Science.gov

Sample records for partial gdh gene

  1. The Saccharomyces cerevisiae Leu3 protein activates expression of GDH1, a key gene in nitrogen assimilation.

    PubMed Central

    Hu, Y; Cooper, T G; Kohlhaw, G B

    1995-01-01

    The Leu3 protein of Saccharomyces cerevisiae has been shown to be a transcriptional regulator of genes encoding enzymes of the branched-chain amino acid biosynthetic pathways. Leu3 binds to upstream activating sequences (UASLEU) found in the promoters of LEU1, LEU2, LEU4, ILV2, and ILV5. In vivo and in vitro studies have shown that activation by Leu3 requires the presence of alpha-isopropylmalate. In at least one case (LEU2), Leu3 actually represses basal-level transcription when alpha-isopropylmalate is absent. Following identification of a UASLEU-homologous sequence in the promoter of GDH1, the gene encoding NADP(+)-dependent glutamate dehydrogenase, we demonstrate that Leu3 specifically interacts with this UASLEU element. We then show that Leu3 is required for full activation of the GDH1 gene. First, the expression of a GDH1-lacZ fusion gene is three- to sixfold lower in a strain lacking the LEU3 gene than in an isogenic LEU3+ strain. Expression is restored to near-normal levels when the leu3 deletion cells are transformed with a LEU3-bearing plasmid. Second, a significant decrease in GDH1-lacZ expression is also seen when the UASLEU of the GDH1-lacZ construct is made nonfunctional by mutation. Third, the steady-state level of GDH1 mRNA decreases about threefold in leu3 null cells. The decrease in GDH1 expression in leu3 null cells is reflected in a diminished specific activity of NADP(+)-dependent glutamate dehydrogenase. We also demonstrate that the level of GDH1-lacZ expression correlates with the cells' ability to generate alpha-isopropylmalate and is lowest in cells unable to produce alpha-isopropylmalate. We conclude that GDH1, which plays an important role in the assimilation of ammonia in yeast cells, is, in part, activated by a Leu3-alpha-isopropylmalate complex. This conclusion suggests that Leu3 participates in transcriptional regulation beyond the branched-chain amino acid biosynthetic pathways. PMID:7799961

  2. The NAD(P)H-utilizing glutamate dehydrogenase of Bacteroides thetaiotaomicron belongs to enzyme family I, and its activity is affected by trans-acting gene(s) positioned downstream of gdhA.

    PubMed Central

    Baggio, L; Morrison, M

    1996-01-01

    Previous studies have suggested that regulation of the enzymes of ammonia assimilation in human colonic Bacteroides species is coordinated differently than in other eubacteria. The gene encoding an NAD(P)H-dependent glutamate dehydrogenase (gdhA) in Bacteroides thetaiotaomicron was cloned and expressed in Escherichia coli by mutant complementation from the recombinant plasmid pANS100. Examination of the predicted GdhA amino acid sequence revealed that this enzyme possesses motifs typical of the family I-type hexameric GDH proteins. Northern blot analysis with a gdhA-specific probe indicated that a single transcript with an electrophoretic mobility of approximately 1.6 kb was produced in both B. thetaiotaomicron and E. coli gdhA+ transformants. Although gdhA transcription was unaffected, no GdhA enzyme activity could be detected in E. coli transformants when smaller DNA fragments from pANS100, which contained the entire gdhA gene, were analyzed. Enzyme activity was restored if these E. coli strains were cotransformed with a second plasmid, which contained a 3-kb segment of DNA located downstream of the gdhA coding region. Frameshift mutagenesis within the DNA downstream of gdhA in pANS100 also resulted in the loss of GdhA enzyme activity. Collectively, these results are interpreted as evidence for the role of an additional gene product(s) in modulating the activity of GDH enzyme activity. Insertional mutagenesis experiments which led to disruption of the gdhA gene on the B. thetaiotaomicron chromosome indicated that gdhA mutants were not glutamate auxotrophs, but attempts to isolate similar mutants with insertion mutations in the region downstream of the gdhA gene were unsuccessful. PMID:8955404

  3. Genetic Analysis of the Gdh and Bg Genes of Animal-Derived Giardia duodenalis Isolates in Northeastern China and Evaluation of Zoonotic Transmission Potential

    PubMed Central

    Shen, Yujuan; Zhang, Weizhe; Wang, Rongjun; Zhao, Wei; Zhang, Longxian; Ling, Hong; Cao, Jianping

    2014-01-01

    Background Giardia duodenalis is a common intestinal parasite that infects humans and many other mammals, mainly distributing in some areas with poor sanitation. The proportion of the human giardiasis burden attributable to G. duodenalis of animal origin differs in different geographical areas. In Mainland China, genetic data of the gdh and bg genes of G. duodenalis from animals are only limited in dogs and cats. The aim of the study was to provide information on the genetic characterizations of animal-derived G. duodenalis isolates (from rabbits, sheep and cattle) at both loci in Heilongjiang Province, Northeastern China, and to assess the potential for zoonotic transmission. Methodology/Principal Findings 61 G. duodenalis isolates from animal feces (dairy and beef cattle, sheep and rabbits) in Heilongjiang Province were characterized at the gdh and bg loci in the present study. The gdh and bg gene sequences of sheep-derived G. duodenalis assemblage AI, and the gdh sequences of rabbit-derived G. duodenalis assemblage B had 100% similarity with those from humans, respectively. Novel subtypes of G. duodenalis were identified, with one and seven subtypes for assemblages A and E at the gdh locus, and two and three subtypes for assemblages B and E at the bg locus, respectively. Three pairs of the same bg sequences of assemblage E were observed in sheep and cattle. Conclusions/Significance This is the first description of genetic characterizations of the gdh and bg genes of G. duodenalis from rabbits, sheep and cattle in Mainland China. Homology analysis of assemblages AI and B implied the possibility of zoonotic transmission. The novel subtypes of assemblages of G. duodenalis may represent the endemic genetic characteristics of G. duodenalis in Heilongjiang Province, China. PMID:24748379

  4. Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66

    PubMed Central

    Naveed, Muhammad; Ahmed, Iftikhar; Khalid, Nauman; Mumtaz, Abdul Samad

    2014-01-01

    Glucose dehydrogenase (GDH; EC 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p ≤ 0.05) promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains in GDH. GDH of Leclercia sp. QAU-66 is one of the main factor that involved in plant growth promotion and provides a solid background for further research in plant growth promoting activities. PMID:25242947

  5. Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66.

    PubMed

    Naveed, Muhammad; Ahmed, Iftikhar; Khalid, Nauman; Mumtaz, Abdul Samad

    2014-01-01

    Glucose dehydrogenase (GDH; EC 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p ≤ 0.05) promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains in GDH. GDH of Leclercia sp. QAU-66 is one of the main factor that involved in plant growth promotion and provides a solid background for further research in plant growth promoting activities. PMID:25242947

  6. Giardia duodenalis genotypes in domestic and wild animals from Romania identified by PCR-RFLP targeting the gdh gene.

    PubMed

    Adriana, Gyӧrke; Zsuzsa, Kalmár; Mirabela Oana, Dumitrache; Mircea, Gherman Călin; Viorica, Mircean

    2016-02-15

    Sixty Giardia duodenalis isolates from domestic (n=49) and wild (n=11) animals (dogs, cats, deers, wolves, raccoon dog and muskrat) were analysed by PCR-RFLP at glutamate dehydrogenase locus (gdh). The isolates were obtained from positive feces samples for Giardia cysts analysed by flotation technique with saturated sodium chloride solution (specific gravity 1.28). Three G. duodenalis genotypes were identified: C (10/60; 16.7%); D (42/60; 70.0%); and E (7/60; 11.7%). In dogs all three genotypes were found, with the following prevalences: 76.9% genotype D (30/39); 23.1% C (9/39); 2.6% genotype E (1/39). One dog was co-infected with C and D genotypes. In cats we identified only G. duodenalis genotype D. Wolves and raccoon dog harbored infection with G. duodenalis genotype D, deers with E type and muskrat C type. This is the first study regarding genotyping of G. duodenalis in cats and wild animals from Romania. To the best of our knowledge, this is the first report of assemblages E in roe deers; assemblage C in wolves and muskrat; and assemblage D in raccoon dog. PMID:26827864

  7. Importance of Glutamate Dehydrogenase (GDH) in Clostridium difficile Colonization In Vivo

    PubMed Central

    Girinathan, Brintha Parasumanna; Braun, Sterling; Sirigireddy, Apoorva Reddy; Lopez, Jose Espinola; Govind, Revathi

    2016-01-01

    Clostridium difficile is the principal cause of antibiotic-associated diarrhea. Major metabolic requirements for colonization and expansion of C. difficile after microbiota disturbance have not been fully determined. In this study, we show that glutamate utilization is important for C. difficile to establish itself in the animal gut. When the gluD gene, which codes for glutamate dehydrogenase (GDH), was disrupted, the mutant C. difficile was unable to colonize and cause disease in a hamster model. Further, from the complementation experiment it appears that extracellular GDH may be playing a role in promoting C. difficile colonization and disease progression. Quantification of free amino acids in the hamster gut during C. difficile infection showed that glutamate is among preferred amino acids utilized by C. difficile during its expansion. This study provides evidence of the importance of glutamate metabolism for C. difficile pathogenesis. PMID:27467167

  8. A nuclear gene with many introns encoding ammonium-inducible chloroplastic NADP-specific glutamate dehydrogenase(s) in Chlorella sorokiniana.

    PubMed

    Cock, J M; Kim, K D; Miller, P W; Hutson, R G; Schmidt, R R

    1991-11-01

    Chlorella sorokiniana possesses ammonium-inducible, chloroplastic, NADP-specific glutamate dehydrogenase (NADP-GDH) homo- or heterohexamers composed of alpha- and/or beta-subunits which were previously shown to derive from precursor protein(s) of identical size. From the present studies, data are consistent with these two subunits being encoded by a single nuclear gene. The NADP-GDH gene is greater than 7 kb in length due to the presence of at least 21 introns, an unusually large number for a eukaryotic microorganism. The exons, identified by comparison with sequences of NADP-GDH cDNA clones, include a region which is highly conserved among NADP-GDH genes. This region in the C. sorokiniana gene is 77% and 73% identical to the corresponding regions in the Escherichia coli and Neurospora crassa NADP-GDH genes, respectively. Seventeen independent NADP-GDH cDNA clones were analyzed by restriction mapping and partial sequencing, and no differences were detected among them. The longest cDNA was fused in frame with lacZ in a Bluescript vector and was expressed in E. coli as NADP-GDH antigen. During a 240 min induction period, under conditions in which both types of subunits were synthesized, only a single (2.2 kb) NADP-GDH mRNA band was detected on northern blots using cDNA probes from the highly conserved and 3'-untranslated regions. Collectively, these results are consistent with a single mRNA encoding a precursor-protein which is differentially processed to yield either an alpha- or beta-subunit. PMID:1718478

  9. The odyssey of a young gene: structure-function studies in human glutamate dehydrogenases reveal evolutionary-acquired complex allosteric regulation mechanisms.

    PubMed

    Zaganas, Ioannis V; Kanavouras, Konstantinos; Borompokas, Nikolas; Arianoglou, Giovanna; Dimovasili, Christina; Latsoudis, Helen; Vlassi, Metaxia; Mastorodemos, Vasileios

    2014-01-01

    Mammalian glutamate dehydrogenase (GDH) catalyzes the reversible inter-conversion of glutamate to α-ketoglutarate and ammonia, interconnecting carbon skeleton and nitrogen metabolism. In addition, it functions as an energy switch by its ability to fuel the Krebs cycle depending on the energy status of the cell. As GDH lies at the intersection of several metabolic pathways, its activity is tightly regulated by several allosteric compounds that are metabolic intermediates. In contrast to other mammals that have a single GDH-encoding gene, humans and great apes possess two isoforms of GDH (hGDH1 and hGDH2, encoded by the GLUD1 and GLUD2 genes, respectively) with distinct regulation pattern, but remarkable sequence similarity (they differ, in their mature form, in only 15 of their 505 amino-acids). The GLUD2 gene is considered a very young gene, emerging from the GLUD1 gene through retro-position only recently (<23 million years ago). The new hGDH2 iso-enzyme, through random mutations and natural selection, is thought to have conferred an evolutionary advantage that helped its persistence through primate evolution. The properties of the two highly homologous human GDHs have been studied using purified recombinant hGDH1 and hGDH2 proteins obtained by expression of the corresponding cDNAs in Sf21 cells. According to these studies, in contrast to hGDH1 that maintains basal activity at 35-40 % of its maximal, hGDH2 displays low basal activity that is highly responsive to activation by rising levels of ADP and/or L-leucine which can also act synergistically. While hGDH1 is inhibited potently by GTP, hGDH2 shows remarkable GTP resistance. Furthermore, the two iso-enzymes are differentially inhibited by estrogens, polyamines and neuroleptics, and also differ in heat-lability. To elucidate the molecular mechanisms that underlie these different regulation patterns of the two iso-enzymes (and consequently the evolutionary adaptation of hGDH2 to a new functional role), we have

  10. Partial structure of the mouse glucokinase gene

    SciTech Connect

    Ishimura-Oka, Kazumi; Chu, Mei-Jin; Sullivan, M.; Oka, Kazuhiro

    1995-10-10

    A complementary DNA for glucokinase (GK) was cloned from mouse liver total RNA by a combination of the polymerase chain reaction (PCR) and mouse liver cDNA library screening. Liver- and {beta}-cell-specific exons 1 were isolated by PCR using mouse and rat genomic DNAs. These clones were then used to screen a mouse genomic library; three genomic clones were isolated and characterized. The mouse GK gene spans over 20 kb, containing 11 exons including a liver- or {beta}-cell-specific exon 1, which encodes a tissue-specific 15-aa peptide at the N-terminus of the protein. Both types of GK contain 465 amino acid residues. The predicted amino acid sequence of mouse {beta}-cell-specific GK showed 98 and 96% identity to the rat and human enzymes, respectively; the corresponding values are 98 and 95% respectively, for the liver-specific GK. Several transcription factor-binding consensus sequences are identified in the 5{prime} flanking region of the mouse GK gene. 21 refs., 1 fig.

  11. The NAD(P)H-dependent glutamate dehydrogenase activities of Prevotella ruminicola B(1)4 can be attributed to one enzyme (GdhA), and gdhA expression is regulated in response to the nitrogen source available for growth.

    PubMed Central

    Wen, Z; Morrison, M

    1996-01-01

    Prevotella ruminicola B(1)4 possesses both NADPH- and NADH-linked glutamate dehydrogenase (GDH) activities, with the greatest specific activity being measured from ammonia-limited cultures. Relative to cells grown in the presence of 1 mM ammonium chloride, the NADPH-dependent activity was decreased approximately 10-fold when peptides were provided as a nitrogen source. Nondenaturing polyacrylamide gel electrophoresis (PAGE) was used to visualize the GDH protein(s) in cell extracts of P. ruminicola. For all growth conditions tested, only one GDH protein was detectable, and its relative abundance, as well as its reactivity with either NAD(P)+ or NAD(P)H, correlated well with the specific activities measured from whole-cell assays. Consistent with the findings from enzyme assays and PAGE activity gels, Northern (RNA) blot analysis revealed that expression of a gene encoding NAD(P)H-GDH activity was greatest in ammonia-grown cultures and that GDH activity is regulated in response to nitrogen source (ammonia versus peptides), probably at the level of transcription. A gene encoding the NAD(P)H-utilizing GDH activity (gdhA) was cloned, and its nucleotide sequence was determined and shown to contain an open reading frame of 1,332 bp which would encode a polypeptide of 48.8 kDa. The deduced amino acid sequence possesses three highly conserved motifs typical of family I GDHs, but several unique amino acid substitutions within these motifs were evident. These results are discussed within the context of ruminal nitrogen metabolism and the growth efficiency of succinate- and propionate-producing anaerobic bacteria. PMID:8837439

  12. Characterization of five partial deletions of the factor VIII gene

    SciTech Connect

    Youssoufian, H.; Antonarakis, S.E.; Aronis, S.; Tsiftis, G.; Phillips, D.G.; Kazazian, H.H. Jr.

    1987-06-01

    Hemophilia A is an X-linked disorder of coagulation caused by a deficiency of factor VIII. By using cloned DNA probes, the authors have characterized the following five different partial deletions of the factor VIII gene from a panel of 83 patients with hemophilia A: (i) a 7-kilobase (kb) deletion that eliminates exon 6; (ii) a 2.5-kb deletion that eliminates 5' sequences of exon 14; (iii) a deletion of at least 7 kb that eliminates exons 24 and 25; (iv) a deletion of at least 16 kb that eliminates exons 23-25; and (v) a 5.5-kb deletion that eliminates exon 22. The first four deletions are associated with severe hemophilia A. By contrast, the last deletion is associated with moderate disease, possibly because of in-frame splicing from adjacent exons. None of those patients with partial gene deletions had circulating inhibitors to factor VIII. One deletion occurred de novo in a germ cell of the maternal grandmother, while a second deletion occurred in a germ cell of the maternal grandfather. These observations demonstrate that de novo deletions of X-linked genes can occur in either male or female gametes.

  13. Interaction between glutamate dehydrogenase (GDH) and L-leucine catabolic enzymes: intersecting metabolic pathways.

    PubMed

    Hutson, Susan M; Islam, Mohammad Mainul; Zaganas, Ioannis

    2011-09-01

    Branched-chain amino acids (BCAAs) catabolism follows sequential reactions and their metabolites intersect with other metabolic pathways. The initial enzymes in BCAA metabolism, the mitochondrial branched-chain aminotransferase (BCATm), which deaminates the BCAAs to branched-chain α-keto acids (BCKAs); and the branched-chain α-keto acid dehydrogenase enzyme complex (BCKDC), which oxidatively decarboxylates the BCKAs, are organized in a supramolecular complex termed metabolon. Glutamate dehydrogenase (GDH1) is found in the metabolon in rat tissues. Bovine GDH1 binds to the pyridoxamine 5'-phosphate (PMP)-form of human BCATm (PMP-BCATm) but not to pyridoxal 5'-phosphate (PLP)-BCATm in vitro. This protein interaction facilitates reamination of the α-ketoglutarate (αKG) product of the GDH1 oxidative deamination reaction. Human GDH1 appears to act like bovine GDH1 but human GDH2 does not show the same enhancement of BCKDC enzyme activities. Another metabolic enzyme is also found in the metabolon is pyruvate carboxylase (PC). Kinetic results suggest that PC binds to the E1 decarboxylase of BCKDC but does not effect BCAA catabolism. The protein interaction of BCATm and GDH1 promotes regeneration of PLP-BCATm which then binds to BCKDC resulting in channeling of the BCKA products from BCATm first half reaction to E1 and promoting BCAA oxidation and net nitrogen transfer from BCAAs. The cycling of nitrogen through glutamate via the actions of BCATm and GDH1 releases free ammonia. Formation of ammonia may be important for astrocyte glutamine synthesis in the central nervous system. In peripheral tissue association of BCATm and GDH1 would promote BCAA oxidation at physiologically relevant BCAA concentrations. PMID:21621574

  14. Mapping of the glucose dehydrogenase gene in Bacillus subtilis.

    PubMed Central

    Chaudhry, G R; Halpern, Y S; Saunders, C; Vasantha, N; Schmidt, B J; Freese, E

    1984-01-01

    A 4.0-kilobase DNA fragment containing the developmentally regulated gene for glucose dehydrogenase (gdh) from Bacillus subtilis was incorporated into the plasmid pGX345, which contains a marker conferring chloramphenicol resistance (cat). The resistance marker of the resulting integration vector was used to map the gdh gene on the B. subtilis chromosome. Using PBS1 transduction, the gene order was determined to be aroI cat (gdh) mtlB dal. The cat (gdh) marker was also cotransformable with mtlB. The genetic location of the gdh gene established by this indirect method was confirmed by the fact that the original phage lambda EF2, containing a 10-kilobase B. subtilis DNA fragment from which the 4-kilobase gdh region had been subcloned, also contained the mtlB gene. Images PMID:6438057

  15. The Q^2 Evolution of the GDH sum Rule (on 3He and the Neutron)

    SciTech Connect

    Gordon Cates

    2002-06-01

    We discuss the extention of the Gerasimov-Drell-Hearn (GDH) sum rule, which pertains to real photons, to include scattering due to virtual photons. We present data from Jefferson Laboratory experiment E94-010 which measured the inclusive scattering of polarized electrons from a polarized 3He target over the quasielastic and resonance regions. From these data we exctract the transverse-transverse interference cross section {sigma}{prime}_TT', and compute the Q^2 depenent extended GDH integral.

  16. Involvement of GDH3-encoded NADP+-dependent Glutamate Dehydrogenase in Yeast Cell Resistance to Stress-induced Apoptosis in Stationary Phase Cells*

    PubMed Central

    Lee, Yong Joo; Kim, Kyung Jin; Kang, Hong Yong; Kim, Hye-Rim; Maeng, Pil Jae

    2012-01-01

    Glutamate metabolism is linked to a number of fundamental metabolic pathways such as amino acid metabolism, the TCA cycle, and glutathione (GSH) synthesis. In the yeast Saccharomyces cerevisiae, glutamate is synthesized from α-ketoglutarate by two NADP+-dependent glutamate dehydrogenases (NADP-GDH) encoded by GDH1 and GDH3. Here, we report the relationship between the function of the NADP-GDH and stress-induced apoptosis. Gdh3-null cells showed accelerated chronological aging and hypersusceptibility to thermal and oxidative stress during stationary phase. Upon exposure to oxidative stress, Gdh3-null strains displayed a rapid loss in viability associated with typical apoptotic hallmarks, i.e. reactive oxygen species accumulation, nuclear fragmentation, DNA breakage, and phosphatidylserine translocation. In addition, Gdh3-null cells, but not Gdh1-null cells, had a higher tendency toward GSH depletion and subsequent reactive oxygen species accumulation than did WT cells. GSH depletion was rescued by exogenous GSH or glutamate. The hypersusceptibility of stationary phase Gdh3-null cells to stress-induced apoptosis was suppressed by deletion of GDH2. Promoter swapping and site-directed mutagenesis of GDH1 and GDH3 indicated that the necessity of GDH3 for the resistance to stress-induced apoptosis and chronological aging is due to the stationary phase-specific expression of GDH3 and concurrent degradation of Gdh1 in which the Lys-426 residue plays an essential role. PMID:23105103

  17. Expression, purification and characterization of human glutamate dehydrogenase (GDH) allosteric regulatory mutations.

    PubMed Central

    Fang, Jie; Hsu, Betty Y L; MacMullen, Courtney M; Poncz, Mortimer; Smith, Thomas J; Stanley, Charles A

    2002-01-01

    Glutamate dehydrogenase (GDH) catalyses the reversible oxidative deamination of l-glutamate to 2-oxoglutarate in the mitochondrial matrix. In mammals, this enzyme is highly regulated by allosteric effectors. The major allosteric activator and inhibitor are ADP and GTP, respectively; allosteric activation by leucine may play an important role in amino acid-stimulated insulin secretion. The physiological significance of this regulation has been highlighted by the identification of children with an unusual hyperinsulinism/hyperammonaemia syndrome associated with dominant mutations in GDH that cause a loss in GTP inhibition. In order to determine the effects of these mutations on the function of the human GDH homohexamer, we studied the expression, purification and characterization of two of these regulatory mutations (H454Y, which affects the putative GTP-binding site, and S448P, which affects the antenna region) and a mutation designed to alter the putative binding site for ADP (R463A). The sensitivity to GTP inhibition was impaired markedly in the purified H454Y (ED(50), 210 microM) and S448P (ED(50), 3.1 microM) human GDH mutants compared with the wild-type human GDH (ED(50), 42 nM) or GDH isolated from heterozygous patient cells (ED(50), 290 and 280 nM, respectively). Sensitivity to ADP or leucine stimulation was unaffected by these mutations, confirming that they interfere specifically with the inhibitory GTP-binding site. Conversely, the R463A mutation completely eliminated ADP activation of human GDH, but had little effect on either GTP inhibition or leucine activation. The effects of these three mutations on ATP regulation indicated that this nucleotide inhibits human GDH through binding of its triphosphate tail to the GTP site and, at higher concentrations, activates the enzyme through binding of the nucleotide to the ADP site. These data confirm the assignment of the GTP and ADP allosteric regulatory sites on GDH based on X-ray crystallography and provide

  18. Leuconostoc pseudomesenteroides WCFur3 partial 16S rRNA gene

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used a partial 535 base pair 16S rRNA gene sequence to identify a bacterial isolate. Fatty acid profiles are consistent with the 16S rRNA gene sequence identification of this bacterium. The isolate was obtained from a compost bin in Fort Collins, Colorado, USA. The 16S rRNA gene sequen...

  19. A note on the change in gene frequency of a selected allele in partial full-sib mating populations

    SciTech Connect

    Caballero, A.

    1996-02-01

    The change in gene frequency of a selected allele in partial full-sib mating populations was analyzed. The implications of these papers is important in terms of the fixation probability of genes because, for the same equilibrium inbreeding coefficient, fixation rates of mutant genes would be larger for partial full-sib mating than for partial selfing. 4 refs.

  20. Identification of a Gene in Staphylococcus xylosus Encoding a Novel Glucose Uptake Protein

    PubMed Central

    Fiegler, Heike; Bassias, Joannis; Jankovic, Ivana; Brückner, Reinhold

    1999-01-01

    By transposon Tn917 mutagenesis, two mutants of Staphylococcus xylosus were isolated that showed higher levels of β-galactosidase activity in the presence of glucose than the wild type. Both transposons integrated in a gene, designated glcU, encoding a protein involved in glucose uptake in S. xylosus, which is followed by a glucose dehydrogenase gene (gdh). Glucose-mediated repression of β-galactosidase, α-glucosidase, and β-glucuronidase activities was partially relieved in the mutant strains, while repression by sucrose or fructose remained as strong as in the wild type. In addition to the pleiotropic regulatory effect, integration of the transposons into glcU reduced glucose dehydrogenase activity, suggesting cotranscription of glcU and gdh. Insertional inactivation of the gdh gene and deletion of the glcU gene without affecting gdh expression showed that loss of GlcU function is exclusively responsible for the regulatory defect. Reduced glucose repression is most likely the consequence of impaired glucose uptake in the glcU mutant strains. With cloned glcU, an Escherichia coli mutant deficient in glucose transport could grow with glucose as sole carbon source, provided a functional glucose kinase was present. Therefore, glucose is internalized by glcU in nonphosphorylated form. A gene from Bacillus subtilis, ycxE, that is homologous to glcU, could substitute for glcU in the E. coli glucose growth experiments and restored glucose repression in the S. xylosus glcU mutants. Three more proteins with high levels of similarity to GlcU and YcxE are currently in the databases. It appears that these proteins constitute a novel family whose members are involved in bacterial transport processes. GlcU and YcxE are the first examples whose specificity, glucose, has been determined. PMID:10438764

  1. Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles.

    PubMed

    Meadows, Sarah K; Dressman, Holly K; Daher, Pamela; Himburg, Heather; Russell, J Lauren; Doan, Phuong; Chao, Nelson J; Lucas, Joseph; Nevins, Joseph R; Chute, John P

    2010-01-01

    In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing radiation. We have recently shown that genome-wide expression analysis of the peripheral blood (PB) can generate gene expression profiles that can predict radiation exposure and distinguish the dose level of exposure following total body irradiation (TBI). However, in the event a radiation-mass casualty scenario, many victims will have heterogeneous exposure due to partial shielding and it is unknown whether PB gene expression profiles would be useful in predicting the status of partially irradiated individuals. Here, we identified gene expression profiles in the PB that were characteristic of anterior hemibody-, posterior hemibody- and single limb-irradiation at 0.5 Gy, 2 Gy and 10 Gy in C57Bl6 mice. These PB signatures predicted the radiation status of partially irradiated mice with a high level of accuracy (range 79-100%) compared to non-irradiated mice. Interestingly, PB signatures of partial body irradiation were poorly predictive of radiation status by site of injury (range 16-43%), suggesting that the PB molecular response to partial body irradiation was anatomic site specific. Importantly, PB gene signatures generated from TBI-treated mice failed completely to predict the radiation status of partially irradiated animals or non-irradiated controls. These data demonstrate that partial body irradiation, even to a single limb, generates a characteristic PB signature of radiation injury and thus may necessitate the use of multiple signatures, both partial body and total body, to accurately assess the status of an individual exposed to radiation. PMID:20634956

  2. Computing the Internode Certainty and Related Measures from Partial Gene Trees

    PubMed Central

    Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis; Stamatakis, Alexandros

    2016-01-01

    We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set. PMID:26915959

  3. Computing the Internode Certainty and Related Measures from Partial Gene Trees.

    PubMed

    Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis; Stamatakis, Alexandros

    2016-06-01

    We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set. PMID:26915959

  4. Expression of chicken CTCF gene in COS-1 cells and partial purification of CTCF protein.

    PubMed

    Kotova, E S; Sorokina, I V; Akopov, S B; Nikolaev, L G; Sverdlov, E D

    2013-08-01

    The chicken gene for transcription factor CTCF was expressed in COS-1 mammalian cells. The CTCF protein containing polyhistidine tag was partially purified using metallo-affinity and ion-exchange chromatography. The expressed protein localized in the cell nucleus and was shown to be functionally active in the electrophoretic mobility shift assay and specifically interacted with anti-CTCF antibodies. PMID:24228875

  5. Statistical completion of a partially identified graph with applications for the estimation of gene regulatory networks.

    PubMed

    Yu, Donghyeon; Son, Won; Lim, Johan; Xiao, Guanghua

    2015-10-01

    We study the estimation of a Gaussian graphical model whose dependent structures are partially identified. In a Gaussian graphical model, an off-diagonal zero entry in the concentration matrix (the inverse covariance matrix) implies the conditional independence of two corresponding variables, given all other variables. A number of methods have been proposed to estimate a sparse large-scale Gaussian graphical model or, equivalently, a sparse large-scale concentration matrix. In practice, the graph structure to be estimated is often partially identified by other sources or a pre-screening. In this paper, we propose a simple modification of existing methods to take into account this information in the estimation. We show that the partially identified dependent structure reduces the error in estimating the dependent structure. We apply the proposed method to estimating the gene regulatory network from lung cancer data, where protein-protein interactions are partially identified from the human protein reference database. The application shows that proposed method identified many important cancer genes as hub genes in the constructed lung cancer network. In addition, we validated the prognostic importance of a newly identified cancer gene, PTPN13, in four independent lung cancer datasets. The results indicate that the proposed method could facilitate studying underlying lung cancer mechanisms and identifying reliable biomarkers for lung cancer prognosis. PMID:25837438

  6. Experimental Tests of the GDH and Other Sum Rules at SLAC

    SciTech Connect

    Bosted, P.E.; /Massachusetts U., Amherst

    2005-06-14

    Recent measurements from SLAC of the polarized nucleon structure functions g{sub 1} and g{sub 2} have been used to experimentally test the Bjorken, Ellis-Jaffe, Burkhardt-Cottingham, and Efremov-Leader-Teryaev sum rules. In the future, the SLAC E159 experiment will extend structure function measurements using real photons to 40 GeV, enabling a definitive test of the high energy convergence of the GDH sum rule for both proton and deuteron targets.

  7. In Vivo Gene Therapy of Hemophilia B: Sustained Partial Correction in Factor IX-Deficient Dogs

    NASA Astrophysics Data System (ADS)

    Kay, Mark A.; Rothenberg, Steven; Landen, Charles N.; Bellinger, Dwight A.; Leland, Frances; Toman, Carol; Finegold, Milton; Thompson, Arthur R.; Read, M. S.; Brinkhous, Kenneth M.; Woo, Savio L. C.

    1993-10-01

    The liver represents a model organ for gene therapy. A method has been developed for hepatic gene transfer in vivo by the direct infusion of recombinant retroviral vectors into the portal vasculature, which results in the persistent expression of exogenous genes. To determine if these technologies are applicable for the treatment of hemophilia B patients, preclinical efficacy studies were done in a hemophilia B dog model. When the canine factor IX complementary DNA was transduced directly into the hepatocytes of affected dogs in vivo, the animals constitutively expressed low levels of canine factor IX for more than 5 months. Persistent expression of the clotting. factor resulted in reductions of whole blood clotting and partial thromboplastin times of the treated animals. Thus, long-term treatment of hemophilia B patients may be feasible by direct hepatic gene therapy in vivo.

  8. Phylogenetic analysis of oryx species using partial sequences of mitochondrial rRNA genes.

    PubMed

    Khan, H A; Arif, I A; Al Farhan, A H; Al Homaidan, A A

    2008-01-01

    We conducted a comparative evaluation of 12S rRNA and 16S rRNA genes of the mitochondrial genome for molecular differentiation among three oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) with respect to two closely related outgroups, addax and roan. Our findings showed the failure of 12S rRNA gene to differentiate between the genus Oryx and addax, whereas a 342-bp partial sequence of 16S rRNA accurately grouped all five taxa studied, suggesting the utility of 16S rRNA segment for molecular phylogeny of oryx at the genus and possibly species levels. PMID:19048493

  9. Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome.

    PubMed

    Barghi, Neda; Concepcion, Gisela P; Olivera, Baldomero M; Lluisma, Arturo O

    2016-02-01

    The evolvability of venom components (in particular, the gene-encoded peptide toxins) in venomous species serves as an adaptive strategy allowing them to target new prey types or respond to changes in the prey field. The structure, organization, and expression of the venom peptide genes may provide insights into the molecular mechanisms that drive the evolution of such genes. Conus is a particularly interesting group given the high chemical diversity of their venom peptides, and the rapid evolution of the conopeptide-encoding genes. Conus genomes, however, are large and characterized by a high proportion of repetitive sequences. As a result, the structure and organization of conopeptide genes have remained poorly known. In this study, a survey of the genome of Conus tribblei was undertaken to address this gap. A partial assembly of C. tribblei genome was generated; the assembly, though consisting of a large number of fragments, accounted for 2160.5 Mb of sequence. A large number of repetitive genomic elements consisting of 642.6 Mb of retrotransposable elements, simple repeats, and novel interspersed repeats were observed. We characterized the structural organization and distribution of conotoxin genes in the genome. A significant number of conopeptide genes (estimated to be between 148 and 193) belonging to different superfamilies with complete or nearly complete exon regions were observed, ~60 % of which were expressed. The unexpressed conopeptide genes represent hidden but significant conotoxin diversity. The conotoxin genes also differed in the frequency and length of the introns. The interruption of exons by long introns in the conopeptide genes and the presence of repeats in the introns may indicate the importance of introns in facilitating recombination, evolution and diversification of conotoxins. These findings advance our understanding of the structural framework that promotes the gene-level molecular evolution of venom peptides. PMID:26423067

  10. Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression

    PubMed Central

    Lehtinen, Sonja; Lees, Jon; Bähler, Jürg; Shawe-Taylor, John; Orengo, Christine

    2015-01-01

    With the growing availability of large-scale biological datasets, automated methods of extracting functionally meaningful information from this data are becoming increasingly important. Data relating to functional association between genes or proteins, such as co-expression or functional association, is often represented in terms of gene or protein networks. Several methods of predicting gene function from these networks have been proposed. However, evaluating the relative performance of these algorithms may not be trivial: concerns have been raised over biases in different benchmarking methods and datasets, particularly relating to non-independence of functional association data and test data. In this paper we propose a new network-based gene function prediction algorithm using a commute-time kernel and partial least squares regression (Compass). We compare Compass to GeneMANIA, a leading network-based prediction algorithm, using a number of different benchmarks, and find that Compass outperforms GeneMANIA on these benchmarks. We also explicitly explore problems associated with the non-independence of functional association data and test data. We find that a benchmark based on the Gene Ontology database, which, directly or indirectly, incorporates information from other databases, may considerably overestimate the performance of algorithms exploiting functional association data for prediction. PMID:26288239

  11. IL-10 induces gene expression in macrophages: partial overlap with IL-5 but not with IL-4 induced genes.

    PubMed

    Stumpo, Rita; Kauer, Manfred; Martin, Stephan; Kolb, Hubert

    2003-10-01

    The hypothesis that IL-10, in addition to down-regulating pro-inflammatory activities of macrophages, induces an alternative state of macrophage reactivity was tested. We therefore conducted a systematic search for genes induced by IL-10 using the method of suppression subtractive hybridisation. Of an initial 1,300 candidate clones obtained, several screening rounds led to the identification of 51 clones which were reproducibly at least twofold up-regulated in mouse J774 macrophages in response to treatment with IL-10. Of these, 41 genes were homologous to known genes involved in cell metabolism or immunoregulation, five contained novel sequences and another five were homologous to ESTs without known function. One major finding was that about 25% of the IL-10 genes were also found expressed in response to IFNgamma, and several of these also reappeared in IL-4 or IL-5 induced mRNA species. Hence, Th1 and Th2 type cytokines may elicit a common basal activation response in macrophages. The second major finding was that 57% of IL-10 induced genes reappeared in IL-5 induced mRNA but no more than 18% were also found in IL-4 induced mRNA of J774 cells. We conclude that the gene expression response to IL-10 in macrophages is partially different from the response to IL-5 and is substantially different from the response to IL-4, which suggests an unexpected diversity of biological phenotypes induced by different Th2 type cytokines. PMID:14561490

  12. Duplication of partial spinosyn biosynthetic gene cluster in Saccharopolyspora spinosa enhances spinosyn production.

    PubMed

    Tang, Ying; Xia, Liqiu; Ding, Xuezhi; Luo, Yushuang; Huang, Fan; Jiang, Yuanwei

    2011-12-01

    Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of insect control agents. Most of the S. spinosa genes involved in spinosyn biosynthesis are found in a contiguous c. 74-kb cluster. To increase the spinosyn production through overexpression of their biosynthetic genes, part of its gene cluster (c. 18 kb) participating in the conversion of the cyclized polyketide to spinosyn was obtained by direct cloning via Red/ET recombination rather than by constructing and screening the genomic library. The resultant plasmid pUCAmT-spn was introduced into S. spinosa CCTCC M206084 from Escherichia coli S17-1 by conjugal transfer. The subsequent single-crossover homologous recombination caused a duplication of the partial gene cluster. Integration of this plasmid enhanced production of spinosyns with a total of 388 (± 25.0) mg L(-1) for spinosyns A and D in the exconjugant S. spinosa trans1 compared with 100 (± 7.7) mg L(-1) in the parental strain. Quantitative real time polymerase chain reaction analysis of three selected genes (spnH, spnI, and spnK) confirmed the positive effect of the overexpression of these genes on the spinosyn production. This study provides a simple avenue for enhancing spinosyn production. The strategies could also be used to improve the yield of other secondary metabolites. PMID:22092858

  13. Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

    PubMed Central

    Lang, Alex H.; Li, Hu; Collins, James J.; Mehta, Pankaj

    2014-01-01

    A common metaphor for describing development is a rugged “epigenetic landscape” where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from spin-glass physics. Each cell fate is a dynamic attractor, yet cells can change fate in response to external signals. Our model suggests that partially reprogrammed cells are a natural consequence of high-dimensional landscapes, and predicts that partially reprogrammed cells should be hybrids that co-express genes from multiple cell fates. We verify this prediction by reanalyzing existing datasets. Our model reproduces known reprogramming protocols and identifies candidate transcription factors for reprogramming to novel cell fates, suggesting epigenetic landscapes are a powerful paradigm for understanding cellular identity. PMID:25122086

  14. In Vivo Gene Transfer Strategies to Achieve Partial Correction of von Willebrand Disease

    PubMed Central

    Wang, Lan; Rosenberg, Jonathan B.; De, Bishnu P.; Ferris, Barbara; Wang, Rui; Rivella, Stefano; Kaminsky, Stephen M.

    2012-01-01

    Abstract von Willebrand disease (VWD), the most common hereditary coagulation disorder, results from mutations in the 52-exon gene for von Willebrand factor (VWF), which encodes an 8.4-kB cDNA. Studies with VWF cDNA plasmids have demonstrated that in vivo gene transfer to the liver will correct the coagulation dysfunction in VWF−/− mice, but the correction is transient. To develop gene therapy for VWF that would mediate long-term expression of the VWF cDNA in liver, we first evaluated segmental pre-mRNA trans-splicing (SPTS) with two adeno-associated virus (AAV) serotype 8 vectors, each delivering one-half of the VWF cDNA. However, although the two vectors functioned well to generate VWF multimers after infection of cells in vitro, the efficiency of SPTS was insufficient to correct the VWF−/− mouse in vivo. As an alternative, we assessed the ability of a lentiviral vector to transfer the intact murine VWF cDNA in vivo directly to the neonatal liver of VWF−/− mice, using generation of VWF multimers, bleeding time, and bleeding volume as efficacy parameters. The VWF lentivirus generated VWF multimers and partially or completely corrected the coagulation defect on a persistent basis in 33% of the treated VWF-deficient mice. On the basis of the concept that partial persistent correction with gene transfer could be beneficial in VWD patients, these observations suggest that lentiviral delivery of VWF cDNA should be explored as a candidate for gene therapy in patients with a severe form of VWD. PMID:22482515

  15. Partial gene deletion in LEC rat: An animal model for Wilson disease

    SciTech Connect

    Wu, J.; Forbes, J.R.; Cox, D.W.

    1994-09-01

    Wilson disease is an inherited disorder of copper transport in which incorporation of copper into ceruloplasmin and excretion of copper into bile are greatly reduced. Copper accumulates to a toxic level in the liver and also in the brain and kidney, causing a spectrum of hepatic and neurological abnormalities. We have recently cloned the gene for Wilson disease (designated ATP7B), which encodes a putative copper-transporting P-type ATPase. The inbred mutant Long-Evans Cinnamon (LEC) rat strain shows similarity to Wilson disease in many clinical and biochemical features. We have cloned cDNAs for the rat homologue (Atp7b) of the human Wilson disease gene (ATP7B) and have shown that the two genes have {approximately}82% identity at the amino acid sequence level. Rat cDNA sequences were used to identify a partial deletion in the Atp7b gene in the LEC rat. The deletion removes at least 750 bp of the coding region at the 3{prime} end, which includes the crucial ATP binding domain and extends downstream of the gene. The proximal breakpoint has been precisely localized at the cDNA level. Our results provide convincing evidence that the LEC rat is an animal model for Wilson disease. This model will be important for studying liver pathophysiology, for developing therapy for Wilson disease, and for studying the pathway of copper transport and its possible interaction with other heavy metals.

  16. PPARγ partial agonist GQ-16 strongly represses a subset of genes in 3T3-L1 adipocytes

    SciTech Connect

    Milton, Flora Aparecida; Cvoro, Aleksandra; Amato, Angelica A.; Sieglaff, Douglas H.; Filgueira, Carly S.; Arumanayagam, Anithachristy Sigamani; Caro Alves de Lima, Maria do; Rocha Pitta, Ivan; Assis Rocha Neves, Francisco de; Webb, Paul

    2015-08-28

    Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor gamma (PPARγ) agonists that improve insulin resistance but trigger side effects such as weight gain, edema, congestive heart failure and bone loss. GQ-16 is a PPARγ partial agonist that improves glucose tolerance and insulin sensitivity in mouse models of obesity and diabetes without inducing weight gain or edema. It is not clear whether GQ-16 acts as a partial agonist at all PPARγ target genes, or whether it displays gene-selective actions. To determine how GQ-16 influences PPARγ activity on a gene by gene basis, we compared effects of rosiglitazone (Rosi) and GQ-16 in mature 3T3-L1 adipocytes using microarray and qRT-PCR. Rosi changed expression of 1156 genes in 3T3-L1, but GQ-16 only changed 89 genes. GQ-16 generally showed weak effects upon Rosi induced genes, consistent with partial agonist actions, but a subset of modestly Rosi induced and strongly repressed genes displayed disproportionately strong GQ-16 responses. PPARγ partial agonists MLR24 and SR1664 also exhibit disproportionately strong effects on transcriptional repression. We conclude that GQ-16 displays a continuum of weak partial agonist effects but efficiently represses some negatively regulated PPARγ responsive genes. Strong repressive effects could contribute to physiologic actions of GQ-16. - Highlights: • GQ-16 is an insulin sensitizing PPARγ ligand with reduced harmful side effects. • GQ-16 displays a continuum of weak partial agonist activities at PPARγ-induced genes. • GQ-16 exerts strong repressive effects at a subset of genes. • These inhibitor actions should be evaluated in models of adipose tissue inflammation.

  17. Radiation and ionization energy loss simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab

    DOE PAGESBeta

    Yan, Xin -Hu; Ye, Yun -Xiu; Chen, Jian -Ping; Lu, Hai -Jiang; Zhu, Peng -Jia; Jiang, Feng -Jian

    2015-07-17

    The radiation and ionization energy loss are presented for single arm Monte Carlo simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab. Radiation and ionization energy loss are discussed formore » $$^{12}C$$ elastic scattering simulation. The relative momentum ratio $$\\frac{\\Delta p}{p}$$ and $$^{12}C$$ elastic cross section are compared without and with radiation energy loss and a reasonable shape is obtained by the simulation. The total energy loss distribution is obtained, showing a Landau shape for $$^{12}C$$ elastic scattering. This simulation work will give good support for radiation correction analysis of the GDH sum rule experiment.« less

  18. Radiation and ionization energy loss simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab

    SciTech Connect

    Yan, Xin -Hu; Ye, Yun -Xiu; Chen, Jian -Ping; Lu, Hai -Jiang; Zhu, Peng -Jia; Jiang, Feng -Jian

    2015-07-17

    The radiation and ionization energy loss are presented for single arm Monte Carlo simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab. Radiation and ionization energy loss are discussed for $^{12}C$ elastic scattering simulation. The relative momentum ratio $\\frac{\\Delta p}{p}$ and $^{12}C$ elastic cross section are compared without and with radiation energy loss and a reasonable shape is obtained by the simulation. The total energy loss distribution is obtained, showing a Landau shape for $^{12}C$ elastic scattering. This simulation work will give good support for radiation correction analysis of the GDH sum rule experiment.

  19. Partial kinetoplast-mitochondrial gene organization and expression in the respiratory deficient plant trypanosomatid Phytomonas serpens.

    PubMed

    Maslov, D A; Nawathean, P; Scheel, J

    1999-04-30

    In plant-dwelling trypanosomatids from the genus Phytomonas, mitochondrial functions, such as cytochrome mediated respiration, ATP production and Krebs cycle, are missing, and cell energetics is based on the glycolysis. Using Blue Native/Tricine-SDS two-dimensional gel electrophoretic analysis, we observed that mitochondrial respiratory Complexes III (cytochrome bc1) and IV (cytochrome c oxidase) were absent in Phytomonas serpens; however, Complex V (ATPase) was present. A deletion of the genes for cytochrome c oxidase subunit III (COIII) and apocytochrome b (Cyb) was identified within the 6234 bp sequenced region of the 31 kb maxicircle kinetoplast DNA. Genes, found in this region, include 12S and 9S ribosomal RNAs, subunits 7, 8 and 9 of NADH dehydrogenase (ND7, ND8 and ND9) and subunit 6 of ATPase (A6 or MURF4), as well as the genes (MURF1, MURF5 and G3) with unknown function. Most genes are actively transcribed and some mRNAs are edited. Fully edited mRNAs for A6 and G3 were abundant, while edited ND7 transcripts were rare, and only partially edited and pre-edited transcripts for ND8 were detected. The data show that the mitochondrial genome of P. serpens is functional, although its functions may be limited to expressing the ATPase and, possibly, NADH dehydrogenase complexes. PMID:10340485

  20. Sequencing of the Reannotated LMNB2 Gene Reveals Novel Mutations in Patients with Acquired Partial Lipodystrophy

    PubMed Central

    Hegele, Robert A.; Cao, Henian; Liu, Dora M.; Costain, Gary A.; Charlton-Menys, Valentine; Rodger, N. Wilson; Durrington, Paul N.

    2006-01-01

    The etiology of acquired partial lipodystrophy (APL, also called “Barraquer-Simons syndrome”) is unknown. Genomic DNA mutations affecting the nuclear lamina protein lamin A cause inherited partial lipodystrophy but are not found in patients with APL. Because it also encodes a nuclear lamina protein (lamin B2) and its genomic structure was recently reannotated, we sequenced LMNB2 as a candidate gene in nine white patients with APL. In four patients, we found three new rare mutations in LMNB2: intron 1 −6G→T, exon 5 c.643G→A (p.R215Q; in two patients), and exon 8 c.1218G→A (p.A407T). The combined frequency of these mutations was 0.222 in the patients with APL, compared with 0.0018 in a multiethnic control sample of 1,100 subjects (P=2.1×10-7) and 0.0045 in a sample of 330 white controls (P=1.2×10-5). These novel heterozygous mutations are the first reported for LMNB2, are the first reported among patients with APL, and indicate how sequencing of a reannotated candidate gene can reveal new disease-associated mutations. PMID:16826530

  1. Isolation and partial characterization of the gene for goose fatty acid synthase.

    PubMed

    Kameda, K; Goodridge, A G

    1991-01-01

    Fatty acid synthase is regulated by diet and hormones, with regulation being primarily transcriptional. In chick embryo hepatocytes in culture, triiodothyronine stimulates accumulation of enzyme and transcription of the gene. Since the 5'-flanking region of this gene is likely involved in hormonal regulation of its expression, we have isolated and partially characterized an avian fatty acid synthase gene. A genomic DNA library was constructed in a cosmid vector and screened with cDNA clones that contained sequence complementary to the 3' end of goose fatty acid synthase mRNA. A genomic clone (approximately 35 kilobase pairs (kb] was isolated, and a 6.5-kb EcoRI fragment thereof contained DNA complementary to the 3' noncoding region of fatty acid synthase mRNA. Additional cosmid libraries were screened with 5' fragments of previously isolated genomic clones, resulting in the isolation of five overlapping cosmid DNAs. The entire region of cloned DNA spans approximately 105 kb. Exon-containing fragments were identified by hybridization with end-labeled poly(A)+ RNA and by hybridization of labeled exon-containing genomic DNA fragments to fatty acid synthase mRNA. A new set of cDNA clones spanning approximately 3.2 kb was isolated from a lambda-ZAP goose liver cDNA library using the 5'-most exon-containing fragment of the 5'-most genomic DNA clone. This region of mRNA contains a 5'-untranslated sequence and a continuous open reading frame which includes a region that codes for the essential cysteine of the beta-ketoacyl synthase domain. The entire fatty acid synthase gene spans about 50 kb. The 5' 15 kb of the gene contain 7 exons. S1 nuclease and primer extension analyses were used to identify a single site for initiation of transcription, 174 nucleotides upstream from the putative translation initiation codon. Putative "TATA" and "CCAAT" boxes are located 28 and 60 base pairs (bp), respectively, upstream of the site of initiation of transcription. The 5'-flanking 597

  2. Identification of Scopulariopsis species by partial 28S rRNA gene sequence analysis.

    PubMed

    Jagielski, Tomasz; Kosim, Kinga; Skóra, Magdalena; Macura, Anna Barbara; Bielecki, Jacek

    2013-01-01

    The genus Scopulariopsis contains over 30 species of mitosporic moulds, which although usually saprophytic may also act as opportunistic pathogens in humans. They have mainly been associated with onychomycosis, and only sporadically reported as a cause of deep tissue infections or systemic disease. Identification of Scopulariopsis species still largely relies on phenotype-based methods. There is a need for a molecular diagnostic approach, that would allow to reliably discriminate between different Scopulariopsis species. The aim of this study was to apply sequence analysis of partial 28S rRNA gene for species identification of Scopulariopsis clinical isolates. Although the method employed did reveal some genetic polymorphism among Scopulariopsis isolates tested, it was not enough for species delineation. For this to be achieved, other genetic loci, within and beyond the rDNA operon, need to be investigated. PMID:24459837

  3. DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy

    PubMed Central

    Li, Deming; Fan, Jinyu; Li, Ziwei; Xu, Cunshuan

    2014-01-01

    Epidermal growth factor (EGF), a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH) rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration. PMID:25071410

  4. Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication

    PubMed Central

    Korithoski, Bryan; Kolaczkowski, Oralia; Mukherjee, Krishanu; Kola, Reema; Earl, Chandra; Kolaczkowski, Bryan

    2015-01-01

    The RIG-like receptors (RLRs) are related proteins that identify viral RNA in the cytoplasm and activate cellular immune responses, primarily through direct protein-protein interactions with the signal transducer, IPS1. Although it has been well established that the RLRs, RIG-I and MDA5, activate IPS1 through binding between the twin caspase activation and recruitment domains (CARDs) on the RLR and a homologous CARD on IPS1, it is less clear which specific RLR CARD(s) are required for this interaction, and almost nothing is known about how the RLR-IPS1 interaction evolved. In contrast to what has been observed in the presence of immune-modulating K63-linked polyubiquitin, here we show that—in the absence of ubiquitin—it is the first CARD domain of human RIG-I and MDA5 (CARD1) that binds directly to IPS1 CARD, and not the second (CARD2). Although the RLRs originated in the earliest animals, both the IPS1 gene and the twin-CARD domain architecture of RIG-I and MDA5 arose much later in the deuterostome lineage, probably through a series of tandem partial-gene duplication events facilitated by tight clustering of RLRs and IPS1 in the ancestral deuterostome genome. Functional differentiation of RIG-I CARD1 and CARD2 appears to have occurred early during this proliferation of RLR and related CARDs, potentially driven by adaptive coevolution between RIG-I CARD domains and IPS1 CARD. However, functional differentiation of MDA5 CARD1 and CARD2 occurred later. These results fit a general model in which duplications of protein-protein interaction domains into novel gene contexts could facilitate the expansion of signaling networks and suggest a potentially important role for functionally-linked gene clusters in generating novel immune-signaling pathways. PMID:26356745

  5. Identification of Genes in a Partially Resistant Genotype of Avena sativa Expressed in Response to Puccinia coronata Infection.

    PubMed

    Loarce, Yolanda; Navas, Elisa; Paniagua, Carlos; Fominaya, Araceli; Manjón, José L; Ferrer, Esther

    2016-01-01

    Cultivated oat (Avena sativa), an important crop in many countries, can suffer significant losses through infection by the fungus Puccinia coronata, the causal agent of crown rust disease. Understanding the molecular basis of existing partial resistance to this disease might provide targets of interest for crop improvement programs. A suppressive subtractive hybridization (SSH) library was constructed using cDNA from the partially resistant oat genotype MN841801-1 after inoculation with the pathogen. A total of 929 genes returned a BLASTx hit and were annotated under different GO terms, including 139 genes previously described as participants in mechanisms related to the defense response and signal transduction. Among these were genes involved in pathogen recognition, cell-wall modification, oxidative burst/ROS scavenging, and abscisic acid biosynthesis, as well genes related to inducible defense responses mediated by salicylic and jasmonic acid (although none of which had been previously reported involved in strong responses). These findings support the hypothesis that basal defense mechanisms are the main systems operating in oat partial resistance to P. coronata. When the expression profiles of 20 selected genes were examined at different times following inoculation with the pathogen, the partially resistant genotype was much quicker in mounting a response than a susceptible genotype. Additionally, a number of genes not previously described in oat transcriptomes were identified in this work, increasing our molecular knowledge of this crop. PMID:27303424

  6. Identification of Genes in a Partially Resistant Genotype of Avena sativa Expressed in Response to Puccinia coronata Infection

    PubMed Central

    Loarce, Yolanda; Navas, Elisa; Paniagua, Carlos; Fominaya, Araceli; Manjón, José L.; Ferrer, Esther

    2016-01-01

    Cultivated oat (Avena sativa), an important crop in many countries, can suffer significant losses through infection by the fungus Puccinia coronata, the causal agent of crown rust disease. Understanding the molecular basis of existing partial resistance to this disease might provide targets of interest for crop improvement programs. A suppressive subtractive hybridization (SSH) library was constructed using cDNA from the partially resistant oat genotype MN841801-1 after inoculation with the pathogen. A total of 929 genes returned a BLASTx hit and were annotated under different GO terms, including 139 genes previously described as participants in mechanisms related to the defense response and signal transduction. Among these were genes involved in pathogen recognition, cell-wall modification, oxidative burst/ROS scavenging, and abscisic acid biosynthesis, as well genes related to inducible defense responses mediated by salicylic and jasmonic acid (although none of which had been previously reported involved in strong responses). These findings support the hypothesis that basal defense mechanisms are the main systems operating in oat partial resistance to P. coronata. When the expression profiles of 20 selected genes were examined at different times following inoculation with the pathogen, the partially resistant genotype was much quicker in mounting a response than a susceptible genotype. Additionally, a number of genes not previously described in oat transcriptomes were identified in this work, increasing our molecular knowledge of this crop. PMID:27303424

  7. Novel glucose dehydrogenase from Mucor prainii: Purification, characterization, molecular cloning and gene expression in Aspergillus sojae.

    PubMed

    Satake, Ryoko; Ichiyanagi, Atsushi; Ichikawa, Keiichi; Hirokawa, Kozo; Araki, Yasuko; Yoshimura, Taro; Gomi, Keiko

    2015-11-01

    Glucose dehydrogenase (GDH) is of interest for its potential applications in the field of glucose sensors. To improve the performance of glucose sensors, GDH is required to have strict substrate specificity. A novel flavin adenine dinucleotide (FAD)-dependent GDH was isolated from Mucor prainii NISL0103 and its enzymatic properties were characterized. This FAD-dependent GDH (MpGDH) exhibited high specificity toward glucose. High specificity for glucose was also observed even in the presence of saccharides such as maltose, galactose and xylose. The molecular masses of the glycoforms of GDH ranged from 90 to 130 kDa. After deglycosylation, a single 80 kDa band was observed. The gene encoding MpGDH was cloned and expressed in Aspergillus sojae. The apparent kcat and Km values of recombinant enzyme for glucose were found to be 749.7 s(-1) and 28.3 mM, respectively. The results indicated that the characteristics of MpGDH were suitable for assaying blood glucose levels. PMID:25912449

  8. Recombinations between Alu repeat sequences that result in partial deletions within the C1 inhibitor gene.

    PubMed

    Ariga, T; Carter, P E; Davis, A E

    1990-12-01

    Genomic DNA sequence analysis was used to define the extent of deletions within the C1 inhibitor gene in two families with type I hereditary angioneurotic edema. Southern blot analysis initially indicated the presence of the partial deletions. One deletion was approximately 2 kb and included exon VII, whereas the other was approximately 8.5 kb and included exons IV-VI. Genomic libraries from an affected member of each family were constructed and clones containing the deletions were analyzed. Sequence analysis of the deletion joints of the mutants and corresponding regions of the normal gene in the two families demonstrated that both deletion joints resulted from recombination of two Alu repetitive DNA elements. Alu repeat sequences from introns VI and VII combined to make a novel Alu in family A, and Alu sequences in introns III and VI were spliced to make a new Alu in family B. The splice sites in the Alu sequences of both mutants were located in the left arm of the Alu element, and both recombination joints overlapped one of the RNA polymerase III promoter sequences. Because the involved Alu sequences, in both instances, were oriented in the same direction, unequal crossingover is the most likely mechanism to account for these mutations. PMID:2276734

  9. The wheat durable, multipathogen resistance gene Lr34 confers partial blast resistance in rice.

    PubMed

    Krattinger, Simon G; Sucher, Justine; Selter, Liselotte L; Chauhan, Harsh; Zhou, Bo; Tang, Mingzhi; Upadhyaya, Narayana M; Mieulet, Delphine; Guiderdoni, Emmanuel; Weidenbach, Denise; Schaffrath, Ulrich; Lagudah, Evans S; Keller, Beat

    2016-05-01

    The wheat gene Lr34 confers durable and partial field resistance against the obligate biotrophic, pathogenic rust fungi and powdery mildew in adult wheat plants. The resistant Lr34 allele evolved after wheat domestication through two gain-of-function mutations in an ATP-binding cassette transporter gene. An Lr34-like fungal disease resistance with a similar broad-spectrum specificity and durability has not been described in other cereals. Here, we transformed the resistant Lr34 allele into the japonica rice cultivar Nipponbare. Transgenic rice plants expressing Lr34 showed increased resistance against multiple isolates of the hemibiotrophic pathogen Magnaporthe oryzae, the causal agent of rice blast disease. Host cell invasion during the biotrophic growth phase of rice blast was delayed in Lr34-expressing rice plants, resulting in smaller necrotic lesions on leaves. Lines with Lr34 also developed a typical, senescence-based leaf tip necrosis (LTN) phenotype. Development of LTN during early seedling growth had a negative impact on formation of axillary shoots and spikelets in some transgenic lines. One transgenic line developed LTN only at adult plant stage which was correlated with lower Lr34 expression levels at seedling stage. This line showed normal tiller formation and more importantly, disease resistance in this particular line was not compromised. Interestingly, Lr34 in rice is effective against a hemibiotrophic pathogen with a lifestyle and infection strategy that is different from obligate biotrophic rusts and mildew fungi. Lr34 might therefore be used as a source in rice breeding to improve broad-spectrum disease resistance against the most devastating fungal disease of rice. PMID:26471973

  10. Partial prevention of hepatic lipid alterations in nude mice by neonatal thymulin gene therapy.

    PubMed

    García de Bravo, Margarita M; Polo, Mónica P; Reggiani, Paula C; Rimoldi, Omar J; Dardenne, Mireille; Goya, Rodolfo G

    2006-08-01

    During adult life athymic (nude) male mice display not only a severe T-cell-related immunodeficiency but also endocrine imbalances and a moderate hyperglycemia. We studied the impact of congenital athymia on hepatic lipid composition and also assessed the ability of neonatal thymulin gene therapy to prevent the effects of athymia. We constructed a recombinant adenoviral vector, RAd-metFTS, expressing a synthetic DNA sequence encoding met-FTS, an analog of the thymic peptide facteur thymique sérique (FTS), whose Zn-bound biologically active form is known as thymulin. On postnatal day 1-2 homozygous (nu/nu) nude and heterozygous (nu/+) mice were injected with 10(8) pfu of RAd-metFTS or RAd-betagal (control vector) intramuscularly. The animals were processed at 52 d of age. Serum thymulin, glycemia, hepatic phospholipid FA composition and free and esterified cholesterol were determined. Adult homozygous male nudes were significantly (P < 0.01) hyperglycemic when compared with their heterozygous counterparts (2.04 vs. 1.40 g/L, respectively). The relative percentage of 16:0, 18:1 n-9, and 18:1n-7 FA was lower, whereas that of 18:0, 20:4n-6, and 22:6n-3 FA was higher, in hepatic phospholipid (PL) of nu/nu animals as compared with their nu/+ counterparts. Some of these alterations, such as that in the relative content of 22:6n-3 in liver PL and the unsaturation index, were completely or partially prevented by neonatal thymulin gene therapy. We conclude that the thymus influences lipid metabolism and that thymulin is involved in this modulatory activity. PMID:17120928

  11. Radiation and ionization energy loss simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab

    NASA Astrophysics Data System (ADS)

    Yan, Xin-Hu; Ye, Yun-Xiu; Chen, Jian-Ping; Lu, Hai-Jiang; Zhu, Peng-Jia; Jiang, Feng-Jian

    2015-07-01

    The radiation and ionization energy loss are presented for single arm Monte Carlo simulation for the GDH sum rule experiment in Hall-A at the Jefferson Lab. Radiation and ionization energy loss are discussed for 12C elastic scattering simulation. The relative momentum ratio \\frac{{Δ p}}{p} and 12C elastic cross section are compared without and with radiative energy loss and a reasonable shape is obtained by the simulation. The total energy loss distribution is obtained, showing a Landau shape for 12C elastic scattering. This simulation work will give good support for radiation correction analysis of the GDH sum rule experiment. Supported by National Natural Science Foundation of China (11135002, 11275083), US Department of Energy contract DE-AC05-84ER-40150 under which Jefferson Science Associates operates the Thomas Jefferson National Accelerator Facility and Natural Science Foundation of An'hui Educational Committee (KJ2012B179)

  12. Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species

    PubMed Central

    Rosselló, Ricardo Antonio; Chen, Chun-Chun; Dai, Rui; Howard, Jason T; Hochgeschwender, Ute; Jarvis, Erich D

    2013-01-01

    Cells are fundamental units of life, but little is known about evolution of cell states. Induced pluripotent stem cells (iPSCs) are once differentiated cells that have been re-programmed to an embryonic stem cell-like state, providing a powerful platform for biology and medicine. However, they have been limited to a few mammalian species. Here we found that a set of four mammalian transcription factor genes used to generate iPSCs in mouse and humans can induce a partially reprogrammed pluripotent stem cell (PRPSCs) state in vertebrate and invertebrate model organisms, in mammals, birds, fish, and fly, which span 550 million years from a common ancestor. These findings are one of the first to show cross-lineage stem cell-like induction, and to generate pluripotent-like cells for several of these species with in vivo chimeras. We suggest that the stem-cell state may be highly conserved across a wide phylogenetic range. DOI: http://dx.doi.org/10.7554/eLife.00036.001 PMID:24015354

  13. Partial Functional Diversification of Drosophila melanogaster Septin Genes Sep2 and Sep5

    PubMed Central

    O’Neill, Ryan S.; Clark, Denise V.

