fusions in prostate cancer.

  13. Missing gene identification using functional coherence scores

    PubMed Central

    Chitale, Meghana; Khan, Ishita K.; Kihara, Daisuke

    2016-01-01

    Reconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile, and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional coherence of proteins. We showed that adding CAS and PAS substantially improve the accuracy of identifying missing genes in the yeast enzyme-enzyme network compared to the cases when only the conventional features, gene expression, phylogenetic profile, were used. Finally, it was also demonstrated that the accuracy improves by considering indirect neighbors to the target enzyme position in the network using a proper network-topology-based weighting scheme. PMID:27552989

  14. Metabolic engineering of Pichia pastoris for production of hyaluronic acid with high molecular weight.

    PubMed

    Jeong, Euijoon; Shim, Woo Yong; Kim, Jung Hoe

    2014-09-20

    The high molecular weight (>1 MDa) of hyaluronic acid (HA) is important for its biological functions. The reported limiting factors for the production of HA with high molecular weight (MW) by microbial fermentation are the insufficient HA precursor pool and cell growth inhibition. To overcome these issues, the Xenopus laevis xhasA2 and xhasB genes encoding hyaluronan synthase 2 (xhasA2) and UDP-glucose dehydrogenase (xhasB), were expressed in Pichia pastoris widely used for production of heterologous proteins. In this study, expression vectors containing various combination cassettes of HA pathway genes including xhasA2 and xhasB from X. laevis as well as UDP-glucose pyrophosphorylase (hasC), UDP-N-acetylglucosamine pyrophosphorylase (hasD) and phosphoglucose isomerase (hasE) from P. pastoris were constructed and tested. First, HA pathway genes were overexpressed using pAO815 and pGAPZB vectors, resulting in the production of 1.2 MDa HA polymers. Second, in order to decrease hyaluronan synthase expression a strong AOX1 promoter in the xhasA2 gene was replaced by a weak AOX2 promoter which increased the mean MW of HA to 2.1 MDa. Finally, the MW of HA polymer was further increased to 2.5 MDa by low-temperature cultivation (26 °C) which reduced cell growth inhibition. The yield of HA production by the P. pastoris recombinant strains in 1L of fermentation culture was 0.8-1.7 g/L.

  15. Is cancer gene therapy an empty suit?

    PubMed Central

    Brenner, Malcolm K; Gottschalk, Stephen; Leen, Ann M; Vera, Juan F

    2014-01-01

    Gene therapy as a treatment for cancer is regarded as high in promise, but low in delivery, a deficiency that has become more obvious with ever-increasing reports of the successful correction of monogenic disorders by this approach. We review the commercial and scientific obstacles that have led to these delays and describe how they are progressively being overcome. Recent and striking successes and correspondingly increased commercial involvement suggest that gene transfer could finally become a powerful method for development of safe and effective cancer therapeutic drugs. PMID:24079872

  16. MATS E-Reporting Final Action

    EPA Pesticide Factsheets

    This page describes the interim final rule that will allow owners or operators of electric generating units to submit to EPA electronic emissions and compliance reports for the Mercury and Air Toxics rule.

  17. A Lifeline Home: Goddard's Final Shuttle Mission

    NASA Video Gallery

    Controllers at Goddard's Network Integration Center share their thoughts as the 30-year-old Shuttle Program comes to an end with the final flight of STS-135, which concluded with a textbook landing...

  18. Expedition 35/36 Final Exams

    NASA Video Gallery

    Three Expedition 35/36 crew members prepare for their final exams in their Sokol launch and entry suits at the Gagarin Cosmonaut Training Center in Star City, Russia. NASA astronaut Chris Cassidy a...

  19. Expedition 36 Final Exams and Training

    NASA Video Gallery

    The Expedition 36 crew members conduct final training at the Gagarin Cosmonaut Training Center before their May 28 launch to the International Space Station. Flight Engineers Karen Nyberg, Fyodor Y...

  20. Final Determination - signed November 23, 1990

    EPA Pesticide Factsheets

    Final determination of the U.S. EPA’s Assistant Administrator for Water pursuant to section 404(c) of the Clean Water Act concerning the Two Forks water supply impoundments in Jefferson and Douglas counties, Colorado.

  1. Data Network Weather Service Reporting - Final Report

    SciTech Connect

    Michael Frey

    2012-08-30

    A final report is made of a three-year effort to develop a new forecasting paradigm for computer network performance. This effort was made in co-ordination with Fermi Lab's construction of e-Weather Center.

  2. Overview of the Final 2013 VGP

    EPA Pesticide Factsheets

    This document is a brief overview of the final 2013 VGP that provides NPDES permit coverage nationwide for discharges incidental to the normal operation of commercial vessels greater than 79 feet in length.

  3. Toxic Substances; Mesityl Oxide; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule establishing testing requirements under section 4(a) of the Toxic Substances Control Act (TSCA) for manufacturers and processors of mesityl oxide (MO; CAS No. 141-97-7).

  4. Final report, Feedback limitations of photosynthesis

    SciTech Connect

    Sharkey, Thomas D.

