Science.gov

Sample records for partial gdh gene

  1. Introduction of the Escherichia coli gdhA gene into Rhizobium phaseoli: effect on nitrogen fixation.

    PubMed Central

    Bravo, A; Becerril, B; Mora, J

    1988-01-01

    Rhizobium phaseoli lacks glutamate dehydrogenase (GDH) and assimilates ammonium by the glutamine synthetase-glutamate synthase pathway. A strain of R. phaseoli harboring the Escherichia coli GDH structural gene (gdhA) was constructed. GDH activity was expressed in R. phaseoli in the free-living state and in symbiosis. Nodules with bacteroids that expressed GDH activity had severe impairment of nitrogen fixation. Also, R. phaseoli cells that lost GDH activity and assimilated ammonium by the glutamine synthetase-glutamate synthase pathway preferentially nodulated Phaseolus vulgaris. PMID:2892830

  2. Nucleotide sequence of the GDH gene coding for the NADP-specific glutamate dehydrogenase of Saccharomyces cerevisiae.

    PubMed

    Nagasu, T; Hall, B D

    1985-01-01

    The isolation of the Saccharomyces cerevisiae gene for NADP-dependent glutamate dehydrogenase (NADP-GDH) by cross hybridization to the Neurospora crassa am gene, known to encode for NADP-GDH is described. Two DNA fragments selected from a yeast genomic library in phage lambda gt11 were shown by restriction analysis to share 2.5 kb of common sequence. A yeast shuttle vector (CV13) carrying either to the cloned fragments complements the gdh- strain of S. cerevisiae and directs substantial overproduction of NADP-GDH. One of the cloned fragments was sequenced, and the deduced amino acid (aa) sequence of the yeast NADP-GDH is 64% homologous to N. crassa, 51% to Escherichia coli and 24% to bovine NADP-GDHs.

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

    PubMed

    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.

  4. Studies on Saccharomyces cerevisiae under carbon-limiting growth transformed with plasmid pCYG4 that carries the gene for NADP-GDH.

    PubMed

    Lima Filho, J L; Ledingham, W M

    1990-02-01

    The gene (GDH1) coding for the NADP-linked glutamate dehydrogenase system (NADP-GDH) has been cloned from Saccharomyces cerevisiae strain. Cells being transformed by the NADP-GDH gene on a 2 micron bared vector (pCYG4) plasmid confering 11-fold higher level on expressed GDH activity over the wild-type cells. The behavior of these cells was investigated under chemostatic growth with a carbon rate-limiting nutrient. Specific growth rates of cells carrying plasmid pCYG4 were found to be slightly slower than wild type cells. Furthermore, the NADP-GDH activity increases proportionally with the dilution rate. In addition, oscillations in the NADP-GDH activity, especially at a dilution rate up to 0.15/h, are probably consequential on the appearance of a changing mixed population (cells with and without plasmids).

  5. The gdhB gene of Pseudomonas aeruginosa encodes an arginine-inducible NAD(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation.

    PubMed

    Lu, C D; Abdelal, A T

    2001-01-01

    The NAD(+)-dependent glutamate dehydrogenase (NAD-GDH) from Pseudomonas aeruginosa PAO1 was purified, and its amino-terminal amino acid sequence was determined. This sequence information was used in identifying and cloning the encoding gdhB gene and its flanking regions. The molecular mass predicted from the derived sequence for the encoded NAD-GDH was 182.6 kDa, in close agreement with that determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme (180 kDa). Cross-linking studies established that the native NAD-GDH is a tetramer of equal subunits. Comparison of the derived amino acid sequence of NAD-GDH from P. aeruginosa with the GenBank database showed the highest homology with hypothetical polypeptides from Pseudomonas putida, Mycobacterium tuberculosis, Rickettsia prowazakii, Legionella pneumophila, Vibrio cholerae, Shewanella putrefaciens, Sinorhizobium meliloti, and Caulobacter crescentus. A moderate degree of homology, primarily in the central domain, was observed with the smaller tetrameric NAD-GDH (protomeric mass of 110 kDa) from Saccharomyces cerevisiae or Neurospora crassa. Comparison with the yet smaller hexameric GDH (protomeric mass of 48 to 55 kDa) of other prokaryotes yielded a low degree of homology that was limited to residues important for binding of substrates and for catalytic function. NAD-GDH was induced 27-fold by exogenous arginine and only 3-fold by exogenous glutamate. Primer extension experiments established that transcription of gdhB is initiated from an arginine-inducible promoter and that this induction is dependent on the arginine regulatory protein, ArgR, a member of the AraC/XyIS family of regulatory proteins. NAD-GDH was purified to homogeneity from a recombinant strain of P. aeruginosa and characterized. The glutamate saturation curve was sigmoid, indicating positive cooperativity in the binding of glutamate. NAD-GDH activity was subject to allosteric control by arginine and citrate, which

  6. Glutamate dehydrogenase isoenzyme 3 (GDH3) of Arabidopsis thaliana is less thermostable than GDH1 and GDH2 isoenzymes.

    PubMed

    Marchi, Laura; Polverini, Eugenia; Degola, Francesca; Baruffini, Enrico; Restivo, Francesco Maria

    2014-10-01

    NAD(H)-glutamate dehydrogenase (GDH; EC 1.4.1.2) is an abundant and ubiquitous enzyme that may exist in different isoenzymic forms. Variation in the composition of the GDH isoenzyme pattern is observed during plant development and specific cell, tissue and organ localization of the different isoforms have been reported. However, the mechanisms involved in the regulation of the isoenzymatic pattern are still obscure. Regulation may be exerted at several levels, i.e. at the level of transcription and translation of the relevant genes, but also when the enzyme is assembled to originate the catalytically active form of the protein. In Arabidopsis thaliana, three genes (GDH1, GDH2 and GDH3) encode three different GDH subunits (β, α and γ) that randomly associate to form a complex array of homo- and hetero-hexamers. In order to asses if the different Arabidopsis GDH isoforms may display different structural properties we have investigated their thermal stability. In particular the stability of GDH1 and GDH3 isoenzymes was studied using site-directed mutagenesis in a heterologous yeast expression system. It was established that the carboxyl terminus of the GDH subunit is involved in the stabilization of the oligomeric structure of the enzyme.

  7. 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

  8. 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.

  9. Role of the complex upstream region of the GDH2 gene in nitrogen regulation of the NAD-linked glutamate dehydrogenase in Saccharomyces cerevisiae.

    PubMed Central

    Miller, S M; Magasanik, B

    1991-01-01

    We analyzed the upstream region of the GDH2 gene, which encodes the NAD-linked glutamate dehydrogenase in Saccharomyces cerevisiae, for elements important for the regulation of the gene by the nitrogen source. The levels of this enzyme are high in cells grown with glutamate as the sole source of nitrogen and low in cells grown with glutamine or ammonium. We found that this regulation occurs at the level of transcription and that a total of six sites are required to cause a CYC1-lacZ fusion to the GDH2 gene to be regulated in the same manner as the NAD-linked glutamate dehydrogenase. Two sites behaved as upstream activation sites (UASs). The remaining four sites were found to block the effects of the two UASs in such a way that the GDH2-CYC1-lacZ fusion was not expressed unless the cells containing it were grown under conditions favorable for the activity of both UASs. This complex regulatory system appears to account for the fact that GDH2 expression is exquisitely sensitive to glutamine, whereas the expression of GLN1, coding for glutamine synthetase, is not nearly as sensitive. Images PMID:1682801

  10. Swi/SNF-GCN5-dependent chromatin remodelling determines induced expression of GDH3, one of the paralogous genes responsible for ammonium assimilation and glutamate biosynthesis in Saccharomyces cerevisiae.

    PubMed

    Avendaño, Amaranta; Riego, Lina; DeLuna, Alexander; Aranda, Cristina; Romero, Guillermo; Ishida, Cecilia; Vázquez-Acevedo, Miriam; Rodarte, Beatriz; Recillas-Targa, Félix; Valenzuela, Lourdes; Zonszein, Sergio; González, Alicia

    2005-07-01

    It is accepted that Saccharomyces cerevisiae genome arose from complete duplication of eight ancestral chromosomes; functionally normal ploidy was recovered because of the massive loss of 90% of duplicated genes. There is evidence that indicates that part of this selective conservation of gene pairs is compelling to yeast facultative metabolism. As an example, the duplicated NADP-glutamate dehydrogenase pathway has been maintained because of the differential expression of the paralogous GDH1 and GDH3 genes, and the biochemical specialization of the enzymes they encode. The present work has been aimed to the understanding of the regulatory mechanisms that modulate GDH3 transcriptional activation. Our results show that GDH3 expression is repressed in glucose-grown cultures, as opposed to what has been observed for GDH1, and induced under respiratory conditions, or under stationary phase. Although GDH3 pertains to the nitrogen metabolic network, and its expression is Gln3p-regulated, complete derepression is ultimately determined by the carbon source through the action of the SAGA and SWI/SNF chromatin remodelling complexes. GDH3 carbon-mediated regulation is over-imposed to that exerted by the nitrogen source, highlighting the fact that operation of facultative metabolism requires strict control of enzymes, like Gdh3p, involved in biosynthetic pathways that use tricarboxylic acid cycle intermediates.

  11. Glucose dehydrogenase polymorphism among ethnic groups of Singapore--with report of two additional alleles (GDH4 and GDH5).

    PubMed

    Saha, N; Bhattacharyya, S P; Yeoh, S C; Chua, S P; Ratnam, S S

    1987-02-01

    Placental glucose dehydrogenase (GDH; E.C.1.1.1.47) polymorphism was studied in 254 Chinese, 104 Malays, and 47 Indians from Singapore using isoelectric focusing. There is suggestive evidence of two additional anodal alleles (GDH4 and GDH5) in addition to the three alleles described in earlier studies. Altogether, 14 phenotypes have been observed in the present investigation, compared with six phenotypes described in earlier studies. It appears that placental GDH is controlled by five codominant autosomal alleles producing 15 possible phenotypes. The gene frequencies of GDH1, GDH2, and GDH3 in these ethnic groups are significantly different from those reported in Caucasians. There were slight differences in the gene frequencies between the three ethnic groups, with those of Indians being nearer to the frequency in Caucasians. In general, the distribution of GDH phenotypes was at Hardy-Weinberg equilibrium in all three ethnic groups studied.

  12. Glutamate dehydrogenase isoenzyme 3 (GDH3) of Arabidopsis thaliana is regulated by a combined effect of nitrogen and cytokinin.

    PubMed

    Marchi, Laura; Degola, Francesca; Polverini, Eugenia; Tercé-Laforgue, Thérèse; Dubois, Frédéric; Hirel, Bertrand; Restivo, Francesco Maria

    2013-12-01

    In higher plants, NAD(H)-glutamate dehydrogenase (GDH; EC 1.4.1.2) is an abundant enzyme that exists in different isoenzymic forms. In Arabidopsis thaliana, three genes (Gdh1, Gdh2 and Gdh3) encode three different GDH subunits (β, α and γ) that randomly associate to form a complex array of homo- and heterohexamers. The modification of the GDH isoenzyme pattern and its regulation was studied during the development of A. thaliana in the gdh1, gdh2 single mutants and the gdh1-2 double mutant, with particular emphasis on GDH3. Investigations showed that the GDH3 isoenzyme could not be detected in closely related Arabidopsis species. The induction and regulation of GDH3 activity in the leaves and roots was investigated following nitrogen deprivation in the presence or absence of sucrose or kinetin. These experiments indicate that GDH3 is likely to play an important role during senescence and nutrient remobilization.

  13. Organ-specific expression of glutamate dehydrogenase (GDH) subunits in yellow lupine.

    PubMed

    Lehmann, Teresa; Dabert, Mirosława; Nowak, Witold

    2011-07-01

    Glutamate dehydrogenase (GDH, EC 1.4.2-4) is present in yellow lupine (Lupinus luteus cv. Juno) in many isoforms. The number and banding pattern of isoenzymes varies with respect to plant organ and developmental stage. To better understand the complex nature of GDH regulation in plants, the levels of GDH transcripts, enzyme activity and isoenzyme patterns in germinating seeds and roots of yellow lupine were examined. The analysis of GDH cDNA sequences in lupine revealed three mRNA types, of which two encoded the β-GDH subunit and one encoded the α-GDH subunit (corresponding to the GDH1(GDH3) and GDH2 genes, respectively). The relative expression of GDH1 and GDH2 genes was analyzed in various lupine organs by using quantitative real-time PCR. Our results indicate that different mRNA types were differently regulated depending on organ type. Although both genes appeared to be ubiquitously expressed in all lupine tissues, the GDH1 transcripts evidently predominated over those of GDH2. Immunochemical analyses confirmed that, during embryo development, varied expression of two GDH subunits takes place. The α-GDH subunit (43kDa) predominated in the early stages of germinating seeds, while the β-GDH subunit (44kDa) was the only GDH polypeptide present in lupine roots. These results firmly support the hypothesis that isoenzyme variability of GDH in yellow lupine is associated with the varied expression of α and β subunits into the complexes of hexameric GDH forms. The presence of several isogenes of GDH in yellow lupine may explain the high number (over 20) of its molecular forms in germinating lupine.

  14. Cellulose production from glucose using a glucose dehydrogenase gene (gdh)-deficient mutant of Gluconacetobacter xylinus and its use for bioconversion of sweet potato pulp.

    PubMed

    Shigematsu, Toru; Takamine, Kazunori; Kitazato, Masaya; Morita, Tetsuya; Naritomi, Takaaki; Morimura, Shigeru; Kida, Kenji

    2005-04-01

    A gene fragment encoding a putative pyrroloquinoline quinone glucose dehydrogenase (PQQ GDH) was cloned from a bacterial cellulose (BC)-forming acetic acid bacterium, Gluconacetobacter xylinus (=Acetobacter xylinum) strain BPR 2001, which was isolated as a high BC producer when using fructose as the carbon source. A GDH-deficient mutant of strain BPR 2001, namely GD-I, was then generated via gene disruption using the cloned gene fragment. Strain GD-I produced no gluconic acid but produced 4.1 g.l(-1) of BC aerobically in medium containing glucose as the carbon source. The ability of strain GD-I to convert glucose to BC was approximately 1.7-fold higher than that of the wild type. Strain GD-I was also able to produce 5.0 g.l(-1) of BC from a saccharified solution, which was derived from sweet potato pulp by enzymatic saccharification. Supplementation of ethanol during aerobic cultivation further increased the concentration of BC produced by strain GD-I to 7.0 g.l(-1). The rate of conversion from glucose to BC under these cultivation conditions was equivalent to that of strain BPR 2001 cultivated with fructose as the carbon source.

  15. 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.

  16. Nucleotide sequence of yeast GDH1 encoding nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase.

    PubMed

    Moye, W S; Amuro, N; Rao, J K; Zalkin, H

    1985-07-15

    The yeast GDH1 gene encodes NADP-dependent glutamate dehydrogenase. This gene was isolated by complementation of an Escherichia coli glutamate auxotroph. NADP-dependent glutamate dehydrogenase was overproduced 6-10-fold in Saccharomyces cerevisiae bearing GDH1 on a multicopy plasmid. The nucleotide sequence of the 1362-base pair coding region and 5' and 3' flanking sequences were determined. Transcription start sites were located by S1 nuclease mapping. Regulation of GDH1 was not maintained when the gene was present on a multicopy plasmid. Protein secondary structure predictions identified a region with potential to form the dinucleotide-binding domain. The amino acid sequences of the yeast and Neurospora crassa enzymes are 63% conserved. Unlike the N. crassa gene, yeast GDH1 has no introns.

  17. Detection and characterisation of Giardia and Cryptosporidium in Hungarian raw, surface and sewage water samples by IFT, PCR and sequence analysis of the SSUrRNA and GDH genes.

    PubMed

    Plutzer, Judit; Karanis, Panagiotis; Domokos, Klarissza; Törökné, Andrea; Márialigeti, Károly

    2008-10-01

    We investigated the prevalence of Giardia and Cryptosporidium species and analysed the genotypes in 36 samples collected from different water sources and various geographic areas in Hungary. Samples were collected from drinking water and sewage treatment plants and from the recreation area of Lake Balaton. The (oo)cysts were purified according to the US EPA 1623 method and they were detected by immunofluorescence test (IFT). Genomic DNA was extracted from all samples and then the GDH target gene for Giardia and the SSUrDNA for both Giardia and for Cryptosporidium species were amplified by PCR. 24 out of 36 samples (67%) were Giardia positive and 15 (42%) were Cryptosporidium positive by IFT. PCR confirmed that 13 out of 36 samples (36%) were Giardia positive and 10 (28%) contained Cryptosporidium. Twelve Giardia and two Cryptosporidium PCR products were successfully sequenced. In seven samples G. lamblia Assemblage A and in one sample Assemblage B and in four cases Assemblages A and B have been found. In one sample C. parvum and in the other separate sample C. meleagridis were detected. Sequence analysis revealed a new subtype of G. duodenalis complex, clustered close to the Assemblage A group. This study provides the first report on simultaneous detection and genotyping of G. duodenalis and Cryptosporidium species from water supplies in Hungary.

  18. Hypoxia promotes mitochondrial glutamine metabolism through HIF1α-GDH pathway in human lung cancer cells.

    PubMed

    Jiang, Zi-Feng; Wang, Min; Xu, Jian-Lin; Ning, Ya-Jing

    2017-01-29

    Drug-resistance is common in human lung cancer therapy. Hypoxia remarkably contributes to drug-resistance in lung cancer but the underlying mechanism remains elusive. Here we demonstrate that hypoxia-induced glutamine metabolism is involved in drug resistance in lung cancer cells. Hypoxia increases glutamine up-take, glutamate to α-ketoglutarate flux and the generation of ATP in lung cancer cells by up-regulating the expression of glutamate dehydrogenase (GDH). Hypoxia-induced expression of GDH relies on the up-regulation of HIF1α but not HIF2α. HIF1α binds the promoter of GDH and promotes the transcription of GDH gene in lung cancer cells. Finally, we show that GDH represses cisplatin-induced cell apoptosis and repression of colony formation, indicating that GDH contributes to drug-resistance in lung cancer cells. In conclusion, HIF1α-GDH pathway regulates glutamine metabolism and ATP production upon hypoxia stress and contributes to drug-resistance in human lung cancer cells.

  19. Control of gdhR Expression in Neisseria gonorrhoeae via Autoregulation and a Master Repressor (MtrR) of a Drug Efflux Pump Operon

    PubMed Central

    Rouquette-Loughlin, Corinne E.; Zalucki, Yaramah M.; Dhulipala, Vijaya L.; Balthazar, Jacqueline T.; Doyle, Raúl G.; Nicholas, Robert A.; Begum, Afrin A.; Raterman, Erica L.; Jerse, Ann E.

    2017-01-01

    ABSTRACT The MtrCDE efflux pump of Neisseria gonorrhoeae contributes to gonococcal resistance to a number of antibiotics used previously or currently in treatment of gonorrhea, as well as to host-derived antimicrobials that participate in innate defense. Overexpression of the MtrCDE efflux pump increases gonococcal survival and fitness during experimental lower genital tract infection of female mice. Transcription of mtrCDE can be repressed by the DNA-binding protein MtrR, which also acts as a global regulator of genes involved in important metabolic, physiologic, or regulatory processes. Here, we investigated whether a gene downstream of mtrCDE, previously annotated gdhR in Neisseria meningitidis, is a target for regulation by MtrR. In meningococci, GdhR serves as a regulator of genes involved in glucose catabolism, amino acid transport, and biosynthesis, including gdhA, which encodes an l-glutamate dehydrogenase and is located next to gdhR but is transcriptionally divergent. We report here that in N. gonorrhoeae, expression of gdhR is subject to autoregulation by GdhR and direct repression by MtrR. Importantly, loss of GdhR significantly increased gonococcal fitness compared to a complemented mutant strain during experimental murine infection. Interestingly, loss of GdhR did not influence expression of gdhA, as reported for meningococci. This variance is most likely due to differences in promoter localization and utilization between gonococci and meningococci. We propose that transcriptional control of gonococcal genes through the action of MtrR and GdhR contributes to fitness of N. gonorrhoeae during infection.

  20. 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

  1. TamA interacts with LeuB, the homologue of Saccharomyces cerevisiae Leu3p, to regulate gdhA expression in Aspergillus nidulans.

    PubMed

    Polotnianka, R; Monahan, B J; Hynes, M J; Davis, M A

    2004-11-01

    Previous studies have shown that expression of the gdhA gene, encoding NADP-linked glutamate dehydrogenase (NADP-GDH), in Aspergillus nidulans is regulated by the major nitrogen regulatory protein AreA and its co-activator TamA. We show here that loss of TamA function has a more severe effect on the levels of gdhA expression than loss of AreA function. Using TamA as the bait in a yeast two-hybrid screen, we have identified a second protein that interacts with TamA. Sequencing analysis and functional studies have shown that this protein, designated LeuB, is a transcriptional activator with similar function to the homologous Leu3p of Saccharomyces cerevisiae. Inactivation of leuB revealed that this gene is involved in the regulation of gdhA, and an areA; leuB double mutant was shown to have similar NADP-GDH levels to a tamA single mutant. The requirement for TamA function to promote gdhA expression is likely to be due to its dual interaction with AreA and LeuB.

  2. Arabidopsis mutant analysis and gene regulation define a nonredundant role for glutamate dehydrogenase in nitrogen assimilation.

    PubMed

    Melo-Oliveira, R; Oliveira, I C; Coruzzi, G M

    1996-05-14

    Glutamate dehydrogenase (GDH) is ubiquitous to all organisms, yet its role in higher plants remains enigmatic. To better understand the role of GDH in plant nitrogen metabolism, we have characterized an Arabidopsis mutant (gdh1-1) defective in one of two GDH gene products and have studied GDH1 gene expression. GDH1 mRNA accumulates to highest levels in dark-adapted or sucrose-starved plants, and light or sucrose treatment each repress GDH1 mRNA accumulation. These results suggest that the GDH1 gene product functions in the direction of glutamate catabolism under carbon-limiting conditions. Low levels of GDH1 mRNA present in leaves of light-grown plants can be induced by exogenously supplied ammonia. Under such conditions of carbon and ammonia excess, GDH1 may function in the direction of glutamate biosynthesis. The Arabidopsis gdh-deficient mutant allele gdh1-1 cosegregates with the GDH1 gene and behaves as a recessive mutation. The gdh1-1 mutant displays a conditional phenotype in that seedling growth is specifically retarded on media containing exogenously supplied inorganic nitrogen. These results suggest that GDH1 plays a nonredundant role in ammonia assimilation under conditions of inorganic nitrogen excess. This notion is further supported by the fact that the levels of mRNA for GDH1 and chloroplastic glutamine synthetase (GS2) are reciprocally regulated by light.

  3. Partial AUC maximization for essential gene prediction using genetic algorithms.

    PubMed

    Hwang, Kyu-Baek; Ha, Beom-Yong; Ju, Sanghun; Kim, Sangsoo

    2013-01-01

    Identifying genes indispensable for an organism's life and their characteristics is one of the central questions in current biological research, and hence it would be helpful to develop computational approaches towards the prediction of essential genes. The performance of a predictor is usually measured by the area under the receiver operating characteristic curve (AUC). We propose a novel method by implementing genetic algorithms to maximize the partial AUC that is restricted to a specific interval of lower false positive rate (FPR), the region relevant to follow-up experimental validation. Our predictor uses various features based on sequence information, protein-protein interaction network topology, and gene expression profiles. A feature selection wrapper was developed to alleviate the over-fitting problem and to weigh each feature's relevance to prediction. We evaluated our method using the proteome of budding yeast. Our implementation of genetic algorithms maximizing the partial AUC below 0.05 or 0.10 of FPR outperformed other popular classification methods.

  4. 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.

  5. Molecular test to determine toxigenic capabilities in GDH-positive, toxin-negative samples: evaluation of the Portrait toxigenic C. difficile assay.

    PubMed

    Finch, L S; Duncan, C M

    2013-01-01

    New recommendations for testing and reporting of Clostridium difficile were introduced in the NHS in 2012. These guidelines have improved identification of potential C. difficile infection (CDI) cases, but questions remain around the management of glutamate dehydrogenase (GDH)-positive, toxin-negative patients. This study aims to assess the introduction of the Portrait C. difficile assay as the third step to identify the presence of the toxigenic C. difficile B (tcdB) gene and thus determine toxigenic capability. Stool samples with a GDH-positive, toxin-negative result were tested using the Portrait analyser to detect the presence of tcdB. A retrospective evaluation was performed, assessing the clinical course of patients who were isolated as a result of the current algorithm using GDH enzyme immunoassay (EIA) and toxin EIA. Of the stool samples tested, 40% carried the tcdB gene. Four tcdB-positive stool samples initially toxin A/B-negative subsequently became positive. Thirteen patients were isolated, four of which did not have the tcdB gene. The total time to 'process' a positive CDI case was 102 hours and cost pounds 592. The additional time and cost of incorporating the Portrait toxigenic C. difficile assay was 105-115 minutes and pounds 46.48 to pounds 51.88. This study confirms that toxigenic capabilities in GDH-positive, toxin-negative specimens can facilitate effective treatment and infection prevention, and results show there is potential value in repeat toxin testing.

  6. GDH1 expression is regulated by GLN3, GCN4, and HAP4 under respiratory growth.

    PubMed

    Riego, Lina; Avendaño, Amaranta; DeLuna, Alexander; Rodríguez, Ekaterina; González, Alicia

    2002-04-26

    In the yeast Saccharomyces cerevisiae, two NADP(+)-dependent glutamate dehydrogenase isoenzymes encoded by GDH1 and GDH3 catalyze the synthesis of glutamate from ammonium and alpha-ketoglutarate. In this work we analyzed GDH1 transcriptional regulation, in order to deepen the studies in regard to its physiological role. Our results indicate that: (i) GDH1 expression is strictly controlled in ethanol-grown cultures, constituting a fine-tuning mechanism that modulates the abundance of Gdh1p monomers under this condition, (ii) GDH1 expression is controlled by transcriptional activators that have been considered as exclusive of either nitrogen (Gln3p and Gcn4p) or carbon metabolism (HAP complex), and (iii) chromatin remodeling complexes play a role in GDH1 expression; ADA2 and ADA3 up-regulated GDH1 expression on ethanol, while that on glucose was ADA3-dependent. SPT3 and SNF2 activated GDH1 expression on either carbon source whereas GCN5 played no role in any condition tested. The above described combinatorial control results in a refined mechanism that coordinates carbon and nitrogen utilization.

  7. Characterization and expression of NAD(H)-dependent glutamate dehydrogenase genes in Arabidopsis.

    PubMed

    Turano, F J; Thakkar, S S; Fang, T; Weisemann, J M

    1997-04-01

    Two distinct cDNA clones encoding NAD(H)-dependent glutamate dehydrogenase (NAD[H]-GDH) in Arabidopsis thaliana were identified and sequenced. The genes corresponding to these cDNA clones were designated GDH1 and GDH2. Analysis of the deduced amino acid sequences suggest that both gene products contain putative mitochondrial transit polypeptides and NAD(H)- and alpha-ketoglutarate-binding domains. Subcellular fractionation confirmed the mitochondrial location of the NAD(H)-GDH isoenzymes. In addition, a putative EF-hand loop, shown to be associated with Ca2+ binding, was identified in the GDH2 gene product but not in the GDH1 gene product. GDH1 encodes a 43.0-kD polypeptide, designated alpha, and GDH2 encodes a 42.5-kD polypeptide, designated beta. The two subunits combine in different ratios to form seven NAD(H)-GDH isoenzymes. The slowest-migrating isoenzyme in a native gel, GDH1, is a homohexamer composed of alpha subunits, and the fastest-migrating isoenzyme, GDH7, is a homohexamer composed of beta subunits. GDH isoenzymes 2 through 6 are heterohexamers composed of different ratios of alpha and beta subunits. NAD(H)-GDH isoenzyme patterns varied among different plant organs and in leaves of plants irrigated with different nitrogen sources or subjected to darkness for 4 d. Conversely, there were little or no measurable changes in isoenzyme patterns in roots of plants treated with different nitrogen sources. In most instances, changes in isoenzyme patterns were correlated with relative differences in the level of alpha and beta subunits. Likewise, the relative difference in the level of alpha or beta subunits was correlated with changes in the level of GDH1 or GDH2 transcript detected in each sample, suggesting that NAD(H)-GDH activity is controlled at least in part at the transcriptional level.

  8. 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.

  9. 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...

  10. Coexpression of Lactobacillus brevis ADH with GDH or G6PDH in Arxula adeninivorans for the synthesis of 1-(R)-phenylethanol.