    2016-01-01

    The septin family of hetero-oligomeric complex-forming proteins can be divided into subgroups, and subgroup members are interchangeable at specific positions in the septin complex. Drosophila melanogaster has five septin genes, including the two SEPT6 subgroup members Sep2 and Sep5. We previously found that Sep2 has a unique function in oogenesis, which is not performed by Sep5. Here, we find that Sep2 is uniquely required for follicle cell encapsulation of female germline cysts, and that Sep2 and Sep5 are redundant for follicle cell proliferation. The five D. melanogaster septins localize similarly in oogenesis, including as rings flanking the germline ring canals. Pnut fails to localize in Sep5; Sep2 double mutant follicle cells, indicating that septin complexes fail to form in the absence of both Sep2 and Sep5. We also find that mutations in septins enhance the mutant phenotype of bazooka, a key component in the establishment of cell polarity, suggesting a link between septin function and cell polarity. Overall, this work suggests that Sep5 has undergone partial loss of ancestral protein function, and demonstrates redundant and unique functions of septins. PMID:27172205

  14. Palynomorphs of Permian Gondwana coal from borehole GDH-38, Barapukuria Coal Basin, Bangladesh

    USGS Publications Warehouse

    Akhtar, A.; Kosanke, R.M.

    2000-01-01

    Thirty-two core samples of Permian Gondwana coal from three coal beds of borehole GDH-38, Barapukuria Coal Basin, Dinajpur, the north-northwestern part of Bangladesh, have been collected for palynological analysis. All samples except one yielded palynomorphs and some samples contain well-preserved and abundant palynomorphs of the gymnospermal and cryptogamic groups that are considered to be useful for future correlation studies. The lower coal bed (331.6-372.5 m) can easily be differentiated from the upper two coal beds by the presence of Alisporites, Cordaitina, Corisaccites, Hamiapollenites, Leuckisporites, Nuskoisporites, Tumoripollenites, Vestgisporites and Vittatina. It is difficult to palynologically differentiate the middle (198.1-208 m) and upper (162.3-172.9 m) coal beds as they contain a very limited number of specimens by which they can be identified. The middle bed is distinguished by the presence of Microbaculispora and Weylandites and the upper bed by the presence of a single taxon Acanthotriletes. Some of the vesiculate or saccate taxa extracted from these coal beds are typical of those occurring in Permian strata of Gondwana in India, South Africa, South America, Russia, Australia and Antarctica. They are thought to be derived from Glossopteris flora, which is characterised by an abundance of Pteridospermic plants of the gymnosperm group. ?? 2000 Elsevier Science Limited. All rights reserved.

  15. Palynomorphs of Permian Gondwana coal from borehole GDH-38, Barapukuria Coal Basin, Bangladesh

    NASA Astrophysics Data System (ADS)

    Akhtar, A.; Kosanke, R. M.

    2000-07-01

    Thirty-two core samples of Permian Gondwana coal from three coal beds of borehole GDH-38, Barapukuria Coal Basin, Dinajpur, the north-northwestern part of Bangladesh, have been collected for palynological analysis. All samples except one yielded palynomorphs and some samples contain well-preserved and abundant palynomorphs of the gymnospermal and cryptogamic groups that are considered to be useful for future correlation studies. The lower coal bed (331.6-372.5 m) can easily be differentiated from the upper two coal beds by the presence of Alisporites, Cordaitina, Corisaccites, Hamiapollenites, Leuckisporites, Nuskoisporites, Tumoripollenites, Vestgisporites and Vittatina. It is difficult to palynologically differentiate the middle (198.1-208 m) and upper (162.3-172.9 m) coal beds as they contain a very limited number of specimens by which they can be identified. The middle bed is distinguished by the presence of Microbaculispora and Weylandites and the upper bed by the presence of a single taxon Acanthotriletes. Some of the vesiculate or saccate taxa extracted from these coal beds are typical of those occurring in Permian strata of Gondwana in India, South Africa, South America, Russia, Australia and Antarctica. They are thought to be derived from Glossopteris flora, which is characterised by an abundance of Pteridospermic plants of the gymnosperm group.

  16. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

    PubMed Central

    2012-01-01

    Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps) genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL) have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad) and susceptible (‘Sloan’) genotypes. There were 1025 single nucleotide polymorphisms (SNPs) in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for resistance to P. sojae

  17. Rat Hepatocytes Weighted Gene Co-Expression Network Analysis Identifies Specific Modules and Hub Genes Related to Liver Regeneration after Partial Hepatectomy

    PubMed Central

    Zhou, Yun; Xu, Jiucheng; Liu, Yunqing; Li, Juntao; Chang, Cuifang; Xu, Cunshuan

    2014-01-01

    The recovery of liver mass is mainly mediated by proliferation of hepatocytes after 2/3 partial hepatectomy (PH) in rats. Studying the gene expression profiles of hepatocytes after 2/3 PH will be helpful to investigate the molecular mechanisms of liver regeneration (LR). We report here the first application of weighted gene co-expression network analysis (WGCNA) to analyze the biological implications of gene expression changes associated with LR. WGCNA identifies 12 specific gene modules and some hub genes from hepatocytes genome-scale microarray data in rat LR. The results suggest that upregulated MCM5 may promote hepatocytes proliferation during LR; BCL3 may play an important role by activating or inhibiting NF-kB pathway; MAPK9 may play a permissible role in DNA replication by p38 MAPK inactivation in hepatocytes proliferation stage. Thus, WGCNA can provide novel insight into understanding the molecular mechanisms of LR. PMID:24743545

  18. Body fat distribution in women with familial partial lipodystrophy caused by mutation in the lamin A/C gene

    PubMed Central

    Monteiro, Luciana Z.; Foss-Freitas, Maria C.; Júnior Montenegro, Renan M.; Foss, Milton C.

    2012-01-01

    Familial partial lipodystrophy (FPLD), Dunnigan variety, is an autosomal dominant disorder caused due to missense mutations in the lamin A/C (LMNA) gene encoding nuclear lamina proteins. Patients with FPLD are predisposed to metabolic complications of insulin resistance such as diabetes. We sought to evaluate and compare body fat distribution with dual-emission X-ray absorptiometry in women with and without FPLD and identify densitometric, clinical and metabolic features. PMID:22276265

  19. The Spin Structure of 3He and the Neutron at Low Q^2: A Measurement of the Generalized GDH Integrand

    SciTech Connect

    Sulkosky, Vincent

    2007-08-01

    Since the 1980's, the study of nucleon (proton or neutron) spin structure has been an active field both experimentally and theoretically. One of the primary goals of this work is to test our understanding of Quantum Chromodynamics (QCD), the fundamental theory of the strong interaction. In the high energy region of asymptotically free quarks, QCD has been verified. However, verifiable predictions in the low energy region are harder to obtain due to the complex interactions between the nucleon's constituents: quarks and gluons. In the non-pertubative regime, low-energy effective field theories such as chiral perturbation theory provide predictions for the spin structure functions in the form of sum rules. Spin-dependent sum rules such as the Gerasimov-Drell-Hearn (GDH) sum rule are important tools available to study nucleon spin structure. Originally derived for real photon absorption, the Gerasimov-Drell-Hearn (GDH) sum rule was first extended for virtual photon absorption in 1989. The extension of the sum rule provides a unique relation, valid at any momentum transfer ($Q^{2}$), that can be used to study the nucleon spin structure and make comparisons between theoretical predictions and experimental data. Experiment E97-110 was performed at the Thomas Jefferson National Accelerator Facility (Jefferson Lab) to examine the spin structure of the neutron and $^{3}$He. The Jefferson Lab longitudinally-polarized electron beam with incident energies between 1.1 and 4.4 GeV was scattered from a longitudinally or transversely polarized $^{3}$He gas target in the Hall A end station. Asymmetries and polarized cross-section differences were measured in the quasielastic and resonance regions to extract the spin structure functions $g_{1}(x,Q^{2})$ and $g_{2}(x,Q^{2})$ at low momentum transfers (0.02 $< Q^{2} <$ 0.3 GeV$^{2}$). The goal of the experiment was to perform a precise measurement of the $Q^{2}$ dependence of the extended GDH integral and of the moments of the neutron

  20. Incorporation of partial polyhedrin homology sequences (PPHS) enhances the production of cloned foreign genes in a baculovirus expression system.

    PubMed

    Gong, Zhaohui; Jin, Yongfeng; Zhang, Yaozhou

    2006-03-01

    Baculovirus expression vector systems (BEVSs) have been used extensively for high-level expression of cloned foreign genes. In many instances, the levels of recombinant protein(s) produced in insect cells and larvae are insufficient for experimental purposes. Thus new techniques and methods are needed to increase significantly the protein expression levels in BEVS. In the present paper, we describe the incorporation of a 15 bp element derived from the 5'-end partial sequence of the polyhedrin gene, which contains the non-coding sequence ATAAAT and the coding sequence ATGCCGAAT, into the 5'-end of the CTB (cholera toxin B subunit)-INS (insulin) fusion gene. With the addition of the PPHS (partial polyhedrin homology sequences), two extra amino acids (Pro-Asn) were added to the N-terminus of the mCTB-INS (modified CTB-INS) fusion protein. This new fusion protein was expressed in both insect cells and larvae using BEVSs. We found that the addition of PPHS enhanced 4-fold the expression of CTB-INS in both insect cells and larvae. Further analysis revealed that the additional two amino acids in mCTB-INS did not significantly affect binding affinity for G(M1) ganglioside. Therefore the PPHS can be used as a constitutive element immediately downstream of the polyhedrin promoter to induce significant increases in the expression levels of cloned foreign genes. PMID:16313236

  1. Partial Sleep Restriction Activates Immune Response-Related Gene Expression Pathways: Experimental and Epidemiological Studies in Humans

    PubMed Central

    Rantanen, Ville; Kronholm, Erkki; Surakka, Ida; van Leeuwen, Wessel M. A.; Lehto, Maili; Matikainen, Sampsa; Ripatti, Samuli; Härmä, Mikko; Sallinen, Mikael; Salomaa, Veikko; Jauhiainen, Matti; Alenius, Harri; Paunio, Tiina; Porkka-Heiskanen, Tarja

    2013-01-01

    Epidemiological studies have shown that short or insufficient sleep is associated with increased risk for metabolic diseases and mortality. To elucidate mechanisms behind this connection, we aimed to identify genes and pathways affected by experimentally induced, partial sleep restriction and to verify their connection to insufficient sleep at population level. The experimental design simulated sleep restriction during a working week: sleep of healthy men (N = 9) was restricted to 4 h/night for five nights. The control subjects (N = 4) spent 8 h/night in bed. Leukocyte RNA expression was analyzed at baseline, after sleep restriction, and after recovery using whole genome microarrays complemented with pathway and transcription factor analysis. Expression levels of the ten most up-regulated and ten most down-regulated transcripts were correlated with subjective assessment of insufficient sleep in a population cohort (N = 472). Experimental sleep restriction altered the expression of 117 genes. Eight of the 25 most up-regulated transcripts were related to immune function. Accordingly, fifteen of the 25 most up-regulated Gene Ontology pathways were also related to immune function, including those for B cell activation, interleukin 8 production, and NF-κB signaling (P<0.005). Of the ten most up-regulated genes, expression of STX16 correlated negatively with self-reported insufficient sleep in a population sample, while three other genes showed tendency for positive correlation. Of the ten most down-regulated genes, TBX21 and LGR6 correlated negatively and TGFBR3 positively with insufficient sleep. Partial sleep restriction affects the regulation of signaling pathways related to the immune system. Some of these changes appear to be long-lasting and may at least partly explain how prolonged sleep restriction can contribute to inflammation-associated pathological states, such as cardiometabolic diseases. PMID:24194869

  2. Trade-off between constitutive and inducible resistance against herbivores is only partially explained by gene expression and glucosinolate production

    PubMed Central

    Rasmann, Sergio; Chassin, Estelle; Bilat, Julia; Glauser, Gaétan; Reymond, Philippe

    2015-01-01

    The hypothesis that constitutive and inducible plant resistance against herbivores should trade-off because they use the same resources and impose costs to plant fitness has been postulated for a long time. Negative correlations between modes of deployment of resistance and defences have been observed across and within species in common garden experiments. It was therefore tested whether that pattern of resistance across genotypes follows a similar variation in patterns of gene expression and chemical defence production. Using the genetically tractable model Arabidopsis thaliana and different modes of induction, including the generalist herbivore Spodoptera littoralis, the specialist herbivore Pieris brassicae, and jasmonate application, constitutive and inducibility of resistance was measured across seven A. thaliana accessions that were previously selected based on constitutive levels of defence gene expression. According to theory, it was found that modes of resistance traded-off among accessions, particularly against S. littoralis, in which accessions investing in high constitutive resistance did not increase it substantially after attack and vice-versa. Accordingly, the average expression of eight genes involved in glucosinolate production negatively predicted larval growth across the seven accessions. Glucosinolate production and genes related to defence induction on healthy and herbivore-damaged plants were measured next. Surprisingly, only a partial correlation between glucosinolate production, gene expression, and the herbivore resistance results was found. These results suggest that the defence outcome of plants against herbivores goes beyond individual molecules or genes but stands on a complex network of interactions. PMID:25716695

  3. Trade-off between constitutive and inducible resistance against herbivores is only partially explained by gene expression and glucosinolate production.

    PubMed

    Rasmann, Sergio; Chassin, Estelle; Bilat, Julia; Glauser, Gaétan; Reymond, Philippe

    2015-05-01

    The hypothesis that constitutive and inducible plant resistance against herbivores should trade-off because they use the same resources and impose costs to plant fitness has been postulated for a long time. Negative correlations between modes of deployment of resistance and defences have been observed across and within species in common garden experiments. It was therefore tested whether that pattern of resistance across genotypes follows a similar variation in patterns of gene expression and chemical defence production. Using the genetically tractable model Arabidopsis thaliana and different modes of induction, including the generalist herbivore Spodoptera littoralis, the specialist herbivore Pieris brassicae, and jasmonate application, constitutive and inducibility of resistance was measured across seven A. thaliana accessions that were previously selected based on constitutive levels of defence gene expression. According to theory, it was found that modes of resistance traded-off among accessions, particularly against S. littoralis, in which accessions investing in high constitutive resistance did not increase it substantially after attack and vice-versa. Accordingly, the average expression of eight genes involved in glucosinolate production negatively predicted larval growth across the seven accessions. Glucosinolate production and genes related to defence induction on healthy and herbivore-damaged plants were measured next. Surprisingly, only a partial correlation between glucosinolate production, gene expression, and the herbivore resistance results was found. These results suggest that the defence outcome of plants against herbivores goes beyond individual molecules or genes but stands on a complex network of interactions. PMID:25716695

  4. Identification and partial characterization of genes that are transactivated by different pathways in quiescent mouse cells stimulated with serum.

    PubMed

    Boeggeman, E; Masibay, A S; Qasba, P K; Sreevalsan, T

    1990-11-01

    We have identified four cDNA clones, cl-1, cl-5, cl-15, and cl-16, that represent genes induced by serum in resting mouse 3T3 cells. Partial sequence analysis of the four cDNAs indicated that cl-15 corresponds to the mouse beta-actin gene. Comparison of the DNA sequences of the other three clones with the sequence data bank (Genbank) showed little homology to other known DNA sequences and thus represent novel genes. The level of the mRNAs corresponding to the four genes began to increase in resting cells following serum stimulation, reached a peak between 5 h and 8 h and then started to decline. Inhibitors of transcription diminished the induction of the mRNAs corresponding to the four genes. Cycloheximide and anisomycin had little effect on the induction of beta actin mRNA while the induction of the other three genes was suppressed by the same inhibitors. 12-O-Tetradecanoylphorbol-13-acetate and the calcium ionophore A23187 enhanced the expression of the cl-16 mRNA while epidermal growth factor, fibroblast growth factor, or insulin enhanced the expression of cl-1- and cl-5-specific transcripts. The level of beta-actin mRNA was elevated in resting cells by epidermal growth factor and 12-O-tetradecanoylphorbol-13-acetate and to a lesser extent by fibroblast growth factor, insulin, and dibutyryl cyclic AMP-elevating agents. Pertussis toxin, an inhibitor of the action of G proteins, did not significantly suppress the activation of the four genes by serum. However, 2-aminopurine, a protein kinase inhibitor, suppressed the induction of the four transcripts in serum-stimulated cells. The possible pathways involved in the activation of these genes in resting cells are discussed. PMID:1978837

  5. The Role of Glutamate Dehydrogenase (GDH) Testing Assay in the Diagnosis of Clostridium difficile Infections: A High Sensitive Screening Test and an Essential Step in the Proposed Laboratory Diagnosis Workflow for Developing Countries like China.

    PubMed

    Cheng, Jing-Wei; Xiao, Meng; Kudinha, Timothy; Xu, Zhi-Peng; Sun, Lin-Ying; Hou, Xin; Zhang, Li; Fan, Xin; Kong, Fanrong; Xu, Ying-Chun

    2015-01-01

    The incidence and severity of Clostridium difficile infection (CDI) in North America and Europe has increased significantly since the 2000s. However, CDI is not widely recognized in China and other developing countries due to limited laboratory diagnostic capacity and low awareness. Most published studies on laboratory workflows for CDI diagnosis are from developed countries, and thus may not be suitable for most developing countries. Therefore, an alternative strategy for developing countries is needed. In this study, we evaluated the performance of the Glutamate Dehydrogenase (GDH) test and its associated workflow on 416 fecal specimens from suspected CDI cases. The assay exhibited excellent sensitivity (100.0%) and specificity (92.8%), compared to culture based method, and thus could be a good screening marker for C. difficile but not for indication of toxin production. The VIDAS CDAB assay, which can detect toxin A/B directly from fecal specimens, showed good specificity (99.7%) and positive predictive value (97.2%), but low sensitivity (45.0%) and negative predictive value (88.3%), compared with PCR-based toxin gene detection. Therefore, we propose a practical and efficient GDH test based workflow strategy for the laboratory diagnosis of CDI in developing countries like China. By applying this new workflow, the CDI laboratory diagnosis rate was notably improved in our center, yet the increasing cost was kept at a minimum level. Furthermore, to gain some insights into the genetic population structure of C. difficile isolates from our hospital, we performed MLST and PCR toxin gene typing. PMID:26659011

  6. The Role of Glutamate Dehydrogenase (GDH) Testing Assay in the Diagnosis of Clostridium difficile Infections: A High Sensitive Screening Test and an Essential Step in the Proposed Laboratory Diagnosis Workflow for Developing Countries like China

    PubMed Central

    Cheng, Jing-Wei; Xiao, Meng; Kudinha, Timothy; Xu, Zhi-Peng; Sun, Lin-Ying; Hou, Xin; Zhang, Li; Fan, Xin; Kong, Fanrong; Xu, Ying-Chun

    2015-01-01

    The incidence and severity of Clostridium difficile infection (CDI) in North America and Europe has increased significantly since the 2000s. However, CDI is not widely recognized in China and other developing countries due to limited laboratory diagnostic capacity and low awareness. Most published studies on laboratory workflows for CDI diagnosis are from developed countries, and thus may not be suitable for most developing countries. Therefore, an alternative strategy for developing countries is needed. In this study, we evaluated the performance of the Glutamate Dehydrogenase (GDH) test and its associated workflow on 416 fecal specimens from suspected CDI cases. The assay exhibited excellent sensitivity (100.0%) and specificity (92.8%), compared to culture based method, and thus could be a good screening marker for C. difficile but not for indication of toxin production. The VIDAS CDAB assay, which can detect toxin A/B directly from fecal specimens, showed good specificity (99.7%) and positive predictive value (97.2%), but low sensitivity (45.0%) and negative predictive value (88.3%), compared with PCR-based toxin gene detection. Therefore, we propose a practical and efficient GDH test based workflow strategy for the laboratory diagnosis of CDI in developing countries like China. By applying this new workflow, the CDI laboratory diagnosis rate was notably improved in our center, yet the increasing cost was kept at a minimum level. Furthermore, to gain some insights into the genetic population structure of C. difficile isolates from our hospital, we performed MLST and PCR toxin gene typing. PMID:26659011

  7. Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes

    PubMed Central

    Hu, Wei; Xia, Zhiqiang; Yan, Yan; Ding, Zehong; Tie, Weiwei; Wang, Lianzhe; Zou, Meiling; Wei, Yunxie; Lu, Cheng; Hou, Xiaowan; Wang, Wenquan; Peng, Ming

    2015-01-01

    Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava. PMID:26579161

  8. Partial cloning of CYP2C23a genes and hepatic protein expression in eight representative avian species.

    PubMed

    Watanabe, K P; Kawai, Y K; Nakayama, S M M; Ikenaka, Y; Mizukawa, H; Takaesu, N; Ito, M; Ikushiro, S-I; Sakaki, T; Ishizuka, M

    2015-04-01

    Large interspecies differences in avian xenobiotic metabolism have been revealed by microsome-based studies, but specific enzyme isoforms in different bird species have not yet been compared. We have previously shown that CYP2C23 genes are the most induced CYP isoforms in chicken liver. In this study, we collected partial CYP2C23a gene sequences from eight avian species (ostrich, blue-eared pheasant, snowy owl, great-horned owl, Chilean flamingo, peregrin falcon, Humboldt penguin, and black-crowned night heron) selected to cover the whole avian lineage: Paleognathae, Galloanserae, and Neoaves. Genetic analysis showed that CYP2C23 genes of Galloanserae species (chicken and blue-eared pheasant) had unique characteristics. We found some duplicated genes (CYP2C23a and CYP2C23b) and two missing amino acid residues in Galloanserae compared to the other two lineages. The genes have lower homology than in other avian lineages, which suggests Galloanserae-specific rapid evolutionary changes. These genetic features suggested that the Galloanserae are not the most representative avian species, considering that the Neoaves comprise more than 95% of birds. Moreover, we succeeded in synthesizing an antipeptide polyclonal antibody against the region of CYP2C23 protein conserved in avians. However, comparative quantitation of CYP2C23 proteins in livers from six species showed that expression levels of these proteins differed no more than fourfold. Further study is needed to clarify the function of avian CYP2C23 proteins. PMID:25229839

  9. Homozygous partial genomic triplication of the parkin gene in early-onset parkinsonism.

    PubMed

    Mata, Ignacio F; Alvarez, Victoria; Coto, Eliecer; Blazquez, Marta; Guisasola, Luis M; Salvador, Carlos; Kachergus, Jennifer M; Lincoln, Sarah J; Farrer, Matthew

    2005-06-01

    Autosomal recessive mutations in the parkin gene are the predominant cause of familial, early-onset parkinsonism; missense mutations involving one or a few nucleotides, exonic deletions and duplications have been described. Here we report a family with two affected brothers. Direct sequencing of parkin did not detect mutations, but semi-quantitative analysis identified a novel exonic rearrangement of exons 2-4. Both patients were homozygous for unique genomic triplications of the parkin gene. PMID:15862897

  10. Engineered Production of Tryprostatins in E. coli through Reconstitution of a Partial ftm Biosynthetic Gene Cluster from Aspergillus sp.

    PubMed Central

    Shah, Gopitkumar R; Wesener, Shane R.; Cheng, Yi-Qiang

    2015-01-01

    Tryprostatin A and B are indole alkaloid-based fungal products that inhibit mammalian cell cycle at the G2/M phase. They are biosynthetic intermediates of fumitremorgins produced by a complex pathway involving a nonribosomal peptide synthetase (FtmA), a prenyltransferase (FtmB), a cytochrome P450 hydroxylase (FtmC), an O-methyltransferase (FtmD), and several additional enzymes. A partial fumitremorgin biosynthetic gene cluster (ftmABCD) from Aspergillus sp. was reconstituted in Escherichia coli BL21(DE3) cells, with or without the co-expression of an Sfp-type phosphopantetheinyltransferase gene (Cv_sfp) from Chromobacterium violaceum No. 968. Several recombinant E. coli strains produced tryprostatin B up to 106 mg/l or tryprostatin A up to 76 mg/l in the fermentation broth under aerobic condition, providing an effective way to prepare those pharmaceutically important natural products biologically. PMID:26640821

  11. Cloning and partial characterization of the mouse glutamine:fructose-6-phosphate amidotransferase (GFAT) gene promoter.

    PubMed Central

    Sayeski, P P; Wang, D; Su, K; Han, I O; Kudlow, J E

    1997-01-01

    Glutamine:fructose-6-phosphate amidotransferase (GFAT) is the enzyme that is rate limiting in the synthesis of glucosamine and hexosamines. Glucosamine has been proposed to contribute to the glucotoxicity of diabetes. Evidence that the gene encoding GFAT is transcriptionally regulated prompted us to clone and characterize its promoter. The position of the mouse GFAT promoter relative to the translational start site was located by primer extension and found to be 149 bp upstream of the translational start site. A 1.9 kb SacI fragment of the GFAT gene was found to contain the promoter and 88 bp of sequence downstream of the transcriptional start site. This promoter segment could drive expression of a luciferase reporter gene, could confer correct transcriptional initiation to the reporter and could confer the EGF-responsiveness previously observed in the native gene. The mouse GFAT promoter lacks a canonical TATA box and has several GC boxes within a highly GC-rich region. Deletional analysis of the promoter indicated that a proximal element extending to -120 relative to the transcriptional start site could confer reporter expression at a level of 57% of the 1.9 kb construct. Detailed analysis of this proximal region by DNase I footprinting, electrophoretic mobility shift assays and site-directed mutagenesis indicated that Sp1 binds to three elements in this proximal promoter segment and plays a vital role in regulation of transcription from this gene. PMID:9060444

  12. Changes in neuronal activity and gene expression in guinea-pig auditory brainstem after unilateral partial hearing loss.

    PubMed

    Dong, S; Mulders, W H A M; Rodger, J; Robertson, D

    2009-03-31

    Spontaneous neural hyperactivity in the central auditory pathway is often associated with deafness, the most common form of which is partial hearing loss. We quantified both peripheral hearing loss and spontaneous activity in single neurons of the contralateral inferior colliculus in a guinea-pig model 1 week after a unilateral partial deafness induced by cochlear mechanical lesion. We also measured mRNA levels of candidate genes in the same animals using quantitative real-time PCR. Spontaneous hyperactivity was most marked in the frequency region of the peripheral hearing loss. Expression of glutamate decarboxylase 1 (GAD1), GABA-A receptor subunit alpha-1 (GABRA1), and potassium channel subfamily K member 15 (KCNK15) was decreased ipsilaterally in the cochlear nucleus and bilaterally in the inferior colliculus. A member of RAB family of small GTPase (RAB3A) was decreased in both ipsilateral cochlear nucleus and contralateral inferior colliculus. RAB3 GTPase activating protein subunit 1 (RAB3GAP1) and glycine receptor subunit alpha-1 (GLRA1) were reduced ipsilaterally in the cochlear nucleus only. These results suggest that a decrease in inhibitory neurotransmission and an increase in membrane excitability may contribute to elevated neuronal spontaneous activity in the auditory brainstem following unilateral partial hearing loss. PMID:19356697

  13. Phylogenetic relationships among the Nymphalidae (Lepidoptera) inferred from partial sequences of the wingless gene.

    PubMed Central

    Brower, A V

    2000-01-01

    A cladistic analysis was performed on a 378 bp region of the wingless gene from 103 nymphalid species and three pierid outgroups in order to infer higher level patterns of relationship among nymphalid subfamilies and tribes. Although the data are highly homoplastic, in many instances the most parsimonious cladograms corroborate traditionally recognized groups. The results suggest that this short gene region provides a useful source of data for phylogenetic inference, provided that adequate effort is made to sample a diversity of taxa. PMID:10902686

  14. Isolation of DNA encoding sucrase genes from Streptococcus salivarius and partial characterization of the enzymes expressed in Escherichia coli.

    PubMed Central

    Houck, C M; Pear, J R; Elliott, R; Perchorowicz, J T

    1987-01-01

    Restriction enzyme fragments containing two sucrase genes have been isolated from a cosmid library of Streptococcus salivarius DNA. The genes were expressed in Escherichia coli cells, and the properties of both enzymes were studied in partially purified protein extracts from E. coli. One gene encoding an invertase-type sucrase was subcloned on a 2.4-kilobase-pair fragment. The sucrase enzyme had a Km for sucrose of 48 mM and a pH optimum of 6.5. The S. salivarius sucrase clone showed no detectable hybridization to a yeast invertase clone. Two overlapping subclones which had 1 kilobase pair of DNA in common were used to localize a fructosyltransferase gene. The fructosyltransferase had a Km of 93 mM and a pH optimum of 7.0. The product of the fructosyltransferase was a levan. A fructosyltransferase clone from Bacillus subtilis did not hybridize to S. salivarius DNA. The properties of the enzymes were compared with those of previously characterized sucrases. Images PMID:3112128

  15. Partial correction of a severe molecular defect in hemophilia A, because of errors during expression of the factor VIII gene

    SciTech Connect

    Young, M.; Antonarakis, S.E.; Inaba, Hiroshi

    1997-03-01

    Although the molecular defect in patients in a Japanese family with mild to moderately severe hemophilia A was a deletion of a single nucleotide T within an A{sub 8}TA{sub 2} sequence of exon 14 of the factor VIII gene, the severity of the clinical phenotype did not correspond to that expected of a frameshift mutation. A small amount of functional factor VIII protein was detected in the patient`s plasma. Analysis of DNA and RNA molecules from normal and affected individuals and in vitro transcription/translation suggested a partial correction of the molecular defect, because of the following: (i) DNA replication/RNA transcription errors resulting in restoration of the reading frame and/or (ii) {open_quotes}ribosomal frameshifting{close_quotes} resulting in the production of normal factor VIII polypeptide and, thus, in a milder than expected hemophilia A. All of these mechanisms probably were promoted by the longer run of adenines, A{sub 10} instead of A{sub 8}TA{sub 2}, after the delT. Errors in the complex steps of gene expression therefore may partially correct a severe frameshift defect and ameliorate an expected severe phenotype. 36 refs., 6 figs.

  16. Electronic structure and metallization of cubic GdH3 under pressure: Ab initio many-body GW calculations

    NASA Astrophysics Data System (ADS)

    Kong, Bo; Zhang, Yachao

    2016-07-01

    The electronic structures of the cubic GdH3 are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G0W0 calculations give a fundamental band gap of 1.72 eV, while GGA+ GW0 or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localization of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn-Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH3 can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G0W0 calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW0 and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G0W0 calculations in the 4f-core case is the closest to the real result. By G0W0 calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH3 occurs around 40 GPa, which might be a satisfied prediction.

  17. Molecular phylogeny of Fusarium inferred from partial RNA polymerase II gene sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Currently there are no robust phylogenetic hypotheses for Fusarium based on large-scale sampling across the breadth of this important group of mycotoxigenic phytopathogens. Nucleotide variation within the second largest RNA polymerase subunit (RPB2) protein-coding gene, however, has clearly demonst...

  18. Convergent evolution of human and bovine haptoglobin: partial duplication of the genes.

    PubMed

    Wicher, Krzysztof B; Fries, Erik

    2007-10-01

    Haptoglobin (Hp) is a hemoglobin-binding plasma protein consisting of two types of chains, called alpha and beta, which originate from a common polypeptide. In humans, but not in other mammals, Hp has been shown to occur in two allelic forms, Hp1 and Hp2, which differ in the length of the alpha-chain. The longer alpha-chain (in Hp2) seems to have arisen by an internal duplication of a gene segment coding for almost the entire alpha-chain of Hp1. In this article we show that Hp of cow (Bos taurus) contains an alpha-chain, the structure of which is similar to that of the human Hp2 alpha-chain. Furthermore, comparison of the structure of bovine Hp and human Hp2 suggests that the bovine gene arose by a duplication of the gene segment homologous to that duplicated in human Hp2. However, a phylogenetic analysis indicates that the two genes were formed independently. The evolutionary pressure that has led to the fixation of the Hps with a longer alpha-chain is not known. PMID:17922076

  19. Partial Antiviral Activities Detection of Chicken Mx Jointing with Neuraminidase Gene (NA) against Newcastle Disease Virus

    PubMed Central

    Zhang, Yani; Fu, Dezhi; Chen, Hao; Zhang, Zhentao; Shi, Qingqing; Elsayed, Ahmed Kamel; Li, Bichun

    2013-01-01

    As an attempt to increase the resistance to Newcastle Disease Virus (NDV) and so further reduction of its risk on the poultry industry. This work aimed to build the eukaryotic gene co-expression plasmid of neuraminidase (NA) gene and myxo-virus resistance (Mx) and detect the gene expression in transfected mouse fibroblasts (NIH-3T3) cells, it is most important to investigate the influence of the recombinant plasmid on the chicken embryonic fibroblasts (CEF) cells. cDNA fragment of NA and mutant Mx gene were derived from pcDNA3.0-NA and pcDNA3.0-Mx plasmid via PCR, respectively, then NA and Mx cDNA fragment were inserted into the multiple cloning sites of pVITRO2 to generate the eukaryotic co-expression plasmid pVITRO2-Mx-NA. The recombinant plasmid was confirmed by restriction endonuclease treatment and sequencing, and it was transfected into the mouse fibroblasts (NIH-3T3) cells. The expression of genes in pVITRO2-Mx-NA were measured by RT-PCR and indirect immunofluorescence assay (IFA). The recombinant plasmid was transfected into CEF cells then RT-PCR and the micro-cell inhibition tests were used to test the antiviral activity for NDV. Our results showed that co-expression vector pVITRO2-Mx-NA was constructed successfully; the expression of Mx and NA could be detected in both NIH-3T3 and CEF cells. The recombinant proteins of Mx and NA protect CEF cells from NDV infection until after 72 h of incubation but the individually mutagenic Mx protein or NA protein protects CEF cells from NDV infection till 48 h post-infection, and co-transfection group decreased significantly NDV infection compared with single-gene transfection group (P<0. 05), indicating that Mx-NA jointing contributed to delaying the infection of NDV in single-cell level and the co-transfection of the jointed genes was more powerful than single one due to their synergistic effects. PMID:23977111

  20. Effects of partial deletion of the wzm and wzt genes on lipopolysaccharide synthesis and virulence of Brucella abortus S19.

    PubMed

    Wang, Xiuran; Wang, Lin; Lu, Tiancheng; Yang, Yanling; Chen, Si; Zhang, Rui; Lang, Xulong; Yan, Guangmou; Qian, Jing; Wang, Xiaoxu; Meng, Lingyi; Wang, Xinglong

    2014-06-01

    Brucellosis is a worldwide human and animal infectious disease, and the effective methods of its control are immunisation of animals by vaccination and elimination. Brucella abortus S19 is one of the popular vaccines with virulence in the control of cattle Brucellosis. In the present study, allelic exchange plasmids of wzm and wzt genes and partial knockout mutants of wzm and wzt were constructed to evaluate the resulting difference in virulence of B. abortus S19. PCR analysis revealed that the target genes were knocked out. The mutants were rough mutants and they could be differentiated from natural infection by the Rose Bengal plate and standard agglutination tests. The molecular weights of lipopolysaccharides of the Δwzm and Δwzt mutants were clustered between 25 and 40 kDa, and 30 and 35 kDa separately, and were markedly different from those in B. abortus S19. The virulence of B. abortus Δwzm and Δwzt was decreased compared with that of B. abortus S19 in mice. All these results identified that there were several differences between the wzm and wzt genes on lipopolysaccharide synthesis and on the virulence of B. abortus. PMID:24718931

  1. Long Noncoding RNA MEG3 Interacts with p53 Protein and Regulates Partial p53 Target Genes in Hepatoma Cells

    PubMed Central

    Zhu, Juanjuan; Liu, Shanshan; Ye, Fuqiang; Shen, Yuan; Tie, Yi; Zhu, Jie; Wei, Lixin; Jin, Yinghua; Fu, Hanjiang; Wu, Yongge; Zheng, Xiaofei

    2015-01-01

    Maternally Expressed Gene 3 (MEG3) encodes a lncRNA which is suggested to function as a tumor suppressor. Previous studies suggested that MEG3 functioned through activation of p53, however, the functional properties of MEG3 remain obscure and their relevance to human diseases is under continuous investigation. Here, we try to illuminate the relationship of MEG3 and p53, and the consequence in hepatoma cells. We find that transfection of expression construct of MEG3 enhances stability and transcriptional activity of p53. Deletion analysis of MEG3 confirms that full length and intact structure of MEG3 are critical for it to activate p53-mediated transactivation. Interestingly, our results demonstrate for the first time that MEG3 can interact with p53 DNA binding domain and various p53 target genes are deregulated after overexpression of MEG3 in hepatoma cells. Furthermore, results of qRT-PCR have shown that MEG3 RNA is lost or reduced in the majority of HCC samples compared with adjacent non-tumorous samples. Ectopic expression of MEG3 in hepatoma cells significantly inhibits proliferation and induces apoptosis. In conclusion, our data demonstrates that MEG3 functions as a tumor suppressor in hepatoma cells through interacting with p53 protein to activate p53-mediated transcriptional activity and influence the expression of partial p53 target genes. PMID:26444285

  2. A partial gene deletion of SLC45A2 causes oculocutaneous albinism in Doberman pinscher dogs.

    PubMed

    Winkler, Paige A; Gornik, Kara R; Ramsey, David T; Dubielzig, Richard R; Venta, Patrick J; Petersen-Jones, Simon M; Bartoe, Joshua T

    2014-01-01

    The first white Doberman pinscher (WDP) dog was registered by the American Kennel Club in 1976. The novelty of the white coat color resulted in extensive line breeding of this dog and her offspring. The WDP phenotype closely resembles human oculocutaneous albinism (OCA) and clinicians noticed a seemingly high prevalence of pigmented masses on these dogs. This study had three specific aims: (1) produce a detailed description of the ocular phenotype of WDPs, (2) objectively determine if an increased prevalence of ocular and cutaneous melanocytic tumors was present in WDPs, and (3) determine if a genetic mutation in any of the genes known to cause human OCA is causal for the WDP phenotype. WDPs have a consistent ocular phenotype of photophobia, hypopigmented adnexal structures, blue irides with a tan periphery and hypopigmented retinal pigment epithelium and choroid. WDPs have a higher prevalence of cutaneous melanocytic neoplasms compared with control standard color Doberman pinschers (SDPs); cutaneous tumors were noted in 12/20 WDP (<5 years of age: 4/12; >5 years of age: 8/8) and 1/20 SDPs (p<0.00001). Using exclusion analysis, four OCA causative genes were investigated for their association with WDP phenotype; TYR, OCA2, TYRP1 and SLC45A2. SLC45A2 was found to be linked to the phenotype and gene sequencing revealed a 4,081 base pair deletion resulting in loss of the terminus of exon seven of SLC45A2 (chr4∶77,062,968-77,067,051). This mutation is highly likely to be the cause of the WDP phenotype and is supported by a lack of detectable SLC45A2 transcript levels by reverse transcriptase PCR. The WDP provides a valuable model for studying OCA4 visual disturbances and melanocytic neoplasms in a large animal model. PMID:24647637

  3. A Partial Gene Deletion of SLC45A2 Causes Oculocutaneous Albinism in Doberman Pinscher Dogs

    PubMed Central

    Winkler, Paige A.; Gornik, Kara R.; Ramsey, David T.; Dubielzig, Richard R.; Venta, Patrick J.; Petersen-Jones, Simon M.; Bartoe, Joshua T.

    2014-01-01

    The first white Doberman pinscher (WDP) dog was registered by the American Kennel Club in 1976. The novelty of the white coat color resulted in extensive line breeding of this dog and her offspring. The WDP phenotype closely resembles human oculocutaneous albinism (OCA) and clinicians noticed a seemingly high prevalence of pigmented masses on these dogs. This study had three specific aims: (1) produce a detailed description of the ocular phenotype of WDPs, (2) objectively determine if an increased prevalence of ocular and cutaneous melanocytic tumors was present in WDPs, and (3) determine if a genetic mutation in any of the genes known to cause human OCA is causal for the WDP phenotype. WDPs have a consistent ocular phenotype of photophobia, hypopigmented adnexal structures, blue irides with a tan periphery and hypopigmented retinal pigment epithelium and choroid. WDPs have a higher prevalence of cutaneous melanocytic neoplasms compared with control standard color Doberman pinschers (SDPs); cutaneous tumors were noted in 12/20 WDP (<5 years of age: 4/12; >5 years of age: 8/8) and 1/20 SDPs (p<0.00001). Using exclusion analysis, four OCA causative genes were investigated for their association with WDP phenotype; TYR, OCA2, TYRP1 and SLC45A2. SLC45A2 was found to be linked to the phenotype and gene sequencing revealed a 4,081 base pair deletion resulting in loss of the terminus of exon seven of SLC45A2 (chr4∶77,062,968–77,067,051). This mutation is highly likely to be the cause of the WDP phenotype and is supported by a lack of detectable SLC45A2 transcript levels by reverse transcriptase PCR. The WDP provides a valuable model for studying OCA4 visual disturbances and melanocytic neoplasms in a large animal model. PMID:24647637

  4. Mucopolysaccharidosis-like phenotype in feline Sandhoff disease and partial correction after AAV gene therapy.

    PubMed

    Gray-Edwards, Heather L; Brunson, Brandon L; Holland, Merrilee; Hespel, Adrien-Maxence; Bradbury, Allison M; McCurdy, Victoria J; Beadlescomb, Patricia M; Randle, Ashley N; Salibi, Nouha; Denney, Thomas S; Beyers, Ronald J; Johnson, Aime K; Voyles, Meredith L; Montgomery, Ronald D; Wilson, Diane U; Hudson, Judith A; Cox, Nancy R; Baker, Henry J; Sena-Esteves, Miguel; Martin, Douglas R

    2015-01-01

    Sandhoff disease (SD) is a fatal neurodegenerative disease caused by a mutation in the enzyme β-N-acetylhexosaminidase. Children with infantile onset SD develop seizures, loss of motor tone and swallowing problems, eventually reaching a vegetative state with death typically by 4years of age. Other symptoms include vertebral gibbus and cardiac abnormalities strikingly similar to those of the mucopolysaccharidoses. Isolated fibroblasts from SD patients have impaired catabolism of glycosaminoglycans (GAGs). To evaluate mucopolysaccharidosis-like features of the feline SD model, we utilized radiography, MRI, echocardiography, histopathology and GAG quantification of both central nervous system and peripheral tissues/fluids. The feline SD model exhibits cardiac valvular and structural abnormalities, skeletal changes and spinal cord compression that are consistent with accumulation of GAGs, but are much less prominent than the severe neurologic disease that defines the humane endpoint (4.5±0.5months). Sixteen weeks after intracranial AAV gene therapy, GAG storage was cleared in the SD cat cerebral cortex and liver, but not in the heart, lung, skeletal muscle, kidney, spleen, pancreas, small intestine, skin, or urine. GAG storage worsens with time and therefore may become a significant source of pathology in humans whose lives are substantially lengthened by gene therapy or other novel treatments for the primary, neurologic disease. PMID:25971245

  5. Spectral sensitivity measurements reveal partial success in restoring missing rod function with gene therapy.

    PubMed

    Ripamonti, Caterina; Henning, G Bruce; Robbie, Scott J; Sundaram, Venki; van den Born, L Ingeborgh; Casteels, Ingele; de Ravel, Thomy J L; Moore, Anthony T; Smith, Alexander J; Bainbridge, James W; Ali, Robin R; Stockman, Andrew

    2015-01-01

    Restored rod visual function after gene therapy can be established unequivocally by demonstrating that, after dark adaptation, spectral sensitivity has the shape characteristic of rods and that this shape collapses to a cone-like shape before rods have recovered after an intense bleach. We used these tests to assess retinal function in eight young adults and children with early-onset severe retinal dystrophy from Phase II of a clinical gene-therapy trial for RPE65 deficiency that involved the subretinal delivery of a recombinant adeno-associated viral vector carrying RPE65. We found substantial improvements in rod sensitivity in two participants: dark-adapted spectral sensitivity was rod-like after treatment and was cone-like before rods had recovered after a bleach. After 40 min of dark adaptation, one participant showed up to 1,000-fold sensitivity improvements 4 months after treatment and the second up to 100-fold improvements 6 months after treatment. The dark-adapted spectral sensitivities of the other six participants remained cone-like and showed little improvement in sensitivity. PMID:26605849

  6. Partial FI gene-independence of lambda-21 hybrid phages specifying chimeric terminases.

    PubMed

    Feiss, M; Frackman, S; Momany, T

    1988-11-01

    The role of the FI gene in the life cycles of a series of lambda-21 hybrid phages that produce chimeric lambda-21 terminases has been examined. An isogenic series of FI+ and FI- derivatives of the hybrids was constructed, and the growth properties of the phages were examined. It was found that three of the four hybrids (hybrids 51, 67, and 33) are able to form plaques and produce a small burst in the absence of the FI gene product (gpFI), but each of the three phages is much healthier in the presence of gpFI. It is concluded that each of the three chimeric terminases is dependent on gpFI. The ability of the FI- hybrids to grow better than lambda FI- is postulated to be due to a minor qualitative or quantitative difference between the chimeric terminases and lambda terminase. The fourth hybrid (54), known from earlier work to produce an infirm terminase, is more dependent on gpFI than the other hybrids and lambda itself. PMID:2973176

  7. Identification and partial characterization of a candidate gene for X-linked retinopathies using a lateral approach

    SciTech Connect

    Wong, P.; MacDonald, I.M.; Sood, R.; Smith, C.; Pilon, R.; Tenniswood, M. )

    1993-03-01

    Using library to library cross-screening the authors have identified a number of genomic clones that harbor X-linked sequences expressed in the human choroid/retina. They describe the characterization of one of these, designated XEH.8 (DXS542), which is localized to Xp11.3-q12. Isolation, partial sequencing, and Northern analysis of the cognate cDNA (XEH.8[sub c]), has shown that the cDNA has some homology to the dystrophin gene and hybridizes to a 10-kb mRNA present in the choroid and retina but not in fibroblasts. This expressed sequence maps to the same region of the X chromosome as several known X-linked ophthalmic diseases, including Norrie disease, retinitis pigmentosa 2, congenital night blindness and Aland Island eye disease. 24 refs., 6 figs.

  8. Evidence of geographical structuring in the Malaysian Snakehead, Channa striata based on partial segment of the CO1 gene

    PubMed Central

    Siti-Balkhis, Abu Bakar; Jamsari, Amirul Firdaus Jamaluddin; Hwai, Tan Shau; Yasin, Zulfigar; Siti-Azizah, Mohd Nor

    2011-01-01

    Channa striata, locally known as “haruan”, is economically important in fisheries and aquaculture industries in several Asian countries. DNA sequencing, based on a partial segment of the Cytochrome oxidase c subunit 1 (CO1) gene, was used to determine genetic variation in C. striata samples from four different populations on the west coast of Peninsular Malaysia. The highest nucleotide and haplotype diversities were observed in the Linggi population (π = 0.0067, h = 0.835), and the lowest in the Timah Tasoh population (π = 0.0008, h = 0.286). Apart from Kajang-Linggi, which was insignificant, FST values were significant (p < 0.05) in all pairwise-population comparisons. Consequently, it is inferred that genetic structuring C. striata populations in this region was largely shaped by a common origin, with secondary influences from geographical factors and isolation. PMID:21931528

  9. Evidence of geographical structuring in the Malaysian Snakehead, Channa striata based on partial segment of the CO1 gene.

    PubMed

    Siti-Balkhis, Abu Bakar; Jamsari, Amirul Firdaus Jamaluddin; Hwai, Tan Shau; Yasin, Zulfigar; Siti-Azizah, Mohd Nor

    2011-07-01

    Channa striata, locally known as "haruan", is economically important in fisheries and aquaculture industries in several Asian countries. DNA sequencing, based on a partial segment of the Cytochrome oxidase c subunit 1 (CO1) gene, was used to determine genetic variation in C. striata samples from four different populations on the west coast of Peninsular Malaysia. The highest nucleotide and haplotype diversities were observed in the Linggi population (π = 0.0067, h = 0.835), and the lowest in the Timah Tasoh population (π = 0.0008, h = 0.286). Apart from Kajang-Linggi, which was insignificant, F(ST) values were significant (p < 0.05) in all pairwise-population comparisons. Consequently, it is inferred that genetic structuring C. striata populations in this region was largely shaped by a common origin, with secondary influences from geographical factors and isolation. PMID:21931528

  10. Partial Gene Deletions of PMP22 Causing Hereditary Neuropathy with Liability to Pressure Palsies

    PubMed Central

    Cho, Sun-Mi; Kim, Yoonjung; Lee, Sang Guk; Yang, Jin-Young

    2014-01-01

    Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal neuropathy that is commonly caused by a reciprocal 1.5 Mb deletion on chromosome 17p11.2, at the site of the peripheral myelin protein 22 (PMP22) gene. Other patients with similar phenotypes have been shown to harbor point mutations or small deletions, although there is some clinical variation across these patients. In this report, we describe a case of HNPP with copy number changes in exon or promoter regions of PMP22. Multiplex ligation-dependent probe analysis revealed an exon 1b deletion in the patient, who had been diagnosed with HNPP in the first decade of life using molecular analysis. PMID:25506001

  11. Partial Gene Deletions of PMP22 Causing Hereditary Neuropathy with Liability to Pressure Palsies.

    PubMed

    Cho, Sun-Mi; Hong, Bo Young; Kim, Yoonjung; Lee, Sang Guk; Yang, Jin-Young; Kim, Juwon; Lee, Kyung-A

    2014-01-01

    Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal neuropathy that is commonly caused by a reciprocal 1.5 Mb deletion on chromosome 17p11.2, at the site of the peripheral myelin protein 22 (PMP22) gene. Other patients with similar phenotypes have been shown to harbor point mutations or small deletions, although there is some clinical variation across these patients. In this report, we describe a case of HNPP with copy number changes in exon or promoter regions of PMP22. Multiplex ligation-dependent probe analysis revealed an exon 1b deletion in the patient, who had been diagnosed with HNPP in the first decade of life using molecular analysis. PMID:25506001

  12. Omega-3 fatty acids partially revert the metabolic gene expression profile induced by long-term calorie restriction.

    PubMed

    López-Domínguez, José Alberto; Cánovas, Ángela; Medrano, Juan F; Islas-Trejo, Alma; Kim, Kyoungmi; Taylor, Sandra L; Villalba, José Manuel; López-Lluch, Guillermo; Navas, Plácido; Ramsey, Jon J

    2016-05-01

    Calorie restriction (CR) consistently extends longevity and delays age-related diseases across several animal models. We have previously shown that different dietary fat sources can modulate life span and mitochondrial ultrastructure, function and membrane fatty acid composition in mice maintained on a 40% CR. In particular, animals consuming lard as the main fat source (CR-Lard) lived longer than CR mice consuming diets with soybean oil (CR-Soy) or fish oil (CR-Fish) as the predominant lipid source. In the present work, a transcriptomic analysis in the liver and skeletal muscle was performed in order to elucidate possible mechanisms underlying the changes in energy metabolism and longevity induced by dietary fat in CR mice. After 8 months of CR, transcription downstream of several mediators of inflammation was inhibited in liver. In contrast, proinflammatory signaling was increased in the CR-Fish versus other CR groups. Dietary fish oil induced a gene expression pattern consistent with increased transcriptional regulation by several cytokines (TNF, GM-CSF, TGF-β) and sex hormones when compared to the other CR groups. The CR-Fish also had lower expression of genes involved in fatty acid biosynthesis and increased expression of mitochondrial and peroxisomal fatty acid β-oxidation genes than the other CR diet groups. Our data suggest that a diet high in n-3 PUFA, partially reverts CR-related changes in gene expression of key processes, such as inflammation and steroid hormone signaling, and this may mitigate life span extension with CR in mice consuming diets high in fish oil. PMID:26875793

  13. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    PubMed

    Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

    2012-05-25

    Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis). PMID:22136768

  14. Purification and partial characterization of the multicomponent dextranase complex of Streptococcus sobrinus and cloning of the dextranase gene.

    PubMed Central

    Barrett, J F; Barrett, T A; Curtiss, R

    1987-01-01

    The presence of proteases in culture supernatant fluids and on the cell surface of Streptococcus sobrinus and the aggregation of multicomponent enzyme complexes make the isolation and characterization of cell surface proteins difficult. We report a simple purification procedure for dextranase and the cloning of the dextranase structural gene. S. sobrinus culture supernatant fluids were precipitated with 70% ammonium sulfate, and the precipitate was dialyzed against sodium acetate buffer and loaded onto a hemoglobin-Sepharose 4B column connected to a blue dextran-agarose column at 4 degrees C. After being washed with low concentrations of salt, the dextranase and the dextran-binding proteins were eluted with 5 M KI and further purified by gel filtration. Two dextranases (molecular weights, 175,000 and 160,000) were purified and partially characterized. The structural gene for the dextranase of S. sobrinus 6715 strain UAB66, serotype g, was cloned into the cosmid vector, pHC79. Clones were selected for expression of dextranase activity by detection of zones of enzyme-mediated hydrolysis of a blue dextran substrate incorporated into minimal medium agar plates. Release of dextranase was achieved by induction of thermoinducible, excision-defective Escherichia coli K-12 lysogens containing recombinant cosmid molecules of S. sobrinus DNA. Recombinant cosmid molecules were repackaged simultaneously into infectious lambdoid particles. Recombinant clones expressing dextranase activity which varied in size from the high-molecular-weight protein produced by S. sobrinus (i.e., 175,000) to lower-molecular-weight forms expressed by S. sobrinus have been identified and partially characterized. Images PMID:3546141

  15. Creation of Mice Bearing a Partial Duplication of HPRT Gene Marked with a GFP Gene and Detection of Revertant Cells In Situ as GFP-Positive Somatic Cells

    PubMed Central

    Noda, Asao; Suemori, Hirofumi; Hirai, Yuko; Hamasaki, Kanya; Kodama, Yoshiaki; Mitani, Hiroshi; Landes, Reid D.; Nakamura, Nori

    2015-01-01

    It is becoming clear that apparently normal somatic cells accumulate mutations. Such accumulations or propagations of mutant cells are thought to be related to certain diseases such as cancer. To better understand the nature of somatic mutations, we developed a mouse model that enables in vivo detection of rare genetically altered cells via GFP positive cells. The mouse model carries a partial duplication of 3’ portion of X-chromosomal HPRT gene and a GFP gene at the end of the last exon. In addition, although HPRT gene expression was thought ubiquitous, the expression level was found insufficient in vivo to make the revertant cells detectable by GFP positivity. To overcome the problem, we replaced the natural HPRT-gene promoter with a CAG promoter. In such animals, termed HPRT-dup-GFP mouse, losing one duplicated segment by crossover between the two sister chromatids or within a single molecule of DNA reactivates gene function, producing hybrid HPRT-GFP proteins which, in turn, cause the revertant cells to be detected as GFP-positive cells in various tissues. Frequencies of green mutant cells were measured using fixed and frozen sections (liver and pancreas), fixed whole mount (small intestine), or by means of flow cytometry (unfixed splenocytes). The results showed that the frequencies varied extensively among individuals as well as among tissues. X-ray exposure (3 Gy) increased the frequency moderately (~2 times) in the liver and small intestine. Further, in two animals out of 278 examined, some solid tissues showed too many GFP-positive cells to score (termed extreme jackpot mutation). Present results illustrated a complex nature of somatic mutations occurring in vivo. While the HPRT-dup-GFP mouse may have a potential for detecting tissue-specific environmental mutagens, large inter-individual variations of mutant cell frequency cause the results unstable and hence have to be reduced. This future challenge will likely involve lowering the background mutation

  16. Phylogenetic analysis of Xanthomonas based on partial rpoB gene sequences and species differentiation by PCR-RFLP.

    PubMed

    Ferreira-Tonin, Mariana; Rodrigues-Neto, Júlio; Harakava, Ricardo; Destéfano, Suzete Aparecida Lanza

    2012-06-01

    The rpoB gene was evaluated as an alternative molecular marker for the differentiation of Xanthomonas species and in order to understand better the phylogenetic relationships within the genus. PCR-RFLP experiments using HaeIII allowed differentiation of Xanthomonas species, particularly those that affect the same plant host such as Xanthomonas albilineans and X. sacchari, pathogenic to sugar cane, Xanthomonas cucurbitae and X. melonis, which cause disease in melon, and Xanthomonas gardneri, X. vesicatoria and X. euvesicatoria/X. perforans, pathogenic to tomato. Phylogenetic relationships within the genus Xanthomonas were also examined by comparing partial rpoB gene sequences (612 nt) and the Xanthomonas species were separated into two main groups. Group I, well supported by bootstrap values of 99 %, comprised X. euvesicatoria, X. perforans, X. alfalfae, X. citri, X. dyei, X. axonopodis, X. oryzae, X. hortorum, X. bromi, X. vasicola, X. cynarae, X. gardneri, X. campestris, X. fragariae, X. arboricola, X. cassavae, X. cucurbitae, X. pisi, X. vesicatoria, X. codiaei and X. melonis. Group II, again well supported by bootstrap values of 99 %, comprised X. albilineans, X. sacchari, X. theicola, X. translucens and X. hyacinthi. The rpoB gene sequence similarity observed among the species in this study ranged from 87.8 to 99.7 %. The results of PCR-RFLP of the rpoB gene indicated that this technique can be used for diagnosis and identification of most Xanthomonas strains, including closely related species within the genus. However, species that showed identical profiles could be differentiated clearly only by sequence analysis. The results obtained in our phylogenetic analysis suggested that the rpoB gene can be used as an alternative molecular marker for genetic relatedness in the genus Xanthomonas. The results of PCR-RFLP of the rpoB gene indicate that this technique can be used for diagnosis and identification of closely related species within the genus, representing

  17. Kernelized partial least squares for feature reduction and classification of gene microarray data

    PubMed Central

    2011-01-01

    Background The primary objectives of this paper are: 1.) to apply Statistical Learning Theory (SLT), specifically Partial Least Squares (PLS) and Kernelized PLS (K-PLS), to the universal "feature-rich/case-poor" (also known as "large p small n", or "high-dimension, low-sample size") microarray problem by eliminating those features (or probes) that do not contribute to the "best" chromosome bio-markers for lung cancer, and 2.) quantitatively measure and verify (by an independent means) the efficacy of this PLS process. A secondary objective is to integrate these significant improvements in diagnostic and prognostic biomedical applications into the clinical research arena. That is, to devise a framework for converting SLT results into direct, useful clinical information for patient care or pharmaceutical research. We, therefore, propose and preliminarily evaluate, a process whereby PLS, K-PLS, and Support Vector Machines (SVM) may be integrated with the accepted and well understood traditional biostatistical "gold standard", Cox Proportional Hazard model and Kaplan-Meier survival analysis methods. Specifically, this new combination will be illustrated with both PLS and Kaplan-Meier followed by PLS and Cox Hazard Ratios (CHR) and can be easily extended for both the K-PLS and SVM paradigms. Finally, these previously described processes are contained in the Fine Feature Selection (FFS) component of our overall feature reduction/evaluation process, which consists of the following components: 1.) coarse feature reduction, 2.) fine feature selection and 3.) classification (as described in this paper) and prediction. Results Our results for PLS and K-PLS showed that these techniques, as part of our overall feature reduction process, performed well on noisy microarray data. The best performance was a good 0.794 Area Under a Receiver Operating Characteristic (ROC) Curve (AUC) for classification of recurrence prior to or after 36 months and a strong 0.869 AUC for

  18. The distribution of DQ genes in the Saharawi population provides only a partial explanation for the high celiac disease prevalence.

    PubMed

    Catassi, C; Doloretta Macis, M; Rätsch, I M; De Virgiliis, S; Cucca, F

    2001-12-01

    Celiac disease (CD) is a multifactorial disorder of the small intestine caused by a permanent dietary intolerance to gluten. The combined presence of the HLA class II DQA1*0501 and DQB1*0201 alleles represents the major genetic component for disease predisposition. It has been shown that the Saharawi refugees living in northern Africa have a very high frequency of CD. In the present study we analysed this population to evaluate the degree of association with CD of the haplotypes and genotypes at the main HLA-DQB1 and DQA1 disease loci. We found a strong association of the DR3, DQB1*0201-DQA1*0501-positive haplotypes and genotypes. A very high frequency of DR3, DQB1*0201-DQA1*0501 was also observed in the general Saharawi population. These results indicate that there is a good correlation between disease prevalence and frequency of the main predisposing haplotype in the background population. However, the correlation is incomplete because similar frequencies of DR3 are also observed in populations such as the Sardinians showing a much lower prevalence of CD. We can conclude that the distribution of DQ genes in the Saharawi population only provides a partial explanation for the high prevalence of CD. Other factors, such as rapidly changing dietary habits and/or non-DQ genes, may also play some role. PMID:11929591

  19. Pathogenesis of growth failure and partial reversal with gene therapy in murine and canine Glycogen Storage Disease type Ia.

    PubMed

    Brooks, Elizabeth Drake; Little, Dianne; Arumugam, Ramamani; Sun, Baodong; Curtis, Sarah; Demaster, Amanda; Maranzano, Michael; Jackson, Mark W; Kishnani, Priya; Freemark, Michael S; Koeberl, Dwight D

    2013-06-01

    Glycogen Storage Disease type Ia (GSD-Ia) in humans frequently causes delayed bone maturation, decrease in final adult height, and decreased growth velocity. This study evaluates the pathogenesis of growth failure and the effect of gene therapy on growth in GSD-Ia affected dogs and mice. Here we found that homozygous G6pase (-/-) mice with GSD-Ia have normal growth hormone (GH) levels in response to hypoglycemia, decreased insulin-like growth factor (IGF) 1 levels, and attenuated weight gain following administration of GH. Expression of hepatic GH receptor and IGF 1 mRNAs and hepatic STAT5 (phospho Y694) protein levels are reduced prior to and after GH administration, indicating GH resistance. However, restoration of G6Pase expression in the liver by treatment with adeno-associated virus 8 pseudotyped vector expressing G6Pase (AAV2/8-G6Pase) corrected body weight, but failed to normalize plasma IGF 1 in G6pase (-/-) mice. Untreated G6pase (-/-) mice also demonstrated severe delay of growth plate ossification at 12 days of age; those treated with AAV2/8-G6Pase at 14 days of age demonstrated skeletal dysplasia and limb shortening when analyzed radiographically at 6 months of age, in spite of apparent metabolic correction. Moreover, gene therapy with AAV2/9-G6Pase only partially corrected growth in GSD-Ia affected dogs as detected by weight and bone measurements and serum IGF 1 concentrations were persistently low in treated dogs. We also found that heterozygous GSD-Ia carrier dogs had decreased serum IGF 1, adult body weights and bone dimensions compared to wild-type littermates. In sum, these findings suggest that growth failure in GSD-Ia results, at least in part, from hepatic GH resistance. In addition, gene therapy improved growth in addition to promoting long-term survival in dogs and mice with GSD-Ia. PMID:23623482

  20. Magnetization and magnetic susceptibilities of GdH3, HoH3, ErH3 and YbH3

    NASA Technical Reports Server (NTRS)

    Flood, D. J.

    1976-01-01

    The magnetic susceptibility of powdered samples of HoH3, ErH3, GdH3 and YbH3 have been measured in the temperature range from 4.2 to 1.2 K. Two broad, local maxima are observed in the variation of chi versus T for GdH3, with maxima in (delta chi delta T) versus T at 1.8 K and 3.3 K. The inverse susceptibilities for HoH3 and ErH3 both obey a Curies-Weiss law over a limited range (4.2 to 2.6K and 4.2 to 2 K respectively) with values for the Weiss constant of -4.25 K and -1.11 K, and effective moments of 8.6 and 7.7 Bohr magnetons respectively. The susceptibility of YbH3 is independent of temperature over the range investigated. High-field magnetization measurements yield extrapolated saturation moments of 7.0 + or - 0.25 Bohr magnetons/ion for GdH3, 6.1 + or - 0.2 Bohr magnetons/ion for HoH3 and 3.74 + or - 0.11 Bohr magnetons/ion for ErH3. In addition, ErH3 exhibits a van Vleck paramagnetism in the high field region.