    1999-07-22

    Final report of research on carbon metabolism of photosynthesis. The feedback from carbon metabolism to primary photosynthetic processes is summarized, and a comprehensive list of published scientific papers is provided.

  5. 2-Ethylhexanoic Acid; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of 2-ethylhexanoic acid (EHA, CAS No. 149-57-5) to conduct testing.

  6. Astronauts Train for Final Shuttle Mission

    NASA Video Gallery

    The crew of STS-135, the final space shuttle mission, rehearsed their launch day process at NASA's Kennedy Space Center in Florida during a Terminal Countdown Demonstration Test that took place Jun...

  7. 31 CFR 92.17 - Final action.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... THE TREASURY UNITED STATES MINT OPERATIONS AND PROCEDURES Assessment of Civil Penalties for Misuse of Words, Letters, Symbols, or Emblems of the United States Mint § 92.17 Final action. (a) In making...

  8. 31 CFR 92.17 - Final action.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... THE TREASURY UNITED STATES MINT OPERATIONS AND PROCEDURES Assessment of Civil Penalties for Misuse of Words, Letters, Symbols, or Emblems of the United States Mint § 92.17 Final action. (a) In making...

  9. 31 CFR 92.17 - Final action.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... THE TREASURY UNITED STATES MINT OPERATIONS AND PROCEDURES Assessment of Civil Penalties for Misuse of Words, Letters, Symbols, or Emblems of the United States Mint § 92.17 Final action. (a) In making...

  10. 31 CFR 92.17 - Final action.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... THE TREASURY UNITED STATES MINT OPERATIONS AND PROCEDURES Assessment of Civil Penalties for Misuse of Words, Letters, Symbols, or Emblems of the United States Mint § 92.17 Final action. (a) In making...

  11. Moonshot Panel Moving Toward Final Report

    Cancer.gov

    An NCI Cancer Currents blog from acting NCI Director Dr. Doug Lowy providing an update on the activities of the National Cancer Moonshot Initiative’s Blue Ribbon Panel and its work to develop a final report.

  12. Triethylene Glycol Monomethyl Ether; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule under section 4 of the Toxic Substances Control Act (TSCA) requiring manufacturers and processors of triethylene glycol monomethyl ether (TGME, CAS No. 112-35-6) to perform developmental neurotoxicity tasting.

  13. Final Determination - signed August 31, 2008

    EPA Pesticide Factsheets

    Final Determination of the U.S. EPA’s Assistant Administrator for Water pursuant to Section 404(c) of the Clean Water Act concerning the proposed Yazoo Backwater area pumps project, Issaquena county, Mississippi.

  14. 77 FR 42077 - Environmental Justice: Final Circular

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-17

    ... TRANSPORTATION Federal Transit Administration Environmental Justice: Final Circular AGENCY: Federal Transit... (hereinafter ``EJ Circular'') on incorporating environmental justice principles into plans, projects, and... recipients of FTA funds on how to fully engage environmental justice populations in the public...

  15. Final focus systems for linear colliders

    SciTech Connect

    Erickson, R.A.

    1987-11-01

    The final focus system of a linear collider must perform two primary functions, it must focus the two opposing beams so that their transverse dimensions at the interaction point are small enough to yield acceptable luminosity, and it must steer the beams together to maintain collisions. In addition, the final focus system must transport the outgoing beams to a location where they can be recycled or safely dumped. Elementary optical considerations for linear collider final focus systems are discussed, followed by chromatic aberrations. The design of the final focus system of the SLAC Linear Collider (SLC) is described. Tuning and diagnostics and steering to collision are discussed. Most of the examples illustrating the concepts covered are drawn from the SLC, but the principles and conclusions are said to be generally applicable to other linear collider designs as well. 26 refs., 17 figs. (LEW)

  16. Research in High Energy Physics. Final report

    SciTech Connect

    Conway, John S.

    2013-08-09

    This final report details the work done from January 2010 until April 2013 in the area of experimental and theoretical high energy particle physics and cosmology at the University of California, Davis.

  17. 49 CFR 190.213 - Final order.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY PIPELINE SAFETY PROGRAMS AND RULEMAKING..., OPS shall issue a final order that includes— (1) A statement of findings and determinations on...

  18. 49 CFR 190.213 - Final order.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY PIPELINE SAFETY PROGRAMS AND RULEMAKING..., OPS shall issue a final order that includes— (1) A statement of findings and determinations on...

  19. Methyl Ethyl Ketoxime; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing this final test rule under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of methyl ethyl ketoxime (MEKO, CAS No. 96-29-7) to perform testing for health effects.

  20. Expedition 32 Final Soyuz Qualification Exams

    NASA Video Gallery

    Expedition 32 Flight Engineers Suni Williams, Yuri Malenchenko and Aki Hoshide take their final Soyuz systems qualification exams at the Gagarin Cosmonaut Training Center in Star City, Russia. The ...