    PubMed

    Rauter, Marion; Prokoph, Alexandra; Kasprzak, Jakub; Becker, Karin; Baronian, Keith; Bode, Rüdiger; Kunze, Gotthard; Vorbrodt, H- Matthias

    2015-06-01

    The yeast Arxula adeninivorans was used for the overexpression of an ADH gene of Lactobacillus brevis coding for (R)-specific alcohol dehydrogenase (LbADH) to synthesise enantiomerically pure 1-(R)-phenylethanol. Glucose dehydrogenase gene from Bacillus megaterium (BmGDH) or glucose 6-phosphate dehydrogenase of Bacillus pumilus (BpG6PDH) were coexpressed in Arxula to regenerate the cofactor NADPH by oxidising glucose or glucose 6-phosphate. The yeast strain expressing LbADH and BpG6PDH produced 5200 U l(-1) ADH and 370 U l(-1) G6PDH activity, whereas the strain expressing LbADH and BmGDH produced 2700 U l(-1) ADH and 170 U l(-1) GDH activity. However, the crude extract of both strains reduced 40 mM acetophenone to pure 1-(R)-phenylethanol with an enantiomeric excess (ee) of >99 % in 60 min without detectable by-products. An increase in yield was achieved using immobilised crude extracts (IEs), Triton X-100 permeabilised cells (PCs) and permeabilised immobilised cells (PICs) with PICs being most stable with GDH regeneration over 52 cycles. Even though the activity and synthesis rate of 1-(R)-phenylethanol with the BpG6PDH and LbADH coexpressing strain was higher, the BmGDH-LbADH strain was more stable over successive reaction cycles. This, combined with its higher total turnover number (TTN) of 391 mol product per mole NADP(+), makes it the preferred strain for continuous reaction systems. The initial non-optimised semi-continuous reaction produced 9.74 g l(-1) day(-1) or 406 g kg(-1) dry cell weight (dcw) day(-1) isolated 1-(R)-phenylethanol with an ee of 100 % and a TTN of 206 mol product per mole NADP(+). In conclusion, A. adeninivorans is a promising host for LbADH and BpG6PDH or BmGDH production and offers a simple method for the production of enantiomerically pure alcohols.

  11. 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.

  12. Spatio-temporal variability in the GDH activity to ammonium excretion ratio in epipelagic marine zooplankton

    NASA Astrophysics Data System (ADS)

    Fernández-Urruzola, I.; Osma, N.; Packard, T. T.; Maldonado, F.; Gómez, M.

    2016-11-01

    Glutamate dehydrogenase (GDH) activities have been widely used in oceanographic research as an index of in situ NH4+ excretion rates (RNH4+) in zooplankton. Here we study the variability in the relationship between the enzymatic rates and the actual rates measured in epipelagic marine zooplankton between several marine ecosystems. Although both measures were significantly correlated across zooplankton assemblages, the regression models yielded different GDH/RNH4+ ratios across ecosystems. Accordingly, the error of a general equation increased up to ±42.5 % when regressing all our data together. Aside from possible interspecific differences, some of the variability was explained by the unequal allometric relation that each rate maintained with protein. Scaling exponents were 1.38 for GDH activities and 0.87 for RNH4+, which would induce uncertainties in the GDH/RNH4+ ratios when organisms with different sizes were considered. Nevertheless, the main factor causing divergence between GDH activities and RNH4+ was the potential prey availability. We compared the excretory metabolism of the zooplankton community at different productivity periods in waters off Gran Canaria, and observed an important decrease in the RNH4+ during stratification. A similar decrease was found in the internal pool of glutamate, which may be critical in the regulation of in vivo rates. Strengthening our knowledge of the relationship between GDH activities and the RNH4+ will lead to more meaningful predictions of phytoplankton regeneration and community nitrogen fluxes across large spatial scales.

  13. GDH3 encodes a glutamate dehydrogenase isozyme, a previously unrecognized route for glutamate biosynthesis in Saccharomyces cerevisiae.

    PubMed

    Avendaño, A; Deluna, A; Olivera, H; Valenzuela, L; Gonzalez, A

    1997-09-01

    It has been considered that the yeast Saccharomyces cerevisiae, like many other microorganisms, synthesizes glutamate through the action of NADP+-glutamate dehydrogenase (NADP+-GDH), encoded by GDH1, or through the combined action of glutamine synthetase and glutamate synthase (GOGAT), encoded by GLN1 and GLT1, respectively. A double mutant of S. cerevisiae lacking NADP+-GDH and GOGAT activities was constructed. This strain was able to grow on ammonium as the sole nitrogen source and thus to synthesize glutamate through an alternative pathway. A computer search for similarities between the GDH1 nucleotide sequence and the complete yeast genome was carried out. In addition to identifying its cognate sequence at chromosome XIV, the search found that GDH1 showed high identity with a previously recognized open reading frame (GDH3) of chromosome I. Triple mutants impaired in GDH1, GLT1, and GDH3 were obtained. These were strict glutamate auxotrophs. Our results indicate that GDH3 plays a significant physiological role, providing glutamate when GDH1 and GLT1 are impaired. This is the first example of a microorganism possessing three pathways for glutamate biosynthesis.

  14. 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

  15. Involvement of GDH3-encoded NADP+-dependent glutamate dehydrogenase in yeast cell resistance to stress-induced apoptosis in stationary phase cells.

    PubMed

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

    2012-12-28

    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.

  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. Isolation and partial characterization of the Drosophila alcohol dehydrogenase gene.

    PubMed Central

    Goldberg, D A

    1980-01-01

    The alcohol dehydrogenase (ADH; alcohol: NAD+ oxidoreductase, EC 1.1.1.1) gene (Adh) of Drosophila melanogaster was isolated by utilizing a mutant strain in which the Adh locus is deleted. Adult RNA from wild-type flies was enriched in ADH sequences by gel electrophoresis and then used to prepare labeled cDNA for screening a bacteriophage lambda library of genomic Drosophila DNA. Of the clones that hybridized in the initial screen, one clone was identified that hybridized with labeled cDNA prepared from a wild-type Drosophila strain but did not hybridize with cDNA prepared from an Adh deletion strain. This clone was shown to contain ADH structural gene sequences by three criteria: in situ hybridization, in vitro translation of mRNA selected by hybridization to the cloned DNA, and comparison of the ADH protein sequence with a nucleotide sequence derived from the cloned DNA. Comparison of the restriction site maps from clones of three different wild-type Drosophila strains revealed the presence of a 200-nucleotide sequence in one strain that was absent from the other two strains. The ADH mRNA sequences were located within the cloned DNA by hybridization mapping experiments. Two intervening sequences were identified within Adh by S1 nuclease mapping experiments. Images PMID:6777776

  18. Sequence and characterization of two Arabidopsis thaliana cDNAs isolated by functional complementation of a yeast gln3 gdh1 mutant.

    PubMed

    Truong, H N; Caboche, M; Daniel-Vedele, F

    1997-06-30

    We have isolated two Arabidopsis thaliana cDNAs by complementation of a yeast gln3 gdh1 strain that is affected in the regulation of nitrogen metabolism. The two clones (RGA1 and RGA2) are homologous to each other and to the SCARECROW (SCR) gene that is involved in regulating an asymmetric cell division in plants. RGA1, RGA2 and SCR share several structural features and may define a new family of genes. RGA1 and RGA2 have been mapped, respectively, to chromosome II and I, and their expression in plant is constitutive.

  19. Identification of homeobox genes expressed during the process of rat liver regeneration after partial hapatectomy

    SciTech Connect

    Mizuta, Ikuko; Ogasawara, Naotake; Yoshikawa, Hiroshi; Sakoyama, Yasuhiko

    1996-02-01

    Homeobox (HBox) genes are well-known to be involved in development and differentiation. To ascertain a role of HBox genes in the process of liver regeneration, we identified HBox genes expressed at various times after partial hepatectomy in rats (at 0 hr, 1 hr, 2 days, and 4 days) by using reverse transcription-polymerase chain reaction (RT-PCR), cloning, and sequencing techniques. By the competitive RT-PCR method using generic primers, expression levels of HBox genes in regenerating livers were estimated at as low as only 0.4-2% of that in 14-day embryonic liver; however, we identified multiple HBox genes at different stages. Comparing sets of HBox genes identified at different stages, we could find two candidates of stage specifically expressed HBox genes (one rat caudal-related gene, RCdx-3, stimulated at 1 hr, and one rat Hox gene, RHoxB5, repressed after hepatectomy) and continuous expression of five Hox genes (RHoxAl, A4, A5, B2, and B3) before and after hepatectomy. These HBox genes are considered to correlate with the process of liver regeneration. 36 refs., 6 figs., 2 tabs.

  20. 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.

  1. 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

    2008-10-28

    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.

  2. Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions.

    PubMed

    Yuan, Yinyin; Li, Chang-Tsun; Windram, Oliver

    2011-04-06

    Inferring regulatory relationships among many genes based on their temporal variation in transcript abundance has been a popular research topic. Due to the nature of microarray experiments, classical tools for time series analysis lose power since the number of variables far exceeds the number of the samples. In this paper, we describe some of the existing multivariate inference techniques that are applicable to hundreds of variables and show the potential challenges for small-sample, large-scale data. We propose a directed partial correlation (DPC) method as an efficient and effective solution to regulatory network inference using these data. Specifically for genomic data, the proposed method is designed to deal with large-scale datasets. It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. The idea is that when a transcription factor is induced artificially within a gene network, the disruption of the network by the induction signifies a genes role in transcriptional regulation. The benchmarking results using GeneNetWeaver, the simulator for the DREAM challenges, provide strong evidence of the outstanding performance of the proposed DPC method. When applied to real biological data, the inferred starch metabolism network in Arabidopsis reveals many biologically meaningful network modules worthy of further investigation. These results collectively suggest DPC is a versatile tool for genomics research. The R package DPC is available for download (http://code.google.com/p/dpcnet/).

  3. IMP2, a gene involved in the expression of glucose-repressible genes in Saccharomyces cerevisiae.

    PubMed

    Lodi, T; Goffrini, P; Ferrero, I; Donnini, C

    1995-09-01

    Two mutants carrying different deletions of the IMP2 coding sequence of Saccharomyces cerevisiae, delta T1, which encodes a protein lacking the last 26 C-terminal amino acids, and delta T2, which completely lacks the coding region, were analysed for derepression of glucose-repressible maltose, galactose, raffinose and ethanol utilization pathways in response to glucose limitation. The role of the IMP2 gene product in the regulation of carbon catabolite repressible enzymes maltase, invertase, alcohol dehydrogenase, NAD-dependent glutamate dehydrogenase (NAD-GDH) and L-lactate:ferricytochrome-c oxidoreductase (L-LCR) was also analysed. The IMP2 gene product is required for the rapid glucose derepression of all above-mentioned carbon source utilization pathways and of all the enzymes except for L-LCR. NAD-GDH is regulated by IMP2 in the opposite way and, in fact, this enzyme was released at higher levels in both imp2 mutants than in the wild-type strain. Therefore, the product of IMP2 appears to be involved in positive and negative regulation. Both deletions result in growth and catalytic defects; in some cases partial modification of the gene product yielded more dramatic effects than its complete absence. Moreover, evidence is provided that the IMP2 gene product regulates galactose- and maltose-inducible genes at the transcriptional level and is a positive regulator of maltase, maltose permease and galactose permease gene expression.

  4. Kinetics of NH(4) Assimilation in Zea mays: Preliminary Studies with a Glutamate Dehydrogenase (GDH1) Null Mutant.

    PubMed

    Magalhães, J R; Ju, G C; Rich, P J; Rhodes, D

    1990-10-01

    In higher plants it is now generally considered that glutamate dehydrogenase (GDH) plays only a small or negligible role in ammonia assimilation. To test this specific point, comparative studies of (15)NH(4) (+) assimilation were undertaken with a GDH1-null mutant of Zea mays and a related (but not strictly isogenic) GDH1-positive wild type from which this mutant was derived. The kinetics of (15)NH(4) (+) assimilation into free amino acids and total reduced nitrogen were monitored in both roots and shoots of 2-week-old seedlings supplied with 5 millimolar 99% ((15)NH(4))(2)SO(4) via the aerated root medium in hydroponic culture over a 24-h period. The GDH1-null mutant, with a 10- to 15-fold lower total root GDH activity in comparison to the wild type, was found to exhibit a 40 to 50% lower rate of (15)NH(4) (+) assimilation into total reduced nitrogen. Observed rates of root ammonium assimilation were 5.9 and 3.1 micromoles per hour per gram fresh weight for the wild type and mutant, respectively. The lower rate of (15)NH(4) (+) assimilation in the mutant was associated with lower rates of labeling of several free amino acids (including glutamate, glutamine-amino N, aspartate, asparagine-amino N, and alanine) in both roots and shoots of the mutant in comparison to the wild type. Qualitatively, these labeling kinetics appear consistent with a reduced flux of (15)N via glutamate in the GDH1-null mutant. However, the responses of the two genotypes to the potent inhibitor of glutamine synthetase, methionine sulfoximine, and differences in morphology of the two genotypes (particularly a lower shoot:root ratio in the GDH1-null mutant) urge caution in concluding that GDH1 is solely responsible for these differences in ammonia assimilation rate.

  5. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming gene

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Li, Hu; Collins, James; Mehta, Pankaj

    2013-03-01

    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 physics, specifically Hopfield neural networks. Each cell fate is a dynamic attractor, yet cells can change fate in response to external signals. Our model suggests that partially reprogrammed cells (cells found in reprogramming experiments but not in vivo) are a natural consequence of high-dimensional landscapes and predicts that partially reprogrammed cells should be hybrids that coexpress genes from multiple cell fates. We verify this prediction by reanalyzing existing data sets. 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.

  6. 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

  7. 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

  8. Absence of PAX6 gene mutations in Gillespie syndrome (partial aniridia, cerebellar ataxia, and mental retardation)

    SciTech Connect

    Glaser, T.; Maas, R.L. ); Ton, C.C.T.; Housman, D.E. ); Mueller, R.; Oliver, C. ); Petzl-Erler, M.L. ); Nevin, N.C. )

    1994-01-01

    The PAX6 gene is expressed at high levels in the developing eye and cerebellum and is mutated in patients with autosomal dominant aniridia. The authors have tested the role of PAX6 mutations in three families with Gillespie syndrome, a rare autosomal recessive condition consisting of partial aniridia, cerebellar ataxia, and mental retardation. Single-strand conformational polymorphism analysis of affected individuals revealed no alteration of PAX6 sequences. In two families, the disease trait segregates independently from chromosome 11p markers flanking PAX6. The authors conclude that Gillespie syndrome is genetically distinct from autosomal dominant aniridia. 28 refs., 2 figs., 1 tab.

  9. 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.

  10. Expression of the human isoform of glutamate dehydrogenase, hGDH2, augments TCA cycle capacity and oxidative metabolism of glutamate during glucose deprivation in astrocytes.

    PubMed

    Nissen, Jakob D; Lykke, Kasper; Bryk, Jaroslaw; Stridh, Malin H; Zaganas, Ioannis; Skytt, Dorte M; Schousboe, Arne; Bak, Lasse K; Enard, Wolfgang; Pääbo, Svante; Waagepetersen, Helle S

    2017-03-01

    A key enzyme in brain glutamate homeostasis is glutamate dehydrogenase (GDH) which links carbohydrate and amino acid metabolism mediating glutamate degradation to CO2 and expanding tricarboxylic acid (TCA) cycle capacity with intermediates, i.e. anaplerosis. Humans express two GDH isoforms, GDH1 and 2, whereas most other mammals express only GDH1. hGDH1 is widely expressed in human brain while hGDH2 is confined to astrocytes. The two isoforms display different enzymatic properties and the nature of these supports that hGDH2 expression in astrocytes potentially increases glutamate oxidation and supports the TCA cycle during energy-demanding processes such as high intensity glutamatergic signaling. However, little is known about how expression of hGDH2 affects the handling of glutamate and TCA cycle metabolism in astrocytes. Therefore, we cultured astrocytes from cerebral cortical tissue of hGDH2-expressing transgenic mice. We measured glutamate uptake and metabolism using [(3) H]glutamate, while the effect on metabolic pathways of glutamate and glucose was evaluated by use of (13) C and (14) C substrates and analysis by mass spectrometry and determination of radioactively labeled metabolites including CO2 , respectively. We conclude that hGDH2 expression increases capacity for uptake and oxidative metabolism of glutamate, particularly during increased workload and aglycemia. Additionally, hGDH2 expression increased utilization of branched-chain amino acids (BCAA) during aglycemia and caused a general decrease in oxidative glucose metabolism. We speculate, that expression of hGDH2 allows astrocytes to spare glucose and utilize BCAAs during substrate shortages. These findings support the proposed role of hGDH2 in astrocytes as an important fail-safe during situations of intense glutamatergic activity. GLIA 2017;65:474-488.

  11. 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.

  12. GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach.

    PubMed

    Baumung, R; Farkas, J; Boichard, D; Mészáros, G; Sölkner, J; Curik, I

    2015-04-01

    GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

  13. 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.

  14. GBF-dependent family genes morphologically suppress the partially active Dictyostelium STATa strain.

    PubMed

    Shimada, Nao; Kanno-Tanabe, Naoko; Minemura, Kakeru; Kawata, Takefumi

    2008-02-01

    Transcription factor Dd-STATa, a functional Dictyostelium homologue of metazoan signal transducers and activators of transcription proteins, is necessary for culmination during development. We have isolated more than 18 putative multicopy suppressors of Dd-STATa using genetic screening. One was hssA gene, whose expression is known to be G-box-binding-factor-dependent and which was specific to prestalk A (pstA) cells, where Dd-STATa is activated. Also, hssA mRNA was expressed in pstA cells in the Dd-STATa-null mutant. At least 40 hssA-related genes are present in the genome and constitute a multigene family. The tagged HssA protein was translated; hssA encodes an unusually high-glycine-serine-rich small protein (8.37 kDa), which has strong homology to previously reported cyclic-adenosine-monophosphate-inducible 2C and 7E proteins. Overexpression of hssA mRNA as well as frame-shifted versions of hssA RNA suppressed the phenotype of the partially active Dd-STATa strain, suggesting that translation is not necessary for suppression. Although overexpression of prespore-specific genes among the family did not suppress the parental phenotype, prestalk-specific family members did. Although overexpression of the hssA did not revert the expression of Dd-STATa target genes, and although its suppression mechanism remains unknown, morphological reversion implies functional relationships between Dd-STATa and hssA.

  15. 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

  16. 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.

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

    DOE PAGES

    Yan, Xin -Hu; Ye, Yun -Xiu; Chen, Jian -Ping; ...

    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 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.

  20. 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.

  1. Plum pox virus induces differential gene expression in the partially resistant stone fruit tree Prunus armeniaca cv. Goldrich.

    PubMed

    Schurdi-Levraud Escalettes, Valérie; Hullot, Clémence; Wawrzy'nczak, Danuta; Mathieu, Elodie; Eyquard, Jean-Philippe; Le Gall, Olivier; Decroocq, Véronique

    2006-06-07

    We investigated the changes in the expression profiles of the partially resistant apricot (Prunus armeniaca L.) cultivar Goldrich following inoculation with Plum pox virus (PPV) using cDNA-amplification fragment length polymorphism (AFLP). Altered expression patterns were detected and twenty-one differentially expressed cDNA had homologies with genes in databases coding for proteins involved in metabolism, signal transduction, defense, stress and intra/intercellular connections. Seven of the modified expressed patterns were further investigated by semi-quantitative RT-PCR or Northern blotting. The expression patterns of five of these genes were confirmed in the partially resistant P. armeniaca cv. 'Goldrich' and assessed in a susceptible genotype. One of these cDNAs, coding for a putative class III chitinase, appeared to be repressed in infected plants of the partially resistant genotype and expressed in the susceptible one which could be related to the partially resistant phenotype. On the contrary, the expression patterns of the genes coding for a transketolase, a kinesin-like and an ankyrin-like protein, were clearly linked to the susceptible interaction. These candidate genes could play a role either in the compatible interaction leading to virus invasion or to the quantitative resistance of apricot to PPV.

  2. Mutational analysis of the androgen receptor gene in two Indian families with partial androgen insensitivity syndrome.

    PubMed

    Nagaraja, M R; Rastogi, Amit; Raman, Rajiva; Gupta, Dinesh K; Singh, S K

    2009-12-01

    Mutation in the androgen receptor gene (AR) is known to cause androgen insensitivity syndrome (AIS). In an X-linked recessive manner, an AR mutation gets transmitted to the offspring through carrier mothers in 70% of cases, the other 30% arising de novo. However, reports on AR mutations amongst Indian patients with AIS are scarce in the literature. This study reports mutations in AR from two Indian families, each having a proband with partial androgen insensitivity syndrome (PAIS) phenotype. Clinical, endocrine and cytogenetic evaluation of these affected children was performed. Mutational analysis was carried out by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis followed by sequencing. The two point mutations were in exon 5: p.M742I, familial in patient 1 and p.V746M de novo in patient 2. These are hitherto unrecognized mutations in our population. Similar mutational studies are suggested in patients with AIS, in order to identify their frequency and clinical severity in our population.

  3. 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

  4. Phylogenetic Relationships of 3 Korean Neodiplostomum Species (Digenea: Neodiplostomidae) Based on Partial CO1 Gene

    PubMed Central

    Pyo, Kyoung-Ho; Yi Lee, Jo Woon; Lee, Jin-Ju; Park, Yun-Kyu; Chai, Jong-Yil

    2014-01-01

    The phylogenetic relationships of the 3 Neodiplostomum spp. (Digenea: Neodiplostomidae) occurring in Korea (N. seoulense, N. leei, and N. boryongense) were analyzed using the partial mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. The adult flukes were recovered from Sprague-Dawley rats (N. seoulense) and newborn chicks (N. leei and N. boryongense) experimentally infected with the neodiplostomula from the grass snake, Rhabdophis tigrinus tigrinus. The genomic DNA was amplified using specific primers, and the sequence of CO1 was obtained. According to the results, the pairwise similarity was 96.1% between N. boryongense and N. seoulense, but was 95.0% between N. boryongense and N. leei and 94.2% between N. leei and N. seoulense. The results demonstrated a closer phylogenetic relationship between N. seoulense and N. boryongense. This high relationship of N. seoulense and N. boryongense may be related to their similar morphologic features including the limited distribution of vitellaria and the presence of a genital cone. N. leei is distinct on the other hand with an extensive distribution of vitellaria and the absence of a genital cone. PMID:25031477

  5. 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

  6. Molecular epidemiology of rabies in Colombia 1994-2005 based on partial nucleoprotein gene sequences.

    PubMed

    Páez, Andrés; Velasco-Villa, Andrés; Rey, Gloria; Rupprecht, Charles E

    2007-12-01

    One hundred and twenty-four rabies viruses (RABV) were isolated from humans and eight species of mammals in Colombia during 1994-2005. To determine the genetic and reservoir-associated diversity cDNA fragments encoding 88 amino acids at the carboxyl terminus of the nucleoprotein were sequenced and used in phylogenetic analyses. Eight genetic lineages (GL) were characterized. GL1, GL2 and GL3 consisted of dog-associated antigenic variant (AV) 1 RABV, isolated in the centre-east, north and southwest of Colombia, respectively. GL1 is apparently extinct in Colombia. The GL4 were AV3, AV8 and non-determined (ND) AV viruses associated with hematophagous bats. The GL5 and GL6 consisted of AV4 viruses. GL6 isolate was found associated with Tadarida brasiliensis bats. GL5 segregated independently. The GL7 and GL8 segregated independently within clades associated with colonial insectivorous and solitary bats, respectively. Both of these were represented by NDAV viruses. Viruses isolated from humans grouped within GL2, GL3 and GL4, which in turn corresponded to AV1, 3, 8 and ND. Dogs and D. rotundus are the two major rabies reservoirs and vectors in Colombia. Insectivorous bats may also be important rabies reservoirs but spillovers to other species are rare. Our data were consistent with previous studies in which partial Psi, G and L gene sequences were analyzed. Our results confirmed the existence of RABV of unclassified AV in Colombia.

  7. Changes in Gene Expression of Arabidopsis Thaliana Cell Cultures Upon Exposure to Real and Simulated Partial- g Forces

    NASA Astrophysics Data System (ADS)

    Fengler, Svenja; Spirer, Ina; Neef, Maren; Ecke, Margret; Hauslage, Jens; Hampp, Rüdiger

    2016-06-01

    Cell cultures of the plant model organism Arabidopsis thaliana were exposed to partial- g forces during parabolic flight and clinostat experiments (0.16 g, 0.38 g and 0.5 g were tested). In order to investigate gravity-dependent alterations in gene expression, samples were metabolically quenched by the fixative RNA later Ⓡ to stabilize nucleic acids and used for whole-genome microarray analysis. An attempt to identify the potential threshold acceleration for the gravity-dependent response showed that the smaller the experienced g-force, the greater was the susceptibility of the cell cultures. Compared to short-term μ g during a parabolic flight, the number of differentially expressed genes under partial- g was lower. In addition, the effect on the alteration of amounts of transcripts decreased during partial- g parabolic flight due to the sequence of the different parabolas (0.38 g, 0.16 g and μ g). A time-dependent analysis under simulated 0.5 g indicates that adaptation occurs within minutes. Differentially expressed genes (at least 2-fold up- or down-regulated in expression) under real flight conditions were to some extent identical with those affected by clinorotation. The highest number of homologuous genes was detected within seconds of exposure to 0.38 g (both flight and clinorotation). To a considerable part, these genes deal with cell wall properties. Additionally, responses specific for clinorotation were observed.

  8. Transcriptome Analysis Highlights Defense and Signaling Pathways Mediated by Rice pi21 Gene with Partial Resistance to Magnaporthe oryzae

    PubMed Central

    Zhang, Yu; Zhao, Jianhua; Li, Yali; Yuan, Zhengjie; He, Haiyan; Yang, Haihe; Qu, Haiyan; Ma, Chenyan; Qu, Shaohong

    2016-01-01

    Rice blast disease is one of the most destructive rice diseases worldwide. The pi21 gene confers partial and durable resistance to Magnaporthe oryzae. However, little is known regarding the molecular mechanisms of resistance mediated by the loss-of-function of Pi21. In this study, comparative transcriptome profiling of the Pi21-RNAi transgenic rice line and Nipponbare with M. oryzae infection at different time points (0, 12, 24, 48, and 72 hpi) were investigated using RNA sequencing. The results generated 43,222 unique genes mapped to the rice genome. In total, 1109 differentially expressed genes (DEGs) were identified between the Pi21-RNAi line and Nipponbare with M. oryzae infection, with 103, 281, 209, 69, and 678 DEGs at 0, 12, 24, 48, and 72 hpi, respectively. Functional analysis showed that most of the DEGs were involved in metabolism, transport, signaling, and defense. Among the genes assigned to plant—pathogen interaction, we identified 43 receptor kinase genes associated with pathogen-associated molecular pattern recognition and calcium ion influx. The expression levels of brassinolide-insensitive 1, flagellin sensitive 2, and elongation factor Tu receptor, ethylene (ET) biosynthesis and signaling genes, were higher in the Pi21-RNAi line than Nipponbare. This suggested that there was a more robust PTI response in Pi21-RNAi plants and that ET signaling was important to rice blast resistance. We also identified 53 transcription factor genes, including WRKY, NAC, DOF, and ERF families that show differential expression between the two genotypes. This study highlights possible candidate genes that may serve a function in the partial rice blast resistance mediated by the loss-of-function of Pi21 and increase our understanding of the molecular mechanisms involved in partial resistance against M. oryzae. PMID:28008334

  9. Transcriptome Analysis Highlights Defense and Signaling Pathways Mediated by Rice pi21 Gene with Partial Resistance to Magnaporthe oryzae.