  1. Review of Adverse Events Associated With False Glucose Readings Measured by GDH-PQQ–Based Glucose Test Strips in the Presence of Interfering Sugars

    PubMed Central

    Frias, Juan P.; Lim, Christine G.; Ellison, John M.; Montandon, Carol M.

    2010-01-01

    OBJECTIVE To assess the implications of falsely elevated glucose readings measured with glucose dehydrogenase pyrroloquinolinequinone (GDH-PQQ) test strips. RESEARCH DESIGN AND METHODS We conducted a review of the Food and Drug Administration's Manufacturer and User Facility Device Experience database and medical literature for adverse events (AEs) associated with falsely elevated glucose readings with GDH-PQQ test strips in the presence of interfering sugars. RESULTS Eighty-two reports were identified: 16 (20%) were associated with death, 46 (56%) with severe hypoglycemia, and 12 (15%) with nonsevere hypoglycemia. In eight reports (10%), the AE was not described. Forty-two events (51%) occurred in the U.S. Although most events occurred in hospitalized patients, at least 14 (17%) occurred in outpatients. Agents most commonly associated with AEs were icodextrin-containing peritoneal dialysate and maltose-containing intravenous immune globulin. CONCLUSIONS GDH-PQQ test strips pose a safety risk to insulin-using patients treated with agents containing or metabolized to interfering sugars. PMID:20351227

  2. Egg yolks inhibit activation of NF-κB and expression of its target genes in adipocytes after partial delipidation

    PubMed Central

    Shen, Qiwen; Riedl, Ken M.; Cole, Rachel M.; Lehman, Christopher; Xu, Lu; Alder, Hansjuerg; Belury, Martha A.; Schwartz, Steven J.; Ziouzenkova, Ouliana

    2015-01-01

    How composition of egg yolk (EY) influences NF-κB, a key transcription pathway in inflammation, remains unclear. We performed partial delipidation of EY that removed 20–30% of cholesterol and triglycerides. The resulting polar and non-polar fractions were termed EY-P and EY-NP. NF-κB activation in response to EY from different suppliers and their fractions was examined in 3T3-L1 adipocytes using a NF-κB response element reporter assay and by analyzing expression of 248 inflammatory genes. Although EY-P and EY contained similar level of vitamins, carotenoids, and fatty acids, only delipidated EY-P fraction suppressed NF-κB via down-regulation of toll like receptor-2 and up-regulation of inhibitory toll interacting protein (Tollip) and lymphocyte antigen 96 (Ly96). Our data suggest that anti-inflammatory activity of lutein and retinol were blunted by non-polar lipids in EY likely via crosstalk between SREBP and NF-κB pathways in adipocytes. Thus, moderate delipidation may improve their beneficial properties of regular eggs. PMID:25620076

  3. Pathogenesis of growth failure and partial reversal with gene therapy in murine and canine Glycogen Storage Disease type Ia

    PubMed Central

    Brooks, Elizabeth Drake; Little, Dianne; Arumugam, Ramamani; Sun, Baodong; Curtis, Sarah; DeMaster, Amanda; Maranzano, Michael; Jackson, Mark W.; Kishnani, Priya; Freemark, Michael S.; Koeberl, Dwight D.

    2013-01-01

    Glycogen Storage Disease type Ia (GSD-Ia) in humans frequently causes delayed bone maturation, decrease in final adult height, and decreased growth velocity. This study evaluates the pathogenesis of growth failure and the effect of gene therapy on growth in GSD-Ia affected dogs and mice. Here we found that homozygous G6pase (−/−) mice with GSD-Ia have normal growth hormone (GH) levels in response to hypoglycemia, decreased insulin-like growth factor (IGF) 1 levels, and attenuated weight gain following administration of GH. Expression of hepatic GH receptor and IGF 1 mRNAs and hepatic STAT5 (phospho Y694) protein levels are reduced prior to and after GH administration, indicating GH resistance. However, restoration of G6Pase expression in the liver by treatment with adeno-associated virus 8 pseudotyped vector expressing G6Pase (AAV2/8-G6Pase) corrected body weight, but failed to normalize plasma IGF 1 in G6pase (−/−) mice. Untreated G6pase (−/−) mice also demonstrated severe delay of growth plate ossification at 12 days of age; those treated with AAV2/8-G6Pase at 14 days of age demonstrated skeletal dysplasia and limb shortening when analyzed radiographically at 6 months of age, in spite of apparent metabolic correction. Moreover, gene therapy with AAV2/9-G6Pase only partially corrected growth in GSD-Ia affected dogs as detected by weight and bone measurements and serum IGF 1 concentrations were persistently low in treated dogs. We also found that heterozygous GSD-Ia carrier dogs had decreased serum IGF 1, adult body weights and bone dimensions compared to wild-type littermates. In sum, these findings suggest that growth failure in GSD-Ia results, at least in part, from hepatic GH resistance. In addition, gene therapy improved growth in addition to promoting long-term survival in dogs and mice with GSD-Ia. PMID:23623482

  4. Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study.

    PubMed

    Liu, Hsi-Che; Shih, Lee-Yung; May Chen, Mei-Ju; Wang, Chien-Chih; Yeh, Ting-Chi; Lin, Tung-Huei; Chen, Chien-Yu; Lin, Chih-Jen; Liang, Der-Cherng

    2011-05-01

    In acute myeloid leukemia (AML), the mixed lineage leukemia (MLL) gene may be rearranged to generate a partial tandem duplication (PTD), or fused to partner genes through a chromosomal translocation (tMLL). In this study, we first explored the differentially expressed genes between MLL-PTD and tMLL using gene expression profiling of our cohort (15 MLL-PTD and 10 tMLL) and one published data set. The top 250 probes were chosen from each set, resulting in 29 common probes (21 unique genes) to both sets. The selected genes include four HOXB genes, HOXB2, B3, B5, and B6. The expression values of these HOXB genes significantly differ between MLL-PTD and tMLL cases. Clustering and classification analyses were thoroughly conducted to support our gene selection results. Second, as MLL-PTD, FLT3-ITD, and NPM1 mutations are identified in AML with normal karyotypes, we briefly studied their impact on the HOXB genes. Another contribution of this study is to demonstrate that using public data from other studies enriches samples for analysis and yields more conclusive results. PMID:21665178

  5. Characterization of full-length and polymerase chain reaction-derived partial-length Gottfried and OSU gene 4 probes for serotypic differentiation of porcine rotaviruses.

    PubMed

    Rosen, B I; Parwani, A V; Gorziglia, M; Larralde, G; Saif, L J

    1992-10-01

    To determine the VP4 (P type) specificity of porcine rotaviruses, full- and partial-length gene 4 probes were produced from cloned Gottfried and OSU porcine rotavirus genomic segment 4 cDNAs. The gene 4 segments from the prototype Gottfried (VP7 serotype 4) and OSU (VP7 serotype 5) porcine rotavirus strains were selected for study because of their distinct P types and the occurrence of rotaviruses with similar serotypes among swine. Partial-length gene 4 cDNAs were produced and amplified by the polymerase chain reaction (PCR) and encompassed portions of the variable region (nucleotides 211 to 612) of VP8 encoded by genomic segment 4. The hybridization stringency conditions necessary for optimal probe specificity and sensitivity were determined by dot or Northern (RNA) blot hybridizations against a diverse group of human and animal rotaviruses of heterologous group A serotypes and against representative group B and C porcine rotaviruses. The PCR-derived gene 4 probes were more specific than the full-length gene 4 probes but demonstrated equivalent sensitivity. The Gottfried PCR-derived probe hybridized with Gottfried, SB2, SB3, and SB5 G serotype 4 porcine rotaviruses. The OSU PCR-derived probe hybridized with OSU, EE, A580, and SB-1A porcine rotaviruses and equine H1 rotavirus. Results of the hybridization reactions of the PCR-derived gene 4 probes with selected porcine rotavirus strains agreed with previous serological or genetic analyses, indicating their suitability as diagnostic reagents. PMID:1328281

  6. Phylogenetic affinities of Diplonema within the Euglenozoa as inferred from the SSU rRNA gene and partial COI protein sequences.

    PubMed

    Maslov, D A; Yasuhira, S; Simpson, L

    1999-03-01

    In order to shed light on the phylogenetic position of diplonemids within the phylum Euglenozoa, we have sequenced small subunit rRNA (SSU rRNA) genes from Diplonema (syn. Isonema) papillatum and Diplonema sp. We have also analyzed a partial sequence of the mitochondrial gene for cytochrome c oxidase subunit I from D. papillatum. With both markers, the maximum likelihood method favored a closer grouping of diplonemids with kinetoplastids, while the parsimony and distance suggested a closer relationship of diplonemids with euglenoids. In each case, the differences between the best tree and the alternative trees were small. The frequency of codon usage in the partial D. papillatum COI was different from both related groups; however, as is the case in kinetoplastids but not in Euglena, both the non-canonical UGA codon and the canonical UGG codon were used to encode tryptophan in Diplonema. PMID:10724517

  7. Partial rescue of a lethal phenotype of fragile bones in transgenic mice with a chimeric antisense gene directed against a mutated collagen gene.

    PubMed Central

    Khillan, J S; Li, S W; Prockop, D J

    1994-01-01

    Previously, transgenic mice were prepared that developed a lethal phenotype of fragile bones because they expressed an internally deleted mini-gene for the pro alpha 1(I) chain of human type I procollagen. The shortened pro alpha 1(I) chains synthesized from the human transgene bound to and produced degradation of normal pro alpha 1(I) chains synthesized from the normal mouse alleles. Here we assembled an antisense gene that was similar to the internally deleted COL1A1 minigene but the 3' half of the gene was inverted so as to code for an antisense RNA. Transgenic mice expressing the antisense gene had a normal phenotype, apparently because the antisense gene contained human sequences instead of mouse sequences. Two lines of mice expressing the antisense gene were bred to two lines of transgenic mice expressing the mini-gene. In mice that inherited both genes, the incidence of the lethal fragile bone phenotype was reduced from 92% to 27%. The effects of the antisense gene were directly demonstrated by an increase in the ratio of normal mouse pro alpha 1(I) chains to human mini-pro alpha 1(I) chains in tissues from mice that inherited both genes and had a normal phenotype. The results raise the possibility that chimeric gene constructs that contain intron sequences and in which only the second half of a gene is inverted may be particularly effective as antisense genes. Images PMID:8022775

  8. New mutations of Saccharomyces cerevisiae that partially relieve both glucose and galactose repression activate the protein kinase Snf1.

    PubMed

    Rodríguez, Cristina; Sanz, Pascual; Gancedo, Carlos

    2003-03-01

    We isolated from Saccharomyces cerevisiae two mutants, esc1-1 and ESC3-1, in which genes FBP1, ICL1 or GDH2 were partially derepressed during growth in glucose or galactose. The isolation was done starting with a triple mutant pyc1 pyc2 mth1 unable to grow in glucose-ammonium medium and selecting for mutants able to grow in the non-permissive medium. HXT1 and HXT2 which encode glucose transporters were expressed at high glucose concentrations in both esc1-1 and ESC3-1 mutants, while derepression of invertase at low glucose concentrations was impaired. REG1, cloned as a suppressor of ESC3-1, was not allelic to ESC3-1. Two-hybrid analysis showed an increased interaction of the protein kinase Snf1 with Snf4 in the ESC3-1 mutant; this was not due to mutations in SNF1 or SNF4. ESC3-1 did not bypass the requirement of Snf1 for derepression. We hypothesize that ESC3-1 either facilitates activation of Snf1 or interferes with its glucose-dependent inactivation. PMID:12702249

  9. Efficient production of α-ketoglutarate in the gdh deleted Corynebacterium glutamicum by novel double-phase pH and biotin control strategy.

    PubMed

    Li, Yanjun; Sun, Lanchao; Feng, Jia; Wu, Ruifang; Xu, Qingyang; Zhang, Chenglin; Chen, Ning; Xie, Xixian

    2016-06-01

    Production of L-glutamate using a biotin-deficient strain of Corynebacterium glutamicum has a long history. The process is achieved by controlling biotin at suboptimal dose in the initial fermentation medium, meanwhile feeding NH4OH to adjust pH so that α-ketoglutarate (α-KG) can be converted to L-glutamate. In this study, we deleted glutamate dehydrogenase (gdh1 and gdh2) of C. glutamicum GKG-047, an L-glutamate overproducing strain, to produce α-KG that is the direct precursor of L-glutamate. Based on the method of L-glutamate fermentation, we developed a novel double-phase pH and biotin control strategy for α-KG production. Specifically, NH4OH was added to adjust the pH at the bacterial growth stage and NaOH was used when the cells began to produce acid; besides adding an appropriate amount of biotin in the initial medium, certain amount of additional biotin was supplemented at the middle stage of fermentation to maintain a high cell viability and promote the carbon fixation to the flux of α-KG production. Under this control strategy, 45.6 g/L α-KG accumulated after 30-h fermentation in a 7.5-L fermentor and the productivity and yield achieved were 1.52 g/L/h and 0.42 g/g, respectively. PMID:26946492

  10. Plasmodium yoelii: identification and partial characterization of an MDR1 gene in an artemisinin-resistant line.

    PubMed

    Ferrer-Rodríguez, Iván; Pérez-Rosado, José; Gervais, Gary W; Peters, Wallace; Robinson, Brian L; Serrano, Adelfa E

    2004-02-01

    The molecular mechanisms by which the malarial parasite has managed to develop resistance to many antimalarial drugs remain to be completely elucidated. Mutations in the pfmdr1 gene of Plasmodium falciparum, as well as an increase in pfmdr1 copy number, have been associated with resistance to the quinoline-containing antimalarial drugs. We investigated the mechanisms of drug resistance in Plasmodium using a collection of P. yoelii lines with different drug resistance profiles. The mdr1 gene of P. yoelii (pymdr1) was identified and characterized. A 2- to 3-fold increase in the pymdr1 gene copy number was observed in the P. yoelii ART line (artemisinin resistant) when compared with the NS parental line. The pymdr1 gene was mapped to a chromosome of 2.1 Mb in all lines analyzed. Reverse transcriptase-polymerase chain reaction and Western blot experiments confirmed the expression of the gene at the RNA and protein levels. PMID:15040683

  11. Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression.

    PubMed

    Pearson, Melanie M; Yep, Alejandra; Smith, Sara N; Mobley, Harry L T

    2011-07-01

    The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In this study, microarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7 days postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis. Across nine microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture. Genes upregulated in vivo encoded mannose-resistant Proteus-like (MR/P) fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism enzymes, and a portion of the tricarboxylic acid (TCA) cycle enzymes. Flagella were downregulated. Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo, while gdhA (glutamate dehydrogenase) was upregulated in vivo. Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression. A gdhA mutant was growth deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection. Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract. PMID:21505083

  12. Partial protoporphyrinogen oxidase (PPOX) gene deletions, due to different Alu-mediated mechanisms, identified by MLPA analysis in patients with variegate porphyria

    PubMed Central

    2013-01-01

    Variegate porphyria (VP) is an autosomal dominantly inherited hepatic porphyria. The genetic defect in the PPOX gene leads to a partial defect of protoporphyrinogen oxidase, the penultimate enzyme of heme biosynthesis. Affected individuals can develop cutaneous symptoms in sun-exposed areas of the skin and/or neuropsychiatric acute attacks. The identification of the genetic defect in VP families is of crucial importance to detect the carrier status which allows counseling to prevent potentially life threatening neurovisceral attacks, usually triggered by factors such as certain drugs, alcohol or fasting. In a total of 31 Swedish VP families sequence analysis had identified a genetic defect in 26. In the remaining five families an extended genetic investigation was necessary. After the development of a synthetic probe set, MLPA analysis to screen for single exon deletions/duplications was performed. We describe here, for the first time, two partial deletions within the PPOX gene detected by MLPA analysis. One deletion affects exon 5 and 6 (c.339-197_616+320del1099) and has been identified in four families, most probably after a founder effect. The other extends from exon 5 to exon 9 (c.339-350_987+229del2609) and was found in one family. We show that both deletions are mediated by Alu repeats. Our findings emphasize the usefulness of MLPA analysis as a complement to PPOX gene sequencing analysis for comprehensive genetic diagnostics in patients with VP. PMID:23324528

  13. High frequency of additional gene mutations in acute myeloid leukemia with MLL partial tandem duplication: DNMT3A mutation is associated with poor prognosis

    PubMed Central

    Kao, Hsiao-Wen; Liang, Der-Cherng; Kuo, Ming-Chung; Wu, Jin-Hou; Dunn, Po; Wang, Po-Nan; Lin, Tung-Liang; Shih, Yu-Shu; Liang, Sung-Tzu; Lin, Tung-Huei; Lai, Chen-Yu; Lin, Chun-Hui; Shih, Lee-Yung

    2015-01-01

    The mutational profiles of acute myeloid leukemia (AML) with partial tandem duplication of mixed-lineage leukemia gene (MLL-PTD) have not been comprehensively studied. We studied 19 gene mutations for 98 patients with MLL-PTD AML to determine the mutation frequency and clinical correlations. MLL-PTD was screened by reverse-transcriptase PCR and confirmed by real-time quantitative PCR. The mutational analyses were performed with PCR-based assays followed by direct sequencing. Gene mutations of signaling pathways occurred in 63.3% of patients, with FLT3-ITD (44.9%) and FLT3-TKD (13.3%) being the most frequent. 66% of patients had gene mutations involving epigenetic regulation, and DNMT3A (32.7%), IDH2 (18.4%), TET2 (18.4%), and IDH1 (10.2%) mutations were most common. Genes of transcription pathways and tumor suppressors accounted for 23.5% and 10.2% of patients. RUNX1 mutation occurred in 23.5% of patients, while none had NPM1 or double CEBPA mutation. 90.8% of MLL-PTD AML patients had at least one additional gene mutation. Of 55 MLL-PTD AML patients who received standard chemotherapy, age older than 50 years and DNMT3A mutation were associated with inferior outcome. In conclusion, gene mutations involving DNA methylation and activated signaling pathway were common co-existed gene mutations. DNMT3A mutation was a poor prognostic factor in MLL-PTD AML. PMID:26375248

  14. Gene Features Selection for Three-Class Disease Classification via Multiple Orthogonal Partial Least Square Discriminant Analysis and S-Plot Using Microarray Data

    PubMed Central

    Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

    2013-01-01

    Motivation DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Results Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub’s leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods. PMID:24386356

  15. A Novel Mutation in Human Androgen Receptor Gene Causing Partial Androgen Insensitivity Syndrome in a Patient Presenting with Gynecomastia at Puberty.

    PubMed

    Koçyiğit, Cemil; Sarıtaş, Serdar; Çatlı, Gönül; Onay, Hüseyin; Dündar, Bumin Nuri

    2016-06-01

    Partial androgen insensitivity syndrome (PAIS) typically presents with micropenis, perineoscrotal hypospadias, and a bifid scrotum with descending or undescending testes and gynecomastia at puberty. It is an X-linked recessive disorder resulting from mutations in the androgen receptor (AR) gene. However, AR gene mutations are found in less than a third of PAIS cases. A 16-year-old boy was admitted with complaints of gynecomastia and sparse facial hair. Family history revealed male relatives from maternal side with similar clinical phenotype. His external genitalia were phenotypically male with pubic hair Tanner stage IV, penoscrotal hypospadias, and a bifid scrotum with bilateral atrophic testes. He had elevated gonadotropins with a normal testosterone level. Chromosome analysis revealed a 46,XY karyotype. Due to the family history suggesting a disorder of X-linked trait, PAIS was considered and molecular analysis of AR gene was performed. DNA sequence analysis revealed a novel hemizygous mutation p.T576I (c.1727C>T) in the AR gene. The diagnosis of PAIS is based upon clinical phenotype and laboratory findings and can be confirmed by detection of a defect in the AR gene. An accurate approach including a detailed family history suggesting an X-linked trait is an important clue for a quick diagnosis. PMID:27087292

  16. Host-mediated gene silencing of a single effector gene from the potato pathogen Phytophthora infestans imparts partial resistance to late blight disease.

    PubMed

    Sanju, Suman; Siddappa, Sundaresha; Thakur, Aditi; Shukla, Pradeep K; Srivastava, Nidhi; Pattanayak, Debasis; Sharma, Sanjeev; Singh, B P

    2015-11-01

    RNA interference (RNAi) has proved a powerful genetic tool for silencing genes in plants. Host-induced gene silencing of pathogen genes has provided a gene knockout strategy for a wide range of biotechnological applications. The RXLR effector Avr3a gene is largely responsible for virulence of oomycete plant pathogen Phytophthora infestans. In this study, we attempted to silence the Avr3a gene of P. infestans through RNAi technology. The P. infestans inoculation resulted in lower disease progression and a reduction in pathogen load, as demonstrated by disease scoring and quantification of pathogen biomass in terms of Pi08 repetitive elements, respectively. Transgenic plants induced moderate silencing of Avr3a, and the presence and/or expression of small interfering RNAs, as determined through Northern hybridization, indicated siRNA targeted against Avr3a conferred moderate resistance to P. infestans. The single effector gene did not provide complete resistance against P. infestans. Although the Avr3a effector gene could confer moderate resistance, for complete resistance, the cumulative effect of effector genes in addition to Avr3a needs to be considered. In this study, we demonstrated that host-induced RNAi is an effective strategy for functional genomics in oomycetes. PMID:26077032

  17. The major and minor chicken vitellogenin genes are each adjacent to partially deleted pseudogene copies of the other.

    PubMed Central

    Silva, R; Fischer, A H; Burch, J B

    1989-01-01

    The major chicken vitellogenin gene (VTGII) has previously been cloned and sequenced. We now report the isolation of genomic clones that encompass a minor chicken vitellogenin gene (VTGIII) which is also expressed in the liver in response to estradiol. Our analysis reveals that a pseudogene for VTGII (psi VTGII) lies 1,426 base pairs upstream of this VTGIII gene. A reevaluation of published sequence data reveals that the converse is also true, namely, that a pseudogene for VTGIII (psi VTGIII) lies 1,345 base pairs downstream of the VTGII gene. Our results show that a 335-base-pair deletion has removed the psi VTGIII promoter and cap site but left residual estrogen response element in a region where nuclease-hypersensitive sites have been reported to be induced in response to estradiol. Images PMID:2796998

  18. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

    PubMed Central

    Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

    2015-01-01

    A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961

  19. Comparisons of mammalian Giardia duodenalis assemblages based on the β-giardin, glutamate dehydrogenase and triose phosphate isomerase genes.

    PubMed

    Scorza, Andrea V; Ballweber, Lora R; Tangtrongsup, Sahatchai; Panuska, Carla; Lappin, Michael R

    2012-10-26

    The objective of this study was to determine and compare the assemblages of Giardia duodenalis isolated from mammalian fecal samples using the β-giardin (bg), glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi) genes. A total of 202 samples, either submitted to the Veterinary Diagnostic Laboratory (Parasitology) at Colorado State University or part of ongoing research studies, were typed. A subset of 50 dog samples were also assessed by the tpi-D-specific primers. Of these, 183 were from dogs, 13 were from cats, two were from llamas, and one each was from a calf, an alpaca, a sheep, and a horse. The majority of the dogs (171 of 183 isolates) in this study were infected with only dog-adapted Assemblage C or D. The tpi-D-specific primers confirmed that 28 of the samples that typed as Assemblage D by the bg and gdh genes were also Assemblage D by the tpi-D-specific primers. Only 12 isolates were Assemblage A alone or Assemblage A and Assemblage C or D. Of the 13 cat isolates, seven were Assemblage F, two were Assemblage D, three were Assemblage A and 1 contained both Assemblages C and D. The calf isolate was Assemblage E (gdh, tpi) and the alpaca (bg, gdh), llamas (gdh), sheep (bg, gdh, tpi) and horse (tpi) isolates were all Assemblage A. When the assemblage could be determined for more than one gene, 91 of 117 dog isolates gave consistent results and 8 of 9 cat isolates gave consistent results. PMID:22652427

  20. Partial deletion of the LAMA3 gene is responsible for hereditary junctional epidermolysis bullosa in the American Saddlebred Horse.

    PubMed

    Graves, K T; Henney, P J; Ennis, R B

    2009-02-01

    Laminin 5 is a heterotrimeric basement membrane protein integral to the structure and function of the dermal-epidermal junction. It consists of three glycoprotein subunits: the alpha3, beta3 and gamma2 chains, which are encoded by the LAMA3, LAMB3 and LAMC2 genes respectively. A mutation in any of these genes results in the condition known as hereditary junctional epidermolysis bullosa (JEB). A 6589-bp deletion spanning exons 24-27 was found in the LAMA3 gene in American Saddlebred foals born with the skin-blistering condition epitheliogenesis imperfecta. The deletion confirms that this autosomal recessive condition in the American Saddlebred Horse can indeed be classified as JEB and corresponds to Herlitz JEB in humans. A diagnostic test was developed and nine of 175 randomly selected American Saddlebred foals from the 2007 foal crop were found to be carriers of the mutation (frequency of 0.026). PMID:19016681

  1. Laminarin modulates the chloroplast antioxidant system to enhance abiotic stress tolerance partially through the regulation of the defensin-like gene expression.

    PubMed

    Wu, Yi-Ru; Lin, Yi-Chen; Chuang, Huey-Wen

    2016-06-01

    Algae wall polysaccharide, laminarin (Lam), has an established role on induction of plant disease resistance. In this study, application of Lam increased Arabidopsis fresh weight and enhanced tolerance to salt and heat stress by stabilizing chloroplast under adverse environment. Transcriptome analysis indicated that, in addition to induced a large number of genes associated with the host defense, genes involved in the regulation of abiotic stress tolerance mostly the heat stress response constituted the largest group of the up-regulated genes. Lam induced expression of IRT1, ZIP8, and copper transporters involved in transport of Fe, Zn, Cu ions associated with the activity of chloroplast antioxidant system. Lam also up-regulated genes involved in the synthesis of terpenoid, a plastidial-derived secondary metabolite with antioxidant activity. Overexpression of a Lam-induced defensin like 202 (DEFL202) resulted in increased chloroplast stability under salt stress and increased plant growth activity after heat stress. Expression of antioxidant enzymes including SOD and ascorbate peroxidase (APX), photosystem PsbA-D1 and ABA-dependent responsive to desiccation 22 (RD22) was induced to higher levels in the transgenic seedlings. In sum, our results suggest that Lam is an potent inducer for induction of chloroplastic antioxidant activity. Lam affect plant abiotic stress tolerance partially through regulation of the DEFL-mediated pathway. PMID:27095402

  2. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

    PubMed Central

    Cristancho, Marco A.; Botero-Rozo, David Octavio; Giraldo, William; Tabima, Javier; Riaño-Pachón, Diego Mauricio; Escobar, Carolina; Rozo, Yomara; Rivera, Luis F.; Durán, Andrés; Restrepo, Silvia; Eilam, Tamar; Anikster, Yehoshua; Gaitán, Alvaro L.

    2014-01-01

    Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates. PMID

  3. Molecular characterization and expression profile of partial TLR4 gene in association to mastitis in crossbred cattle.

    PubMed

    Panigrahi, Manjit; Sharma, Arjava; Bhushan, Bharat

    2014-01-01

    Crossbred cattle are more prone to mastitis in comparison to indigenous cattle. Toll-like receptor 4 (TLR4) recognizes pathogen ligands, for example, lipopolysaccharide (LPS) endotoxin from Escherichia coli and mediates signaling to initiate innate and adaptive immune responses. Mutations in TLR4 can compromise the host immune response to certain pathogens, so it may be a potential candidate for marker assisted selection to enhance mastitis resistance in dairy cattle. Hence, in this study role of bovine TLR4 gene in mastitis resistance was investigated by association as well as expression profiling analysis in crossbred cattle. The animals were divided into mastitis affected and unaffected groups on the basis of history of animals and California Mastitis Test (CMT). PCR-SSCP and Sequence analysis revealed three genotypes of coreceptor binding region 1 (CRBR1) fragment of TLR4 gene namely AA, AB, and BB in both groups of cattle. The logistic regression model did not show any significant effect of these genotypes on the occurrence of clinical mastitis. Moreover, in vitro challenge of peripheral blood mononuclear cells (PBMCs) with LPS failed to show any association of the genotypes with TLR4 gene expression. In a nutshell, in the present study enough evidence was not found for association of the SNP variants of CRBR1 fragment of TLR4 gene with mastitis susceptibility in crossbred cattle. PMID:24669869

  4. SPATULA and ALCATRAZ, are partially redundant, functionally diverging bHLH genes required for Arabidopsis gynoecium and fruit development.

    PubMed

    Groszmann, Michael; Paicu, Teodora; Alvarez, John P; Swain, Steve M; Smyth, David R

    2011-12-01

    The Arabidopsis gynoecium is a complex organ that facilitates fertilization, later developing into a dehiscent silique that protects seeds until their dispersal. Identifying genes important for development is often hampered by functional redundancy. We report unequal redundancy between two closely related genes, SPATULA (SPT) and ALCATRAZ (ALC), revealing previously unknown developmental roles for each. SPT is known to support septum, style and stigma development in the flower, whereas ALC is involved in dehiscence zone development in the fruit. ALC diverged from a SPT-like ancestor following gene duplication coinciding with the At-β polyploidy event. Here we show that ALC is also involved in early gynoecium development, and SPT in later valve margin generation in the silique. Evidence includes the increased severity of early gynoecium disruption, and of later valve margin defects, in spt-alc double mutants. In addition, a repressive version of SPT (35S:SPT-SRDX) disrupts both structures. Consistent with redundancy, ALC and SPT expression patterns overlap in these tissues, and the ALC promoter carries two atypical E-box elements identical to one in SPT required for valve margin expression. Further, SPT can heterodimerize with ALC, and 35S:SPT can fully complement dehiscence defects in alc mutants, although 35S:ALC can only partly complement spt gynoecium disruptions, perhaps associated with its sequence simplification. Interactions with FRUITFULL and SHATTERPROOF genes differ somewhat between SPT and ALC, reflecting their different specializations. These two genes are apparently undergoing subfunctionalization, with SPT essential for earlier carpel margin tissues, and ALC specializing in later dehiscence zone development. PMID:21801252

  5. The HLA-B*83:01 allele is generated by a gene conversion event including whole of exon 2 and partial introns 1 and 2 between B*44 and B*56 alleles.

    PubMed

    Cervera, I; Herraiz, M A; Vidart, J A; Peñaloza, J; Martinez-Laso, J

    2011-02-01

    Several studies have indicated the gene conversion as the most important mechanism about the MHC polymorphism generation when intron sequences are studied. The data obtained confirm that the B*83:01 allele is generated by gene conversion event including exon 2 and partial intron 1 and 2 between B*44 and B*56 alleles. PMID:21199389

  6. Sense and antisense transcripts of the developmentally regulated murine hsp70.2 gene are expressed in distinct and only partially overlapping areas in the adult brain

    NASA Technical Reports Server (NTRS)

    Murashov, A. K.; Wolgemuth, D. J.

    1996-01-01

    We have examined the spatial pattern of expression of a member of the hsp70 gene family, hsp70.2, in the mouse central nervous system. Surprisingly, RNA blot analysis and in situ hybridization revealed abundant expression of an 'antisense' hsp70.2 transcript in several areas of adult mouse brain. Two different transcripts recognized by sense and antisense riboprobes for the hsp70.2 gene were expressed in distinct and only partially overlapping neuronal populations. RNA blot analysis revealed low levels of the 2.7 kb transcript of hsp70.2 in several areas of the brain, with highest signal in the hippocampus. Abundant expression of a slightly larger (approximately 2.8 kb) 'antisense' transcript was detected in several brain regions, notably in the brainstem, cerebellum, mesencephalic tectum, thalamus, cortex, and hippocampus. In situ hybridization revealed that the sense and antisense transcripts were both predominantly neuronal and localized to the same cell types in the granular layer of the cerebellum, trapezoid nucleus of the superior olivary complex, locus coeruleus and hippocampus. The hsp70.2 antisense transcripts were particularly abundant in the frontal cortex, dentate gyrus, subthalamic nucleus, zona incerta, superior and inferior colliculi, central gray, brainstem, and cerebellar Purkinje cells. Our findings have revealed a distinct cellular and spatial localization of both sense and antisense transcripts, demonstrating a new level of complexity in the function of the heat shock genes.

  7. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones.

    PubMed Central

    Newman, T; de Bruijn, F J; Green, P; Keegstra, K; Kende, H; McIntosh, L; Ohlrogge, J; Raikhel, N; Somerville, S; Thomashow, M

    1994-01-01

    High-throughput automated partial sequencing of anonymous cDNA clones provides a method to survey the repertoire of expressed genes from an organism. Comparison of the coding capacity of these expressed sequence tags (ESTs) with the sequences in the public data bases results in assignment of putative function to a significant proportion of the ESTs. Thus, the more than 13,400 plant ESTs that are currently available provide a new resource that will facilitate progress in many areas of plant biology. These opportunities are illustrated by a description of the results obtained from analysis of 1500 Arabidopsis ESTs from a cDNA library prepared from equal portions of poly(A+) mRNA from etiolated seedlings, roots, leaves, and flowering inflorescences. More than 900 different sequences were represented, 32% of which showed significant nucleotide or deduced amino acid sequences similarity to previously characterized genes or proteins from a wide range of organisms. At least 165 of the clones had significant deduced amino acid sequence homology to proteins or gene products that have not been previously characterized from higher plants. A summary of methods for accessing the information and materials generated by the Arabidopsis cDNA sequencing project is provided. PMID:7846151

  8. The inactivation of the sortilin gene leads to a partial disruption of prosaposin trafficking to the lysosomes

    SciTech Connect

    Zeng, Jibin; Racicott, Jesse; Morales, Carlos R.

    2009-11-01

    Lysosomes are intracellular organelles which contain enzymes and activator proteins involved in the digestion and recycling of a variety of cellular and extracellular substances. We have identified a novel sorting receptor, sortilin, which is involved in the lysosomal trafficking of the sphingolipid activator proteins, prosaposin and GM{sub 2}AP, and the soluble hydrolases cathepsin D, cathepsin H, and acid sphingomyelinase. Sortilin belongs to a growing family of receptors with homology to the yeast Vps10 protein, which acts as a lysosomal sorting receptor for carboxypeptidase Y. In this study we examined the effects of the sortilin gene inactivation in mice. The inactivation of this gene did not yield any noticeable lysosomal pathology. To determine the existence of an alternative receptor complementing the sorting function of sortilin, we quantified the concentration of prosaposin in the lysosomes of the nonciliated epithelial cells lining the efferent ducts. These cells were chosen because they express sortilin and have a large number of lysosomes containing prosaposin. In addition, the nonciliated cells are known to endocytose luminal prosaposin that is synthesized and secreted by Sertoli cells into the seminiferous luminal fluids. Consequently, the nonciliated cells are capable of targeting both exogenous and endogenous prosaposin to the lysosomes. Using electron microscope immunogold labeling and quantitative analysis, our results demonstrate that inactivation of the sortilin gene produces a significant decrease of prosaposin in the lysosomes. When luminal prosaposin was excluded from the efferent ducts, the level of prosaposin in lysosomes was even lower in the mutant mice. Nonetheless, a significant amount of prosaposin continues to reach the lysosomal compartment. These results strongly suggest the existence of an alternative receptor that complements the function of sortilin and explains the lack of lysosomal storage disorders in the sortilin

  9. Cloning and partial characterization of two chromosomal loci from Bacteroides ovatus that contain genes essential for growth on guar gum.

    PubMed Central

    Valentine, P J; Arnold, P; Salyers, A A

    1992-01-01

    Previously, we isolated three transposon insertion mutants of Bacteroides ovatus (M-4, M-5, and M-7) that were unable to grow on the branched polysaccharide guar gum. In this study, we used a tetracycline resistance gene on the transposon to clone chromosomal DNA adjacent to the transposon insertions in each of the three mutants. Restriction analysis of the flanking chromosomal DNA in M-4 and M-7 revealed that the insertions in these two mutants were in the same location. The cloned DNA adjacent to the insertions in M-5 and M-7 was used as a hybridization probe to clone the wild-type loci. Two clones of about 10 kbp in size were obtained. Restriction analysis showed that these two clones did not overlap. The clone of the M-5 locus appeared to contain all of the genes affected by the M-5 insertion, but we were unable to demonstrate complementation of the M-5 mutation because of the instability of the clone in this background. Analysis of the clone of the M-7 locus showed that it contained a guar gum-regulated promoter, but the transcript originating from this promoter was not affected by the transposon insertion. Thus, the M-7 locus apparently contains at least two separate transcriptional units, the one defined by this promoter and the one interrupted by the transposon insertion. Insertion mutations downstream of the guar gum-regulated promoter demonstrated that there were essential guar gum utilization genes in this region. The M-7 mutant was eliminated by the wild type in the intestinal tracts of germfree mice.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:1622223

  10. SNPs in DNA repair or oxidative stress genes and late subcutaneous fibrosis in patients following single shot partial breast irradiation

    PubMed Central

    2012-01-01

    Background The aim of this study was to evaluate the potential association between single nucleotide polymorphisms related response to radiotherapy injury, such as genes related to DNA repair or enzymes involved in anti-oxidative activities. The paper aims to identify marker genes able to predict an increased risk of late toxicity studying our group of patients who underwent a Single Shot 3D-CRT PBI (SSPBI) after BCS (breast conserving surgery). Methods A total of 57 breast cancer patients who underwent SSPBI were genotyped for SNPs (single nucleotide polymorphisms) in XRCC1, XRCC3, GST and RAD51 by Pyrosequencing technology. Univariate analysis (ORs and 95% CI) was performed to correlate SNPs with the risk of developing ≥ G2 fibrosis or fat necrosis. Results A higher significant risk of developing ≥ G2 fibrosis or fat necrosis in patients with: polymorphic variant GSTP1 (Ile105Val) (OR = 2.9; 95%CI, 0.88-10.14, p = 0.047). Conclusions The presence of some SNPs involved in DNA repair or response to oxidative stress seem to be able to predict late toxicity. Trial Registration ClinicalTrials.gov: NCT01316328 PMID:22272830

  11. Partial sequencing of Bm86 gene for studying the phylogeny of an Indian isolate of Rhipicephalus (Boophilus) microplus tick.

    PubMed

    Anbarasi, P; Latha, B R; Dhinakar Raj, G; Sreekumar, C; Senthuran, S

    2014-09-01

    Tick gut glycoprotein, designated as Bm86, found on the luminal surface of the plasma membrane of gut epithelial cells of Boophilus microplus, which is a concealed antigen, has been used as vaccine candidate molecule for immunization against ticks. To better understand the molecular diversity of Bm86 gene in ticks, a portion of the cDNA was sequenced from an Indian isolate of B. microplus. Comparison of nucleotide sequence revealed that Indian isolate had 97 % homology (18 polymorphisms) with that of the Australian isolate and 96 % homology (20 polymorphisms) with that of the Cuban vaccine strain. Further, the Indian isolate differed from the Cuban vaccine isolate at 7 amino acid loci, including 5 substitutions (at residues 88, 94, 175, 176 and 177) and 2 deletions (at 183 and 184). However, protein prediction studies did not show any difference in the putative antigenic epitopes of the protein expressed. PMID:25035581

  12. Partial deletion of the AGXT gene (EX1_EX7del): A new genotype in hyperoxaluria type 1.

    PubMed

    Nogueira, P K; Vuong, T S; Bouton, O; Maillard, A; Marchand, M; Rolland, M O; Cochat, P; Bozon, D

    2000-04-01

    Primary hyperoxaluria type 1 (PH1) is a rare autosomal (2q37.3) recessive metabolic disease caused by a deficiency of the hepatic peroxisomal enzyme alanine:glyoxylate amino transferase. Molecular heterogeneity is important in PH1 as most of the patients (if the parents are unrelated) are compound heterozygotes for rare mutations. We describe the first large deletion in the AGXT gene, removing exons 1 to 7 (EX1_EX7del) that was responsible for one case of severe PH1. This 10 kb deletion was identified by Southern blotting of genomic DNA digested by Xba I and hybridized with different exonic probes. Both parents (from Turkey) are first cousin and carry the deletion. It is of note that the presently reported patient did not exhibit any AGT catalytic activity and even so, he progressed towards end-stage renal disease only at 19 years old. PMID:10737993

  13. Human liver mitochondrial carnitine palmitoyltransferase I: characterization of its cDNA and chromosomal localization and partial analysis of the gene.

    PubMed Central

    Britton, C H; Schultz, R A; Zhang, B; Esser, V; Foster, D W; McGarry, J D

    1995-01-01

    Using the cDNA for rat liver mitochondrial carnitine palmitoyltransferase I (CPT I; EC 2.3.1.21) as a probe, we isolated its counterpart as three overlapping clones from a human liver cDNA library. Both the nucleotide sequence of the human cDNA and the predicted primary structure of the protein (773 aa) proved to be very similar to those of the rat enzyme (82% and 88% identity, respectively). The CPT I mRNA size was also found to be the same (approximately 4.7 kb) in both species. Screening of a human genomic library with the newly obtained cDNA yielded a positive clone of approximately 6.5 kb which, upon partial analysis, was found to contain at least two complete exons linked by a 2.3-kb intron. Oligonucleotide primers specific to upstream and downstream regions of one of the exon/intron junctions were tested in PCRs with DNA from a panel of somatic cell hybrids, each containing a single human chromosome. The results allowed unambiguous assignment of the human liver CPT I gene to the q (long) arm of chromosome 11. Additional experiments established that liver and fibroblasts express the same isoform of mitochondrial CPT I, legitimizing the use of fibroblast assays in the differential diagnosis of the "muscle" and "hepatic" forms of CPT deficiency. The data provide insights into the structure of a human CPT I isoform and its corresponding gene and establish unequivocally that CPT I and CPT II are distinct gene products. Availability of the human CPT I cDNA should open the way to an understanding of the genetic basis of inherited CPT I deficiency syndromes, how the liver CPT I gene is regulated, and which tissues other than liver express this particular variant of the enzyme. Images Fig. 4 Fig. 5 PMID:7892212

  14. Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae

    NASA Technical Reports Server (NTRS)

    Springer, E.; Sachs, M. S.; Woese, C. R.; Boone, D. R.

    1995-01-01

    Representatives of the family Methanosarcinaceae were analyzed phylogenetically by comparing partial sequences of their methyl-coenzyme M reductase (mcrI) genes. A 490-bp fragment from the A subunit of the gene was selected, amplified by the PCR, cloned, and sequenced for each of 25 strains belonging to the Methanosarcinaceae. The sequences obtained were aligned with the corresponding portions of five previously published sequences, and all of the sequences were compared to determine phylogenetic distances by Fitch distance matrix methods. We prepared analogous trees based on 16S rRNA sequences; these trees corresponded closely to the mcrI trees, although the mcrI sequences of pairs of organisms had 3.01 +/- 0.541 times more changes than the respective pairs of 16S rRNA sequences, suggesting that the mcrI fragment evolved about three times more rapidly than the 16S rRNA gene. The qualitative similarity of the mcrI and 16S rRNA trees suggests that transfer of genetic information between dissimilar organisms has not significantly affected these sequences, although we found inconsistencies between some mcrI distances that we measured and and previously published DNA reassociation data. It is unlikely that multiple mcrI isogenes were present in the organisms that we examined, because we found no major discrepancies in multiple determinations of mcrI sequences from the same organism. Our primers for the PCR also match analogous sites in the previously published mcrII sequences, but all of the sequences that we obtained from members of the Methanosarcinaceae were more closely related to mcrI sequences than to mcrII sequences, suggesting that members of the Methanosarcinaceae do not have distinct mcrII genes.

  15. Adenoviral gene transfer of endothelial nitric-oxide synthase (eNOS) partially restores normal pulmonary arterial pressure in eNOS-deficient mice

    PubMed Central

    Champion, Hunter C.; Bivalacqua, Trinity J.; Greenberg, Stanley S.; Giles, Thomas D.; Hyman, Albert L.; Kadowitz, Philip J.

    2002-01-01

    It has been shown that mice deficient in the gene coding for endothelial nitric-oxide synthase (eNOS) have increased pulmonary arterial pressure and pulmonary vascular resistance. In the present study, the effect of transfer to the lung of an adenoviral vector encoding the eNOS gene (AdCMVeNOS) on pulmonary arterial pressure and pulmonary vascular resistance was investigated in eNOS-deficient mice. One day after intratracheal administration of AdCMVeNOS to eNOS−/− mice, there was an increase in eNOS protein, cGMP levels, and calcium-dependent conversion of l-arginine to l-citrulline in the lung. The increase in eNOS protein and activity in eNOS−/− mice was associated with a reduction in mean pulmonary arterial pressure and pulmonary vascular resistance when compared with values in eNOS-deficient mice treated with vehicle or a control adenoviral vector coding for β-galactosidase, AdCMVβgal. These data suggest that in vivo gene transfer of eNOS to the lung in eNOS−/− mice can increase eNOS staining, eNOS protein, calcium-dependent NOS activity, and cGMP levels and partially restore pulmonary arterial pressure and pulmonary vascular resistance to near levels measured in eNOS+/+ mice. Thus, the major finding in this study is that in vivo gene transfer of eNOS to the lung in large part corrects a genetic deficiency resulting from eNOS deletion and may be a useful therapeutic intervention for the treatment of pulmonary hypertensive disorders in which eNOS activity is reduced. PMID:12237402

  16. A novel large regulator RNA, B2, partially overlaps the HEF1/NEDD9/Cas-L gene.

    PubMed

    Malleter, Marine; Jacquot, Catherine; Moreau, Dimitri; Tomasoni, Christophe; Tsvetanova, Marianna; Chinou, Ioanna; Juge, Marcel; Pineau, Alain; Le Pape, Patrice; Roussakis, Christos

    2010-06-01

    The non-coding RNAs are new players in cellular and molecular biology. Indeed, quantitative and functional non-coding RNA has long been underestimated. There is a great diversity and it seems that much of the genome is transcribed into RNA, while only 1.2% of DNA information is translated into proteins. Non-coding RNA has been categorized according to different specifications so large non-coding RNA includes RNA with 300 to more than 10,000 bp. In this study, we propose a new non-coding RNA named B2 discovered by differential display. B2 is a nuclear RNA which is 51,011 bp long with no significant open reading frame. This RNA has a continuous homology with the genomic DNA of the HEF1/ NEDD9/Cas-L gene located on 6p24-p25. This homology has enabled us to characterize its structure by choosing overlapping fragments to perform several RT-PCRs. B2 RNA extends from 10 kb upstream of exon 1 of the HEF1 gene on the 5' end to exon 4 HEF1 on the 3' end. In addition, a strategic choice of PCR primers enabled us to determine the location of B2 in the subcellular compartment and then real-time PCR revealed overexpression of B2 and HEF1 in certain tissues such as thymus, cervix, liver, and spleen (among the 20 tissues analysed). B2 seems especially interesting in that it can regulate apoptosis and cell proliferation by modulating HEF1. In addition, the fact that cytostatic treatments can induce B2 reinforces the interest in this new potential target in the development of anticancer treatments. These results show that this novel non-coding RNA is an attractive target. PMID:20428794

  17. Partial activation of gene activity and chromatin remodeling of the human 14q32.1 serpin gene cluster by HNF-1 alpha and HNF-4 in fibroblast microcell hybrids.

    PubMed

    Rollini, P; Xu, L; Fournier, R E

    1999-07-01

    The genes encoding alpha 1-antitrypsin (alpha 1AT, gene symbol P I) and corticosteroid-binding globulin (CBG) are part of a cluster of serine protease inhibitor (serpin) genes on human chromosome 14q32.1. Both genes are highly expressed in the liver and in cultured hepatoma cells, and the approximately 100-kb region around these genes contains an extensive array of expression-associated DNase I-hypersensitive sites (DHSs). Activation of human alpha 1AT and CBG transcription occurred when human chromosome 14 was transferred from nonexpressing cells to rat hepatoma cells. This activation event was accompanied by long-range chromatin reorganization of the entire region and the de novo formation of 17 expression-associated DHSs. Both gene activation and chromatin remodeling in hepatic cells required the liver-enriched transactivators hepatocyte nuclear factors-1 alpha and -4 (HNF-1 alpha and HNF-4). In this study, we tested whether ectopic expression of HNF-1 alpha and HNF-4 in nonexpressing cells could activate alpha 1AT and/or CBG transcription, and we monitored the chromatin structure of the locus in stably transfected fibroblasts. We report that both alpha 1AT and CBG mRNAs were expressed in fibroblast transfectants that stably expressed HNF-1 alpha and HNF-4, but expression was only approximately 1-10% of that observed in hepatic cells. Gene activation in these cells was accompanied by partial chromatin remodeling, as 6 of 17 expression-associated DHSs were formed. The potential implications of these results are discussed. PMID:11586788

  18. [On the phylogenetic relationship of Corvinae birds (Aves, Corvidae) from data of partial sequencing of cytochrome b gene mitochondrial DNA].

    PubMed

    Kriukov, A P; Odati, S

    2000-09-01

    To establish phylogenetic relationships within the corvine birds at the interspecific and intergeneric levels, the sequence of the mitochondrial DNA cytochrome b gene was analyzed. The NJ, UPGMA, and MP trees showed similar clustering. Relationships between the jungle crow, on the one hand, and the rook and Australian raven, on the other hand, were closer than between the jungle crow and the hooded and carrion crows. Mitochondrial genome of Australian raven displayed the closest similarity to the ancestral genome of the genus Corvus. Populations inhabiting the eastern part of the carrion crow C. corone orientations area were statistically significantly subdivided into three lineages. These data also confirmed the hypothesis on the location of the carrion crow ancestral lineage in the southeastern part of the area. In general, the transition and transversion substitution levels, their relationships, and distribution over codon positions were similar to that already reported for birds. Synonymous transitions in the third codon position were the prevailing substitution type. Using standard calibration scales, the time of divergence between species and genera within the corvine family was estimated to be 3.1-4 and 3.8-8.8 Myr, respectively. The divergence time between the examined corvine birds and birds of paradise constituted from 8 to 10 Myr. PMID:11042813

  19. Transgenic Expression of the piRNA-Resistant Masculinizer Gene Induces Female-Specific Lethality and Partial Female-to-Male Sex Reversal in the Silkworm, Bombyx mori.

    PubMed

    Sakai, Hiroki; Sumitani, Megumi; Chikami, Yasuhiko; Yahata, Kensuke; Uchino, Keiro; Kiuchi, Takashi; Katsuma, Susumu; Aoki, Fugaku; Sezutsu, Hideki; Suzuki, Masataka G

    2016-08-01

    In Bombyx mori (B. mori), Fem piRNA originates from the W chromosome and is responsible for femaleness. The Fem piRNA-PIWI complex targets and cleaves mRNAs transcribed from the Masc gene. Masc encodes a novel CCCH type zinc-finger protein and is required for male-specific splicing of B. mori doublesex (Bmdsx) transcripts. In the present study, several silkworm strains carrying a transgene, which encodes a Fem piRNA-resistant Masc mRNA (Masc-R), were generated. Forced expression of the Masc-R transgene caused female-specific lethality during the larval stages. One of the Masc-R strains weakly expressed Masc-R in various tissues. Females heterozygous for the transgene expressed male-specific isoform of the Bombyx homolog of insulin-like growth factor II mRNA-binding protein (ImpM) and Bmdsx. All examined females showed a lower inducibility of vitellogenin synthesis and exhibited abnormalities in the ovaries. Testis-like tissues were observed in abnormal ovaries and, notably, the tissues contained considerable numbers of sperm bundles. Homozygous expression of the transgene resulted in formation of the male-specific abdominal segment in adult females and caused partial male differentiation in female genitalia. These results strongly suggest that Masc is an important regulatory gene of maleness in B. mori. PMID:27579676

  20. Rapid Origin Determination of the Northern Mauxia Shrimp (Acetes chinensis) Based on Allele Specific Polymerase Chain Reaction of Partial Mitochondrial 16S rRNA Gene

    PubMed Central

    Kang, Jung-Ha; Noh, Eun-Soo; Park, Jung-Youn; An, Chel-Min; Choi, Jung-Hwa; Kim, Jin-Koo

    2015-01-01

    Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis′ economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis′ origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3′-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China. PMID:25656197

  1. Rapid Origin Determination of the Northern Mauxia Shrimp (Acetes chinensis) Based on Allele Specific Polymerase Chain Reaction of Partial Mitochondrial 16S rRNA Gene.

    PubMed

    Kang, Jung-Ha; Noh, Eun-Soo; Park, Jung-Youn; An, Chel-Min; Choi, Jung-Hwa; Kim, Jin-Koo

    2015-04-01

    Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China. PMID:25656197

  2. A gene-centric analysis of activated partial thromboplastin time and activated protein C resistance using the HumanCVD focused genotyping array

    PubMed Central

    Gaunt, Tom R; Lowe, Gordon DO; Lawlor, Debbie A; Casas, Juan-Pablo; Day, Ian NM

    2013-01-01

    Activated partial thromboplastin time (aPTT) is an important routine measure of intrinsic blood coagulation. Addition of activated protein C (APC) to the aPTT test to produce a ratio, provides one measure of APC resistance. The associations of some genetic mutations (eg, factor V Leiden) with these measures are established, but associations of other genetic variations remain to be established. The objective of this work was to test for association between genetic variants and blood coagulation using a high-density genotyping array. Genetic association with aPTT and APC resistance was analysed using a focused genotyping array that tests approximately 50 000 single-nucleotide polymorphisms (SNPs) in nearly 2000 cardiovascular candidate genes, including coagulation pathway genes. Analyses were conducted on 2544 European origin women from the British Women's Heart and Health Study. We confirm associations with aPTT at the coagulation factor XII (F12)/G protein-coupled receptor kinase 6 (GRK6) and kininogen 1 (KNG1)/histidine-rich glycoprotein (HRG) loci, and identify novel SNPs at the ABO locus and novel locus kallikrein B (KLKB1)/F11. In addition, we confirm association between APC resistance and factor V Leiden mutation, and identify novel SNP associations with APC resistance in the HRG and F5/solute carrier family 19 member 2 (SLC19A2) regions. In conclusion, variation at several genetic loci influences intrinsic blood coagulation as measured by both aPTT and APC resistance. PMID:23188048

  3. Partial characterization of genes whose transcripts accumulate preferentially in cell clusters at the earliest stage of carrot somatic embryogenesis.

    PubMed

    Yasuda, H; Nakajima, M; Ito, T; Ohwada, T; Masuda, H

    2001-04-01

    We attempted to identify genes that are preferentially expressed immediately after somatic cells divide to form cell clusters at the earliest stage of carrot somatic embryogenesis when they are not or barely expressed in non-embryogenic suspension-cultured cells in the presence of 2,4-D. Using the differential display technique, we isolated three cDNA clones, designated No. 43, No. 87 and No. 93. The No. 43 transcript was preferentially expressed in the earliest cell clusters, its level decreased drastically at the globular and heart-shaped and torpedo-shaped stages, and it was not detected in non-embryogenic suspension-cultured cells. No. 43 cDNA encoded a protein with homology to thaumatin-like proteins and the deduced positions of seven cysteine residues in the 63 amino acid sequence from the carboxyl terminus were identical to those in thaumatin-like proteins. The full-length nucleotide sequence of No. 93 cDNA was determined and its product was about 80% homologous to precursor of the 14 kDa proline-rich DC 2.15 protein of carrot at the amino acid level. However, the deduced amino acid sequence lacked the characteristic core of repeating Pro-X motifs found in DC 2.15. The No. 93 transcript accumulated preferentially in the earliest cell clusters but it was also detected at a low level in non-embryogenic suspension-cultured cells, unlike DC 2.15 transcripts that begin to accumulate in heart-shaped embryos before their level falls in torpedo-shaped embryos. No. 87 transcripts were expressed preferentially in the earliest cell clusters that has been incubated with 2,4-D but were also detected at a low level in suspension-cultured cells subcultured in the continued presence of 2,4-D. The No. 87 cDNA exhibited no significant homology to any sequences in databases. PMID:11430432

  4. Partial correction of the CFTR-dependent ABPA mouse model with recombinant adeno-associated virus gene transfer of truncated CFTR gene.

    PubMed

    Mueller, Christian; Torrez, Daniel; Braag, Sofia; Martino, Ashley; Clarke, Tracy; Campbell-Thompson, Martha; Flotte, Terence R

    2008-01-01

    Recently, we have developed a model of airway inflammation in a CFTR knockout mouse utilizing Aspergillus fumigatus crude protein extract (Af-cpe) to mimic allergic bronchopulmonary aspergillosis (ABPA) 1, an unusual IgE-mediated hypersensitivity syndrome seen in up to 15% of cystic fibrosis (CF) patients and rarely elsewhere. We hypothesized that replacement of CFTR via targeted gene delivery to airway epithelium would correct aberrant epithelial cytokine signaling and ameliorate the ABPA phenotype in CFTR-deficient (CFTR 489X - /-, FABP-hCFTR + / +) mice. CFTR knockout mice underwent intra-tracheal (IT) delivery of recombinant adeno-associated virus serotype 5 (rAAV5Delta-264CFTR) or rAAV5-GFP at 2.58 x 10(12) viral genomes/mouse. All mice were then sensitized with two serial injections (200 microg) of crude Af antigen via the intra-peritoneal (IP) route. Untreated mice were sensitized without virus exposure. Challenges were performed 2 weeks after final sensitization, using a 0.25% solution containing Aspergillus fumigatus crude protein extract delivered by inhalation on three consecutive days. The rAAV5Delta-264CFTR-treated mice had lower total serum IgE levels (172513 ng/ml +/- 1312) than rAAV5-GFP controls (26 892 ng/ml +/- 3715) (p = 0.037) and non-treated, sensitized controls (24 816 +/- 4219 ng/ml). Serum IgG1 levels also were lower in mice receiving the CFTR vector. Interestingly, splenocytes from rAAV5Delta-264CFTR-treated mice secreted less IL-13, INFg, TNFa, RANTES and GM-CSF after ConA stimulation. Gene therapy with rAAV5Delta-264CFTR attenuated the hyper-IgE response in this reproducible CF mouse model of ABPA, with systemic effects also evident in the cytokine response of stimulated splenocytes. PMID:18023072

  5. Four-locus phylogeny of Fusarium avenaceum and related species and their species-specific identification based on partial phosphate permease gene sequences.

    PubMed

    Stakheev, Alexander A; Khairulina, Dina R; Zavriev, Sergey K

    2016-05-16

    The fungus Fusarium avenaceum and its closest relatives are responsible for contamination of agricultural plants and their products by mycotoxins such as enniatins and moniliformin. Precise identification of mycotoxin producers is necessary for estimation of the accumulation risk of those compounds and for preventing the consumption of highly contaminated products. Nucleic acids amplification-based techniques proved to be the most rapid and reliable approach for pathogen diagnostics and identification. In this study partial phosphate permease gene (PHO) sequences were determined for Fusarium avenaceum (including one isolate identified as F. arthrosporioides), F. tricinctum, F. acuminatum and F. torulosum. Phylogenetic analysis of 40 isolates of those species from different climates and geographical regions of Russia and some neighboring countries based on sequences of PHO, translation elongation factor 1 alpha (TEF1α), beta-tubulin (β-TUB), enniatin synthetase (Esyn1) genes and combined data set demonstrated that the PHO gene possesses the highest rate of variability among them and can be considered as an informative marker for phylogenetic studies of these species. According to the combined data set phylogeny, the isolates of each species formed clusters with a high bootstrap support. Analysis of PHO sequences revealed a high intraspecific variability of F. avenaceum: there were 5 independent clusters on the dendrogram, including one cluster which was closer to F. torulosum than to other F. avenaceum isolates. Variable sites in PHO sequences have been used for the design of species-specific primers and a fluorescent hydrolysis probe. The specificity of the assay was shown for DNA samples extracted from 68 isolates of 23 Fusarium species. Quantitative PCR approach was applied to estimate the contamination rate of 17 naturally infected oat and barley samples, previously characterized by microbiological procedures. PMID:26974249

  6. Immunohistochemical analyses of cell cycle progression and gene expression of biliary epithelial cells during liver regeneration after partial hepatectomy of the mouse

    PubMed Central

    Fukuda, Tatsuya; Fukuchi, Tomokazu; Yagi, Shinomi; Shiojiri, Nobuyoshi

    2015-01-01

    The liver has a remarkable regeneration capacity, and, after surgical removal of its mass, the remaining tissue undergoes rapid regeneration through compensatory growth of its constituent cells. Although hepatocytes synchronously proliferate under the control of various signaling molecules from neighboring cells, there have been few detailed analyses on how biliary cells regenerate for their cell population after liver resection. The present study was undertaken to clarify how biliary cells regenerate after partial hepatectomy of mice through extensive analyses of their cell cycle progression and gene expression using immunohistochemical and RT-PCR techniques. When expression of PCNA, Ki67 antigen, topoisomerase IIα and phosphorylated histone H3, which are cell cycle markers, was immunohistochemically examined during liver regeneration, hepatocytes had a peak of the S phase and M phase at 48–72 h after resection. By contrast, biliary epithelial cells had much lower proliferative activity than that of hepatocytes, and their peak of the S phase was delayed. Mitotic figures were rarely detectable in biliary cells. RT-PCR analyses of gene expression of biliary markers such as Spp1 (osteopontin), Epcam and Hnf1b demonstrated that they were upregulated during liver regeneration. Periportal hepatocytes expressed some of biliary markers, including Spp1 mRNA and protein. Some periportal hepatocytes had downregulated expression of HNF4α and HNF1α. Gene expression of Notch signaling molecules responsible for cell fate decision of hepatoblasts to biliary cells during development was upregulated during liver regeneration. Notch signaling may be involved in biliary regeneration. PMID:26633692

  7. Partial Attenuation of Respiratory Syncytial Virus with a Deletion of a Small Hydrophobic Gene Is Associated with Elevated Interleukin-1β Responses

    PubMed Central

    Russell, Ryan F.; McDonald, Jacqueline U.; Ivanova, Maria; Zhong, Ziyun; Bukreyev, Alexander

    2015-01-01

    ABSTRACT The small hydrophobic (SH) gene of respiratory syncytial virus (RSV), a major cause of infant hospitalization, encodes a viroporin of unknown function. SH gene knockout virus (RSV ΔSH) is partially attenuated in vivo, but not in vitro, suggesting that the SH protein may have an immunomodulatory role. RSV ΔSH has been tested as a live attenuated vaccine in humans and cattle, and here we demonstrate that it protected against viral rechallenge in mice. We compared the immune response to infection with RSV wild type and RSV ΔSH in vivo using BALB/c mice and in vitro using epithelial cells, neutrophils, and macrophages. Strikingly, the interleukin-1β (IL-1β) response to RSV ΔSH infection was greater than to wild-type RSV, in spite of a decreased viral load, and when IL-1β was blocked in vivo, the viral load returned to wild-type levels. A significantly greater IL-1β response to RSV ΔSH was also detected in vitro, with higher-magnitude responses in neutrophils and macrophages than in epithelial cells. Depleting macrophages (with clodronate liposome) and neutrophils (with anti-Ly6G/1A8) demonstrated the contribution of these cells to the IL-1β response in vivo, the first demonstration of neutrophilic IL-1β production in response to viral lung infection. In this study, we describe an increased IL-1β response to RSV ΔSH, which may explain the attenuation in vivo and supports targeting the SH gene in live attenuated vaccines. IMPORTANCE There is a pressing need for a vaccine for respiratory syncytial virus (RSV). A number of live attenuated RSV vaccine strains have been developed in which the small hydrophobic (SH) gene has been deleted, even though the function of the SH protein is unknown. The structure of the SH protein has recently been solved, showing it is a pore-forming protein (viroporin). Here, we demonstrate that the IL-1β response to RSV ΔSH is greater in spite of a lower viral load, which contributes to the attenuation in vivo. This

  8. Measurement of the doubly-polarized 3He → (γ → , n) pp reaction at 16.5 MeV and its implications for the GDH sum rule

    NASA Astrophysics Data System (ADS)

    Laskaris, G.; Yan, X.; Mueller, J. M.; Zimmerman, W. R.; Xiong, W.; Ahmed, M. W.; Averett, T.; Chu, P.-H.; Deltuva, A.; Flower, C.; Fonseca, A. C.; Gao, H.; Golak, J.; Heideman, J. N.; Karwowski, H. J.; Meziane, M.; Sauer, P. U.; Skibiński, R.; Strakovsky, I. I.; Weller, H. R.; Witała, H.; Wu, Y. K.