  1. Final Determination - signed March 1, 1990

    EPA Pesticide Factsheets

    Final Determination of the U.S. Environmental Protection Agency's Assistant Administrator for Water pursuant to Section 404(c) of the Clean Water Act concerning the proposed Big River water supply impoundment in Kent county, RI.

  2. 1977 National Debate Tournament Final Debate

    ERIC Educational Resources Information Center

    Rives, Stanley G., ed.; Boaz, John K., ed.

    1977-01-01

    Presents a transcript of the final debate of the Thirty-First National Debate Tournament sponsored by the American Forensic Association in 1977. Focuses on the necessity and desirability of requiring airbags to promote automobile safety. (MH)

  3. Final Determination - signed March 21, 1988

    EPA Pesticide Factsheets

    Information about final determination of the U.S. EPA's Assistant Administrator for water, concerning wetlands owned by the Russo Development Corporation in Carlstadt, New Jersey pursuant to section 404(c) of the Clean Water Act.

  4. Norcal Prototype LNG Truck Fleet: Final Results

    SciTech Connect

    Not Available

    2004-07-01

    U.S. DOE and National Renewable Energy Laboratory evaluated Norcal Waste Systems liquefied natural gas (LNG) waste transfer trucks. Trucks had prototype Cummins Westport ISXG engines. Report gives final evaluation results.

  5. Federal Register notice: Isopropanol; Final Test Rule

    EPA Pesticide Factsheets

    EPA is issuing a final test rule, under section 4 of the Toxic Substances Control Act (TSCA), requiring manufacturers and processors of isopropanol (CAS No. 87-83-0) to perform testing for health effects.

  6. Finally, Proof That Hearing Aids Help

    MedlinePlus

    ... news/fullstory_163889.html Finally, Proof That Hearing Aids Help High-quality digital devices provide 'significant benefit' ... but solid evidence about the value of hearing aids has been lacking -- until now. New research findings " ...

  7. Health care for homeless veterans. Final rule.

    PubMed

    2011-08-23

    This final rule establishes regulations for contracting with community-based treatment facilities in the Health Care for Homeless Veterans (HCHV) program of the Department of Veterans Affairs (VA). The HCHV program assists certain homeless veterans in obtaining treatment from non-VA community-based providers. The final rule formalizes VA's policies and procedures in connection with this program and clarifies that veterans with substance use disorders may qualify for the program.

  8. Health insurance premium tax credit. Final regulations.

    PubMed

    2013-02-01

    This document contains final regulations relating to the health insurance premium tax credit enacted by the Patient Protection and Affordable Care Act and the Health Care and Education Reconciliation Act of 2010.These final regulations provide guidance to individuals related to employees who may enroll in eligible employer-sponsored coverage and who wish to enroll in qualified health plans through Affordable Insurance Exchanges (Exchanges) and claim the premium tax credit.

  9. 21 CFR 26.81 - Final provisions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Final provisions. 26.81 Section 26.81 Food and...Frameworkâ Provisions § 26.81 Final provisions. (a) The sectoral annexes referred to in § 26.80(a), as well... this part is derived. (b) For a given product or sector, the provisions contained in subparts A and...

  10. Final Technical Report 09 LW 112

    SciTech Connect

    Lenhoff, R J

    2010-11-28

    Since the development of new antibiotics is out-paced by the emergence of bacterial resistance to existing antibiotics, it is crucial to understand the genetic mechanisms underlying resistance existing antibiotics. At the center of this mystery is a poorly understood phenomenon, heteroresistance: the coexistence of multiple subpopulations with varying degrees of antibiotic resistance. A better understanding of the fundamental basis of heteroresistance could result in sorely needed breakthroughs in treatment options. This project proposed to leverage a novel microfluidic (microchemostat) technology to probe the heteroresistance phenomenon in bacteria, with the aim of restoring the efficacy of existing {beta}-lactam antibiotics. The clinically important bacteria Methicillin Resistant S. aureus (MRSA) was used as the test case of bacteria that exhibits antibiotic heteroresistance. MRSA is difficult to treat because it is resistant to all {beta}-lactam antibiotics, as well as other classes of antimicrobials. Whereas {beta}-lactams such as methicillin and oxacillin are the preferred antibiotics to treat S. aureus infections due to their efficacy and low side effects, accurate determination and use of oxacillin/methicillin dosage is hampered by heteroresistance. In fact, invasive MRSA infections now account for about 95,000 deaths per year, a number that exceeds the deaths due to either influenza or HIV (12). In some MRSA strains, two subpopulations of cells may coexist: both populations carry the mecA gene that confers resistance, but mecA is differentially expressed so that only a small number of cells are observed during in vitro testing. Why this occurs is not understood. Prior experiments have sought to explain this phenomenon with conflicting results, with technology being the primary barrier to test the system sufficiently. This is the final report on work accomplished under the Lab-wide LDRD project 09-LW-112. This project was awarded to Frederick Balagadde who

  11. Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

    PubMed Central

    Wissler, Lothar; Gadau, Jürgen; Simola, Daniel F.; Helmkampf, Martin; Bornberg-Bauer, Erich