    PubMed

    Zhang, Yu; Zhao, Jianhua; Li, Yali; Yuan, Zhengjie; He, Haiyan; Yang, Haihe; Qu, Haiyan; Ma, Chenyan; Qu, Shaohong

    2016-01-01

    Rice blast disease is one of the most destructive rice diseases worldwide. The pi21 gene confers partial and durable resistance to Magnaporthe oryzae. However, little is known regarding the molecular mechanisms of resistance mediated by the loss-of-function of Pi21. In this study, comparative transcriptome profiling of the Pi21-RNAi transgenic rice line and Nipponbare with M. oryzae infection at different time points (0, 12, 24, 48, and 72 hpi) were investigated using RNA sequencing. The results generated 43,222 unique genes mapped to the rice genome. In total, 1109 differentially expressed genes (DEGs) were identified between the Pi21-RNAi line and Nipponbare with M. oryzae infection, with 103, 281, 209, 69, and 678 DEGs at 0, 12, 24, 48, and 72 hpi, respectively. Functional analysis showed that most of the DEGs were involved in metabolism, transport, signaling, and defense. Among the genes assigned to plant-pathogen interaction, we identified 43 receptor kinase genes associated with pathogen-associated molecular pattern recognition and calcium ion influx. The expression levels of brassinolide-insensitive 1, flagellin sensitive 2, and elongation factor Tu receptor, ethylene (ET) biosynthesis and signaling genes, were higher in the Pi21-RNAi line than Nipponbare. This suggested that there was a more robust PTI response in Pi21-RNAi plants and that ET signaling was important to rice blast resistance. We also identified 53 transcription factor genes, including WRKY, NAC, DOF, and ERF families that show differential expression between the two genotypes. This study highlights possible candidate genes that may serve a function in the partial rice blast resistance mediated by the loss-of-function of Pi21 and increase our understanding of the molecular mechanisms involved in partial resistance against M. oryzae.

  10. Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow.

    PubMed

    Guirao-Rico, Sara; Sánchez-Gracia, Alejandro; Charlesworth, Deborah

    2017-03-01

    DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.

  11. 16S rRNA partial gene sequencing for the differentiation and molecular subtyping of Listeria species.

    PubMed

    Hellberg, Rosalee S; Martin, Keely G; Keys, Ashley L; Haney, Christopher J; Shen, Yuelian; Smiley, R Derike

    2013-12-01

    Use of 16S rRNA partial gene sequencing within the regulatory workflow could greatly reduce the time and labor needed for confirmation and subtyping of Listeria monocytogenes. The goal of this study was to build a 16S rRNA partial gene reference library for Listeria spp. and investigate the potential for 16S rRNA molecular subtyping. A total of 86 isolates of Listeria representing L. innocua, L. seeligeri, L. welshimeri, and L. monocytogenes were obtained for use in building the custom library. Seven non-Listeria species and three additional strains of Listeria were obtained for use in exclusivity and food spiking tests. Isolates were sequenced for the partial 16S rRNA gene using the MicroSeq ID 500 Bacterial Identification Kit (Applied Biosystems). High-quality sequences were obtained for 84 of the custom library isolates and 23 unique 16S sequence types were discovered for use in molecular subtyping. All of the exclusivity strains were negative for Listeria and the three Listeria strains used in food spiking were consistently recovered and correctly identified at the species level. The spiking results also allowed for differentiation beyond the species level, as 87% of replicates for one strain and 100% of replicates for the other two strains consistently matched the same 16S type.

  12. 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)

  13. 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.

  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. A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip.

    PubMed

    Roselli, Sandro; Olry, Alexandre; Vautrin, Sonia; Coriton, Olivier; Ritchie, Dave; Galati, Gianni; Navrot, Nicolas; Krieger, Célia; Vialart, Guilhem; Bergès, Hélène; Bourgaud, Frédéric; Hehn, Alain

    2017-03-01

    Furanocoumarins are specialized metabolites that are involved in the defense of plants against phytophagous insects. The molecular and functional characterization of the genes involved in their biosynthetic pathway is only partially complete. Many recent reports have described gene clusters responsible for the biosynthesis of specialized metabolites in plants. To investigate possible co-localization of the genes involved in the furanocoumarin pathway, we sequenced parsnip BAC clones spanning two different gene loci. We found that two genes previously identified in this pathway, CYP71AJ3 and CYP71AJ4, were located on the same BAC, whereas a third gene, PsPT1, belonged to a different BAC clone. Chromosome mapping using fluorescence in situ hybridization (FISH) indicated that PsPT1 and the CYP71AJ3-CYP71AJ4 clusters are located on two different chromosomes. Sequencing the BAC clone harboring PsPT1 led to the identification of a gene encoding an Fe(II) α-ketoglutarate-dependent dioxygenase (PsDIOX) situated in the neighborhood of PsPT1 and confirmed the occurrence of a second gene cluster involved in the furanocoumarin pathway. This enzyme metabolizes p-coumaroyl CoA, leading exclusively to the synthesis of umbelliferone, an important intermediate compound in furanocoumarin synthesis. This work provides an insight into the genomic organization of genes from the furanocoumarin biosynthesis pathway organized in more than one gene cluster. It also confirms that the screening of a genomic library and the sequencing of BAC clones represent a valuable tool to identify genes involved in biosynthetic pathways dedicated to specialized metabolite synthesis.

  16. Partial Least Squares Based Gene Expression Analysis in EBV- Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders.

    PubMed

    Wu, Sa; Zhang, Xin; Li, Zhi-Ming; Shi, Yan-Xia; Huang, Jia-Jia; Xia, Yi; Yang, Hang; Jiang, Wen-Qi

    2013-01-01

    Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

  17. Human speech- and reading-related genes display partially overlapping expression patterns in the marmoset brain.

    PubMed

    Kato, Masaki; Okanoya, Kazuo; Koike, Taku; Sasaki, Erika; Okano, Hideyuki; Watanabe, Shigeru; Iriki, Atsushi

    2014-06-01

    Language is a characteristic feature of human communication. Several familial language impairments have been identified, and candidate genes for language impairments already isolated. Studies comparing expression patterns of these genes in human brain are necessary to further understanding of these genes. However, it is difficult to examine gene expression in human brain. In this study, we used a non-human primate (common marmoset; Callithrix jacchus) as a biological model of the human brain to investigate expression patterns of human speech- and reading-related genes. Expression patterns of speech disorder- (FoxP2, FoxP1, CNTNAP2, and CMIP) and dyslexia- (ROBO1, DCDC2, and KIAA0319) related genes were analyzed. We found the genes displayed overlapping expression patterns in the ocular, auditory, and motor systems. Our results enhance understanding of the molecular mechanisms underlying language impairments.

  18. Phasic-like stimulation of the medial forebrain bundle augments striatal gene expression despite methamphetamine-induced partial dopamine denervation.

    PubMed

    Howard, Christopher D; Pastuzyn, Elissa D; Barker-Haliski, Melissa L; Garris, Paul A; Keefe, Kristen A

    2013-05-01

    Methamphetamine-induced partial dopamine depletions are associated with impaired basal ganglia function, including decreased preprotachykinin mRNA expression and impaired transcriptional activation of activity-regulated, cytoskeleton-associated (Arc) gene in striatum. Recent work implicates deficits in phasic dopamine signaling as a potential mechanism linking methamphetamine-induced dopamine loss to impaired basal ganglia function. This study thus sought to establish a causal link between phasic dopamine transmission and altered basal ganglia function by determining whether the deficits in striatal neuron gene expression could be restored by increasing phasic dopamine release. Three weeks after pretreatment with saline or a neurotoxic regimen of methamphetamine, rats underwent phasic- or tonic-like stimulation of ascending dopamine neurons. Striatal gene expression was examined using in situ hybridization histochemistry. Phasic-like, but not tonic-like, stimulation induced immediate-early genes Arc and zif268 in both groups, despite the partial striatal dopamine denervation in methamphetamine-pretreated rats, with the Arc expression occurring in presumed striatonigral efferent neurons. Phasic-like stimulation also restored preprotachykinin mRNA expression. These results suggest that disruption of phasic dopamine signaling likely underlies methamphetamine-induced impairments in basal ganglia function, and that restoring phasic dopamine signaling may be a viable approach to manage long-term consequences of methamphetamine-induced dopamine loss on basal ganglia functions.

  19. Partial Gene Sequencing of CYP1A, Vitellogenin, and Metallothionein in Mosquitofish Gambusia yucatana and Gambusia sexradiata.

    PubMed

    Vázquez-Euán, Roberto; Escalante-Herrera, Karla S; Rodríguez-Fuentes, Gabriela

    2017-01-01

    Ground characteristics in the Yucatan Peninsula make recovery and treatment of wastewater very expensive. This situation has contributed to an increase of pollutants in the aquifer. Unfortunately, studies related to the effects of those pollutants in native organisms are scarce. The aim of this work was to obtain partial sequences of widely known genes used as biomarkers of pollutant effect in Gambusia yucatana and Gambusia sexradiata. The studied genes were: cytochrome P450 1A (CYP1A); vitellogenin (VTG); metallothionein (MT), and two housekeeping genes, 18S and β-actin. From reported sequences of Gambusia affinis, primers were designed and amplification was done in the local Gambusia species exposed for 48 h to gasoline (100 µL/L, stirred for 24 h pre-exposure). Preliminary results revealed partial sequences of all genes with an approximate average length of 200 bp. BLAST analysis of found sequences indicated a minimum of 97% identity with reported sequences for G. affinis or Gambusia holbrooki showing great similarity.

  20. A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes.

    PubMed Central

    Warren, R F; Henk, A; Mowery, P; Holub, E; Innes, R W

    1998-01-01

    Recognition of pathogens by plants is mediated by several distinct families of functionally variable but structurally related disease resistance (R) genes. The largest family is defined by the presence of a putative nucleotide binding domain and 12 to 21 leucine-rich repeats (LRRs). The function of these LRRs has not been defined, but they are speculated to bind pathogen-derived ligands. We have isolated a mutation in the Arabidopsis RPS5 gene that indicates that the LRR region may interact with other plant proteins. The rps5-1 mutation causes a glutamate-to-lysine substitution in the third LRR and partially compromises the function of several R genes that confer bacterial and downy mildew resistance. The third LRR is relatively well conserved, and we speculate that it may interact with a signal transduction component shared by multiple R gene pathways. PMID:9724691

  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. Gene- and strand-specific repair in vitro: Partial purification of a transcription-repair coupling factor

    SciTech Connect

    Selby, C.P.; Sancar, A. )

    1991-09-15

    In eukaryotic and prokaryotic cells, actively transcribed genes and, in some instances, the template strand of these genes have been found to be repaired 2-10 times more rapidly than nontranscribed genes or the coding strand of transcribed genes. The authors demonstrate here gene- and template strand-specific repair synthesis in vitro by using an Escherichia coli cell-free extract and a plasmid carrying a gene with the strong tac promoter. Strand-specific repair of UV, 4{prime}-hydroxymethyl-4,5{prime}, 8-trimethylpsoralen, and cis-dicholorodiammine platinum(II) damage was dependent upon transcription and a functional nucleotide excision repair system and was stimulated by 6% (wt/vol) polyethylene glycol. A defined system consisting of the transcription and repair proteins in highly purified form did not perform strand-specific repair; however, active fractions of extract conferred strand specificity to the defined system. Transcription-repair coupling activity was partially purified from extract by successive DEAE-agarose and gel filtration chromatography. The coupling factor is heat-labile, with an estimated M{sub r} of 100,000.

  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.

  4. 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.

  5. Partial mitochondrial gene arrangements support a close relationship between Tardigrada and Arthropoda.

    PubMed

    Ryu, Shi Hyun; Lee, Ji Min; Jang, Kuem-Hee; Choi, Eun Hwa; Park, Shin Ju; Chang, Cheon Young; Kim, Won; Hwang, Ui Wook

    2007-12-31

    Regions (about 3.7-3.8 kb) of the mitochondrial genomes (rrnL-cox1) of two tardigrades, a heterotardigrade, Batillipes pennaki, and a eutardigrade, Pseudobiotus spinifer, were sequenced and characterized. The gene order in Batillipes was rrnL-V-rrnS-Q-I-M-nad2-W-C-Y-cox1, and in Pseudobiotus it was rrnL-V-rrnS-Q-M-nad2-W-C-Y-cox1. With the exception of the trnI gene, the two tardigrade regions have the same gene content and order. Their gene orders are strikingly similar to that of the chelicerate Limulus polyphemus (rrnL-V-rrnS-CR-I-Q-M-nad2-W-C-Y-cox1), which is considered to be ancestral for arthropods. Although the tardigrades do not have a distinct control region (CR) within this segment, the trnI gene in Pseudobiotus is located between rrnL-trnL1 and trnL2-nad1, and the trnI gene in Batillipes is located between trnQ and trnM. In addition, the 106-bp region between trnQ and trnM in Batillipes not only contains two plausible trnI genes with opposite orientations, but also exhibits some CR-like characteristics. The mitochondrial gene arrangements of 183 other protostomes were compared. 60 (52.2%) of the 115 arthropods examined have the M-nad2-W-C-Y-cox1 arrangement, and 88 (76.5%) the M-nad2-W arrangement, as found in the tardigrades. In contrast, no such arrangement was seen in the 70 non-arthropod protostomes studied. These are the first non-sequence molecular data that support the close relationship of tardigrades and arthropods.

  6. [Cloning and analysis of geldanamycin partial biosynthetic gene cluster of Streptomyces hygroscopicus 17997].

    PubMed

    He, Wei-Qing; Wang, Yi-Guang

    2006-11-01

    A geldanamycin (GDM) producing strain, Streptomyces hygroscopicus 17997, was isolated from Yunnan China soil by our institute researchers. GDM is an ansamycin antibiotic, which has the ability to bind with Hsp90 (Heat Shock Protein 90) and alter its function. Hsp90 is a chaperone protein involved in the regulation of the cell cycle, cell growth, cell survival, apoptosis, and oncogenesis. So it plays a key role in regulating the physiology of cells exposed to environmental stress and in maintaining the malignant phenotype of tumor cells. As an inhibitor of Hsp90, GDM possesses potent antitumor and antivirus bioactivity, but the hypato-toxicity and poor solubility in water limits its clinical use. Two GDM derivatives, 17-(Allylamino)-17-demethoxygeldanamycin (17-AAG) and 17-dimethylamino-ethylamino-17-demethoxygeldanamycin (17-DMAG), both showing lesser hepato-toxicity, are now in Phase II and Phase I clinic trials. In order to accomplish the structure modification of GDM by genetic means, an attempt to obtain the biosynthetic gene cluster of GDM from S. hygroscopicus 17997 was made. In this study, a pair of primers was designed according to a conserved sequence of one of possible post-PKS (polyketides synthase) modification genes, the carbamoyltransferase (CT) gene (gdmN) in GDM biosynthesis. The 732 bp PCR product was obtained from the S. hygroscopicus 17997 genomic DNA. Through the colony-PCR Binary Search Method, using the CT gene primers, six positive cosmid clones, CT1-6, were identified from the S. hygroscopicus 17997 cosmid genomic library. The CT gene containing fragments were verified and localized by Southern blot. The CT-4 positive cosmid was then sub-cloned and sequenced. Approximately 28.356kb of foreign gene sequence from CT-4 cosmid and by further PCR extension reaction was obtained. Based on BLAST analysis, this sequence contains 13 possible ORFs and their deduced functions are believed to be involved in GDM production. The ORF1 encoding products

  7. Sequence analysis of a few species of termites (Order: Isoptera) on the basis of partial characterization of COII gene.

    PubMed

    Sobti, Ranbir Chander; Kumari, Mamtesh; Sharma, Vijay Lakshmi; Sodhi, Monika; Mukesh, Manishi; Shouche, Yogesh

    2009-11-01

    The present study was aimed to get the nucleotide sequences of a part of COII mitochondrial gene amplified from individuals of five species of Termites (Isoptera: Termitidae: Macrotermitinae). Four of them belonged to the genus Odontotermes (O. obesus, O. horni, O. bhagwatii and Odontotermes sp.) and one to Microtermes (M. obesi). Partial COII gene fragments were amplified by using specific primers. The sequences so obtained were characterized to calculate the frequencies of each nucleotide bases and a high A + T content was observed. The interspecific pairwise sequence divergence in Odontotermes species ranged from 6.5% to 17.1% across COII fragment. M. obesi sequence diversity ranged from 2.5 with Odontotermes sp. to 19.0% with O. bhagwatii. Phylogenetic trees drawn on the basis of distance neighbour-joining method revealed three main clades clustering all the individuals according to their genera and families.

  8. Gene dosage effect for fumarate hydratase (FH; E.C. 4.2.1.2) in partial trisomy 1.

    PubMed

    Braunger, R; Kling, H; Krone, W; Schmid, M; Olert, J

    1977-08-31

    A strain of fibroblasts partially trisomic for the larger part of 1q (Norwood and Hoehn, 1974) contains about 1.5 times as much fumarate hydratase (FH) as various control-strains. This gene dosage effect was ascertained by (1) comparative measurements of the specific activity; (2) relating the specific activity of FH to that of reference enzymes, not influenced by the chromosomal anomaly; and (3) by immunoprecipitation methods, using a rabbit antiserum against pig heart FH which cross-reacts with the human enzyme. Among others, this gene dosage effect can be demonstrated numerically by the following parameters: Ratio of the average specific activity of FH in the trisomic strain to that of the control strains: 1.53. Corresponding ratio after dividing FH activity by that of reference enzymes; for acid phosphatase: 1.58, for glutamate dehydrogenase: 1.53. Average ratio of the immunoprecipitation areas obtained upon radial immunodiffusion according to Mancini et al. (1965): 1.56.

  9. Dihydroflavonol 4-Reductase Genes from Freesia hybrida Play Important and Partially Overlapping Roles in the Biosynthesis of Flavonoids

    PubMed Central

    Li, Yueqing; Liu, Xingxue; Cai, Xinquan; Shan, Xiaotong; Gao, Ruifang; Yang, Song; Han, Taotao; Wang, Shucai; Wang, Li; Gao, Xiang

    2017-01-01

    Dihydroflavonol-4-reductase (DFR) is a key enzyme in the reduction of dihydroflavonols to leucoanthocyanidins in both anthocyanin biosynthesis and proanthocyanidin accumulation. In many plant species, it is encoded by a gene family, however, how the different copies evolve either to function in different tissues or at different times or to specialize in the use of different but related substrates needs to be further investigated, especially in monocot plants. In this study, a total of eight putative DFR-like genes were firstly cloned from Freesia hybrida. Phylogenetic analysis showed that they were classified into different branches, and FhDFR1, FhDFR2, and FhDFR3 were clustered into DFR subgroup, whereas others fell into the group with cinnamoyl-CoA reductase (CCR) proteins. Then, the functions of the three FhDFR genes were further characterized. Different spatio-temporal transcription patterns and levels were observed, indicating that the duplicated FhDFR genes might function divergently. After introducing them into Arabidopsis dfr (tt3-1) mutant plants, partial complementation of the loss of cyanidin derivative synthesis was observed, implying that FhDFRs could convert dihydroquercetin to leucocyanidin in planta. Biochemical assays also showed that FhDFR1, FhDFR2, and FhDFR3 could utilize dihydromyricetin to generate leucodelphinidin, while FhDFR2 could also catalyze the formation of leucocyanidin from dihydrocyanidin. On the contrary, neither transgenic nor biochemical analysis demonstrated that FhDFR proteins could reduce dihydrokaempferol to leucopelargonidin. These results were consistent with the freesia flower anthocyanin profiles, among which delphinidin derivatives were predominant, with minor quantities of cyanidin derivatives and undetectable pelargonidin derivatives. Thus, it can be deduced that substrate specificities of DFRs were the determinant for the categories of anthocyanins aglycons accumulated in F. hybrida. Furthermore, we also found that

  10. 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.

  11. 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

  12. Partial Reconstruction of the Ergot Alkaloid Pathway by Heterologous Gene Expression in Aspergillus nidulans

    PubMed Central

    Ryan, Katy L.; Moore, Christopher T.; Panaccione, Daniel G.

    2013-01-01

    Ergot alkaloids are pharmaceutically and agriculturally important secondary metabolites produced by several species of fungi. Ergot alkaloid pathways vary among different fungal lineages, but the pathway intermediate chanoclavine-I is evolutionarily conserved among ergot alkaloid producers. At least four genes, dmaW, easF, easE, and easC, are necessary for pathway steps prior to chanoclavine-I; however, the sufficiency of these genes for chanoclavine-I synthesis has not been established. A fragment of genomic DNA containing dmaW, easF, easE, and easC was amplified from the human-pathogenic, ergot alkaloid-producing fungus Aspergillus fumigatus and transformed into Aspergillus nidulans, a model fungus that does not contain any of the ergot alkaloid synthesis genes. HPLC and LC-MS analyses demonstrated that transformed A. nidulans strains produced chanoclavine-I and an earlier pathway intermediate. Aspergillus nidulans transformants containing dmaW, easF, and either easE or easC did not produce chanoclavine-I but did produce an early pathway intermediate and, in the case of the easC transformant, an additional ergot alkaloid-like compound. We conclude that dmaW, easF, easE, and easC are sufficient for the synthesis of chanoclavine-I in A. nidulans and expressing ergot alkaloid pathway genes in A. nidulans provides a novel approach to understanding the early steps in ergot alkaloid synthesis. PMID:23435153

  13. 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

  14. High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust.

    PubMed

    Yeo, F K S; Bouchon, R; Kuijken, R; Loriaux, A; Boyd, C; Niks, R E; Marcel, T C

    2017-01-01

    Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.

  15. MDR-1 and MRP2 Gene Polymorphisms in Mexican Epileptic Pediatric Patients with Complex Partial Seizures

    PubMed Central

    Escalante-Santiago, David; Feria-Romero, Iris Angélica; Ribas-Aparicio, Rosa María; Rayo-Mares, Dario; Fagiolino, Pietro; Vázquez, Marta; Escamilla-Núñez, Consuelo; Grijalva-Otero, Israel; López-García, Miguel Angel; Orozco-Suárez, Sandra

    2014-01-01

    Although the Pgp efflux transport protein is overexpressed in resected tissue of patients with epilepsy, the presence of polymorphisms in MDR1/ABCB1 and MRP2/ABCC2 in patients with antiepileptic-drugs resistant epilepsy (ADR) is controversial. The aim of this study was to perform an exploratory study to identify nucleotide changes and search new and reported mutations in patients with ADR and patients with good response (CTR) to antiepileptic drugs (AEDs) in a rigorously selected population. We analyzed 22 samples In Material and Methods, from drug-resistant patients with epilepsy and 7 samples from patients with good response to AEDs. Genomic DNA was obtained from leukocytes. Eleven exons in both genes were genotyped. The concentration of drugs in saliva and plasma was determined. The concentration of valproic acid in saliva was lower in ADR than in CRT. In ABCB1, five reported SNPs and five unreported nucleotide changes were identified; rs2229109 (GA) and rs2032582 (AT and AG) were found only in the ADR. Of six SNPs associated with the ABCC2 that were found in the study population, rs3740066 (TT) and 66744T > A (TG) were found only in the ADR. The strongest risk factor in the ABCB1 gene was identified as the TA genotype of rs2032582, whereas for the ABCC2 gene the strongest risk factor was the T allele of rs3740066. The screening of SNPs in ACBC1 and ABCC2 indicates that the Mexican patients with epilepsy in this study display frequently reported ABCC1 polymorphisms; however, in the study subjects with a higher risk factor for drug resistance, new nucleotide changes were found in the ABCC2 gene. Thus, the population of Mexican patients with AED-resistant epilepsy (ADR) used in this study exhibits genetic variability with respect to those reported in other study populations; however, it is necessary to explore this polymorphism in a larger population of patients with ADR. PMID:25346718

  16. MDR-1 and MRP2 Gene Polymorphisms in Mexican Epileptic Pediatric Patients with Complex Partial Seizures.

    PubMed

    Escalante-Santiago, David; Feria-Romero, Iris Angélica; Ribas-Aparicio, Rosa María; Rayo-Mares, Dario; Fagiolino, Pietro; Vázquez, Marta; Escamilla-Núñez, Consuelo; Grijalva-Otero, Israel; López-García, Miguel Angel; Orozco-Suárez, Sandra

    2014-01-01

    Although the Pgp efflux transport protein is overexpressed in resected tissue of patients with epilepsy, the presence of polymorphisms in MDR1/ABCB1 and MRP2/ABCC2 in patients with antiepileptic-drugs resistant epilepsy (ADR) is controversial. The aim of this study was to perform an exploratory study to identify nucleotide changes and search new and reported mutations in patients with ADR and patients with good response (CTR) to antiepileptic drugs (AEDs) in a rigorously selected population. We analyzed 22 samples In Material and Methods, from drug-resistant patients with epilepsy and 7 samples from patients with good response to AEDs. Genomic DNA was obtained from leukocytes. Eleven exons in both genes were genotyped. The concentration of drugs in saliva and plasma was determined. The concentration of valproic acid in saliva was lower in ADR than in CRT. In ABCB1, five reported SNPs and five unreported nucleotide changes were identified; rs2229109 (GA) and rs2032582 (AT and AG) were found only in the ADR. Of six SNPs associated with the ABCC2 that were found in the study population, rs3740066 (TT) and 66744T > A (TG) were found only in the ADR. The strongest risk factor in the ABCB1 gene was identified as the TA genotype of rs2032582, whereas for the ABCC2 gene the strongest risk factor was the T allele of rs3740066. The screening of SNPs in ACBC1 and ABCC2 indicates that the Mexican patients with epilepsy in this study display frequently reported ABCC1 polymorphisms; however, in the study subjects with a higher risk factor for drug resistance, new nucleotide changes were found in the ABCC2 gene. Thus, the population of Mexican patients with AED-resistant epilepsy (ADR) used in this study exhibits genetic variability with respect to those reported in other study populations; however, it is necessary to explore this polymorphism in a larger population of patients with ADR.

  17. Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes.

    PubMed

    Springer, Michael; Wykoff, Dennis D; Miller, Nicole; O'Shea, Erin K

    2003-11-01

    A cell's ability to generate different responses to different levels of stimulus is an important component of an adaptive environmental response. Transcriptional responses are frequently controlled by transcription factors regulated by phosphorylation. We demonstrate that differential phosphorylation of the budding yeast transcription factor Pho4 contributes to differential gene expression. When yeast cells are grown in high-phosphate growth medium, Pho4 is phosphorylated on four critical residues by the cyclin-CDK complex Pho80-Pho85 and is inactivated. When yeast cells are starved for phosphate, Pho4 is dephosphorylated and fully active. In intermediate-phosphate conditions, a form of Pho4 preferentially phosphorylated on one of the four sites accumulates and activates transcription of a subset of phosphate-responsive genes. This Pho4 phosphoform binds differentially to phosphate-responsive promoters and helps to trigger differential gene expression. Our results demonstrate that three transcriptional outputs can be generated by a pathway whose regulation is controlled by one kinase, Pho80-Pho85, and one transcription factor, Pho4. Differential phosphorylation of Pho4 by Pho80-Pho85 produces phosphorylated forms of Pho4 that differ in their ability to activate transcription, contributing to multiple outputs.

  18. Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes

    PubMed Central

    Miller, Nicole

    2003-01-01

    A cell's ability to generate different responses to different levels of stimulus is an important component of an adaptive environmental response. Transcriptional responses are frequently controlled by transcription factors regulated by phosphorylation. We demonstrate that differential phosphorylation of the budding yeast transcription factor Pho4 contributes to differential gene expression. When yeast cells are grown in high-phosphate growth medium, Pho4 is phosphorylated on four critical residues by the cyclin–CDK complex Pho80–Pho85 and is inactivated. When yeast cells are starved for phosphate, Pho4 is dephosphorylated and fully active. In intermediate-phosphate conditions, a form of Pho4 preferentially phosphorylated on one of the four sites accumulates and activates transcription of a subset of phosphate-responsive genes. This Pho4 phosphoform binds differentially to phosphate-responsive promoters and helps to trigger differential gene expression. Our results demonstrate that three transcriptional outputs can be generated by a pathway whose regulation is controlled by one kinase, Pho80–Pho85, and one transcription factor, Pho4. Differential phosphorylation of Pho4 by Pho80–Pho85 produces phosphorylated forms of Pho4 that differ in their ability to activate transcription, contributing to multiple outputs. PMID:14624238

  19. Structure and partial genomic sequence of the human E2F1 gene.

    PubMed

    Neuman, E; Sellers, W R; McNeil, J A; Lawrence, J B; Kaelin, W G

    1996-09-16

    The E2F family of transcription factors appears to play a critical role in the transcription of certain genes required for cell cycle progression. E2F1, the first cloned member of this family, is regulated during the cell cycle at the mRNA level by changes in transcription of the E2F1 gene and at the protein level by complex formation with proteins such as the retinoblastoma gene product (pRB), cyclin A and DP1. E2F1 can override a pRB-induced G1/S block and can behave as an oncogene in certain cells. E2F1 was cloned and was found to contain seven exons. The dinucleotides at the 5' and 3' splice sites of intron 4 do not agree with consensus splice site sequences. Fluorescence in situ hybridization localized E2F1 to chromosome 20q11. Knowledge of the organization of E2F1 may facilitate identification of additional E2F family members, as well as detection of E2F1 abnormalities in human tumors.

  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.

  1. 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.