    2015-11-01

    We report new measurements of the double-polarized photodisintegration of 3He at an incident photon energy of 16.5 MeV, carried out at the High Intensity γ-ray Source (HIγS) facility located at Triangle Universities Nuclear Laboratory (TUNL). The spin-dependent double-differential cross sections and the contribution from the three-body channel to the Gerasimov-Drell-Hearn (GDH) integrand were extracted and compared with the state-of-the-art three-body calculations. The calculations, which include the Coulomb interaction and are in good agreement with the results of previous measurements at 12.8 and 14.7 MeV, deviate from the new cross section results at 16.5 MeV. The GDH integrand was found to be about one standard deviation larger than the maximum value predicted by the theories.

  9. Analysis of cellulose synthase genes from domesticated apple identifies collinear genes WDR53 and CesA8A: partial co-expression, bicistronic mRNA, and alternative splicing of CESA8A

    PubMed Central

    Guerriero, Gea; Spadiut, Oliver; Kerschbamer, Christine; Giorno, Filomena; Baric, Sanja; Ezcurra, Inés

    2016-01-01

    Cellulose synthase (CesA) genes constitute a complex multigene family with six major phylogenetic clades in angiosperms. The recently sequenced genome of domestic apple, Malus×domestica, was mined for CesA genes, by blasting full-length cellulose synthase protein (CESA) sequences annotated in the apple genome against protein databases from the plant models Arabidopsis thaliana and Populus trichocarpa. Thirteen genes belonging to the six angiosperm CesA clades and coding for proteins with conserved residues typical of processive glycosyltransferases from family 2 were detected. Based on their phylogenetic relationship to Arabidopsis CESAs, as well as expression patterns, a nomenclature is proposed to facilitate further studies. Examination of their genomic organization revealed that MdCesA8-A is closely linked and co-oriented with WDR53, a gene coding for a WD40 repeat protein. The WDR53 and CesA8 genes display conserved collinearity in dicots and are partially co-expressed in the apple xylem. Interestingly, the presence of a bicistronic WDR53–CesA8A transcript was detected in phytoplasma-infected phloem tissues of apple. The bicistronic transcript contains a spliced intergenic sequence that is predicted to fold into hairpin structures typical of internal ribosome entry sites, suggesting its potential cap-independent translation. Surprisingly, the CesA8A cistron is alternatively spliced and lacks the zinc-binding domain. The possible roles of WDR53 and the alternatively spliced CESA8 variant during cellulose biosynthesis in M.×domestica are discussed. PMID:23048131

  10. A glucose bio-battery prototype based on a GDH/poly(methylene blue) bioanode and a graphite cathode with an iodide/tri-iodide redox couple.

    PubMed

    Wang, Jen-Yuan; Nien, Po-Chin; Chen, Chien-Hsiao; Chen, Lin-Chi; Ho, Kuo-Chuan

    2012-07-01

    A glucose bio-battery prototype independent of oxygen is proposed based on a glucose dehydrogenase (GDH) bioanode and a graphite cathode with an iodide/tri-iodide redox couple. At the bioanode, a NADH electrocatalyst, poly(methylene blue) (PMB), which can be easily grown on the electrode (screen-printed carbon paste electrode, SPCE) by electrodeposition, is harnessed and engineered. We find that carboxylated multi-walled carbon nanotubes (MWCNTs) are capable of significantly increasing the deposition amount of PMB and thus enhancing the PMB's electrocatalysis of NADH oxidation and the glucose bio-battery's performance. The choice of the iodide/tri-iodide redox couple eliminates the dependence of oxygen for this bio-battery, thus enabling the bio-battery with a constant current-output feature similar to that of the solar cells. The present glucose bio-battery prototype can attain a maximum power density of 2.4 μW/cm(2) at 25 °C. PMID:22541949

  11. Helicity-dependent reaction γd → π0d near the η-threshold and its contribution to the E-asymmetry and the GDH sum rule for the deuteron

    NASA Astrophysics Data System (ADS)

    Darwish, Eed M.; Hemmdan, A.; El-Shamy, N. T.

    2015-08-01

    The helicity-dependent coherent π0-photoproduction in the reaction γd → π0d near the η-threshold is investigated. The calculations are performed within an approach which includes the reaction amplitudes of the impulse approximation (IA), two-step process with intermediate πN- and ηN-rescattering, and the higher order terms in the multiple scattering series for the intermediate ηNN interaction. The contribution of γd → π0d to the deuteron spin asymmetry is calculated and its contribution to the Gerasimov-Drell-Hearn (GDH) integral is explicitly evaluated by integration up to a photon energy of 900 MeV. In addition, the helicity E-asymmetry is calculated. The results revealed that the doubly polarized differential cross-sections and the helicity E-asymmetry are sensitive to the interference of rescattering effects, specially at photon energies 600-800 MeV and extreme backward pion angles. The sensitivity of the obtained results for the GDH integral to the choice of NN potential model governing the deuteron wave function is discussed. We find that the deviation among results obtained for the deuteron GDH integral using different deuteron wave functions is quite large.

  12. Effects of repeated adolescent stress and serotonin transporter gene partial knockout in mice on behaviors and brain structures relevant to major depression

    PubMed Central

    Spinelli, Simona; Müller, Tanja; Friedel, Miriam; Sigrist, Hannes; Lesch, Klaus-Peter; Henkelman, Mark; Rudin, Markus; Seifritz, Erich; Pryce, Christopher R.

    2013-01-01

    In humans, exposure to stress during development is associated with structural and functional alterations of the prefrontal cortex (PFC), amygdala (AMY), and hippocampus (HC) and their circuits of connectivity, and with an increased risk for developing major depressive disorder particularly in carriers of the short (s) variant of the serotonin transporter (5-HTT) gene-linked polymorphic region (5-HTTLPR). Although changes in these regions are found in carriers of the s allele and/or in depressed patients, evidence for a specific genotype × developmental stress effect on brain structure and function is limited. Here, we investigated the effect of repeated stress exposure during adolescence in mice with partial knockout of the 5-HTT gene (HET) vs. wildtype (WT) on early-adulthood behavioral measures and brain structure [using magnetic resonance imaging (MRI)] relevant to human major depression. Behaviorally, adolescent stress (AS) increased anxiety and decreased activity and did so to a similar degree in HET and WT. In a probabilistic reversal learning task, HET-AS mice achieved fewer reversals than did HET-No-AS mice. 5-HTT genotype and AS were without effect on corticosterone stress response. In terms of structural brain differences, AS reduced the volume of two long-range white matter tracts, the optic tract (OT) and the cerebral peduncle (CP), in WT mice specifically. In a region-of-interest analysis, AS was associated with increased HC volume and HET genotype with a decreased frontal lobe volume. In conclusion, we found that 5-HTT and AS genotype exerted long-term effects on behavior and development of brain regions relevant to human depression. PMID:24427124

  13. Codon-Optimized NADH Oxidase Gene Expression and Gene Fusion with Glycerol Dehydrogenase for Bienzyme System with Cofactor Regeneration

    PubMed Central

    Zhou, Qiang; Wang, Shizhen

    2015-01-01

    NADH oxidases (NOXs) play an important role in maintaining balance of NAD+/NADH by catalyzing cofactors regeneration. The expression of nox gene from Lactobacillus brevis in Escherichia coli BL21 (BL21 (DE3)) was studied. Two strategies, the high AT-content in the region adjacent to the initiation codon and codon usage of the whole gene sequence consistent with the host, obtained the NOX activity of 59.9 U/mg and 73.3 U/mg (crude enzyme), with enhanced expression level of 2.0 and 2.5-folds, respectively. Purified NOX activity was 213.8 U/mg. Gene fusion of glycerol dehydrogenase (GDH) and NOX formed bifuctional multi-enzymes for bioconversion of glycerol coupled with coenzyme regeneration. Kinetic parameters of the GDH-NOX for each substrate, glycerol and NADH, were calculated as Vmax(Glycerol) 20 μM/min, Km(Glycerol) 19.4 mM, Vmax (NADH) 12.5 μM/min and Km (NADH) 51.3 μM, respectively, which indicated the potential application of GDH-NOX for quick glycerol analysis and dioxyacetone biosynthesis. PMID:26115038

  14. Flavobacterium johnsoniae gldN and gldO are partially redundant genes required for gliding motility and surface localization of SprB.

    PubMed

    Rhodes, Ryan G; Samarasam, Mudiarasan Napoleon; Shrivastava, Abhishek; van Baaren, Jessica M; Pochiraju, Soumya; Bollampalli, Sreelekha; McBride, Mark J

    2010-03-01

    Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Mutations in gldN cause a partial defect in gliding. A novel bacteriophage selection strategy was used to aid construction of a strain with a deletion spanning gldN and the closely related gene gldO in an otherwise wild-type F. johnsoniae UW101 background. Bacteriophage transduction was used to move a gldN mutation into F. johnsoniae UW101 to allow phenotypic comparison with the gldNO deletion mutant. Cells of the gldN mutant formed nonspreading colonies on agar but retained some ability to glide in wet mounts. In contrast, cells of the gldNO deletion mutant were completely nonmotile, indicating that cells require GldN, or the GldN-like protein GldO, to glide. Recent results suggest that Porphyromonas gingivalis PorN, which is similar in sequence to GldN, has a role in protein secretion across the outer membrane. Cells of the F. johnsoniae gldNO deletion mutant were defective in localization of the motility protein SprB to the cell surface, suggesting that GldN may be involved in secretion of components of the motility machinery. Cells of the gldNO deletion mutant were also deficient in chitin utilization and were resistant to infection by bacteriophages, phenotypes that may also be related to defects in protein secretion. PMID:20038590

  15. Flavobacterium johnsoniae gldN and gldO Are Partially Redundant Genes Required for Gliding Motility and Surface Localization of SprB▿ †

    PubMed Central

    Rhodes, Ryan G.; Samarasam, Mudiarasan Napoleon; Shrivastava, Abhishek; van Baaren, Jessica M.; Pochiraju, Soumya; Bollampalli, Sreelekha; McBride, Mark J.

    2010-01-01

    Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Mutations in gldN cause a partial defect in gliding. A novel bacteriophage selection strategy was used to aid construction of a strain with a deletion spanning gldN and the closely related gene gldO in an otherwise wild-type F. johnsoniae UW101 background. Bacteriophage transduction was used to move a gldN mutation into F. johnsoniae UW101 to allow phenotypic comparison with the gldNO deletion mutant. Cells of the gldN mutant formed nonspreading colonies on agar but retained some ability to glide in wet mounts. In contrast, cells of the gldNO deletion mutant were completely nonmotile, indicating that cells require GldN, or the GldN-like protein GldO, to glide. Recent results suggest that Porphyromonas gingivalis PorN, which is similar in sequence to GldN, has a role in protein secretion across the outer membrane. Cells of the F. johnsoniae gldNO deletion mutant were defective in localization of the motility protein SprB to the cell surface, suggesting that GldN may be involved in secretion of components of the motility machinery. Cells of the gldNO deletion mutant were also deficient in chitin utilization and were resistant to infection by bacteriophages, phenotypes that may also be related to defects in protein secretion. PMID:20038590

  16. Epilepsy (partial)

    PubMed Central

    2011-01-01

    Introduction About 3% of people will be diagnosed with epilepsy during their lifetime, but about 70% of people with epilepsy eventually go into remission. Methods and outcomes We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of starting antiepileptic drug treatment following a single seizure? What are the effects of drug monotherapy in people with partial epilepsy? What are the effects of additional drug treatments in people with drug-resistant partial epilepsy? What is the risk of relapse in people in remission when withdrawing antiepileptic drugs? What are the effects of behavioural and psychological treatments for people with epilepsy? What are the effects of surgery in people with drug-resistant temporal lobe epilepsy? We searched: Medline, Embase, The Cochrane Library, and other important databases up to July 2009 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). Results We found 83 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. Conclusions In this systematic review we present information relating to the effectiveness and safety of the following interventions: antiepileptic drugs after a single seizure; monotherapy for partial epilepsy using carbamazepine, gabapentin, lamotrigine, levetiracetam, phenobarbital, phenytoin, sodium valproate, or topiramate; addition of second-line drugs for drug-resistant partial epilepsy (allopurinol, eslicarbazepine, gabapentin, lacosamide, lamotrigine, levetiracetam, losigamone, oxcarbazepine, retigabine, tiagabine, topiramate, vigabatrin, or zonisamide); antiepileptic drug withdrawal for people with partial or

  17. nkx2.1 and nkx2.4 genes function partially redundant during development of the zebrafish hypothalamus, preoptic region, and pallidum

    PubMed Central

    Manoli, Martha; Driever, Wolfgang

    2014-01-01

    During ventral forebrain development, orthologs of the homeodomain transcription factor Nkx2.1 control patterning of hypothalamus, preoptic region, and ventral telencephalon. However, the relative contributions of Nkx2.1 and Nkx2.4 to prosencephalon development are poorly understood. Therefore, we analyzed functions of the previously uncharacterized nkx2.4-like zgc:171531 as well as of the presumed nkx2.1 orthologs nkx2.1a and nkx2.1b in zebrafish forebrain development. Our results show that zgc:171531 and nkx2.1a display overlapping expression patterns and a high sequence similarity. Together with a high degree of synteny conservation, these findings indicate that both these genes indeed are paralogs of nkx2.4. As a result, we name zgc:171531 now nkx2.4a, and changed the name of nkx2.1a to nkx2.4b, and of nkx2.1b to nkx2.1. In nkx2.1, nkx2.4a, and nkx2.4b triple morpholino knockdown (nkx2TKD) embryos we observed a loss of the rostral part of prosomere 3 and its derivative posterior tubercular and hypothalamic structures. Furthermore, there was a loss of rostral and intermediate hypothalamus, while a residual preoptic region still develops. The reduction of the ventral diencephalon was accompanied by a ventral expansion of the dorsally expressed pax6, revealing a dorsalization of the basal hypothalamus. Within the telencephalon we observed a loss of pallidal markers, while striatum and pallium are forming. At the neuronal level, nkx2TKD morphants lacked several neurosecretory neuron types, including avp, crh, and pomc expressing cells in the hypothalamus, but still form oxt neurons in the preoptic region. Our data reveals that, while nkx2.1, nkx2.4a, and nkx2.4b genes act partially redundant in hypothalamic development, nkx2.1 is specifically involved in the development of rostral ventral forebrain including the pallidum and preoptic regions, whereas nkx2.4a and nkx2.4b control the intermediate and caudal hypothalamus. PMID:25520628

  18. Hyperosmia, ectrodactyly, mild intellectual disability, and other defects in a male patient with an X-linked partial microduplication and overexpression of the KAL1 gene.

    PubMed

    Sowińska-Seidler, Anna; Piwecka, Monika; Olech, Ewelina; Socha, Magdalena; Latos-Bieleńska, Anna; Jamsheer, Aleksander

    2015-05-01

    Loss-of-function mutations of the KAL1 gene are a known cause of Kallmann syndrome, a disorder characterized by the coexistence of hypogonadotropic hypogonadism and anosmia/hiposmia. On the other hand, neither complete nor partial duplications of KAL1 have been reported in the literature; thus, clinical symptoms associated with such alterations remain unknown. Ectrodactyly is a clinically and genetically heterogeneous abnormality presenting with hypoplasia of the central rays of the extremity, which, in around 68% of cases, has unknown underlying molecular defect. In this paper, we report on a sporadic male patient manifesting hyperosmia and ectrodactyly accompanied by additional symptoms involving mild intellectual disability, unilateral hearing loss, genital anomalies, stocky build, and facial dysmorphism. Using a combination of high-resolution array comparative genomic hybridization (array CGH) and breakpoint analysis, we detected a hemizygous tandem duplication of 110,967 bp on Xp22.31, encompassing the promoter region and the first two exons of KAL1. In order to confirm pathogenicity of the duplication, we tested the level of KAL1 transcript in blood lymphocytes, showing 79 times higher expression in the proband compared to controls. We, therefore, hypothesize that olfactory hypersensitivity in our proband directly results from KAL1 overproduction. Additionally, a literature review allowed us to conclude that KAL1 protein at high levels may interfere with FGFR1 signaling activity, most probably indirectly giving rise to ectrodactyly, intellectual disability, and genital anomalies. Noteworthy, those symptoms overlap with Hartsfield syndrome caused by FGFR1 loss-of-function mutations. To conclude, our paper highlights the role of KAL1 in embryogenesis and provides data on the contribution of KAL1 overexpression to human pathology. PMID:25339597

  19. Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences.

    PubMed

    Ghebremedhin, B; Layer, F; König, W; König, B

    2008-03-01

    The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (approximately 931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (approximately 97%), rpoB (approximately 86%), hsp60 (approximately 82%), and sodA (approximately 78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification. PMID:18174295

  20. Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences▿

    PubMed Central

    Ghebremedhin, B.; Layer, F.; König, W.; König, B.

    2008-01-01

    The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (∼97%), rpoB (∼86%), hsp60 (∼82%), and sodA (∼78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification. PMID:18174295

  1. Anaplasma phagocytophilum in Questing Ixodes ricinus Ticks: Comparison of Prevalences and Partial 16S rRNA Gene Variants in Urban, Pasture, and Natural Habitats

    PubMed Central

    Pfister, Kurt; Thiel, Claudia; Herb, Ingrid; Mahling, Monia; Silaghi, Cornelia

    2013-01-01

    Urban, natural, and pasture areas were investigated for prevalences and 16S rRNA gene variants of Anaplasma phagocytophilum in questing Ixodes ricinus ticks. The prevalences differed significantly between habitat types, and year-to-year variations in prevalence and habitat-dependent occurrence of 16S rRNA gene variants were detected. PMID:23263964

  2. Identification and Partial Characterization of Extracellular Aspartic Protease Genes from Metschnikowia pulcherrima IWBT Y1123 and Candida apicola IWBT Y1384

    PubMed Central

    Reid, Vernita J.; Theron, Louwrens W.; du Toit, Maret

    2012-01-01

    The extracellular acid proteases of non-Saccharomyces wine yeasts may fulfill a number of roles in winemaking, which include increasing the available nitrogen sources for the growth of fermentative microbes, affecting the aroma profile of the wine, and potentially reducing protein haze formation. These proteases, however, remain poorly characterized, especially at genetic level. In this study, two extracellular aspartic protease-encoding genes were identified and sequenced, from two yeast species of enological origin: one gene from Metschnikowia pulcherrima IWBT Y1123, named MpAPr1, and the other gene from Candida apicola IWBT Y1384, named CaAPr1. In silico analysis of these two genes revealed a number of features peculiar to aspartic protease genes, and both the MpAPr1 and CaAPr1 putative proteins showed homology to proteases of yeast genera. Heterologous expression of MpAPr1 in Saccharomyces cerevisiae YHUM272 confirmed that it encodes an aspartic protease. MpAPr1 production, which was shown to be constitutive, and secretion were confirmed in the presence of bovine serum albumin (BSA), casein, and grape juice proteins. The MpAPr1 gene was found to be present in 12 other M. pulcherrima strains; however, plate assays revealed that the intensity of protease activity was strain dependent and unrelated to the gene sequence. PMID:22820332

  3. Cloning, sequencing and partial characterisation of sorbitol transporter (srlT) gene encoding phosphotransferase system, glucitol/sorbitol-specific IIBC components of Erwinia herbicola ATCC 21998.

    PubMed

    Qazi, P H; Johri, S; Verma, V; Khan, L; Qazi, G N

    2004-09-01

    A DNA fragment of approximately 1500 bp, harbouring the sorbitol transport gene (srlT), was amplified from the chromosomal DNA of Erwinia herbicola ATCC 21998 by PCR and cloned in Escherichia coli JM109. Degenerate oligonucleotide primers used were designed based on the conserved regions in the gene sequences within the gut operon of E. coli (Gene Bank accession no. J02708) and the srl operon of Erwinia amylovora (Gene Bank accession no. Y14603). The cloned DNA fragment was sequenced and found to contain an open reading frame of 1473 nucleotides coding for a protein of 491 amino acids, corresponding to a mass of 52410 Da. The nucleotide sequence of this ORF was highly homologous to that of the gutA gene of Escherichia coli gut operon, the srlE gene of Shigella flexrni and the sorbitol transporter gene sequence of Escherichia coli K12 (Gene Bank accession nos. J02708, AE016987 and D90892 respectively). The protein sequence showed significant homology to that of the phosphotransferase system i.e. the glucitol/sorbitol-specific IIBC components of Escherichia coli and Erwinia amylovora (P56580, O32522). The cloned DNA fragment was introduced into a pRA90 vector and the recombinant was used for developing srlT mutants of Erwinia herbicola, by homologous recombination. Mutants obtained were unable to grow on minimal medium with sorbitol. The insertion of the pRA90 vector inside the srlT gene sequence of the mutants was confirmed by DNA-DNA hybridisation. PMID:15560368

  4. Establishment of a recessive mutant small-eye rat with lens involution and retinal detachment associated with partial deletion and rearrangement of the Cryba1 gene.

    PubMed

    Yamada, Toshiyuki; Nanashima, Naoki; Shimizu, Takeshi; Nakazawa, Yosuke; Nakazawa, Mitsuru; Tsuchida, Shigeki

    2015-10-15

    From our stock of SDRs (Sprague-Dawley rats), we established a mutant strain having small opaque eyes and named it HiSER (Hirosaki small-eye rat). The HiSER phenotype is progressive and autosomal recessive. In HiSER eyes, disruption and involution of the lens, thickening of the inner nuclear layer, detachment and aggregation of the retina, rudimentary muscle in the ciliary body and cell infiltration in the vitreous humour were observed. Genetic linkage analysis using crossing with Brown Norway rat suggested that the causative gene(s) is located on chromosome 10. Microarray analysis showed that the expression level of the Cryba1 gene encoding βA3/A1-crystallin on chromosome 10 was markedly decreased in HiSER eyes. Genomic PCR revealed deletion of a 3.6-kb DNA region encompassing exons 4-6 of the gene in HiSERs. In HiSER eyes, a chimaeric transcript of the gene containing exons 1-3 and an approximately 250-bp sequence originating from the 3'-UTR of the Nufip2 gene, located downstream of the breakpoint in the opposite direction, was present. Whereas the chimaeric transcript was expressed in HiSER eyes, neither normal nor chimaeric βA3/A1-crystallin proteins were detected by Western blot analysis. Real-time RT (reverse transcription)-PCR analysis revealed that expression level of the Nufip2 gene in the HiSER eye was 40% of that in the SDR eye. These results suggest that the disappearance of the βA3/A1-crystallin protein and, in addition, down-regulation of the Nufip2 gene as a consequence of gene rearrangement causes the HiSER phenotype. PMID:26303524

  5. Control of human carnitine palmitoyltransferase II gene transcription by peroxisome proliferator-activated receptor through a partially conserved peroxisome proliferator-responsive element.

    PubMed Central

    Barrero, María J; Camarero, Nuria; Marrero, Pedro F; Haro, Diego

    2003-01-01

    The expression of several genes involved in fatty acid metabolism is regulated by peroxisome proliferator-activated receptors (PPARs). To gain more insight into the control of carnitine palmitoyltransferase (CPT) gene expression, we examined the transcriptional regulation of the human CPT II gene. We show that the 5'-flanking region of this gene is transcriptionally active and binds PPARalpha in vivo in a chromatin immunoprecipitation assay. In addition, we characterized the peroxisome proliferator-responsive element (PPRE) in the proximal promoter of the CPT II gene, which appears to be a novel PPRE. The sequence of this PPRE contains one half-site which is a perfect consensus sequence (TGACCT) but no clearly recognizable second half-site (CAGCAC); this part of the sequence contains only one match to the consensus, which seems to be irrelevant for the binding of PPARalpha. As expected, other members of the nuclear receptor superfamily also bind to this element and repress the activation mediated by PPARalpha, thus showing that the interplay between several nuclear receptors may regulate the entry of fatty acids into the mitochondria, a crucial step in their metabolism. PMID:12408750

  6. Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.

    PubMed

    Benachenhou-Lahfa, N; Forterre, P; Labedan, B

    1993-04-01

    The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the

  7. A Core MYC Gene Expression Signature Is Prominent in Basal-Like Breast Cancer but Only Partially Overlaps the Core Serum Response

    PubMed Central

    Chandriani, Sanjay; Frengen, Eirik; Cowling, Victoria H.; Pendergrass, Sarah A.; Perou, Charles M.; Whitfield, Michael L.; Cole, Michael D.

    2009-01-01

    Background The MYC oncogene contributes to induction and growth of many cancers but the full spectrum of the MYC transcriptional response remains unclear. Methodology/Principal Findings Using microarrays, we conducted a detailed kinetic study of genes that respond to MYCN or MYCNΔMBII induction in primary human fibroblasts. In parallel, we determined the response to steady state overexpression of MYCN and MYCNΔMBII in the same cell type. An overlapping set of 398 genes from the two protocols was designated a ‘Core MYC Signature’ and used for further analysis. Comparison of the Core MYC Signature to a published study of the genes induced by serum stimulation revealed that only 7.4% of the Core MYC Signature genes are in the Core Serum Response and display similar expression changes to both MYC and serum. Furthermore, more than 50% of the Core MYC Signature genes were not influenced by serum stimulation. In contrast, comparison to a panel of breast cancers revealed a strong concordance in gene expression between the Core MYC Signature and the basal-like breast tumor subtype, which is a subtype with poor prognosis. This concordance was supported by the higher average level of MYC expression in the same tumor samples. Conclusions/Significance The Core MYC Signature has clinical relevance as this profile can be used to deduce an underlying genetic program that is likely to contribute to a clinical phenotype. Therefore, the presence of the Core MYC Signature may predict clinical responsiveness to therapeutics that are designed to disrupt MYC-mediated phenotypes. PMID:19690609

  8. Partial HPRT Deficiency with a Novel Mutation of the HPRT Gene in Combination with Four Previously Reported Variants Associated with Hyperuricemia.

    PubMed

    Kurajoh, Masafumi; Koyama, Hidenori; Hatayama, Miki; Okazaki, Hirokazu; Shoji, Takuhito; Moriwaki, Yuji; Yamamoto, Tetsuya; Nakayama, Tomitaka; Namba, Mitsuyoshi

    2015-01-01

    A 15-year-old boy was referred to our department due to gout. The laboratory findings showed hyperuricemia with a decreased erythrocyte hypoxanthine phosphoribosyl transferase (HPRT) activity. The HPRT cDNA sequence was revealed to be 206A>T, which has not been previously reported. In addition, direct sequencing of genomic DNA showed the patient to possess four variants reported to be associated with hyperuricemia. This is the first case report of partial HPRT deficiency due to a novel HPRT mutation accompanied by variants associated with hyperuricemia. Combination treatment consisting of benzbromarone and febuxostat had a significant effect in reducing the urate level in our patient. PMID:26073243

  9. Disruption of the splicing enhancer sequence within exon 27 of the dystrophin gene by a nonsense mutation induces partial skipping of the exon and is responsible for Becker muscular dystrophy.

    PubMed Central

    Shiga, N; Takeshima, Y; Sakamoto, H; Inoue, K; Yokota, Y; Yokoyama, M; Matsuo, M

    1997-01-01

    The mechanism of exon skipping induced by nonsense mutations has not been well elucidated. We now report results of in vitro splicing studies which disclosed that a particular example of exon skipping is due to disruption of a splicing enhancer sequence located within the exon. A nonsense mutation (E1211X) due to a G to T transversion at the 28th nucleotide of exon 27 (G3839T) was identified in the dystrophin gene of a Japanese Becker muscular dystrophy case. Partial skipping of the exon resulted in the production of truncated dystrophin mRNA, although the consensus sequences for splicing at both ends of exon 27 were unaltered. To determine how E1211X induced exon 27 skipping, the splicing enhancer activity of purine-rich region within exon 27 was examined in an in vitro splicing system using chimeric doublesex gene pre-mRNA. The mutant sequence containing G3839T abolished splicing enhancer activity of the wild-type purine-rich sequence for the upstream intron in this chimeric pre-mRNA. An artificial polypurine oligonucleotide mimicking the purine-rich sequence of exon 27 also showed enhancer activity that was suppressed by the introduction of a T nucleotide. Furthermore, the splicing enhancer activity was more markedly inhibited when a nonsense codon was created by the inserted T residue. This is the first evidence that partial skipping of an exon harboring a nonsense mutation is due to disruption of a splicing enhancer sequence. PMID:9410897

  10. Disruption of the splicing enhancer sequence within exon 27 of the dystrophin gene by a nonsense mutation induces partial skipping of the exon and is responsible for Becker muscular dystrophy.

    PubMed

    Shiga, N; Takeshima, Y; Sakamoto, H; Inoue, K; Yokota, Y; Yokoyama, M; Matsuo, M

    1997-11-01

    The mechanism of exon skipping induced by nonsense mutations has not been well elucidated. We now report results of in vitro splicing studies which disclosed that a particular example of exon skipping is due to disruption of a splicing enhancer sequence located within the exon. A nonsense mutation (E1211X) due to a G to T transversion at the 28th nucleotide of exon 27 (G3839T) was identified in the dystrophin gene of a Japanese Becker muscular dystrophy case. Partial skipping of the exon resulted in the production of truncated dystrophin mRNA, although the consensus sequences for splicing at both ends of exon 27 were unaltered. To determine how E1211X induced exon 27 skipping, the splicing enhancer activity of purine-rich region within exon 27 was examined in an in vitro splicing system using chimeric doublesex gene pre-mRNA. The mutant sequence containing G3839T abolished splicing enhancer activity of the wild-type purine-rich sequence for the upstream intron in this chimeric pre-mRNA. An artificial polypurine oligonucleotide mimicking the purine-rich sequence of exon 27 also showed enhancer activity that was suppressed by the introduction of a T nucleotide. Furthermore, the splicing enhancer activity was more markedly inhibited when a nonsense codon was created by the inserted T residue. This is the first evidence that partial skipping of an exon harboring a nonsense mutation is due to disruption of a splicing enhancer sequence. PMID:9410897

  11. Expression of a partially deleted gene of human type II procollagen (COL2A1) in transgenic mice produces a chondrodysplasia

    SciTech Connect

    Vandenberg, P.; Khillan, J.S.; Prockop, D.J.; Helminen, H.; Kontusaari, S.; Ala-Kokko, L. )

    1991-09-01

    A minigene version of the human gene for type II procollagen (COL2AI) was prepared that lacked a large central region containing 12 of the 52 exons and therefore 291 of the 1523 codons of the gene. The construct was modeled after sporadic in-frame deletions of collagen genes that cause synthesis of shortened pro{alpha} chains that associate with normal pro{alpha} chains and thereby cause degradation of the shortened and normal pro{alpha} chains through a process called procollagen suicide. The gene construct was used to prepare five lines of transgenic mice expressing the minigene. A large proportion of the mice expressing the minigene developed a phenotype of a chondrodysplasia with dwarfism, short and thick limbs, a short snout, a cranial bulge, a cleft palate, and delayed mineralization of bone. A number of mice died shortly after birth. Microscopic examination of cartilage revealed decreased density and organization of collagen fibrils. In cultured chondrocytes from the transgenic mice, the minigene was expressed as shortened pro{alpha}1(II) chains that were disulfide-linked to normal mouse pro{alpha}1(II) chains. Therefore, the phenotype is probably explained by depletion of the endogenous mouse type II procollagen through the phenomenon of procollagen suicide.

  12. Comparison of Traditional Phenotypic Identification Methods with Partial 5′ 16S rRNA Gene Sequencing for Species-Level Identification of Nonfermenting Gram-Negative Bacilli▿

    PubMed Central

    Cloud, Joann L.; Harmsen, Dag; Iwen, Peter C.; Dunn, James J.; Hall, Gerri; LaSala, Paul Rocco; Hoggan, Karen; Wilson, Deborah; Woods, Gail L.; Mellmann, Alexander

    2010-01-01

    Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5′ 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB. PMID:20164273

  13. Modeling partial monosomy for human chromosome 21q11.2-q21.1 reveals haploinsufficient genes influencing behavior and fat deposition.

    PubMed

    Migdalska, Anna M; van der Weyden, Louise; Ismail, Ozama; White, Jacqueline K; Sánchez-Andrade, Gabriela; Logan, Darren W; Arends, Mark J; Adams, David J

    2012-01-01

    Haploinsufficiency of part of human chromosome 21 results in a rare condition known as Monosomy 21. This disease displays a variety of clinical phenotypes, including intellectual disability, craniofacial dysmorphology, skeletal and cardiac abnormalities, and respiratory complications. To search for dosage-sensitive genes involved in this disorder, we used chromosome engineering to generate a mouse model carrying a deletion of the Lipi-Usp25 interval, syntenic with 21q11.2-q21.1 in humans. Haploinsufficiency for the 6 genes in this interval resulted in no gross morphological defects and behavioral analysis performed using an open field test, a test of anxiety, and tests for social interaction were normal in monosomic mice. Monosomic mice did, however, display impaired memory retention compared to control animals. Moreover, when fed a high-fat diet (HFD) monosomic mice exhibited a significant increase in fat mass/fat percentage estimate compared with controls, severe fatty changes in their livers, and thickened subcutaneous fat. Thus, genes within the Lipi-Usp25 interval may participate in memory retention and in the regulation of fat deposition. PMID:22276124

  14. GQ-16, a TZD-Derived Partial PPARγ Agonist, Induces the Expression of Thermogenesis-Related Genes in Brown Fat and Visceral White Fat and Decreases Visceral Adiposity in Obese and Hyperglycemic Mice

    PubMed Central

    Coelho, Michella S.; de Lima, Caroline L.; Royer, Carine; Silva, Janaina B.; Oliveira, Fernanda C. B.; Christ, Camila G.; Pereira, Sidney A.; Bao, Sonia N.; Lima, Maria C. A.; Pitta, Marina G. R.; Pitta, Ivan R.; Neves, Francisco A. R.; Amato, Angélica A.

    2016-01-01

    Background Beige adipocytes comprise a unique thermogenic cell type in the white adipose tissue (WAT) of rodents and humans, and play a critical role in energy homeostasis. In this scenario, recruitment of beige cells has been an important focus of interest for the development of novel therapeutic strategies to treat obesity. PPARγ activation by full agonists (thiazolidinediones, TZDs) drives the appearance of beige cells, a process so-called browning of WAT. However, this does not translate into increased energy expenditure, and TZDs are associated with weight gain. Partial PPARγ agonists, on the other hand, do not induce weight gain, but have not been shown to drive WAT browning. The present study was designed to investigate the effects of GQ-16 on BAT and on browning of WAT in obese mice. Methods Male Swiss mice with obesity and hyperglycemia induced by high fat diet were treated with vehicle, rosiglitazone (4 mg/kg/d) or the TZD-derived partial PPARγ agonist GQ-16 (40 mg/kg/d) for 14 days. Fasting blood glucose, aspartate aminotransferase, alanine aminotransferase and lipid profile were measured. WAT and brown adipose tissue (BAT) depots were excised for determination of adiposity, relative expression of Ucp-1, Cidea, Prdm16, Cd40 and Tmem26 by RT-qPCR, histological analysis, and UCP-1 protein expression analysis by immunohistochemistry. Liver samples were also removed for histological analysis and determination of hepatic triglyceride content. Results GQ-16 treatment reduced high fat diet-induced weight gain in mice despite increasing energy intake. This was accompanied by reduced epididymal fat mass, reduced liver triglyceride content, morphological signs of increased BAT activity, increased expression of thermogenesis-related genes in interscapular BAT and epididymal WAT, and increased UCP-1 protein expression in interscapular BAT and in epididymal and inguinal WAT. Conclusion This study suggests for the first time that a partial PPARγ agonist may

  15. Vaccinia virus recombinants encoding the truncated structural gene region of Venezuelan equine encephalitis virus (VEEV) give solid protection against peripheral challenge but only partial protection against airborne challenge with virulent VEEV.

    PubMed

    Phillpotts, R J; Lescott, T L; Jacobs, S C

    2000-10-01

    Vaccinia virus (VV) recombinants that contain the genes encoding the Venezuelan equine encephalitis virus (VEEV) structural gene region (C-E3-E2-6 K-E1) solidly protect mice against peripheral challenge with virulent VEEV, but provide only partial protection against airborne challenge. To improve upon these results we focussed on the principal antigens involved in protection. VV recombinants encoding the structural genes E3-E2-6 K-E1, E3-E2-6 K or 6 K-E1 were prepared and evaluated for their ability to protect Balb/c mice after a single dorsal scarification with 10(8) PFU against peripheral or airborne challenge with virulent VEEV. The antibody response was also examined. Our experiments provide new evidence that truncates of the VEEV structural region (E3-E2-6 K-E1, E3-E2-6 K), cloned and expressed in VV, protect against challenge with virulent virus. They also confirm the important role of E2 in protection. However, we were unable to improve upon previously reported levels of protection against airborne challenge. A substantial level of circulating antibodies and the presence of local IgA (not always induced by mucosal immunization) (Greenway et al., 1992) appear essential for protection against the airborne virus. Current VV-VEEV recombinants seem unable to elicit this level of immune response and further improvements are therefore required to increase the immunogenicity of VV-VEEV vaccines. PMID:11252667

  16. Exposure to Bisphenol-A during Pregnancy Partially Mimics the Effects of a High-Fat Diet Altering Glucose Homeostasis and Gene Expression in Adult Male Mice

    PubMed Central

    García-Arevalo, Marta; Alonso-Magdalena, Paloma; Rebelo Dos Santos, Junia; Quesada, Ivan; Carneiro, Everardo M.; Nadal, Angel

    2014-01-01

    Bisphenol-A (BPA) is one of the most widespread EDCs used as a base compound in the manufacture of polycarbonate plastics. The aim of our research has been to study how the exposure to BPA during pregnancy affects weight, glucose homeostasis, pancreatic β-cell function and gene expression in the major peripheral organs that control energy flux: white adipose tissue (WAT), the liver and skeletal muscle, in male offspring 17 and 28 weeks old. Pregnant mice were treated with a subcutaneous injection of 10 µg/kg/day of BPA or a vehicle from day 9 to 16 of pregnancy. One month old offspring were divided into four different groups: vehicle treated mice that ate a normal chow diet (Control group); BPA treated mice that also ate a normal chow diet (BPA); vehicle treated animals that had a high fat diet (HFD) and BPA treated animals that were fed HFD (HFD-BPA). The BPA group started to gain weight at 18 weeks old and caught up to the HFD group before week 28. The BPA group as well as the HFD and HFD-BPA ones presented fasting hyperglycemia, glucose intolerance and high levels of non-esterified fatty acids (NEFA) in plasma compared with the Control one. Glucose stimulated insulin release was disrupted, particularly in the HFD-BPA group. In WAT, the mRNA expression of the genes involved in fatty acid metabolism, Srebpc1, Pparα and Cpt1β was decreased by BPA to the same extent as with the HFD treatment. BPA treatment upregulated Pparγ and Prkaa1 genes in the liver; yet it diminished the expression of Cd36. Hepatic triglyceride levels were increased in all groups compared to control. In conclusion, male offspring from BPA-treated mothers presented symptoms of diabesity. This term refers to a form of diabetes which typically develops in later life and is associated with obesity. PMID:24959901

  17. Identification of genotypes of Giardia intestinalis isolates from dogs in Japan by direct sequencing of the PCR amplified glutamate dehydrogenase gene.

    PubMed

    Abe, Niichiro; Kimata, Isao; Iseki, Motohiro

    2003-01-01

    Giardia has been detected in domestic dogs in Japan, but the genotype of isolates has remained unclear because identification has relied on conventional microscopy. Here we tried to identify the genotypes of four isolates from dogs in Japan by direct sequencing of the PCR amplified Giardia glutamate dehydrogenase (GDH) gene. The primer pair GDHF3 and GDHB5, targeting the GDH gene, was designed to prime a region of the GDH gene sequence conserved in the strains found to have the dog-specific genotype. The specific PCR product (approximately 220 bp), amplified with this primer pair, was only observed when Giardia DNA was used as the template. The sequences of the diagnostic fragments were identical among the isolates from dogs, and were differed by 15 bp or 1 bp from the strains, which were found to be the dog-specific genotypes, Assemblage C or D respectively. To verify the identity of the amplified DNA, a phylogenetic analysis was performed. Consequently, the sequence of the isolates from dogs clearly clustered with the strain found to be Assemblage D with neighbor-joining analyses. Therefore, all the isolates from dogs examined were identified as the dog-specific genotype, Assemblage D. In the present study, we revealed the genotype of Giardia isolates in Japan, and showed that direct sequencing of the PCR product amplified with the primer pair GDHF3 and GDHB5 was a useful tool for distinguishing between the zoonotic and dog-specific genotypes. PMID:12576701

  18. A computer program for fast and easy typing of a partial endoglucanase gene sequence into genospecies and sequevars 1&2 of the Ralstonia solanacearum species complex.

    PubMed

    Stulberg, Michael J; Huang, Qi

    2016-04-01

    The phytopathogen Ralstonia solanacearum is a species complex that contains race 3 biovar 2 strains belonging to phylotype IIB sequevars 1 and 2 that are quarantined or select agent pathogens. Recently, the R. solanacearum species complex strains have been reclassified into three genospecies: R. solanacearum, Ralstonia pseudosolanacearum and Ralstonia syzygii. An unidentified R. solanacearum strain is considered a select agent in the US until proven to be a non-race 3 biovar 2 (non-phylotype IIB sequevars 1&2). Currently, sequevars of R. solanacearum species complex strains can only be determined by phylogenetic analysis of a partial endoglucanase (egl) sequence of approximately 700-bp in length. Such analysis, however, requires expert knowledge to properly trim the sequence, to include the correct reference strains, and to interpret the results. By comparing GenBank egl sequences of representative R. solanacearum species-complex strains, we identified genospecies- and sequevar 1 and 2-specific single nucleotide polymorphisms (SNPs). We also designed primers to amplify a shorter, 526-bp, egl fragment from R. solanacearum species complex strains for easy sequencing of the amplicon, and to facilitate direct and specific amplification of egl from R. solanacearum-infected plant samples without the need of bacterial isolation. We wrote a computer program (Ralstonia solanacearum typing program) that analyzes a minimum 400-bp user-input egl sequence from a R. solanacearum strain for egl homology and SNP content to determine 1) whether it belongs to the R. solanacearum species complex, 2) if so, to which genospecies, and 3) whether it is of the sequevar type (sequevars 1 and 2) associated with the select agent/quarantined R. solanacearum strain. The program correctly typed all 371 tested egl sequences with known sequevars, obtained either from GenBank or through personal communication. Additionally, the program successfully typed 25 R. solanacearum strains in our

  19. The evolutionary history of the genus Timarcha (Coleoptera, Chrysomelidae) inferred from mitochondrial COII gene and partial 16S rDNA sequences.

    PubMed

    Gómez-Zurita, J; Juan, C; Petitpierre, E

    2000-02-01

    The apterous genus Timarcha consists of three subgenera and more than 100 species in its Palearctic distribution, with specialized feeding on few plant families. Fifty-four sequences sampled from 31 taxa of the genus plus three outgroup leaf beetles were studied for their complete cytochrome oxidase II (COII) and a fragment of 16S rDNA mitochondrial genes, representing a total of about 1200 bp. Phylogenetic analyses using maximum-parsimony and distance methods for each gene separately and for the combined data set gave compatible topologies. The subgenus Metallotimarcha consistently appears in a basal position and is well differentiated from the remaining Timarcha, but no clear monophyletic grouping of Timarchostoma and Timarcha s. str. subgenera can be deduced from our analysis. Calibration of the molecular clock has been done using the opening of the Gibraltar Strait after the Messinian salinity crisis (about 5.5 MYA) as the biogeographic event causing disjunction of two particular taxa. Accordingly, the COII evolutionary rate has been estimated to be of 0.76 x 10(-8) substitution/site/year in Timarcha. Relation between phylogeny and host-plant use indicates widening of trophic regime as a derived character in Timarcha. PMID:10679162

  20. Genotyping of a miso and soy sauce fermentation yeast, Zygosaccharomyces rouxii, based on sequence analysis of the partial 26S ribosomal RNA gene and two internal transcribed spacers.

    PubMed

    Suezawa, Yasuhiko; Suzuki, Motofumi; Mori, Haruhiko

    2008-09-01

    We analyzed sequences of the D1D2 domain of the 26S ribosomal RNA gene (26S rDNA sequence), the internal transcribed spacer 1, the 5.8S ribosomal RNA gene, and the internal transcribed spacer 2 (the ITS sequence) from 46 strains of miso and soy sauce fermentation yeast, Zygosaccharomyces rouxii and a closely related species, Z. mellis, for typing. Based on the 26S rDNA sequence analysis, the Z. rouxii strains were of two types, and the extent of sequence divergence between them was 2.6%. Based on the ITS sequence analysis, they were divided into seven types (I-VII). Between the type strain (type I) and type VI, in particular, a 12% difference was detected. The occurrence of these nine genotypes with a divergence of more than 1% in these two sequences suggests that Z. rouxii is a species complex including novel species and hybrids. Z. mellis strains were of two types (type alpha and type beta) based on the ITS sequence. Z. rouxii could clearly be distinguished from Z. mellis by 26S rDNA and ITS sequence analyses, but not by the 16% NaCl tolerance, when used as the sole key characteristic for differentiation between the two species. PMID:18776675

  1. Partial correction of the dwarf phenotype by non-viral transfer of the growth hormone gene in mice: Treatment age is critical.

    PubMed

    Higuti, Eliza; Cecchi, Cláudia R; Oliveira, Nélio A J; Lima, Eliana R; Vieira, Daniel P; Aagaard, Lars; Jensen, Thomas G; Jorge, Alexander A L; Bartolini, Paolo; Peroni, Cibele N

    2016-02-01

    Non-viral transfer of the growth hormone gene to different muscles of immunodeficient dwarf (lit/scid) mice is under study with the objective of improving phenotypic correction via this particular gene therapy approach. Plasmid DNA was administered into the exposed quadriceps or non-exposed tibialis cranialis muscle of lit/scid mice followed by electroporation, monitoring several growth parameters. In a 6-month bioassay, 50μg DNA were injected three times into the quadriceps muscle of 80-day old mice. A 50% weight increase, with a catch-up growth of 21%, together with a 16% increase for nose-to-tail and tail lengths (catch-up=19-21%) and a 24-28% increase for femur length (catch-up=53-60%), were obtained. mIGF1 serum levels were ~7-fold higher than the basal levels for untreated mice, but still ~2-fold lower than in non-dwarf scid mice. Since treatment age was found to be particularly important in a second bioassay utilizing 40-day old mice, these pubertal mice were compared in a third bioassay with adult (80-day old) mice, all treated twice with 50μg DNA injected into each tibialis cranialis muscle, via a less invasive approach. mIGF1 concentrations at the same level as co-aged scid mice were obtained 15days after administration in pubertal mice. Catch-up growth, based on femur length (77%), nose-to-tail (36%) and tail length (39%) increases was 40 to 95% higher than those obtained upon treating adult mice. These data pave the way for the development of more effective pre-clinical assays in pubertal dwarf mice for the treatment of GH deficiency via plasmid-DNA muscular administration. PMID:26774398

  2. Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes

    PubMed Central

    Khosravi, Azar Dokht; Shahraki, Abdolrazagh Hashemi; Heidarieh, Parvin; Sheikhi, Nasrin

    2015-01-01

    Background Acinetobacter spp. is a diverse group of Gram-negative bacteria which are ubiquitous in soil and water, and an important cause of nosocomial infections. The purpose of this study was to identify a collection of Acinetobacter spp. clinical isolates accurately and to investigate their antibiotic susceptibility patterns. Materials and Methods A total of 197 non-duplicate clinical isolates of Acinetobacter spp. isolates identified using conventional biochemical tests. The molecular technique of PCR-RFLP and sequence analysis of rpoB and 16S rRNA genes was applied for species identification. Antimicrobial susceptibility test was performed with a disk diffusion assay. Results Based on 16S rRNA and rpoB genes analysis separately, most of clinical isolates can be identified with high bootstrap values. However, the identity of the isolate 555T was uncertain due to high similarity of A. grimontii and A. junii. Identification by concatenation of 16S rRNA and rpoB confirmed the identity of clinical isolates of Acenitobacer to species level confidently. Accordingly, the isolate 555T assigned as A. grimontii due to 100% similarity to A. grimontii. Moreover, this isolate showed 98.64% to A. junii. Besides, the identity of the isolates 218T and 364T was confirmed as Genomic species 3 and A. calcoaceticus respectively. So, the majority of Acinetobacter spp. isolates, were identified as: A. baumannii (131 isolates, 66%), A. calcoaceticus (9 isolates, 4.5%), and A. genomosp 16 (8 isolates, 4%). The rest of identified species showed the lower frequencies. In susceptibility test, 105 isolates (53%), presented high antibiotic resistance of 90% to ceftriaxone, piperacillin, piperacillin tazobactam, amikacin, and 81% to ciprofloxacin. Conclusion Sequence analysis of the 16S rRNA and rpoB spacer simultaneously was able to do identification of Acinetobacter spp. to species level. A.baumannii was identified as the most prevalent species with high antibiotic resistance. Other

  3. The Presence of Clitoromegaly in the Nonclassical Form of 21-Hydroxylase Deficiency Could Be Partially Modulated by the CAG Polymorphic Tract of the Androgen Receptor Gene

    PubMed Central

    Garcia Gomes, Larissa; Bugano Diniz Gomes, Diogo; Marcondes, José Antônio Miguel; Madureira, Guiomar; de Mendonca, Berenice Bilharinho; Bachega, Tânia A. Sartori Sanchez

    2016-01-01

    Background In the nonclassical form (NC), good correlation has been observed between genotypes and 17OH-progesterone (17-OHP) levels. However, this correlation was not identified with regard to the severity of hyperandrogenic manifestations, which could depend on interindividual variability in peripheral androgen sensitivity. Androgen action is modulated by the polymorphic CAG tract (nCAG) of the androgen receptor (AR) gene and by polymorphisms in 5α-reductase type 2 (SRD5A2) enzyme, both of which are involved in the severity of hyperandrogenic disorders. Objectives To analyze whether nCAG-AR and SRD5A2 polymorphisms influence the severity of the nonclassical phenotype. Patients NC patients (n = 114) diagnosed by stimulated-17OHP ≥10 ng/mL were divided into groups according to the beginning of hyperandrogenic manifestations (pediatric and adolescent/adult) and CYP21A2 genotypes (C/C: homozygosis for mild mutations; A/C: compound heterozygosis for severe/mild mutations). Methods CYP21A2 mutations were screened by allelic-specific PCR, MLPA and/or sequencing. HpaII-digested and HpaII-undigested DNA samples underwent GeneScan analysis to study nCAG, and the SRD5A2 polymorphisms were screened by RLFP. Results Mean nCAG did not differ among pediatric, adolescent/adult and asymptomatic subjects. In the C/C genotype, we observed a significantly lower frequency of longer CAG alleles in pediatric patients than in adolescent/adults (p = 0.01). In patients carrying the A/C genotype, the frequencies of shorter and longer CAG alleles did not differ between pediatric patients and adolescent/adults (p>0.05). Patients with clitoromegaly had significantly lower weighted CAG biallelic mean than those without it: 19.1±2.7 and 21.6±2.5, respectively (p = 0.007), independent of the CYP21A2 genotype's severity. The SRD5A2 polymorphisms were not associated with the variability of hyperandrogenic NC phenotypes. Conclusions In this series, we observed a modulatory effect of the CAG

  4. Isolation and partial sequence of the A-protein gene of Thermus thermophilus cytochrome c/sub 1/aa/sub 3/

    SciTech Connect

    Fee, J.A.; Mather, M.W.; Springer, P.; Hensel, S.; Buse, G.

    1988-01-01

    Thermus thermophilus is a strictly aerobic eubacterium which grows optimally near 70/degree/C. Its respiratory system is very similar to that of eukaryotic mitochondria, and the organism has proven to be a particularly good source of stable, comparatively simple respiratory enzymes. There are at least two terminal oxidases: The recently discovered cytochrome ba/sub 3//sup 3/ and cytochrome c/sub 1/aa/sub 3//sup 2/. Cytochrome ba/sub 3/ is analog of aa/sub 3/ in which the heme A of cytochrome a is replaced with protoporphyrin IX (heme B) while its order redox components appear to be largely identical to those of the now classical mammalian cytochrome aa/sub 3/; it has only a single 35 kD protein subunit. Cytochrome c/sub 1/aa/sub 3/ consists of two polypeptides. The /approximately/33 kD C-protein covalently binds one heme C, while the /approximately/55 kD protein is thought to bind the four canonical redox centers of aa/sub 3/, two heme A, and two Cu. Toward our goal of unequivocally establishing the distribution of the metal centers in cytochrome c/sub 1/aa/sub 3/, we have isolated the structural gene of the A-protein. 20 refs., 4 figs.

  5. Investigation on the partial resistance of Cpkk2 knock out strain of Cryphonectria parasitica to Cryphonectria hypovirus 1 infection in presence of Geneticin and Geneticin resistance gene.

    PubMed

    Turina, Massimo; Rossi, Marika; Moretti, Marino

    2016-07-01

    We have recently characterized the central components of the three MAP kinase cascades present in Cryphonectria parasitica : the MEK genes cpkk1, cpkk2 and cpkk3. When we attempted to infect through anastomosis the three knock out strains with Cryphonectria hypovirus 1 (CHV1), only the deletion strain of Cpkk2, the yeast Ste7 homologue, involved in mating and filamentous growth, could not be infected. We then proceeded to attempt virus infection through transformation of Δcpkk2 protoplasts using an infectious cDNA clone able to establish virus infection through transformation. In this case, a very limited number of strains could be recovered as stable transformants compared to the efficiency of control transformations with plasmid carrying only the antibiotic marker. Furthermore, transformants carrying actively replicating virus could be isolated only if the selection marker Geneticin was used during the very initial selection process, and not maintained throughout the growth of the colonies. Moreover, Δcpkk2 isolates that maintained the virus lost Geneticin resistance. We therefore unveiled a specific negative interaction among virus infection, presence of Geneticin in the growth media, and lack of Cpkk2 MEK in the fungal host. PMID:26643512

  6. Mice trisomic for a bacterial artificial chromosome with the single-minded 2 gene (Sim2) show phenotypes similar to some of those present in the partial trisomy 16 mouse models of Down syndrome.

    PubMed

    Chrast, R; Scott, H S; Madani, R; Huber, L; Wolfer, D P; Prinz, M; Aguzzi, A; Lipp, H P; Antonarakis, S E

    2000-07-22

    The Drosophila single-minded (sim) transcription factor, is a master regulator of fruitfly neurogenesis. Recently, we have cloned and mapped a human homolog of sim, SIM2, to chromosome 21 in the so-called 'Down syndrome chromosomal region'. Three copies of SIM2 may contribute to some Down syndrome (DS) phenotypes because of the mapping position function as transcriptional repressor, temporal and spatial expression pattern of mouse Sim2, and the potentially analogous role of human SIM2 to that of Drosophila sim during neurogenesis. In order to validate this hypothesis in vivo, we have created the first bacterial artificial chromosome transgenic mice overexpressing a gene possibly involved in DS with only one or two additional copies of mouse Sim2. The transgene was shown to be expressed in the same spatial pattern as the endogenous gene. The mice develop normally, are fertile and do not show detectable histopathological abnormalities. However, detailed analysis of their behavior revealed anxiety-related/reduced exploratory behaviour and sensitivity to pain, phenotypes similar to those also present in other partial trisomy 16 mouse models of DS. Our data therefore suggest that overexpression of SIM2 contributes to some of the complex DS phenotypes. PMID:10915774

  7. Hb St. Jozef, A Val-->Leu N-terminal mutation leading to retention of the methionine, and partial acetylation found in the globin gene in Cis with a -alpha3.7 thalassemia deletion.

    PubMed

    Harteveld, Cornelis L; Versteegh, Florens G A; van Leer, Eduard H G; Starreveld, Jaap S; Kok, Peter J M J; van Rooijen-Nijdam, Irene; van Delft, Peter; Zanella-Cleon, Isabelle; Becchi, Michel; Wajcman, Henri; Giordano, Piero C

    2007-01-01

    We report a new hemoglobin (Hb) variant found in a 6-year-old girl of Moroccan origin, living in the Dutch city of Gouda. The child was referred because of microcytic and hypochromic parameters. A normal zinc protoporphyirin (ZPP) value excluded iron deficiency and gap-polymerase chain reaction (gap-PCR) revealed a heterozygosity for the common -alpha(3.7) thalassemia deletion, partially justifying the hematological picture. The Hb pattern on alkaline electrophoresis and capillary electrophoresis was normal, while a fraction of 9% preceding the Hb A peak, remained visible on different high performance liquid chromatography (HPLC) devices. This fraction, located in front of the Hb A peak, is usually considered as a Hb A derivate that becomes more expressed in older samples. However, the sample was freshly collected and the peak unusually evident. Therefore, direct sequencing of the alpha-globin genes was performed revealing a GTG-->CTG transversion at codon 1 of the alpha1-globin gene or of the hybrid gene. This point mutation induces a single amino acid substitution from valine to leucine. Electrospray-mass spectrometry (ES-MS) analysis revealed, in addition to this substitution, that the N-terminal methionine was retained and that about 20% of the variant was acetylated. As expected for an association with a -alpha(3.7)-thalassemia (thal) deletion, the non acetylated and acetylated abnormal alpha chain amounted to 32% of the total alpha chains. Family studies revealed that the mutated codon was located in cis of the deletion. PMID:17654068

  8. Partial (focal) seizure

    MedlinePlus

    ... Jacksonian seizure; Seizure - partial (focal); Temporal lobe seizure; Epilepsy - partial seizures ... Abou-Khalil BW, Gallagher MJ, Macdonald RL. Epilepsies. In: Daroff RB, ... 6th ed. Philadelphia, PA: Elsevier Saunders; 2012:chap 67. ...

  9. Partial (focal) seizure

    MedlinePlus

    ... Jacksonian seizure; Seizure - partial (focal); Temporal lobe seizure; Epilepsy - partial seizures ... Abou-Khalil BW, Gallagher MJ, Macdonald RL. Epilepsies. In: Daroff ... Practice . 7th ed. Philadelphia, PA: Elsevier; 2016:chap 101. ...

  10. Partial tooth gear bearings

    NASA Technical Reports Server (NTRS)

    Vranish, John M. (Inventor)

    2010-01-01

    A partial gear bearing including an upper half, comprising peak partial teeth, and a lower, or bottom, half, comprising valley partial teeth. The upper half also has an integrated roller section between each of the peak partial teeth with a radius equal to the gear pitch radius of the radially outwardly extending peak partial teeth. Conversely, the lower half has an integrated roller section between each of the valley half teeth with a radius also equal to the gear pitch radius of the peak partial teeth. The valley partial teeth extend radially inwardly from its roller section. The peak and valley partial teeth are exactly out of phase with each other, as are the roller sections of the upper and lower halves. Essentially, the end roller bearing of the typical gear bearing has been integrated into the normal gear tooth pattern.

  11. Abiotic Stresses Downregulate Key Genes Involved in Nitrogen Uptake and Assimilation in Brassica juncea L.

    PubMed Central

    Goel, Parul; Singh, Anil Kumar

    2015-01-01

    Abiotic stresses such as salinity, drought and extreme temperatures affect nitrogen (N) uptake and assimilation in plants. However, little is known about the regulation of N pathway genes at transcriptional level under abiotic stress conditions in Brassica juncea. In the present work, genes encoding nitrate transporters (NRT), ammonium transporters (AMT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), asparagines synthetase (ASN) were cloned from Brassica juncea L. var. Varuna. The deduced protein sequences were analyzed to predict their subcellular localization, which confirmed localization of all the proteins in their respective cellular organelles. The protein sequences were also subjected to conserved domain identification, which confirmed presence of characteristic domains in all the proteins, indicating their putative functions. Moreover, expression of these genes was studied after 1h and 24h of salt (150 mM NaCl), osmotic (250 mM Mannitol), cold (4°C) and heat (42°C) stresses. Most of the genes encoding nitrate transporters and enzymes responsible for N assimilation and remobilization were found to be downregulated under abiotic stresses. The expression of BjAMT1.2, BjAMT2, BjGS1.1, BjGDH1 and BjASN2 was downregulated after 1hr, while expression of BjNRT1.1, BjNRT2.1, BjNiR1, BjAMT2, BjGDH1 and BjASN2 was downregulated after 24h of all the stress treatments. However, expression of BjNRT1.1, BjNRT1.5 and BjGDH2 was upregulated after 1h of all stress treatments, while no gene was found to be upregulated after 24h of stress treatments, commonly. These observations indicate that expression of most of the genes is adversely affected under abiotic stress conditions, particularly under prolonged stress exposure (24h), which may be one of the reasons of reduction in plant growth and development under abiotic stresses. PMID:26605918

  12. Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4

    PubMed Central

    Cortellino, Salvatore; Wang, Chengbing; Wang, Baolin; Bassi, Maria Rosaria; Caretti, Elena; Champeval, Delphine; Calmont, Amelie; Jarnik, Michal; Burch, John; Zaret, Kenneth; Larue, Lionel; Bellacosa, Alfonso

    2009-01-01

    Primary cilia are assembled and maintained by evolutionarily conserved intraflagellar transport (IFT) proteins that are involved in the coordinated movement of macromolecular cargo from the basal body to the cilium tip and back. The IFT machinery is organized in two structural complexes named complex A and complex B. Recently, inactivation in the mouse germline of Ift genes belonging to complex B revealed a requirement of ciliogenesis, or proteins involved in ciliogenesis, for Sonic Hedgehog (Shh) signaling in mammals. Here we report on a complex A mutant mouse, defective for the Ift122 gene. Ift122-null embryos show multiple developmental defects (exencephaly, situs viscerum inversus, delay in turning, hemorrhage and defects in limb development) that result in lethality. In the node, primary cilia were absent or malformed in homozygous mutant and heterozygous embryos, respectively. Impairment of the Shh pathway was apparent in both neural tube patterning (expansion of motoneurons and rostro-caudal level-dependent contraction or expansion of the dorso-lateral interneurons), and limb patterning (ectrosyndactyly). These phenotypes are distinct from both complex B IFT mutant embryos and embryos defective for the ciliary protein hennin/Arl13b, and suggest reduced levels of both Gli2/Gli3 activator and Gli3 repressor functions. We conclude that complex A and complex B factors play similar but distinct roles in ciliogenesis and Shh/Gli3 signaling. PMID:19000668

  13. Detection of Multiple Budding Yeast Cells and a Partial Sequence of 43-kDa Glycoprotein Coding Gene of Paracoccidioides brasiliensis from a Case of Lacaziosis in a Female Pacific White-Sided Dolphin (Lagenorhynchus obliquidens).

    PubMed

    Minakawa, Tomoko; Ueda, Keiichi; Tanaka, Miyuu; Tanaka, Natsuki; Kuwamura, Mitsuru; Izawa, Takeshi; Konno, Toshihiro; Yamate, Jyoji; Itano, Eiko Nakagawa; Sano, Ayako; Wada, Shinpei

    2016-08-01

    Lacaziosis, formerly called as lobomycosis, is a zoonotic mycosis, caused by Lacazia loboi, found in humans and dolphins, and is endemic in the countries on the Atlantic Ocean, Indian Ocean and Pacific Ocean of Japanese coast. Susceptible Cetacean species include the bottlenose dolphin (Tursiops truncatus), the Indian Ocean bottlenose dolphin (T. aduncus), and the estuarine dolphin (Sotalia guianensis); however, no cases have been recorded in other Cetacean species. We diagnosed a case of Lacaziosis in a Pacific white-sided dolphin (Lagenorhynchus obliquidens) nursing in an aquarium in Japan. The dolphin was a female estimated to be more than 14 years old at the end of June 2015 and was captured in a coast of Japan Sea in 2001. Multiple, lobose, and solid granulomatous lesions with or without ulcers appeared on her jaw, back, flipper and fluke skin, in July 2014. The granulomatous skin lesions from the present case were similar to those of our previous cases. Multiple budding and chains of round yeast cells were detected in the biopsied samples. The partial sequence of 43-kDa glycoprotein coding gene confirmed by a nested PCR and sequencing, which revealed a different genotype from both Amazonian and Japanese lacaziosis in bottlenose dolphins, and was 99 % identical to those derived from Paracoccidioides brasiliensis; a sister fungal species to L. loboi. This is the first case of lacaziosis in Pacific white-sided dolphin. PMID:26883513

  14. Gene cloning and characterization of the very large NAD-dependent l-glutamate dehydrogenase from the psychrophile Janthinobacterium lividum, isolated from cold soil.