    2013-01-01

    Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome. Several case studies demonstrated that orphans can contribute to lineage-specific adaptation. Here, we study orphan genes by comparing 30 arthropod genomes, focusing in particular on seven recently sequenced ant genomes. This setup allows analyzing a major metazoan taxon and a comparison between social Hymenoptera (ants and bees) and nonsocial Diptera (flies and mosquitoes). First, we find that recently split lineages undergo accelerated genomic reorganization, including the rapid gain of many orphan genes. Second, between the two insect orders Hymenoptera and Diptera, orphan genes are more abundant and emerge more rapidly in Hymenoptera, in particular, in leaf-cutter ants. With respect to intragenomic localization, we find that ant orphan genes show little clustering, which suggests that orphan genes in ants are scattered uniformly over the genome and between nonorphan genes. Finally, our results indicate that the genetic mechanisms creating orphan genes—such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements—act at different rates in insects, primates, and plants. In Formicidae, the majority of orphan genes has their origin in intergenic regions, pointing to a high rate of de novo gene formation or generalized gene loss, and support a recently proposed dynamic model of frequent gene birth and death. PMID:23348040

  12. Transcription Factors in Xylem Development. Final report

    SciTech Connect

    Sederoff, Ronald; Whetten, Ross; O'Malley, David; Campbell, Malcolm

    1999-07-01

    Answers to the following questions are answered in this report. do the two pine Byb proteins previously identified as candidate transcription factors bind to DNA and activate transcription? In what cell types are tehse Myb proteins expressed? Are these proteins localized to the nucleus? Do other proteins in pine xylem interact with these Myb proteins? Does altered expression of these genes have an impact on xylogenesis, specifically the expression of monolignol biosynthetic genes?

  13. Informative Gene Selection and Direct Classification of Tumor Based on Chi-Square Test of Pairwise Gene Interactions

    PubMed Central

    Zhang, Hongyan; Li, Lanzhi; Luo, Chao; Sun, Congwei; Chen, Yuan; Dai, Zhijun; Yuan, Zheming

    2014-01-01

    In efforts to discover disease mechanisms and improve clinical diagnosis of tumors, it is useful to mine profiles for informative genes with definite biological meanings and to build robust classifiers with high precision. In this study, we developed a new method for tumor-gene selection, the Chi-square test-based integrated rank gene and direct classifier (χ2-IRG-DC). First, we obtained the weighted integrated rank of gene importance from chi-square tests of single and pairwise gene interactions. Then, we sequentially introduced the ranked genes and removed redundant genes by using leave-one-out cross-validation of the chi-square test-based Direct Classifier (χ2-DC) within the training set to obtain informative genes. Finally, we determined the accuracy of independent test data by utilizing the genes obtained above with χ2-DC. Furthermore, we analyzed the robustness of χ2-IRG-DC by comparing the generalization performance of different models, the efficiency of different feature-selection methods, and the accuracy of different classifiers. An independent test of ten multiclass tumor gene-expression datasets showed that χ2-IRG-DC could efficiently control overfitting and had higher generalization performance. The informative genes selected by χ2-IRG-DC could dramatically improve the independent test precision of other classifiers; meanwhile, the informative genes selected by other feature selection methods also had good performance in χ2-DC. PMID:25140319

  14. Gene regulation in cancer gene therapy strategies.

    PubMed

    Scanlon, Ian; Lehouritis, Panos; Niculescu-Duvaz, Ion; Marais, Richard; Springer, Caroline J

    2003-10-01

    Regulation of expression in gene therapy is considered to be a very desirable goal, preventing toxic effects and improving biological efficacy. A variety of systems have been reported in an ever widening range of applications, this paper describes these systems with specific reference to cancer gene therapy.

  15. Human Gene Therapy: Genes without Frontiers?

    ERIC Educational Resources Information Center

    Simon, Eric J.

    2002-01-01

    Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

  16. 75 FR 42819 - Notice of Availability of a Final Environmental Assessment (Final EA) and a Finding of No...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-22

    ... Federal Aviation Administration Notice of Availability of a Final Environmental Assessment (Final EA) and...: Notice of Availability of a Final Environmental Assessment (Final EA) and Finding of No Significant...)/Record of Decision (ROD) based on the Final Environmental Assessment (Final EA) for the Proposed...

  17. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.

    PubMed Central

    Bellen, Hugo J; Levis, Robert W; Liao, Guochun; He, Yuchun; Carlson, Joseph W; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P Robin; Schulze, Karen L; Rubin, Gerald M; Hoskins, Roger A; Spradling, Allan C

    2004-01-01

    The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool. PMID:15238527

  18. Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

    PubMed

    Narang, Vipin; Ramli, Muhamad Azfar; Singhal, Amit; Kumar, Pavanish; de Libero, Gennaro; Poidinger, Michael; Monterola, Christopher

    2015-01-01

    Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs). Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data) accompanying this manuscript.