  2. 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

  3. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability

    PubMed Central

    Paolella, Brenton R; Gibson, William J; Urbanski, Laura M; Alberta, John A; Zack, Travis I; Bandopadhayay, Pratiti; Nichols, Caitlin A; Agarwalla, Pankaj K; Brown, Meredith S; Lamothe, Rebecca; Yu, Yong; Choi, Peter S; Obeng, Esther A; Heckl, Dirk; Wei, Guo; Wang, Belinda; Tsherniak, Aviad; Vazquez, Francisca; Weir, Barbara A; Root, David E; Cowley, Glenn S; Buhrlage, Sara J; Stiles, Charles D; Ebert, Benjamin L; Hahn, William C; Reed, Robin; Beroukhim, Rameen

    2017-01-01

    Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency. DOI: http://dx.doi.org/10.7554/eLife.23268.001 PMID:28177281

  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.

  5. Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

    PubMed Central

    2010-01-01

    Background Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. Results The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. Conclusions The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases. PMID:20691110

  6. 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.

  7. 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.

  8. 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

  9. Cloning, partial sequence, expression, and antigenic analysis of the filamentous hemagglutinin gene of Bordetella pertussis.

    PubMed Central

    Delisse-Gathoye, A M; Locht, C; Jacob, F; Raaschou-Nielsen, M; Heron, I; Ruelle, J L; de Wilde, M; Cabezon, T

    1990-01-01

    The gene coding for the filamentous hemagglutinin (FHA), one of the main factors involved in mediating adherence of Bordetella pertussis to ciliated host cells, was cloned in Escherichia coli, and the 3,500-base-pair nucleotide sequence encoding the amino-terminal region was determined. Molecular cloning, together with the characterization of recombinant FHA-related proteins produced in E. coli, revealed that the primary translation product is a protein of about 370 kilodaltons (kDa). The mature 220-kDa FHA polypeptide secreted by B. pertussis is most probably generated by proteolytic processing that eliminates a carboxy-terminal portion of about 150 kDa. The 1,087 amino-terminal residues of the predicted FHA sequence showed a number of remarkable features. Extensive homology to the Serratia marcescens and Proteus mirabilis hemolysin proteins was found between amino acids 91 and 205 of the FHA sequence, suggesting involvement of this FHA domain in host cell binding or secretion of FHA from B. pertussis. In addition, two regions containing repetitive amino acid sequences were identified. One region, extending from residues 382 to 664, was formed by six repeats, and a second, extending from residues 701 to 912, contained three repeats. The reactivities of several recombinant FHA-derived proteins with a panel of monoclonal antibodies identified at least four epitopes composing an immunoreactive domain present in the carboxy-terminal moiety of the mature FHA. Images PMID:1696934

  10. Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences.

    PubMed

    Stefanoviac, S; Jager, M; Deutsch, J; Broutin, J; Masselot, M

    1998-05-01

    The conifers, which traditionally comprise seven families, are the largest and most diverse group of living gymnosperms. Efforts to systematize this diversity without a cladistic phylogenetic framework have often resulted in the segregation of certain genera and/or families from the conifers. In order to understand better the relationships between the families, we performed cladistic analyses using a new data set obtained from 28S rRNA gene sequences. These analyses strongly support the monophyly of conifers including Taxaceae. Within the conifers, the Pinaceae are the first to diverge, being the sister group of the rest of conifers. A recently discovered Australian genus Wollemia is confirmed to be a natural member of the Araucariaceae. The Taxaceae are nested within the conifer clade, being the most closely related to the Cephalotaxaceae. The Taxodiaceae and Cupressaceae together form a monophyletic group. Sciadopitys should be considered as constituting a separate family. These relationships are consistent with previous cladistic analyses of morphological and molecular (18S rRNA, rbcL) data. Furthermore, the well-supported clade linking the Araucariaceae and Podocarpaceae, which has not been previously reported, suggests that the common ancestor of these families, both having the greatest diversity in the Southern Hemisphere, inhabited Gondwanaland.

  11. The equine herpesvirus 1 gene 63 RING finger protein partially complements Vmw110, its herpes simplex virus type 1 counterpart.

    PubMed

    Everett, R; Orr, A; Elliott, M

    1995-09-01

    All alpha herpesviruses of known DNA sequence have been found to encode a protein with similarities to immediate early protein Vmw110 (ICP0) of herpes simplex virus type 1 (HSV-1). The conserved portion of this family of proteins is a characteristic zinc binding module, known as a RING finger or C3HC4 domain. Examples of RING finger domains occur in many other proteins of diverse evolutionary origin and function. Recently, the solution structure of the equine herpesvirus 1 (EHV-1) RING finger protein, encoded by gene 63, has been solved. To investigate whether this structure could be considered to be a paradigm of herpesvirus RING domains, we have constructed a recombinant HSV-1 which expresses the EHV-1 gene 63 protein (EHVg63) in place of Vmw110. Comparison of the growth properties of the recombinant with those of wild-type and Vmw110-defective viruses indicates that EHVg63 is able to fulfil partially, but not completely, the roles of Vmw110 during virus growth in tissue culture.

  12. Cloning, sequencing and expression of the Schwanniomyces occidentalis NADP-dependent glutamate dehydrogenase gene.

    PubMed

    De Zoysa, P A; Connerton, I F; Watson, D C; Johnston, J R

    1991-08-01

    The cloned NADP-specific glutamate dehydrogenase (GDH) genes of Aspergillus nidulans (gdhA) and Neurospora crassa (am) have been shown to hybridize under reduced stringency conditions to genomic sequences of the yeast Schwanniomyces occidentalis. Using 5' and 3' gene-specific probes, a unique 5.1 kb BclI restriction fragment that encompasses the entire Schwanniomyces sequence has been identified. A recombinant clone bearing the unique BclI fragment has been isolated from a pool of enriched clones in the yeast/E. coli shuttle vector pWH5 by colony hybridization. The identity of the plasmid clone was confirmed by functional complementation of the Saccharomyces cerevisiae gdh-1 mutation. The nucleotide sequence of the Schw. occidentalis GDH gene, which consists of 1380 nucleotides in a continuous reading frame of 459 amino acids, has been determined. The predicted amino acid sequence shows considerable homology with GDH proteins from other fungi and significant homology with all other available GDH sequences.

  13. 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.

  14. 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.

  15. A complete alpha1,3-galactosyltransferase gene is present in the human genome and partially transcribed.

    PubMed

    Lantéri, Marion; Giordanengo, Valérie; Vidal, Frédérique; Gaudray, Patrick; Lefebvre, Jean-Claude

    2002-12-01

    The synthesis of Galalpha1-3Gal-terminated oligosaccharides (alpha-Gal) epitopes has been interrupted during the course of evolution, starting with Old World primates. Partial sequences similar to the alpha1,3-galactosyltransferase (alpha1,3GalT) gene, which governs the synthesis of alpha-Gal epitopes, have been detected in the human genome and were found to correspond to pseudogenes. We completed the sequence of the human alpha1,3GalT pseudogene present on chromosome 9 and found it to be organized like the murine alpha1,3GalT gene. In human cell lines and several normal and tumor tissues we detected truncated transcripts corresponding to this pseudogene. Considering these mRNAs, translation of an open reading frame containing the first four translated exons but missing the two catalytic exons could predict a truncated alpha1,3GalT polypeptide that should be enzymatically inactive. We show that transcription of human alpha1,3GalT is prematurely terminated at the level of a strong transcriptional stop signal in the middle of intron VII. We were able to reproduce this effect in vitro by subcloning the implicated DNA region upstream from a reporter cDNA. The premature transcriptional arrest of human alpha1,3-GalT gene leads to an ectopic splicing event and to the connection of a short intronic sequence downstream from translated exons. Finally, we show that these truncated transcripts are overexpressed in cell lines with modifications of O-glycans.

  16. [Genetic polymorphism for GOT and GDH loci of Scotch pine seed embryos in the area of nitrogen emissions from the chemical enterprise].

    PubMed

    Korshikov, I I; Demkovich, A E

    2011-01-01

    Variability for the loci GOT and GDH of seed embryos of three subpopulations of Pinus sylvestris L. exposed to the emissions from the chemical enterprise manufacturing nitrogen fertilizers was studied during four years. The trend to heterozygosity reduction and increased occurrence of the cases of significant deviation of the distribution of genotypes from the theoretically expected one was shown.

  17. Novel mutations within the RFX-B gene and partial rescue of MHC and related genes through exogenous class II transactivator in RFX-B-deficient cells.

    PubMed

    Nagarajan, U M; Peijnenburg, A; Gobin, S J; Boss, J M; van den elsen, P J

    2000-04-01

    MHC class II deficiency or bare lymphocyte syndrome is a severe combined immunodeficiency caused by defects in MHC-specific regulatory factors. Fibroblasts derived from two recently identified bare lymphocyte syndrome patients, EBA and FZA, were found to contain novel mutations in the RFX-B gene. RFX-B encodes a component of the RFX transcription factor that functions in the assembly of multiple transcription factors on MHC class II promoters. Unlike RFX5- and RFXAP-deficient cells, transfection of exogenous class II transactivator (CIITA) into these RFX-B-deficient fibroblasts resulted in the induction of HLA-DR and HLA-DP and, to a lesser extent, HLA-DQ. Similarly, CIITA-mediated induction of MHC class I, beta2-microglobulin, and invariant chain genes was also found in these RFX-B-deficient fibroblasts. Expression of wild-type RFX-B completely reverted the noted deficiencies in these cells. Transfection of CIITA into Ramia cells, a B cell line that does not produce a stable RFX-B mRNA, resulted in induction of an MHC class II reporter, suggesting that CIITA overexpression may partially override the RFX-B defect.

  18. Gene profiling approach to establish the molecular bases for partial versus full activation of naïve CD8 T lymphocytes.

    PubMed

    Verdeil, Gréory; Puthier, Denis; Nguyen, Catherine; Schmitt-Verhulst, Anne-Marie; Auphan-Anezin, Nathalie

    2002-12-01

    When initial antigen encounter involves optimal antigenic and costimulatory stimuli, naïve CD8 T cells undergo a developmental program that leads to their activation, expansion and acquisition of effector functions (including production of IL-2, IFNgamma and expression of cytolytic effector molecules). A subset of the activated CD8 T cells thrives as long-lived memory cells. Encounter of tissue-associated, and in particular tumor-associated antigen, may often be suboptimal in terms of antigenicity and costimulation, however. We previously developed a model of naïve CD8 T cells from transgenic mice expressing an alloreactive TCR for which a mutant alloantigen behaved as a partial agonist, inducing only some of the effector functions induced by the native alloantigen. To ascertain the molecular bases for the establishment of divergent fates within the same naïve CD8 T cells, we have used cDNA microarrays to monitor sequential gene expression patterns in conditions of full or partial response of these naïve CD8 T cells. Of the 5000 different genes monitored on the array, 18% showed changes in expression in activated versus naïve CD8 T cells, independent of whether stimulation was with full or partial agonist. These included antigen-induced upregulated as well as downregulated genes. Clusters of genes that were differentially expressed were also identified, being either (i) weakly versus strongly, or (ii) transiently versus stably expressed in response to partial and full agonist, respectively. They included (i) genes encoding costimulatory molecules and (ii) genes controlling cytolytic function, cytokine production, and chemokines. Therefore, the cDNA microarray approach was a sensitive tool to provide an exhaustive picture of T cell activation as it could discriminate quantitative, qualitative and dynamic differences in mRNA expression profiles between fully or partially activated T cells.

  19. Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance.

    PubMed

    Geffroy, V; Sévignac, M; De Oliveira, J C; Fouilloux, G; Skroch, P; Thoquet, P; Gepts, P; Langin, T; Dron, M

    2000-03-01

    Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.

  20. Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.

    PubMed

    Tang, Weihong; Schwienbacher, Christine; Lopez, Lorna M; Ben-Shlomo, Yoav; Oudot-Mellakh, Tiphaine; Johnson, Andrew D; Samani, Nilesh J; Basu, Saonli; Gögele, Martin; Davies, Gail; Lowe, Gordon D O; Tregouet, David-Alexandre; Tan, Adrian; Pankow, James S; Tenesa, Albert; Levy, Daniel; Volpato, Claudia B; Rumley, Ann; Gow, Alan J; Minelli, Cosetta; Yarnell, John W G; Porteous, David J; Starr, John M; Gallacher, John; Boerwinkle, Eric; Visscher, Peter M; Pramstaller, Peter P; Cushman, Mary; Emilsson, Valur; Plump, Andrew S; Matijevic, Nena; Morange, Pierre-Emmanuel; Deary, Ian J; Hicks, Andrew A; Folsom, Aaron R

    2012-07-13

    Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are clinical tests commonly used to screen for coagulation-factor deficiencies. One genome-wide association study (GWAS) has been reported previously for aPTT, but no GWAS has been reported for PT. We conducted a GWAS and meta-analysis to identify genetic loci for aPTT and PT. The GWAS for aPTT was conducted in 9,240 individuals of European ancestry from the Atherosclerosis Risk in Communities (ARIC) study, and the GWAS for PT was conducted in 2,583 participants from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS) and the Lothian Birth Cohorts (LBC) of 1921 and 1936. Replication was assessed in 1,041 to 3,467 individuals. For aPTT, previously reported associations with KNG1, HRG, F11, F12, and ABO were confirmed. A second independent association in ABO was identified and replicated (rs8176704, p = 4.26 × 10(-24)). Pooling the ARIC and replication data yielded two additional loci in F5 (rs6028, p = 3.22 × 10(-9)) and AGBL1 (rs2469184, p = 3.61 × 10(-8)). For PT, significant associations were identified and confirmed in F7 (rs561241, p = 3.71 × 10(-56)) and PROCR/EDEM2 (rs2295888, p = 5.25 × 10(-13)). Assessment of existing gene expression and coronary artery disease (CAD) databases identified associations of five of the GWAS loci with altered gene expression and two with CAD. In summary, eight genetic loci that account for ∼29% of the variance in aPTT and two loci that account for ∼14% of the variance in PT were detected and supported by functional data.

  1. Genetic Associations for Activated Partial Thromboplastin Time and Prothrombin Time, their Gene Expression Profiles, and Risk of Coronary Artery Disease

    PubMed Central

    Tang, Weihong; Schwienbacher, Christine; Lopez, Lorna M.; Ben-Shlomo, Yoav; Oudot-Mellakh, Tiphaine; Johnson, Andrew D.; Samani, Nilesh J.; Basu, Saonli; Gögele, Martin; Davies, Gail; Lowe, Gordon D.O.; Tregouet, David-Alexandre; Tan, Adrian; Pankow, James S.; Tenesa, Albert; Levy, Daniel; Volpato, Claudia B.; Rumley, Ann; Gow, Alan J.; Minelli, Cosetta; Yarnell, John W.G.; Porteous, David J.; Starr, John M.; Gallacher, John; Boerwinkle, Eric; Visscher, Peter M.; Pramstaller, Peter P.; Cushman, Mary; Emilsson, Valur; Plump, Andrew S.; Matijevic, Nena; Morange, Pierre-Emmanuel; Deary, Ian J.; Hicks, Andrew A.; Folsom, Aaron R.

    2012-01-01

    Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are clinical tests commonly used to screen for coagulation-factor deficiencies. One genome-wide association study (GWAS) has been reported previously for aPTT, but no GWAS has been reported for PT. We conducted a GWAS and meta-analysis to identify genetic loci for aPTT and PT. The GWAS for aPTT was conducted in 9,240 individuals of European ancestry from the Atherosclerosis Risk in Communities (ARIC) study, and the GWAS for PT was conducted in 2,583 participants from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS) and the Lothian Birth Cohorts (LBC) of 1921 and 1936. Replication was assessed in 1,041 to 3,467 individuals. For aPTT, previously reported associations with KNG1, HRG, F11, F12, and ABO were confirmed. A second independent association in ABO was identified and replicated (rs8176704, p = 4.26 × 10−24). Pooling the ARIC and replication data yielded two additional loci in F5 (rs6028, p = 3.22 × 10−9) and AGBL1 (rs2469184, p = 3.61 × 10−8). For PT, significant associations were identified and confirmed in F7 (rs561241, p = 3.71 × 10−56) and PROCR/EDEM2 (rs2295888, p = 5.25 × 10−13). Assessment of existing gene expression and coronary artery disease (CAD) databases identified associations of five of the GWAS loci with altered gene expression and two with CAD. In summary, eight genetic loci that account for ∼29% of the variance in aPTT and two loci that account for ∼14% of the variance in PT were detected and supported by functional data. PMID:22703881

  2. Analysis of partial sequences of genes coding for 16S rRNA of actinomycetes isolated from Casuarina equisetifolia nodules in Mexico.

    PubMed Central

    Niner, B M; Brandt, J P; Villegas, M; Marshall, C R; Hirsch, A M; Valdés, M

    1996-01-01

    Filamentous bacteria isolated from surface-sterilized nodules of Casuarina equisetifolia trees in México were capable of reducing acetylene, a diagnostic test for nitrogenase, but were unable to nodulate their host. Analysis of partial 16S rRNA gene sequences suggests that the Mexican isolates are not Frankia strains but members of a novel clade. PMID:8702297

  3. 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

  4. 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

  5. The Long-Term Outcome of Boys With Partial Androgen Insensitivity Syndrome and a Mutation in the Androgen Receptor Gene

    PubMed Central

    Lucas-Herald, A.; Bertelloni, S.; Juul, A.; Bryce, J.; Jiang, J.; Rodie, M.; Sinnott, R.; Boroujerdi, M.; Lindhardt Johansen, M.; Hiort, O.; Holterhus, P. M.; Cools, M.; Guaragna-Filho, G.; Guerra-Junior, G.; Weintrob, N.; Hannema, S.; Drop, S.; Guran, T.; Darendeliler, F.; Nordenstrom, A.; Hughes, I. A.; Acerini, C.; Tadokoro-Cuccaro, R.

    2016-01-01

    Background: In boys with suspected partial androgen insensitivity syndrome (PAIS), systematic evidence that supports the long-term prognostic value of identifying a mutation in the androgen receptor gene (AR) is lacking. Objective: To assess the clinical characteristics and long-term outcomes in young men with suspected PAIS in relation to the results of AR analysis. Methods: Through the International Disorders of Sex Development Registry, clinical information was gathered on young men suspected of having PAIS (n = 52) who presented before the age of 16 years and had genetic analysis of AR. Results: The median ages at presentation and at the time of the study were 1 month (range, 1 day to 16 years) and 22 years (range, 16 to 52 years), respectively. Of the cohort, 29 men (56%) had 20 different AR mutations reported. At diagnosis, the median external masculinization scores were 7 and 6 in cases with and without AR mutation, respectively (P = .9), and median current external masculinization scores were 9 and 10, respectively (P = .28). Thirty-five men (67%) required at least one surgical procedure, and those with a mutation were more likely to require multiple surgeries for hypospadias (P = .004). All cases with an AR mutation had gynecomastia, compared to 9% of those without an AR mutation. Of the six men who had a mastectomy, five (83%) had an AR mutation. Conclusions: Boys with genetically confirmed PAIS are likely to have a poorer clinical outcome than those with XY DSD, with normal T synthesis, and without an identifiable AR mutation. Routine genetic analysis of AR to confirm PAIS informs long-term prognosis and management. PMID:27403927

  6. Comparison of green and albino individuals of the partially mycoheterotrophic orchid Epipactis helleborine on molecular identities of mycorrhizal fungi, nutritional modes and gene expression in mycorrhizal roots.

    PubMed

    Suetsugu, Kenji; Yamato, Masahide; Miura, Chihiro; Yamaguchi, Katsushi; Takahashi, Kazuya; Ida, Yoshiko; Shigenobu, Shuji; Kaminaka, Hironori

    2017-03-01

    Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf-bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on (15) N and (13) C abundances and gene expression in their mycorrhizae by RNA-seq and cDNA de novo assembly. Molecular identification of mycorrhizal fungi showed that green and albino E. helleborine harboured similar mycobionts, mainly Wilcoxina. Stable isotope analyses indicated that albino E. helleborine plants were fully mycoheterotrophic, whereas green individuals were partially mycoheterotrophic. Gene expression analyses showed that genes involved in antioxidant metabolism were upregulated in the albino variants, which indicates that these plants experience greater oxidative stress than the green variants, possibly due to a more frequent lysis of intracellular pelotons. It was also found that some genes involved in the transport of some metabolites, including carbon sources from plant to fungus, are higher in albino than in green variants. This result may indicate a bidirectional carbon flow even in the mycoheterotrophic symbiosis. The genes related to mycorrhizal symbiosis in autotrophic orchids and arbuscular mycorrhizal plants were also upregulated in the albino variants, indicating the existence of common molecular mechanisms among the different mycorrhizal types.

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

    PubMed

    Kao, Hsiao-Wen; Liang, D 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

    2015-10-20

    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.

  8. Screening, diversity and partial sequence comparison of vegetative insecticidal protein (vip3A) genes in the local isolates of Bacillus thuringiensis Berliner.

    PubMed

    Asokan, R; Swamy, H M Mahadeva; Arora, D K

    2012-04-01

    Characterization, direct sequencing of the PCR amplicon and phylogenetic relationship was done to discover a novel Vip protein genes of the Bt isolates, to improve the prospects for insect control, more Vip proteins should be sought out and researched to predict their insecticidal activity. Characterization was based on direct sequencing of PCR amplicon using primers specific to vip3A gene was presented here. 12 out of 18 isolates screened were positive for vip gene-specific primers. Homology search for the partial sequences using BLAST showed that 11 isolates had high similarity to vip3Aa gene and only one fragment with vip3Ae gene (25-100% at nucleotide and amino acid level). Phylogenetic analysis showed that the gene sequences were responsible for geographic separation for divergence within vip genes, consistent with the evaluation of distinct bacterial population. Despite the geographical distances, strains harbouring vip genes have originated from common ancestors may significantly contribute to control resistant insect pests. Some strains have evolved to be quite distinct and others remain as members of closely related groups. The reported method is a powerful tool to find novel Vip3A proteins from large-scale Bt strains which is effective in terms of time and cost. Further the Vip proteins produced by different strains of B. thuringiensis are unique in terms of the sequence divergence and hence may also differ in their insecticidal activities.

  9. 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.

  10. 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

  11. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p.

    PubMed

    Davidsson, Josef; Johansson, Bertil

    2016-03-03

    To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes-ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21-exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material.

  12. Partial deficiency of isoleucine impairs root development and alters transcript levels of the genes involved in branched-chain amino acid and glucosinolate metabolism in Arabidopsis.

    PubMed

    Yu, Hailan; Zhang, Fengxia; Wang, Guodong; Liu, Yule; Liu, Dong

    2013-01-01

    Isoleucine is one of the branched-chain amino acids (BCAAs) that are essential substrates for protein synthesis in all organisms. Although the metabolic pathway for isoleucine has been well characterized in higher plants, it is not known whether it plays a specific role in plant development. In this study, an Arabidopsis mutant, lib (low isoleucine biosynthesis), that has defects in both cell proliferation and cell expansion processes during root development, was characterized. The lib mutant carries a T-DNA insertion in the last exon of the OMR1 gene that encodes a threonine deaminase/dehydratase (TD). TD catalyses the deamination and dehydration of threonine, which is the first and also the committed step in the biosynthesis of isoleucine. This T-DNA insertion results in a partial deficiency of isoleucine in lib root tissues but it does not affect its total protein content. Application of exogenous isoleucine or introduction of a wild-type OMR1 gene into the lib mutant can completely rescue the mutant phenotypes. These results reveal an important role for isoleucine in plant development. In addition, microarray analysis indicated that the partial deficiency of isoleucine in the lib mutant triggers a decrease in transcript levels of the genes encoding the major enzymes involved in the BCAA degradation pathway; the analysis also indicated that many genes involved in the biosynthesis of methionine-derived glucosinolates are up-regulated.

  13. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p

    PubMed Central

    Davidsson, Josef; Johansson, Bertil

    2016-01-01

    ABSTRACT To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes—ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21—exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material. PMID:26890086

  14. Transcriptional control of vitamin C defective 2 and tocopherol cyclase genes by light and plastid-derived signals: the partial involvement of GENOMES UNCOUPLED 1.

    PubMed

    Tanaka, Hiroyuki; Maruta, Takanori; Tamoi, Masahiro; Yabuta, Yukinori; Yoshimura, Kazuya; Ishikawa, Takahiro; Shigeoka, Shigeru

    2015-02-01

    Previous findings have suggested that light and plastid-derived signals are involved in the regulation of biosynthetic pathways for l-ascorbic acid (AsA) and tocopherols (Toc). Photosynthetic electron transport (PET) activity, plastid gene expression (PGE), and the tetrapyrrole metabolism have been identified as signals that regulate nuclear gene expression through the GENOMES UNCOUPLED 1 (GUN1) protein. Here, we examined the effects of disrupting GUN1 on these pathways. The expression of vitamin C defective 2 (VTC2) and tocopherol cyclase (TC) genes, which encode key enzymes in the AsA and Toc biosynthetic pathways, respectively, was affected by illumination and darkness in parallel with the levels of both these antioxidants. However, the GUN1 disruption had no effect on these biosynthetic pathways under light-dark conditions. All treatments that inhibited PET, PGE, and the tetrapyrrole metabolism interrupted both biosynthetic pathways; however, this was partially mitigated by the GUN1 disruption. The expression patterns of VTC2 and TC reflected the levels of both antioxidants under most of the conditions examined. Our results suggest that the transcriptional control of VTC2 and TC by light and plastid-derived signals is important for the regulation of the biosynthetic pathways, and that GUN1 is at least partially involved in the plastid-derived signals-dependent regulation.

  15. 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

  16. Androgen Activation of the Folate Receptor α Gene through Partial Tethering of the Androgen Receptor by C/EBPα○

    PubMed Central

    Sivakumaran, Suneethi; Zhang, Juan; Kelley, Karen M.M.; Gonit, Mesfin; Hao, Hong; Ratnam, Manohar

    2010-01-01

    The folate receptor α (FRα) is critical for normal embryonic and fetal development. The receptor has a relatively narrow tissue specificity which includes the visceral endoderm and the placenta and mediates delivery of folate, inadequacy of which results in termination of pregnancy or developmental defects. We have previously reported that the FRα gene is negatively and directly regulated by estrogen and positively but indirectly by progesterone and glucocorticoid. To further investigate hormonal control of this gene and in view of the growing evidence for the importance of the androgen receptor (AR) in endometrial and placental functions, we examined the response of the FRα gene to androgen. Here we demonstrate that the FRα gene is directly activated by androgen. The P4 promoter of the FRα gene is the target of hormone-dependent activation by the androgen receptor (AR) in a manner that is co-activator-dependent. The site of functional association of AR in the FRα gene maps to a 35bp region occurring ~1500bp upstream of the target promoter. The functional elements within this region are an androgen response element (ARE) half-site and a non-canonical C/EBP element that cooperate to recruit AR in a manner that is dependent on the DNA-bound C/EBPα. Since the placenta is rich in C/EBPα, the findings underscore the multiplicity of mechanisms by which the FRα gene is under the exquisite control of steroid hormones. PMID:20817090

  17. 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

    2016-06-05

    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.

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

    PubMed Central

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

    2016-01-01

    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

  19. 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

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

    PubMed

    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.

  1. 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.

  2. Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical Laboratory▿

    PubMed Central

    Simmon, Keith E.; Croft, Ann C.; Petti, Cathy A.

    2006-01-01

    Laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. With the emergence of 16S rRNA gene sequencing as an identification tool, we evaluated the usefulness of SmartGene IDNS, a 16S rRNA sequence database and software program for microbial identification. Identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the SmartGene and MicroSeq databases. Of 300 isolates, SmartGene identified 295 (98%) to the genus level and 262 (87%) to the species level, with 5 (2%) being inconclusive. MicroSeq identified 271 (90%) to the genus level and 223 (74%) to the species level, with 29 (10%) being inconclusive. SmartGene and MicroSeq agreed on the genus for 233 (78%) isolates and the species for 212 (71%) isolates. Conventional methods identified 291 (97%) isolates to the genus level and 208 (69%) to the species level, with 9 (3%) being inconclusive. SmartGene, MicroSeq, and conventional identifications agreed for 193 (64%) of the results. Twenty-seven microorganisms were not represented in MicroSeq, compared to only 2 not represented in SmartGene. Overall, SmartGene IDNS provides comprehensive and accurate identification of a diverse group of bacteria and has the added benefit of being a user-friendly program that can be modified to meet the unique needs of clinical laboratories. PMID:17050811

  3. Construction of 4"-isovalerylspiramycin-I-producing strain by in-frame partial deletion of 3-O-acyltransferase gene in Streptomyces spiramyceticus WSJ-1, the bitespiramycin producer.