    PubMed

    Kawakami, Ryushi; Sakuraba, Haruhiko; Ohshima, Toshihisa

    2007-08-01

    NAD-dependent l-glutamate dehydrogenase (NAD-GDH) activity was detected in cell extract from the psychrophile Janthinobacterium lividum UTB1302, which was isolated from cold soil and purified to homogeneity. The native enzyme (1,065 kDa, determined by gel filtration) is a homohexamer composed of 170-kDa subunits (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis). Consistent with these findings, gene cloning and sequencing enabled deduction of the amino acid sequence of the subunit, which proved to be comprised of 1,575 amino acids with a combined molecular mass of 169,360 Da. The enzyme from this psychrophile thus appears to belong to the GDH family characterized by very large subunits, like those expressed by Streptomyces clavuligerus and Pseudomonas aeruginosa (about 180 kDa). The entire amino acid sequence of the J. lividum enzyme showed about 40% identity with the sequences from S. clavuligerus and P. aeruginosa enzymes, but the central domains showed higher homology (about 65%). Within the central domain, the residues related to substrate and NAD binding were highly conserved, suggesting that this is the enzyme's catalytic domain. In the presence of NAD, but not in the presence of NADP, this GDH exclusively catalyzed the oxidative deamination of l-glutamate. The stereospecificity of the hydride transfer to NAD was pro-S, which is the same as that of the other known GDHs. Surprisingly, NAD-GDH activity was markedly enhanced by the addition of various amino acids, such as l-aspartate (1,735%) and l-arginine (936%), which strongly suggests that the N- and/or C-terminal domains play regulatory roles and are involved in the activation of the enzyme by these amino acids. PMID:17526698

  15. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing.

    PubMed

    Naveed, Muhammad; Mubeen, Samavia; Khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

    2014-01-01

    In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization. PMID:25477935

  16. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

    PubMed Central

    Naveed, Muhammad; Mubeen, Samavia; khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

    2014-01-01

    In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization. PMID:25477935

  17. Physics of Partially Ionized Plasmas

    NASA Astrophysics Data System (ADS)

    Krishan, Vinod

    2016-05-01

    Figures; Preface; 1. Partially ionized plasmas here and everywhere; 2. Multifluid description of partially ionized plasmas; 3. Equilibrium of partially ionized plasmas; 4. Waves in partially ionized plasmas; 5. Advanced topics in partially ionized plasmas; 6. Research problems in partially ionized plasmas; Supplementary matter; Index.

  18. A codon-usage variant in the (GGN){sub n} trinucleotide polymorphism of the androgen receptor gene as an aid in the prenatal diagnosis of ambiguous genitalia due to partial androgen insensitivity

    SciTech Connect

    Lumbroso, R.; Vasiliou, M.; Beitel, L.K.

    1994-09-01

    Exon 1 at the X-linked androgen receptor (AR) locus encodes an N-terminal modulatory domain that contains two large homopolyamino acid tracts: (CAG;glutamine;Gln){sub 11-33} and (GGN;Glycine;Cly){sub 15-27}. Certain AR mutations cause partial androgen insensitivity (PAI) with frank genital ambiguity that may engender appreciable parental anxiety and patient morbidity. If the AR mutation in a PAI family is unknown, the AR`s intragenic trinucleotide repeat polymorphisms may be used for prenatal diagnosis. However, intergenerational instability of repeat-size may be worrisome, particularly when the information alleles differ by only a few repeats. Here, we report the discovery of a codon-usage (silent substitution) variant in the GGN repeat, and describe its use as a source of complementary information for prenatal diagnosis. The standard sense sequence of the (GGN){sub n} tract is (GGT){sub 3} GGG(GGT){sub 2} (GGC){sub 9-21}. On 4 of 27 X chromosomes we noted that the internal GGT sequence was expanded to 3 or 4 repeats. We used an internal (GGT){sub 4} repeat in a total (GGN){sub 24} tract together with a (CAG){sub 20} tract to distinguish an X chromosome with a mutant AR allele from another X chromosome, bearing a normal allele, that had an internal (GGT){sub 2} repeat in a total (GGN){sub 23} tract together with a (CAG){sub 21} tract. Subsequently, we found the base change leading to a pathogenic amino acid substitution (M779I) in codon 6 of the mutant AR gene in an affected maternal aunt and the fetus at risk. This confirmed the prenatal diagnosis based on the intragenic trinucleotide repeat polymorphisms, and it strengthened the prediction of external genital ambiguity using our previous experience with M779I in another family.

  19. Why arthroscopic partial meniscectomy?

    PubMed

    Lyu, Shaw-Ruey

    2015-09-01

    "Arthroscopic Partial Meniscectomy versus Sham Surgery for a Degenerative Meniscal Tear" published in the New England Journal of Medicine on December 26, 2013 draws the conclusion that arthroscopic partial medial meniscectomy provides no significant benefit over sham surgery in patients with a degenerative meniscal tear and no knee osteoarthritis. This result argues against the current practice of performing arthroscopic partial meniscectomy (APM) in patients with a degenerative meniscal tear. Since the number of APM performed has been increasing, the information provided by this study should lead to a change in clinical care of patients with a degenerative meniscus tear. PMID:26488013

  20. Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67.

    PubMed

    Wagh, Jitendra; Shah, Sonal; Bhandari, Praveena; Archana, G; Kumar, G Naresh

    2014-06-01

    Gluconic acid secretion mediated by the direct oxidation of glucose by pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase (GDH) is responsible for mineral phosphate solubilization in Gram-negative bacteria. Herbaspirillum seropedicae Z67 (ATCC 35892) genome encodes GDH apoprotein but lacks genes for the biosynthesis of its cofactor PQQ. In this study, pqqE of Erwinia herbicola (in plasmid pJNK1) and pqq gene clusters of Pseudomonas fluorescens B16 (pOK53) and Acinetobacter calcoaceticus (pSS2) were over-expressed in H. seropedicae Z67. Transformants Hs (pSS2) and Hs (pOK53) secreted micromolar levels of PQQ and attained high GDH activity leading to secretion of 33.46 mM gluconic acid when grown on 50 mM glucose while Hs (pJNK1) was ineffective. Hs (pJNK1) failed to solubilize rock phosphate, while Hs (pSS2) and Hs (pOK53) liberated 125.47 μM and 168.07 μM P, respectively, in minimal medium containing 50 mM glucose under aerobic conditions. Moreover, under N-free minimal medium, Hs (pSS2) and Hs (pOK53) not only released significant P but also showed enhanced growth, biofilm formation, and exopolysaccharide (EPS) secretion. However, indole acetic acid (IAA) production was suppressed. Thus, the addition of the pqq gene cluster, but not pqqE alone, is sufficient for engineering phosphate solubilization in H. seropedicae Z67 without compromising growth under nitrogen-fixing conditions. PMID:24682480

  1. Partial knee replacement - slideshow

    MedlinePlus

    ... page: //medlineplus.gov/ency/presentations/100225.htm Partial knee replacement - series To use the sharing features on ... A.M. Editorial team. Related MedlinePlus Health Topics Knee Replacement A.D.A.M., Inc. is accredited ...

  2. Partial knee replacement

    MedlinePlus

    Most people recover quickly and have much less pain than they did before surgery. People who have a partial knee replacement recover faster than those who have a total knee replacement. Many people are able to walk ...

  3. Twisted partially pure spinors

    NASA Astrophysics Data System (ADS)

    Herrera, Rafael; Tellez, Ivan

    2016-08-01

    Motivated by the relationship between orthogonal complex structures and pure spinors, we define twisted partially pure spinors in order to characterize spinorially subspaces of Euclidean space endowed with a complex structure.

  4. PARTIAL TORUS INSTABILITY

    SciTech Connect

    Olmedo, Oscar; Zhang Jie

    2010-07-20

    Flux ropes are now generally accepted to be the magnetic configuration of coronal mass ejections (CMEs), which may be formed prior to or during solar eruptions. In this study, we model the flux rope as a current-carrying partial torus loop with its two footpoints anchored in the photosphere, and investigate its stability in the context of the torus instability (TI). Previous studies on TI have focused on the configuration of a circular torus and revealed the existence of a critical decay index of the overlying constraining magnetic field. Our study reveals that the critical index is a function of the fractional number of the partial torus, defined by the ratio between the arc length of the partial torus above the photosphere and the circumference of a circular torus of equal radius. We refer to this finding as the partial torus instability (PTI). It is found that a partial torus with a smaller fractional number has a smaller critical index, thus requiring a more gradually decreasing magnetic field to stabilize the flux rope. On the other hand, a partial torus with a larger fractional number has a larger critical index. In the limit of a circular torus when the fractional number approaches 1, the critical index goes to a maximum value. We demonstrate that the PTI helps us to understand the confinement, growth, and eventual eruption of a flux-rope CME.

  5. GDH Integral on the Proton from Asymmetries

    SciTech Connect

    Yelena Prok

    2004-05-01

    Inclusive double spin electron asymmetries have been measured by scattering polarized electrons off the solid polarized {sup 15}NH{sub 3} target in Hall B of Jefferson Lab in 2000-2001. The virtual photon asymmetry A{sub 1} (x), the longitudinal spin structure function, g{sub 1} (x, Q{sup 2}), and the first moment, {Gamma}{sub 1}{sup p}, have been evaluated for a kinematic range of 0.05 {ge} Q{sup 2} {ge} 4.5 GeV{sup 2}. The extracted results complement the existing data in the resonance region, extending it to lower and higher Q{sup 2} regions. The results are important in the study of Q{sup 2} evolution of nucleon structure from the hadronic to partonic degrees of freedom.

  6. Improvement of a Sulfolobus-E. coli shuttle vector for heterologous gene expression in Sulfolobus acidocaldarius.

    PubMed

    Hwang, Sungmin; Choi, Kyoung-Hwa; Yoon, Naeun; Cha, Jaeho

    2015-02-01

    A Sulfolobus-E. coli shuttle vector for an efficient expression of the target gene in S. acidocaldarius strain was constructed. The plasmid-based vector pSM21 and its derivative pSM21N were generated based on the pUC18 and Sulfolobus cryptic plasmid pRN1. They carried the S. solfataricus P2 pyrEF gene for the selection marker, a multiple cloning site (MCS) with C-terminal histidine tag, and a constitutive promoter of the S. acidocaldarius gdhA gene for strong expression of the target gene, as well as the pBR322 origin and ampicillin-resistant gene for E. coli propagation. The advantage of pSM21 over other Sulfolobus shuttle vectors is that it contains a MCS and a histidine tag for the simple and easy cloning of a target gene as well as one-step purification by histidine affinity chromatography. For successful expression of the foreign genes, two genes from archaeal origins (PH0193 and Ta0298) were cloned into pSM21N and the functional expression was examined by enzyme activity assay. The recombinant PH0193 was successfully expressed under the control of the gdhA promoter and purified from the cultures by His-tag affinity chromatography. The yield was approximately 1 mg of protein per liter of cultures. The enzyme activity measurements of PH0913 and Ta0298 revealed that both proteins were expressed as an active form in S. acidocaldarius. These results indicate that the pSM21N shuttle vector can be used for the functional expression of foreign archaeal genes that form insoluble aggregates in the E. coli system. PMID:25293629

  7. Partial spread OFDM

    NASA Astrophysics Data System (ADS)

    Elghariani, Ali; Zoltowski, Michael D.

    2012-05-01

    In this paper, partial spread OFDM system has been presented and its performance has been studied when different detection techniques are employed, such as minimum mean square error (MMSE), grouped Maximum Likelihood (ML) and approximated integer quadratic programming (IQP) techniques . The performance study also includes applying two different spreading matrices, Hadamard and Vandermonde. Extensive computer simulation have been implemented and important results show that partial spread OFDM system improves the BER performance and the frequency diversity of OFDM compared to both non spread and full spread systems. The results from this paper also show that partial spreading technique combined with suboptimal detector could be a better solution for applications that require low receiver complexity and high information detectability.

  8. Methanol partial oxidation reformer

    DOEpatents

    Ahmed, S.; Kumar, R.; Krumpelt, M.

    1999-08-17

    A partial oxidation reformer is described comprising a longitudinally extending chamber having a methanol, water and an air inlet and an outlet. An igniter mechanism is near the inlets for igniting a mixture of methanol and air, while a partial oxidation catalyst in the chamber is spaced from the inlets and converts methanol and oxygen to carbon dioxide and hydrogen. Controlling the oxygen to methanol mole ratio provides continuous slightly exothermic partial oxidation reactions of methanol and air producing hydrogen gas. The liquid is preferably injected in droplets having diameters less than 100 micrometers. The reformer is useful in a propulsion system for a vehicle which supplies a hydrogen-containing gas to the negative electrode of a fuel cell. 7 figs.

  9. Methanol partial oxidation reformer

    DOEpatents

    Ahmed, Shabbir; Kumar, Romesh; Krumpelt, Michael

    1999-01-01

    A partial oxidation reformer comprising a longitudinally extending chamber having a methanol, water and an air inlet and an outlet. An igniter mechanism is near the inlets for igniting a mixture of methanol and air, while a partial oxidation catalyst in the chamber is spaced from the inlets and converts methanol and oxygen to carbon dioxide and hydrogen. Controlling the oxygen to methanol mole ratio provides continuous slightly exothermic partial oxidation reactions of methanol and air producing hydrogen gas. The liquid is preferably injected in droplets having diameters less than 100 micrometers. The reformer is useful in a propulsion system for a vehicle which supplies a hydrogen-containing gas to the negative electrode of a fuel cell.

  10. Methanol partial oxidation reformer

    DOEpatents

    Ahmed, Shabbir; Kumar, Romesh; Krumpelt, Michael

    2001-01-01

    A partial oxidation reformer comprising a longitudinally extending chamber having a methanol, water and an air inlet and an outlet. An igniter mechanism is near the inlets for igniting a mixture of methanol and air, while a partial oxidation catalyst in the chamber is spaced from the inlets and converts methanol and oxygen to carbon dioxide and hydrogen. Controlling the oxygen to methanol mole ratio provides continuous slightly exothermic partial oxidation reactions of methanol and air producing hydrogen gas. The liquid is preferably injected in droplets having diameters less than 100 micrometers. The reformer is useful in a propulsion system for a vehicle which supplies a hydrogen-containing gas to the negative electrode of a fuel cell.

  11. Methanol partial oxidation reformer

    DOEpatents

    Ahmed, S.; Kumar, R.; Krumpelt, M.

    1999-08-24

    A partial oxidation reformer is described comprising a longitudinally extending chamber having a methanol, water and an air inlet and an outlet. An igniter mechanism is near the inlets for igniting a mixture of methanol and air, while a partial oxidation catalyst in the chamber is spaced from the inlets and converts methanol and oxygen to carbon dioxide and hydrogen. Controlling the oxygen to methanol mole ratio provides continuous slightly exothermic partial oxidation reactions of methanol and air producing hydrogen gas. The liquid is preferably injected in droplets having diameters less than 100 micrometers. The reformer is useful in a propulsion system for a vehicle which supplies a hydrogen-containing gas to the negative electrode of a fuel cell. 7 figs.

  12. Oxygen partial pressure sensor

    DOEpatents

    Dees, D.W.

    1994-09-06

    A method for detecting oxygen partial pressure and an oxygen partial pressure sensor are provided. The method for measuring oxygen partial pressure includes contacting oxygen to a solid oxide electrolyte and measuring the subsequent change in electrical conductivity of the solid oxide electrolyte. A solid oxide electrolyte is utilized that contacts both a porous electrode and a nonporous electrode. The electrical conductivity of the solid oxide electrolyte is affected when oxygen from an exhaust stream permeates through the porous electrode to establish an equilibrium of oxygen anions in the electrolyte, thereby displacing electrons throughout the electrolyte to form an electron gradient. By adapting the two electrodes to sense a voltage potential between them, the change in electrolyte conductivity due to oxygen presence can be measured. 1 fig.

  13. Oxygen partial pressure sensor

    DOEpatents

    Dees, Dennis W.

    1994-01-01

    A method for detecting oxygen partial pressure and an oxygen partial pressure sensor are provided. The method for measuring oxygen partial pressure includes contacting oxygen to a solid oxide electrolyte and measuring the subsequent change in electrical conductivity of the solid oxide electrolyte. A solid oxide electrolyte is utilized that contacts both a porous electrode and a nonporous electrode. The electrical conductivity of the solid oxide electrolyte is affected when oxygen from an exhaust stream permeates through the porous electrode to establish an equilibrium of oxygen anions in the electrolyte, thereby displacing electrons throughout the electrolyte to form an electron gradient. By adapting the two electrodes to sense a voltage potential between them, the change in electrolyte conductivity due to oxygen presence can be measured.

  14. Partial Participation Revisited.

    ERIC Educational Resources Information Center

    Ferguson, Dianne L.; Baumgart, Diane

    1991-01-01

    This article reanalyzes the principle of partial participation in integrated educational programing for students with severe or profound disabilities. The article presents four "error patterns" in how the concept has been used, some reasons why such error patterns have occurred, and strategies for avoiding these errors. (Author/JDD)

  15. Partial gravity habitat study

    NASA Technical Reports Server (NTRS)

    Capps, Stephen; Lorandos, Jason; Akhidime, Eval; Bunch, Michael; Lund, Denise; Moore, Nathan; Murakawa, Kiosuke

    1989-01-01

    The purpose of this study is to investigate comprehensive design requirements associated with designing habitats for humans in a partial gravity environment, then to apply them to a lunar base design. Other potential sites for application include planetary surfaces such as Mars, variable-gravity research facilities, and a rotating spacecraft. Design requirements for partial gravity environments include locomotion changes in less than normal earth gravity; facility design issues, such as interior configuration, module diameter, and geometry; and volumetric requirements based on the previous as well as psychological issues involved in prolonged isolation. For application to a lunar base, it is necessary to study the exterior architecture and configuration to insure optimum circulation patterns while providing dual egress; radiation protection issues are addressed to provide a safe and healthy environment for the crew; and finally, the overall site is studied to locate all associated facilities in context with the habitat. Mission planning is not the purpose of this study; therefore, a Lockheed scenario is used as an outline for the lunar base application, which is then modified to meet the project needs. The goal of this report is to formulate facts on human reactions to partial gravity environments, derive design requirements based on these facts, and apply the requirements to a partial gravity situation which, for this study, was a lunar base.

  16. Partial Androgen Insensitivity Syndrome Presenting with Gynecomastia

    PubMed Central

    Lee, Sung Won; Kwak, Dong Shin; Jung, In Sub; Kwak, Joo Hee; Park, Jung Hwan; Hong, Sang Mo; Lee, Chang Bum; Park, Yong Soo; Kim, Dong Sun; Choi, Woong Hwan

    2015-01-01

    Gynecomastia is a benign enlargement of the male breast caused by the proliferation of glandular breast tissue. Determining the various causes of gynecomastia such as physiological causes, drugs, systemic diseases, and endocrine disorders is important. Androgen insensitivity syndrome (AIS) is a rare endocrine disorder presenting with gynecomastia and is a disorder of male sexual differentiation caused by mutations within the androgen receptor gene. All individuals with AIS have the 46 XY karyotype, although AIS phenotypes can be classified as mild, partial or complete and can differ among both males and females including ambiguous genitalia or infertility in males. We experienced a case of partial AIS presenting with gynecomastia and identified the androgen receptor gene mutation. PMID:25433660

  17. Partially coherent ultrafast spectrography

    NASA Astrophysics Data System (ADS)

    Bourassin-Bouchet, C.; Couprie, M.-E.

    2015-03-01

    Modern ultrafast metrology relies on the postulate that the pulse to be measured is fully coherent, that is, that it can be completely described by its spectrum and spectral phase. However, synthesizing fully coherent pulses is not always possible in practice, especially in the domain of emerging ultrashort X-ray sources where temporal metrology is strongly needed. Here we demonstrate how frequency-resolved optical gating (FROG), the first and one of the most widespread techniques for pulse characterization, can be adapted to measure partially coherent pulses even down to the attosecond timescale. No modification of experimental apparatuses is required; only the processing of the measurement changes. To do so, we take our inspiration from other branches of physics where partial coherence is routinely dealt with, such as quantum optics and coherent diffractive imaging. This will have important and immediate applications, such as enabling the measurement of X-ray free-electron laser pulses despite timing jitter.

  18. Partially integrated exhaust manifold

    DOEpatents

    Hayman, Alan W; Baker, Rodney E

    2015-01-20

    A partially integrated manifold assembly is disclosed which improves performance, reduces cost and provides efficient packaging of engine components. The partially integrated manifold assembly includes a first leg extending from a first port and terminating at a mounting flange for an exhaust gas control valve. Multiple additional legs (depending on the total number of cylinders) are integrally formed with the cylinder head assembly and extend from the ports of the associated cylinder and terminate at an exit port flange. These additional legs are longer than the first leg such that the exit port flange is spaced apart from the mounting flange. This configuration provides increased packaging space adjacent the first leg for any valving that may be required to control the direction and destination of exhaust flow in recirculation to an EGR valve or downstream to a catalytic converter.

  19. Partially coherent ultrafast spectrography

    PubMed Central

    Bourassin-Bouchet, C.; Couprie, M.-E.

    2015-01-01

    Modern ultrafast metrology relies on the postulate that the pulse to be measured is fully coherent, that is, that it can be completely described by its spectrum and spectral phase. However, synthesizing fully coherent pulses is not always possible in practice, especially in the domain of emerging ultrashort X-ray sources where temporal metrology is strongly needed. Here we demonstrate how frequency-resolved optical gating (FROG), the first and one of the most widespread techniques for pulse characterization, can be adapted to measure partially coherent pulses even down to the attosecond timescale. No modification of experimental apparatuses is required; only the processing of the measurement changes. To do so, we take our inspiration from other branches of physics where partial coherence is routinely dealt with, such as quantum optics and coherent diffractive imaging. This will have important and immediate applications, such as enabling the measurement of X-ray free-electron laser pulses despite timing jitter. PMID:25744080

  20. Partial quantum logics revisited

    NASA Astrophysics Data System (ADS)

    Vetterlein, Thomas

    2011-01-01

    Partial Boolean algebras (PBAs) were introduced by Kochen and Specker as an algebraic model reflecting the mutual relationships among quantum-physical yes-no tests. The fact that not all pairs of tests are compatible was taken into special account. In this paper, we review PBAs from two sides. First, we generalise the concept, taking into account also those yes-no tests which are based on unsharp measurements. Namely, we introduce partial MV-algebras, and we define a corresponding logic. Second, we turn to the representation theory of PBAs. In analogy to the case of orthomodular lattices, we give conditions for a PBA to be isomorphic to the PBA of closed subspaces of a complex Hilbert space. Hereby, we do not restrict ourselves to purely algebraic statements; we rather give preference to conditions involving automorphisms of a PBA. We conclude by outlining a critical view on the logico-algebraic approach to the foundational problem of quantum physics.

  1. Role of nitrogen-metabolism genes expressed during pathogenicity of the alkalinizing Colletotrichum gloeosporioides and their differential expression in acidifying pathogens.

    PubMed

    Miyara, I; Shnaiderman, C; Meng, X; Vargas, W A; Diaz-Minguez, J M; Sherman, A; Thon, M; Prusky, D

    2012-09-01

    Pathogens can actively alter fruit pH around the infection site, signaling modulation of pathogenicity-factor expression, as found for alkalinizing (Colletotrichum and Alternaria spp.) and acidifying (Penicillium, Botrytis, and Sclerotinia spp.) fungi. The nitrogen-metabolism genes GDH2, GS1, GLT, and MEP genes are differentially expressed during colonization by Colletotrichum gloeosporioides, and a Δgdh2 strain reduces ammonia accumulation and pathogenicity. We analyzed the contribution of transporters GLT and MEPB to C. gloeosporiodes pathogenicity. Germinating spores of Δglt strains showed reduced appressorium formation; those of ΔmepB mutants showed rapid ammonia uptake and accumulation inside the hyphae, indicating deregulated uptake. Both mutants reduced pathogenicity, indicating that these transporters function during alkalinizing species pathogenicity. We compared the expressions of these genes in C. gloeosporioides and Sclerotinia sclerotiorum, and found five to 10-fold higher expression at the transcript level in the former. Interestingly, GLT and MEPB in the alkalinizing species showed no and very low sequence identity, respectively, with their counterparts in the acidifying species. Knockout analysis of GLT and MEPB and their differential transcript regulation in the alkalinizing and acidifying species suggest that the ammonia accumulation contributing to pathogenicity in the former is modulated by factors at the gene-regulation levels that are lacking in the acidifying species. PMID:22571816

  2. The microbial gene diversity along an elevation gradient of the Tibetan grassland.

    PubMed

    Yang, Yunfeng; Gao, Ying; Wang, Shiping; Xu, Depeng; Yu, Hao; Wu, Linwei; Lin, Qiaoyan; Hu, Yigang; Li, Xiangzhen; He, Zhili; Deng, Ye; Zhou, Jizhong

    2014-02-01

    Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4(+)-N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics. PMID:23985745

  3. The microbial gene diversity along an elevation gradient of the Tibetan grassland

    PubMed Central

    Yang, Yunfeng; Gao, Ying; Wang, Shiping; Xu, Depeng; Yu, Hao; Wu, Linwei; Lin, Qiaoyan; Hu, Yigang; Li, Xiangzhen; He, Zhili; Deng, Ye; Zhou, Jizhong

    2014-01-01

    Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics. PMID:23985745

  4. General classification of partially polarized partially coherent beams

    NASA Astrophysics Data System (ADS)

    Martinez-Herrero, Rosario; Piquero, Gemma; Mejias, Pedro M.

    2003-05-01

    The behavior of the so-called generalized degree of polarization of partially coherent partially polarized beams upon free propagation is investigated. On the basis of this parameter a general classification scheme of partially polarized beams is proposed. The results are applied to certain classes of fields of special interest.

  5. Experts' Understanding of Partial Derivatives Using the Partial Derivative Machine

    ERIC Educational Resources Information Center

    Roundy, David; Weber, Eric; Dray, Tevian; Bajracharya, Rabindra R.; Dorko, Allison; Smith, Emily M.; Manogue, Corinne A.

    2015-01-01

    Partial derivatives are used in a variety of different ways within physics. Thermodynamics, in particular, uses partial derivatives in ways that students often find especially confusing. We are at the beginning of a study of the teaching of partial derivatives, with a goal of better aligning the teaching of multivariable calculus with the needs of…

  6. Characterisation of full-length mitochondrial copies and partial nuclear copies (numts) of the cytochrome b and cytochrome c oxidase subunit I genes of Toxoplasma gondii, Neospora caninum, Hammondia heydorni and Hammondia triffittae (Apicomplexa: Sarcocystidae).

    PubMed

    Gjerde, Bjørn

    2013-04-01

    Genomic DNA was extracted from three oocyst isolates of Hammondia triffittae from foxes and two oocyst isolates of Hammondia heydorni from dogs, as well as from cell culture-derived tachyzoites of Toxoplasma gondii (RH strain) and Neospora caninum (NC-Liverpool strain), and examined by PCR with primers targeting the cytochrome b (cytb) and the cytochrome c oxidase subunit I (cox1) genes in order to characterise both genes and, if possible, the remainder of the mitochondrial genome of these species. Several primers were designed and used in various combinations to amplify regions within and between both genes and to determine gene order. When certain forward primers targeting cytb were used in combination with certain reverse primers targeting cox1, two overlapping sequences were obtained for each species and isolate studied, which showed that a full-length copy of cytb was followed 36-37 bp downstream by a full-length copy of cox1, and these sequences are believed to represent the true mitochondrial genes and the gene order in the mitochondrial genome of the four species examined. The cytb of T. gondii, N. caninum, H. heydorni and H. triffittae comprised a total of 1,080 bp (359 amino acids) and used ATG and TAA as start and stop codon, respectively. The cox1 of these species also used TAA as stop codon, whereas the most likely start codon was ATG, resulting in a gene comprising 1,491 bp (496 amino acids). Pair-wise sequence comparisons based on either cytb or cox1 clearly separated T. gondii from N. caninum and both of these species from the two Hammondia species, whereas the latter two species were 100 % identical at cytb and shared 99.3 % identity at cox1. Phylogenetic analyses using the maximum-likelihood method confirmed these findings and placed T. gondii in a clade separate from the three other species and all four Toxoplasmatinae in a sister clade to Eimeria spp. PCR with other primers and/or primer pairs than those used to obtain the full

  7. Analysis of gene expression changes, caused by exposure to nitrite, in metabolic and antioxidant enzymes in the red claw crayfish, Cherax quadricarinatus.

    PubMed

    Jiang, Qichen; Zhang, Wenyi; Tan, Hongyue; Pan, Dongmei; Yang, Yuanhao; Ren, Qian; Yang, Jiaxin

    2014-06-01

    We evaluated the effect of acute exposure to nitrite on expression of antioxidant and metabolic enzyme genes in gill tissue of advanced juvenile Cherax quadricarinatus. A 48h nitrite exposure was conducted, using four test concentrations (NO2-N=0.5, 1, 1.5 and 2mg L(-1)) plus a control group. The relative mRNA expression of mitochondrial manganese superoxide dismutase (mMnSOD), cytosolic MnSOD (cMnSOD), extracellular copper/zinc SOD (exCu/ZnSOD), catalase (CAT), glutathione S-transferase (GST), arginine kinase (AK), glutamate dehydrogenase (GDH), mitochondrial malate dehydrogenase (mMDH), Na(+)/K(+)-ATPase α-subunit and phosphoenolpyruvate carboxykinase (PEPCK) in gill tissue was measured. Significantly increased mRNA expression was observed for all the antioxidant enzymes after 12 and 24h. After 48h, they all decreased at high nitrite concentrations. The gene expression levels of AK, GDH, mMDH and Na(+)/K(+)-ATPase α-subunit showed similar trends as the antioxidant enzymes. Significant depression of gene expression levels of PEPCK occurred throughout the experimental time at high nitrite concentrations. The results indicated that nitrite could induce oxidative and metabolic stress in C. quadricarinatus, in a time dependent manner, which suggests they could be helpful in predicting sublethal nitrite toxicity and useful in environmental monitoring studies. PMID:24680578

  8. Partially segmented deformable mirror

    DOEpatents

    Bliss, Erlan S.; Smith, James R.; Salmon, J. Thaddeus; Monjes, Julio A.

    1991-01-01

    A partially segmented deformable mirror is formed with a mirror plate having a smooth and continuous front surface and a plurality of actuators to its back surface. The back surface is divided into triangular areas which are mutually separated by grooves. The grooves are deep enough to make the plate deformable and the actuators for displacing the mirror plate in the direction normal to its surface are inserted in the grooves at the vertices of the triangular areas. Each actuator includes a transducer supported by a receptacle with outer shells having outer surfaces. The vertices have inner walls which are approximately perpendicular to the mirror surface and make planar contacts with the outer surfaces of the outer shells. The adhesive which is used on these contact surfaces tends to contract when it dries but the outer shells can bend and serve to minimize the tendency of the mirror to warp.

  9. Partially segmented deformable mirror

    DOEpatents

    Bliss, E.S.; Smith, J.R.; Salmon, J.T.; Monjes, J.A.

    1991-05-21

    A partially segmented deformable mirror is formed with a mirror plate having a smooth and continuous front surface and a plurality of actuators to its back surface. The back surface is divided into triangular areas which are mutually separated by grooves. The grooves are deep enough to make the plate deformable and the actuators for displacing the mirror plate in the direction normal to its surface are inserted in the grooves at the vertices of the triangular areas. Each actuator includes a transducer supported by a receptacle with outer shells having outer surfaces. The vertices have inner walls which are approximately perpendicular to the mirror surface and make planar contacts with the outer surfaces of the outer shells. The adhesive which is used on these contact surfaces tends to contract when it dries but the outer shells can bend and serve to minimize the tendency of the mirror to warp. 5 figures.

  10. Partial oxidation catalyst

    DOEpatents

    Krumpelt, Michael; Ahmed, Shabbir; Kumar, Romesh; Doshi, Rajiv

    2000-01-01

    A two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion. The dehydrogenation portion is a group VIII metal and the oxide-ion conducting portion is selected from a ceramic oxide crystallizing in the fluorite or perovskite structure. There is also disclosed a method of forming a hydrogen rich gas from a source of hydrocarbon fuel in which the hydrocarbon fuel contacts a two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion at a temperature not less than about 400.degree. C. for a time sufficient to generate the hydrogen rich gas while maintaining CO content less than about 5 volume percent. There is also disclosed a method of forming partially oxidized hydrocarbons from ethanes in which ethane gas contacts a two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion for a time and at a temperature sufficient to form an oxide.

  11. Characterization of Pseudomonas putida Genes Responsive to Nutrient Limitation

    SciTech Connect

    Syn, Chris K.; Magnuson, Jon K.; Kingsley, Mark T.; Swarup, Sanjay

    2004-06-01

    The low bioavailability of nutrients and oxygen in the soil environment has hampered successful expression of biodegradation/biocontrol genes that are driven by promoters highly active during routine laboratory conditions of high nutrient- and oxygen-availability. Hence, in the present study, expression of the gus-tagged genes in 12 Tn5-gus mutants of the soil microbe Pseudomonas putida PNL-MK25 was examined under various conditions chosen to mimic the soil environment: low carbon, phosphate, nitrate, or oxygen, and in the rhizosphere. Based on their expression profiles, three nutrient-responsive mutant (NRM) strains, NRM5, NRM7, and NRM17, were selected for identification of the tagged genes. In the mutant strain NRM5, expression of the glutamate dehydrogenase (gdhA) gene was increased between 4.9- to 26.4-fold under various low nutrient conditions. In NRM7, expression of the novel NADPH:quinone oxidoreductase-like (nql) gene was consistently amongst the highest and was synergistically upregulated by low nutrient and anoxic conditions. The cyoD gene in NRM17, which encodes the fourth subunit of the cytochrome o ubiquinol oxidase complex, had decreased expression in low nutrient conditions but its absolute expression levels was still amongst the highest. Additionally, it was independent of oxygen availability, in contrast to that in E. coli.

  12. Arabidopsis genes, AtNPR1, AtTGA2 and AtPR-5, confer partial resistance to soybean cyst nematode (Heterodera glycines) when overexpressed in transgenic soybean roots

    PubMed Central

    2014-01-01

    Background Extensive studies using the model system Arabidopsis thaliana to elucidate plant defense signaling and pathway networks indicate that salicylic acid (SA) is the key hormone triggering the plant defense response against biotrophic and hemi-biotrophic pathogens, while jasmonic acid (JA) and derivatives are critical to the defense response against necrotrophic pathogens. Several reports demonstrate that SA limits nematode reproduction. Results Here we translate knowledge gained from studies using Arabidopsis to soybean. The ability of thirty-one Arabidopsis genes encoding important components of SA and JA synthesis and signaling in conferring resistance to soybean cyst nematode (SCN: Heterodera glycines) are investigated. We demonstrate that overexpression of three of thirty-one Arabidoposis genes in transgenic soybean roots of composite plants decreased the number of cysts formed by SCN to less than 50% of those found on control roots, namely AtNPR1(33%), AtTGA2 (38%), and AtPR-5 (38%). Three additional Arabidopsis genes decreased the number of SCN cysts by 40% or more: AtACBP3 (53% of the control value), AtACD2 (55%), and AtCM-3 (57%). Other genes having less or no effect included AtEDS5 (77%), AtNDR1 (82%), AtEDS1 (107%), and AtPR-1 (80%), as compared to control. Overexpression of AtDND1 greatly increased susceptibility as indicated by a large increase in the number of SCN cysts (175% of control). Conclusions Knowledge of the pathogen defense system gained from studies of the model system, Arabidopsis, can be directly translated to soybean through direct overexpression of Arabidopsis genes. When the genes, AtNPR1, AtGA2, and AtPR-5, encoding specific components involved in SA regulation, synthesis, and signaling, are overexpressed in soybean roots, resistance to SCN is enhanced. This demonstrates functional compatibility of some Arabidopsis genes with soybean and identifies genes that may be used to engineer resistance to nematodes. PMID:24739302

  13. Pseudo Boolean Programming for Partially Ordered Genomes

    NASA Astrophysics Data System (ADS)

    Angibaud, Sébastien; Fertin, Guillaume; Thévenin, Annelyse; Vialette, Stéphane

    Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to different maps with some unordered genes. Starting from a partial order between genes of a genome, one method to find a total order consists in optimizing a given measure between a linear extension of this partial order and a given total order of a close and well-known genome. However, for most common measures, the problem turns out to be NP-hard. In this paper, we propose a (0,1)-linear programming approach to compute a linear extension of one genome that maximizes the number of common intervals (resp. the number of adjacencies) between this linear extension and a given total order. Next, we propose an algorithm to find linear extensions of two partial orders that maximize the number of adjacencies.

  14. The Recently Identified Isoleucine Conjugate of cis-12-Oxo-Phytodienoic Acid Is Partially Active in cis-12-Oxo-Phytodienoic Acid-Specific Gene Expression of Arabidopsis thaliana.

    PubMed

    Arnold, Monika D; Gruber, Cornelia; Floková, Kristýna; Miersch, Otto; Strnad, Miroslav; Novák, Ondřej; Wasternack, Claus; Hause, Bettina

    2016-01-01

    Oxylipins of the jasmonate family are active as signals in plant responses to biotic and abiotic stresses as well as in development. Jasmonic acid (JA), its precursor cis-12-oxo-phytodienoic acid (OPDA) and the isoleucine conjugate of JA (JA-Ile) are the most prominent members. OPDA and JA-Ile have individual signalling properties in several processes and differ in their pattern of gene expression. JA-Ile, but not OPDA, is perceived by the SCFCOI1-JAZ co-receptor complex. There are, however, numerous processes and genes specifically induced by OPDA. The recently identified OPDA-Ile suggests that OPDA specific responses might be mediated upon formation of OPDA-Ile. Here, we tested OPDA-Ile-induced gene expression in wild type and JA-deficient, JA-insensitive and JA-Ile-deficient mutant background. Tests on putative conversion of OPDA-Ile during treatments revealed only negligible conversion. Expression of two OPDA-inducible genes, GRX480 and ZAT10, by OPDA-Ile could be detected in a JA-independent manner in Arabidopsis seedlings but less in flowering plants. The data suggest a bioactivity in planta of OPDA-Ile. PMID:27611078

  15. Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences.

    PubMed

    Pchelin, Ivan M; Zlatogursky, Vasily V; Rudneva, Mariya V; Chilina, Galina A; Rezaei-Matehkolaei, Ali; Lavnikevich, Dmitry M; Vasilyeva, Natalya V; Taraskina, Anastasia E

    2016-09-01

    Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique. PMID:27071492

  16. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    Content-based multimedia indexing, retrieval, and processing as well as multimedia databases demand the structuring of the media content (image, audio, video, text, etc.), one significant goal being to associate the identity of the content to the individual segments of the signals. In this paper, we specifically address the problem of speaker clustering, the task of assigning every speech utterance in an audio stream to its speaker. We offer a complete treatment to the idea of partially supervised speaker clustering, which refers to the use of our prior knowledge of speakers in general to assist the unsupervised speaker clustering process. By means of an independent training data set, we encode the prior knowledge at the various stages of the speaker clustering pipeline via 1) learning a speaker-discriminative acoustic feature transformation, 2) learning a universal speaker prior model, and 3) learning a discriminative speaker subspace, or equivalently, a speaker-discriminative distance metric. We study the directional scattering property of the Gaussian mixture model (GMM) mean supervector representation of utterances in the high-dimensional space, and advocate exploiting this property by using the cosine distance metric instead of the euclidean distance metric for speaker clustering in the GMM mean supervector space. We propose to perform discriminant analysis based on the cosine distance metric, which leads to a novel distance metric learning algorithm—linear spherical discriminant analysis (LSDA). We show that the proposed LSDA formulation can be systematically solved within the elegant graph embedding general dimensionality reduction framework. Our speaker clustering experiments on the GALE database clearly indicate that 1) our speaker clustering methods based on the GMM mean supervector representation and vector-based distance metrics outperform traditional speaker clustering methods based on the “bag of acoustic features” representation and statistical

  17. Controllability of the better chosen partial networks

    NASA Astrophysics Data System (ADS)

    Liu, Xueming; Pan, Linqiang

    2016-08-01

    How to control large complex networks is a great challenge. Recent studies have proved that the whole network can be sufficiently steered by injecting control signals into a minimum set of driver nodes, and the minimum numbers of driver nodes for many real networks are high, indicating that it is difficult to control them. For some large natural and technological networks, it is impossible and not feasible to control the full network. For example, in biological networks like large-scale gene regulatory networks it is impossible to control all the genes. This prompts us to explore the question how to choose partial networks that are easy for controlling and important in networked systems. In this work, we propose a method to achieve this goal. By computing the minimum driver nodes densities of the partial networks of Erdös-Rényi (ER) networks, scale-free (SF) networks and 23 real networks, we find that our method performs better than random method that chooses nodes randomly. Moreover, we find that the nodes chosen by our method tend to be the essential elements of the whole systems, via studying the nodes chosen by our method of a real human signaling network and a human protein interaction network and discovering that the chosen nodes from these networks tend to be cancer-associated genes. The implementation of our method shows some interesting connections between the structure and the controllability of networks, improving our understanding of the control principles of complex systems.

  18. Partial hepatectomy in mice.

    PubMed

    Nevzorova, Y A; Tolba, R; Trautwein, C; Liedtke, C

    2015-04-01

    The surgical procedure of two-thirds partial hepatectomy (PH) in rodents was first described more than 80 years ago by Higgins and Anderson. Nevertheless, this technique is still a state-of-the-art method for the community of liver researchers as it allows the in-depth analysis of signalling pathways involved in liver regeneration and hepatocarcinogenesis. The importance of PH as a key method in experimental hepatology has even increased in the last decade due to the increasing availability of genetically-modified mouse strains. Here, we propose a standard operating procedure (SOP) for the implementation of PH in mice, which is based on our experience of more than 10 years. In particular, the SOP offers all relevant background information on the PH model and provides comprehensive guidelines for planning and performing PH experiments. We provide established recommendations regarding optimal age and gender of animals, use of appropriate anaesthesia and biometric calculation of the experiments. We finally present an easy-to-follow step-by-step description of the complete surgical procedure including required materials, critical steps and postoperative management. This SOP especially takes into account the latest changes in animal welfare rules in the European Union but is still in agreement with current international regulations. In summary, this article provides comprehensive information for the legal application, design and implementation of PH experiments. PMID:25835741

  19. Partial covariate adjusted regression

    PubMed Central

    Şentürk, Damla; Nguyen, Danh V.

    2008-01-01

    Covariate adjusted regression (CAR) is a recently proposed adjustment method for regression analysis where both the response and predictors are not directly observed (Şentürk and Müller, 2005). The available data has been distorted by unknown functions of an observable confounding covariate. CAR provides consistent estimators for the coefficients of the regression between the variables of interest, adjusted for the confounder. We develop a broader class of partial covariate adjusted regression (PCAR) models to accommodate both distorted and undistorted (adjusted/unadjusted) predictors. The PCAR model allows for unadjusted predictors, such as age, gender and demographic variables, which are common in the analysis of biomedical and epidemiological data. The available estimation and inference procedures for CAR are shown to be invalid for the proposed PCAR model. We propose new estimators and develop new inference tools for the more general PCAR setting. In particular, we establish the asymptotic normality of the proposed estimators and propose consistent estimators of their asymptotic variances. Finite sample properties of the proposed estimators are investigated using simulation studies and the method is also illustrated with a Pima Indians diabetes data set. PMID:20126296

  20. Recombinant adenovirus encoding the HA gene from swine H3N2 influenza virus partially protects mice from challenge with heterologous virus: A/HK/1/68 (H3N2).

    PubMed

    Tang, M; Harp, J A; Wesley, R D

    2002-11-01

    Immunization with recombinant adenoviral vaccine that induces potent immunity has been applied to many infectious diseases. We report here developing a recombinant adenoviral vaccine encoding the HA gene from swine H3N2 influenza virus (SIV). Two replication-defective recombinant adenoviruses were generated: (1) rAd-HA: recombinant adenovirus encoding the HA gene from swine H3N2 influenza virus, and (2) rAd-vector: a control recombinant adenovirus containing adenovirus and transfer plasmids without a foreign HA gene. Mice given rAd-HA developed high titers of neutralizing and hemagglutination inhibition antibodies to SIV in comparison to mice inoculated with rAd-vector or PBS as early as 2 weeks after immunization, and these antibodies were substantially increased in the mice given rAd-HA within the next 3 weeks following the first dose. However, these antibodies were not able to neutralize the virus, A/HK/68 (H3N2), used for challenge. Nonetheless mice immunized with one or two doses of rAd-HA were protected from lethal challenge with heterologous virus, A/HK/1/68 (H3N2). A statistically significant ( P < 0.03) difference between survival rates of rAd-HA mice vs. rAd-vector or PBS mice was observed. PMID:12417948

  1. Characterization and Structure Prediction of Partial Length Protein Sequences of pcoA, pcoR and chrB Genes from Heavy Metal Resistant Bacteria from the Klip River, South Africa

    PubMed Central

    Chihomvu, Patience; Stegmann, Peter; Pillay, Michael

    2015-01-01

    The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. Copper and chromate resistance determinants were cloned and sequenced. Open reading frames (ORFs) related to the genes CopA and CopR were identified in E. coli KR29, PcoA in Lysinibacillus sp. KR25 and none related to chromate resistance were detected. The 3D-models predicted by I-TASSER disclose that the PcoA proteins consist of β-sheets, which form a part of the cupredoxin domain of the CopA copper resistance family of genes. The model for PcoR_29 revealed the presence of a helix turn helix; this forms part of a DNA binding protein, which is part of a heavy metal transcriptional regulator. The bacterial strains were cured using ethidium bromide. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E. coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element, which was not detected using gel electrophoresis. PMID:25837632

  2. Cloning and expression of the gene encoding catalytic subunit of thermostable glucose dehydrogenase from Burkholderia cepacia in Escherichia coli.

    PubMed

    Inose, Ken; Fujikawa, Masako; Yamazaki, Tomohiko; Kojima, Katsuhiro; Sode, Koji

    2003-02-21

    We have cloned a 1620-nucleotide gene encoding the catalytic subunit (alpha subunit) of a thermostable glucose dehydrogenase (GDH) from Burkholderia cepacia. The FAD binding motif was found in the N-terminal region of the alpha subunit. The deduced primary structure of the alpha subunit showed about 48% identity to the catalytic subunits of sorbitol dehydrogenase (SDH) from Gluconobacter oxydans and 2-keto-D-gluconate dehydrogenases (2KGDH) from Erwinia herbicola and Pantoea citrea. The alpha subunit of B. cepacia was expressed in Escherichia coli in its active water-soluble form, showing maximum dye-mediated GDH activity at 70 degrees C, retaining high thermal stability. A putative open reading frame (ORF) of 507 nucleotides was also found upstream of the alpha subunit encoding an 18-kDa peptide, designated as gamma subunit. The deduced primary structure of gamma subunit showed about 30% identity to the small subunits of the SDH from G. oxydans and 2KGDHs from E. herbicola and P. citrea. PMID:12573242

  3. CHRFAM7A, a human-specific and partially duplicated α7-nicotinic acetylcholine receptor gene with the potential to specify a human-specific inflammatory response to injury

    PubMed Central

    Costantini, Todd W.; Dang, Xitong; Coimbra, Raul; Eliceiri, Brian P.; Baird, Andrew

    2015-01-01

    Conventional wisdom presumes that the α7nAChR product of CHRNA7 expression mediates the ability of the vagus nerve to regulate the inflammatory response to injury and infection. Yet, 15 years ago, a 2nd structurally distinct and human-specific α7nAChR gene was discovered that has largely escaped attention of the inflammation research community. The gene, originally called dupα7nAChR but now known as CHRFAM7A, has been studied exhaustively in psychiatric research because of its association with mental illness. However, dupα7nAChR/CHRFAM7A expression is relatively low in human brain but elevated in human leukocytes. Furthermore, α7nAChR research in human tissues has been confounded by cross-reacting antibodies and nonspecific oligonucleotide primers that crossreact in immunoblotting, immunohistochemistry, and RT-PCR. Yet, 3 independent reports show the human-specific CHRFAM7A changes cell responsiveness to the canonical α7nAChR/CHRNA7 ion-gated channel. Because of its potential for the injury research community, its possible significance to human leukocyte biology, and its relevance to human inflammation, we review the discovery and structure of the dupα7nAChR/CHRFAM7A gene, the distribution of its mRNA, and its biologic activities and then discuss its possible role(s) in specifying human inflammation and injury. In light of emerging concepts that point to a role for human-specific genes in complex human disease, the existence of a human-specific α7nAChR regulating inflammatory responses in injury underscores the need for caution in extrapolating findings in the α7nAChR literature to man. To this end, we discuss the translational implications of a uniquely human α7nAChR-like gene on new drug target discovery and therapeutics development for injury, infection, and inflammation. PMID:25473097

  4. Partial lipodystrophy in coeliac disease.

    PubMed Central

    O'Mahony, D; O'Mahony, S; Whelton, M J; McKiernan, J

    1990-01-01

    The association of coeliac disease and partial lipodystrophy is described. The patient also had deficiencies of serum IgA and C3 complement (the latter associated with partial lipodystrophy). In addition, there was subclinical dermatitis herpetiformis confirmed by skin biopsy. The facial wasting of fully developed partial lipodystrophy may be misinterpreted as a sign of malabsorption but the facial, upper limb, and truncal lipodystrophy contrasts with normal pelvic and lower limb appearances. Images Figure 1 Figure 2 PMID:2379878

  5. Trigonometric Integrals via Partial Fractions

    ERIC Educational Resources Information Center

    Chen, H.; Fulford, M.

    2005-01-01

    Parametric differentiation is used to derive the partial fractions decompositions of certain rational functions. Those decompositions enable us to integrate some new combinations of trigonometric functions.

  6. Low partial discharge vacuum feedthrough

    NASA Technical Reports Server (NTRS)

    Benham, J. W.; Peck, S. R.

    1979-01-01

    Relatively discharge free vacuum feedthrough uses silver-plated copper conductor jacketed by carbon filled silicon semiconductor to reduce concentrated electric fields and minimize occurrence of partial discharge.

  7. Experts' understanding of partial derivatives using the partial derivative machine

    NASA Astrophysics Data System (ADS)

    Roundy, David; Weber, Eric; Dray, Tevian; Bajracharya, Rabindra R.; Dorko, Allison; Smith, Emily M.; Manogue, Corinne A.

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] Partial derivatives are used in a variety of different ways within physics. Thermodynamics, in particular, uses partial derivatives in ways that students often find especially confusing. We are at the beginning of a study of the teaching of partial derivatives, with a goal of better aligning the teaching of multivariable calculus with the needs of students in STEM disciplines. In this paper, we report on an initial study of expert understanding of partial derivatives across three disciplines: physics, engineering, and mathematics. We report on the central research question of how disciplinary experts understand partial derivatives, and how their concept images of partial derivatives differ, with a focus on experimentally measured quantities. Using the partial derivative machine (PDM), we probed expert understanding of partial derivatives in an experimental context without a known functional form. In particular, we investigated which representations were cued by the experts' interactions with the PDM. Whereas the physicists and engineers were quick to use measurements to find a numeric approximation for a derivative, the mathematicians repeatedly returned to speculation as to the functional form; although they were comfortable drawing qualitative conclusions about the system from measurements, they were reluctant to approximate the derivative through measurement. On a theoretical front, we found ways in which existing frameworks for the concept of derivative could be expanded to include numerical approximation.

  8. Are Electron Partial Waves Real

    NASA Astrophysics Data System (ADS)

    Yenen, O.; McLaughlin, K. W.

    2005-05-01

    Experiments determining the partial wave content of electrons are uncommon. The standard approach to partial wave expansion of the wavefunction of electrons often ignores their spin. In this non-relativistic approximation the partial waves are labeled by their orbital angular momentum quantum number, e.g. d-waves. As our previous work has shown, this non-relativistic approximation usually fails for photoelectrons. Partial waves should be further specified by their total angular momentum. With d-waves for example, one would need to distinguish between d3/2 and d5/2 partial waves. Although energetically degenerate, fully relativistic d3/2 and d5/2 partial waves of photoelectrons have fundamentally different angular distributions. Using experimental and theoretical methods we have developed, we obtain partial wave probabilities of photoelectrons from polarization measurements of ionic fluorescence. We found that for selected states of the residual ion, there are energy regions where the photoelectron is in a single partial wave with predictable angular distributions.

  9. Highly expressed amino acid biosynthesis genes revealed by global gene expression analysis of Salmonella enterica serovar Enteritidis during growth in whole egg are not essential for this growth.

    PubMed

    Jakočiūnė, Džiuginta; Herrero-Fresno, Ana; Jelsbak, Lotte; Olsen, John Elmerdahl

    2016-05-01

    Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common cause of egg borne salmonellosis in many parts of the world. This study analyzed gene expression of this bacterium during growth in whole egg, and whether highly expressed genes were essential for the growth. High quality RNA was extracted from S. Enteritidis using a modified RNA-extraction protocol. Global gene expression during growth in whole egg was compared to growth in LB-medium using DNA array method. Twenty-six genes were significantly upregulated during growth in egg; these belonged to amino acid biosynthesis, di/oligopeptide transport system, biotin synthesis, ferrous iron transport system, and type III secretion system. Significant downregulation of 15 genes related to formate hydrogenlyase (FHL) and trehalose metabolism was observed. The results suggested that S. Enteritidis is starved for amino-acids, biotin and iron when growing in egg. However, site specific mutation of amino acid biosynthesis genes asnA (17.3 fold upregulated), asnB (18.6 fold upregulated), asnA/asnB and, serA (12.0 fold upregulated) and gdhA (3.7 fold upregulated), did not result in growth attenuation, suggesting that biosynthesis using the enzymes encoded from these genes may represent the first choice for S. Enteritidis when growing in egg, but when absent, the bacterium could use alternative ways to obtain the amino acids. PMID:26945769

  10. High Productivity Implantation ''PARTIAL IMPLANT''

    SciTech Connect

    Hino, Masayoshi; Miyamoto, Naoki; Sakai, Shigeki; Matsumoto, Takao

    2008-11-03

    The patterned ion implantation 'PARTIAL IMPLANT' has been developed as a productivity improvement tool. The Partial Implant can form several different ion dose areas on the wafer surface by controlling the speed of wafer moving and the stepwise rotation of twist axis. The Partial Implant system contains two implant methods. One method is 'DIVIDE PARTIAL IMPLANT', that is aimed at reducing the consumption of the wafer. The Divide Partial Implant evenly divides dose area on one wafer surface into two or three different dose part. Any dose can be selected in each area. So the consumption of the wafer for experimental implantation can be reduced. The second method is 'RING PARTIAL IMPLANT' that is aimed at improving yield by correcting electrical characteristic of devices. The Ring Partial Implant can form concentric ion dose areas. The dose of wafer external area can be selected to be within plus or minus 30% of dose of wafer central area. So the electrical characteristic of devices can be corrected by controlling dose at edge side on the wafer.

  11. Computer copings for partial coverage.

    PubMed

    Denissen, H; van der Zel, J; Reisig, J; Vlaar, S; de Ruiter, W; van Waas, R

    1999-04-01

    Partial coverage posterior tooth preparations are very complex surfaces for computer surface digitization, computer design, and manufacture of ceramic copings. The aim of this study was therefore to determine whether the Computer Integrated Crown Reconstruction (Cicero) system was compatible with a proposed partial coverage preparation design and capable of producing ceramic copings. Posterior teeth were prepared for partial coverage copings with deep gingival chamfers in the proximal boxes and around the functional cusps (buccal of mandibular and lingual of maxillary posterior teeth). The nonfunctional cusps (lingual of mandibular and buccal of maxillary posterior teeth) were prepared with broad bevels following the inclined occlusal plane pattern. Optical impressions were taken of stone dies by means of a fast laser-line scanning method that measured the three-dimensional geometry of the partial coverage preparation. Computers digitized the images, and designed and produced the ceramic copings. The Cicero system digitized the partial coverage preparation surfaces precisely with a minor coefficient of variance of 0.2%. The accuracy of the surface digitization, the design, and the computer aided milling showed that the system was capable of producing partial coverage copings with a mean marginal gap of 74 microns. This value was obtained before optimizing the marginal fit by means of porcelain veneering. In summary, Cicero computer technology, i.e., surface digitization, coping design, and manufacture, was compatible with the described partial coverage preparations for posterior teeth. PMID:11351490

  12. Coherent-mode decomposition of partially polarized, partially coherent sources

    NASA Astrophysics Data System (ADS)

    Gori, Franco; Santarsiero, Massimo; Simon, Raja; Piquero, Gemma; Borghi, Riccardo; Guattari, Giorgio

    2003-01-01

    It is shown that any partially polarized, partially coherent source can be expressed in terms of a suitable superposition of transverse coherent modes with orthogonal polarization states. Such modes are determined through the solution of a system of two coupled integral equations. An example, for which the modal decomposition is obtained in closed form in terms of fully linearly polarized Hermite Gaussian modes, is given.

  13. Coherent-mode decomposition of partially polarized, partially coherent sources.

    PubMed

    Gori, Franco; Santarsiero, Massimo; Simon, Raja; Piquero, Gemma; Borghi, Riccardo; Guattari, Giorgio

    2003-01-01

    It is shown that any partially polarized, partially coherent source can be expressed in terms of a suitable superposition of transverse coherent modes with orthogonal polarization states. Such modes are determined through the solution of a system of two coupled integral equations. An example, for which the modal decomposition is obtained in closed form in terms of fully linearly polarized Hermite Gaussian modes, is given. PMID:12542320

  14. Partial heterologous protection by low pathogenic H9N2 virus against natural H9N2-PB1 gene reassortant highly pathogenic H5N1 virus in chickens.

    PubMed

    Dash, Sandeep Kumar; Kumar, Manoj; Kataria, Jag Mohan; Nagarajan, Shanmugasundaram; Tosh, Chakradhar; Murugkar, Harshad V; Kulkarni, Diwakar D

    2016-06-01

    Low pathogenic avian influenza H9N2 and highly pathogenic avian influenza H5N1 viruses continue to co-circulate in chickens. Prior infection with low pathogenic avian influenza can modulate the outcome of H5N1 infection. In India, low pathogenic H9N2 and highly pathogenic H5N1 avian influenza viruses are co-circulating in poultry. Herein, by using chickens with prior infection of A/chicken/India/04TI05/2012 (H9N2) virus we explored the outcome of infection with H5N1 virus A/turkey/India/10CA03/2012 natural PB1 gene reassortant from H9N2. Four groups (E1-E4) of SPF chickens (n = 6) prior inoculated with 10(6) EID50 of H9N2 virus were challenged with 10(6) EID50 of H5N1 natural reassortant (PB1-H9N2) virus at days 1 (group E1); 3 (group E2); 7 (group E3) and 14 (group E4) post H9N2 inoculation. The survival percentage in groups E1-E4 was 0, 100, 66.6 and 50%, respectively. Virus shedding periods for groups E1-E4 were 3, 4, 7 and 9 days, respectively post H5N1 challenge. Birds of group E1 and E2 were shedding both H9N2 and H5N1 viruses and mean viral RNA copy number was higher in oropharyngeal swabs than cloacal swabs. In group, E3 and E4 birds excreted only H5N1 virus and mean viral RNA copy number was higher in most cloacal swabs than oral swabs. These results indicate that prior infection with H9N2 virus could protect from lethal challenge of reassortant H5N1 virus as early as with three days prior H9N2 inoculation and protection decreased in groups E3 and E4 as time elapsed. However, prior infection with H9N2 did not prevent infection with H5N1 virus and birds continue to excrete virus in oropharyngeal and cloacal swabs. Amino acid substitution K368E was found in HA gene of excreted H5N1 virus of group E3. Hence, concurrent infection can also cause emergence of viruses with mutations leading to virus evolution. The results of this study are important for the surveillance and epidemiological data analysis where both H9N2 and H5N1 viruses are co-circulating. PMID

  15. Clines with partial panmixia across a geographical barrier.

    PubMed

    Nagylaki, Thomas

    2016-06-01

    In geographically structured populations, partial global panmixia can be regarded as the limiting case of long-distance migration. In the presence of a geographical barrier, an exact, discrete model for the evolution of the gene frequencies at a multiallelic locus under viability selection, local adult migration, and partial panmixia is formulated. For slow evolution, from this model a spatially unidimensional continuous approximation (a system of integro-partial differential equations with discontinuities at the barrier) is derived. For (i) the step-environment, (ii) homogeneous, isotropic migration on the entire line, and (iii) two alleles without dominance, an explicit solution for the unique polymorphic equilibrium is found. In most natural limiting cases, asymptotic expressions are obtained for the gene frequencies on either side of the barrier. PMID:26808902

  16. Overexpression of a partial fragment of the salt-responsive gene OsNUC1 enhances salt adaptation in transgenic Arabidopsis thaliana and rice (Oryza sativa L.) during salt stress.

    PubMed

    Sripinyowanich, Siriporn; Chamnanmanoontham, Nontalee; Udomchalothorn, Thanikarn; Maneeprasopsuk, Somporn; Santawee, Panudda; Buaboocha, Teerapong; Qu, Li-Jia; Gu, Hongya; Chadchawan, Supachitra

    2013-12-01

    The rice (Oryza sativa L.) nucleolin gene, OsNUC1, transcripts were expressed in rice leaves, flowers, seeds and roots but differentially expressed within and between two pairs of salt-sensitive and salt-resistant rice lines when subjected to salt stress. Salt-resistant lines exhibited higher OsNUC1 transcript expression levels than salt-sensitive lines during 0.5% (w/v) NaCl salt stress for 6d. Two sizes of OsNUC1 full-length cDNA were found in the rice genome database and northern blot analysis confirmed their existence in rice tissues. The longer transcript (OsNUC1-L) putatively encodes for a protein with a serine rich N-terminal, RNA recognition motifs in the central domain and a glycine- and arginine-rich repeat in the C-terminal domain, while the shorter one (OsNUC1-S) putatively encodes for the similar protein without the N-terminus. Without salt stress, OsNUC1-L expressing Arabidopsis thaliana Atnuc1-L1 plants displayed a substantial but incomplete revertant phenotype, whereas OsNUC1-S expression only induced a weak effect. However, under 0.5% (w/v) NaCl salt stress they displayed a higher relative growth rate, longer root length and a lower H2O2 level than the wild type plants, suggesting a higher salt resistance. Moreover, they displayed elevated AtSOS1 and AtP5CS1 transcript levels. We propose that OsNUC1-S plays an important role in salt resistance during salt stress, a new role for nucleolin in plants. PMID:24157209

  17. Molecular Identification of Sibling Species of Sclerodermus (Hymenoptera: Bethylidae) That Parasitize Buprestid and Cerambycid Beetles by Using Partial Sequences of Mitochondrial DNA Cytochrome Oxidase Subunit 1 and 28S Ribosomal RNA Gene

    PubMed Central

    Jiang, Yuan; Yang, Zhongqi; Wang, Xiaoyi; Hou, Yuxia

    2015-01-01

    The species belonging to Sclerodermus (Hymenoptera: Bethylidae) are currently the most important insect natural enemies of wood borer pests, mainly buprestid and cerambycid beetles, in China. However, some sibling species of this genus are very difficult to distinguish because of their similar morphological features. To address this issue, we conducted phylogenetic and genetic analyses of cytochrome oxidase subunit I (COI) and 28S RNA gene sequences from eight species of Sclerodermus reared from different wood borer pests. The eight sibling species were as follows: S. guani Xiao et Wu, S. sichuanensis Xiao, S. pupariae Yang et Yao, and Sclerodermus spp. (Nos. 1–5). A 594-bp fragment of COI and 750-bp fragment of 28S were subsequently sequenced. For COI, the G-C content was found to be low in all the species, averaging to about 30.0%. Sequence divergences (Kimura-2-parameter distances) between congeneric species averaged to 4.5%, and intraspecific divergences averaged to about 0.09%. Further, the maximum sequence divergences between congeneric species and Sclerodermus sp. (No. 5) averaged to about 16.5%. All 136 samples analyzed were included in six reciprocally monophyletic clades in the COI neighbor-joining (NJ) tree. The NJ tree inferred from the 28S rRNA sequence yielded almost identical results, but the samples from S. guani, S. sichuanensis, S. pupariae, and Sclerodermus spp. (Nos. 1–4) clustered together and only Sclerodermus sp. (No. 5) clustered separately. Our findings indicate that the standard barcode region of COI can be efficiently used to distinguish morphologically similar Sclerodermus species. Further, we speculate that Sclerodermus sp. (No. 5) might be a new species of Sclerodermus. PMID:25782000

  18. Transcriptional inhibition of p21WAF1/CIP1 gene (CDKN1) expression by survivin is at least partially p53-dependent: evidence for survivin acting as a transcription factor or co-factor.