  19. The BDGP gene disruption project: Single transposon insertions associated with 40 percent of Drosophila genes

    SciTech Connect

    Bellen, Hugo J.; Levis, Robert W.; Liao, Guochun; He, Yuchun; Carlson, Joseph W.; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P. Robin; Schulze, Karen L.; Rubin, Gerald M.; Hoskins, Roger A.; Spradling, Allan C.

    2004-01-13

    The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in more than 30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6,300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7,140 lines. It now includes individual lines predicted to disrupt 5,362 of the 13,666 currently annotated Drosophila genes (39 percent). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene mis-expression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

  20. Minimal gene selection for classification and diagnosis prediction based on gene expression profile

    PubMed Central

    Mehridehnavi, Alireza; Ziaei, Lia

    2013-01-01

    Background: Up to date different methods have been used in order to dimensions reduction, classification, clustering and prediction of cancers based on gene expression profiling. The aim of this study is extracting most significant genes and classifying of Diffuse Large B-cell Lymphoma (DLBCL) patients on the basis of their gene expression profiles. Materials and Methods: We studied 40 DLBCL patients and 4026 genes. We utilized Artificial Neural Network (ANN) for classification of patients in two groups: Germinal center and Activated like. As we were faced with low number of patients (40) and numerous genes (4026), we tried to deploy one optimum network and achieve to minimum error. Moreover we used signal to noise (S/N) ratio as a main tool for dimension reduction. We tried to select suitable training data and so to train just one network instead of 26 networks. Finally, we extracted two most significant genes. Result: In this study two most significant genes based on their S/N ratios were selected. After selection of suitable training samples, the training and testing error were 0 and 7% respectively. Conclusion: We have shown that the use of two most significant genes based on their S/N ratios and selection of suitable training samples can lead to classify DLBCL patients with a rather good result. Actually with the aid of mentioned methods we could compensate lack of enough number of patients, improve accuracy of classifying and reduce complication of computations and so running time. PMID:23977654

  1. Plant Biofilm Inhibitors to Discover Biofilm Genes

    DTIC Science & Technology

    2011-04-08

    REPORT Final Report for Plant Biofilm Inhibitors to Discover Biofilm Genes 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: To control biofilms , we have...synthesized the natural biofilm inhibitor (5Z)-4-bromo-5-(bromomethylene) -3-butyl-2(5H)-furanone from the red alga Delisea pulchra and determined that...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS biofilms , biofilm inhibitors Thomas K. Wood Texas Engineering

  2. Human gene therapy.

    PubMed

    Sandhu, J S; Keating, A; Hozumi, N

    1997-01-01

    Human gene therapy and its application for the treatment of human genetic disorders, such as cystic fibrosis, cancer, and other diseases, are discussed. Gene therapy is a technique in which a functioning gene is inserted into a human cell to correct a genetic error or to introduce a new function to the cell. Many methods, including retroviral vectors and non-viral vectors, have been developed for both ex vivo and in vivo gene transfer into cells. Vectors need to be developed that efficiently transfer genes to target cells, and promoter systems are required that regulate gene expression according to physiologic needs of the host cell. There are several safety and ethical issues related to manipulating the human genome that need to be resolved. Current gene therapy efforts focus on gene insertion into somatic cells only. Gene therapy has potential for the effective treatment of genetic disorders, and gene transfer techniques are being used for basic research, for example, in cancer, to examine the underlying mechanism of disease. There are still many technical obstacles to be overcome before human gene therapy can become a routine procedure. The current human genome project provides the sequences of a vast number of human genes, leading to the identification, characterization, and understanding of genes that are responsible for many human diseases.

  3. Current status of haemophilia gene therapy.

    PubMed

    High, K H; Nathwani, A; Spencer, T; Lillicrap, D

    2014-05-01

    After many reports of successful gene therapy studies in small and large animal models of haemophilia, we have, at last, seen the first signs of success in human patients. These very encouraging results have been achieved with the use of adeno-associated viral (AAV) vectors in patients with severe haemophilia B. Following on from these initial promising studies, there are now three ongoing trials of AAV-mediated gene transfer in haemophilia B all aiming to express the factor IX gene from the liver. Nevertheless, as discussed in the first section of this article, there are still a number of significant hurdles to overcome if haemophilia B gene therapy is to become more widely available. The second section of this article deals with the challenges relating to factor VIII gene transfer. While the recent results in haemophilia B are extremely encouraging, there is, as yet, no similar data for factor VIII gene therapy. It is widely accepted that this therapeutic target will be significantly more problematic for a variety of reasons including accommodating the larger factor VIII cDNA, achieving adequate levels of transgene expression and preventing the far more frequent complication of antifactor VIII immunity. In the final section of the article, the alternative approach of lentiviral vector-mediated gene transfer is discussed. While AAV-mediated approaches to transgene delivery have led the way in clinical haemophilia gene therapy, there are still a number of potential advantages of using an alternative delivery vehicle including the fact that ex vivo host cell transduction will avoid the likelihood of immune responses to the vector. Overall, these are exciting times for haemophilia gene therapy with the likelihood of further clinical successes in the near future.