    PubMed

    Ma, Chunyan; Zhou, Hongxia; Li, Jingyan; Dai, Jianlu; He, Weiqing; Wang, Hongyuan; Wu, Linzhuan; Wang, Yiguang

    2011-01-01

    Bitespiramycin (BT), a multi-component antibiotic consisted mainly of 4"-isovalerylspiramycin I, II and III, is produced by Streptomyces spiramyceticus WSJ-1, a recombinant spiramycin-production strain that harbored the 4"-O-acyltransferase gene (ist) from Streptomyces mycarofaciens 1748, which could isovalerylate the 4"-OH of spiramycin. To eliminate the production of components 4"-isovalerylspiramycin II and III, therefore reducing the component complexity of BT, inactivation of the sspA gene, which encodes the 3-O-acyltransferase responsible for the acylation of spiramycin I to spiramycin II and III, was performed in Streptomyces spiramyceticus WSJ-1, by in-frame partial deletion. The resulting strain, Streptomyces spiramyceticus WSJ-2, is a 4"-isovalerylspiramycin-I-producing strain as expected.

  4. Detection of a true breeding homeotic gene mutant Pps-1 with partially petaloid sepals in opium poppy (Papaver somniferum L.) and its genetic behavior.

    PubMed

    Dhawan, Om Prakash; Dubey, Mukesh Kumar; Khanuja, Suman Preet Singh

    2007-01-01

    A spontaneous true breeding homeotic gene mutant Pps-1 with distinct partial petaloid sepals was detected in the population of downy mildew (DM)-resistant elite accession I-14 during our studies for the identification of disease resistance sources in opium poppy. The trait was found to be stable and inherited truly in the subsequent generations. Genetic studies were carried out through systematic reciprocal crosses with the parental wild-type genotype I-14, and segregation pattern of phenotypic characteristics in F(1) and F(2) populations clearly indicated single recessive nuclear gene control of the mutant character. The studies have demonstrated that the mutant phenotype is due to mutations at the Pps-1 locus that possibly corresponds to B-class function (according to ABC model) with negative control function. The mutant Pps-1 being single-whorl homeotic mutant might greatly help in providing insight into mechanisms of flower development in opium poppy.

  5. New insights from X-ray photoelectron spectroscopy into the chemistry of covalent enzyme immobilization, with glutamate dehydrogenase (GDH) on silicon dioxide as an example.

    PubMed

    Longo, Luigia; Vasapollo, Giuseppe; Guascito, Maria Rachele; Malitesta, Cosimino

    2006-05-01

    A three-step process for immobilization of glutamate dehydrogenase (GDH) on the surface of silicon dioxide has been studied by X-ray photoelectron spectroscopy (XPS). The enzyme layer was deposited on the silicon dioxide surface after first exposing the surface to 3-aminopropyltriethoxysilane (3-APTS) and reacting the silylated surface with glutaraldehyde (GA). Fine XPS analysis, performed after each step of the chemical procedure, revealed unknown details of the step-by-step construction of the enzyme layer under different experimental conditions.

  6. Partial deletion of both the spermine synthase gene and the Pex gene in the X-linked hypophosphatemic, gyro (Gy) mouse.

    PubMed

    Meyer, R A; Henley, C M; Meyer, M H; Morgan, P L; McDonald, A G; Mills, C; Price, D K

    1998-03-15

    Gy, along with Hyp, is a dominant mutation of the normal gene Pex causing X-linked hypophosphatemia in the mouse. Hemizygous Gy male mice, however, have greater defects in survival, bodily growth, skeletal mineralization, and neurological function than those found in heterozygous Gy females or in Hyp mice. Since the gene for spermine synthase is immediately upstream of the homologous human gene PEX, we compared the effects of the Gy and Hyp mutations on both the spermine synthase gene and the Pex gene. Barely detectable levels of spermine (< 5% of normal) with elevated levels of its precursor, spermidine, were found in organs of Gy male mice compared to normal male littermates. Neither Gy females nor Hyp male mice were significantly affected. Four missing introns of the spermine synthase gene were identified in Gy male mice, suggesting extensive gene disruption. A pseudogene for spermine synthase was also identified in the mouse genome. Pex mRNA was found in several but not all tissues studied in adult normal mice. Pex mRNA was altered in both Gy and Hyp mice. All male Hyp mice were lacking the 3' end of the Pex message, whereas all male Gy mice were deficient at the 5' end. In summary, the Gy mutation is associated with a recessively expressed mutation of the spermine synthase gene, leading to spermine deficiency, and a dominantly expressed mutation of the Pex gene, leading to hypophosphatemia. Alterations in two contiguous genes in Gy may explain the additional phenotypic abnormalities present in the Gy male mouse.

  7. 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.

  8. Identification, classification, and partial characterization of genes in humans and other vertebrates homologous to a fish membrane progestin receptor

    PubMed Central

    Zhu, Yong; Bond, Jason; Thomas, Peter

    2003-01-01

    Recently we discovered a previously uncharacterized gene with the characteristics of a membrane progestin receptor (mPR) in a fish model, spotted seatrout. Here, we report the identification, cloning, and characteristics of other members of this hitherto unknown family of putative mPRs from several vertebrate species, including human, mouse, pig, Xenopus, zebrafish, and Fugu, with highly conserved nucleotide and deduced amino acid sequences and similar structures to the spotted seatrout mPR. The 13 vertebrate genes identified seem to belong to an unknown gene family. Phylogenetic analysis indicates these cDNAs comprise three distinct groups (named α, β, and γ) within this gene family. Structural analyses of the translated cDNAs suggest they encode membrane proteins with seven transmembrane domains. The transcript sizes of the human α, β, and γ putative mPR mRNAs varied from 2.8 to 5.8 kb and showed distinct distributions in reproductive, neural, kidney and intestinal tissues, respectively. Recombinant human α, γ, and mouse β proteins produced in an Escherichia coli expression system demonstrated high affinity (Kd = 20–30 nM) saturable binding for progesterone. Further analysis of binding to the γ-subtype revealed binding was specific for progestins and was displaceable, with rapid rates of association and dissociation (t1/2 = 2–8 min). These results suggest this is a new family of steroid receptors unrelated to nuclear steroid receptors, but instead having characteristics of G protein-coupled receptors. PMID:12601167

  9. A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana.

    PubMed

    Jailani, A Abdul Kader; Solanki, Vikas; Roy, Anirban; Sivasudha, T; Mandal, Bikash

    2017-03-02

    A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. benthamiana. The qRT-PCR analysis showed 23 fold increase of GFP over actin at 10days post inoculation (dpi), which increased to 45 fold at 14dpi and thereafter the GFP expression was significantly declined. Further, we show that when the most of the CP sequence is deleted retaining only the first 105 nucleotides, the shortened vector containing GFP in frame of original CP open reading frame (ORF) resulted in 234 fold increase of GFP expression over actin at 5dpi in N. benthamiana without the formation of virions and disease symptoms. Our study demonstrated that a simple manipulation of CP gene in the CGMMV genome while preserving the translational frame of CP resulted in developing a virus-free, rapid and efficient foreign protein expression system in the plant. The CGMMV based vectors developed in this study may be potentially useful for the production of edible vaccines in cucurbits.

  10. 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

  11. Partial least squares regression, support vector machine regression, and transcriptome-based distances for prediction of maize hybrid performance with gene expression data.

    PubMed

    Fu, Junjie; Falke, K Christin; Thiemann, Alexander; Schrag, Tobias A; Melchinger, Albrecht E; Scholten, Stefan; Frisch, Matthias

    2012-03-01

    The performance of hybrids can be predicted with gene expression data from their parental inbred lines. Implementing such prediction approaches in breeding programs promises to increase the efficiency of hybrid breeding. The objectives of our study were to compare the accuracy of prediction models employing multiple linear regression (MLR), partial least squares regression (PLS), support vector machine regression (SVM), and transcriptome-based distances (D(B)). For a factorial of 7 flint and 14 dent maize lines, the grain yield of the hybrids was assessed and the gene expression of the parental lines was profiled with a 56k microarray. The accuracy of the prediction models was measured by the correlation between predicted and observed yield employing two cross-validation schemes. The first modeled the prediction of hybrids when testcross data are available for both parental lines (type 2 hybrids), and the second modeled the prediction of hybrids when no testcross data for the parental lines were available (type 0 hybrids). MLR, SVM, and PLS resulted in a high correlation between predicted and observed yield for type 2 hybrids, whereas for type 0 hybrids D(B) had greater prediction accuracy. The regression methods were robust to the choice of the set of profiled genes and required only a few hundred genes. In contrast, for an accurate hybrid prediction with D(B), 1,000-1,500 genes were required, and the prediction accuracy depended strongly on the set of profiled genes. We conclude that for prediction within one set of genetic material MLR is a promising approach, and for transferring prediction models from one set of genetic material to a related one, the transcriptome-based distance D(B) is most promising.

  12. Polyvariant mutant cystic fibrosis transmembrane conductance regulator genes. The polymorphic (Tg)m locus explains the partial penetrance of the T5 polymorphism as a disease mutation.

    PubMed Central

    Cuppens, H; Lin, W; Jaspers, M; Costes, B; Teng, H; Vankeerberghen, A; Jorissen, M; Droogmans, G; Reynaert, I; Goossens, M; Nilius, B; Cassiman, J J

    1998-01-01

    In congenital bilateral absence of the vas deferens patients, the T5 allele at the polymorphic Tn locus in the CFTR (cystic fibrosis transmembrane conductance regulator) gene is a frequent disease mutation with incomplete penetrance. This T5 allele will result in a high proportion of CFTR transcripts that lack exon 9, whose translation products will not contribute to apical chloride channel activity. Besides the polymorphic Tn locus, more than 120 polymorphisms have been described in the CFTR gene. We hypothesized that the combination of particular alleles at several polymorphic loci might result in less functional or even insufficient CFTR protein. Analysis of three polymorphic loci with frequent alleles in the general population showed that, in addition to the known effect of the Tn locus, the quantity and quality of CFTR transcripts and/or proteins was affected by two other polymorphic loci: (TG)m and M470V. On a T7 background, the (TG)11 allele gave a 2.8-fold increase in the proportion of CFTR transcripts that lacked exon 9, and (TG)12 gave a sixfold increase, compared with the (TG)10 allele. T5 CFTR genes derived from patients were found to carry a high number of TG repeats, while T5 CFTR genes derived from healthy CF fathers harbored a low number of TG repeats. Moreover, it was found that M470 CFTR proteins matured more slowly, and that they had a 1.7-fold increased intrinsic chloride channel activity compared with V470 CFTR proteins, suggesting that the M470V locus might also play a role in the partial penetrance of T5 as a disease mutation. Such polyvariant mutant genes could explain why apparently normal CFTR genes cause disease. Moreover, they might be responsible for variation in the phenotypic expression of CFTR mutations, and be of relevance in other genetic diseases. PMID:9435322

  13. 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.

  14. Molecular phylogenetic relationships of puffer fish inferred from partial sequences of cytochrome b gene and restriction fragment length polymorphism analysis.

    PubMed

    Hsieh, Yu-Wen; Hwang, Deng-Fwu

    2004-06-30

    Phylogenetic relationships among puffer fish were investigated by comparing cytochrome b gene sequences and restriction endonuclease assays of 16 species from Taiwan. DNA was prepared for sequencing by PCR. No variation in sequences was detected among individuals within each species. Direct estimates of mitochondrial cytochrome b gene sequence divergence among 16 puffer fish were from 3.41 to 31.78%. Different restriction patterns were found among 16 puffer fish with 10 restriction endonucleases, whereas no variation in patterns was detected among individuals within each species. The polymorphisms obtained by RFLP have provided a new set of genetic markers for the accurate identification of sibling puffer species. It is the first molecularly based study of puffer diversity and sheds light on the evolution and taxonomy of this major puffer fish family.

  15. 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.

  16. Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment

    PubMed Central

    Henriques, Ana C.; Azevedo, Rui M.S.

    2016-01-01

    Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea. PMID:27761315

  17. Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment.

    PubMed

    Henriques, Ana C; Azevedo, Rui M S; De Marco, Paolo

    2016-01-01

    Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea.

  18. 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

  19. 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.

  20. 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

  1. In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

    PubMed Central

    Fouhy, Fiona; O’Connell Motherway, Mary; Fitzgerald, Gerald F.; Ross, R. Paul; Stanton, Catherine; van Sinderen, Douwe; Cotter, Paul D.

    2013-01-01

    Bifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria. PMID:24324818

  2. Partially Hydrolyzed Poly(n-propyl-2-oxazoline): Synthesis, Aqueous Solution Properties, and Preparation of Gene Delivery Systems.

    PubMed

    Mees, Maarten; Haladjova, Emi; Momekova, Denitsa; Momekov, Georgi; Shestakova, Pavletta S; Tsvetanov, Christo B; Hoogenboom, Richard; Rangelov, Stanislav

    2016-11-14

    Random copolymers of n-propyl-2-oxazoline and ethylenimine (PPrOx-PEI) were prepared by partial acidic hydrolysis of poly(n-propyl-2-oxazoline) (PPrOx). Dynamic and electrophoretic light scattering and diffusion-ordered NMR spectroscopy were utilized to investigate aqueous solution properties of the copolymers. Above a specific cloud point temperature, well-defined nanoparticles were formed. The latter consisted of a core composed predominantly of PPrOx and a thin positively charged shell from PEI moieties that mediated formation of polyplexes with DNA. The polyplexes were prepared at 65 °C at varying N/P (amine-to-phosphate groups) ratios. They underwent structural changes upon temperature variations 65-25-37 °C depending on N/P. At N/P < 2, the polyplex particles underwent minor changes because of formation of a surface layer of DNA that acted as a barrier and prevented swelling and disintegration of the initial particles. Dramatic rearrangements at N/P ≥ 2 resulting in large swollen microgel particles were overcome by coating of the polyplex particles with a cross-linked polymeric shell. The shell retained the colloidal stability and preserved the physicochemical parameters of the initial polyplex particles while it reduced the high surface potential values. Progressive loss of cytotoxicity upon complexation with DNA and coating of polyplex particles was displayed.

  3. Two new species of photosymbiotic ascidians of the genus Diplosoma from the Ryukyu Archipelago, with partial sequences of the COI gene.

    PubMed

    Hirose, Euichi; Oka, Atsushi T; Hirose, Mamiko

    2009-05-01

    Two new species of Diplosoma are described from coral reefs in the Ryukyu Archipelago, Japan: D. watanabei sp. nov. and D. gumavirens sp. nov. Colonies of both species are green due to algal symbionts of Prochloron, which are distributed in the common cloacal cavity. Both species are characterized by the point of emergence of the retractor muscle and a unique combination of stigma numbers among the four rows of the branchial sac. There are three adhesive papillae in the embryos of D. watanabei, as in most ascidian embryos and larvae, whereas the pre-hatching embryos of D. gumavirens sp. nov. posses 12-16 adhesive papillae. Partial sequences of the cytochrome c oxidase subunit I (COI) gene discriminated the new species from each other and from congeners.

  4. Novel point mutation in the splice donor site of exon-intron junction 6 of the androgen receptor gene in a patient with partial androgen insensitivity syndrome.

    PubMed

    Sammarco, I; Grimaldi, P; Rossi, P; Cappa, M; Moretti, C; Frajese, G; Geremia, R

    2000-09-01

    Androgen receptor (AR) gene mutations have been shown to cause androgen insensitivity syndrome with altered sexual differentiation in XY individuals, ranging from a partial insensitivity with male phenotype and azoospermia to a complete insensitivity with female phenotype and the absence of pubic and axillary sexual hair after puberty. In this study we present an 11-yr-old XY girl, with clinical manifestations peculiar for impaired androgen biological action, including female phenotype, blind-ending vagina, small degree of posterior labial fusion, and absence of uterus, fallopian tubes, and ovaries. At the time of the diagnosis the patient had a FSH/LH ratio according to the puberal stage, undetectable 17beta-estradiol, and high levels of testosterone (80.1 ng/mL). After bilateral gonadectomy, performed at the age of 11 yr, histological examination showed small embryonic seminiferous tubules containing prevalently Sertoli cells and occasional spermatogonia together with abundant fibrous tissue. Molecular study of the patient showed a guanine to thymine transversion in position +5 of the donor splice site in the junction between exon 6 and intron 6 of the AR gene. The result of RT-PCR amplification of the AR messenger ribonucleic acid from cultured genital skin fibroblasts of the patient suggests that splicing is defective, and intron 6 is retained in most of the receptor messenger ribonucleic acid molecules. We show by immunoblotting that most of the expressed protein lacks part of the C-terminal hormone-binding domain, and a small amount of normal receptor is observed. This is probably responsible for the reduced binding capacity in genital skin fibroblasts of the patient. The molecular basis of the alteration in this case is a novel, uncommon mutation, leading to a phenotype indicative of a partial androgen insensitivity syndrome, Quigley's grade 5.

  5. 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.

  6. Molecular cloning of eucaryotic genes required for excision repair of UV-irradiated DNA: isolation and partial characterization of the RAD3 gene of Saccharomyces cerevisiae.

    PubMed Central

    Naumovski, L; Friedberg, E C

    1982-01-01

    We describe the molecular cloning of a 6-kilobase (kb) fragment of yeast chromosomal DNA containing the RAD3 gene of Saccharomyces cerevisiae. When present in the autonomously replicating yeast cloning vector YEp24, this fragment transformed two different UV-sensitive, excision repair-defective rad3 mutants of S. cerevisiae to UV resistance. The same result was obtained with a variety of other plasmids containing a 4.5-kb subclone of the 6-kb fragment. The UV sensitivity of mutants defective in the RAD1, RAD2, RAD4, and RAD14 loci was not affected by transformation with these plasmids. The 4.5-kb fragment was subcloned into the integrating yeast vector YIp5, and the resultant plasmid was used to transform the rad3-1 mutant to UV resistance. Both genetic and physical studies showed that this plasmid integrated by homologous recombination into the rad3 site uniquely. We conclude from these studies that the cloned DNA that transforms the rad3-1 mutant to UV resistance contains the yeast chromosomal RAD3 gene. The 4.5-kb fragment was mapped by restriction analysis, and studies on some of the subclones generated from this fragment indicate that the RAD3 gene is at least 1.5 kb in size. Images PMID:6749808

  7. Hereditary fructose intolerance: functional study of two novel ALDOB natural variants and characterization of a partial gene deletion.

    PubMed

    Esposito, Gabriella; Imperato, Maria Rosaria; Ieno, Luigi; Sorvillo, Rosa; Benigno, Vincenzo; Parenti, Giancarlo; Parini, Rossella; Vitagliano, Luigi; Zagari, Adriana; Salvatore, Francesco

    2010-12-01

    Hereditary fructose intolerance (HFI) is an autosomal recessive metabolic disease caused by impaired functioning of human liver aldolase (ALDOB). At least 54 subtle/point mutations and only two large intragenic deletions have been found in the ALDOB gene. Here we report two novel ALDOB variants (p.R46W and p.Y343H) and an intragenic deletion that we found in patients with suspected HFI. The residual catalytic activity of the recombinant p.R46W and p.Y343H variants toward F1P was particularly altered. We also characterized a large intragenic deletion that we found in six unrelated patients. This is the first report of six unrelated patients sharing the same ALDOB deletion, thus indicating a founder effect for this allele in our geographic area. Because this deletion involves ALDOB exon 5, it can mimic worldwide common pathogenic genotypes, that is, homozygous p.A150P and p.A175D. Finally, the identification of only one ALDOB mutation in symptomatic patients suggests that HFI symptoms can, albeit rarely, appear also in heterozygotes. Therefore, an excessive and continuous fructose dietary intake may have deleterious effects even in apparently asymptomatic HFI carriers.

  8. Membrane immunoglobulin expressed by retroviral vector gene transfer mimics partial function of the B-cell receptor in vivo.

    PubMed

    Lu, Jing; Chen, Feng; Xu, Zhen; Zhang, Lingling; Xu, Peng; Liu, Depei; Liang, Chihchuan

    2016-01-01

    Activation of B-cells is initiated by the ligation of B-cell receptors by its cognate antigen, inducing a series of signal cascades. Understanding the molecular mechanisms of these important events is a crucial goal for immunologists. Chimeric B cell receptors provide a powerful tool for analysis of B-cell signal function. However, this method can only be used in tool cells, but cannot be used for in vivo study. Here, we constructed a retroviral vector to encode both heavy chains and light chains of a membrane immunoglobulin, and expressed them in primary B-cells using retroviral gene transfer. Our results demonstrate that the membrane immunoglobulin expressed by retroviral vectors transfer can initiate B-cell receptor-mediated signaling, resulting in the phosphorylation of Syk and Erk1/2 proteins. The results showed that B-cells expressing membrane immunoglobulin can make proliferative responses to cognate antigen both in vitro and in vivo. Therefore, we provide a methodology for rapidly analyzing the downstream signals of B-cell receptors both in vitro and in vivo, which could expedite the identification of proteins involved in B-cell function.

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

    PubMed

    Gaunt, Tom R; Lowe, Gordon D O; Lawlor, Debbie A; Casas, Juan-Pablo; Day, Ian N M

    2013-07-01

    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.

  10. 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 Central

    Chikami, Yasuhiko; Yahata, Kensuke; Uchino, Keiro; Kiuchi, Takashi; Katsuma, Susumu; Aoki, Fugaku; Sezutsu, Hideki; Suzuki, Masataka G.

    2016-01-01

    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

  11. Repression of nitrogen catabolic genes by ammonia and glutamine in nitrogen-limited continuous cultures of Saccharomyces cerevisiae.

    PubMed

    ter Schure, E G; Silljé, H H; Vermeulen, E E; Kalhorn, J W; Verkleij, A J; Boonstra, J; Verrips, C T

    1998-05-01

    Growth of Saccharomyces cerevisiae on ammonia and glutamine decreases the expression of many nitrogen catabolic genes to low levels. To discriminate between ammonia- and glutamine-driven repression of GAP1, PUT4, GDH1 and GLN1, a gln1-37 mutant was used. This mutant is not able to convert ammonia into glutamine. Glutamine-limited continuous cultures were used to completely derepress the expression of GAP1, PUT4, GDH1 and GLN1. Following an ammonia pulse, the expression of GAP1, PUT4 and GDH1 decreased while the intracellular glutamine concentration remained constant, both in the cytoplasm and in the vacuole. Therefore, it was concluded that ammonia causes gene repression independent of the intracellular glutamine concentration. The expression of GLN1 was not decreased by an ammonia pulse but solely by a glutamine pulse. Analysis of the mRNA levels of ILV5 and HIS4 showed that the response of the two biosynthetic genes, GDH1 and GLN1, to ammonia and glutamine in the wild-type and gln1-37 was not due to changes in general transcription of biosynthetic genes. Ure2p has been shown to be an essential element for nitrogen-regulated gene expression. Deletion of URE2 in the gln1-37 background prevented repression of gene expression by ammonia, showing that the ammonia-induced repression is not caused by a general stress response but represents a specific signal for nitrogen catabolite regulation.

  12. 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.

  13. A de novo 2.78-Mb duplication on chromosome 21q22.11 implicates candidate genes in the partial trisomy 21 phenotype

    PubMed Central

    Weisfeld-Adams, James D; Tkachuk, Amanda K; Maclean, Kenneth N; Meeks, Naomi L; Scott, Stuart A

    2016-01-01

    Down syndrome (DS) is the most common genetic cause of intellectual disability (ID) and in the majority of cases is the result of complete trisomy 21. The hypothesis that the characteristic DS clinical features are due to a single DS critical region (DSCR) at distal chromosome 21q has been refuted by recently reported segmental trisomy 21 cases characterised by microarray-based comparative genomic hybridisation (aCGH). These rare cases have implicated multiple regions on chromosome 21 in the aetiology of distinct features of DS; however, the map of chromosome 21 copy-number aberrations and their associated phenotypes remains incompletely defined. We report a child with ID who was deemed very high risk for DS on antenatal screening (1 in 13) and has partial, but distinct, dysmorphologic features of DS without congenital heart disease (CHD). Oligonucleotide aCGH testing of the proband detected a previously unreported de novo 2.78-Mb duplication on chromosome 21q22.11 that includes 16 genes; however, this aberration does not harbour any of the historical DSCR genes (APP, DSCR1, DYRK1A and DSCAM). This informative case implicates previously under-recognised candidate genes (SOD1, SYNJ1 and ITSN1) in the pathogenesis of specific DS clinical features and supports a critical region for CHD located more distal on chromosome 21q. In addition, this unique case illustrates how the increasing resolution of microarray and high-throughput sequencing technologies can continue to reveal new biology and enhance understanding of widely studied genetic diseases that were originally described over 50 years ago. PMID:27840696

  14. Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae.

    PubMed

    Daugherty, J R; Rai, R; el Berry, H M; Cooper, T G

    1993-01-01

    We demonstrate that expression of the UGA1, CAN1, GAP1, PUT1, PUT2, PUT4, and DAL4 genes is sensitive to nitrogen catabolite repression. The expression of all these genes, with the exception of UGA1 and PUT2, also required a functional GLN3 protein. In addition, GLN3 protein was required for expression of the DAL1, DAL2, DAL7, GDH1, and GDH2 genes. The UGA1, CAN1, GAP1, and DAL4 genes markedly increased their expression when the DAL80 locus, encoding a negative regulatory element, was disrupted. Expression of the GDH1, PUT1, PUT2, and PUT4 genes also responded to DAL80 disruption, but much more modestly. Expression of GLN1 and GDH2 exhibited parallel responses to the provision of asparagine and glutamine as nitrogen sources but did not follow the regulatory responses noted above for the nitrogen catabolic genes such as DAL5. Steady-state mRNA levels of both genes did not significantly decrease when glutamine was provided as nitrogen source but were lowered by the provision of asparagine. They also did not respond to disruption of DAL80.

  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. Molecular and phylogenetic characterizations of an Eimeria krijgsmanni Yakimoff & Gouseff, 1938 (Apicomplexa: Eimeriidae) mouse intestinal protozoan parasite by partial 18S ribosomal RNA gene sequence analysis.

    PubMed

    Takeo, Toshinori; Tanaka, Tetsuya; Matsubayashi, Makoto; Maeda, Hiroki; Kusakisako, Kodai; Matsui, Toshihiro; Mochizuki, Masami; Matsuo, Tomohide

    2014-08-01

    Previously, we characterized an undocumented strain of Eimeria krijgsmanni by morphological and biological features. Here, we present a detailed molecular phylogenetic analysis of this organism. Namely, 18S ribosomal RNA gene (rDNA) sequences of E. krijgsmanni were analyzed to incorporate this species into a comprehensive Eimeria phylogeny. As a result, partial 18S rDNA sequence from E. krijgsmanni was successfully determined, and two different types, Type A and Type B, that differed by 1 base pair were identified. E. krijgsmanni was originally isolated from a single oocyst, and thus the result show that the two types might have allelic sequence heterogeneity in the 18S rDNA. Based on phylogenetic analyses, the two types of E. krijgsmanni 18S rDNA formed one of two clades among murine Eimeria spp.; these Eimeria clades reflected morphological similarity among the Eimeria spp. This is the third molecular phylogenetic characterization of a murine Eimeria spp. in addition to E. falciformis and E. papillata.

  17. 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.

  18. 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.

  19. Hap2-3-5-Gln3 determine transcriptional activation of GDH1 and ASN1 under repressive nitrogen conditions in the yeast Saccharomyces cerevisiae.

    PubMed

    Hernández, Hugo; Aranda, Cristina; López, Geovani; Riego, Lina; González, Alicia

    2011-03-01

    The transcriptional activation response relies on a repertoire of transcriptional activators, which decipher regulatory information through their specific binding to cognate sequences, and their capacity to selectively recruit the components that constitute a given transcriptional complex. We have addressed the possibility of achieving novel transcriptional responses by the construction of a new transcriptional regulator--the Hap2-3-5-Gln3 hybrid modulator--harbouring the HAP complex polypeptides that constitute the DNA-binding domain (Hap2-3-5) and the Gln3 activation domain, which usually act in an uncombined fashion. The results presented in this paper show that transcriptional activation of GDH1 and ASN1 under repressive nitrogen conditions is achieved through the action of the novel Hap2-3-5-Gln3 transcriptional regulator. We propose that the combination of the Hap DNA-binding and Gln3 activation domains results in a hybrid modulator that elicits a novel transcriptional response not evoked when these modulators act independently.

  20. 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

  1. Identification and partial characterization of extracellular aspartic protease genes from Metschnikowia pulcherrima IWBT Y1123 and Candida apicola IWBT Y1384.