    PubMed

    Tang, Lei; Ling, Xiang; Liu, Wensheng; Das, Gokul M; Li, Fengzhi

    2012-05-01

    Growing evidence suggests a role for the antiapoptotic protein survivin in promotion of cancer cell G1/S transition and proliferation. However, the underlying mechanism is unclear. Further, although upregulation of p21(WAF1/CIP1) by p53 plays an important role in p53-mediated cell G1 arrests in response to various distresses, it is unknown whether survivin plays a role in the regulation of p21(WAF1/CIP1) expression. Here, we report that exogenous expression of survivin in p53-wild type MCF-7 breast cancer cells inhibits the expression of p21(WAF1/CIP1) protein, mRNA and promoter activity, while the survivin C84A mutant and antisense failed to do so. Cotransfection experiments in the p53 mutant H1650 lung cancer cell line showed that survivin neutralizes p53-induced p21(WAF1/CIP1) expression and promoter activity. Importantly, genetically silencing of endogenous survivin using lentiviral survivin shRNA also enhances endogenous p21 in p53 wild type cancer cells, suggesting the physiological relevance of the fining. We further demonstrated that both p53 and survivin interacts on the two p53-binding sites in the p21(WAF1/CIP1) promoter (-2313 to -2212; -1452 to -1310), and survivin physically interacts with p53 in cancer cells. Together, we propose that survivin may act as a transcription factor or cofactor to interact with p53 on the p21(WAF1/CIP1) promoter leading to the inhibition of p21(WAF1/CIP1) expression at least in part by neutralizing p53-mediated transcriptional activation of the p21 gene. PMID:22503977

  19. Genes and Gene Therapy

    MedlinePlus

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

  20. 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 ...

  1. Transcriptional inhibition of p21{sup WAF1/CIP1} gene (CDKN1) expression by survivin is at least partially p53-dependent: Evidence for survivin acting as a transcription factor or co-factor

    SciTech Connect

    Tang, Lei; Ling, Xiang; Liu, Wensheng; Das, Gokul M.; Li, Fengzhi

    2012-05-04

    } expression at least in part by neutralizing p53-mediated transcriptional activation of the p21 gene.

  2. Laparoscopic total and partial nephrectomy.

    PubMed

    Lee, Benjamin R

    2002-01-01

    Laparoscopic radical nephrectomy has established its role as a standard of care for the management of renal neoplasms. Long term follow-up has demonstrated laparoscopic radical nephrectomy has shorter patient hospitalization and effective cancer control, with no significant difference in survival compared with open radical nephrectomy. For renal masses less than 4cm, partial nephrectomy is indicated for patients with a solitary kidney or who demonstrate impairment of contralateral renal function. The major technical issue for success of laparoscopic partial nephrectomy is bleeding control and several techniques have been developed to achieve better hemostatic control. Development of new laparoscopic techniques for partial nephrectomy can be divided into 2 categories: hilar control and warm ischemia vs. no hilar control. Development of a laparoscopic Satinsky clamp has achieved en bloc control of the renal hilum in order to allow cold knife excision of the mass, with laparoscopic repair of the collecting system, if needed. Combination of laparoscopic partial nephrectomy with ablative techniques has achieved successful excision of renal masses with adequate hemostasis without hilar clamping. Other techniques without hilar control have been investigated and included the use of a microwave tissue coagulator. In conclusion, laparoscopic radical nephrectomy for renal cell carcinoma has clearly demonstrated low morbidity and equivalent cancer control. The rates for local recurrences and metastatic spread are low and actuarial survival high. Furthermore, laparoscopic partial nephrectomy has demonstrated to be technically feasible, with low morbidity. With short term outcomes demonstrating laparoscopic partial nephrectomy as an efficacious procedure, the role of laparoscopic partial nephrectomy should continue to increase. PMID:15748397

  3. Complete characterization of partially coherent and partially polarized optical fields.

    PubMed

    Basso, Gabriel; Oliveira, Luimar; Vidal, Itamar

    2014-03-01

    We suggest a method to access the second-order, or two-point, Stokes parameters of a partially coherent and partially polarized Gaussian model optical field from an intensity interferometry experiment. Through a remarkably simple experimental arrangement, it is possible to measure the two-point and one-point Stokes parameters simultaneously, allowing the reconstruction of the coherence matrix and the polarization matrix, thus completely characterizing the optical field both statistically and locally on the observation plane. Developments, automation, and applications are pointed out. PMID:24690711

  4. Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation.

    PubMed

    Ha, Min Jin; Sun, Wei

    2014-09-01

    Motivated by the problem of construction of gene co-expression network, we propose a statistical framework for estimating high-dimensional partial correlation matrix by a three-step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non-zero entries of the partial correlation matrix by hypothesis testing. Finally we re-estimate the partial correlation coefficients at these non-zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein-protein interactions than the Graphic Lasso. PMID:24845967

  5. Multiple-subgenotype infections of Giardia intestinalis detected in Palestinian clinical cases using a subcloning approach.

    PubMed

    Hussein, Amjad I A; Yamaguchi, Tomohiro; Nakamoto, Kentaro; Iseki, Motohiro; Tokoro, Masaharu

    2009-09-01

    To evaluate the geographic distribution of Giardia intestinalis genotypes in Nablus, West Bank, Palestine, a genotyping study was performed using clinical fecal samples. Microscopic examination confirmed that 8 of 69 (11.6%) samples were G. intestinalis positive, and subsequent genotyping analyses targeting the small-subunit ribosomal RNA (18S rRNA) and glutamate dehydrogenase (GDH) genes revealed the G. intestinalis genotypes within the 8 samples. Of these 8 samples, 6 were clustered with assemblage A-II and the remaining 2 samples were clustered with assemblage B by 18S rRNA gene analysis; however, direct sequencing of the GDH gene segments from the latter 2 samples showed a mixed infection profile. To assess those samples, we employed a subcloning approach and successfully isolated 6 independent assemblage B subgenotypes. These partial GDH gene sequences (393 bp) had 15 single-nucleotide polymorphisms, all of which were synonymous transition substitutions at the third nucleotide position of codons. From the results, we concluded that the highly polymorphic gene loci such as GDH gene locus might provide us an opportunity to obtain a detailed molecular data even from the samples with multiple-subgenotype mixed infections. Therefore, subcloning approach is recommended in genotyping studies, especially in those conducted in giardiasis-endemic areas, where the repeated and cumulative infections could be commonly expected. PMID:19361570

  6. Distal Partial Trisomy 15q26 and Partial Monosomy 16p13.3 in a 36-Year-Old Male with Clinical Features of Both Chromosomal Abnormalities.

    PubMed

    Cox, Devin M; Butler, Merlin G

    2015-01-01

    We report a 36-year-old Caucasian male identified with distal partial trisomy 15q and partial monosomy 16p from an unbalanced chromosome translocation detected by microarray and FISH analysis. He had a history of developmental delay and intellectual disability, chronic anemia, tall and slender stature, thoracic scoliosis and lumbar lordosis, and dysmorphic features. The distal partial trisomy 15q included the insulin-like growth factor 1 receptor gene involved with growth, while genes in the distal partial monosomy 16p region are involved with alpha hemoglobin production, intellectual disability, dysmorphic features, and acromegaly. The chromosome derivative found in our patient contains genes known to play a role in his phenotype. PMID:25871641

  7. Landsliding in partially saturated materials

    USGS Publications Warehouse

    Godt, J.W.; Baum, R.L.; Lu, N.

    2009-01-01

    [1] Rainfall-induced landslides are pervasive in hillslope environments around the world and among the most costly and deadly natural hazards. However, capturing their occurrence with scientific instrumentation in a natural setting is extremely rare. The prevailing thinking on landslide initiation, particularly for those landslides that occur under intense precipitation, is that the failure surface is saturated and has positive pore-water pressures acting on it. Most analytic methods used for landslide hazard assessment are based on the above perception and assume that the failure surface is located beneath a water table. By monitoring the pore water and soil suction response to rainfall, we observed shallow landslide occurrence under partially saturated conditions for the first time in a natural setting. We show that the partially saturated shallow landslide at this site is predictable using measured soil suction and water content and a novel unified effective stress concept for partially saturated earth materials. Copyright 2009 by the American Geophysical Union.

  8. Partial integration raises antitrust concerns.

    PubMed

    Brock, T H; Kamoie, B E

    2000-11-01

    Recently, providers have begun to explore a new model of integrated delivery system, the partially integrated IDS. Typically, a partially integrated IDS is a joint venture, owned by a core group of providers that maintains complete financial and operational independence outside the joint venture. The IDS contracts with other providers to furnish services that the part-owners do not furnish. A partially integrated IDS raises antitrust concerns because the participating providers may be seen as competitors banding together to set prices jointly for healthcare services. Therefore, to minimize their antitrust exposure, providers that are considering this model should be careful to structure the IDS in accordance with the relevant Federal antitrust laws (i.e., Section 1 of the Sherman Act), taking into account the Federal antitrust agencies' various guidelines and enforcement policies. PMID:11688054

  9. Partial Priapism Treated with Pentoxifylline

    PubMed Central

    Cooper, Meghan A.; Carrion, Rafael E.; Yang, Christopher

    2015-01-01

    ABSTRACT Main findings: A 26-year-old man suffering from partial priapism was successfully treated with a regimen including pentoxifylline, a nonspecific phosphodiesterase inhibitor that is often used to conservatively treat Peyronie's disease. Case hypothesis: Partial priapism is an extremely rare urological condition that is characterized by thrombosis within the proximal segment of a single corpus cavernosum. There have only been 36 reported cases to date. Although several factors have been associated with this unusual disorder, such as trauma or bicycle riding, the etiology is still not completely understood. Treatment is usually conservative and consists of a non-steroidal anti-inflammatory and anti-thrombotic. Promising future implications: This case report supports the utilization of pentoxifylline in patients with partial priapism due to its anti-fibrogenic and anti-thrombotic properties. PMID:26401875

  10. Full and partial gauge fixing

    SciTech Connect

    Shirzad, A.

    2007-08-15

    Gauge fixing may be done in different ways. We show that using the chain structure to describe a constrained system enables us to use either a full gauge, in which all gauged degrees of freedom are determined, or a partial gauge, in which some first class constraints remain as subsidiary conditions to be imposed on the solutions of the equations of motion. We also show that the number of constants of motion depends on the level in a constraint chain in which the gauge fixing condition is imposed. The relativistic point particle, electromagnetism, and the Polyakov string are discussed as examples and full or partial gauges are distinguished.

  11. Partial pressure analysis of plasmas

    SciTech Connect

    Dylla, H.F.

    1984-11-01

    The application of partial pressure analysis for plasma diagnostic measurements is reviewed. A comparison is made between the techniques of plasma flux analysis and partial pressure analysis for mass spectrometry of plasmas. Emphasis is given to the application of quadrupole mass spectrometers (QMS). The interface problems associated with the coupling of a QMS to a plasma device are discussed including: differential-pumping requirements, electromagnetic interferences from the plasma environment, the detection of surface-active species, ion source interactions, and calibration procedures. Example measurements are presented from process monitoring of glow discharge plasmas which are useful for cleaning and conditioning vacuum vessels.

  12. PARTIAL RESISTANCE IN THE LINUM-MELAMPSORA HOST–PATHOGEN SYSTEM: DOES PARTIAL RESISTANCE MAKE THE RED QUEEN RUN SLOWER?

    PubMed Central

    Antonovics, Janis; Thrall, Peter H.; Burdon, Jeremy J.; Laine, Anna-Liisa

    2011-01-01

    Five levels of disease expression were scored in a cross-inoculation study of 120 host and 60 pathogen lines of wild flax Linum marginale and its rust fungus Melampsora lini sampled from six natural populations. Patterns of partial resistance showed clear evidence of gene-for-gene interactions, with particular levels of partial resistance occurring in specific host–pathogen combinations. Sympatric and putatively more highly coevolved host–pathogen combinations had a lower frequency of partial resistance types relative to allopatric combinations. Sympatric host–pathogen combinations also showed a lower diversity of resistance responses, but there was a trend toward a greater fraction of this variance being determined by pathogen-genotype × host-genotype interactions. In this system, there was no evidence that partial resistances slow host–pathogen coevolution. The analyses show that if variation is generated by among population host or pathogen dispersal, then coevolution occurs largely by pathogens overcoming the partial resistances that are generated. PMID:21029078

  13. Apparatus for generating partially coherent radiation

    DOEpatents

    Naulleau, Patrick P.

    2005-02-22

    Techniques for generating partially coherent radiation and particularly for converting effectively coherent radiation from a synchrotron to partially coherent EUV radiation suitable for projection lithography.

  14. Partial least squares Cox regression for genome-wide data.

    PubMed

    Nygård, Ståle; Borgan, Ornulf; Lingjaerde, Ole Christian; Størvold, Hege Leite

    2008-06-01

    Most methods for survival prediction from high-dimensional genomic data combine the Cox proportional hazards model with some technique of dimension reduction, such as partial least squares regression (PLS). Applying PLS to the Cox model is not entirely straightforward, and multiple approaches have been proposed. The method of Park etal. (Bioinformatics 18(Suppl. 1):S120-S127, 2002) uses a reformulation of the Cox likelihood to a Poisson type likelihood, thereby enabling estimation by iteratively reweighted partial least squares for generalized linear models. We propose a modification of the method of Park et al. (2002) such that estimates of the baseline hazard and the gene effects are obtained in separate steps. The resulting method has several advantages over the method of Park et al. (2002) and other existing Cox PLS approaches, as it allows for estimation of survival probabilities for new patients, enables a less memory-demanding estimation procedure, and allows for incorporation of lower-dimensional non-genomic variables like disease grade and tumor thickness. We also propose to combine our Cox PLS method with an initial gene selection step in which genes are ordered by their Cox score and only the highest-ranking k% of the genes are retained, obtaining a so-called supervised partial least squares regression method. In simulations, both the unsupervised and the supervised version outperform other Cox PLS methods. PMID:18188699

  15. Leadership in Partially Distributed Teams

    ERIC Educational Resources Information Center

    Plotnick, Linda

    2009-01-01

    Inter-organizational collaboration is becoming more common. When organizations collaborate they often do so in partially distributed teams (PDTs). A PDT is a hybrid team that has at least one collocated subteam and at least two subteams that are geographically distributed and communicate primarily through electronic media. While PDTs share many…

  16. Partially molten magma ocean model

    SciTech Connect

    Shirley, D.N.

    1983-02-15

    The properties of the lunar crust and upper mantle can be explained if the outer 300-400 km of the moon was initially only partially molten rather than fully molten. The top of the partially molten region contained about 20% melt and decreased to 0% at 300-400 km depth. Nuclei of anorthositic crust formed over localized bodies of magma segregated from the partial melt, then grew peripherally until they coverd the moon. Throughout most of its growth period the anorthosite crust floated on a layer of magma a few km thick. The thickness of this layer is regulated by the opposing forces of loss of material by fractional crystallization and addition of magma from the partial melt below. Concentrations of Sr, Eu, and Sm in pristine ferroan anorthosites are found to be consistent with this model, as are trends for the ferroan anorthosites and Mg-rich suites on a diagram of An in plagioclase vs. mg in mafics. Clustering of Eu, Sr, and mg values found among pristine ferroan anorthosites are predicted by this model.

  17. The partial-birth stratagem.

    PubMed

    1998-06-01

    In Wisconsin, physicians stopped performing abortions when a Federal District Court Judge refused to issue a temporary restraining order against the state's newly enacted "partial birth" abortion ban that was couched in such vague language it actually covered all abortions. While ostensibly attempting to ban late-term "intact dilation and extraction," the language of the law did not refer to that procedure or to late terms. Instead, it prohibited all abortions in which a physician "partially vaginally delivers a living child, causes the death of the partially delivered child with the intent to kill the child and then completes the delivery of the child." The law also defined "child" as "a human being from the time of fertilization" until birth. It is clear that this abortion ban is unconstitutional under Row v. Wade, and this unconstitutionality is compounded by the fact that the law allowed no exception to protect a woman's health, which is required by Roe for abortion bans after fetal viability. Wisconsin is only one of about 28 states that have enacted similar laws, and only two have restricted the ban to postviability abortions. Many of these laws have been struck down in court, and President Clinton has continued to veto the Federal partial-birth bill. The Wisconsin Judge acknowledged that opponents of the ban will likely prevail when the case is heard, but his action in denying the temporary injunction means that many women in Wisconsin will not receive timely medical care. The partial birth strategy is really only another anti-abortion strategy. PMID:12348556

  18. Wettability of partially suspended graphene.

    PubMed

    Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; Dujardin, Erik; Rahman, Atikur; Black, Charles T; Checco, Antonio

    2016-01-01

    The dependence of the wettability of graphene on the nature of the underlying substrate remains only partially understood. Here, we systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Further, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquid interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle. PMID:27072195

  19. Wettability of partially suspended graphene

    DOE PAGESBeta

    Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; Dujardin, Erik; Rahman, Atikur; Black, Charles T.; Checco, Antonio

    2016-04-13

    Dependence on the wettability of graphene on the nature of the underlying substrate remains only partially understood. We systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Moreover, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquidmore » interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle.« less

  20. Wettability of partially suspended graphene

    PubMed Central

    Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; Dujardin, Erik; Rahman, Atikur; Black, Charles T.; Checco, Antonio

    2016-01-01

    The dependence of the wettability of graphene on the nature of the underlying substrate remains only partially understood. Here, we systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Further, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquid interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle. PMID:27072195

  1. Partial hydatidiform mole: ultrasonographic features.

    PubMed

    Woo, J S; Hsu, C; Fung, L L; Ma, H K

    1983-05-01

    Four patients with partial hyatidiform mole managed at the Queen Mary Hospital, Hong Kong, are described. The diagnosis of blighted ovum or missed abortion was made on the sonographic findings prior to suction evacuation. The dominant features in these cases consisted of a relatively large central transonic area bearing the appearance of an empty gestational sac and surrounded by a thick rim of low-level placenta-like echoes; in contrast with the case of the blighted ovum, a well-defined echogenic sac wall is absent. In another 9 patients with molar pregnancy managed during the same period, the more typical 'snow-storm' vesicular appearance was present. It was concluded that the anembryonic appearance described should alert the sonologist and clinician to the possible diagnosis of partial hydatitiform mole. The evacuated material from the uterine cavity should be examined morphologically and if possible cytogenetically. PMID:6578773

  2. Wettability of partially suspended graphene

    NASA Astrophysics Data System (ADS)

    Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; Dujardin, Erik; Rahman, Atikur; Black, Charles T.; Checco, Antonio

    2016-04-01

    The dependence of the wettability of graphene on the nature of the underlying substrate remains only partially understood. Here, we systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Further, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquid interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle.

  3. Partial stabilization-based guidance.

    PubMed

    Shafiei, M H; Binazadeh, T

    2012-01-01

    A novel nonlinear missile guidance law against maneuvering targets is designed based on the principles of partial stability. It is demonstrated that in a real approach which is adopted with actual situations, each state of the guidance system must have a special behavior and asymptotic stability or exponential stability of all states is not realistic. Thus, a new guidance law is developed based on the partial stability theorem in such a way that the behaviors of states in the closed-loop system are in conformity with a real guidance scenario that leads to collision. The performance of the proposed guidance law in terms of interception time and control effort is compared with the sliding mode guidance law by means of numerical simulations. PMID:21963401

  4. Gene Cloning and mRNA Expression of Glutamate Dehydrogenase in the Liver, Brain, and Intestine of the Swamp Eel, Monopterus albus (Zuiew), Exposed to Freshwater, Terrestrial Conditions, Environmental Ammonia, or Salinity Stress

    PubMed Central

    Tok, Chia Y.; Chew, Shit F.; Ip, Yuen K.

    2011-01-01

    The swamp eel, Monopterus albus, is an obligatory air-breathing teleost which can undergo long period of emersion, has high environmental and tissue ammonia tolerance, and can survive in brackish water. We obtained a cDNA sequence of glutamate dehydrogenase (gdh), which consisted of a 133-bp 5′ UTR, a complete coding sequence region spanning 1629 bp and a 3′ UTR of approximately 717 bp, from the liver, intestine, and brain of M. albus. The translated Gdh amino acid sequence had 542 residues, and it formed a monophyletic clade with Bostrychus sinensis Gdh1a, Tetraodon nigroviridis Gdh1a, Chaenocephalus aceratus Gdh1a, Salmo salar Gdh1a1 and Gdh1a2, and O. mykiss Gdh1a. One day of exposure to terrestrial conditions or 75 mmol l−1 NH4Cl, but not to water at salinity 20, resulted in a significant increase in mRNA expression of gdh1a and Gdh amination activity in the liver of M. albus. However, exposure to brackish water, but not to terrestrial conditions or 75 mmol l−1 NH4Cl, led to a significant increase in the mRNA expression of gdh1a and Gdh amination activity in the intestine. By contrast, all the three experimental conditions had no significant effects on the mRNA expression of gdh1a in the brain of M. albus, despite a significant decrease in the Gdh amination activity in the brain of fish exposed to 75 mmol l−1 NH4Cl for 6 days. Our results indicate for the first time that the mRNA expression of gdh1a was differentially up-regulated in the liver and intestine of M. albus in response to ammonia toxicity and salinity stress, respectively. The increases in mRNA expression of gdh1a and Gdh amination activity would probably lead to an increase in glutamate production in support of increased glutamine synthesis for the purpose of ammonia detoxification or cell volume regulation under these two different environmental conditions. PMID:22319499

  5. Positive partial transpose from spectra

    SciTech Connect

    Hildebrand, Roland

    2007-11-15

    In this paper we solve the following problem. Let H{sub nm} be a Hilbert space of dimension nm, and let A be a positive semidefinite self-adjoint linear operator on H{sub nm}. Under which conditions on the spectrum has A a positive partial transpose (is PPT) with respect to any partition H{sub n} x H{sub m} of the space H{sub nm} as a tensor product of an n-dimensional and an m-dimensional Hilbert space? We show that the necessary and sufficient conditions can be expressed as a set of linear matrix inequalities (LMIs) on the eigenvalues of A.

  6. Partial coalescence of soap bubbles

    NASA Astrophysics Data System (ADS)

    Harris, Daniel M.; Pucci, Giuseppe; Bush, John W. M.

    2015-11-01

    We present the results of an experimental investigation of the merger of a soap bubble with a planar soap film. When gently deposited onto a horizontal film, a bubble may interact with the underlying film in such a way as to decrease in size, leaving behind a smaller daughter bubble with approximately half the radius of its progenitor. The process repeats up to three times, with each partial coalescence event occurring over a time scale comparable to the inertial-capillary time. Our results are compared to the recent numerical simulations of Martin and Blanchette and to the coalescence cascade of droplets on a fluid bath.

  7. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on...

  8. Variation in chromosome constitution of the Xiaoyan series partial amphiploids and its relations to stripe rust and stem rust resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the tertiary gene pool of wheat, tall wheatgrass Thinopyrum ponticum (2n = 10x = 70) is an excellent source of resistance genes against numerous wheat diseases. The creation of wheat-Th. ponticum partial amphiploids is an intermediate step for transferring the useful genes from Th. ponticum to w...

  9. A partially duplicated discoid lateral meniscus.

    PubMed

    Kim, S J; Lee, Y T; Choi, C H; Kim, D W

    1998-01-01

    Partially duplicated discoid lateral meniscus has not been previously reported. We present a case of a partially duplicated discoid lateral meniscus with a peripheral tear of the meniscus and a concomitant cartilage lesion of the lateral femoral condyle. PMID:9681547

  10. Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

    PubMed Central

    Navarro-Costa, Paulo; Pereira, Luísa; Alves, Cíntia; Gusmão, Leonor; Proença, Carmen; Marques-Vidal, Pedro; Rocha, Tiago; Correia, Sónia C; Jorge, Sónia; Neves, António; Soares, Ana P; Nunes, Joaquim; Calhaz-Jorge, Carlos; Amorim, António; Plancha, Carlos E; Gonçalves, João

    2007-01-01

    Background The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility. Results The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles. Conclusion Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator. PMID:17903263

  11. Partial coalescence of soap bubbles

    NASA Astrophysics Data System (ADS)

    Pucci, G.; Harris, D. M.; Bush, J. W. M.

    2015-06-01

    We present the results of an experimental investigation of the merger of a soap bubble with a planar soap film. When gently deposited onto a horizontal film, a bubble may interact with the underlying film in such a way as to decrease in size, leaving behind a smaller daughter bubble with approximately half the radius of its progenitor. The process repeats up to three times, with each partial coalescence event occurring over a time scale comparable to the inertial-capillary time. Our results are compared to the recent numerical simulations of Martin and Blanchette ["Simulations of surfactant effects on the dynamics of coalescing drops and bubbles," Phys. Fluids 27, 012103 (2015)] and to the coalescence cascade of droplets on a fluid bath.

  12. Partial Return Yoke for MICE

    SciTech Connect

    Witte H.; Plate, S

    2013-05-03

    The international Muon Ionization Cooling Experiment (MICE) is a large scale experiment which is presently assembled at the Rutherford Appleton Laboratory in Didcot, UK. The purpose of MICE is to demonstrate the concept of ionization cooling experimentally. Ionization cooling is an important accelerator concept which will be essential for future HEP experiments such as a potential Muon Collider or a Neutrino Factory. The MICE experiment will house up to 18 superconducting solenoids, all of which produce a substantial amount of magnetic flux. Recently it was realized that this magnetic flux leads to a considerable stray magnetic field in the MICE hall. This is a concern as technical equipment in the MICE hall may may be compromised by this. In July 2012 a concept called partial return yoke was presented to the MICE community, which reduces the stray field in the MICE hall to a safe level. This report summarizes the general concept, engineering considerations and the expected shielding performance.

  13. Partially coherent lensfree tomographic microscopy⋄

    PubMed Central

    Isikman, Serhan O.; Bishara, Waheb; Ozcan, Aydogan

    2012-01-01

    Optical sectioning of biological specimens provides detailed volumetric information regarding their internal structure. To provide a complementary approach to existing three-dimensional (3D) microscopy modalities, we have recently demonstrated lensfree optical tomography that offers high-throughput imaging within a compact and simple platform. In this approach, in-line holograms of objects at different angles of partially coherent illumination are recorded using a digital sensor-array, which enables computing pixel super-resolved tomographic images of the specimen. This imaging modality, which forms the focus of this review, offers micrometer-scale 3D resolution over large imaging volumes of, for example, 10–15 mm3, and can be assembled in light weight and compact architectures. Therefore, lensfree optical tomography might be particularly useful for lab-on-a-chip applications as well as for microscopy needs in resource-limited settings. PMID:22193016

  14. Otto Stern, the Gdh Sum Rule and Various Spin Crises

    NASA Astrophysics Data System (ADS)

    Drechsel, D.

    2001-02-01

    The history of spin and anomalous magnetic moment is full of puzzles and "crises" from the first observations in the 1920's to the present day. The Gerasimov-Drell-Hearn sum rule connects the anomalous magnetic moment with the helicity dependent cross section for photoproduction, and as such checks the internal consistency of our understanding of the nucleon spin structure. Various generalizations of the sum rule have been proposed for the case of virtual photons, thus interpolating from the real photon point to deep inelastic scattering. A series of recent and newly proposed experiments with beam and target/recoil polarization will study this transition between the coherent spin-dependent response and the incoherent response of the partons in the scaling region.

  15. GDH Integral on the Proton from Cross Section Differences

    SciTech Connect

    Alexander Skabelin

    2002-02-01

    We studied the inclusive reaction {rvec e} {rvec p} {yields} e{prime}X with a 2.5 GeV and a 4.2 GeV incident beam of polarized electrons. The virtual photon four momentum squared, Q{sup 2}, varied from 0.2 GeV{sup 2}/c{sup 2} to 1 GeV{sup 2}/c{sup 2} and the center of mass total energy W ranged up to 2 GeV. The measurement was performed at the CEBAF Large Acceptance Spectrometer (CLAS) of the Thomas Jefferson National Accelerator Facility during the Fall of 1998. A cryogenic NH{sub 3} target was used as a source of protons polarized in the direction of the incident electron beam. For the first time, proton spin structure functions were studied with precision in the resonance region. The data indicate that a dramatic change in the spin structure occurs between the deep inelastic high Q{sup 2} region and the region of low Q{sup 2} where photons become nearly real.

  16. SOX genes: architects of development.

    PubMed Central

    Prior, H. M.; Walter, M. A.

    1996-01-01

    Development in higher organisms involves complex genetic regulation at the molecular level. The emerging picture of development control includes several families of master regulatory genes which can affect the expression of down-stream target genes in developmental cascade pathways. One new family of such development regulators is the SOX gene family. The SOX genes are named for a shared motif called the SRY box a region homologous to the DNA-binding domain of SRY, the mammalian sex determining gene. Like SRY, SOX genes play important roles in chordate development. At least a dozen human SOX genes have been identified and partially characterized (Tables 1 and 2). Mutations in SOX9 have recently been linked to campomelic dysplasia and autosomal sex reversal, and other SOX genes may also be associated with human disease. Images FIG. 1 FIG. 2 PMID:8827711

  17. Temperature- and nitrogen source-dependent regulation of GlnR target genes in Listeria monocytogenes.

    PubMed

    Kaspar, Daniela; Auer, Franziska; Schardt, Jakob; Schindele, Franziska; Ospina, Alberto; Held, Claudia; Ehrenreich, Armin; Scherer, Siegfried; Müller-Herbst, Stefanie

    2014-06-01

    The ubiquitous pathogen Listeria monocytogenes lives either saprophytically in the environment or within cells in a vertebrate host, thus adapting its lifestyle to its ecological niche. Growth experiments at 24 and 37 °C (environmental and host temperature) with ammonium or glutamine as nitrogen sources revealed that ammonium is the preferred nitrogen source of L. monocytogenes. Reduced growth on glutamine is more obvious at 24 °C. Global transcriptional microarray analyses showed that the most striking difference in temperature-dependent transcription was observed for central nitrogen metabolism genes, glnR (glutamine synthetase repressor GlnR), glnA (glutamine synthetase GlnA), amtB (ammonium transporter AmtB), glnK (PII regulatory protein GlnK), and gdh (glutamate dehydrogenase) when cells were grown on glutamine. When grown on ammonium, both at 24 and 37 °C, the transcriptional level of these genes resembles that of cells grown with glutamine at 37 °C. Electrophoretic mobility shift assay studies and qPCR analyses in the wild-type L. monocytogenes and the deletion mutant L. monocytogenes ∆glnR revealed that the transcriptional regulator GlnR is directly involved in temperature- and nitrogen source-dependent regulation of the respective genes. Glutamine, a metabolite known to influence GlnR activity, seems unlikely to be the (sole) intracellular signal mediating this temperature-and nitrogen source-dependent metabolic adaptation. PMID:24801548

  18. A role for partial endothelial-mesenchymal transitions in angiogenesis?

    PubMed

    Welch-Reardon, Katrina M; Wu, Nan; Hughes, Christopher C W

    2015-02-01

    The contribution of epithelial-to-mesenchymal transitions (EMT) in both developmental and pathological conditions has been widely recognized and studied. In a parallel process, governed by a similar set of signaling and transcription factors, endothelial-to-mesenchymal transitions (EndoMT) contribute to heart valve formation and the generation of cancer-associated fibroblasts. During angiogenic sprouting, endothelial cells express many of the same genes and break down basement membrane; however, they retain intercellular junctions and migrate as a connected train of cells rather than as individual cells. This has been termed a partial endothelial-to-mesenchymal transition. A key regulatory check-point determines whether cells undergo a full or a partial epithelial-to-mesenchymal transitions/endothelial-to-mesenchymal transition; however, very little is known about how this switch is controlled. Here we discuss these developmental/pathological pathways, with a particular focus on their role in vascular biology. PMID:25425619

  19. A role for partial endothelial-mesenchymal transitions in angiogenesis?

    PubMed Central

    Welch-Reardon, Katrina M.; Wu, Nan; Hughes, Christopher C.W.

    2016-01-01

    The contribution of epithelial-to-mesenchymal transitions (EMT) in both developmental and pathological conditions has been widely recognized and studied. In a parallel process, governed by a similar set of signaling and transcription factors, endothelial-to-mesenchymal transitions (EndoMT) contribute to heart valve formation and the generation of cancer-associated-fibroblasts. During angiogenic sprouting endothelial cells express many of the same genes and break down basement membrane, however they retain intercellular junctions and migrate as a connected “train” of cells rather than as individual cells. This has been termed a partial EndoMT. A key regulatory check-point determines whether cells undergo a full or a partial EMT/EndoMT, however, very little is known about how this switch is controlled. Here we discuss these developmental/pathologic pathways, with a particular focus on their role in vascular biology. PMID:25425619

  20. Partial ADAMTS13 deficiency in atypical hemolytic uremic syndrome

    PubMed Central

    Feng, Shuju; Eyler, Stephen J.; Zhang, Yuzhou; Maga, Tara; Nester, Carla M.; Kroll, Michael H.

    2013-01-01

    Complement dysregulation leads to atypical hemolytic uremic syndrome (aHUS), while ADAMTS13 deficiency causes thrombotic thrombocytopenic purpura. We investigated whether genetic variations in the ADAMTS13 gene partially explain the reduced activity known to occur in some patients with aHUS. We measured complement activity and ADAMTS13 function, and completed mutation screening of multiple complement genes and ADAMTS13 in a large cohort of aHUS patients. In over 50% of patients we identified complement gene mutations. Surprisingly, 80% of patients also carried at least 1 nonsynonymous change in ADAMTS13, and in 38% of patients, multiple ADAMTS13 variations were found. Six of the 9 amino acid substitutions in ADAMTS13 were common single nucleotide polymorphisms; however, 3 variants—A747V, V832M, and R1096H— were rare, with minor allele frequencies of 0.0094%, 0.5%, and 0.32%, respectively. Reduced complement and ADAMTS13 activity (<60% of normal activity) were found in over 60% and 50% of patients, respectively. We concluded that partial ADAMTS13 deficiency is a common finding in aHUS patients and that genetic screening and functional tests of ADAMTS13 should be considered in these patients. PMID:23847193

  1. Genes and gene regulation

    SciTech Connect

    MacLean, N.

    1988-01-01

    Genetics has long been a central topic for biologists, and recent progress has captured the public imagination as well. This book addresses questions that are at the leading edge of this continually advancing discipline. In tune with the increasing emphasis on molecular biology and genetic engineering, this text emphasizes the molecular aspects of gene expression, and the evolution of gene sequence organization and control. It reviews the genetic material of viruses, bacteria, and of higher organisms. Cells and organisms are compared in terms of gene numbers, their arrangements within a cell, and the control mechanisms which regulate the activity of genes.

  2. Channeled partial Mueller matrix polarimetry

    NASA Astrophysics Data System (ADS)

    Alenin, Andrey S.; Tyo, J. S.

    2015-09-01

    In prior work,1,2 we introduced methods to treat channeled systems in a way that is similar to Data Reduction Method (DRM), by focusing attention on the Fourier content of the measurement conditions. Introduction of Q enabled us to more readily extract the performance of the system and thereby optimize it to obtain reconstruction with the least noise. The analysis tools developed for that exercise can be expanded to be applicable to partial Mueller Matrix Polarimeters (pMMPs), which were a topic of prior discussion as well. In this treatment, we combine the principles involved in both of those research trajectories and identify a set of channeled pMMP families. As a result, the measurement structure of such systems is completely known and the design of a channeled pMMP intended for any given task becomes a search over a finite set of possibilities, with the additional channel rotation allowing for a more desirable Mueller element mixing.

  3. GLSMs for partial flag manifolds

    NASA Astrophysics Data System (ADS)

    Donagi, Ron; Sharpe, Eric

    2008-12-01

    In this paper we outline some aspects of nonabelian gauged linear sigma models. First, we review how partial flag manifolds (generalizing Grassmannians) are described physically by nonabelian gauged linear sigma models, paying attention to realizations of tangent bundles and other aspects pertinent to (0, 2) models. Second, we review constructions of Calabi-Yau complete intersections within such flag manifolds, and properties of the gauged linear sigma models. We discuss a number of examples of nonabelian GLSMs in which the Kähler phases are not birational, and in which at least one phase is realized in some fashion other than as a complete intersection, extending previous work of Hori-Tong. We also review an example of an abelian GLSM exhibiting the same phenomenon. We tentatively identify the mathematical relationship between such non-birational phases, as examples of Kuznetsov's homological projective duality. Finally, we discuss linear sigma model moduli spaces in these gauged linear sigma models. We argue that the moduli spaces being realized physically by these GLSMs are precisely Quot and hyperquot schemes, as one would expect mathematically.

  4. Quantum states with strong positive partial transpose

    SciTech Connect

    Chruscinski, Dariusz; Jurkowski, Jacek; Kossakowski, Andrzej

    2008-02-15

    We construct a large class of bipartite M x N quantum states which defines a proper subset of states with positive partial transposes (PPTs). Any state from this class has PPT but the positivity of its partial transposition is recognized with respect to canonical factorization of the original density operator. We propose to call elements from this class states with strong positive partial transposes (SPPTs). We conjecture that all SPPT states are separable.

  5. 20% PARTIAL SIBERIAN SNAKE IN THE AGS.

    SciTech Connect

    Huang, H; Bai, M; Brown, K A; Glenn, W; Luccio, A U; Mackay, W W; Montag, C; Ptitsyn, V; Roser, T; Tsoupas, N; Zeno, K; Ranjbar, V; Spinka, H; Underwood, D

    2002-11-06

    An 11.4% partial Siberian snake was used to successfully accelerate polarized proton through a strong intrinsic depolarizing spin resonance in the AGS. No noticeable depolarization was observed. This opens up the possibility of using a 20% to 30% partial Siberian snake in the AGS to overcome all weak and strong depolarizing spin resonances. Some design and operation issues of the new partial Siberian snake are discussed.

  6. Partial sequence analysis of 130 randomly selected maize cDNA clones.

    PubMed Central

    Keith, C S; Hoang, D O; Barrett, B M; Feigelman, B; Nelson, M C; Thai, H; Baysdorfer, C

    1993-01-01

    As part of a project to identify novel maize (Zea mays L. cv B73) genes functionally, we have partially sequenced 130 randomly selected clones from a maize leaf cDNA library. Data base comparisons revealed seven previously sequenced maize cDNAs and 18 cDNAs with sequence similarity to related maize genes or to genes from other organisms. One hundred five cDNAs show little or no similarity to previously sequenced genes. Our results also establish the suitability of this library for large-scale sequencing in terms of its large insert size, proper insert orientation, and low duplication rate. PMID:8278499

  7. Partial Derivatives of the Lambert Problem

    NASA Technical Reports Server (NTRS)

    Arora, Nitin; Russell, Ryan P.; Strange, Nathan

    2014-01-01

    A procedure for deriving analytic partial derivatives of the Lambert problem is presented. Using the universal, cosine based Lambert formulation; first order partial derivatives of the velocities with respect to the positions and times are developed. Taking advantage of inherent symmetries and intermediate variables, the derivatives are expressed in a computationally efficient form. The added cost of computing these partials is found to be approximately 10% to approximately 60% of the Lambert compute cost. The availability of analytic partial derivatives increases optimization speed, efficiency and allows for trajectory optimization formulations that implicitly enforce continuity constraints via embedded Lambert problems.

  8. Partially entangled states bridge in quantum teleportation

    NASA Astrophysics Data System (ADS)

    Cai, Xiao-Fei; Yu, Xu-Tao; Shi, Li-Hui; Zhang, Zai-Chen

    2014-10-01

    The traditional method for information transfer in a quantum communication system using partially entangled state resource is quantum distillation or direct teleportation. In order to reduce the waiting time cost in hop-by-hop transmission and execute independently in each node, we propose a quantum bridging method with partially entangled states to teleport quantum states from source node to destination node. We also prove that the designed specific quantum bridging circuit is feasible for partially entangled states teleportation across multiple intermediate nodes. Compared to two traditional ways, our partially entanglement quantum bridging method uses simpler logic gates, has better security, and can be used in less quantum resource situation.

  9. 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 ...

  10. Partial oxidation of sewage sludge

    SciTech Connect

    McMahon, M.A.; Martin, M.C.; McKenzie, K.W.

    1993-07-27

    A process is described comprising: (1) splitting a stream of dewatered sewage sludge having a solids content in the range of about 17-40 wt.% into a first stream and a second stream; (2) drying the first stream of dewatered sewage sludge to produce a stream of dried sewage sludge having a solids content in the range of about 75-99 wt.%: (3) grinding the dried sewage sludge from (2) to a particle size so that 100 wt% passes through ASTM E11 Standard Sieve Designation 1.40 mm; (4) mixing about 2-8 parts by dry weight aqueous slurry of solid carbonaceous fuel having a solids content of about 50-70 wt. % with each part by weight of said second stream of dewatered sewage sludge from (1); (5) heating the solid carbonaceous fuel-sewage slurry from (4) to a temperature of about 140-212 F; and mixing together 3-9 parts by dry weight of the solid carbonaceous fuel-sewage sludge slurry from (4) with each part by weight of dried sewage sludge from (2) to produce a pumpable fuel slurry comprising sewage sludge and solid carbonaceous fuel and having a solids content in the range of about 45-70 wt. %; and (6) reacting the fuel slurry from (5) in the reaction zone of a partial oxidation gas generator at a temperature in the range of about 1800-3500 F and a pressure in the range of about 1-35 atmospheres, and in the presence of free-oxygen containing gas, thereby producing a hot raw effluent gas stream of synthesis gas, reducing gas or fuel gas; (7) cooling, cleaning and purifying said raw effluent gas stream to produce a stream of fuel gas; (8) burning the fuel gas from (7) with air in a combustor of a gas turbine, and passing the hot exhaust gas through an expansion turbine which drives an electric generator; and (9) passing the hot exhaust gas from (8) in indirect heat exchange with water to produce steam for use in drying said first stream of dewatered sewage sludge in (2) and/or for heating said solid carbonaceous fuel-sewage slurry is (5) by indirect heat exchange.

  11. Merging Partially Labelled Trees: Hardness and a Declarative Programming Solution.

    PubMed

    Labarre, Anthony; Verwer, Sicco

    2014-01-01

    Intraspecific studies often make use of haplotype networks instead of gene genealogies to represent the evolution of a set of genes. Cassens et al. proposed one such network reconstruction method, based on the global maximum parsimony principle, which was later recast by the first author of the present work as the problem of finding a minimum common supergraph of a set of t partially labelled trees. Although algorithms have been proposed for solving that problem on two graphs, the complexity of the general problem on trees remains unknown. In this paper, we show that the corresponding decision problem is NP-complete for t=3. We then propose a declarative programming approach to solving the problem to optimality in practice, as well as a heuristic approach, both based on the idpsystem, and assess the performance of both methods on randomly generated data. PMID:26355785

  12. Partial characterization of new adenoviruses found in lizards.

    PubMed

    Ball, Inna; Behncke, Helge; Schmidt, Volker; Geflügel, F T A; Papp, Tibor; Stöhr, Anke C; Marschang, Rachel E

    2014-06-01

    In the years 2011-2012, a consensus nested polymerase chain reaction was used for the detection of adenovirus (AdV) infection in reptiles. During this screening, three new AdVs were detected. One of these viruses was detected in three lizards from a group of green striped tree dragons (Japalura splendida). Another was detected in a green anole (Anolis carolinensis). A third virus was detected in a Jackson's chameleon (Chamaeleo jacksonii). Analysis of a portion of the DNA-dependent DNA polymerase genes of each of these viruses revealed that they all were different from one another and from all previously described reptilian AdVs. Phylogenetic analysis of the partial DNA polymerase gene sequence showed that all newly detected viruses clustered within the genus Atadenovirus. This is the first description of AdVs in these lizard species. PMID:25000689

  13. Nested hierarchical controller with partial autonomy

    NASA Technical Reports Server (NTRS)

    Meystel, A.

    1987-01-01

    The problem of computer architecture for intelligent robots with partial autonomy is addressed. A robot with partial autonomy is considered a degenerated case of a fully autonomous robot. Thus, the problem of man-machine communication is formulated, and the conditions are determined for generating a language for such a communication. The duties of the master are determined.

  14. 47 CFR 5.69 - Partial grants.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Partial grants. 5.69 Section 5.69...) Applications and Licenses § 5.69 Partial grants. In cases in which the Commission grants an application in part... interference that may result to a station if designated application or applications are subsequently...

  15. 47 CFR 5.69 - Partial grants.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Partial grants. 5.69 Section 5.69...) Applications and Licenses § 5.69 Partial grants. In cases in which the Commission grants an application in part... interference that may result to a station if designated application or applications are subsequently...

  16. Evaluating Models for Partially Clustered Designs

    ERIC Educational Resources Information Center

    Baldwin, Scott A.; Bauer, Daniel J.; Stice, Eric; Rohde, Paul

    2011-01-01

    Partially clustered designs, where clustering occurs in some conditions and not others, are common in psychology, particularly in prevention and intervention trials. This article reports results from a simulation comparing 5 approaches to analyzing partially clustered data, including Type I errors, parameter bias, efficiency, and power. Results…

  17. A Primer on Partial Correlation Coefficients.

    ERIC Educational Resources Information Center

    Waliczek, Tina M.

    Part and partial correlation coefficients are used to measure the strength of a relationship between a dependent variable and an independent variable while controlling for one or more other variables. The present paper discusses the uses and limitations of partial correlations and presents a small heuristic data set to illustrate the discussion.…

  18. Exploring Partial Order of European Countries

    ERIC Educational Resources Information Center

    Annoni, Paola; Bruggemann, Rainer

    2009-01-01

    Partial Order Theory has been recently more and more employed in applied science to overcome the intrinsic disadvantage hidden in aggregation, if a multiple attribute system is available. Despite its numerous positive features, there are many practical cases where the interpretation of the partial order can be rather troublesome. In these cases…

  19. Removable partial overdentures for the irradiated patient

    SciTech Connect

    Rosenberg, S.W. )

    1990-10-01

    Patients who have received radiotherapy to the head and neck area must avoid dental extractions and seek simplicity in treatment and home care follow-up. For partially edentulous patients, removable partial overdenture therapy can fulfill these goals while maintaining the high level of function and aesthetics desired by patients.11 references.

  20. On the partial/line{partial} -Lemma and Bott-Chern cohomology

    NASA Astrophysics Data System (ADS)

    Angella, Daniele; Tomassini, Adriano

    2013-04-01

    On a compact complex manifold $X$, we prove a Fr\\"olicher-type inequality for Bott-Chern cohomology and we show that the equality holds if and only if $X$ satisfies the $\\partial\\overline{\\partial}$-Lemma.

  1. Kinetics of a Fast Moving Partial Dislocation

    NASA Astrophysics Data System (ADS)

    Daphalapurkar, Nitin; Ramesh, K. T.

    2013-03-01

    Plastic deformation in materials under extreme stresses requires a kinetic description of moving dislocations. The velocities with which the partial dislocations can propagate under an applied stress has implications for plasticity at high strain rates, specifically, the rate of plastic deformation and the rate-sensitivity. In this work, we focus our attention on motion of a twinning partial dislocation in a face-centered cubic (FCC) material, Ni. We use molecular dynamics simulations to simulate the velocity of a propagating twinning partial dislocation and investigate the effect of applied shear stress. Results suggest a limiting value for the speeds of a propagating partial dislocation. The material speeds based on the nonlinear part (under high stresses) of the stress-strain curve are shown to have an influence on the velocity with which a partial dislocation can propagate. Predicted velocities from simulations will be related to observations from high rate impact experiments. Supported by Hopkins Extreme Materials Institute

  2. gltB gene and regulation of nitrogen metabolism by glutamine synthetase in Escherichia coli.

    PubMed Central

    Pahel, G; Zelenetz, A D; Tyler, B M

    1978-01-01

    A mutant (gltB) of Escherichia coli lacking glutamate synthase (GOGAT) was unable to utilize a wide variety of compounds as sole nitrogen source (e.g., arginine, proline, gamma-aminobutyrate, and glycine). Among revertants of these Asm- strains selected on one of these compounds (e.g., arginine, proline, or gamma-aminobutyrate) were those that produce glutamine synthetase (GS) constitutively (GlnC phenotype). These revertants had a pleiotropically restored ability to grow on compounds that are metabolized to glutamate. This suggested that the expression of the genes responsible for the metabolism of these nitrogen sources was regulated by GS. An examination of the regulation of proline oxidase confirmed this hypothesis. The differential sensitivities of GlnC and wild-type strains to low concentrations (0.1 mM) of the glutamine analog L-methionine-DL-sulfoximine supported the conclusion that the synthesis of a glutamine permease was also positively controlled by GS. During the course of this study we found that the reported position of the locus (gltB) for glutamate synthase is incorrect. We have relocated this gene to be 44% linked to the argG locus by P1 transduction. Further mapping has shown that the locus previously called aspB is in reality the gltB locus and that the "suppressor" of the aspB mutation (A. M. Reiner, J. Bacteriol. 97:1431-1436, 1969) is the locus for glutamate dehydrogenase (gdhA). PMID:22535

  3. Partially Observed Mixtures of IRT Models: An Extension of the Generalized Partial-Credit Model

    ERIC Educational Resources Information Center

    Von Davier, Matthias; Yamamoto, Kentaro

    2004-01-01

    The generalized partial-credit model (GPCM) is used frequently in educational testing and in large-scale assessments for analyzing polytomous data. Special cases of the generalized partial-credit model are the partial-credit model--or Rasch model for ordinal data--and the two parameter logistic (2PL) model. This article extends the GPCM to the…

  4. Circulant states with positive partial transpose

    SciTech Connect

    Chruscinski, Dariusz; Kossakowski, Andrzej

    2007-09-15

    We construct a large class of quantum dxd states which are positive under partial transposition (so called PPT states). The construction is based on certain direct sum decomposition of the total Hilbert space displaying characteristic circular structure - that is why we call them circulant states. It turns out that partial transposition maps any such decomposition into another one and hence both original density matrix and its partially transposed partner share similar cyclic properties. This class contains many well-known examples of PPT states from the literature and gives rise to a huge family of completely new states.

  5. Partially coherent contrast-transfer-function approximation.

    PubMed

    Nesterets, Yakov I; Gureyev, Timur E

    2016-04-01

    The contrast-transfer-function (CTF) approximation, widely used in various phase-contrast imaging techniques, is revisited. CTF validity conditions are extended to a wide class of strongly absorbing and refracting objects, as well as to nonuniform partially coherent incident illumination. Partially coherent free-space propagators, describing amplitude and phase in-line contrast, are introduced and their properties are investigated. The present results are relevant to the design of imaging experiments with partially coherent sources, as well as to the analysis and interpretation of the corresponding images. PMID:27140752

  6. Method for partially coating laser diode facets

    NASA Technical Reports Server (NTRS)

    Dholakia, Anil R. (Inventor)

    1990-01-01

    Bars of integral laser diode devices cleaved from a wafer are placed with their p regions abutting and n regions abutting. A thin BeCu mask having alternate openings and strips of the same width as the end facets is used to mask the n region interfaces so that multiple bars can be partially coated over their exposed p regions with a reflective or partial reflective coating. The partial coating permits identification of the emitting facet from the fully coated back facet during a later device mounting procedure.

  7. Complex partial status epilepticus: a recurrent problem.

    PubMed Central

    Cockerell, O C; Walker, M C; Sander, J W; Shorvon, S D

    1994-01-01

    Twenty patients with complex partial status epilepticus were identified retrospectively from a specialist neurology hospital. Seventeen patients experienced recurrent episodes of complex partial status epilepticus, often occurring at regular intervals, usually over many years, and while being treated with effective anti-epileptic drugs. No unifying cause for the recurrences, and no common epilepsy aetiologies, were identified. In spite of the frequency of recurrence and length of history, none of the patients showed any marked evidence of cognitive or neurological deterioration. Complex partial status epilepticus is more common than is generally recognised, should be differentiated from other forms of non-convulsive status, and is often difficult to treat. PMID:8021671

  8. Fluctuation theorem for partially masked nonequilibrium dynamics.

    PubMed

    Shiraishi, Naoto; Sagawa, Takahiro

    2015-01-01

    We establish a generalization of the fluctuation theorem for partially masked nonequilibrium dynamics. We introduce a partial entropy production with a subset of all possible transitions, and show that the partial entropy production satisfies the integral fluctuation theorem. Our result reveals the fundamental properties of a broad class of autonomous as well as nonautonomous nanomachines. In particular, our result gives a unified fluctuation theorem for both autonomous and nonautonomous Maxwell's demons, where mutual information plays a crucial role. Furthermore, we derive a fluctuation-dissipation theorem that relates nonequilibrium stationary current to two kinds of equilibrium fluctuations. PMID:25679593

  9. Fluctuation theorem for partially masked nonequilibrium dynamics

    NASA Astrophysics Data System (ADS)

    Shiraishi, Naoto; Sagawa, Takahiro

    2015-01-01

    We establish a generalization of the fluctuation theorem for partially masked nonequilibrium dynamics. We introduce a partial entropy production with a subset of all possible transitions, and show that the partial entropy production satisfies the integral fluctuation theorem. Our result reveals the fundamental properties of a broad class of autonomous as well as nonautonomous nanomachines. In particular, our result gives a unified fluctuation theorem for both autonomous and nonautonomous Maxwell's demons, where mutual information plays a crucial role. Furthermore, we derive a fluctuation-dissipation theorem that relates nonequilibrium stationary current to two kinds of equilibrium fluctuations.

  10. Partially decentralized control for ALSTOM gasifier.

    PubMed

    Tan, Wen; Lou, Guannan; Liang, Luping

    2011-07-01

    The gasifier plays a key role in the operation of the whole IGCC power plant. It is a typical multivariable control system with strict constraints on the inputs and outputs which makes it very difficult to control. This paper presents a partially decentralized controller design method based on the stabilizer idea. The method only requires identifying some closed-loop transfer functions and solving an H(∞) optimization problem. The final partially decentralized controller is easy to implement and test in practice. Two partially decentralized controllers are designed for the ALSTOM gasifier benchmark problem, and simulation results show that they both meet the design specifications. PMID:21356534

  11. Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora root and stem rot caused by Phytophthora sojae Kaufmann and Gerdmann is one of the most severe soybean [Glycine max (L.) Merr] diseases in the US. Partial resistance is as effective in managing this disease as single-gene (Rps) mediated resistance and is more durable. The objective of t...

  12. Identification of quantitative trait loci conditioning partial resistance to Phytophthora sojae in soybean PI 407861A

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving resistance for Phytophthora root and stem rot is an important goal in soybean [Glycine max (L.) Merr.] breeding. Partial resistance can be as effective in managing this disease as single-gene (Rps) mediated resistance and is more durable. The objective of this study was to identify QTL con...

  13. [Disseminated BCG disease revealing a partial deficiency in receptor 1 interferon gamma].

    PubMed

    Antonietti, J; Retornaz, K; Bernasconi, A; Laporte, R-J; Minodier, P; Bustamante, J-C; Dubus, J-C

    2015-09-01

    We report on a case of disseminated BCGitis with an unusual presentation in a 4-month-old infant revealing a syndrome of Mendelian susceptibility to mycobacteria due to a partial dominant mutation of the interferon gamma receptor 1 gene. PMID:26251056

  14. Identification and Validation of Quantitative Trait Loci for Partial Resistance to Crown Rust in Oat.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Management of oat crown rust disease with host resistance is challenging because major gene resistance is generally short-lived. Partial resistance in productive oat cultivars could benefit oat growers by providing more durable resistance. The objective of this study was to validate and discover qua...

  15. Color Discriminability for Partially Seeing Children

    ERIC Educational Resources Information Center

    Myers, William A.

    1971-01-01

    Investigated was whether partially seeing children see the Snellen E, printed in selected colored inks on various colored backgrounds, at different distances in terms of initial recognition and best focus. (Author)

  16. Prolonged partial epilepsy: a case report

    SciTech Connect

    Wilson, M.A.

    1980-11-01

    The case study of a patient with prolonged partial epilepsy is presented. There was a discrepancy between the extent of the abnormality seen on the radionuclide angiogram and that seen on the static brain scan.

  17. [Prevention: the success of a partial denture].

    PubMed

    van Loveren, C

    2009-11-01

    After the placement of removable partial dentures, additional caries and periodontal problems may arise in the remaining dentition. These problems are the result of insufficient oral hygiene. Oral hygiene may be hampered by wearing the removable partial denture. The design of the removable partial denture should be carried out according to modern concepts of preventive dentistry. Before placing a removable partial denture, the patient's mouth should be thoroughly healthy and the patient should be instructed properly on adequate oral care. Furthermore, the patient should be aware of his/her own responsibility for maintenance. If cleaning twice a day with fluoride tooth-paste provides insufficient protection, care can be supported by daily use of a fluoride containing antimicrobial mouthrinse. Little effect can be expected from professionally applied fluoride or chlorhexidine solutions. PMID:19999672

  18. Partial ASL extensions for stochastic programming.

    Energy Science and Technology Software Center (ESTSC)

    2010-03-31

    partially completed extensions for stochastic programming to the AMPL/solver interface library (ASL).modeling and experimenting with stochastic recourse problems. This software is not primarily for military applications

  19. Partial Knee with Personalized Patient Care

    MedlinePlus Videos and Cool Tools

    Oxford® Partial Knee with Signature™ Personalized Patient Care You must have Javascript enabled in your web browser. View Program Transcript Click Here to view the OR-Live, Inc. Privacy Policy and ...

  20. 38 CFR 36.4305 - Partial disbursement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) LOAN GUARANTY Guaranty or Insurance of Loans to Veterans With Electronic Reporting § 36.4305 Partial... and percentage of the guaranty and the amount of the loan for the purposes of insurance or...

  1. 38 CFR 36.4305 - Partial disbursement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) LOAN GUARANTY Guaranty or Insurance of Loans to Veterans With Electronic Reporting § 36.4305 Partial... and percentage of the guaranty and the amount of the loan for the purposes of insurance or...

  2. Inconspicuous retention for removable partial dentures.

    PubMed

    King, G E; Barco, M T; Olson, R J

    1978-05-01

    Many dentists and patients believe that removable partial dentures have an unesthetic appearance when they replace anterior teeth because of the visible clasps. Two methods of obtaining inconspicuous retention have been described. PMID:349140

  3. Free fall - A partial unique motion environment

    NASA Technical Reports Server (NTRS)

    Graybiel, A.

    1980-01-01

    Conditions leading to the elicitation of motion sickness have been divided into two main categories: partial motion environments, in which head movements are required to elicit motion sickness, and complete motion environments, in which independent movements of the head are not required for the production of symptoms. It is postulated that, according to this categorization, free fall constitutes a partial motion environment. In support of this hypothesis evidence is reviewed from Skylab missions, experiments in parabolic flight, and ground-based studies.

  4. Partial nephrectomy in a patient with dwarfism.

    PubMed

    Farber, Nicholas J; Dubin, Justin; Parihar, Jaspreet; Han, Chris; Lasser, Michael S

    2016-08-01

    We describe the case of a 50-year-old male with achondroplastic dwarfism who presents with a renal mass in his left kidney concerning for renal cell carcinoma. The patient successfully underwent a robotic partial nephrectomy, which revealed a T1a renal cell carcinoma. The tumor was excised successfully without any intraoperative complications demonstrating that a robotic partial nephrectomy is technically both safe and effective in patients with achondroplastic dwarfism. PMID:27544562

  5. A compilation of partial sequences of randomly selected cDNA clones from the rat incisor.

    PubMed

    Matsuki, Y; Nakashima, M; Amizuka, N; Warshawsky, H; Goltzman, D; Yamada, K M; Yamada, Y

    1995-01-01

    The formation of tooth organs is regulated by a series of developmental programs. We have initiated a genome project with the ultimate goal of identifying novel genes important for tooth development. As an initial approach, we constructed a unidirectional cDNA library from the non-calcified portion of incisors of 3- to 4-week-old rats, sequenced cDNA clones, and classified their sequences by homology search through the GenBank data base and the PIR protein data base. Here, we report partial DNA sequences obtained by automated DNA sequencing on 400 cDNA clones randomly selected from the library. Of the sequences determined, 51% represented sequences of new genes that were not related to any previously reported gene. Twenty-six percent of the clones strongly matched genes and proteins in the data bases, including amelogenin, alpha 1(I) and alpha 2(I) collagen chains, osteonectin, and decorin. Nine percent of clones revealed partial sequence homology to known genes such as transcription factors and cell surface receptors. A significant number of the previously identified genes were expressed redundantly and were found to encode extracellular matrix proteins. Identification and cataloging of cDNA clones in these tissues are the first step toward identification of markers expressed in a tissue- or stage-specific manner, as well as the genetic linkage study of tooth anomalies. Further characterization of the clones described in this paper should lead to the discovery of novel genes important for tooth development. PMID:7876422

  6. Partial melting of subducting oceanic crust

    NASA Astrophysics Data System (ADS)

    Peacock, Simon M.; Rushmer, Tracy; Thompson, Alan Bruce

    1994-01-01

    The conditions under which partial melting of subducting oceanic crust occurs can be determined by combining a partial melting model for basaltic compositions with two-dimensional thermal models of subduction zones. For porosities of approximately 1% containing H2O the amount of partial melt generated at the wet basaltic solidus is limited to less than 5 vol%. At higher temperatures (approximately 1000 C at 1.5 GPa) large amounts of partial melt, up to 50 vol%, form by the breakdown of amphibole and the release of structurally bound H2O. In most subduction zones, substantial partial melting of subducting oceanic crust will only occur if high shear stresses (greater than approximately 100 MPa) can be maintained by rocks close to, or above, their melting temperatures. In the absence of high shear stresses, substantial melting of the oceanic crust will only occur during subduction of very young (less than 5 Ma) oceanic lithosphere. Partial melting of hydrated basalt (amphibolites) derived from the mid-ocean ridge has been proposed as being responsible for the generation of certain recent high-Al andesitic to dacitic volcanic rocks (adakites). Three of these volcanic suites (Mount St. Helens, southern Chile, and Panama) occur in volcanic arcs where oceanic crust less than 25 Ma is being subducted at rates of 1 - 3 cm/yr and the calculated thermal regime is several hundreds of degrees hotter than more typical subduction zone environments. However, oceanic lithosphere is not currently being subducted beneath Baja and New Guinea, where recent adakites are also present, suggesting that some adakite magmas may form by water-undersaturated partial melting of underplated mafic lower crust or previously subducted oceanic crust. Further experimental work on compositions representative of oceanic crust is required to define the depth of possible adakite source regions more accurately.

  7. Partial Volume Correction in Quantitative Amyloid Imaging

    PubMed Central

    Su, Yi; Blazey, Tyler M.; Snyder, Abraham Z.; Raichle, Marcus E.; Marcus, Daniel S.; Ances, Beau M.; Bateman, Randall J.; Cairns, Nigel J.; Aldea, Patricia; Cash, Lisa; Christensen, Jon J.; Friedrichsen, Karl; Hornbeck, Russ C.; Farrar, Angela M.; Owen, Christopher J.; Mayeux, Richard; Brickman, Adam M.; Klunk, William; Price, Julie C.; Thompson, Paul M.; Ghetti, Bernardino; Saykin, Andrew J.; Sperling, Reisa A.; Johnson, Keith A.; Schofield, Peter R.; Buckles, Virginia; Morris, John C.; Benzinger, Tammie. LS.