  4. Rotavirus gene structure and function.

    PubMed Central

    Estes, M K; Cohen, J

    1989-01-01

    Knowledge of the structure and function of the genes and proteins of the rotaviruses has expanded rapidly. Information obtained in the last 5 years has revealed unexpected and unique molecular properties of rotavirus proteins of general interest to virologists, biochemists, and cell biologists. Rotaviruses share some features of replication with reoviruses, yet antigenic and molecular properties of the outer capsid proteins, VP4 (a protein whose cleavage is required for infectivity, possibly by mediating fusion with the cell membrane) and VP7 (a glycoprotein), show more similarities with those of other viruses such as the orthomyxoviruses, paramyxoviruses, and alphaviruses. Rotavirus morphogenesis is a unique process, during which immature subviral particles bud through the membrane of the endoplasmic reticulum (ER). During this process, transiently enveloped particles form, the outer capsid proteins are assembled onto particles, and mature particles accumulate in the lumen of the ER. Two ER-specific viral glycoproteins are involved in virus maturation, and these glycoproteins have been shown to be useful models for studying protein targeting and retention in the ER and for studying mechanisms of virus budding. New ideas and approaches to understanding how each gene functions to replicate and assemble the segmented viral genome have emerged from knowledge of the primary structure of rotavirus genes and their proteins and from knowledge of the properties of domains on individual proteins. Localization of type-specific and cross-reactive neutralizing epitopes on the outer capsid proteins is becoming increasingly useful in dissecting the protective immune response, including evaluation of vaccine trials, with the practical possibility of enhancing the production of new, more effective vaccines. Finally, future analyses with recently characterized immunologic and gene probes and new animal models can be expected to provide a basic understanding of what regulates the

  5. Gene therapy for blindness.

    PubMed

    Sahel, José-Alain; Roska, Botond

    2013-07-08

    Sight-restoring therapy for the visually impaired and blind is a major unmet medical need. Ocular gene therapy is a rational choice for restoring vision or preventing the loss of vision because most blinding diseases originate in cellular components of the eye, a compartment that is optimally suited for the delivery of genes, and many of these diseases have a genetic origin or genetic component. In recent years we have witnessed major advances in the field of ocular gene therapy, and proof-of-concept studies are under way to evaluate the safety and efficacy of human gene therapies. Here we discuss the concepts and recent advances in gene therapy in the retina. Our review discusses traditional approaches such as gene replacement and neuroprotection and also new avenues such as optogenetic therapies. We conjecture that advances in gene therapy in the retina will pave the way for gene therapies in other parts of the brain.

  6. Scientists Spot 'Teetotaler' Gene

    MedlinePlus

    ... gov/news/fullstory_162265.html Scientists Spot 'Teetotaler' Gene Discovery might one day lead to drugs to ... HealthDay News) -- Scientists say they've identified a gene variant that dampens the desire to drink alcohol. ...

  7. Genes and Hearing Loss

    MedlinePlus

    ... gametes (reproductive cells). One gamete will carry the mutant form of the gene of interest, and the ... by having parents who are heterozygous carriers for mutant forms of the gene in question but are ...

  8. Gene-gene and gene-sex epistatic interactions of DNMT1, DNMT3A and DNMT3B in autoimmune thyroid disease.

    PubMed

    Cai, Tian-Tian; Zhang, Jian; Wang, Xuan; Song, Rong-Hua; Qin, Qiu; Muhali, Fatuma-Said; Zhou, Jiao-Zhen; Xu, Jian; Zhang, Jin-An

    2016-07-30

    The aim of this study was to investigate the associations of DNA methyltransferases (DNMTs) polymorphisms with susceptibility to autoimmune thyroid diseases (AITDs) and to test gene-gene/gene-sex epistasis interactions. Eight single-nucleotide polymorphisms (SNPs) in DNMT1, DNMT3A and DNMT3B were selected and genotyped by multiplex polymerase chain reaction combined with ligase detection reaction method (PCR-LDR). A total of 685 Graves' disease (GD) patients, 353 Hashimoto's thyroiditis (HT) patients and 909 healthy controls were included in the final analysis. Epistasis was tested by additive model, multiplicative model and general multifactor dimensionality reduction (general MDR). Rs2424913 (DNMT3B) and rs2228611 (DNMT1) were associated with susceptibility to AITD and GD in the dominant and overdominant model, respectively (rs2424913: P=0.009 for AITD, P=0.0041 for GD; rs2228611: P=0.035 for AITD, P=0.043 for GD). Multiplicative and multiple high dimensional gene-gene or gene-sex interactions were also observed in this study. We have found evidence for a potential role of rs2424913 (DNMT3B) and rs2228611 (DNMT1) in AITD susceptibility and identified novel gene-gene/gene-sex interactions in AITD. Our study may highlight sex and genes of DNMTs family as contributors to the pathogenesis of AITD.

  9. Myocardial gene therapy

    NASA Astrophysics Data System (ADS)

    Isner, Jeffrey M.