    PubMed

    Reid, Vernita J; Theron, Louwrens W; du Toit, Maret; Divol, Benoit

    2012-10-01

    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.

  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. 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.

  4. Molecular cloning, partial genomic structure and functional characterization of succinic semialdehyde dehydrogenase genes from the parasitic insects Lucilia cuprina and Ctenocephalides felis.

    PubMed

    Rothacker, B; Werr, M; Ilg, T

    2008-06-01

    The enzyme succinic semialdehyde dehydrogenase (SSADH; EC1.2.1.24) is a component of the gamma-aminobutyric acid degradation pathway in mammals and is essential for development and function of the nervous system. Here we report the identification, cDNA cloning and functional expression of SSADH from the parasitic insects Lucilia cuprina and Ctenocephalides felis. The recombinant proteins possess potent NAD+-dependent SSADH activity, while their catalytic efficiency for other aldehyde substrates is lower. A genomic copy of the L. cuprina SSADH gene contains two introns, while a genomic gene version of C. felis is devoid of introns. In contrast to the single copy SSADH genes in Drosophila melanogaster and mammals, in L. cuprina and C. felis, multiple SSADH gene copies are present in the genome.

  5. A gain-of-function mutation of plastidic invertase alters nuclear gene expression with sucrose treatment partially via GENOMES UNCOUPLED1-mediated signaling.

    PubMed

    Maruta, Takanori; Miyazaki, Nozomi; Nosaka, Ryota; Tanaka, Hiroyuki; Padilla-Chacon, Daniel; Otori, Kumi; Kimura, Ayako; Tanabe, Noriaki; Yoshimura, Kazuya; Tamoi, Masahiro; Shigeoka, Shigeru

    2015-05-01

    Plastid gene expression (PGE) is one of the signals that regulate the expression of photosynthesis-associated nuclear genes (PhANGs) via GENOMES UNCOUPLED1 (GUN1)-dependent retrograde signaling. We recently isolated Arabidopsis sugar-inducible cotyledon yellow-192 (sicy-192), a gain-of-function mutant of plastidic invertase, and showed that following the treatment of this mutant with sucrose, the expression of PhANGs as well as PGE decreased, suggesting that the sicy-192 mutation activates a PGE-evoked and GUN1-mediated retrograde pathway. To clarify the relationship between the sicy-192 mutation, PGE, and GUN1-mediated pathway, plastid and nuclear gene expression in a double mutant of sicy-192 and gun1-101, a null mutant of GUN1 was studied. Plastid-encoded RNA polymerase (PEP)-dependent PGE was markedly suppressed in the sicy-192 mutant by the sucrose treatment, but the suppression as well as cotyledon yellow phenotype was not mitigated by GUN1 disruption. Microarray analysis revealed that the altered expression of nuclear genes such as PhANG in the sucrose-treated sicy-192 mutant was largely dependent on GUN1. The present findings demonstrated that the sicy-192 mutation alters nuclear gene expression with sucrose treatment via GUN1, which is possibly followed by inhibiting PEP-dependent PGE, providing a new insight into the role of plastid sugar metabolism in nuclear gene expression.

  6. Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

    PubMed Central

    Dobešová, E; Malinská, H; Matyášek, R; Leitch, A R; Soltis, D E; Soltis, P S; Kovařík, A

    2015-01-01

    To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely different rRNA gene dosages. Plant 33B had ~400 rRNA genes at the D-genome locus, which is typical for T. mirus, accounting for ~25% of total rDNA. We observed characteristic expression dominance of T. dubius-origin genes in all organs. Its sister plant 33A harboured a homozygous macrodeletion that reduced the number of T. dubius-origin genes to about 70 copies (~4% of total rDNA). It showed biparental rDNA expression in root, flower and callus, but not in leaf where D-genome rDNA dominance was maintained. There was upregulation of minor rDNA variants in some tissues. The RNA polymerase I promoters of reactivated T. porrifolius-origin rRNA genes showed reduced DNA methylation, mainly at symmetrical CG and CHG nucleotide motifs. We hypothesise that active, decondensed rDNA units are most likely to be deleted via recombination. The silenced homeologs could be used as a ‘first reserve' to ameliorate mutational damage and contribute to evolutionary success of polyploids. Deletion and reactivation cycles may lead to bidirectional homogenisation of rRNA arrays in the long term. PMID:25537492

  7. Molecular cloning and characterization of a mammalian excision repair gene that partially restores UV resistance to xeroderma pigmentosum complementation group D cells

    SciTech Connect

    Arrand, J.E.; Bone, N.M.; Johnson, R.T. )

    1989-09-01

    A hamster DNA repair gene has been isolated by cosmid rescue after two rounds of transfection of an immortalized xeroderma pigmentosum (XP) complementation group D cell line with neomycin-resistance gene (neo)-tagged normal hamster DNA and selection with G418 and ultraviolet irradiation. The functional length of the sequence has been defined as 11.5 kilobase pairs by measurement of the region of overlap between two hamster DNA-containing cosmids, cloned by selection for the integrated neo gene, that are able to confer an increase in resistance to ultraviolet irradiation on two XP-D cell line but not on an XP-A line. Detailed molecular characterization of the hamster repair gene has revealed no obvious similarities to two human excision repair genes (ERCC1 and ERCC2) that correct repair-defective hamster cells but have no effect on XP cells. Hybridization analyses of normal human and XP cell genomic DNAs and mRNAs, using a cosmid-clone probe from which repeated sequences have been removed, show that homologues are present and expressed in all cases.

  8. Regulation of the laminin beta 1 (LAMB1), retinoic acid receptor beta, and bone morphogenetic protein 2 genes in mutant F9 teratocarcinoma cell lines partially deficient in cyclic AMP-dependent protein kinase activity.

    PubMed

    Shen, J; Li, C; Gudas, L J

    1997-12-01

    We stably transfected a gene encoding a dominant negative regulatory subunit of cyclic AMP (cAMP)-dependent protein kinase A (PKA) into F9 cells and generated cell lines partially deficient in PKA activity (DN16 and DN19). In these cell lines, the retinoic acid (RA) receptor beta and laminin beta(1) chain (LAMB1) genes were regulated normally by RA alone, indicating that in the absence of exogenous modulation of cAMP levels, the PKA signaling pathway does not seem to play a major role in the RA-associated regulation of these genes. However, alterations in gene regulation were observed when the mutant cell lines were treated with a combination of RA and cAMP analogues. Moreover, in the DN16 cell line, which exhibits the lowest PKA activity among the mutant cell lines [22% of wild type (WT) at 1 microM cAMP], there was a significant decrease in the cAMP-associated activation of the LAMB1 gene DNase I hypersensitivity site 2 enhancer, as measured by chloramphenicol acetyl transferase assays. Using electrophoretic mobility shift assays, less protein binding was observed at one of the motifs (C2) within this enhancer region in the DN16 cells as compared to the F9 WT cells after treatment of the cells with RA and cAMP analogues for 24 h. Furthermore, no increase in C2 binding was observed when extracts from RA-treated F9 ST or DN16 cells were subjected to in vitro phosphorylation, suggesting that PKA is involved in the induction of the C2-binding protein in RA-treated cells. In contrast to the results with RA receptor beta and LAMB1, the effects of cAMP analogues on the RA-associated regulation of the bone morphogenetic protein 2 gene were not altered in the cell lines that exhibited reduced PKA activity. These results suggest that a partial reduction in PKA activity is not sufficient to abrogate the effects of cAMP analogues on all of the genes regulated by RA.

  9. Glucose dehydrogenase polymorphism in man.

    PubMed

    King, J; Cook, P J

    1981-05-01

    An isoelectric focusing method for human GDH is described which reveals seven GDH phenotypes. Family studies demonstrate that the variation is genetically determined by three alleles at an autosomal locus with gene frequencies GDH1 = 0.723, GDH2 = 0.194, GDH3 = 0.083. Linkage analysis shows that GDH may be closely linked to PGD on chromosome 1.

  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 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

  11. Partial resistance of Medicago truncatula to Aphanomyces euteiches is associated with protection of the root stele and is controlled by a major QTL rich in proteasome-related genes.

    PubMed

    Djébali, Naceur; Jauneau, Alain; Ameline-Torregrosa, Carine; Chardon, Fabien; Jaulneau, Valérie; Mathé, Catherine; Bottin, Arnaud; Cazaux, Marc; Pilet-Nayel, Marie-Laure; Baranger, Alain; Aouani, Mohamed Elarbi; Esquerré-Tugayé, Marie-Thérèse; Dumas, Bernard; Huguet, Thierry; Jacquet, Christophe

    2009-09-01

    A pathosystem between Aphanomyces euteiches, the causal agent of pea root rot disease, and the model legume Medicago truncatula was developed to gain insights into mechanisms involved in resistance to this oomycete. The F83005.5 French accession and the A17-Jemalong reference line, susceptible and partially resistant, respectively, to A. euteiches, were selected for further cytological and genetic analyses. Microscopy analyses of thin root sections revealed that a major difference between the two inoculated lines occurred in the root stele, which remained pathogen free in A17. Striking features were observed in A17 roots only, including i) frequent pericycle cell divisions, ii) lignin deposition around the pericycle, and iii) accumulation of soluble phenolic compounds. Genetic analysis of resistance was performed on an F7 population of 139 recombinant inbred lines and identified a major quantitative trait locus (QTL) near the top of chromosome 3. A second study, with near-isogenic line responses to A. euteiches confirmed the role of this QTL in expression of resistance. Fine-mapping allowed the identification of a 135-kb sequenced genomic DNA region rich in proteasome-related genes. Most of these genes were shown to be induced only in inoculated A17. Novel mechanisms possibly involved in the observed partial resistance are proposed.

  12. 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.

  13. Hypermethylation of CpG islands in the mouse asparagine synthetase gene: relationship to asparaginase sensitivity in lymphoma cells. Partial methylation in normal cells.

    PubMed

    Peng, H; Shen, N; Qian, L; Sun, X L; Koduru, P; Goodwin, L O; Issa, J P; Broome, J D

    2001-09-14

    We have sequenced the promoter region of the murine asparagine synthetase gene and examined its methylation profile in the CpG islands of L-asparaginase-sensitive 6C3HED cells (asparagine auxotrophs) and resistant variants (prototrophs). In the former, complete methylation of the CpG island is correlated with failure of expression of mRNA: cells of the latter possess both methylated and unmethylated alleles, as do cells of the intrinsically asparagine-independent lines L1210 and EL4. A similar phenomenon was seen in normal splenic cells of adult mice. This was age related: no methylation was found in weanlings, but up to 45% of gene copies in animals 18 weeks or older were methylated. It was also tissue related, with methylation occurring rarely in liver cells. The relationship of these changes to oncogenesis is considered.

  14. In vivo transfer of hepatocyte growth factor gene accelerates proliferation of hepatic oval cells in a 2-acetylaminofluorene/partial hepatectomy model in rats.

    PubMed

    Shiota, G; Kunisada, T; Oyama, K; Udagawa, A; Nomi, T; Tanaka, K; Tsutsumi, A; Isono, M; Nakamura, T; Hamada, H; Sakatani, T; Sell, S; Sato, K; Ito, H; Kawasaki, H

    2000-03-31

    To clarify the effect of hepatocyte growth factor (HGF) on proliferation of hepatic oval cells, we transferred HGF gene into liver of the Solt-Farber rat model. Male Fisher 344 rats were infected with a recombinant adenovirus carrying the cDNA for HGF (pAxCAHGF) from tail vein. HGF mRNA showed its peak at 4 days, and diminished thereafter. The total and proliferating cell nuclear antigen-positive hepatic oval cells were significantly elevated in HGF-transferred rats, in which stem cell factor and c-kit mRNA increased at each time point. Our results suggest that in vivo transfer of the HGF gene into liver accelerates proliferation of hepatic oval cells in the Solt-Farber model in rats.

  15. Partial Complementation of the UV Sensitivity of Deinococcus Radiodurans Excision Repair Mutants by the Cloned denv Gene of Bacteriophage T4

    DTIC Science & Technology

    1990-07-19

    ligated with the denV gene containing fragment from pTACdenV using T4 DNA ligase . T4 DNA ligase catalyzes the formation of phosphodiester bonds between...MgClj, lOmM DTT, 1 ug DNA, 0. 5mM ATP, 50 ug/ml BSA and 1 U T4 DNA ligase . Incubation was at 15°C overnight. Transformation of E. coli with DNA

  16. 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.

  17. 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

  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. 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.

  20. 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

  1. 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

    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.

  2. AB283. SPR-10 Down-regulation of ryanodine receptor gene expression in murine urinary bladder smooth muscle following partial bladder outlet obstruction

    PubMed Central

    Boopathi, Ettickan; Javed, Elham; Addya, Shankar; Fortina, Paolo; Zderic, Stephen; Wein, Alan; Chacko, Samuel

    2016-01-01

    Objective Urinary bladder smooth muscle (UBSM) displays spontaneous action potentials and this potential is related to the phasic nature of spontaneous contractions in this tissue. The amplitude of a phasic contraction depends on the increase in Ca2+ entry caused by membrane depolarization. Ryanodine receptors (RyRs) in UBSM decreases the force production by decreasing the frequency of phasic contractions through interactions with large-conductance Ca2+-activated K+ (BK) and small-conductance Ca2+-activated K+ (SK) channels. Microarray and network analysis were employed to determine the changes in mRNA in 14-day obstructed murine bladders. We found that obstruction significantly down-regulated the RyRs in bladder smooth muscle (BSM). Methods Male C57Bl/6 mice were surgically obstructed and kept for 14 days. Sham-operated mice served as a control. Bladders were excised; urothelium scraped off with a scalpel, and the serosa was removed. BSM obtained from PBOO and sham control animals were used for microarray and western blotting Results Pathway-based analysis of these gene signatures showed significant number of under-expressed genes in obstructed bladder and they were mapped to proteins involved in calcium signaling. We focused our work on RyR protein expression in BSM. There was a four-fold reduction of RyR3 in BSM in 14-day obstructed groups as shown by microarray and immunoblotting compared to that of sham-operated animals. Conclusions These results confirm that the RyR gene expression is down-regulated in obstructed murine bladder smooth muscle. Funding Source(s) None

  3. The Mitochondrial SDHD Gene Is Required for Early Embryogenesis, and Its Partial Deficiency Results in Persistent Carotid Body Glomus Cell Activation with Full Responsiveness to Hypoxia

    PubMed Central

    Piruat, José I.; Pintado, C. Oscar; Ortega-Sáenz, Patricia; Roche, Marta; López-Barneo, José

    2004-01-01

    The SDHD gene encodes one of the two membrane-anchoring proteins of the succinate dehydrogenase (complex II) of the mitochondrial electron transport chain. This gene has recently been proposed to be involved in oxygen sensing because mutations that cause loss of its function produce hereditary familiar paraganglioma, a tumor of the carotid body (CB), the main arterial chemoreceptor that senses oxygen levels in the blood. Here, we report the generation of a SDHD knockout mouse, which to our knowledge is the first mammalian model lacking a protein of the electron transport chain. Homozygous SDHD−/− animals die at early embryonic stages. Heterozygous SDHD+/− mice show a general, noncompensated deficiency of succinate dehydrogenase activity without alterations in body weight or major physiological dysfunction. The responsiveness to hypoxia of CBs from SDHD+/− mice remains intact, although the loss of an SDHD allele results in abnormal enhancement of resting CB activity due to a decrease of K+ conductance and persistent Ca2+ influx into glomus cells. This CB overactivity is linked to a subtle glomus cell hypertrophy and hyperplasia. These observations indicate that constitutive activation of SDHD+/− glomus cells precedes CB tumor transformation. They also suggest that, contrary to previous beliefs, mitochondrial complex II is not directly involved in CB oxygen sensing. PMID:15572694

  4. Partial characterization of an rpoD-like gene of Lactococcus lactis subsp. lactis ML3 with a polymerase chain reaction-based approach.

    PubMed

    Gansel, X; Dutreix, M; Hartke, A; Boutibonnes, P; Auffray, Y

    1993-11-01

    With degenerated oligonucleotide primers for conserved regions of bacterial sigma factor proteins, a 117-bp internal DNA fragment of an rpoD-like gene of Lactococcus lactis subsp. lactis ML3 was amplified by the polymerase chain reaction (PCR). The DNA sequence of this PCR product was determined by cycle sequencing, and the deduced amino acid sequence of this internal fragment showed an extensive homology with the known sigma factor sequences from six other microorganisms and present a 13-amino acid region corresponding to the typical "RpoD box" of primary sigma factors. This PCR product was used as a probe to specifically detect sigma homologs in Pediococcus acidilactici, Leuconostoc lactis, Lactobacillus helveticus, Lactobacillus acidophilus, Enterococcus faecalis, Streptococcus thermophilus, and Lactococcus lactis subsp. cremoris. These data are consistent with the existence of a high similarity between the primary sigma factors from diverse Gram-positive microorganisms.

  5. 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.

  6. 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. ...

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. Misexpression of AtTX12 encoding a Toll/interleukin-1 receptor domain induces growth defects and expression of defense-related genes partially independently of EDS1 in Arabidopsis

    PubMed Central

    Song, Sang-Kee

    2016-01-01

    In this study, a tissue-specific GAL4/UAS activation tagging system was used for the characterization of genes which could induce lethality when ubiquitously expressed. A dominant mutant exhibiting stunted growth was isolated and named defective root development 1-D (drd1-D). The T-DNA tag was located within the promoter region of AtTX12, which is predicted to encode a truncated nucleotide-binding leucine-rich repeat (NLR) protein, containing a Toll/interleukin-1 receptor (TIR) domain. The transcript levels of AtTX12 and defense-related genes were elevated in drd1-D, and the misexpression of AtTX12 recapitulated the drd1-D phenotypes. In the presence of ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), a key transducer of signals triggered by TIR-type NLRs, a low-level of AtTX12 misexpression induced strong defective phenotypes including seedling lethality whereas, in the absence of EDS1, a high-level of AtTX12 misexpression induced weak growth defects like dwarfism, suggesting that AtTX12 might function mainly in an EDS1-dependent and partially in an EDS1-independent manner. [BMB Reports 2016; 49(12): 693–698] PMID:27802841

  12. Specific and sensitive detection of Nosema bombi (Microsporidia: Nosematidae) in bumble bees (Bombus spp.; Hymenoptera: Apidae) by PCR of partial rRNA gene sequences.

    PubMed

    Klee, Julia; Tek Tay, Wee; Paxton, Robert J

    2006-02-01

    A polymerase chain reaction (PCR) based method was developed for the specific and sensitive diagnosis of the microsporidian parasite Nosema bombi in bumble bees (Bombus spp.). Four primer pairs, amplifying ribosomal RNA (rRNA) gene fragments, were tested on N. bombi and the related microsporidia Nosema apis and Nosema ceranae, both of which infect honey bees. Only primer pair Nbombi-SSU-Jf1/Jr1 could distinguish N. bombi (323bp amplicon) from these other bee parasites. Primer pairs Nbombi-SSU-Jf1/Jr1 and ITS-f2/r2 were then tested for their sensitivity with N. bombi spore concentrations from 10(7) down to 10 spores diluted in 100 microl of either (i) water or (ii) host bumble bee homogenate to simulate natural N. bombi infection (equivalent to the DNA from 10(6) spores down to 1 spore per PCR). Though the N. bombi-specific primer pair Nbombi-SSU-Jf1/Jr1 was relatively insensitive, as few as 10 spores per extract (equivalent to 1 spore per PCR) were detectable using the N. bombi-non-specific primer pair ITS-f2/r2, which amplifies a short fragment of approximately 120 bp. Testing 99 bumble bees for N. bombi infection by light microscopy versus PCR diagnosis with the highly sensitive primer pair ITS-f2/r2 showed the latter to be more accurate. PCR diagnosis of N. bombi using a combination of two primer pairs (Nbombi-SSU-Jf1/Jr1 and ITS-f2/r2) provides increased specificity, sensitivity, and detection of all developmental stages compared with light microscopy.

  13. Genes

    MedlinePlus

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

  14. A new genus and species of Brachycoeliidae (Digenea) from Chiropterotriton sp. (Caudata: Plethodontidae) in Mexico and its phylogenetic position within the Plagiorchiida based on partial sequences of the 28S ribosomal RNA gene.

    PubMed

    de León, G Pérez-Ponce; Mendoza-Garfias, B; Razo-Mendivil, U; Parra-Olea, G

    2011-02-01

    Parabrachycoelium longicaecum n. gen., n. sp. (Digenea: Brachycoeliidae) is described from the intestine of a plethodontid salamander Chiropterotriton sp. Hosts were collected in bromeliads at the cloud forest of Tlaquilpa, Veracruz, Mexico. Members of the Brachycoeliidae Looss, 1899 (sensu Yamaguti, 1971) are characterized by having a spined tegument; ceca usually short, not passing level of gonads, but longer in some species; gonads posterior to, or in region of, acetabulum, with ovary anterior to testes; a well developed cirrus pouch containing a bipartite seminal vesicle; and uterus occupying entire hind-body posterior to testes. However, this combination of morphological traits prevents the inclusion of the new taxon in any of the genera in that family; a new genus was, therefore, erected to accommodate the new species. The new taxon is readily distinguished from members belonging to Brachycoelium Dujardin, 1845, Mesocoelium Odhner, 1910, and Tremiorchis Mehra and Negi, 1925, by having long ceca extending into the posterior third of the body, slightly surpassing the testes, and vitellaria extending along the body. The new species morphologically resembles Caudouterina rhyacotritoni Martin, 1966, a digenean parasitizing a plethodontid salamander; however, the latter species lacks spines in the tegument and is actually placed within the Allocreadiidae. To demonstrate further the phylogenetic position of the new taxon, we sequenced the D1-D3 regions of 28S rRNA gene and conducted a phylogenetic analysis of available sequences for the order to which brachycoeliids belong (Plagiorchiida). Sequence divergence of the partial 28S rRNA gene confirms its distinction from the aforementioned brachycoeliids, and the phylogenetic position within the Plagiorchiida places the new species as closely related to a clade formed by Brachycoelium + Mesocoelium. Divergence levels and phylogenetic position within the Plagiorchiida verifies the validity of the new genus and its

  15. Gene Copy-Number Variations (CNVs) and Protein Levels of Complement C4A and C4B as Novel Biomarkers for Partial Disease Remissions in New-Onset Type 1 Diabetes Patients

    PubMed Central

    Kingery, Suzanne E.; Wu, Yee Ling; Zhou, Bi; Hoffman, Robert P.; Yu, C. Yung

    2014-01-01

    Objective To determine the roles of complement C4A and C4B gene CNVs and their plasma protein concentrations in residual insulin secretion and loss of pancreatic beta-cell function in new-onset type 1 diabetes patients. Methods We studied 34 patients of European ancestry with new-onset type 1 diabetes, aged between 3 and 17 years (10.7±3.45), at Nationwide Children's Hospital in Columbus, Ohio. Gene copy-number and size variations of complement C4A and C4B were determined by genomic Southern blot analyses. C4A and C4B protein phenotypes were elucidated by immunofixation and radial immunodiffusion. Two-digit HLA-DRB1 genotypes were determined by sequence-specific PCR. At 1 month and 9-month post diagnosis, stimulated C-peptide levels were measured after a standardized mixed-meal tolerance test. Results The diploid gene copy-numbers of C4A varied from 0 to 4, and those of C4B from 0 to 3. Patients with higher copy-number of C4A or higher C4A plasma protein concentrations at diagnosis had higher C-peptide levels at 1 month post diagnosis (p=0.008; p=0.008). When controlled by the Z-score of body-mass index, C4A copy-numbers, C4A protein concentrations, the age of disease-onset, the number of HLA-DR3 but not DR4 alleles were significant parameters in determining C-peptide levels. At 9-month post diagnosis, 42.3% of patients remained in partial remission, and these patients were characterized by lower total C4B copy-numbers or lower C4B protein concentrations (p=0.02, p=0.0004). Conclusions C4A appears to associate with the protection of residual beta-cell function in new-onset type 1 diabetes; C4B is correlated with the end of disease remission at 9-month post diagnosis. PMID:22151770

  16. Partial Torus Instability

    NASA Astrophysics Data System (ADS)

    Olmedo, Oscar; Zhang, J.

    2010-05-01

    Flux ropes are now generally accepted to be the magnetic configuration of Coronal Mass Ejections (CMEs), which may be formed prior 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 instability 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. 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 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, the partial torus with a larger fractional number has a larger critical index. In the limit of a circular torus when the fractional number approaches one, the critical index goes to a maximum value that depends on the distribution of the external magnetic field. We demonstrate that the partial torus instability helps us to understand the confinement, growth, and eventual eruption of a flux rope CME.

  17. Partial knee replacement - slideshow

    MedlinePlus

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

  18. 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.

  19. Partially coherent nonparaxial beams.

    PubMed

    Duan, Kailiang; Lü, Baida

    2004-04-15

    The concept of a partially coherent nonparaxial beam is proposed. A closed-form expression for the propagation of nonparaxial Gaussian Schell model (GSM) beams in free space is derived and applied to study the propagation properties of nonparaxial GSM beams. It is shown that for partially coherent nonparaxial beams a new parameter f(sigma) has to be introduced, which together with the parameter f, determines the beam nonparaxiality.

  20. 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.

  1. Partial Torus Instability

    NASA Astrophysics Data System (ADS)

    Olmedo, Oscar; Zhang, Jie

    2010-07-01

    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.

  2. Molecular characterization, function and regulation of ammonium transporters (Amt) and ammonium-metabolizing enzymes (GS, NADP-GDH) in the ectomycorrhizal fungus Hebeloma cylindrosporum.

    PubMed

    Javelle, Arnaud; Morel, Mélanie; Rodríguez-Pastrana, Blanca-Rosa; Botton, Bernard; André, Bruno; Marini, Anne-Marie; Brun, Annick; Chalot, Michel

    2003-01-01

    External hyphae, which play a key role in nitrogen nutrition of trees, are considered as the absorbing structures of the ectomycorrhizal symbiosis. Here, we have cloned and characterized Hebeloma cylindrosporum AMT1, GLNA and GDHA genes, which encode a third ammonium transporter, a glutamine synthetase and an NADP-dependent glutamate dehydrogenase respectively. Amt1 can fully restore the pseudohyphal growth defect of a Saccharomyces cerevisiae mep2 mutant, and this is the first evidence that a heterologous member of the Mep/Amt family complements this dimorphic change defect. Dixon plots of the inhibition of methylamine uptake by ammonium indicate that Amt1 has a much higher affinity than the two previously characterized members (Amt2 and Amt3) of the Amt/Mep family in H. cylindrosporum. We also identified the intracellular nitrogen pool(s) responsible for the modulation of expression of AMT1, AMT2, AMT3, GDHA and GLNA. In response to exogenously supplied ammonium or glutamine, AMT1, AMT2 and GDHA were downregulated and, therefore, these genes are subjected to nitrogen repression in H. cylindrosporum. Exogenously supplied nitrate failed to induce a downregulation of the five mRNAs after transfer of mycelia from a N-starved condition. Our results demonstrate that glutamine is the main effector for AMT1 and AMT2 repression, whereas GDHA repression is controlled by intracellular ammonium, independently of the intracellular glutamine or glutamate concentration. Ammonium transport activity may be controlled by intracellular NH4+. AMT3 and GLNA are highly expressed but not highly regulated. A model for ammonium assimilation in H. cylindrosporum is presented.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Partially strong WW scattering

    SciTech Connect

    Cheung Kingman; Chiang Chengwei; Yuan Tzuchiang

    2008-09-01

    What if only a light Higgs boson is discovered at the CERN LHC? Conventional wisdom tells us that the scattering of longitudinal weak gauge bosons would not grow strong at high energies. However, this is generally not true. In some composite models or general two-Higgs-doublet models, the presence of a light Higgs boson does not guarantee complete unitarization of the WW scattering. After partial unitarization by the light Higgs boson, the WW scattering becomes strongly interacting until it hits one or more heavier Higgs bosons or other strong dynamics. We analyze how LHC experiments can reveal this interesting possibility of partially strong WW scattering.

  11. Partial polarizer filter

    NASA Technical Reports Server (NTRS)

    Title, A. M. (Inventor)

    1978-01-01

    A birefringent filter module comprises, in seriatum. (1) an entrance polarizer, (2) a first birefringent crystal responsive to optical energy exiting the entrance polarizer, (3) a partial polarizer responsive to optical energy exiting the first polarizer, (4) a second birefringent crystal responsive to optical energy exiting the partial polarizer, and (5) an exit polarizer. The first and second birefringent crystals have fast axes disposed + or -45 deg from the high transmitivity direction of the partial polarizer. Preferably, the second crystal has a length 1/2 that of the first crystal and the high transmitivity direction of the partial polarizer is nine times as great as the low transmitivity direction. To provide tuning, the polarizations of the energy entering the first crystal and leaving the second crystal are varied by either rotating the entrance and exit polarizers, or by sandwiching the entrance and exit polarizers between pairs of half wave plates that are rotated relative to the polarizers. A plurality of the filter modules may be cascaded.