    2014-01-01

    Amyloid imaging is a valuable tool for research and diagnosis in dementing disorders. As positron emission tomography (PET) scanners have limited spatial resolution, measured signals are distorted by partial volume effects. Various techniques have been proposed for correcting partial volume effects, but there is no consensus as to whether these techniques are necessary in amyloid imaging, and, if so, how they should be implemented. We evaluated a two-component partial volume correction technique and a regional spread function technique using both simulated and human Pittsburgh compound B (PiB) PET imaging data. Both correction techniques compensated for partial volume effects and yielded improved detection of subtle changes in PiB retention. However, the regional spread function technique was more accurate in application to simulated data. Because PiB retention estimates depend on the correction technique, standardization is necessary to compare results across groups. Partial volume correction has sometimes been avoided because it increases the sensitivity to inaccuracy in image registration and segmentation. However, our results indicate that appropriate PVC may enhance our ability to detect changes in amyloid deposition. PMID:25485714

  8. Partial volume correction in quantitative amyloid imaging.

    PubMed

    Su, Yi; Blazey, Tyler M; Snyder, Abraham Z; Raichle, Marcus E; Marcus, Daniel S; Ances, Beau M; Bateman, Randall J; Cairns, Nigel J; Aldea, Patricia; Cash, Lisa; Christensen, Jon J; Friedrichsen, Karl; Hornbeck, Russ C; Farrar, Angela M; Owen, Christopher J; Mayeux, Richard; Brickman, Adam M; Klunk, William; Price, Julie C; Thompson, Paul M; Ghetti, Bernadino; Saykin, Andrew J; Sperling, Reisa A; Johnson, Keith A; Schofield, Peter R; Buckles, Virginia; Morris, John C; Benzinger, Tammie L S

    2015-02-15

    Amyloid imaging is a valuable tool for research and diagnosis in dementing disorders. As positron emission tomography (PET) scanners have limited spatial resolution, measured signals are distorted by partial volume effects. Various techniques have been proposed for correcting partial volume effects, but there is no consensus as to whether these techniques are necessary in amyloid imaging, and, if so, how they should be implemented. We evaluated a two-component partial volume correction technique and a regional spread function technique using both simulated and human Pittsburgh compound B (PiB) PET imaging data. Both correction techniques compensated for partial volume effects and yielded improved detection of subtle changes in PiB retention. However, the regional spread function technique was more accurate in application to simulated data. Because PiB retention estimates depend on the correction technique, standardization is necessary to compare results across groups. Partial volume correction has sometimes been avoided because it increases the sensitivity to inaccuracy in image registration and segmentation. However, our results indicate that appropriate PVC may enhance our ability to detect changes in amyloid deposition. PMID:25485714

  9. Incremental fusion of partial biometric information

    NASA Astrophysics Data System (ADS)

    Abboud, Ali J.; Jassim, Sabah A.

    2012-06-01

    Existing face recognition schemes are mostly based on extracting biometric feature vectors either from whole face images, or from a fixed facial region (e.g., eyes, nose, and mouth). Extreme variation in quality conditions between biometric enrolment and verification stages badly affects the performance of face recognition systems. Such problems have partly motivated several investigations into the use of partial facial features for face recognition. Nevertheless, partial face recognition is potentially useful in several applications, for instance, it used in forensics for detectives to identify individuals after some accidents such as fire or explosion. In this paper, we propose a scheme to fuse the biometric information of partial face images incrementally based on their recognition accuracy (or discriminative power) ranks. Such fusion scheme uses the optimal ratio of full/partial face images in each different quality condition. We found that such scheme is also useful for full face images to enhance authentication accuracy significantly. Nevertheless, it reduces the required storage requirements and processing time of the biometric system. Our experiments show that the required ratio of full/partial facial images to achieve optimal performance varies from (5%) to (80%) according to the quality conditions whereas the authentication accuracy improves significantly for low quality biometric samples.

  10. NO formation in counterflow partially premixed flames

    SciTech Connect

    Mungekar, Hemant; Atreya, Arvind

    2007-02-15

    An experimental and computational study of NO formation in low-strain-rate partially premixed methane counterflow flames is reported. For progressive fuel-side partial premixing the peak NO concentration increased and the NO distribution along the stagnation streamline broadened. New temperature-dependent emissivity data for a SiO{sub 2}-coated Pt thermocouple was used to estimate the radiation correction for the thermocouple, thus improving the accuracy of the reported flame temperature. Flame structure computations with GRIMech 3.00 showed good agreement between measured and computed concentration distributions of NO and OH radical. With progressive partial premixing the contribution of the thermal NO pathway to NO formation increases. The emission index of NO (EINO) first increased and then decreased, reaching its peak value for the level of partial premixing that corresponds to location of the nonpremixed reaction zone at the stagnation plane. The observation of a maximum in EINO at a level of partial premixing corresponding to the nonpremixed reaction zone at the stagnation plane seems to be a consistent feature of low (<20 s{sup -1})-strain-rate counterflow flames. (author)

  11. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population.

    PubMed

    Allard, Alix; Bink, Marco C A M; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean-Michel; di Guardo, Mario; Di Pierro, Erica A; Laurens, François; van de Weg, Eric W; Costes, Evelyne

    2016-04-01

    In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6-21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase. PMID:27034326

  12. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

    PubMed Central

    Allard, Alix; Bink, Marco C.A.M.; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean-Michel; di Guardo, Mario; Di Pierro, Erica A.; Laurens, François; van de Weg, Eric W.; Costes, Evelyne

    2016-01-01

    In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase. PMID:27034326

  13. Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background WC1 co-receptors belong to the scavenger receptor cysteine-rich superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ '' T cells. Our previous study identified partial sequences for 13 different WC1 genes by annota...

  14. Thin film oxygen partial pressure sensor

    NASA Technical Reports Server (NTRS)

    Wortman, J. J.; Harrison, J. W.; Honbarrier, H. L.; Yen, J.

    1972-01-01

    The development is described of a laboratory model oxygen partial pressure sensor using a sputtered zinc oxide thin film. The film is operated at about 400 C through the use of a miniature silicon bar. Because of the unique resistance versus temperature relation of the silicon bar, control of the operational temperature is achieved by controlling the resistance. A circuit for accomplishing this is described. The response of sputtered zinc oxide films of various thicknesses to oxygen, nitrogen, argon, carbon dioxide, and water vapor caused a change in the film resistance. Over a large range, film conductance varied approximately as the square root of the oxygen partial pressure. The presence of water vapor in the gas stream caused a shift in the film conductance at a given oxygen partial pressure. A theoretical model is presented to explain the characteristic features of the zinc oxide response to oxygen.

  15. Telecloning of qudits via partially entangled states

    NASA Astrophysics Data System (ADS)

    Araneda, Gabriel; Cisternas, Nataly; Delgado, Aldo

    2016-08-01

    We study the process of quantum telecloning of d-dimensional pure quantum states using partially entangled pure states as quantum channel. This process efficiently mixes optimal universal symmetric cloning with quantum teleportation. It is shown that it is possible to implement universal symmetric telecloning in a probabilistic way using unambiguous state discrimination and quantum state separation schemes. It is also shown that other strategies, such as minimum error discrimination, lead to a decrease in the fidelity of the copies and that certain partially entangled pure states with maximal Schmidt rank lead to an average telecloning fidelity which is always above the optimal fidelity of measuring and preparation of quantum states. We also discuss the case of partially entangled pure states with non-maximal Schmidt rank. The results presented here are valid for arbitrary numbers of copies of a single-input qudit state of any dimension.

  16. Virtual environment application with partial gravity simulation

    NASA Technical Reports Server (NTRS)

    Ray, David M.; Vanchau, Michael N.

    1994-01-01

    To support manned missions to the surface of Mars and missions requiring manipulation of payloads and locomotion in space, a training facility is required to simulate the conditions of both partial and microgravity. A partial gravity simulator (Pogo) which uses pneumatic suspension is being studied for use in virtual reality training. Pogo maintains a constant partial gravity simulation with a variation of simulated body force between 2.2 and 10 percent, depending on the type of locomotion inputs. this paper is based on the concept and application of a virtual environment system with Pogo including a head-mounted display and glove. The reality engine consists of a high end SGI workstation and PC's which drive Pogo's sensors and data acquisition hardware used for tracking and control. The tracking system is a hybrid of magnetic and optical trackers integrated for this application.

  17. On partially massless theory in 3 dimensions

    SciTech Connect

    Alexandrov, Sergei; Deffayet, Cédric

    2015-03-24

    We analyze the first-order formulation of the ghost-free bigravity model in three-dimensions known as zwei-dreibein gravity. For a special choice of parameters, it was argued to have an additional gauge symmetry and give rise to a partially massless theory. We provide a thorough canonical analysis and identify that whether the theory becomes partially massless depends on the form of the stability condition of the secondary constraint responsible for the absence of the ghost. Generically, it is found to be an equation for a Lagrange multiplier implying that partially massless zwei-dreibein gravity does not exist. However, for special backgrounds this condition is identically satisfied leading to the presence of additional symmetries, which however disappear at quadratic order in perturbations.

  18. Partial connectivity increases cultural accumulation within groups

    PubMed Central

    Boyd, Robert

    2016-01-01

    Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population’s ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups. PMID:26929364

  19. Robotic partial nephrectomy: current technique and outcomes.

    PubMed

    Wang, Liang; Lee, Benjamin R

    2013-09-01

    Over the past decade, management of the T1 renal mass has focused on nephron-sparing surgery. Robotic partial nephrectomy has played an increasing role in the technique of preserving renal function by decreasing warm ischemia time, as well as optimizing outcomes of hemorrhage and fistula. Robot-assisted partial nephrectomy is designed to provide a minimally-invasive nephron-sparing surgical option utilizing reconstructive capability, decreasing intracorporeal suturing time, technical feasibility and safety. Ultimately, its benefits are resulting in its dissemination across institutions. Articulated instrumentation and three-dimensional vision facilitate resection, collecting system reconstruction and renorrhaphy, leading to decreased warm ischemia time while preserving oncological outcomes. The aim of the present review was to present our surgical sequence and technique, as well as review the current status of robot-assisted partial nephrectomy. PMID:23635467

  20. Telecloning of qudits via partially entangled states

    NASA Astrophysics Data System (ADS)

    Araneda, Gabriel; Cisternas, Nataly; Delgado, Aldo

    2016-05-01

    We study the process of quantum telecloning of d-dimensional pure quantum states using partially entangled pure states as quantum channel. This process efficiently mixes optimal universal symmetric cloning with quantum teleportation. It is shown that it is possible to implement universal symmetric telecloning in a probabilistic way using unambiguous state discrimination and quantum state separation schemes. It is also shown that other strategies, such as minimum error discrimination, lead to a decrease in the fidelity of the copies and that certain partially entangled pure states with maximal Schmidt rank lead to an average telecloning fidelity which is always above the optimal fidelity of measuring and preparation of quantum states. We also discuss the case of partially entangled pure states with non-maximal Schmidt rank. The results presented here are valid for arbitrary numbers of copies of a single-input qudit state of any dimension.

  1. Phase retrieval from one partial derivative.

    PubMed

    Matías Di Martino, J; Flores, Jorge L; Pfeiffer, Franz; Scherer, Kai; Ayubi, Gastón A; Ferrari, José A

    2013-11-15

    Phase objects can be characterized using well-known methods such as shear interferometry and deflectometry, which provide information on the partial derivatives of the phase. It is often believed that for phase retrieval it is strictly necessary to have knowledge of two partial derivatives in orthogonal directions. In the praxis, this implies that the measurements have to be performed along two dimensions, which often requires a rotation of the object or rotation of the shear direction. This is time consuming and errors can be easily generated from the process of rotation, especially for image registration in the axial direction. In the present Letter, we will demonstrate that only one partial derivative often suffices to recover the phase, and we will discuss under which conditions that is possible. Simulations and validation experiments are presented. PMID:24322139

  2. Partial connectivity increases cultural accumulation within groups.

    PubMed

    Derex, Maxime; Boyd, Robert

    2016-03-15

    Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population's ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups. PMID:26929364

  3. Partial characterization of a major autolysin from Mycobacterium phlei.

    PubMed

    Li, Z S; Beveridge, T J; Betts, J; Clarke, A J

    1999-01-01

    Autolytic enzyme profiles of fast- and slow-growing mycobacteria were examined using SDS-PAGE zymography with incorporated mycobacterial peptidoglycan sacculi as substrate. Each species tested (Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium aurum, Mycobacterium fortuitum and Mycobacterium kansasii) appeared to produce a different set of enzymes on the basis of differing number and molecular masses. A major autolysin from M. phlei was purified to apparent homogeneity by DEAE-cellulose chromatography, preparative gel electrophoresis and Mono Q FPLC. This enzyme had an estimated molecular mass of 38 kDa, an isoelectric point of 5.5 and a pH optimum of pH 7.5. Digestion of purified peptidoglycan by the enzyme resulted in the appearance of reducing sugars, suggesting that the 38 kDa autolysin is a beta-glycosidase. Partial internal amino acid sequence of the autolysin was determined and should facilitate identification, cloning and overexpression of the encoding gene. PMID:10206696

  4. Adult case of partial trisomy 9q

    PubMed Central

    2010-01-01

    Background Complete and partial trisomy 9 is the fourth most common chromosomal disorder. It is also associated with various congenital characteristics affecting the cranio-facial, skeletal, central nervous, gastrointestinal, cardiac and renal systems. Very few cases have been reported in adults. Partial trisomy 9q is also associated with short stature, poor growth and growth hormone deficiency. This is the first reported case of an extensive endocrinology investigation of short stature in trisomy 9q and the outcome of growth hormone treatment. Case Presentation The case involves a 23-year-old female of pure partial trisomy 9q. The case involves a 23-year old female with pure partial trisomy 9q involving a duplication of 9q22.1 to q32, de novo, confirmed by genetic studies using fluorescene in situ hybridization (FISH) method. The diagnosis was at 6 years of age. She did not demonstrate all the congenital morphologies identified with trisomy 9q disorders especially in relation to multi-organ morphologies. There is also a degree of associated intellectual impairment. At prepuberty, she was referred for poor growth and was diagnosed with partial growth hormone deficiency. She responded very well to treatment with growth hormone and is currently living an independent life with some support. Conclusions Trisomy 9q is associated with short stature and failure to thrive. Growth hormone deficiency should be identified in cases of trisomy 9q and treatment offered. This is the first reported case of response to growth hormone replacement in partial trisomy 9. PMID:20158889

  5. Cloning and overexpression of an NADH-dependent alcohol dehydrogenase gene from Candida maris involved in (R)-selective reduction of 5-acetylfuro[2,3-c]pyridine.

    PubMed

    Kawano, Shigeru; Yano, Miho; Hasegawa, Junzo; Yasohara, Yoshihiko

    2011-01-01

    5-((R)-1-Hydroxyethyl)-furo[2,3-c]pyridine ((R)-FPH) is a useful chiral building block in the synthesis of pharmaceuticals. An NADH-dependent alcohol dehydrogenase (AFPDH) isolated from Candida maris catalyzed the reduction of 5-acetylfuro[2,3-c]pyridine (AFP) to (R)-FPH with 100% enantiomeric excess. The gene encoding AFPDH was cloned and sequenced. The AFPDH gene comprises 762 bp and encodes a polypeptide of 27,230 Da. The deduced amino acid sequence showed a high degree of similarity to those of other members of the short-chain alcohol dehydrogenase superfamily. The AFPDH gene was overexpressed in Escherichia coli under the control of the lac promoter. One L of the cultured broth of an E. coli transformant coexpressing AFPDH and the glucose dehydrogenase (GDH) gene reduced 250 g of AFP to (R)-FPH in an organic solvent two-phase system. Under coupling with NADH regeneration using 2-propanol, 1 L of the cultured broth of an E. coli transformant expressing the AFPDH gene reduced 150 g of AFP to (R)-FPH. The optical purity of the (R)-FPH formed was 100% enantiomeric excess under both reaction conditions. PMID:22056439

  6. Partial gravity - Human impacts on facility design

    NASA Technical Reports Server (NTRS)

    Capps, Stephen; Moore, Nathan

    1990-01-01

    Partial gravity affects the body differently than earth gravity and microgravity environments. The main difference from earth gravity is human locomotion; while the main dfference from microgravity is the specific updown orientation and reach envelopes which increase volume requirements. Much data are available on earth gravity and microgravity design; however, very little information is available on human reactions to reduced gravity levels in IVA situations (without pressure suits). Therefore, if humans commit to permanent lunar habitation, much research should be conducted in the area of partial gravity effects on habitat design.

  7. Solute partial molal volumes in supercritical fluids

    SciTech Connect

    Eckert, C.A.; Ziger, D.H.; Johnston, K.P.; Kim, S.

    1986-06-05

    A novel technique is described for the measurement of the partial molal volume at infinite dilution of solutes in supercritical fluids. Results are reported for five systems from 2/sup 0/C above the solvent critical temperature up to 15/sup 0/C above, at pressures from just above the critical pressure to 350 bars. The solute partial molal volumes are small and positive at high pressures, but very large and negative in the highly compressible near-critical region. The results are interpreted in terms of solvent structure and intermolecular forces.

  8. Oral hygiene for the partially edentulous.

    PubMed

    Bassiouny, M A; Grant, A A

    1981-04-01

    THE EFFECTIVENESS of a proximal brush on the interdental hygiene for partially edentulous individuals was investigated. Nineteen partially edentulous adults participated in a crossover study. Three groups were instructed to use the toothbrush alone or a toothbrush combined with either toothpicks or proximal brush. The effectiveness of the cleansing devices was measured by the amount of plaque remaining on the examined surfaces. The results indicated that the cleaning efficiency of the proximal brush is greater than that of the toothpicks on the proximal surfaces of teeth adjacent to edentulous areas. On the other hand, the toothpicks were more effective on the proximal surfaces of teeth in contact. PMID:6939841

  9. Digital generation of partially coherent vortex beams.

    PubMed

    Perez-Garcia, Benjamin; Yepiz, Adad; Hernandez-Aranda, Raul I; Forbes, Andrew; Swartzlander, Grover A

    2016-08-01

    We present an experimental technique to generate partially coherent vortex beams with an arbitrary azimuthal index using only a spatial light modulator. Our approach is based on digitally simulating the intrinsic randomness of broadband light passing through a spiral phase plate. We illustrate the versatility of the technique by generating partially coherent beams with different coherence lengths and orbital angular momentum content, without any moving optical device. Consequently, we study its cross-correlation function in a wavefront folding interferometer. The comparison with theoretical predictions yields excellent agreement. PMID:27472596

  10. [Simple partial frontal nonconvulsive status epilepticus].

    PubMed

    Thomas, P; Mottin, Y

    1997-07-01

    Non convulsive status epilepticus (NCSE) of frontal origin is a rare cause of mental confusion. The present case of possible frontal-onset NCSE proved to have a neuropsychological examination that was suggestive either of a disruption of attentional function or a left prefrontal dysfunction, exhibiting disturbances of immediate memory and logical programmation, perseverations and affective disinhibition. Vigilance was not impaired. This case was therefore, on a nosographic point of view, more consistent with a simple partial status epilepticus with cognitive and affective symptomatology rather than with a complex partial status epilepticus of extra-temporal origin. PMID:9684010

  11. Partially coherent interferometric biometry in cataract surgery

    NASA Astrophysics Data System (ADS)

    Drexler, Wolfgang; Findl, Oliver; Menapace, Rupert; Hitzenberger, Christoph K.; Fercher, Adolf F.

    1999-02-01

    In an earlier study we showed that precise axial eye length measurement on cataract eyes is possible with the dual beam partial coherence interferometry technique (PCI). A high correlation with the standard ultrasound technique has been obtained. Recently, in a prospective study, partially coherent interferometry and ultrasound biometry were compared in cataract surgery using the SRK II formula based on US applanation biometry. Three months after surgery PCI was repeated and refractive outcome was determined. The use of PCI would have improved refractive outcome by about 30%.

  12. DEVICE FOR CONTROL OF OXYGEN PARTIAL PRESSURE

    DOEpatents

    Bradner, H.; Gordon, H.S.

    1957-12-24

    A device is described that can sense changes in oxygen partial pressure and cause a corresponding mechanical displacement sufficient to actuate meters, valves and similar devices. A piston and cylinder arrangement contains a charge of crystalline metal chelate pellets which have the peculiar property of responding to variations in the oxygen content of the ambient atmosphere by undergoing a change in dimension. A lever system amplifies the relative displacement of the piston in the cylinder, and actuates the controlled valving device. This partial pressure oxygen sensing device is useful in controlled chemical reactions or in respiratory devices such as the oxygen demand meters for high altitude aircraft.

  13. Laparoscopic sleeve gastrectomy in partial situs inversus

    PubMed Central

    Borude, S; Jadhav, S; Shaikh, T; Nath, SR

    2012-01-01

    Laparoscopic surgery in a patient with Partial Situs Inversus may pose interesting challenges to the surgeon. Here we report a case of a morbidly obese young female with partial situs inversus who underwent Laparoscopic Vertical Sleeve Gastrectomy (LSG). The peri-operative challenges very many and these have been enumerated. The mirror image approach is recommended in such cases for a successful surgery which was not employed in this case. Postoperative barium swallow was normal and the patient has been on regular follow up. PMID:24960136

  14. Advanced high frequency partial discharge measuring system

    NASA Technical Reports Server (NTRS)

    Karady, George G.

    1994-01-01

    This report explains the Advanced Partial Discharge Measuring System in ASU's High Voltage Laboratory and presents some of the results obtained using the setup. While in operation an insulation is subjected to wide ranging temperature and voltage stresses. Hence, it is necessary to study the effect of temperature on the behavior of partial discharges in an insulation. The setup described in this report can be used to test samples at temperatures ranging from -50 C to 200 C. The aim of conducting the tests described herein is to be able to predict the behavior of an insulation under different operating conditions in addition to being able to predict the possibility of failure.

  15. Partial siamese twin as potential organ donor

    PubMed Central

    Kapoor, Rakesh; Maheshwari, Ruchir; Srivastava, Aneesh; Sharma, Raj K.

    2010-01-01

    During evaluation of a partial Siamese twin for removal of nonviable parasitic part in an 8-year-old male child, a fully functional kidney was found. The functional status of the extra kidney was found to be within acceptable limits for the purpose of transplant, which was subsequently done in a 24-year-old patient with end-stage renal disease. The recipient is healthy 19 months after the surgery. The possibility of using organs from a partial Siamese twin makes this a unique case report. PMID:20877612

  16. Partially overlapping primer-based PCR for genome walking.

    PubMed

    Li, Haixing; Ding, Dongqin; Cao, Yusheng; Yu, Bo; Guo, Liang; Liu, Xiaohua

    2015-01-01

    Current genome walking methods are cumbersome to perform and can result in non-specific products. Here, we demonstrate the use of partially overlapping primer-based PCR (POP-PCR), a direct genome walking technique for the isolation of unknown flanking regions. This method exploits the partially overlapping characteristic at the 3' ends of a set of POP primers (walking primers), which guarantees that the POP primer only anneals to the POP site of the preceding PCR product at relatively low temperatures. POP primer adaptation priming at the genomic DNA/POP site occurs only once due to one low-/reduced-stringency cycle in each nested PCR, resulting in the synthesis of a pool of single-stranded DNA molecules. Of this pool, the target single-stranded DNA is replicated to the double-stranded form bound by the specific primer and the POP primer in the subsequent high-stringency cycle due to the presence of the specific primer-binding site. The non-target single stranded DNA does not become double stranded due to the absence of a binding site for any of the primers. Therefore, the POP-PCR enriches target DNA while suppressing non-target products. We successfully used POP-PCR to retrieve flanking regions bordering the gadA locus in Lactobacillus brevis NCL912, malQ in Pichia pastoris GS115, the human aldolase A gene, and hyg in rice. PMID:25811779

  17. Partial dosage compensation in Strepsiptera, a sister group of beetles.

    PubMed

    Mahajan, Shivani; Bachtrog, Doris

    2015-02-01

    Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species. PMID:25601100

  18. Partial Dosage Compensation in Strepsiptera, a Sister Group of Beetles

    PubMed Central

    Mahajan, Shivani; Bachtrog, Doris

    2015-01-01

    Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X’s in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species. PMID:25601100

  19. 77 FR 61724 - Partial Approval and Partial Disapproval of Air Quality Implementation Plans for Florida...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-11

    ...EPA is taking final action to partially approve and partially disapprove revisions to the State Implementation Plans (SIPs) for Florida, Mississippi, and South Carolina submitted on September 23, 2009, October 6, 2009, and September 18, 2009, respectively. EPA is approving the determinations, contained in those submittals, that the existing SIPs for Florida, Mississippi, and South Carolina are......

  20. 77 FR 1417 - Partial Approval and Partial Disapproval of Air Quality Implementation Plans; California; San...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-10

    .... Proposed Action On September 9, 2011 (76 FR 55842), EPA proposed to partially approve and partially... approval/disapproval October 1, 2010 (75 FR 60623). SJVUAPCD is scheduled to adopt amendments to Rule 4352.../disapproval January 26, 2010, (75 FR 3996). SJVUAPCD submitted amendments to EPA on July 28, 2011 and...

  1. Methods for producing partially digested restriction DNA fragments and for producing a partially modified PCR product

    DOEpatents

    Wong, Kwong-Kwok

    2000-01-01

    The present invention is an improved method of making a partially modified PCR product from a DNA fragment with a polymerase chain reaction (PCR). In a standard PCR process, the DNA fragment is combined with starting deoxynucleoside triphosphates, a primer, a buffer and a DNA polymerase in a PCR mixture. The PCR mixture is then reacted in the PCR producing copies of the DNA fragment. The improvement of the present invention is adding an amount of a modifier at any step prior to completion of the PCR process thereby randomly and partially modifying the copies of the DNA fragment as a partially modified PCR product. The partially modified PCR product may then be digested with an enzyme that cuts the partially modified PCR product at unmodified sites thereby producing an array of DNA restriction fragments.

  2. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  3. Partial wave analysis using graphics processing units

    NASA Astrophysics Data System (ADS)

    Berger, Niklaus; Beijiang, Liu; Jike, Wang

    2010-04-01

    Partial wave analysis is an important tool for determining resonance properties in hadron spectroscopy. For large data samples however, the un-binned likelihood fits employed are computationally very expensive. At the Beijing Spectrometer (BES) III experiment, an increase in statistics compared to earlier experiments of up to two orders of magnitude is expected. In order to allow for a timely analysis of these datasets, additional computing power with short turnover times has to be made available. It turns out that graphics processing units (GPUs) originally developed for 3D computer games have an architecture of massively parallel single instruction multiple data floating point units that is almost ideally suited for the algorithms employed in partial wave analysis. We have implemented a framework for tensor manipulation and partial wave fits called GPUPWA. The user writes a program in pure C++ whilst the GPUPWA classes handle computations on the GPU, memory transfers, caching and other technical details. In conjunction with a recent graphics processor, the framework provides a speed-up of the partial wave fit by more than two orders of magnitude compared to legacy FORTRAN code.

  4. Absolute partial photoionization cross sections of ozone.

    SciTech Connect

    Berkowitz, J.; Chemistry

    2008-04-01

    Despite the current concerns about ozone, absolute partial photoionization cross sections for this molecule in the vacuum ultraviolet (valence) region have been unavailable. By eclectic re-evaluation of old/new data and plausible assumptions, such cross sections have been assembled to fill this void.

  5. Some Considerations on the Partial Credit Model

    ERIC Educational Resources Information Center

    Verhelst, N. D.; Verstralen, H. H. F. M.

    2008-01-01

    The Partial Credit Model (PCM) is sometimes interpreted as a model for stepwise solution of polytomously scored items, where the item parameters are interpreted as difficulties of the steps. It is argued that this interpretation is not justified. A model for stepwise solution is discussed. It is shown that the PCM is suited to model sums of binary…

  6. Partially Correct Constructs Illuminate Students' Inconsistent Answers

    ERIC Educational Resources Information Center

    Ron, Gila; Dreyfus, Tommy; Hershkowitz, Rina

    2010-01-01

    We present a view of knowledge construction processes, focusing on partially correct constructs. Motivated by unexpected and seemingly inconsistent quantitative data based on the written reports of students working on an elementary probability task, we analyze in detail the knowledge construction processes of a representative student. We show how…

  7. Partial Automated Alignment and Integration System

    NASA Technical Reports Server (NTRS)

    Kelley, Gary Wayne (Inventor)

    2014-01-01

    The present invention is a Partial Automated Alignment and Integration System (PAAIS) used to automate the alignment and integration of space vehicle components. A PAAIS includes ground support apparatuses, a track assembly with a plurality of energy-emitting components and an energy-receiving component containing a plurality of energy-receiving surfaces. Communication components and processors allow communication and feedback through PAAIS.

  8. Some Partial Models for Urban Problems.

    ERIC Educational Resources Information Center

    Guthrie, Harold W.

    This paper focuses on partial models for solving urban problems to contrast our achievements as social scientists with our aspirations as prescribers of public policy. The objectives of this paper are (1) to review some of the reasons that an ideal set of solutions for urban problems has not been produced by social scientists and (2) to describe…

  9. Partial spin reversal in magnetic deflagration

    NASA Astrophysics Data System (ADS)

    Vélez, S.; Subedi, P.; Macià, F.; Li, S.; Sarachik, M. P.; Tejada, J.; Mukherjee, S.; Christou, G.; Kent, A. D.

    2014-04-01

    The reversal of spins in a magnetic material as they relax toward equilibrium is accompanied by the release of Zeeman energy, which can lead to accelerated spin relaxation and the formation of a well-defined self-sustained propagating spin-reversal front known as magnetic deflagration. To date, studies of Mn12-acetate single crystals have focused mainly on deflagration in large longitudinal magnetic fields, and they found a fully spin-reversed final state. We report a systematic study of the effect of a transverse magnetic field on magnetic deflagration, and we demonstrate that in small longitudinal fields the final state consists of only partially reversed spins. Further, we measured the front speed as a function of applied magnetic field. The theory of magnetic deflagration, together with a modification that takes into account partial spin reversal, fits the transverse field dependence of the front speed but not its dependence on the longitudinal field. The most significant result of this study is the finding of a partially spin-reversed final state, which is evidence that the spins at the deflagration front are also only partially reversed.

  10. Conservation Development in the Partially Sighted Child.

    ERIC Educational Resources Information Center

    Swanson, Lee; And Others

    1979-01-01

    A comparative study of conservation development in partially sighted, sighted, and sighted blindfolded children at four age levels was assessed. Conservation on tasks of mass, weight, and volume were evaluated using Piaget and Inhelder's prediction, judgment, and explanation questions. The significant differences were found between groups, task,…

  11. Partially redundant apertures for infrared stellar imaging

    NASA Astrophysics Data System (ADS)

    Aitken, G. J. M.; Corteggiani, J. P.; Gay, J.

    1981-06-01

    Spectral-bandwidth constraints to ensure controlled amounts of redundancy are established for a class of two-dimensional partially redundant arrays (PRA's). In the IR, where speckle statistics are poor, the telescope-atmosphere modulation transfer function is determined solely by the PRA geometry. Signal-to-noise-ratio estimates, an optimum aperture criterion, and a six-element PRA example are presented.

  12. PARTIALLY SEEING PROGRAM, 1966-1967.

    ERIC Educational Resources Information Center

    Lake County Special Education District, Gurnee, IL.

    THIS ADMINISTRATIVE OUTLINE OF THE PARTIALLY SEEING PROGRAM IN LAKE COUNTY, ILLINOIS, PRESENTS THE DUTIES AND RESPONSIBILITIES OF THE TWO ITINERANT TEACHERS AND THEIR IMMEDIATE SUPERVISORS. THE PROGRAM'S PHILOSOPHY, GOALS, HISTORY AND PLACEMENT IN THE COUNTY'S ORGANIZATIONAL STRUCTURE IS PRESENTED. THE ITINERANT TEACHER'S ADMINISTRATIVE…

  13. A Partial Theory of Executive Succession.

    ERIC Educational Resources Information Center

    Thiemann, Francis C.

    This study has two purposes: (1) To construct a partial theory of succession, and (2) to utilize a method of theory construction which combines some of the concepts of Hans Zetterberg with the principles of formal symbolic logic. A bibliography on succession in complex organizations with entries on descriptive and empirical studies from various…

  14. Partial Derivative Automata Formalized in Coq

    NASA Astrophysics Data System (ADS)

    Almeida, José Bacelar; Moreira, Nelma; Pereira, David; de Sousa, Simão Melo

    In this paper we present a computer assisted proof of the correctness of a partial derivative automata construction from a regular expression within the Coq proof assistant. This proof is part of a formalization of Kleene algebra and regular languages in Coq towards their usage in program certification.

  15. Partial least squares for dependent data

    PubMed Central

    Singer, Marco; Krivobokova, Tatyana; Munk, Axel; de Groot, Bert

    2016-01-01

    We consider the partial least squares algorithm for dependent data and study the consequences of ignoring the dependence both theoretically and numerically. Ignoring nonstationary dependence structures can lead to inconsistent estimation, but a simple modification yields consistent estimation. A protein dynamics example illustrates the superior predictive power of the proposed method. PMID:27279662

  16. Accommodating blind and partially sighted clients

    PubMed Central

    England, Gary; Gebbels, Tim; Whelan, Chantelle; Freeman, Sarah

    2014-01-01

    Veterinary surgeons provide an important service to blind and partially sighted guide dog owners. By adopting basic disability awareness and visual impairment training, practices can ensure that the assistance needs of those clients are met, facilitating access to veterinary care. PMID:25642013

  17. Partially Decentralized Control Architectures for Satellite Formations

    NASA Technical Reports Server (NTRS)

    Carpenter, J. Russell; Bauer, Frank H.

    2002-01-01

    In a partially decentralized control architecture, more than one but less than all nodes have supervisory capability. This paper describes an approach to choosing the number of supervisors in such au architecture, based on a reliability vs. cost trade. It also considers the implications of these results for the design of navigation systems for satellite formations that could be controlled with a partially decentralized architecture. Using an assumed cost model, analytic and simulation-based results indicate that it may be cheaper to achieve a given overall system reliability with a partially decentralized architecture containing only a few supervisors, than with either fully decentralized or purely centralized architectures. Nominally, the subset of supervisors may act as centralized estimation and control nodes for corresponding subsets of the remaining subordinate nodes, and act as decentralized estimation and control peers with respect to each other. However, in the context of partially decentralized satellite formation control, the absolute positions and velocities of each spacecraft are unique, so that correlations which make estimates using only local information suboptimal only occur through common biases and process noise. Covariance and monte-carlo analysis of a simplified system show that this lack of correlation may allow simplification of the local estimators while preserving the global optimality of the maneuvers commanded by the supervisors.

  18. Partially Quenched Chiral Perturbation Theory to NNLO

    SciTech Connect

    Laehde, Timo; Bijnens, Johan; Danielsson, Niclas

    2006-07-11

    This paper summarizes the recent calculations of the masses and decay constants of the pseudoscalar mesons at the two-loop level, or NNLO, in Partially Quenched Chiral Perturbation theory (PQ{chi}PT). Possible applications include chiral extrapolations of Lattice QCD, as well as the determination of the low-energy constants (LEC:s) of QCD.

  19. Canonical coordinates for partial differential equations

    NASA Technical Reports Server (NTRS)

    Hunt, L. R.; Villarreal, Ramiro

    1987-01-01

    Necessary and sufficient conditions are found under which operators of the form Sigma(m, j=1) X(2)sub j + X sub 0 can be made constant coefficient. In addition, necessary and sufficient conditions are derived which classify those linear partial differential operators that can be moved to the Kolmogorov type.

  20. Canonical coordinates for partial differential equations

    NASA Technical Reports Server (NTRS)

    Hunt, L. R.; Villarreal, Ramiro

    1988-01-01

    Necessary and sufficient conditions are found under which operators of the form Sigma (m, j=1) x (2) sub j + X sub O can be made constant coefficient. In addition, necessary and sufficient conditions are derived which classify those linear partial differential operators that can be moved to the Kolmogorov type.

  1. Partial Data Traces: Efficient Generation and Representation

    SciTech Connect

    Mueller, F; De Supinski, B R; McKee, S A; Yoo, A

    2001-08-20

    Binary manipulation techniques are increasing in popularity. They support program transformations tailored toward certain program inputs, and these transformations have been shown to yield performance gains beyond the scope of static code optimizations without profile-directed feedback. They even deliver moderate gains in the presence of profile-guided optimizations. In addition, transformations can be performed on the entire executable, including library routines. This work focuses on program instrumentation, yet another application of binary manipulation. This paper reports preliminary results on generating partial data traces through dynamic binary rewriting. The contributions are threefold. First, a portable method for extracting precise data traces for partial executions of arbitrary applications is developed. Second, a set of hierarchical structures for compactly representing these accesses is developed. Third, an efficient online algorithm to detect regular accesses is introduced. The authors utilize dynamic binary rewriting to selectively collect partial address traces of regions within a program. This allows partial tracing of hot paths for only a short time during program execution in contrast to static rewriting techniques that lack hot path detection and also lack facilities to limit the duration of data collection. Preliminary results show reductions of three orders of a magnitude of inline instrumentation over a dual process approach involving context switching. They also report constant size representations for regular access patters in nested loops. These efforts are part of a larger project to counter the increasing gap between processor and main memory speeds by means of software optimization and hardware enhancements.

  2. Partial purification and characterization of an aminopeptidase from Eimeria tenella.

    PubMed

    Fetterer, R H; Miska, K B; Barfield, R C

    2005-12-01

    Our previous investigation demonstrated the expression in Eimeria tenella sporulated oocysts of an aminopeptidase (AP) with strong homology to AP N. To further understand the role of proteases during development, we investigated the molecular and biochemical properties of E. tenella AP. Greater than 95% AP activity was present in a soluble extract during sporulation of oocysts with highest activity in fully sporulated oocysts. The AP activity was inhibited by the AP inhibitors bestatin and 1,6-phenanthroline, but not by serine protease inhibitors. The AP had specificity for synthetic endopeptidase substrates that contain arginine, alanine, or glycine at the N terminus. Partial purification of the enzyme yielded a major protein band with an Mr of about 106 kDa and an isoelectric point (Ip) of 5.1. Reverse transcription-polymerase chain reaction indicated that the gene for AP is expressed during sporulation, but expression is absent or greatly reduced in the sporozoites and merozoites. On the basis of the deduced gene structure, the predicted Mr is 110 kDa with a pI of 5.59. Database search indicates that the E. tenella AP shares significant homology with the AP from Apicomplexan taxa: Toxoplasma gondii, Cryptosporidium parvum, and Cryptosporidium hominis. Together, these results confirm the presence of a cytosolic AP related to AP N, which is expressed and active during sporulation of E. tenella oocysts. PMID:16539006

  3. Partial Rectangular Metric Spaces and Fixed Point Theorems

    PubMed Central

    2014-01-01

    The purpose of this paper is to introduce the concept of partial rectangular metric spaces as a generalization of rectangular metric and partial metric spaces. Some properties of partial rectangular metric spaces and some fixed point results for quasitype contraction in partial rectangular metric spaces are proved. Some examples are given to illustrate the observed results. PMID:24672366

  4. Planarian Immobilization, Partial Irradiation, and Tissue Transplantation

    PubMed Central

    Guedelhoefer IV, Otto C.; Sánchez Alvarado, Alejandro

    2012-01-01

    The planarian, a freshwater flatworm, has proven to be a powerful system for dissecting metazoan regeneration and stem cell biology1,2. Planarian regeneration of any missing or damaged tissues is made possible by adult stem cells termed neoblasts3. Although these stem cells have been definitively shown to be pluripotent and singularly capable of reconstituting an entire animal4, the heterogeneity within the stem cell population and the dynamics of their cellular behaviors remain largely unresolved. Due to the large number and wide distribution of stem cells throughout the planarian body plan, advanced methods for manipulating subpopulations of stem cells for molecular and functional study in vivo are needed. Tissue transplantation and partial irradiation are two methods by which a subpopulation of planarian stem cells can be isolated for further study. Each technique has distinct advantages. Tissue transplantation allows for the introduction of stem cells, into a naïve host, that are either inherently genetically distinct or have been previously treated pharmacologically. Alternatively, partial irradiation allows for the isolation of stem cells within a host, juxtaposed to tissue devoid of stem cells, without the introduction of a wound or any breech in tissue integrity. Using these two methods, one can investigate the cell autonomous and non-autonomous factors that control stem cell functions, such as proliferation, differentiation, and migration. Both tissue transplantation5,6 and partial irradiation7 have been used historically in defining many of the questions about planarian regeneration that remain under study today. However, these techniques have remained underused due to the laborious and inconsistent nature of previous methods. The protocols presented here represent a large step forward in decreasing the time and effort necessary to reproducibly generate large numbers of grafted or partially irradiated animals with efficacies approaching 100 percent. We

  5. Effects of hydrogen partial pressure on autotrophic growth and product formation of Acetobacterium woodii.

    PubMed

    Kantzow, Christina; Weuster-Botz, Dirk

    2016-08-01

    Low aqueous solubility of the gases for autotrophic fermentations (e.g., hydrogen gas) results in low productivities in bioreactors. A frequently suggested approach to overcome mass transfer limitation is to increase the solubility of the limiting gas in the reaction medium by increasing the partial pressure in the gas phase. An increased inlet hydrogen partial pressure of up to 2.1 bar (total pressure of 3.5 bar) was applied for the autotrophic conversion of hydrogen and carbon dioxide with Acetobacterium woodii in a batch-operated stirred-tank bioreactor with continuous gas supply. Compared to the autotrophic batch process with an inlet hydrogen partial pressure of 0.4 bar (total pressure of 1.0 bar) the final acetate concentration after 3.1 days was reduced to 50 % (29.2 g L(-1) compared to 59.3 g L(-1)), but the final formate concentration was increased by a factor of 18 (7.3 g L(-1) compared to 0.4 g L(-1)). Applying recombinant A. woodii strains overexpressing either genes for enzymes in the methyl branch of the Wood-Ljungdahl pathway or the genes phosphotransacetylase and acetate kinase at an inlet hydrogen partial pressure of 1.4 bar reduced the final formate concentration by up to 40 % and increased the final dry cell mass and acetate concentrations compared to the wild type strain. Solely the overexpression of the two genes for ATP regeneration at the end of the Wood-Ljungdahl pathway resulted in an initial switch off of formate production at increased hydrogen partial pressure until the maximum of the hydrogen uptake rate was reached. PMID:27059835

  6. Partially polarized Gaussian Schell-model beams

    NASA Astrophysics Data System (ADS)

    Gori, F.; Santarsiero, M.; Piquero, G.; Borghi, R.; Mondello, A.; Simon, R.

    2001-01-01

    We consider a class of beams that are both partially polarized and partially coherent from the spatial standpoint. They are characterized by a correlation matrix whose elements have the same form as the mutual intensity of a Gaussian Schell-model beam. We focus our attention on those beams that would appear identical to ordinary Gaussian Schell-model beams in a scalar treatment. After establishing some inequalities that limit the choice of the matrix parameters, we study the main effects of propagation. Starting from the source plane, in which the beam is assumed to be uniformly polarized, we find that in the course of propagation the degree of polarization generally becomes non-uniform across a typical section of the beam. Furthermore, we find that the intensity distribution at the output of an arbitrarily oriented linear polarizer is Gaussian shaped at the source plane whereas it can be quite different at other planes.

  7. Surgical repair of partial atrioventricular defect.

    PubMed

    El-Rassi, Issam; Charafedine, Fatimah; Majdalani, Mariane; Arabi, Mariam; Khater, Daniele; Bitar, Fadi

    2015-01-01

    Long-term survival rate of patients operated for partial atrioventricular (AV) canal is lower than that of the general population, and late complications are relatively significant: between 10 and 30% of operated patients present with left AV valve regurgitation, and up to 25% have to be reoperated for valve repair or replacement, left ventricular outflow tract obstruction or residual atrial septal defect. Because the left AV valve regurgitation is the most common complication following surgery, technical details in the surgical management of the mitral valve are the most important aspects of this procedure; for example, the decision to close the cleft and to perform an annuloplasty. The presence of mitral valve anomalies in 7-28% of the cases complicates further the surgical management of these valves. This article will describe in detail the operative technique of partial AV canal repair, and review the relevant literature. PMID:26685152

  8. Optimal partial deterministic quantum teleportation of qubits

    SciTech Connect

    Mista, Ladislav Jr.; Filip, Radim

    2005-02-01

    We propose a protocol implementing optimal partial deterministic quantum teleportation for qubits. This is a teleportation scheme realizing deterministically an optimal 1{yields}2 asymmetric universal cloning where one imperfect copy of the input state emerges at the sender's station while the other copy emerges at receiver's possibly distant station. The optimality means that the fidelities of the copies saturate the asymmetric cloning inequality. The performance of the protocol relies on the partial deterministic nondemolition Bell measurement that allows us to continuously control the flow of information among the outgoing qubits. We also demonstrate that the measurement is optimal two-qubit operation in the sense of the trade-off between the state disturbance and the information gain.

  9. Local cerebral metabolism during partial seizures

    SciTech Connect

    Engel, J. Jr.; Kuhl, D.E.; Phelps, M.E.; Rausch, R.; Nuwer, M.

    1983-04-01

    Interictal and ictal fluorodeoxyglucose scans were obtained with positron CT from four patients with spontaneous recurrent partial seizures, one with epilepsia partialis continua, and one with a single partial seizure induced by electrical stimulation of the hippocampus. Ictal metabolic patterns were different for each patient studied. Focal and generalized increased and decreased metabolism were observed. Ictal hypermetabolism may exceed six times the interictal rate and could represent activation of excitatory or inhibitory synapses in the epileptogenic region and its projection fields. Hypometabolism seen on ictal scans most likely reflects postictal depression and may indicate projection fields of inhibited neurons. No quantitative relationship between alterations in metabolism and EEG or behavioral measurements of ictal events could be demonstrated.

  10. The Lockheed alternate partial polarizer universal filter

    NASA Technical Reports Server (NTRS)

    Title, A. M.

    1976-01-01

    A tunable birefringent filter using an alternate partial polarizer design has been built. The filter has a transmission of 38% in polarized light. Its full width at half maximum is .09A at 5500A. It is tunable from 4500 to 8500A by means of stepping motor actuated rotating half wave plates and polarizers. Wave length commands and thermal compensation commands are generated by a PPD 11/10 minicomputer. The alternate partial polarizer universal filter is compared with the universal birefringent filter and the design techniques, construction methods, and filter performance are discussed in some detail. Based on the experience of this filter some conclusions regarding the future of birefringent filters are elaborated.

  11. Applications of partially quenched chiral perturbation theory

    SciTech Connect

    Golterman, M.F.; Leung, K.C.

    1998-05-01

    Partially quenched theories are theories in which the valence- and sea-quark masses are different. In this paper we calculate the nonanalytic one-loop corrections of some physical quantities: the chiral condensate, weak decay constants, Goldstone boson masses, B{sub K}, and the K{sup +}{r_arrow}{pi}{sup +}{pi}{sup 0} decay amplitude, using partially quenched chiral perturbation theory. Our results for weak decay constants and masses agree with, and generalize, results of previous work by Sharpe. We compare B{sub K} and the K{sup +} decay amplitude with their real-world values in some examples. For the latter quantity, two other systematic effects that plague lattice computations, namely, finite-volume effects and unphysical values of the quark masses and pion external momenta, are also considered. We find that typical one-loop corrections can be substantial. {copyright} {ital 1998} {ital The American Physical Society}

  12. Retinal pigment epithelial change and partial lipodystrophy.

    PubMed Central

    Davis, T. M.; Holdright, D. R.; Schulenberg, W. E.; Turner, R. C.; Joplin, G. F.

    1988-01-01

    Cuticular drusen and retinal pigment epithelial changes were found incidentally in a 27 year old Lebanese woman during assessment of partial lipodystrophy. Her vision was normal despite involvement of both maculae. The patient had hypocomplementaemia, but serum C3 nephritic factor was absent and renal function was normal. She had impaired glucose tolerance and a continuous infusion of glucose with model assessment (CIGMA) test revealed low normal tissue insulin sensitivity and high normal pancreatic beta cell function. Mild fasting hypertriglyceridaemia (2.0 mmol/l) may have been secondary to impaired insulin sensitivity. Endocrine function was otherwise normal apart from a completely absent growth hormone response to adequate hypoglycaemia. The simultaneous occurrence of partial lipodystrophy and retinal pigmentary epithelial and basement membrane changes appears to be a newly recognized syndrome. Images Figure 1 Figure 2 PMID:3255937

  13. Benign idiopathic partial epilepsy and brain lesion.

    PubMed

    Stephani, U; Doose, H

    1999-03-01

    A 14-year-old girl had severe head trauma from a dog bite at the age of 9 days. This resulted in extensive brain damage, tetraplegia, mental retardation, and epilepsy. The seizures were of rolandic type, and the EEG showed multifocal sharp waves. The course was benign. The initial diagnosis of a pure symptomatic epilepsy was revised after demonstrating typical benign focal sharp waves in the EEG of the healthy sister. Thus a phenocopy of a benign partial epilepsy by the brain lesion could be excluded with sufficient certainty. This observation allows the conclusion that the genetic disposition underlying the sharp-wave trait characteristic of benign partial epilepsies can be involved also in the pathogenesis of seemingly pure symptomatic epilepsies. EEG studies on siblings of such patients are needed to exclude possible phenocopies. PMID:10080522

  14. Partial Data Traces: Efficient Generation and Representation

    SciTech Connect

    Mueller,F; Mohan,T; de R. Supinski, B; McKee,S A; Yoo,A

    2001-07-16

    Binary manipulation techniques are increasing in popularity. They support program transformations tailored toward certain program inputs, and these transformations have been shown to yield performance gains beyond the scope of static code optimizations without profile-directed feedback. They even deliver moderate gains in the presence of profile-guided optimizations. In addition, transformations can be performed on the entire executable, including library routines. This work focuses on program instrumentation, yet another application of binary manipulation. This paper reports preliminary results on generating partial data traces through dynamic binary rewriting. The contributions are threefold. First, a portable method for extracting precise data traces for partial executions of arbitrary applications is developed. Second, a set of hierarchical structures for compactly representing these accesses is developed. Third, an efficient online algorithm to detect regular accesses is introduced. These efforts are part of a larger project to counter the increasing gap between processor and main memory speeds by means of software optimization and hardware enhancements.

  15. Apparatus for generating partially coherent radiation

    DOEpatents

    Naulleau, Patrick P.

    2004-09-28

    The effective coherence of an undulator beamline can be tailored to projection lithography requirements by using a simple single moving element and a simple stationary low-cost spherical mirror. The invention is particularly suited for use in an illuminator device for an optical image processing system requiring partially coherent illumination. The illuminator includes: (i) source of coherent or partially coherent radiation which has an intrinsic coherence that is higher than the desired coherence; (ii) a reflective surface that receives incident radiation from said source; (iii) means for moving the reflective surface through a desired range of angles in two dimensions wherein the rate of the motion is fast relative to integration time of said image processing system; and (iv) a condenser optic that re-images the moving reflective surface to the entrance plane of said image processing system, thereby, making the illumination spot in said entrance plane essentially stationary.

  16. Multiple teleportation via partially entangled GHZ state

    NASA Astrophysics Data System (ADS)

    Xiong, Pei-Ying; Yu, Xu-Tao; Zhan, Hai-Tao; Zhang, Zai-Chen

    2016-08-01

    Quantum teleportation is important for quantum communication. We propose a protocol that uses a partially entangled Greenberger-Horne-Zeilinger (GHZ) state for single hop teleportation. Quantum teleportation will succeed if the sender makes a Bell state measurement, and the receiver performs the Hadamard gate operation, applies appropriate Pauli operators, introduces an auxiliary particle, and applies the corresponding unitary matrix to recover the transmitted state.We also present a protocol to realize multiple teleportation of partially entangled GHZ state without an auxiliary particle. We show that the success probability of the teleportation is always 0 when the number of teleportations is odd. In order to improve the success probability of a multihop, we introduce the method used in our single hop teleportation, thus proposing a multiple teleportation protocol using auxiliary particles and a unitary matrix. The final success probability is shown to be improved significantly for the method without auxiliary particles for both an odd or even number of teleportations.

  17. Distributed acoustic sensing: towards partial discharge monitoring

    NASA Astrophysics Data System (ADS)

    Rohwetter, Philipp; Eisermann, René; Krebber, Katerina

    2015-09-01

    We report on the successful application of distributed acoustic sensing (DAS) to the detection of partial discharge (PD). A detection limit of about 1 nC discharge magnitude was achieved for PD in a real-scale model of a high voltage termination. Dedicated ultrasonic fibre-optic transducers were interrogated using coherent optical time-domain Rayleigh backscatter reflectometry (C-OTDR). Random quadrature demodulation was employed for retrieving relevant acoustic information from the raw C-OTDR backscatter traces. To our knowledge, our results are a first-time demonstration that quasi-distributed fibre-optic acoustic sensing is a candidate technology for the acoustic partial discharge monitoring of power cable joints and terminations.

  18. Dynamic partial FPGA reconfiguration in space applications

    NASA Astrophysics Data System (ADS)

    Graczyk, Rafal; Stolarski, Marcin; Palau, Marie-Catherine; Orleanski, Piotr

    2012-05-01

    Design and implementation of hardware mock-up of high performance system for general avionics testing in reconfigurable FPGAs. Strong emphasis is put on exploiting dynamic partial reconfiguration capability as a method for functionality multiplexing and fault mitigation. Additionally, dynamic reconfiguration can be used for fault injection which makes Single Event Upset in configuration memory simulation possible. LEON3 processors are used to create an avionic systems test-bed, for testing the mock-ups of real system flight software and testing dynamic full and partial reconfiguration. Experiments with different means of reconfiguration are performed to measure reconfiguration times and stability of software. Several solutions for whole system reconfiguration controller have been implemented and tested.

  19. Inviscid Partial Coalescence from Bubbles to Drops

    NASA Astrophysics Data System (ADS)

    Zhang, F. H.; Taborek, P.; Burton, J.; Khoo, B. C.; Lim, K. M.; Thoroddsen, S. T.

    2010-11-01

    Coalescence of bubbles (drops) not only coarse the bubble (drop) sizes, but sometimes produces satellite bubbles (droplets), known as partial coalescence. To explore links between the drop and bubble cases, we experimentally study the partial coalescence of pressurized xenon gas bubbles in nano de-ionized water using high-speed video imaging. The size of these satellites relative to their mother bubbles is found to increase with the density ratio of the gas to the liquid. Moreover, sub-satellite bubbles are sometimes observed, whose size is also found to increase with the density ratio, while keeps about one quarter of the primary satellite. The time duration from start of the coalescence to formation of the satellites, scaled by the capillary time, increases with the density ratio too. In addition, as the size ratio of the father bubble to the mother bubble increases moderately, their coalescence proceeds faster and the sub-satellite is prone to form and relatively larger.

  20. Class of positive partial transposition states

    SciTech Connect

    Chruscinski, Dariusz; Kossakowski, Andrzej

    2006-08-15

    We construct a class of quantum bipartite d(multiply-in-circle sign)d states which are positive under partial transposition (PPT states). This class is invariant under the maximal commutative subgroup of U(d) and contains as special cases many well-known examples of PPT states. States from our class provide criteria for testing the indecomposability of positive maps. Such maps are crucial for constructing entanglement witnesses.

  1. The partially filled viscous ring damper.

    NASA Technical Reports Server (NTRS)

    Alfriend, K. T.

    1973-01-01

    The problem of a spinning satellite with a partially filled viscous ring damper is investigated. It is shown that there are two distinct modes of motion, the nutation-synchronous mode and spin-synchronous mode. From an approximate solution of the equations of motion a time constant is obtained for each mode. From a consideration of the fluid dynamics several methods are developed for determining the damping constant.

  2. Lifted Partially Premixed Flames in Microgravity

    NASA Technical Reports Server (NTRS)

    Lock, Andrew J.; Ganguly, Ranjan; Puri, Ishwar K.; Aggarwal, Suesh K.; Hegde, Uday

    2004-01-01

    Lifted Double and Triple flames are established in the UIC-NASA Partially Premixed microgravity rig. The flames examined in this paper are established above a coannular burner because its axisymmetric geometry allows for future implementation of other non-intrusive optical diagnostic techniques easily. Both burner-attached stable flames and lifted flames are established at normal and microgravity conditions in the drop tower facility.

  3. Partial differential equation models in macroeconomics.

    PubMed

    Achdou, Yves; Buera, Francisco J; Lasry, Jean-Michel; Lions, Pierre-Louis; Moll, Benjamin

    2014-11-13

    The purpose of this article is to get mathematicians interested in studying a number of partial differential equations (PDEs) that naturally arise in macroeconomics. These PDEs come from models designed to study some of the most important questions in economics. At the same time, they are highly interesting for mathematicians because their structure is often quite difficult. We present a number of examples of such PDEs, discuss what is known about their properties, and list some open questions for future research. PMID:25288811

  4. Pseudopotential Method for Higher Partial Wave Scattering

    SciTech Connect

    Idziaszek, Zbigniew; Calarco, Tommaso

    2006-01-13

    We present a zero-range pseudopotential applicable for all partial wave interactions between neutral atoms. For p and d waves, we derive effective pseudopotentials, which are useful for problems involving anisotropic external potentials. Finally, we consider two nontrivial applications of the p-wave pseudopotential: we solve analytically the problem of two interacting spin-polarized fermions confined in a harmonic trap, and we analyze the scattering of p-wave interacting particles in a quasi-two-dimensional system.

  5. Partial Dynamical Symmetry in Nuclear Systems

    SciTech Connect

    Escher, J E

    2003-06-02

    Partial dynamical symmetry (PDS) extends and complements the concepts of exact and dynamical symmetry. It allows one to remove undesired constraints from an algebraic theory, while preserving some of the useful aspects of a dynamical symmetry, and to study the effects of symmetry breaking in a controlled manner. An example of a PDS in an interacting fermion system is presented. The associated PDS Hamiltonians are closely related with a realistic quadrupole-quadrupole interaction and provide new insights into this important interaction.

  6. Collagen dynamics of partial small bowel obstruction

    SciTech Connect

    Stromberg, B.V.; Klein, L.

    1984-08-01

    The response of intestinal collagen to obstruction and stress was studied in the rat. Partial small bowel obstructions were created. Preobstruction collagen was measured by injection of tritium labeled proline. New collagen formation after obstruction occurred was followed by injection of carbon-14 labeled proline. At 3 weeks, collagen fractions were identified. Throughout the study, preexisting preobstruction intestinal collagen was metabolically stable with no breakdown or remodeling demonstrable. New collagen formation was rapid and occurred to the largest degree close to the obstruction.

  7. Partial discharge testing under direct voltage conditions

    NASA Technical Reports Server (NTRS)

    Bever, R. S.; Westrom, J. L.

    1982-01-01

    DC partial discharge (PD) (corona) testing is performed using a multichannel analyzer for pulse storing, and data is collected during increase of voltage and at quiescent voltage levels. Thus high voltage ceramic disk capacitors were evaluated by obtaining PD data interspersed during an accelerated life test. Increased PD activity was found early in samples that later failed catastrophically. By this technique, trends of insulation behavior are revealed sensitively and nondestructively in high voltage dc components.

  8. Observability of discretized partial differential equations

    NASA Technical Reports Server (NTRS)

    Cohn, Stephen E.; Dee, Dick P.

    1988-01-01

    It is shown that complete observability of the discrete model used to assimilate data from a linear partial differential equation (PDE) system is necessary and sufficient for asymptotic stability of the data assimilation process. The observability theory for discrete systems is reviewed and applied to obtain simple observability tests for discretized constant-coefficient PDEs. Examples are used to show how numerical dispersion can result in discrete dynamics with multiple eigenvalues, thereby detracting from observability.

  9. Anisotropic pure-phase plates for quality improvement of partially coherent, partially polarized beams.

    PubMed

    Martínez-Herrero, Rosario; Mejías, Pedro M; Piquero, Gemma

    2003-03-01

    From a theoretical point of view, the use of anisotropic pure-phase plates (APP) is considered in order to improve the quality parameter of certain partially coherent, partially polarized beams. It is shown that, to optimize the beam-quality parameter, the phases of the two Cartesian components of the field at the output of the APP plate should be identical and should exhibit a quadratic dependence on the radial polar coordinate. PMID:12630845

  10. Anisotropic pure-phase plates for quality improvement of partially coherent, partially polarized beams

    NASA Astrophysics Data System (ADS)

    MartíNez-Herrero, Rosario; MejíAs, Pedro M.; Piquero, Gemma

    2003-03-01

    From a theoretical point of view, the use of anisotropic pure-phase plates (APP) is considered in order to improve the quality parameter of certain partially coherent, partially polarized beams. It is shown that, to optimize the beam-quality parameter, the phases of the two Cartesian components of the field at the output of the APP plate should be identical and should exhibit a quadratic dependence on the radial polar coordinate.

  11. Conformal Visualization for Partially-Immersive Platforms

    PubMed Central

    Petkov, Kaloian; Papadopoulos, Charilaos; Zhang, Min; Kaufman, Arie E.; Gu, Xianfeng

    2010-01-01

    Current immersive VR systems such as the CAVE provide an effective platform for the immersive exploration of large 3D data. A major limitation is that in most cases at least one display surface is missing due to space, access or cost constraints. This partially-immersive visualization results in a substantial loss of visual information that may be acceptable for some applications, however it becomes a major obstacle for critical tasks, such as the analysis of medical data. We propose a conformal deformation rendering pipeline for the visualization of datasets on partially-immersive platforms. The angle-preserving conformal mapping approach is used to map the 360°3D view volume to arbitrary display configurations. It has the desirable property of preserving shapes under distortion, which is important for identifying features, especially in medical data. The conformal mapping is used for rasterization, realtime raytracing and volume rendering of the datasets. Since the technique is applied during the rendering, we can construct stereoscopic images from the data, which is usually not true for image-based distortion approaches. We demonstrate the stereo conformal mapping rendering pipeline in the partially-immersive 5-wall Immersive Cabin (IC) for virtual colonoscopy and architectural review. PMID:26279083

  12. Multichannel cochlear implants in partially ossified cochleas.

    PubMed

    Balkany, T; Gantz, B; Nadol, J B

    1988-01-01

    Deposition of bone within the fluid spaces of the cochlea is encountered commonly in cochlear implant candidates and previously has been considered a relative contraindication to the use of multichannel intracochlear electrodes. This contraindication has been based on possible mechanical difficulty with electrode insertion as well as uncertainty about the potential benefit of the multichannel device in the patient. Fifteen profoundly deaf patients with partial ossification of the basal turn of the cochlea received implants with long intracochlear electrodes (11, Nucleus; 1, University of California at San Francisco/Storz; and 3, Symbion/Inneraid). In 11 cases, ossification had been predicted preoperatively by computed tomographic scan. Electrodes were completely inserted in 14 patients, and partial insertion was accomplished in one patient. All patients currently are using their devices and nine of 12 postlingually deaf patients have achieved some degree of open-set speech discrimination. This series demonstrates that in experienced hands, insertion of long multichannel electrodes into partially ossified cochleas is possible and that results are similar to those achieved in patients who have nonossified cochleas. PMID:3140705

  13. Acute renal injury after partial hepatectomy

    PubMed Central

    Peres, Luis Alberto Batista; Bredt, Luis Cesar; Cipriani, Raphael Flavio Fachini

    2016-01-01

    Currently, partial hepatectomy is the treatment of choice for a wide variety of liver and biliary conditions. Among the possible complications of partial hepatectomy, acute kidney injury (AKI) should be considered as an important cause of increased morbidity and postoperative mortality. Difficulties in the data analysis related to postoperative AKI after liver resections are mainly due to the multiplicity of factors to be considered in the surgical patients, moreover, there is no consensus of the exact definition of AKI after liver resection in the literature, which hampers comparison and analysis of the scarce data published on the subject. Despite this multiplicity of risk factors for postoperative AKI after partial hepatectomy, there are main factors that clearly contribute to its occurrence. First factor relates to large blood losses with renal hypoperfusion during the operation, second factor relates to the occurrence of post-hepatectomy liver failure with consequent distributive circulatory changes and hepatorenal syndrome. Eventually, patients can have more than one factor contributing to post-operative AKI, and frequently these combinations of acute insults can be aggravated by sepsis or exposure to nephrotoxic drugs. PMID:27478539

  14. Energy considerations in the partial space elevator

    NASA Astrophysics Data System (ADS)

    Woo, Pamela; Misra, Arun K.