    2002-01-01

    Gene therapy is proving likely to be a viable alternative to conventional therapies in coronary artery disease and heart failure. Phase 1 clinical trials indicate high levels of safety and clinical benefits with gene therapy using angiogenic growth factors in myocardial ischaemia. Although gene therapy for heart failure is still at the pre-clinical stage, experimental data indicate that therapeutic angiogenesis using short-term gene expression may elicit functional improvement in affected individuals.

  10. Rules on determining hearing appearances. Final rule.

    PubMed

    2013-05-21

    This final rule is another step in our continual efforts to handle workloads more effectively and efficiently. We are publishing final rules for portions of the rules we proposed in October 2007 that relate to persons, other than the claimant or any other party to the hearing, appearing by telephone. We are also clarifying that the administrative law judge (ALJ) will allow the claimant or any other party to a hearing to appear by telephone under certain circumstances when the claimant or other party requests to make his or her appearance in that manner. We expect that these final rules will make the hearings process more efficient and help us continue to reduce the hearings backlog. In addition, we made some minor editorial changes to our regulations that do not have any effect on the rights of claimants or any other parties.

  11. Antiperspirant drug products for over-the-counter human use; final monograph. Final rule.

    PubMed

    2003-06-09

    The Food and Drug Administration (FDA) is issuing a final rule in the form of a final monograph establishing conditions under which over-the-counter (OTC) antiperspirant drug products are generally recognized as safe and effective and not misbranded as part of FDA's ongoing review of OTC drug products. FDA is issuing this final rule after considering public comments on its proposed regulation, issued as a tentative final monograph (TFM), and all new data and information on antiperspirant drug products that have come to the agency's attention.

  12. Housekeeping genes tend to show reduced upstream sequence conservation

    PubMed Central

    Farré, Domènec; Bellora, Nicolás; Mularoni, Loris; Messeguer, Xavier; Albà, M Mar

    2007-01-01

    Background Understanding the constraints that operate in mammalian gene promoter sequences is of key importance to understand the evolution of gene regulatory networks. The level of promoter conservation varies greatly across orthologous genes, denoting differences in the strength of the evolutionary constraints. Here we test the hypothesis that the number of tissues in which a gene is expressed is related in a significant manner to the extent of promoter sequence conservation. Results We show that mammalian housekeeping genes, expressed in all or nearly all tissues, show significantly lower promoter sequence conservation, especially upstream of position -500 with respect to the transcription start site, than genes expressed in a subset of tissues. In addition, we evaluate the effect of gene function, CpG island content and protein evolutionary rate on promoter sequence conservation. Finally, we identify a subset of transcription factors that bind to motifs that are specifically over-represented in housekeeping gene promoters. Conclusion This is the first report that shows that the promoters of housekeeping genes show reduced sequence conservation with respect to genes expressed in a more tissue-restricted manner. This is likely to be related to simpler gene expression, requiring a smaller number of functional cis-regulatory motifs. PMID:17626644

  13. Evaluating the evaluation of cancer driver genes

    PubMed Central

    Tokheim, Collin J.; Papadopoulos, Nickolas; Kinzler, Kenneth W.; Vogelstein, Bert; Karchin, Rachel

    2016-01-01

    Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard, that is, bona fide driver gene mutations. Here, we establish an evaluation framework that can be applied to driver gene prediction methods. We used this framework to compare the performance of eight such methods. One of these methods, described here, incorporated a machine-learning–based ratiometric approach. We show that the driver genes predicted by each of the eight methods vary widely. Moreover, the P values reported by several of the methods were inconsistent with the uniform values expected, thus calling into question the assumptions that were used to generate them. Finally, we evaluated the potential effects of unexplained variability in mutation rates on false-positive driver gene predictions. Our analysis points to the strengths and weaknesses of each of the currently available methods and offers guidance for improving them in the future. PMID:27911828

  14. Evaluating the evaluation of cancer driver genes.

    PubMed

    Tokheim, Collin J; Papadopoulos, Nickolas; Kinzler, Kenneth W; Vogelstein, Bert; Karchin, Rachel

    2016-12-13

    Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard, that is, bona fide driver gene mutations. Here, we establish an evaluation framework that can be applied to driver gene prediction methods. We used this framework to compare the performance of eight such methods. One of these methods, described here, incorporated a machine-learning-based ratiometric approach. We show that the driver genes predicted by each of the eight methods vary widely. Moreover, the P values reported by several of the methods were inconsistent with the uniform values expected, thus calling into question the assumptions that were used to generate them. Finally, we evaluated the potential effects of unexplained variability in mutation rates on false-positive driver gene predictions. Our analysis points to the strengths and weaknesses of each of the currently available methods and offers guidance for improving them in the future.

  15. Strategies in Gene Therapy for Glioblastoma

    PubMed Central

    Kwiatkowska, Aneta; Nandhu, Mohan S.; Behera, Prajna; Chiocca, E. Antonio; Viapiano, Mariano S.