  12. Dilemmas of partial cooperation.

    PubMed

    Stark, Hans-Ulrich

    2010-08-01

    Related to the often applied cooperation models of social dilemmas, we deal with scenarios in which defection dominates cooperation, but an intermediate fraction of cooperators, that is, "partial cooperation," would maximize the overall performance of a group of individuals. Of course, such a solution comes at the expense of cooperators that do not profit from the overall maximum. However, because there are mechanisms accounting for mutual benefits after repeated interactions or through evolutionary mechanisms, such situations can constitute "dilemmas" of partial cooperation. Among the 12 ordinally distinct, symmetrical 2 x 2 games, three (barely considered) variants are correspondents of such dilemmas. Whereas some previous studies investigated particular instances of such games, we here provide the unifying framework and concisely relate it to the broad literature on cooperation in social dilemmas. Complementing our argumentation, we study the evolution of partial cooperation by deriving the respective conditions under which coexistence of cooperators and defectors, that is, partial cooperation, can be a stable outcome of evolutionary dynamics in these scenarios. Finally, we discuss the relevance of such models for research on the large biodiversity and variation in cooperative efforts both in biological and social systems.

  13. Partial correction of the CNS lysosomal storage defect in a mouse model of juvenile neuronal ceroid lipofuscinosis by neonatal CNS administration of an adeno-associated virus serotype rh.10 vector expressing the human CLN3 gene.

    PubMed

    Sondhi, Dolan; Scott, Emma C; Chen, Alvin; Hackett, Neil R; Wong, Andrew M S; Kubiak, Agnieszka; Nelvagal, Hemanth R; Pearse, Yewande; Cotman, Susan L; Cooper, Jonathan D; Crystal, Ronald G

    2014-03-01

    Juvenile neuronal ceroid lipofuscinosis (JNCL or CLN3 disease) is an autosomal recessive lysosomal storage disease resulting from mutations in the CLN3 gene that encodes a lysosomal membrane protein. The disease primarily affects the brain with widespread intralysosomal accumulation of autofluorescent material and fibrillary gliosis, as well as the loss of specific neuronal populations. As an experimental treatment for the CNS manifestations of JNCL, we have developed a serotype rh.10 adeno-associated virus vector expressing the human CLN3 cDNA (AAVrh.10hCLN3). We hypothesized that administration of AAVrh.10hCLN3 to the Cln3(Δex7/8) knock-in mouse model of JNCL would reverse the lysosomal storage defect, as well as have a therapeutic effect on gliosis and neuron loss. Newborn Cln3(Δex7/8) mice were administered 3 × 10(10) genome copies of AAVrh.10hCLN3 to the brain, with control groups including untreated Cln3(Δex7/8) mice and wild-type littermate mice. After 18 months, CLN3 transgene expression was detected in various locations throughout the brain, particularly in the hippocampus and deep anterior cortical regions. Changes in the CNS neuronal lysosomal accumulation of storage material were assessed by immunodetection of subunit C of ATP synthase, luxol fast blue staining, and periodic acid-Schiff staining. For all parameters, Cln3(Δex7/8) mice exhibited abnormal lysosomal accumulation, but AAVrh.10hCLN3 administration resulted in significant reductions in storage material burden. There was also a significant decrease in gliosis in AAVrh.10hCLN3-treated Cln3(Δex7/8) mice, and a trend toward improved neuron counts, compared with their untreated counterparts. These data demonstrate that AAVrh.10 delivery of a wild-type cDNA to the CNS is not harmful and instead provides a partial correction of the neurological lysosomal storage defect of a disease caused by a lysosomal membrane protein, indicating that this may be an effective therapeutic strategy for JNCL and

  14. Cloning of a yeast gene coding for the glutamate synthase small subunit (GUS2) by complementation of Saccharomyces cerevisiae and Escherichia coli glutamate auxotrophs.

    PubMed

    González, A; Membrillo-Hernández, J; Olivera, H; Aranda, C; Macino, G; Ballario, P

    1992-02-01

    A Saccharomyces cerevisiae glutamate auxotroph, lacking NADP-glutamate dehydrogenase (NADP-GDH) and glutamate synthase (GOGAT) activities, was complemented with a yeast genomic library. Clones were obtained which still lacked NADP-GDH but showed GOGAT activity. Northern analysis revealed that the DNA fragment present in the complementing plasmids coded for a 1.5kb mRNA. Since the only GOGAT enzyme so far purified from S. cerevisiae is made up of a small and a large subunit, the size of the mRNA suggested that the cloned DNA fragment could code for the GOGAT small subunit. Plasmids were purified and used to transform Escherichia coli glutamate auxotrophs. Transformants were only recovered when the recipient strain was an E. coli GDH-less mutant lacking the small GOGAT subunit. These data show that we have cloned the structural gene coding for the yeast small subunit (GUS2). Evidence is also presented indicating that the GOGAT enzyme which is synthesized in the E. coli transformants is a hybrid comprising the large E. coli subunit and the small S. cerevisiae subunit.

  15. 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

  16. 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

  17. Laparoscopic partial splenic resection.

    PubMed

    Uranüs, S; Pfeifer, J; Schauer, C; Kronberger, L; Rabl, H; Ranftl, G; Hauser, H; Bahadori, K

    1995-04-01

    Twenty domestic pigs with an average weight of 30 kg were subjected to laparoscopic partial splenic resection with the aim of determining the feasibility, reliability, and safety of this procedure. Unlike the human spleen, the pig spleen is perpendicular to the body's long axis, and it is long and slender. The parenchyma was severed through the middle third, where the organ is thickest. An 18-mm trocar with a 60-mm Endopath linear cutter was used for the resection. The tissue was removed with a 33-mm trocar. The operation was successfully concluded in all animals. No capsule tears occurred as a result of applying the stapler. Optimal hemostasis was achieved on the resected edges in all animals. Although these findings cannot be extended to human surgery without reservations, we suggest that diagnostic partial resection and minor cyst resections are ideal initial indications for this minimally invasive approach.

  18. Hierarchical partial order ranking.

    PubMed

    Carlsen, Lars

    2008-09-01

    Assessing the potential impact on environmental and human health from the production and use of chemicals or from polluted sites involves a multi-criteria evaluation scheme. A priori several parameters are to address, e.g., production tonnage, specific release scenarios, geographical and site-specific factors in addition to various substance dependent parameters. Further socio-economic factors may be taken into consideration. The number of parameters to be included may well appear to be prohibitive for developing a sensible model. The study introduces hierarchical partial order ranking (HPOR) that remedies this problem. By HPOR the original parameters are initially grouped based on their mutual connection and a set of meta-descriptors is derived representing the ranking corresponding to the single groups of descriptors, respectively. A second partial order ranking is carried out based on the meta-descriptors, the final ranking being disclosed though average ranks. An illustrative example on the prioritization of polluted sites is given.

  19. 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.

  20. Partially integrated exhaust manifold

    SciTech Connect

    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.

  1. Activated partial thromboplastin time.

    PubMed

    Ignjatovic, Vera

    2013-01-01

    Activated partial thromboplastin time (APTT) is a commonly used coagulation assay that is easy to perform, is affordable, and is therefore performed in most coagulation laboratories, both clinical and research, worldwide. The APTT is based on the principle that in citrated plasma, the addition of a platelet substitute, factor XII activator, and CaCl2 allows for formation of a stable clot. The time required for the formation of a stable clot is recorded in seconds and represents the actual APTT result.

  2. Laparoscopic partial adrenalectomy.

    PubMed

    Ikeda, Y; Takami, H; Tajima, G; Sasaki, Y; Takayama, J; Kurihara, H; Niimi, M

    2002-01-01

    Since corticosteroids are indispensable hormones, partial or cortical-sparing adrenalectomies may be adopted for the surgical treatment of adrenal diseases. In this article, we describe the technique and results of these procedures. Laparoscopic partial or cortical-sparing adrenalectomy has been performed in 10 patients. Seven cases had an aldosterone-producing adenoma (APA) and three had a pheochromocytoma. Three cases with an APA and a case with a pheochromocytoma had tumors located far from the adrenal central vein, and the vein could be preserved. Four cases with an APA and two with a pheochromocytoma had tumors located close to the adrenal central vein, and it was necessary to section the central vein to resect them. All endoscopic procedures were performed successfully. There were no postoperative complications. At follow-up, adrenal 131I-adosterol scintigrams showed the preservation of remnant adrenal function in all patients. Laparoscopic partial or cortical-sparing adrenal surgery was safely performed, and adrenal function was preserved irrespective of whether the adrenal central vein could be preserved or not. We consider this to be a useful operative technique for selected cases.

  3. Partial Androgen Insensitivity Syndrome Presenting with Gynecomastia.

    PubMed

    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; Ahn, You Hern

    2015-06-01

    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.

  4. Partial Southwest Elevation Mill #5 West (Part 3), Partial ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Partial Southwest Elevation - Mill #5 West (Part 3), Partial Southwest Elevation - Mill #5 West (with Section of Courtyard) (Parts 1 & 2) - Boott Cotton Mills, John Street at Merrimack River, Lowell, Middlesex County, MA

  5. Paternalism and partial autonomy.

    PubMed Central

    O'Neill, O

    1984-01-01

    A contrast is often drawn between standard adult capacities for autonomy, which allow informed consent to be given or withheld, and patients' reduced capacities, which demand paternalistic treatment. But patients may not be radically different from the rest of us, in that all human capacities for autonomous action are limited. An adequate account of paternalism and the role that consent and respect for persons can play in medical and other practice has to be developed within an ethical theory that does not impose an idealised picture of unlimited autonomy but allows for the variable and partial character of actual human autonomy. PMID:6520849

  6. 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…

  7. GDH Integral on the Proton from Asymmetries

    SciTech Connect

    Prok, Yelena

    2004-05-01

    Inclusive double spin electron asymmetries have been measured by scattering polarized electrons off the solid polarized 15NH3 target in Hall B of Jefferson Lab in 2000-2001. The virtual photon asymmetry A1 (x), the longitudinal spin structure function, g1 (x, Q2), and the first moment, γ1p, have been evaluated for a kinematic range of 0.05 ≥ Q2 ≥ 4.5 GeV2. The extracted results complement the existing data in the resonance region, extending it to lower and higher Q2 regions. The results are important in the study of Q2 evolution of nucleon structure from the hadronic to partonic degrees of freedom.

  8. Is Titan Partially Differentiated?

    NASA Astrophysics Data System (ADS)

    Mitri, G.; Pappalardo, R. T.; Stevenson, D. J.

    2009-12-01

    The recent measurement of the gravity coefficients from the Radio Doppler data of the Cassini spacecraft has improved our knowledge of the interior structure of Titan (Rappaport et al. 2008 AGU, P21A-1343). The measured gravity field of Titan is dominated by near hydrostatic quadrupole components. We have used the measured gravitational coefficients, thermal models and the hydrostatic equilibrium theory to derive Titan's interior structure. The axial moment of inertia gives us an indication of the degree of the interior differentiation. The inferred axial moment of inertia, calculated using the quadrupole gravitational coefficients and the Radau-Darwin approximation, indicates that Titan is partially differentiated. If Titan is partially differentiated then the interior must avoid melting of the ice during its evolution. This suggests a relatively late formation of Titan to avoid the presence of short-lived radioisotopes (Al-26). This also suggests the onset of convection after accretion to efficiently remove the heat from the interior. The outer layer is likely composed mainly of water in solid phase. Thermal modeling indicates that water could be present also in liquid phase forming a subsurface ocean between an outer ice I shell and a high pressure ice layer. Acknowledgments: This work was conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration.

  9. Furnace brazing under partial vacuum

    NASA Technical Reports Server (NTRS)

    Mckown, R. D.

    1979-01-01

    Brazing furnace utilizing partial-vacuum technique reduces tooling requirements and produces better bond. Benefit in that partial vacuum helps to dissociate metal oxides that inhibit metal flow and eliminates heavy tooling required to hold parts together during brazing.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Robot-assisted partial nephrectomy: Superiority over laparoscopic partial nephrectomy.

    PubMed

    Shiroki, Ryoichi; Fukami, Naohiko; Fukaya, Kosuke; Kusaka, Mamoru; Natsume, Takahiro; Ichihara, Takashi; Toyama, Hiroshi

    2016-02-01

    Nephron-sparing surgery has been proven to positively impact the postoperative quality of life for the treatment of small renal tumors, possibly leading to functional improvements. Laparoscopic partial nephrectomy is still one of the most demanding procedures in urological surgery. Laparoscopic partial nephrectomy sometimes results in extended warm ischemic time and severe complications, such as open conversion, postoperative hemorrhage and urine leakage. Robot-assisted partial nephrectomy exploits the advantages offered by the da Vinci Surgical System to laparoscopic partial nephrectomy, equipped with 3-D vision and a better degree in the freedom of surgical instruments. The introduction of the da Vinci Surgical System made nephron-sparing surgery, specifically robot-assisted partial nephrectomy, safe with promising results, leading to the shortening of warm ischemic time and a reduction in perioperative complications. Even for complex and challenging tumors, robotic assistance is expected to provide the benefit of minimally-invasive surgery with safe and satisfactory renal function. Warm ischemic time is the modifiable factor during robot-assisted partial nephrectomy to affect postoperative kidney function. We analyzed the predictive factors for extended warm ischemic time from our robot-assisted partial nephrectomy series. The surface area of the tumor attached to the kidney parenchyma was shown to significantly affect the extended warm ischemic time during robot-assisted partial nephrectomy. In cases with tumor-attached surface area more than 15 cm(2) , we should consider switching robot-assisted partial nephrectomy to open partial nephrectomy under cold ischemia if it is imperative. In Japan, a nationwide prospective study has been carried out to show the superiority of robot-assisted partial nephrectomy to laparoscopic partial nephrectomy in improving warm ischemic time and complications. By facilitating robotic technology, robot-assisted partial nephrectomy

  15. 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

  16. Removable partial denture occlusion.

    PubMed

    Ivanhoe, John R; Plummer, Kevin D

    2004-07-01

    No single occlusal morphology, scheme, or material will successfully treat all patients. Many patients have been treated, both successfully and unsuccessfully, using widely varying theories of occlusion, choices of posterior tooth form, and restorative materials. Therefore, experience has demonstrated that there is no one righ r way to restore the occlusion of all patients. Partially edentulous patients have many and varied needs. Clinicians must understand the healthy physiologic gnathostomatic system and properly diagnose what is or may become pathologic. Henderson [3] stated that the occlusion of the successfully treated patient allows the masticating mechanism to carry out its physiologic functions while the temporomandibular joints, the neuromuscular mechanism, the teeth and their supporting structures remain in a good state of health. Skills in diagnosis and treatment planning are of utmost importance in treating these patients, for whom the clinician's goals are not only an esthetic and functional restoration but also a lasting harmonious state. Perhaps this was best state by DeVan [55] more than 60 years ago in his often-quoted objective. "The patient's fundamental need is the continued meticulous restoration of what is missing, since what is lost is in a sense irretrievably lost." Because it is clear that there is no one method, no one occlusal scheme, or one material that guarantees success for all patients, recommendations for consideration when establishing or reestablishing occlusal schemes have been presented. These recommendations must be used in conjunction with other diagnostic and technical skills.

  17. Partially solidified systems

    NASA Astrophysics Data System (ADS)

    The evolution of magmas is a topic of considerable importance in geology and geophysics because it affects volcanology, igneous petrology, geothermal energy sources, mantle convection, and the thermaland chemical evolution of the earth. The dynamics and evolution of magmas are strongly affected by the presence of solid crystals that occur either in suspension in liquid or as a rigid porous matrix through which liquid magma can percolate. Such systems are physically complex and difficult to model mathematically. Similar physical situations are encountered by metallurgists who study the solidification of molten alloys, and applied mathematicians have long been interested in such moving boundary problems. Clearly, it would be of mutual benefit to bring together scientists, engineers, and mathematicians with a common interest in such systems. Such a meeting is being organized as a North Atlantic Treaty Organization (NATO) Advanced Research Workshop on the Structure and Dynamics of Partially Solidified Systems, to be held at Stanford University's Fallen Leaf Lodge at Tahoe, Calif., May 12-16, 1986 The invited speakers and their topics are

  18. Partial disassembly of peroxisomes

    PubMed Central

    1985-01-01

    Rat liver peroxisomes were subjected to a variety of procedures intended to partially disassemble or damage them; the effects were analyzed by recentrifugation into sucrose gradients, enzyme analyses, electron microscopy, and SDS PAGE. Freezing and thawing or mild sonication released some matrix proteins and produced apparently intact peroxisomal "ghosts" with crystalloid cores and some fuzzy fibrillar content. Vigorous sonication broke open the peroxisomes but the membranes remained associated with cores and fibrillar and amorphous matrix material. The density of both ghosts and more severely damaged peroxisomes was approximately 1.23. Pyrophosphate (pH 9) treatment solubilized the fibrillar content, yielding ghosts that were empty except for cores. Some matrix proteins such as catalase and thiolase readily leak from peroxisomes. Other proteins were identified that remain in mechanically damaged peroxisomes but are neither core nor membrane proteins because they can be released by pyrophosphate treatment. These constitute a class of poorly soluble matrix proteins that appear to correspond to the fibrillar material observed morphologically. All of the peroxisomal beta-oxidation enzymes are located in the matrix, but they vary greatly in how easily they leak out. Palmitoyl coenzyme A synthetase is in the membrane, based on its co-distribution with the 22-kilodalton integral membrane polypeptide. PMID:2989301

  19. Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes.

    PubMed Central

    Eardly, B D; Young, J P; Selander, R K

    1992-01-01

    Phenotypic and DNA sequence comparisons are presented for eight Rhizobium isolates that were cultured from field-grown alfalfa (Medicago sativa L.) in Oregon. These isolates were previously shown to nodulate both alfalfa and common bean (Phaseolus vulgaris (L.) Savi.). The objective of the present study was to determine their phylogenetic relationships to the normal symbionts of these plants, Rhizobium meliloti and Rhizobium leguminosarum biovar phaseoli, respectively. Phenotypically, the Oregon isolates more nearly resemble strains from P. vulgaris than those from M. sativa. For example, even though nitrogen fixation levels were low with both host species, the symbiotic efficiency of a representative Rhizobium isolate (Or 191) with common bean was twice that observed with alfalfa. Comparative sequencing of a 260-bp segment of the 16S rRNA gene (directly sequenced after amplification by the polymerase chain reaction) demonstrated that Or 191 is not closely related to the type strain of R. meliloti (ATCC 9930), R. leguminosarum (ATCC 10004), or Rhizobium tropici (CIAT 899). Instead, sequence comparisons of the 16S gene indicated that Or 191 belongs to a distinct and previously unrecognized taxonomic group that includes strains that have previously been called R. leguminosarum bv. phaseoli type I. Unlike type I strains, however, Or 191 has only a single copy of the nifH gene (type I strains have three), and the nucleotide sequence of this gene is substantially different from those of other rhizobial and nonrhizobial nifH genes examined thus far. Images PMID:1377901

  20. 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.

  1. 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

  2. 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.

  3. [Lymphocyte metabolism in patients with acute pancreatitis with different genotypes of GSTM1 and GSTT1 genes].

    PubMed

    Markova, E V; Zotova, N V; Savchenko, A A; Titova, N M; Slepov, E V; Cherdantsev, D V; Konovalenko, A N

    2006-01-01

    In this study, we have investigated correlation between enzymatic activity of NAD(P)-dependent dehydrogenases of lymphocytes and polymorphic variants of glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) genes in the group of unrelated patients with acute pancreatitis in comparison with healthy Russians from Krasnoyarsk. Thus, genotype GSTM1 0/0 is the marker of predisposition to the acute pancreatitis, wheras polymorphism of the GSTT1 gene is not involved in the development of the pancreatitis, at least in our group. The bioluminescence analysis showed statistically significant decrease of the levels of G3PD, NAD(+)MDH and the increase of NADH(+)LDH, NAD(+)GDH, NADH(+)GDH in lymphocytes of pancreatic group. Development of pancreatitis in patients with different genotypes GSTM1 and GSTT1 genes showed the rearrangement of the basic intracellular processes: dominance of a plastic metabolism in the patients with GSTM1--deletions and predominance of energetic processes at GSTT1 0 - pancreatitis.

  4. 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.

  5. NAD(H)-dependent glutamate dehydrogenase is essential for the survival of Arabidopsis thaliana during dark-induced carbon starvation.

    PubMed

    Miyashita, Yo; Good, Allen G

    2008-01-01

    Interconversion between glutamate and 2-oxoglutarate, which can be catalysed by glutamate dehydrogenase (GDH), is a key reaction in plant carbon (C) and nitrogen (N) metabolism. However, the physiological role of plant GDH has been a controversial issue for several decades. To elucidate the function of GDH, the expression of GDH in various tissues of Arabidopsis thaliana was studied. Results suggested that the expression of two Arabidopsis GDH genes was differently regulated depending on the organ/tissue types and cellular C availability. Moreover, Arabidopsis mutants defective in GDH genes were identified and characterized. The two isolated mutants, gdh1-2 and gdh2-1, were crossed to make a double knockout mutant, gdh1-2/gdh2-1, which contained negligible levels of NAD(H)-dependent GDH activity. Phenotypic analysis on these mutants revealed an increased susceptibility of gdh1-2/gdh2-1 plants to C-deficient conditions. This conditional phenotype of the double knockout mutant supports the catabolic role of GDH and its role in fuelling the TCA cycle during C starvation. The reduced rate of glutamate catabolism in the gdh2-1 and gdh1-2/gdh2-1 plants was also evident by the growth retardation of these mutants when glutamate was supplied as the alternative N source. Furthermore, amino acid profiles during prolonged dark conditions were significantly different between WT and the gdh mutant plants. For instance, glutamate levels increased in WT plants but decreased in gdh1-2/gdh2-1 plants, and aberrant accumulation of several amino acids was detected in the gdh1-2/gdh2-1 plants. These results suggest that GDH plays a central role in amino acid breakdown under C-deficient conditions.

  6. Gene therapy for retinitis pigmentosa and Leber congenital amaurosis caused by defects in AIPL1: effective rescue of mouse models of partial and complete Aipl1 deficiency using AAV2/2 and AAV2/8 vectors

    PubMed Central

    Tan, Mei Hong; Smith, Alexander J.; Pawlyk, Basil; Xu, Xiaoyun; Liu, Xiaoqing; Bainbridge, James B.; Basche, Mark; McIntosh, Jenny; Tran, Hoai Viet; Nathwani, Amit; Li, Tiansen; Ali, Robin R.

    2009-01-01

    Defects in the photoreceptor-specific gene encoding aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) are clinically heterogeneous and present as Leber Congenital Amaurosis, the severest form of early-onset retinal dystrophy and milder forms of retinal dystrophies such as juvenile retinitis pigmentosa and dominant cone-rod dystrophy. [Perrault, I., Rozet, J.M., Gerber, S., Ghazi, I., Leowski, C., Ducroq, D., Souied, E., Dufier, J.L., Munnich, A. and Kaplan, J. (1999) Leber congenital amaurosis. Mol. Genet. Metab., 68, 200–208.] Although not yet fully elucidated, AIPL1 is likely to function as a specialized chaperone for rod phosphodiesterase (PDE). We evaluate whether AAV-mediated gene replacement therapy is able to improve photoreceptor function and survival in retinal degeneration associated with AIPL1 defects. We used two mouse models of AIPL1 deficiency simulating three different rates of photoreceptor degeneration. The Aipl1 hypomorphic (h/h) mouse has reduced Aipl1 levels and a relatively slow degeneration. Under light acceleration, the rate of degeneration in the Aipl1 h/h mouse is increased by 2–3-fold. The Aipl1−/− mouse has no functional Aipl1 and has a very rapid retinal degeneration. To treat the different rates of degeneration, two pseudotypes of recombinant adeno-associated virus (AAV) exhibiting different transduction kinetics are used for gene transfer. We demonstrate restoration of cellular function and preservation of photoreceptor cells and retinal function in Aipl1 h/h mice following gene replacement therapy using an AAV2/2 vector and in the light accelerated Aipl1 h/h model and Aipl1−/− mice using an AAV2/8 vector. We have thus established the potential of gene replacement therapy in varying rates of degeneration that reflect the clinical spectrum of disease. This is the first gene replacement study to report long-term rescue of a photoreceptor-specific defect and to demonstrate effective rescue of a rapid photoreceptor

  7. Partial reversion at the bobbed locus of Drosophila melanogaster.

    PubMed

    Terracol, R; Iturbide, Y; Prud'Homme, N

    1990-01-01

    In Drosophila melanogaster the tandemly arranged repetitive sequences coding for 18S and 28S rRNA are heterogenous at the level of the spacers between units and insertions that interrupt many 28S rRNA genes. This heterogeneity contrasts with the homogeneity of the regions transcribed into 18S and 28S rRNA. Homogenization and evolution of repetitive genes are usually explained by conversion, amplification events or unequal crossovers. In this paper we studied the change in rDNA patterns associated with partial reversion of bobbed mutations. In most cases, no increase in rDNA gene number, but a new repartition of gene types were found.

  8. Age-related changes in the gene expression profile of antigen-specific mouse CD8+ T cells can be partially reversed by blockade of the BTLA/CD160 pathways during vaccination

    PubMed Central

    Dawany, Noor; Parzych, Elizabeth M; Showe, Louise C; Ertl, Hildegund CJ

    2016-01-01

    We analyzed gene expression profiles of young and aged mouse CD8+ T cells specific for the nucleoprotein (NP) of influenza A/PR8/34 virus. CD8+ T cells were stimulated either by the NP antigen expressed in its native form or fused into the herpes virus (HSV)-1 glycoprotein D (gD) protein, which blocks signaling through the immunoinhibitory B and T lymphocyte attenuator (BTLA) and CD160 pathways. We show that NP-specific CD8+ T cells from aged mice exhibit numerous differences in gene expression compared to NP-specific CD8+ T cells from young mice, including a significant reduction of expression in genes involved in T cell receptor (TcR) and CD28 signaling. We also show that these changes can be reversed in a sub-population (∼50%) of the aged mice by a BTLA/CD160 checkpoint blockade. These results suggest that BTLA/CD160 checkpoint blockade has potential value as a vaccine additive to induce better CD8+ T cell responses in the aged. PMID:27922818

  9. Organization and partial sequence of a DNA region of the Rhizobium leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC, nifA, nifB and a novel open reading frame.

    PubMed Central

    Grönger, P; Manian, S S; Reiländer, H; O'Connell, M; Priefer, U B; Pühler, A

    1987-01-01

    By hybridization and heteroduplex studies the fixABC and nifA genes of the Rhizobium leguminosarum symbiotic plasmid pRL6JI have been identified. DNA sequencing of the region containing nifA showed an open reading frame of 1557 bp encoding a protein of 56, 178 D. Based on sequence homology, this ORF was confirmed to correspond to the nifA gene. Comparison of three nifA proteins (Klebsiella pneumoniae, Rhizobium meliloti, Rhizobium leguminosarum) revealed only a weak relationship in their N-terminal regions, whereas the C-terminal parts exhibited strong homology. Sequence analysis also showed that the R. leguminosarum nifA gene is followed by nifB and preceded by fixC with an open reading frame inserted in between. This novel ORF of 294 bp was found to be highly conserved also in R. meliloti. No known promoter and termination signals could be defined on the sequenced R. leguminosarum fragment. Images PMID:3029674

  10. 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

  11. Experimental generating the partially coherent and partially polarized electromagnetic source.

    PubMed

    Ostrovsky, Andrey S; Rodríguez-Zurita, Gustavo; Meneses-Fabián, Cruz; Olvera-Santamaría, Miguel A; Rickenstorff-Parrao, Carolina

    2010-06-07

    The technique for generating the partially coherent and partially polarized source starting from the completely coherent and completely polarized laser source is proposed and analyzed. This technique differs from the known ones by the simplicity of its physical realization. The efficiency of the proposed technique is illustrated with the results of physical experiment in which an original technique for characterizing the coherence and polarization properties of the generated source is employed.

  12. Partial-Payload Support Structure

    NASA Technical Reports Server (NTRS)

    Mitchell, R.; Freeman, M.