    2014-06-01

    The space elevator has been proposed as an alternate method for space transportation. A partial elevator is composed of a tether of several hundreds of kilometres, held vertically in tension between two end masses, with its centre of orbit placed at the geosynchronous orbit. A spacecraft can dock at the lower end, and then use the climber on the elevator to ascend to higher altitudes. In this paper, energy calculations are performed, to determine whether a partial elevator can provide sufficient savings in operational costs, compared to the traditional rocket-powered launch. The energy required to launch a spacecraft from a Low Earth Orbit (LEO) to the geostationary orbit (GEO) is calculated for two trajectories. In the first trajectory, the spacecraft travels from LEO to GEO via a Hohmann transfer. In the second trajectory, the spacecraft travels from LEO to the lower end of the partial space elevator with a Hohmann transfer, and then uses the elevator to climb to GEO. The total energy required is compared between the two trajectories. The effects of tether length, spacecraft-to-climber mass ratio, altitude of LEO, and tether material are investigated.

  15. Viscous fingering with partial miscible fluids

    NASA Astrophysics Data System (ADS)

    Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

    2015-11-01

    When a less viscous fluid displaces a more viscous fluid, the contrast in viscosity destabilizes the interface between the two fluids, leading to the formation of fingers. Studies of viscous fingering have focused on fluids that are either fully miscible or perfectly immiscible. In practice, however, the miscibility of two fluids can change appreciably with temperature and pressure, and often falls into the case of partial miscibility, where two fluids have limited solubility in each other. Following our recent work for miscible (Jha et al., PRL 2011, 2013) and immiscible systems (Cueto-Felgueroso and Juanes, PRL 2012, JFM 2014), here we propose a phase-field model for fluid-fluid displacements in a Hele-Shaw cell, when the two fluids have limited (but nonzero) solubility in one another. Partial miscibility is characterized through the design of thermodynamic free energy of the two-fluid system. We elucidate the key dimensionless groups that control the behavior of the system. We present high-resolution numerical simulations of the model applied to the viscous fingering problem. On one hand, we demonstrate the effect of partial miscibility on the hydrodynamic instability. On the other, we elucidate the role of the degree of fingering on the rate of mutual fluid dissolution.

  16. Eslicarbazepine acetate for partial-onset seizures.

    PubMed

    Rauchenzauner, Markus; Luef, Gerhard

    2011-12-01

    Eslicarbazepine acetate (ESL), a new voltage-gated sodium channel blocker that is chemically related to carbamazepine and partially metabolized to oxcarbazepine, has attracted attention as results of previous Phase II and III studies demonstrated and confirmed efficacy and tolerability of ESL 800 and 1200 mg once daily as add-on therapy for adult patients with drug-resistant partial-onset seizures. In children, efficacy data point towards a dose-dependent decrease in seizure frequency and tolerability analyses showed a low incidence of mild drug-related adverse effects at 5 and 15 mg/kg/day. The most frequently reported adverse effects were dizziness, somnolence, headache, diplopia, nausea and vomiting. The convenience of once-daily dosing and a short/simple titration regimen in combination with a comparative efficacy and tolerability profile might promote ESL as a valid alternative to the current adjunctive antiepileptic drug therapy armamentarium for drug-resistant partial seizures in adults. Since clinical trials in children and adolescents on ESL efficacy and safety are ongoing and data already published are far from conclusive, the therapeutic value of ESL in this special population has to be established in the near future. PMID:22091592

  17. Partial-Vacuum-Gasketed Electrochemical Corrosion Cell

    NASA Technical Reports Server (NTRS)

    Bonifas, Andrew P.; Calle, Luz M.; Hintze, Paul E.

    2006-01-01

    An electrochemical cell for making corrosion measurements has been designed to prevent or reduce crevice corrosion, which is a common source of error in prior such cells. The present cell (see figure) includes an electrolyte reservoir with O-ring-edged opening at the bottom. In preparation for a test, the reservoir, while empty, is pressed down against a horizontal specimen surface to form an O-ring seal. A purge of air or other suitable gas is begun in the reservoir, and the pressure in the reservoir is regulated to maintain a partial vacuum. While maintaining the purge and partial vacuum, and without opening the interior of the reservoir to the atmosphere, the electrolyte is pumped into the reservoir. The reservoir is then slowly lifted a short distance off the specimen. The level of the partial vacuum is chosen such that the differential pressure is just sufficient to keep the electrolyte from flowing out of the reservoir through the small O-ring/specimen gap. Electrochemical measurements are then made. Because there is no gasket (and, hence, no crevice between the specimen and the gasket), crevice corrosion is unlikely to occur.

  18. Acute renal injury after partial hepatectomy.

    PubMed

    Peres, Luis Alberto Batista; Bredt, Luis Cesar; Cipriani, Raphael Flavio Fachini

    2016-07-28

    Currently, partial hepatectomy is the treatment of choice for a wide variety of liver and biliary conditions. Among the possible complications of partial hepatectomy, acute kidney injury (AKI) should be considered as an important cause of increased morbidity and postoperative mortality. Difficulties in the data analysis related to postoperative AKI after liver resections are mainly due to the multiplicity of factors to be considered in the surgical patients, moreover, there is no consensus of the exact definition of AKI after liver resection in the literature, which hampers comparison and analysis of the scarce data published on the subject. Despite this multiplicity of risk factors for postoperative AKI after partial hepatectomy, there are main factors that clearly contribute to its occurrence. First factor relates to large blood losses with renal hypoperfusion during the operation, second factor relates to the occurrence of post-hepatectomy liver failure with consequent distributive circulatory changes and hepatorenal syndrome. Eventually, patients can have more than one factor contributing to post-operative AKI, and frequently these combinations of acute insults can be aggravated by sepsis or exposure to nephrotoxic drugs. PMID:27478539

  19. Sorting network for the partial selection problem

    NASA Astrophysics Data System (ADS)

    Belzile, Jean; Savaria, Yvon; Haccoun, David

    Sorting networks and switching networks are widely used in the communication world. Partial selection networks have applications in areas where a single answer is desired but several paths are explored such as in suboptimal breadth-first tree searching algorithms. A technique is introduced which permits the evaluation of any network in terms of average selection and in terms of the number of elements that are always in the partial selection set. The Banyan network was examined using the method and it was found that the quality of the selection decreases as the size of the input set grows. It was also shown that the sorting networks such as the Banyan are not necessarily the best choices for selection problems. Networks which partially sort two sets and then compare the two sets together can achieve much better selection. These two types of network offer a higher number of guaranteed items than the Banyan network for all considered values of elements. Finally, it was noted that deterministic pre-ordering, if present, can also be used to configure a network.

  20. Autosomal Trisomies and Partial Trisomy Syndromes

    PubMed Central

    Zaleski, W. A.

    1963-01-01

    The establishing of 46 chromosomes as the normal complement in man and the report of the sex chromatin bodies in buccal smears were followed by reports of trisomies and other abnormal patterns of the X and Y chromosomes in Klinefelter's and Turner's syndromes. Abnormal autosomal complements were described in mongolism, in the E-trisomy syndrome, the D-trisomy syndrome, in the Sturge-Weber syndrome, Waldenstrom's macroglobulinemia, benign congenital hypotonia, atrial septal defect and in the schizoid personality. Certain of these conditions, as well as the “oral-facial-digital” syndrome, were also found to exist as partial trisomies. The mechanism of a trisomy is one of non-disjunction and of partial trisomy translocation or insertion. Two cases of the partial trisomy in the E group are described; these are of especial interest because of the familial incidence, longer survival and male sex occurrence, features which are rarely seen in the full E-trisomy syndrome. ImagesFig. 4Fig. 5Fig. 6 PMID:20327419

  1. Bilateral Laparoscopic Partial Nephrectomies: A Case Report

    PubMed Central

    Panuganti, Sravan; Kavoussi, Louis Raphael

    2015-01-01

    Abstract Although laparoscopy is a recognized operative approach to the management of renal masses, there is currently no standardized approach to manage bilateral synchronous renal masses. We present a case of synchronous bilateral renal masses, identified during work-up for flank pain, and managed simultaneously with laparoscopic partial nephrectomies. The patient is a 42-year-old Caucasian male found to have bilateral renal masses during evaluation for left flank pain. Cross-sectional imaging studies showed a 7.0 × 7.3 × 5.2 cm anterior, mid-to-lower pole mass on the left kidney and a 1.5 × 1.9 × 1.6 cm medial lower pole mass on the right kidney. He underwent bilateral laparoscopic partial nephrectomy at the same setting, with an uncomplicated postoperative course. Pathology report revealed clear cell renal-cell carcinoma (ccRCC) on both sides. He had normal renal function and no evidence of recurrence in the first 6 months of follow-up. This case demonstrates the possibility and safety of performing bilateral laparoscopic partial nephrectomies in one operative session. Our review of the literature supports the role of genetic counseling and the need for long-term surveillance in young patients having RCC.

  2. Partial rotor-to-stator rub demonstration

    NASA Technical Reports Server (NTRS)

    Grissom, R.

    1985-01-01

    A rotor radial rub typically occurs in seals or at a blade tip or shroud when there is insufficient clearance, high vibration, or the shaft equilibrium position has been displaced to effectively limit the clearance (eccentricity). There are two extreme cases of radial rubs: full annular rub, when the rotor maintains continuous contact with the seal, etc.; and a partial rub, when the contact occurs during a fraction of the precession period. They both involve similar physical phenomena such as friction and modification of stiffness. In partial rubs with consecutive impacts, a significant average value of radial force is generated. This results in shaft average displacement in the direction opposite the rub location. The rotor rig demonstrates the characteristics of a partial lateral rub of varying severity and location. These characteristics include: (1) subharmonic components as a function of rotative speed/first balance resonance ratio and radial force; (2) higher harmonic content as a function of severity; (3) increased average rotor stiffness resulting in increased first balance resonance speed; and (4) change in overall orbital pattern as a sum of the unbalance response (1x) and subharmonic response (1nx).

  3. Partial molecular volumes of lipids and cholesterol

    PubMed Central

    Greenwood, Alexander I.; Tristram-Nagle, Stephanie; Nagle, John F.

    2009-01-01

    Volumetric measurements are reported for fully hydrated lipid/cholesterol bilayer mixtures using the neutral flotation method. Apparent specific volume data were obtained with the lipids DOPC, POPC and DMPC at T = 30 °C, DPPC at 50 °C, and brain sphingomyelin (BSM) at 45 and 24 °C for mole fractions of cholesterol x from 0 to 0.5. Unlike previous cholesterol mixture studies, we converted our raw data to partial molecular volume VL of the lipid and VC of the cholesterol. The partial molecular volumes were constant for POPC and DOPC as x was varied, but had sharp breaks for the other lipids at values of xC near 0.25 ± 0.05. Results for x < xC clearly exhibit the condensation effect of cholesterol on DPPC, DMPC and BSM when measured at temperatures above their main transition temperatures TM. The break points at xC are compared to phase diagrams in the literature. For x > xC the values of the partial molecular volumes of cholesterol clustered near 630 ± 10 Å3 in all the lipids when measured for T > TM; we suggest that this is the most appropriate measure of the bare volume of cholesterol in lipid bilayers. PMID:16737691

  4. Partial transfer entropy on rank vectors

    NASA Astrophysics Data System (ADS)

    Kugiumtzis, D.

    2013-06-01

    For the evaluation of information flow in bivariate time series, information measures have been employed, such as the transfer entropy (TE), the symbolic transfer entropy (STE), defined similarly to TE but on the ranks of the components of the reconstructed vectors, and the transfer entropy on rank vectors (TERV), similar to STE but forming the ranks for the future samples of the response system with regard to the current reconstructed vector. Here we extend TERV for multivariate time series, and account for the presence of confounding variables, called partial transfer entropy on ranks (PTERV). We investigate the asymptotic properties of PTERV, and also partial STE (PSTE), construct parametric significance tests under approximations with Gaussian and gamma null distributions, and show that the parametric tests cannot achieve the power of the randomization test using time-shifted surrogates. Using simulations on known coupled dynamical systems and applying parametric and randomization significance tests, we show that PTERV performs better than PSTE but worse than the partial transfer entropy (PTE). However, PTERV, unlike PTE, is robust to the presence of drifts in the time series and it is also not affected by the level of detrending.

  5. Partial entrainment of gravel bars during floods

    USGS Publications Warehouse

    Konrad, C.P.; Booth, D.B.; Burges, S.J.; Montgomery, D.R.

    2002-01-01

    Spatial patterns of bed material entrainment by floods were documented at seven gravel bars using arrays of metal washers (bed tags) placed in the streambed. The observed patterns were used to test a general stochastic model that bed material entrainment is a spatially independent, random process where the probability of entrainment is uniform over a gravel bar and a function of the peak dimensionless shear stress ??*0 of the flood. The fraction of tags missing from a gravel bar during a flood, or partial entrainment, had an approximately normal distribution with respect to ??*0 with a mean value (50% of the tags entrained) of 0.085 and standard deviation of 0.022 (root-mean-square error of 0.09). Variation in partial entrainment for a given ??*0 demonstrated the effects of flow conditioning on bed strength, with lower values of partial entrainment after intermediate magnitude floods (0.065 < ??*0 < 0.08) than after higher magnitude floods. Although the probability of bed material entrainment was approximately uniform over a gravel bar during individual floods and independent from flood to flood, regions of preferential stability and instability emerged at some bars over the course of a wet season. Deviations from spatially uniform and independent bed material entrainment were most pronounced for reaches with varied flow and in consecutive floods with small to intermediate magnitudes.

  6. Functional activity of the porcine Gnrhr2 gene promoter in testis-derived cells is partially conferred by nuclear factor-κB, specificity protein 1 and 3 (SP1/3) and overlapping early growth response 1/SP1/3 binding sites.

    PubMed

    Brauer, Vanessa M; Wiarda-Bell, Jocelyn R; Desaulniers, Amy T; Cederberg, Rebecca A; White, Brett R

    2016-08-10

    Unlike the classical gonadotropin-releasing hormone (GnRH1), the second mammalian isoform (GnRH2) is ubiquitously expressed, suggesting a divergent function. Indeed, we demonstrated that GnRH2 governs LH-independent testosterone secretion in porcine testes via interaction with its receptor (GnRHR2) on Leydig cells. Transient transfections with luciferase reporter vectors containing 3009bp of 5' flanking sequence for the porcine Gnrhr2 gene (-3009pGL3) revealed promoter activity in all 15 cell lines examined, including swine testis-derived (ST) cells. Therefore, ST cells were utilized to explore the molecular mechanisms underlying transcriptional regulation of the porcine Gnrhr2 gene in the testis. Reporter plasmids containing progressive 5' deletions of the Gnrhr2 promoter indicated that the -708/-490 region contained elements critical to promoter activity. Electrophoretic mobility shift assays (EMSAs) with radiolabeled oligonucleotides spanning the -708/-490bp region and ST nuclear extracts, identified specific binding complexes for the -513/-490, -591/-571 and -606/-581bp segments of promoter. Antibody addition to EMSAs indicated that the p65 and p52 subunits of nuclear factor-κB (NF-κB) comprised the specific complex bound to the oligonucleotide probe for the -513/-490bp promoter region, specificity protein (SP) 1 and 3 bound the -591/-571bp probe and early growth response 1 (EGR1), SP1 and SP3 bound the -606/-581 radiolabeled oligonucleotide. Transient transfections with vectors containing mutations of the NF-κB (-499/-493), SP1/3 (-582/-575) or overlapping EGR1/SP1/3 (-597/-587) binding sites reduced luciferase activity by 26%, 61% and 56%, respectively (P<0.05). Thus, NF-κB, SP1/3 and overlapping EGR1/SP1/3 binding sites are critical to expression of the porcine Gnrhr2 gene in ST cells. PMID:27134031

  7. Partial Transition Warming Remanence ("Inverse TRM")

    NASA Astrophysics Data System (ADS)

    Dunlop, D. J.

    2001-12-01

    "Inverse TRM" (ITRM) produced by warming magnetite through the Verwey transition was discovered by Nagata et al. (1963), who speculated that the NRM of magnetite-bearing meteorites could be in part ITRM acquired by warming in the Earth's magnetic field after impact rather than a record of extraterrestrial fields. New results are reported here for ITRM and partial ITRM (acquired over narrow intervals of temperature during warming), including tests of partial ITRM additivity and reciprocity intended to lay the groundwork for an ITRM Thellier-analog cooling method of paleointensity determination. Memory ratios for ITRM low-temperature demagnetization (LTD) ranged from 0.254 to 0.092 for 0.6-135 um magnetites. ITRM was less resistant to LTD than TRM, leaving an ITRM memory similar to remanence after 15 mT AF cleaning. However, ITRM memory was much more stable against thermal demagnetization than the original ITRM and would contaminate NRM up to the highest steps of paleointensity determination. Next the thermal demagnetization of total ITRM and of a partial ITRM produced by switching off the field partway through warming from 77 K to 300 K were compared for nine magnetite size fractions. For the 1-14 um magnetites, 75-85% of the ITRM decayed quasi-linearly from 25 to 550oC, then dropped to zero by 570oC. The 20, 110 and 135 um magnetites demagnetized in two stages: a 50% loss from 20-250oC, a leveling out until 500oC, and a final plunge to zero above 550oC. Partial ITRMs of 0.6-20 um magnetites were more resistant to thermal demagnetization than total ITRMs. The decay was still quasi-linear or two-stage, but twice as much remanence survived at 550oC. The most stable part of ITRM seems to be acquired in the earliest stages of the Verwey transition, well below 120 K. The final experiments studied sets of neighbouring partial ITRMs, using 12 narrow T intervals from 20 to 300 K. The reciprocity law was obeyed for all samples: pITRM(T1, T2) was completely erased by zero

  8. Quantitative trait loci for partial resistance to Pseudomonas syringae pv. maculicola in Arabidopsis thaliana

    PubMed Central

    Rant, Jenni C; Arraiano, Lia S; Chabannes, Matthieu; Brown, James K M

    2013-01-01

    Segregation of partial resistance to Pseudomonas syringae pv. maculicola (Psm) ES4326 was studied in the recombinant inbred population created from accessions (ecotypes) Columbia (Col-4), the more susceptible parent, and Landsberg (Ler-0). Plants were spray inoculated with lux-transformed bacteria in experiments to measure susceptibility. The amount of disease produced on a range of Col × Ler lines by spray inoculation was highly correlated with that produced by pressure infiltration of bacteria into the apoplast. Quantitative trait locus (QTL) analysis identified four loci that contributed to partial resistance: QRps.JIC-1.1, QRps.JIC-2.1, QRps.JIC-3.1 and QRps.JIC-5.1 on chromosomes 1, 2, 3 and 5, respectively. QRps.JIC-3.1, located 8.45 cM from the top of the consensus genetic map of chromosome 3, had a large, approximately additive effect on partial resistance, explaining 50% of the genetic variation in this population. Fine mapping narrowed the region within which this QTL was located to 62 genes. A list of candidate genes included several major classes of resistance gene. PMID:23724899

  9. Management of 46, XY partial gonadal dysgenesis--revisited.

    PubMed

    Crone, Julia; Amann, Gabriele; Gheradini, Rainer; Kirchlechner, Veronika; Fékété, Claire-Nihoul

    2002-06-28

    46, XY partial gonadal dysgenesis is a rare condition characterized by a varying degree of testicular dysgenesis, ambiguous genitalia, and usually absence of regression of Müllerian structures. The management of patients with these disorders warrants revisiting, owing to recent molecular biological findings and to reports on the long-term outcome of individuals with ambiguous genitalia. We report on a patient with 46, XY chromosomes, presence of the "sex-determining region of Y chromosome" (SRY) gene, scrotal gonads, fallopain tubes, uterus, vagina, and ambiguous genitalia with a penisoid, perineal hypospadia and sinus urogenitalis. Gonadal biopsy revealed virtually normal testicular tissue in both gonads. Removal of the gonads during surgery for a cystic adnex tumor revealed clear signs of partial gonadal dysgenesis. The decision to raise the child as a male was made by parents and physicians caring for the patient. Administration of testosterone, removal of the uterus and adnexes, in addition to repair of the hypospadia permitted an almost normal penis to be formed with normal male micturition. In the management of affected patients it has to be considered that establishing the diagnosis may be extremely tricky, even with the use of gonadal biopsies. The decision on sex assignment may be even more difficult, since future gender identity, limitations of genital reconstructive surgery and the potential for development of gonadal tumors have to be taken into consideration. While in the past, female sex assignment was commonly recommended for such patients, raising them in a male gender role is now considered. Parents should be involved in the decision that is ultimately based on extensive analysis of the individual case. PMID:12422582

  10. Effects of methyl mercury on the activity and gene expression of mouse Langerhans islets and glucose metabolism.

    PubMed

    Maqbool, Faheem; Bahadar, Haji; Niaz, Kamal; Baeeri, Maryam; Rahimifard, Mahban; Navaei-Nigjeh, Mona; Ghasemi-Niri, Seyedeh Farnaz; Abdollahi, Mohammad

    2016-07-01

    Mercury (Hg) is a well-known heavy metal and causes various toxic effects. It is abundantly present in fish in the form of methyl mercury (MeHg). Also, various other forms of mercury can enter human body either from environment like inhalation or through dental amalgams. The present study was designed to assess MeHg induced toxicity in mouse plasma and pancreatic islets with respect to insulin secretion, oxidative balance, glucose tolerance, gene expression, caspases 3 and 9 activities. MeHg was dissolved in tap water and administered at doses 2.5, 5 and 10 mg/kg/day, for 4 weeks. In mice, MeHg significantly caused increase in plasma insulin as well as C-peptides. Glucose intolerance, insulin resistance and hyperglycemia are main consequences of our study that correlate with the gene expression changes of glucose homeostasis as well. MeHg caused increase lipid peroxidation in a dose-dependent manner in plasma as well as pancreatic islets. In addition, total thiol molecules and ferrous reducing antioxidant power in MeHg treated group was decreased in plasma as well as pancreatic islets. Caspases 3 and 9 activities of pancreatic islets were upregulated in MeHg exposed animals. Reactive oxygen species were extremely high in pancreatic islets of MeHg treated groups. MeHg disrupted gluconeogenesis/glycogenolysis pathways and insulin secretory functions of islets by targeting GDH, GLUT2 and GCK genes of pancreatic islets. In conclusion, the current study revealed that insulin pathways, oxidative balance and glucose metabolism encoded genetic makeup are susceptible to MeHg toxicity and the subsequent oxidative stress and alternations in gene expression could lead toward functional abnormalities in other organs. PMID:27178136

  11. Programmed cell death and the gene behind spinal muscular atrophy.

    PubMed Central

    Robinson, A

    1995-01-01

    A gene involved in the development of spinal muscular atrophy (SMA) has been found on human chromosome 5 after a 4-year search. Named the neuronal apoptosis inhibitor protein (NAIP) gene, it is believed to inhibit the normal process of apoptosis--the disintegration of single cells that results from programmed cell death--in motor neurons. The researchers who found the NAIP gene also discovered that healthy people carry one complete copy of the gene along with many other partial copies. Many children with SMA have the partial copies but not the complete gene. This discovery facilitates the accurate genetic diagnosis of SMA. But gene therapy for SMA will not be possible until researchers find a suitable vector to stably introduce activated and intact copies of the gene into the motor neurons of children with SMA in time to stop motor neuron loss. Images p1460-a PMID:7585374

  12. Turbulent flame propagation in partially premixed flames

    NASA Technical Reports Server (NTRS)

    Poinsot, T.; Veynante, D.; Trouve, A.; Ruetsch, G.

    1996-01-01

    Turbulent premixed flame propagation is essential in many practical devices. In the past, fundamental and modeling studies of propagating flames have generally focused on turbulent flame propagation in mixtures of homogeneous composition, i.e. a mixture where the fuel-oxidizer mass ratio, or equivalence ratio, is uniform. This situation corresponds to the ideal case of perfect premixing between fuel and oxidizer. In practical situations, however, deviations from this ideal case occur frequently. In stratified reciprocating engines, fuel injection and large-scale flow motions are fine-tuned to create a mean gradient of equivalence ratio in the combustion chamber which provides additional control on combustion performance. In aircraft engines, combustion occurs with fuel and secondary air injected at various locations resulting in a nonuniform equivalence ratio. In both examples, mean values of the equivalence ratio can exhibit strong spatial and temporal variations. These variations in mixture composition are particularly significant in engines that use direct fuel injection into the combustion chamber. In this case, the liquid fuel does not always completely vaporize and mix before combustion occurs, resulting in persistent rich and lean pockets into which the turbulent flame propagates. From a practical point of view, there are several basic and important issues regarding partially premixed combustion that need to be resolved. Two such issues are how reactant composition inhomogeneities affect the laminar and turbulent flame speeds, and how the burnt gas temperature varies as a function of these inhomogeneities. Knowledge of the flame speed is critical in optimizing combustion performance, and the minimization of pollutant emissions relies heavily on the temperature in the burnt gases. Another application of partially premixed combustion is found in the field of active control of turbulent combustion. One possible technique of active control consists of pulsating

  13. Estimation of partial decoupling of cavity events

    SciTech Connect

    Garbin, H.D.

    1993-03-01

    One proven method of evading the detection of a nuclear test is to decouple the explosion with a large air-filled cavity. Past tests have shown it is possible to substantially reduce the seismic energy emanating from a nuclear explosion by as much as two, orders of magnitude. The problem is not whether it can be done; the problem is the expense involved in mining a large cavity to fully decouple any reasonable size test. It has been suggested that partial decoupling may exist so some fraction of decoupling may be attained between factors of 1 to 100. MISTY ECHO and MINERAL QUARRY are two nuclear tests which were instrumented to look at this concept. MISTY ECHO was a nuclear explosion conducted in an 11 m hemispherical cavity such that the walls were over driven and reacted in a non-linear manner. MINERAL QUARRY was a nearby tamped event that is used as a reference to compare with MISTY ECHO. The scaled cavity radius of MISTY ECHO was greater than 2m/kt{sup l/3}. Both of these tests had free-field accelerometers located within 400 m of their respective sources. Analysis of surface ground motion is inconclusive on the question of partial decoupling. This is due to the difference in medium properties that the ray paths take to the surface. The free-field configuration alleviates this concern. The analysis consists of cube-root signal MINERAL QUARRYs signal to MISTY ECHO`s yield and calculating the ratio of the Fourier amplitudes of both the acceleration and the reduced displacement potentials. The results do not indicate the presence of partial decoupling. In fact, there is a coupling enhancement factor of 2.

  14. Estimation of partial decoupling of cavity events

    SciTech Connect

    Garbin, H.D.

    1993-03-01

    One proven method of evading the detection of a nuclear test is to decouple the explosion with a large air-filled cavity. Past tests have shown it is possible to substantially reduce the seismic energy emanating from a nuclear explosion by as much as two, orders of magnitude. The problem is not whether it can be done; the problem is the expense involved in mining a large cavity to fully decouple any reasonable size test. It has been suggested that partial decoupling may exist so some fraction of decoupling may be attained between factors of 1 to 100. MISTY ECHO and MINERAL QUARRY are two nuclear tests which were instrumented to look at this concept. MISTY ECHO was a nuclear explosion conducted in an 11 m hemispherical cavity such that the walls were over driven and reacted in a non-linear manner. MINERAL QUARRY was a nearby tamped event that is used as a reference to compare with MISTY ECHO. The scaled cavity radius of MISTY ECHO was greater than 2m/kt[sup l/3]. Both of these tests had free-field accelerometers located within 400 m of their respective sources. Analysis of surface ground motion is inconclusive on the question of partial decoupling. This is due to the difference in medium properties that the ray paths take to the surface. The free-field configuration alleviates this concern. The analysis consists of cube-root signal MINERAL QUARRYs signal to MISTY ECHO's yield and calculating the ratio of the Fourier amplitudes of both the acceleration and the reduced displacement potentials. The results do not indicate the presence of partial decoupling. In fact, there is a coupling enhancement factor of 2.

  15. Gravity Effects Observed In Partially Premixed Flames

    NASA Technical Reports Server (NTRS)

    Puri, Ishwar K.; Aggarwal, Suresh K.; Lock, Andrew J.; Gauguly, Ranjan; Hegde, Uday

    2003-01-01

    Partially premixed flames (PPFs) contain a rich premixed fuel air mixture in a pocket or stream, and, for complete combustion to occur, they require the transport of oxidizer from an appropriately oxidizer-rich (or fuel-lean) mixture that is present in another pocket or stream. Partial oxidation reactions occur in fuel-rich portions of the mixture and any remaining unburned fuel and/or intermediate species are consumed in the oxidizer-rich portions. Partial premixing, therefore, represents that condition when the equivalence ratio (phi) in one portion of the flowfield is greater than unity, and in another section its value is less than unity. In general, for combustion to occur efficiently, the global equivalence ratio is in the range fuel-lean to stoichiometric. These flames can be established by design by placing a fuel-rich mixture in contact with a fuel-lean mixture, but they also occur otherwise in many practical systems, which include nonpremixed lifted flames, turbulent nonpremixed combustion, spray flames, and unwanted fires. Other practical applications of PPFs are reported elsewhere. Although extensive experimental studies have been conducted on premixed and nonpremixed flames under microgravity, there is a absence of previous experimental work on burner stabilized PPFs in this regard. Previous numerical studies by our group employing a detailed numerical model showed gravity effects to be significant on the PPF structure. We report on the results of microgravity experiments conducted on two-dimensional (established on a Wolfhard-Parker slot burner) and axisymmetric flames (on a coannular burner) that were investigated in a self-contained multipurpose rig. Thermocouple and radiometer data were also used to characterize the thermal transport in the flame.

  16. Partial diel vertical migrations in pelagic fish.

    PubMed

    Mehner, Thomas; Kasprzak, Peter

    2011-07-01

    1. Field studies on diel vertical migration (DVM) usually report uniform behaviour with population-wide ascents and descents during crepuscular periods. This contrasts partial seasonal migrations of many animal populations, where individuals choose either the resident or the migrant strategy depending on population density, feeding opportunity and predation risk in the resident and migrant habitats. 2. We tested whether DVM of freshwater zooplanktivorous fish (Coregonus spp.) resembles partial migrations. Twenty-eight hydroacoustic surveys were performed in the deep Lake Stechlin (Germany) between 2000 and 2010, with samplings encompassing all months between March and December. Zooplankton samples were simultaneously taken in epilimnetic and hypolimnetic layers. Fish obtained from depth-stratified samplings by a midwater trawl were used to test for individual differences between residents and migrants. 3. We show for the first time that DVMs of freshwater fish resemble patterns of partial migrations often found in seasonal environments. Across all samplings, 7-33% of fish did not ascend at dusk, but exhibited the resident strategy. The proportion or residents increased at low zooplankton feeding rates in the daytime habitat and during months when the temperature difference between daytime and night-time habitats was minor. 4. Slightly larger size and higher caloric density of migrants over residents in one of the coexisting Coregonus species suggested that individual differences contributed to the migration strategy performed. However, these results were based on one sample only, and extrapolation to the entire data set is not possible. 5. Our results are indirect evidence that the balance between migrants and residents may primarily depend on the trade-off between feeding gains and metabolic and predation costs of migration. However, the results also suggest that the global fitness consequences for the resident and migrant strategies may not be identical

  17. A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa

    DOE PAGESBeta

    Dalal, Jyoti; Lopez, Harry; Vasani, Naresh B.; Hu, Zhaohui; Swift, Jennifer E.; Yalamanchili, Roopa; Dvora, Mia; Lin, Xiuli; Xie, Deyu; Qu, Rongda; et al

    2015-10-29

    Camelina sativa is an oilseed crop with great potential for biofuel production on marginal land. The seed oil from camelina has been converted to jet fuel and improved fuel efficiency in commercial and military test flights. Hydrogenation-derived renewable diesel from camelina is environmentally superior to that from canola due to lower agricultural inputs, and the seed meal is FDA approved for animal consumption. However, relatively low yield makes its farming less profitable. Our study is aimed at increasing camelina seed yield by reducing carbon loss from photorespiration via a photorespiratory bypass. Genes encoding three enzymes of the Escherichia coli glycolatemore » catabolic pathway were introduced: glycolate dehydrogenase (GDH), glyoxylate carboxyligase (GCL) and tartronic semialdehyde reductase (TSR). These enzymes compete for the photorespiratory substrate, glycolate, convert it to glycerate within the chloroplasts, and reduce photorespiration. As a by-product of the reaction, CO2 is released in the chloroplast, which increases photosynthesis. Camelina plants were transformed with either partial bypass (GDH), or full bypass (GDH, GCL and TSR) genes. Furthermore, transgenic plants were evaluated for physiological and metabolic traits.« less

  18. A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa

    SciTech Connect

    Dalal, Jyoti; Lopez, Harry; Vasani, Naresh B.; Hu, Zhaohui; Swift, Jennifer E.; Yalamanchili, Roopa; Dvora, Mia; Lin, Xiuli; Xie, Deyu; Qu, Rongda; Sederoff, Heike W.

    2015-10-29

    Camelina sativa is an oilseed crop with great potential for biofuel production on marginal land. The seed oil from camelina has been converted to jet fuel and improved fuel efficiency in commercial and military test flights. Hydrogenation-derived renewable diesel from camelina is environmentally superior to that from canola due to lower agricultural inputs, and the seed meal is FDA approved for animal consumption. However, relatively low yield makes its farming less profitable. Our study is aimed at increasing camelina seed yield by reducing carbon loss from photorespiration via a photorespiratory bypass. Genes encoding three enzymes of the Escherichia coli glycolate catabolic pathway were introduced: glycolate dehydrogenase (GDH), glyoxylate carboxyligase (GCL) and tartronic semialdehyde reductase (TSR). These enzymes compete for the photorespiratory substrate, glycolate, convert it to glycerate within the chloroplasts, and reduce photorespiration. As a by-product of the reaction, CO2 is released in the chloroplast, which increases photosynthesis. Camelina plants were transformed with either partial bypass (GDH), or full bypass (GDH, GCL and TSR) genes. Furthermore, transgenic plants were evaluated for physiological and metabolic traits.

  19. Thermal conductivity of partially ionized gas mixtures

    NASA Astrophysics Data System (ADS)

    Armaly, B. F.; Sutton, K.

    1981-06-01

    A method is proposed for predicting the translational component of the thermal conductivity of partially ionized gas mixtures. It is approximate but simple in form and offers a significant improvement over commonly utilized approximations. It does not require large computer run times nor storage, thus it is suitable for use with complex flow fields and heat transfer calculations. Results for gas mixtures which are representative of the atmosphere of Jupiter, Earth, and Venus are presented and they compare favorably with results from detailed kinetic theory analyses.

  20. Viscosity of multicomponent partially ionized gas mixtures

    NASA Astrophysics Data System (ADS)

    Armaly, B. F.; Sutton, K.

    1980-07-01

    An approximate method is proposed for predicting the viscosity of partially ionized gas mixtures. This technique expresses the viscosity of a mixture in terms of the viscosities of the individual pure components, is simple in form, and does not require large computer run times or storage. Thus, the technique is suitable for use with complex flowfields and heat-transfer calculations. Results for gas mixtures which are representative of the atmospheres of Jupiter, Earth, and Venus, are presented and it is shown that the results compare favorably with detailed kinetic-theory analyses.

  1. Multiple Partial Siberian Snakes in the AGS

    SciTech Connect

    Takano, J.; Ahrens, L. A.; Bai, M.; Brown, K.; Courant, E. D.; Gardner, C. J.; Glenn, J. W.; Huang, H.; Luccio, A. U.; MacKay, W. W.; Okamura, M.; Roser, T.; Tepikian, S.; Tsoupas, N.; Yip, K.; Zelenski, A.; Zeno, K.; Hattori, T.; Lin, F.

    2007-06-13

    Polarized protons are accelerated up to 24.3 GeV in the Alternating Gradient Synchrotron (AGS) at Brookhaven National Laboratory (BNL). To accelerate the beam with preserving the polarization, two different types of helical dipole partial Siberian snake have been installed to the AGS. One is a superconducting magnet (Cold Snake, CSNK), and the other is a normal conducting one (Warm Snake, WSNK). With these snake magnets, the polarization at the AGS extraction achieved 65%. However, the AGS has spin mismatches at the injection and extraction. This description shows calculated results to have better spin matching with using two or three snakes.

  2. Regioselective Mitsunobu Reaction of Partially Protected Uridine.

    PubMed

    Szlenkier, Maurycy; Kamel, Karol; Boryski, Jerzy

    2016-08-01

    Mitsunobu reaction of partially acylated uridine proceeds with high regioselectivity for intramolecular SN2 anhydro linkage closuring. Under the reaction conditions, an isomeric mixture of diacyl uridine derivatives with either free 2'- or 3'-hydroxyl group was transformed into a single cyclonucleosidic product, 2,2'-anhydro-3',5'-di-O-acyluridine. This paper presents a possible mechanism of the reactions, the explanation of observed phenomenon based on semiempirical and density functional theory (DFT) calculations and possible utility of this synthetic pathway. PMID:27351239

  3. Partial Melting in the Inner Core

    NASA Astrophysics Data System (ADS)

    Hernlund, J. W.

    2014-12-01

    The inner core boundary (ICB) is often considered to be permeable to flow, because solid iron could melt as it upwells across the ICB. Such a mechanism has been proposed to accompany inner core convective processes (including translation from a freezing to melting hemisphere), and has also been invoked to explain the formation of a dense Fe-rich liquid F-layer above the ICB. However, the conceptions of ICB melting invoked thus far are extremely simplistic, and neglect the many lessons learned from melting in other geological contexts. Owing to some degree of solid solution in relatively incompatible light alloys in solid iron, the onset of melting in the inner core will likely occur as a partial melt, with the liquid being enriched in these light alloys relative to the co-existing solid. Such a partial melt is then subject to upward migration/percolation out of the solid matrix owing to the buoyancy of melt relative to solid. Removal of melt and viscous compaction of the pore space results in an iron-enriched dense solid, whose negative buoyancy will oppose whatever buoyancy forces initially gave rise to upwelling. Either the negative buoyancy will balance these other forces and cause upwelling to cease, or else the solid will become so depleted in light alloys that it is unable to undergo further melting. Thus a proper accounting of partial melting results in a very different melting regime in the inner core, and suppression of upwelling across the ICB. Any fluid that is able to escape into the outer core from inner core partial melting will likely be buoyant because in order to be a melt it should be enriched in incompatiable alloys relative to whatever is freezing at the ICB. Therefore inner core melting is unlikely to contribute to the formation of an F-layer, but instead will tend to de-stabilize it. I will present models that illustrate these processes, and propose that the F-layer is a relic of incomplete mixing of the core during Earth's final stages of

  4. [Partial lease squares approach to functional analysis].

    PubMed

    Preda, C

    2006-01-01

    We extend the partial least squares (PLS) approach to functional data represented in our models by sample paths of stochastic process with continuous time. Due to the infinite dimension, when functional data are used as a predictor for linear regression and classification models, the estimation problem is an ill-posed one. In this context, PLS offers a simple and efficient alternative to the methods based on the principal components of the stochastic process. We compare the results given by the PLS approach and other linear models using several datasets from economy, industry and medical fields. PMID:17124795

  5. Partial Arc Curvilinear Direct Drive Servomotor

    NASA Technical Reports Server (NTRS)

    Sun, Xiuhong (Inventor)

    2014-01-01

    A partial arc servomotor assembly having a curvilinear U-channel with two parallel rare earth permanent magnet plates facing each other and a pivoted ironless three phase coil armature winding moves between the plates. An encoder read head is fixed to a mounting plate above the coil armature winding and a curvilinear encoder scale is curved to be co-axis with the curvilinear U-channel permanent magnet track formed by the permanent magnet plates. Driven by a set of miniaturized power electronics devices closely looped with a positioning feedback encoder, the angular position and velocity of the pivoted payload is programmable and precisely controlled.

  6. Particle image fields and partial coherence

    NASA Technical Reports Server (NTRS)

    Rubinstein, Robert; Greenberg, Paul S.

    1990-01-01

    The accuracy of Young's fringe method for reducing velocity field data is compromized by a spatially incoherent background field which originates in the random locations of the seeding particles. The probability density function for the spatial frequency cutoff of this background is derived as a function of the particle count, the distribution governing the power in each frequency interval is derived, and conditions are found under which the Van Cittert-Zernike theorem applies. The background field resembles the far field of a partially coherent source in the high particle count limit, but departs significantly at low and moderate counts.

  7. The algebraic structure of quantum partial isometries

    NASA Astrophysics Data System (ADS)

    Banica, Teodor

    2016-03-01

    The partial isometries of ℝN, ℂN form compact semigroups O˜N,U˜N. We discuss here the liberation question for these semigroups, and for their discrete versions H˜N,K˜N. Our main results concern the construction of half-liberations H˜N×,K˜ N×,O˜ N×,U˜ N× and of liberations H˜N+,K˜ N+,O˜ N+,U˜ N+. We include a detailed algebraic and probabilistic study of all these objects, justifying our “half-liberation” and “liberation” claims.

  8. Partial stability and stabilisation of Boolean networks

    NASA Astrophysics Data System (ADS)

    Chen, Hong-Wei; Sun, Liang-Jie; Liu, Yang

    2016-07-01

    In this paper, we investigate the stability of Boolean networks and the stabilisation of Boolean control networks with respect to part of the system's states. First, an algebraic expression of the Boolean (control) network is derived by the semi-tensor product of matrices. Then, some necessary and sufficient conditions for partial stability of Boolean networks are given. Finally, the stabilisation of Boolean control networks by a free control sequence and a state-feedback control is investigated and the respective necessary and sufficient conditions are obtained. Examples are provided to illustrate the efficiency of the obtained results.

  9. Partially resolved super transition array method

    NASA Astrophysics Data System (ADS)

    Wilson, Brian G.; Iglesias, Carlos A.; Chen, Mau H.

    2015-03-01

    The partially resolved transition array model for radiative transitions between ordinary electronic configurations is extended to the super configuration approach. The specific application incorporates intermediate coupling effects into transition arrays to describe the transition from LS to JJ coupling without the ad hoc approximations introduced in past formulations. More generally, the extended concept permits stepwise refinement of the super transition array method towards the line-by-line limit in ordinary configurations. Thus, the formalism forms a framework for a hybrid scheme to combine detailed line accounting and statistical methods.

  10. PARTIAL TRISOMY 4p AND PARTIAL MONOSOMY 13q: CASE REPORT AND A LITERATURE REVIEW.

    PubMed

    Puvabanditsin, S; Herrera-Garcia, G; Gengel, N; Hussein, K; February, M; Mayne, J; Mehta, R

    2016-01-01

    We report on a term first born dichorionic-diamniotic twin with deletion of the distal long arm of chromosome 13, partial trisomy of the short arm of chromosome 4, intrauterine growth retardation, and multiple anomalies including microcephaly, colpocephaly, absent corpus callosum, bulbous tip of the nose, large and low set ears, macroglossia, thin upper lip, double outlet right ventricle, atria/ventricular septal defect, cleft mitral valve, pulmonary stenosis, single umbilical artery, multicystic dysplastic left kidney, sacral dimple, anterior displacement of anus, simian creases, abnormal thumb (congenital clasped thumb), overlapping toes, and congenital hypothyroidism. This is the first report of a patient with partial trisomy 4p and partial monosomy 13q. PMID:27192890

  11. Partial spatial coherence and partial polarization in random evanescent fields on lossless interfaces.

    PubMed

    Norrman, Andreas; Setälä, Tero; Friberg, Ari T

    2011-03-01

    We consider partial spatial coherence and partial polarization of purely evanescent optical fields generated in total internal reflection at an interface of two dielectric (lossless) media. Making use of the electromagnetic degree of coherence, we show that, in such fields, the coherence length can be notably shorter than the light's vacuum wavelength, especially at a high-index-contrast interface. Physical explanation for this behavior, analogous to the generation of incoherent light in a multimode laser, is provided. We also analyze the degree of polarization by using a recent three-dimensional formulation and show that the field may be partially polarized at a subwavelength distance from the surface even though it is fully polarized farther away. The degree of polarization can assume values unattainable by beamlike fields, indicating that electromagnetic evanescent waves generally are genuine three-dimensional fields. The results can find applications in near-field optics and nanophotonics. PMID:21383821

  12. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns

    PubMed Central

    Hastie, Trevor; Tibshirani, Robert; Eisen, Michael B; Alizadeh, Ash; Levy, Ronald; Staudt, Louis; Chan, Wing C; Botstein, David; Brown, Patrick

    2000-01-01

    Background: Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called 'gene shaving'. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other widely used methods for analyzing gene expression studies in that genes may belong to more than one cluster, and the clustering may be supervised by an outcome measure. The technique can be 'unsupervised', that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings. Results: We illustrate the use of the gene shaving method to analyze gene expression measurements made on samples from patients with diffuse large B-cell lymphoma. The method identifies a small cluster of genes whose expression is highly predictive of survival. Conclusions: The gene shaving method is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worth further investigation. PMID:11178228

  13. Gene Therapy

    PubMed Central

    Baum, Bruce J

    2014-01-01

    Applications of gene therapy have been evaluated in virtually every oral tissue, and many of these have proved successful at least in animal models. While gene therapy will not be used routinely in the next decade, practitioners of oral medicine should be aware of the potential of this novel type of treatment that doubtless will benefit many patients with oral diseases. PMID:24372817

  14. Trichoderma genes

    DOEpatents

    Foreman, Pamela; Goedegebuur, Frits; Van Solingen, Pieter; Ward, Michael

    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.

  15. Partially sparse imaging of stationary indoor scenes

    NASA Astrophysics Data System (ADS)

    Ahmad, Fauzia; Amin, Moeness G.; Dogaru, Traian

    2014-12-01

    In this paper, we exploit the notion of partial sparsity for scene reconstruction associated with through-the-wall radar imaging of stationary targets under reduced data volume. Partial sparsity implies that the scene being imaged consists of a sparse part and a dense part, with the support of the latter assumed to be known. For the problem at hand, sparsity is represented by a few stationary indoor targets, whereas the high scene density is defined by exterior and interior walls. Prior knowledge of wall positions and extent may be available either through building blueprints or from prior surveillance operations. The contributions of the exterior and interior walls are removed from the data through the use of projection matrices, which are determined from wall- and corner-specific dictionaries. The projected data, with enhanced sparsity, is then processed using l 1 norm reconstruction techniques. Numerical electromagnetic data is used to demonstrate the effectiveness of the proposed approach for imaging stationary indoor scenes using a reduced set of measurements.

  16. Partial Facetectomy for Lumbar Foraminal Stenosis

    PubMed Central

    Kang, Kevin; Rodriguez-Olaverri, Juan Carlos; Razi, Afshin; Farcy, Jean Pierre

    2014-01-01

    Background. Several different techniques exist to address the pain and disability caused by isolated nerve root impingement. Failure to adequately decompress the lumbar foramen may lead to failed back surgery syndrome. However, aggressive treatment often causes spinal instability or may require fusion for satisfactory results. We describe a novel technique for decompression of the lumbar nerve root and demonstrate its effectiveness in relief of radicular symptoms. Methods. Partial facetectomy was performed by removal of the medial portion of the superior facet in patients with lumbar foraminal stenosis. 47 patients underwent the procedure from 2001 to 2010. Those who demonstrated neurogenic claudication without spinal instability or central canal stenosis and failed conservative management were eligible for the procedure. Functional level was recorded for each patient. These patients were followed for an average of 3.9 years to evaluate outcomes. Results. 27 of 47 patients (57%) reported no back pain and no functional limitations. Eight of 47 patients (17%) reported moderate pain, but had no limitations. Six of 47 patients (13%) continued to experience degenerative symptoms. Five of 47 patients (11%) required additional surgery. Conclusions. Partial facetectomy is an effective means to decompress the lumbar nerve root foramen without causing spinal instability. PMID:25110591

  17. Quantum dynamics in the partial Wigner picture

    NASA Astrophysics Data System (ADS)

    Beck, Geoffrey M.; Sergi, Alessandro

    2013-10-01

    Recently we have shown how the partial Wigner representation of quantum mechanics can be used to study hybrid quantum models where a system with a finite number of energy levels is coupled to linear or nonlinear oscillators (Beck and Sergi 2013 Phys. Lett. A 377 1047). The purpose of this work is to provide a detailed derivation of the partially Wigner-transformed quantum equations of motion for nonlinear oscillator subsystems under the action of general polynomial potentials. Such equations can be written in terms of a propagator, which can then be expanded in a power series. The linear terms of the series describe quantum-classical dynamics while the nonlinear terms provide the corrections needed to restore the fully quantum character of the evolution. In the case of polynomial potentials and position dependent couplings, the number of nonlinear terms is finite and the corrections can be calculated explicitly. In this work we show how to implement numerically the above scheme where, in principle, no assumption about the strength of the coupling must be taken. We illustrate the formalism by studying a two-level system interacting with an asymmetric quartic oscillator. We integrate the quantum dynamics of the total system and provide a comparison with the case of the quantum-classical dynamics of the quartic oscillator. The approach presented here is expected to be effective for studying hybrid quantum circuits in quantum information theory and for witnessing the quantum-to-classical transition in nano-oscillators coupled to pseudo-spins.

  18. Sintering aids for yttria partially stabilized zirconia

    SciTech Connect

    Montross, C.S.

    1987-01-01

    High-purity yttria partially stabilized zirconia does not sinter readily. Commercial production of the powder and finished parts has allowed contamination by silica and aluminosilicates to enhance the sintering via a liquid-phase mechanism at 1400/sup 0/C. This research analyzed several simple metal oxides as possible nonglassy sintering aids to enhance the sintering of high-purity yttria partially stabilized zirconia, Y-PSZ, without the deleterious effects of the glass contamination. Of the metal oxides analyzed: iron oxide, bismuth oxide, chromia, niobia, tantala, tungsten oxide and mullite, only one metal oxide, iron oxide resulted in enhanced sintering. The iron oxide doped Y-PSZ exhibited better sinterability than high purity Y-PSZ and equivalent/better sinterability than glass doped Y-PSZ. The iron oxide doped Y-PSZ had a higher tetragonal content at lower sintering temperatures and at lower densities than glass doped Y-PSZ. This resulted in higher fracture toughness at lower temperatures than the glass doped Y-PSZ. Additionally, the iron oxide doped Y-PSZ showed a better resistance to low temperature high humidity degradation than glass doped Y-PSZ under identical conditions. Problems of bloating common to high surface area ultra fine powders and exhibited by the glass doped Y-PSZ were not alleviated by the use of the nonglassy metal oxide sintering aids.

  19. Preparation of partially decaffeinated instant green tea.

    PubMed

    Ye, Jian-Hui; Liang, Yue-Rong; Jin, Jing; Liang, Hue-Ling; Du, Ying-Ying; Lu, Jian-Liang; Ye, Qian; Lin, Chen

    2007-05-01

    The caffeine level of instant tea extracted from decaffeinated leaf tea with 4.0 mg g-1 caffeine is commonly above 10.0 mg g-1, the maximum limit of caffeine for decaffeinated instant tea. Further removal of caffeine by active carbon (AC) from the green tea extract was investigated. It showed that the removal of caffeine from the tea extract solutions depended on the treatment time and tea extract concentration while the ethanol concentration and pH had little effect on the removal of caffeine. According to the removal of caffeine and the ratio of total catechins to caffeine in the tested samples, the optimum decaffeination conditions were determined to be as follows: tea extract concentration 15-30 g L-1 for common tea extract but higher for partially decaffeinated tea leaf extract; ratio of tea solution to AC, 100 mL:4 g; treatment time, 4 h; and natural tea extract pH. Instant tea powder extracted from partially decaffeinated leaf tea with a caffeine level of 4.03 mg g-1 and further decaffeinated by AC had a caffeine level of 7.81 mg g-1, which was 31% lower than that without AC treatment. PMID:17407319

  20. Partial pressure analysis in space testing

    NASA Technical Reports Server (NTRS)

    Tilford, Charles R.

    1994-01-01

    For vacuum-system or test-article analysis it is often desirable to know the species and partial pressures of the vacuum gases. Residual gas or Partial Pressure Analyzers (PPA's) are commonly used for this purpose. These are mass spectrometer-type instruments, most commonly employing quadrupole filters. These instruments can be extremely useful, but they should be used with caution. Depending on the instrument design, calibration procedures, and conditions of use, measurements made with these instruments can be accurate to within a few percent, or in error by two or more orders of magnitude. Significant sources of error can include relative gas sensitivities that differ from handbook values by an order of magnitude, changes in sensitivity with pressure by as much as two orders of magnitude, changes in sensitivity with time after exposure to chemically active gases, and the dependence of the sensitivity for one gas on the pressures of other gases. However, for most instruments, these errors can be greatly reduced with proper operating procedures and conditions of use. In this paper, data are presented illustrating performance characteristics for different instruments and gases, operating parameters are recommended to minimize some errors, and calibrations procedures are described that can detect and/or correct other errors.

  1. Energetics and mechanics for partial gravity locomotion.

    PubMed

    Newman, D J; Alexander, H L; Webbon, B W

    1994-09-01

    The role of gravitational acceleration on human locomotion is not clearly understood. It is hypothesized that the mechanics and energetics of locomotion depend upon the prevailing gravity level. A unique human-rated underwater treadmill and an adjustable ballasting harness were used to stimulate partial gravity environments. This study has two research aspects, biomechanics and energetics. Vertical forces which are exerted by subjects on the treadmill-mounted, split-plate force platform show that peak vertical force and stride frequency significantly decrease (p < 0.05) as the gravity level is reduced, while ground contact time is independent of gravity level. A loping gait is employed over a wide range of speeds (approximately 1.5 m/s to approximately 2.3 m/s) suggesting a change in the mechanics for lunar (1/6 G) and Martian (3/8 G) locomotion. As theory predicts, locomotion energy requirements for partial gravity levels are significantly less than at 1 G (p < 0.05). PMID:7818450

  2. An Ultrasonic Clamp for Bloodless Partial Nephrectomy

    NASA Astrophysics Data System (ADS)

    Lafon, Cyril; Bouchoux, Guillaume; Murat, François Joseph; Birer, Alain; Theillère, Yves; Chapelon, Jean Yves; Cathignol, Dominique

    2007-05-01

    Maximum conservation of the kidney is preferable through partial nephrectomy for patients at risk of disease recurrence of renal cancers. Haemostatic tools are needed in order to achieve bloodless surgery and reduce post surgery morbidity. Two piezo-ceramic transducers operating at a frequency of 4 MHz were mounted on each arm of a clamp. When used for coagulation purposes, two transducers situated on opposite arms of the clamp were driven simultaneously. Heat delivery was optimized as each transducers mirrored back to targeted tissues the wave generated by the opposite transducer. Real-time treatment monitoring with an echo-based technique was also envisaged with this clamp. Therapy was periodically interrupted so one transducer could generate a pulse. The echo returning from the opposite transducer was treated. Coagulation necroses were obtained in vitro on substantial thicknesses (23-38mm) of pig liver over exposure durations ranging from 30s to 130s, and with acoustic intensities of less than 15W/cm2 per transducer. Both kidneys of two pigs were treated in vivo with the clamp (14.5W/cm2 for 90s), and the partial nephrectomies performed proved to be bloodless. In vitro and in vivo, wide transfixing lesions corresponded to an echo energy decrease superior to -10dB and parabolic form of the time of flight versus treatment time. In conclusion, this ultrasound clamp has proven to be an excellent mean for achieving monitored haemostasis in kidney.

  3. Partial volume correction using cortical surfaces

    NASA Astrophysics Data System (ADS)

    Blaasvær, Kamille R.; Haubro, Camilla D.; Eskildsen, Simon F.; Borghammer, Per; Otzen, Daniel; Ostergaard, Lasse R.

    2010-03-01

    Partial volume effect (PVE) in positron emission tomography (PET) leads to inaccurate estimation of regional metabolic activities among neighbouring tissues with different tracer concentration. This may be one of the main limiting factors in the utilization of PET in clinical practice. Partial volume correction (PVC) methods have been widely studied to address this issue. MRI based PVC methods are well-established.1 Their performance depend on the quality of the co-registration of the MR and PET dataset, on the correctness of the estimated point-spread function (PSF) of the PET scanner and largely on the performance of the segmentation method that divide the brain into brain tissue compartments.1, 2 In the present study a method for PVC is suggested, that utilizes cortical surfaces, to obtain detailed anatomical information. The objectives are to improve the performance of PVC, facilitate a study of the relationship between metabolic activity in the cerebral cortex and cortical thicknesses, and to obtain an improved visualization of PET data. The gray matter metabolic activity after performing PVC was recovered by 99.7 - 99.8 % , in relation to the true activity when testing on simple simulated data with different PSFs and by 97.9 - 100 % when testing on simulated brain PET data at different cortical thicknesses. When studying the relationship between metabolic activities and anatomical structures it was shown on simulated brain PET data, that it is important to correct for PVE in order to get the true relationship.

  4. Partial Northeast Elevation Mill #5 East & #5 West ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Partial Northeast Elevation - Mill #5 East & #5 West (Part 4), Typical Floor - Partial Plan Mill #5 East & #5 West (Part 4) - Boott Cotton Mills, John Street at Merrimack River, Lowell, Middlesex County, MA

  5. Genetics Home Reference: autosomal dominant partial epilepsy with auditory features

    MedlinePlus

    ... Genetics Home Health Conditions ADPEAF autosomal dominant partial epilepsy with auditory features Enable Javascript to view the ... Open All Close All Description Autosomal dominant partial epilepsy with auditory features ( ADPEAF ) is an uncommon form ...

  6. Partial oxidation power plant with reheating and method thereof

    DOEpatents

    Newby, R.A.; Yang, W.C.; Bannister, R.L.

    1999-08-10

    A system and method are disclosed for generating power having an air compression/partial oxidation system, a turbine, and a primary combustion system. The air compression/partial oxidation system receives a first air stream and a fuel stream and produces a first partially oxidized fuel stream and a first compressed air stream therefrom. The turbine expands the first partially oxidized fuel stream while being cooled by the first compressed air stream to produce a heated air stream. The heated air stream is injected into the expanding first partially oxidized fuel stream, thereby reheating it in the turbine. A second partially oxidized fuel stream is emitted from the turbine. The primary combustion system receives said second partially oxidized fuel stream and a second air stream, combusts said second partially oxidized fuel stream, and produces rotating shaft power and an emission stream therefrom. 2 figs.

  7. Partial oxidation power plant with reheating and method thereof

    DOEpatents

    Newby, Richard A.; Yang, Wen-Ching; Bannister, Ronald L.

    1999-01-01

    A system and method for generating power having an air compression/partial oxidation system, a turbine, and a primary combustion system. The air compression/partial oxidation system receives a first air stream and a fuel stream and produces a first partially oxidized fuel stream and a first compressed air stream therefrom. The turbine expands the first partially oxidized fuel stream while being cooled by the first compressed air stream to produce a heated air stream. The heated air stream is injected into the expanding first partially oxidized fuel stream, thereby reheating it in the turbine. A second partially oxidized fuel stream is emitted from the turbine. The primary combustion system receives said second partially oxidized fuel stream and a second air stream, combusts said second partially oxidized fuel stream, and produces rotating shaft power and an emission stream therefrom.

  8. Precision metal occlusal surfaces for removable partial dentures.

    PubMed

    Barco, M T; Synnott, S A

    1989-01-01

    The prosthodontist is often limited in developing the desired occlusal pattern when integrating removable partial dentures with natural dentitions or fixed partial dentures. A technique that allows the development of an esthetic, accurate metal occlusal surface for a removable partial denture is described. The occlusion developed allows an occlusal harmony with the removable partial denture that is not possible with stock denture teeth or metal occlusal surfaces developed with stock denture teeth. PMID:2700630

  9. 42 CFR 488.715 - Partial extended surveys.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 5 2013-10-01 2013-10-01 false Partial extended surveys. 488.715 Section 488.715... (CONTINUED) STANDARDS AND CERTIFICATION SURVEY, CERTIFICATION, AND ENFORCEMENT PROCEDURES Survey and Certification of Home Health Agencies § 488.715 Partial extended surveys. A partial extended survey is...

  10. 42 CFR 488.715 - Partial extended surveys.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 5 2014-10-01 2014-10-01 false Partial extended surveys. 488.715 Section 488.715... (CONTINUED) STANDARDS AND CERTIFICATION SURVEY, CERTIFICATION, AND ENFORCEMENT PROCEDURES Survey and Certification of Home Health Agencies § 488.715 Partial extended surveys. A partial extended survey is...

  11. 40 CFR 721.10146 - Partially fluorinated condensation polymer (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Partially fluorinated condensation... Specific Chemical Substances § 721.10146 Partially fluorinated condensation polymer (generic). (a) Chemical... as partially fluorinated condensation polymer (PMN P-07-87) is subject to reporting under...

  12. 40 CFR 721.10146 - Partially fluorinated condensation polymer (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Partially fluorinated condensation... Specific Chemical Substances § 721.10146 Partially fluorinated condensation polymer (generic). (a) Chemical... as partially fluorinated condensation polymer (PMN P-07-87) is subject to reporting under...

  13. 40 CFR 721.10146 - Partially fluorinated condensation polymer (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Partially fluorinated condensation... Specific Chemical Substances § 721.10146 Partially fluorinated condensation polymer (generic). (a) Chemical... as partially fluorinated condensation polymer (PMN P-07-87) is subject to reporting under...

  14. A Potential Cost Effective Liquefaction Mitigation Countermeasure: Induced Partial Saturation

    SciTech Connect

    Bian Hanbing; Jia Yun; Shahrour, Isam

    2008-07-08

    This work is devoted to illustrate the potential liquefaction mitigation countermeasure: Induced Partial Saturation. Firstly the potential liquefaction mitigation method is briefly introduced. Then the numerical model for partially saturated sandy soil is presented. At last the dynamic responses of liquefiable free filed with different water saturation is given. It shows that the induced partial saturation is efficiency for preventing the liquefaction.

  15. 48 CFR 819.502-3 - Partial set-asides.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Partial set-asides. 819... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 819.502-3 Partial set-asides. When... particular procurement will be partially set aside for small business participation, the solicitation...

  16. 48 CFR 1319.502-3 - Partial set-asides.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Partial set-asides. 1319... PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 1319.502-3 Partial set-asides. A partial set... and one small) will respond with offers unless the set-aside is authorized by the designee set...

  17. Thin film devices used as oxygen partial pressure sensors

    NASA Technical Reports Server (NTRS)

    Canady, K. S.; Wortman, J. J.

    1970-01-01

    Electrical conductivity of zinc oxide films to be used in an oxygen partial pressure sensor is measured as a function of temperature, oxygen partial pressure, and other atmospheric constituents. Time response following partial pressure changes is studied as a function of temperature and environmental changes.

  18. 48 CFR 49.112-1 - Partial payments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Government will process applications for partial payments promptly. A subcontractor shall submit its... in preparing its own settlement proposal. (b) Amount of partial payment. Before approving any partial payment, the TCO shall obtain any desired accounting, engineering, or other specialized reviews of...

  19. 48 CFR 49.112-1 - Partial payments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Government will process applications for partial payments promptly. A subcontractor shall submit its... in preparing its own settlement proposal. (b) Amount of partial payment. Before approving any partial payment, the TCO shall obtain any desired accounting, engineering, or other specialized reviews of...

  20. Apparatus for the concurrent inspection of partially completed welds

    DOEpatents

    Smartt, Herschel B.; Johnson, John A.; Larsen, Eric D.; Bitsoi, Rodney J.; Perrenoud, Ben C.; Miller, Karen S.; Pace, David P.

    2002-01-01

    An apparatus for the concurrent inspection of partially completed welds is described in which is utilized in combination with a moveable welder for forming a partially completed weld, and an ultrasonic generator mounted on a moveable welder in which is reciprocally moveable along a path of travel which is laterally disposed relative to the partially completed weld.