    2013-01-01

    Glioblastoma (GBM) is the most aggressive form of brain cancer, with a dismal prognosis and extremely low percentage of survivors. Novel therapies are in dire need to improve the clinical management of these tumors and extend patient survival. Genetic therapies for GBM have been postulated and attempted for the past twenty years, with variable degrees of success in pre-clinical models and clinical trials. Here we review the most common approaches to treat GBM by gene therapy, including strategies to deliver tumor-suppressor genes, suicide genes, immunomodulatory cytokines to improve immune response, and conditionally-replicating oncolytic viruses. The review focuses on the strategies used for gene delivery, including the most common and widely used vehicles (i.e., replicating and non-replicating viruses) as well as novel therapeutic approaches such as stem cell-mediated therapy and nanotechnologies used for gene delivery. We present an overview of these strategies, their targets, different advantages, and challenges for success. Finally, we discuss the potential of gene therapy-based strategies to effectively attack such a complex genetic target as GBM, alone or in combination with conventional therapy. PMID:24202446

  16. Gene mutations in chronic lymphocytic leukemia.

    PubMed

    Amin, Nisar A; Malek, Sami N

    2016-04-01

    The recent discovery of genes mutated in chronic lymphocytic leukemia (CLL) has stimulated new research into the role of these genes in CLL pathogenesis. CLL cases carry approximately 5-20 mutated genes per exome, a lower number than detected in many human tumors. Of the recurrently mutated genes in CLL, all are mutated in 10% or less of patients when assayed in unselected CLL cohorts at diagnosis. Mutations in TP53 are of major clinical relevance, are often associated with del17p and gain in frequency over time. TP53 mutated and associated del17p states substantially lower response rates, remission duration, and survival in CLL. Mutations in NOTCH1 and SF3B1 are recurrent, often associated with progressive CLL that is also IgVH unmutated and ZAP70-positive and are under investigation as targets for novel therapies and as factors influencing CLL outcome. There are an estimated 20-50 additional mutated genes with frequencies of 1%-5% in CLL; more work is needed to identify these and to study their significance. Finally, of the major biological aberration categories influencing CLL as a disease, gene mutations will need to be placed into context with regard to their ultimate role and importance. Such calibrated appreciation necessitates studies incorporating multiple CLL driver aberrations into biological and clinical analyses.

  17. X-43A Final Flight Observations

    NASA Technical Reports Server (NTRS)

    Grindle, Laurie

    2011-01-01

    The presentation will provide an overview of the final flight of the NASA X-43A project. The project consisted of three flights, two planned for Mach 7 and one for Mach 10. The first flight, conducted on June 2, 2001, was unsuccessful and resulted in a nine-month mishap investigation. A two-year return to flight effort ensued and concluded when the second Mach 7 flight was successfully conducted on March 27, 2004. The third and final flight, which occurred on November 16, 2004, was the first Mach 10 flight demonstration of an airframe-integrated, scramjet-powered, hypersonic vehicle. As such, the final flight presented first time technical challenges in addition to final flight project closeout concerns. The goals and objectives for the third flight as well as those for the project will be presented. The configuration of the Hyper-X stack including the X-43A, Hyper-X launch vehicle, and Hyper-X research vehicle adapter wil also be presented. Mission differences, vehicle modifications and lessons learned from the first and second flights as they applied to the third flight will also be discussed. Although X-43A flight 3 was always planned to be the final flight of the X-43A project, the X-43 program had two other vehicles and corresponding flight phases in X-43C and X-43B. Those other projects never manifested under the X-43 banner and X-43A flight 3 also became the final flight of X-43 program.

  18. Reading and Generalist Genes

    ERIC Educational Resources Information Center

    Haworth, Claire M. A.; Meaburn, Emma L.; Harlaar, Nicole; Plomin, Robert

    2007-01-01

    Twin-study research suggests that many (but not all) of the same genes contribute to genetic influence on diverse learning abilities and disabilities, a hypothesis called "generalist genes". This generalist genes hypothesis was tested using a set of 10 DNA markers (single nucleotide polymorphisms [SNPs]) found to be associated with early reading…

  19. Updating fire safety standards. Final rule; affirmation.

    PubMed

    2011-11-16

    This document affirms as final, without changes, a provision included in a final rule with request for comments that amended the Department of Veterans Affairs (VA) regulations concerning community residential care facilities, contract facilities for certain outpatient and residential services, and State home facilities. That provision established a five-year period within which all covered buildings with nursing home facilities existing as of June 25, 2001, must conform to the automatic sprinkler requirement of the 2009 edition of the National Fire Protection Association (NFPA) 101. This rule helps ensure the safety of veterans in the affected facilities.

  20. Comprehensive Child Welfare Information System. Final rule.

    PubMed

    2016-06-02

    This final rule replaces the Statewide and Tribal Automated Child Welfare Information Systems (S/TACWIS) rule with the Comprehensive Child Welfare Information System (CCWIS) rule. The rule also makes conforming amendments in rules in related requirements. This rule will assist title IV-E agencies in developing information management systems that leverage new innovations and technology in order to better serve children and families. More specifically, this final rule supports the use of cost-effective, innovative technologies to automate the collection of high-quality case management data and to promote its analysis, distribution, and use by workers, supervisors, administrators, researchers, and policy makers.