    1984-01-01

    Partial-payload support structure (PPSS) is modular, bridge like structure supporting experiments weighing up to 2 tons. PPSS handles such experiments more economically than standard Spacelab pallet system.

  13. Partial arthrodeses of the wrist.

    PubMed

    Marcuzzi, A; Cristiani, G; Castagnini, L; Castagnetti, C; Caroli, A

    1995-01-01

    The authors report 16 cases of partial arthrodeses of the wrist for the treatment of Kienboeck's disease, pseudarthrosis of the scaphoid, rotatory subluxation of the scaphoid, rheumatoid arthritis, etc. Based on the good results obtained (76.6%) the authors believe that partial arthrodeses constitute the type of treatment indicated for the treatment of pathologies that involve only some of the carpal bones, and they also emphasize that this type of surgery represents a valid alternative to total arthrodesis of the wrist.

  14. Analysis of yeast isolates related to Metschnikowia pulcherrima using the partial sequences of the large subunit rDNA and the actin gene; description of Metschnikowia andauensis sp. nov.

    PubMed

    Molnár, Orsolya; Prillinger, Hansjörg

    2005-10-01

    Thirty-two yeast isolates were cultured from guts or excrements of three different pests of corn or from the stem of healthy corn. The strains were analyzed using MSP-PCR (micro/minisatellite-primed polymerase chain reaction), sequences of the D1/D2 region of the large subunit rDNA and a 979 bp long part of the actin gene (act-1). They seem to belong to three groups that are all sister groups of Metschnikowia pulcherrima, M. fructicola and M. chrysoperlae. A new species, Metschnikowia andauensis (HA 1657T) is described. In contrast to M. pulcherrima and M. fructicola, M. andauensis is well separated in the act-1 phylogenetic tree too.

  15. Partial Correlation Estimation by Joint Sparse Regression Models

    PubMed Central

    Peng, Jie; Wang, Pei; Zhou, Nengfeng; Zhu, Ji

    2009-01-01

    In this paper, we propose a computationally efficient approach —space(Sparse PArtial Correlation Estimation)— for selecting non-zero partial correlations under the high-dimension-low-sample-size setting. This method assumes the overall sparsity of the partial correlation matrix and employs sparse regression techniques for model fitting. We illustrate the performance of space by extensive simulation studies. It is shown that space performs well in both non-zero partial correlation selection and the identification of hub variables, and also outperforms two existing methods. We then apply space to a microarray breast cancer data set and identify a set of hub genes which may provide important insights on genetic regulatory networks. Finally, we prove that, under a set of suitable assumptions, the proposed procedure is asymptotically consistent in terms of model selection and parameter estimation. PMID:19881892

  16. Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies

    PubMed Central

    2014-01-01

    Background The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations. Results Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly

  17. 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.

  18. 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.

  19. Partial synchronization and partial amplitude death in mesoscale network motifs.

    PubMed

    Poel, Winnie; Zakharova, Anna; Schöll, Eckehard

    2015-02-01

    We study the interplay between network topology and complex space-time patterns and introduce a concept to analytically predict complex patterns in networks of Stuart-Landau oscillators with linear symmetric and instantaneous coupling based solely on the network topology. These patterns consist of partial amplitude death and partial synchronization and are found to exist in large variety for all undirected networks of up to 5 nodes. The underlying concept is proved to be robust with respect to frequency mismatch and can also be extended to larger networks. In addition it directly links the stability of complete in-phase synchronization to only a small subset of topological eigenvalues of a network.

  20. Detection of Cryptosporidium species in feces or gastric contents from snakes and lizards as determined by polymerase chain reaction analysis and partial sequencing of the 18S ribosomal RNA gene.

    PubMed

    Richter, Barbara; Nedorost, Nora; Maderner, Anton; Weissenböck, Herbert

    2011-05-01

    Cryptosporidiosis is a well-known gastrointestinal disease of snakes and lizards. In the current study, 672 samples (feces and/or gastric contents or regurgitated food items) of various snakes and lizards were examined for the presence of cryptosporidia by polymerase chain reaction (PCR) assay targeting a part of the 18S ribosomal RNA gene. A consecutive sequencing reaction was used to identify the cryptosporidian species present in PCR-positive samples. Cryptosporidium varanii (saurophilum) was detected in 17 out of 106 (16%) samples from corn snakes (Pantherophis guttatus) and in 32 out of 462 (7%) samples from leopard geckos (Eublepharis macularius). Cryptosporidium serpentis was found in 8 out of 462 (2%) leopard gecko samples, but in no other reptile. The Cryptosporidium sp. "lizard genotype" was present in 1 leopard gecko sample, and 1 sample from a corn snake showed a single nucleotide mismatch to this genotype. Pseudoparasitic cryptosporidian species were identified in 5 out of 174 (3%) ophidian samples, but not in lizards. Other sequences did not show complete similarity to previously published Cryptosporidium sequences. The results stress the importance for diagnostic methods to be specific for Cryptosporidium species especially in snakes and show a relatively high prevalence of C. varanii in leopard geckos and corn snakes.

  1. 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.

  2. 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

  3. Designing successful removable partial dentures.

    PubMed

    Daher, Tony; Hall, Dan; Goodacre, Charles J

    2006-03-01

    In today's busy dental offices, removable partial denture design is often abdicated by dentists, both as a result of a lack of experience and consensus of design and because of educational failure on the part of dental schools. The result is delegation of the clinical design process to the lab technician. The lack of clinical data provided to the dental technician jeopardizes the quality of care. This article will focus on a logical and simple approach to this problem, making removable partial denture design simple and predictably achievable. The clinical evidence related to removable partial denture design will be described, along with a checklist to simplify the process and make it practical and applicable to everyday clinical practice.

  4. 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

  5. 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.

  6. Partially coherent vectorial nonparaxial beams.

    PubMed

    Duan, Kailiang; Lü, Baida

    2004-10-01

    Generalized vectorial Rayleigh-Sommerfeld diffraction integrals are developed for the cross-spectral-density matrices of spatially partially coherent beams. Using the Gaussian Schell-model (GSM) beam as an example, we derive the expressions for the propagation of cross-spectral-density matrices and intensity of partially coherent vectorial nonparaxial beams, and the corresponding far-field asymptotic forms, beyond the paraxial approximation. The propagation of the vectorial nonparaxial GSM beams are evaluated and analyzed. It is shown that a 3 x 3 cross-spectral-density matrix or a vector theory is required for the exact description of nonparaxial GSM beams.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Covert Reinforcement: A Partial Replication.

    ERIC Educational Resources Information Center

    Ripstra, Constance C.; And Others

    A partial replication of an investigation of the effect of covert reinforcement on a perceptual estimation task is described. The study was extended to include an extinction phase. There were five treatment groups: covert reinforcement, neutral scene reinforcement, noncontingent covert reinforcement, and two control groups. Each subject estimated…

  12. 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…

  13. Partial polarization by quantum distinguishability

    NASA Astrophysics Data System (ADS)

    Lahiri, Mayukh; Hochrainer, Armin; Lapkiewicz, Radek; Lemos, Gabriela Barreto; Zeilinger, Anton

    2017-03-01

    We establish that a connection exists between wave-particle duality of photons and partial polarization of a light beam. We perform a two-path lowest-order (single photon) interference experiment and demonstrate both theoretically and experimentally that the degree of polarization of the light beam emerging from an output of the interferometer depends on path distinguishability. In our experiment, we are able to change the quantum state of the emerging photon from a pure state to a fully mixed state without any direct interaction with the photon. Although most lowest-order interference experiments can be explained by classical theory, our experiment has no genuine classical analog. Our results show that a case exists where the cause of partial polarization is beyond the scope of classical theory.

  14. 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

  15. Wettability of partially suspended graphene

    DOE PAGES

    Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; ...

    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

  16. Wettability of partially suspended graphene

    SciTech Connect

    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-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.

  17. Matching games with partial information

    NASA Astrophysics Data System (ADS)

    Laureti, Paolo; Zhang, Yi-Cheng

    2003-06-01

    We analyze different ways of pairing agents in a bipartite matching problem, with regard to its scaling properties and to the distribution of individual “satisfactions”. Then we explore the role of partial information and bounded rationality in a generalized Marriage Problem, comparing the benefits obtained by self-searching and by a matchmaker. Finally we propose a modified matching game intended to mimic the way consumers’ information makes firms to enhance the quality of their products in a competitive market.

  18. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K. ); Warnow, T.J. )

    1993-01-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n[sup 3]) time and from POM experiments in O(n[sup 4]) time.

  19. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K.; Warnow, T.J.

    1993-03-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n{sup 3}) time and from POM experiments in O(n{sup 4}) time.

  20. Microflora of partially processed lettuce.

    PubMed

    Magnuson, J A; King, A D; Török, T

    1990-12-01

    Bacteria, yeasts, and molds isolated from partially processed iceberg lettuce were taxonomically classified. The majority of bacterial isolates were gram-negative rods. Pseudomonas, Erwinia, and Serratia species were commonly found. Yeasts most frequently isolated from lettuce included members of the genera Candida, Cryptococcus, Pichia, Torulaspora, and Trichosporon. Comparatively few molds were isolated; members of the genera Rhizopus, Cladosporium, Phoma, Aspergillus, and Penicillium were identified.

  1. 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

    2016-05-02

    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.

  2. 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 ...

  3. Partial androgen insensitivity syndrome with thermolability in the androgen receptor.

    PubMed

    Hiraoka, Kenji; Kawauchi, Akihiro; Soh, Jintetsu; Ohe, Hiroshi; Shima, Hiroki; Miki, Tsuneharu

    2006-01-01

    We report case of partial androgen insensitivity syndrome in a 12-year-old boy referred to our clinic complaining of bilateral gynecomastia and left undescended testicle. Laparoscopy for undescended testicle and bilateral mastectomy were performed, and the left testicle was absent. When skin fibroblasts of the scrotum obtained during surgery were cultured to analyse the androgen receptors, a slight thermolability was observed. Genomic examination of the androgen receptor gene could not detect any mutations.

  4. Laparoscopic radical and partial cystectomy

    PubMed Central

    Challacombe, Ben J.; Rose, Kristen; Dasgupta, Prokar

    2005-01-01

    Radical cystectomy remains the standard treatment for muscle invasive organ confined bladder carcinoma. Laparoscopic radical cystoprostatectomy (LRC) is an advanced laparoscopic procedure that places significant demands on the patient and the surgeon alike. It is a prolonged procedure which includes several technical steps and requires highly developed laparoscopic skills including intra-corporeal suturing. Here we review the development of the technique, the indications, complications and outcomes. We also examine the potential benefits of robotic-assisted LRC and explore the indications and technique of laparoscopic partial cystectomy. PMID:21206662

  5. 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.

  6. Sparse partial least squares regression for simultaneous dimension reduction and variable selection.

    PubMed

    Chun, Hyonho; Keleş, Sündüz

    2010-01-01

    Partial least squares regression has been an alternative to ordinary least squares for handling multicollinearity in several areas of scientific research since the 1960s. It has recently gained much attention in the analysis of high dimensional genomic data. We show that known asymptotic consistency of the partial least squares estimator for a univariate response does not hold with the very large p and small n paradigm. We derive a similar result for a multivariate response regression with partial least squares. We then propose a sparse partial least squares formulation which aims simultaneously to achieve good predictive performance and variable selection by producing sparse linear combinations of the original predictors. We provide an efficient implementation of sparse partial least squares regression and compare it with well-known variable selection and dimension reduction approaches via simulation experiments. We illustrate the practical utility of sparse partial least squares regression in a joint analysis of gene expression and genomewide binding data.

  7. Performance of partial statistics in individual-based landscape genetics.

    PubMed

    Kierepka, E M; Latch, E K

    2015-05-01

    Individual-based landscape genetic methods have become increasingly popular for quantifying fine-scale landscape influences on gene flow. One complication for individual-based methods is that gene flow and landscape variables are often correlated with geography. Partial statistics, particularly Mantel tests, are often employed to control for these inherent correlations by removing the effects of geography while simultaneously correlating measures of genetic differentiation and landscape variables of interest. Concerns about the reliability of Mantel tests prompted this study, in which we use simulated landscapes to evaluate the performance of partial Mantel tests and two ordination methods, distance-based redundancy analysis (dbRDA) and redundancy analysis (RDA), for detecting isolation by distance (IBD) and isolation by landscape resistance (IBR). Specifically, we described the effects of suitable habitat amount, fragmentation and resistance strength on metrics of accuracy (frequency of correct results, type I/II errors and strength of IBR according to underlying landscape and resistance strength) for each test using realistic individual-based gene flow simulations. Mantel tests were very effective for detecting IBD, but exhibited higher error rates when detecting IBR. Ordination methods were overall more accurate in detecting IBR, but had high type I errors compared to partial Mantel tests. Thus, no one test outperformed another completely. A combination of statistical tests, for example partial Mantel tests to detect IBD paired with appropriate ordination techniques for IBR detection, provides the best characterization of fine-scale landscape genetic structure. Realistic simulations of empirical data sets will further increase power to distinguish among putative mechanisms of differentiation.

  8. 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.

  9. Modeling Partial Attacks with Alloy

    NASA Astrophysics Data System (ADS)

    Lin, Amerson; Bond, Mike; Clulow, Jolyon

    The automated and formal analysis of cryptographic primitives, security protocols and Application Programming Interfaces (APIs) up to date has been focused on discovering attacks that completely break the security of a system. However, there are attacks that do not immediately break a system but weaken the security sufficiently for the adversary. We term these attacks partial attacks and present the first methodology for the modeling and automated analysis of this genre of attacks by describing two approaches. The first approach reasons about entropy and was used to simulate and verify an attack on the ECB|ECB|OFB triple-mode DES block-cipher. The second approach reasons about possibility sets and was used to simulate and verify an attack on the personal identification number (PIN) derivation algorithm used in the IBM 4758 Common Cryptographic Architecture.

  10. Partial Dynamical Symmetry in Molecules

    NASA Astrophysics Data System (ADS)

    Ping, Jia-Lun; Chen, Jin-Quan

    1997-03-01

    It is shown that any Hamiltonian involving only one- and two-bond interactions for a molecule withnbonds and having a point groupPas its symmetry group may have theSn⊃Ppartial dynamical symmetry, i.e., the Hamiltonian can be solved analytically for a part of the states, called the unique states. For example, theXY6molecule has theS6⊃Ohpartial dynamical symmetry. The model of Iachello and Oss forncoupled anharmonic oscillators is revisited in terms of the partial dynamical symmetry. The energies are obtained analytically for the nine unique levels of theXY6molecule and the structures of the eigenstates are disclosed for the first time, while for non-unique states they are obtained by diagonalizing the Hamiltonian in theS6⊃Ohsymmetry adapted basis with greatly reduced dimension.

  11. Partial masslessness and conformal gravity

    NASA Astrophysics Data System (ADS)

    Deser, S.; Joung, E.; Waldron, A.

    2013-05-01

    We use conformal, but ghostful, Weyl gravity to study its ghost-free, second derivative, partially massless (PM) spin-2 component in the presence of Einstein gravity with positive cosmological constant. Specifically, we consider both gravitational- and self-interactions of PM via the fully nonlinear factorization of conformal gravity’s Bach tensor into Einstein times Schouten operators. We find that extending PM beyond linear order suffers from familiar higher spin consistency obstructions: it propagates only in Einstein backgrounds, and the conformal gravity route generates only the usual safe, Noether, cubic order vertices. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Higher spin theories and holography’.

  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. Partial Synchronization of Interconnected Boolean Networks.

    PubMed

    Chen, Hongwei; Liang, Jinling; Lu, Jianquan

    2017-01-01

    This paper addresses the partial synchronization problem for the interconnected Boolean networks (BNs) via the semi-tensor product (STP) of matrices. First, based on an algebraic state space representation of BNs, a necessary and sufficient criterion is presented to ensure the partial synchronization of the interconnected BNs. Second, by defining an induced digraph of the partial synchronized states set, an equivalent graphical description for the partial synchronization of the interconnected BNs is established. Consequently, the second partial synchronization criterion is derived in terms of adjacency matrix of the induced digraph. Finally, two examples (including an epigenetic model) are provided to illustrate the efficiency of the obtained results.

  14. 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...

  15. 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...

  16. 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

  17. 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

    ... AGENCY 40 CFR Part 52 Partial Approval and Partial Disapproval of Air Quality Implementation Plans for... partially disapprove revisions to the State Implementation Plans (SIPs) for Florida, Mississippi, and South... address the 2006 PM 2.5 NAAQS or any requirements related to that NAAQS. Today's partial disapproval...

  18. 76 FR 4601 - Determinations Concerning Need for Error Correction, Partial Approval and Partial Disapproval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

    ... AGENCY 40 CFR Part 52 RIN 2060-AQ66 Determinations Concerning Need for Error Correction, Partial Approval and Partial Disapproval, and Federal Implementation Plan Regarding Texas Prevention of Significant... Determination Concerning the Need for Error Correction, Partial Approval and Partial Disapproval, and...

  19. Partial fasciectomy for Dupuytren's contractures.

    PubMed

    Mavrogenis, Andreas F; Spyridonos, Sarantis G; Ignatiadis, Ioannis A; Antonopoulos, Dimitrios; Papagelopoulos, Panayiotis J

    2009-01-01

    One hundred ninety-six patients with Dupuytren's contractures were treated by partial fasciectomy and adequate postoperative rehabilitation. All patients had flexion contracture of the proximal interphalangeal joint of >20 degrees ; 93 patients had flexion contracture of the associated metacarpophalangeal joint of >30 degrees ; 143 patients had risk factors for Dupuytren's disease. Primary skin closure and splinting were done in all patients. Range of motion was begun by the 1st week. Splinting was discontinued by the 2nd week, followed by night-time splinting until the 8th week. The mean follow-up was 6.6 years (range, 2-9 years). At the latest examination, 72.5% of the patients had complete range of motion of the metacarpophalangeal and proximal interphalangeal joints; 20.2% had 5 degrees -10 degrees of extension deficit and 7.3% had recurrent contractures of >20 degrees at the proximal interphalangeal joint and were subjected to reoperation. Complications included digital neurovascular injury in 5%, complex regional pain syndrome in 10.1%, and wound-healing problems and superficial infections in 15.1%.

  20. 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.

  1. The future of partial nephrectomy.

    PubMed

    Malthouse, Theo; Kasivisvanathan, Veeru; Raison, Nicholas; Lam, Wayne; Challacombe, Ben

    2016-12-01

    Innovation in recent times has accelerated due to factors such as the globalization of communication; but there are also more barriers/safeguards in place than ever before as we strive to streamline this process. From the first planned partial nephrectomy completed in 1887, it took over a century to become recommended practice for small renal tumours. At present, identified areas for improvement/innovation are 1) to preserve renal parenchyma, 2) to optimise pre-operative eGFR and 3) to reduce global warm ischaemia time. All 3 of these, are statistically significant predictors of post-operative renal function. Urologists, have a proud history of embracing innovation & have experimented with different clamping techniques of the renal vasculature, image guidance in robotics, renal hypothermia, lasers and new robots under development. The DaVinci model may soon no longer have a monopoly on this market, as it loses its stranglehold with novel technology emerging including added features, such as haptic feedback with reduced costs. As ever, our predictions of the future may well fall wide of the mark, but in order to progress, one must open the mind to the possibilities that already exist, as evolution of existing technology often appears to be a revolution in hindsight.

  2. NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles.

    PubMed

    DeLuna, A; Avendano, A; Riego, L; Gonzalez, A

    2001-11-23

    In the yeast Saccharomyces cerevisiae, two NADP(+)-dependent glutamate dehydrogenases (NADP-GDHs) encoded by GDH1 and GDH3 catalyze the synthesis of glutamate from ammonium and alpha-ketoglutarate. The GDH2-encoded NAD(+)-dependent glutamate dehydrogenase degrades glutamate producing ammonium and alpha-ketoglutarate. Until very recently, it was considered that only one biosynthetic NADP-GDH was present in S. cerevisiae. This fact hindered understanding the physiological role of each isoenzyme and the mechanisms involved in alpha-ketoglutarate channeling for glutamate biosynthesis. In this study, we purified and characterized the GDH1- and GDH3-encoded NADP-GDHs; they showed different allosteric properties and rates of alpha-ketoglutarate utilization. Analysis of the relative levels of these proteins revealed that the expression of GDH1 and GDH3 is differentially regulated and depends on the nature of the carbon source. Moreover, the physiological study of mutants lacking or overexpressing GDH1 or GDH3 suggested that these genes play nonredundant physiological roles. Our results indicate that the coordinated regulation of GDH1-, GDH3-, and GDH2-encoded enzymes results in glutamate biosynthesis and balanced utilization of alpha-ketoglutarate under fermentative and respiratory conditions. The possible relevance of the duplicated NADP-GDH pathway in the adaptation to facultative metabolism is discussed.

  3. Predicting changes of reaction networks with partial kinetic information.

    PubMed

    Niehren, Joachim; Versari, Cristian; John, Mathias; Coutte, François; Jacques, Philippe

    2016-11-01

    We wish to predict changes of reaction networks with partial kinetic information that lead to target changes of their steady states. The changes may be either increases or decreases of influxes, reaction knockouts, or multiple changes of these two kinds. Our prime applications are knockout prediction tasks for metabolic and regulation networks. In a first step, we propose a formal modeling language for reaction networks with partial kinetic information. The modeling language has a graphical syntax reminiscent to Petri nets. Each reaction in a model comes with a partial description of its kinetics, based on a similarity relation on kinetic functions that we introduce. Such partial descriptions are able to model the regulation of existing metabolic networks for which precise kinetic knowledge is usually not available. In a second step, we develop prediction algorithms that can be applied to any reaction network modeled in our language. These algorithms perform qualitative reasoning based on abstract interpretation, by which the kinetic unknowns are abstracted away. Given a reaction network, abstract interpretation produces a finite domain constraint in a novel class. We show how to solve these finite domain constraints with an existing finite domain constraint solver, and how to interpret the solution sets as predictions of multiple reaction knockouts that lead to a desired change of the steady states. We have implemented the prediction algorithm and integrated it into a prediction tool. This journal article extends the two conference papers John et al. (2013) and Niehren et al. (2015) while adding a new prediction algorithm for multiple gene knockouts. An application to single gene knockout prediction for surfactin overproduction was presented in Coutte et al. (2015). It illustrates the adequacy of the model-based predictions made by our algorithm in the wet lab.

  4. Partially Blind Signatures Based on Quantum Cryptography

    NASA Astrophysics Data System (ADS)

    Cai, Xiao-Qiu; Niu, Hui-Fang

    2012-12-01

    In a partially blind signature scheme, the signer explicitly includes pre-agreed common information in the blind signature, which can improve the availability and performance. We present a new partially blind signature scheme based on fundamental properties of quantum mechanics. In addition, we analyze the security of this scheme, and show it is not possible to forge valid partially blind signatures. Moreover, the comparisons between this scheme and those based on public-key cryptography are also discussed.

  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. 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.

  7. Changes in Gene Expression of E. coli under Conditions of Modeled Reduced Gravity

    NASA Astrophysics Data System (ADS)

    Vukanti, Raja; Mintz, Eric; Leff, Laura

    2008-06-01

    Relatively few studies have examined bacterial responses to the reduced gravity conditions that are experienced by bacteria grown in space. In this study, whole genome expression of Escherichia coli K12 under clinorotation (which models some of the conditions found under reduced gravity) was analyzed. We hypothesized that phenotypic differences at cellular and population levels under clinorotation (hereafter referred to as modeled reduced gravity) are directly coupled to changes in gene expression. Further, we hypothesized that these responses may be due to indirect effects of these environmental conditions on nutrient accessibility for bacteria. Overall, 430 genes were identified as significantly different between modeled reduced gravity conditions and controls. Up-regulated genes included those involved in the starvation response ( csiD, cspD, ygaF, gabDTP, ygiG, fliY, cysK) and redirecting metabolism under starvation ( ddpX, acs, actP, gdhA); responses to multiple stresses, such as acid stress ( asr, yhiW), osmotic stress ( yehZYW), oxidative stress ( katE, btuDE); biofilm formation ( lldR, lamB, yneA, fadB, ydeY); curli biosynthesis ( csgDEF), and lipid biosynthesis ( yfbEFG). Our results support the previously proposed hypothesis that under conditions of modeled reduced gravity, zones of nutrient depletion develop around bacteria eliciting responses similar to entrance into stationary phase which is generally characterized by expression of starvation inducible genes and genes associated with multiple stress responses.

  8. 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.

  9. Generalized partial dynamical symmetry in nuclei.

    PubMed

    Leviatan, A; Isacker, P Van

    2002-11-25

    We introduce the notion of a generalized partial dynamical-symmetry for which part of the eigenstates have part of the dynamical symmetry. This general concept is illustrated with the example of Hamiltonians with a partial dynamical O(6) symmetry in the framework of the interacting boson model. The resulting spectrum and electromagnetic transitions are compared with empirical data in 162Dy.

  10. Partial dynamical symmetry in a fermion system

    PubMed

    Escher; Leviatan

    2000-02-28

    The relevance of the partial dynamical symmetry concept for an interacting fermion system is demonstrated. Hamiltonians with partial SU(3) symmetry are presented in the framework of the symplectic shell model of nuclei and shown to be closely related to the quadrupole-quadrupole interaction. Implications are discussed for the deformed light nucleus 20Ne.

  11. 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...

  12. 49 CFR 234.106 - Partial activation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Partial activation. 234.106 Section 234.106..., DEPARTMENT OF TRANSPORTATION GRADE CROSSING SIGNAL SYSTEM SAFETY AND STATE ACTION PLANS Response to Reports of Warning System Malfunction § 234.106 Partial activation. Upon receipt of a credible report of...

  13. [Laparoscopic partial nephrectomy: technique and outcomes].

    PubMed

    Colombo, J R; Gill, I S

    2006-05-01

    The indication of laparoscopic partial nephrectomy (LPN) has evolved considerably, and the technique is approaching established status at our institution. Over the past 5 years, the senior author has performed more than 450 laparoscopic partial nephrectomies at the Cleveland Clinic. Herein we present our current technique, review contemporary data and oncological outcomes of LPN.

  14. [Voice function in patients after partial laryngectomy].

    PubMed

    Kosztyła-Hojna, B; Chodynicki, S; Lazarczyk, B; Tupalska, M; Mikiel, W

    1998-01-01

    103 patients with cancer of the larynx treated with partial laryngectomy were presented. Voice quality before and after surgery was compared. Voice was analysed by subjective and objective-spectrographic methods. Partial laryngectomies consisted of: vertical, horizontal and supraglottic subtotal procedures. The least dysphony was found in horizontal laryngectomy, the biggest--in supraglottic subtotal laryngectomy.

  15. 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.

  16. 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...

  17. 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.

  18. 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.

  19. 77 FR 43018 - Partial Approval and Partial Disapproval of Air Quality Implementation Plans for Florida...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-23

    ... AGENCY 40 CFR Part 52 Partial Approval and Partial Disapproval of Air Quality Implementation Plans for... partially disapprove revisions to the State Implementation Plans (SIPs) for Florida, Mississippi, and South... enforcement'' of such NAAQS. Section 110(a)(2) includes a list of specific elements that `` ach such...

  20. 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…

  1. Partial Granger causality--eliminating exogenous inputs and latent variables.

    PubMed

    Guo, Shuixia; Seth, Anil K; Kendrick, Keith M; Zhou, Cong; Feng, Jianfeng

    2008-07-15

    Attempts to identify causal interactions in multivariable biological time series (e.g., gene data, protein data, physiological data) can be undermined by the confounding influence of environmental (exogenous) inputs. Compounding this problem, we are commonly only able to record a subset of all related variables in a system. These recorded variables are likely to be influenced by unrecorded (latent) variables. To address this problem, we introduce a novel variant of a widely used statistical measure of causality--Granger causality--that is inspired by the definition of partial correlation. Our 'partial Granger causality' measure is extensively tested with toy models, both linear and nonlinear, and is applied to experimental data: in vivo multielectrode array (MEA) local field potentials (LFPs) recorded from the inferotemporal cortex of sheep. Our results demonstrate that partial Granger causality can reveal the underlying interactions among elements in a network in the presence of exogenous inputs and latent variables in many cases where the existing conditional Granger causality fails.

  2. GDH Integral on the Proton from Cross Section Differences

    SciTech Connect

    Skabelin, Alexander

    2002-02-01

    We studied the inclusive reaction $\\vec{e}$ $\\vec{p}$ → e'X with a 2.5 GeV and a 4.2 GeV incident beam of polarized electrons. The virtual photon four momentum squared, Q2, varied from 0.2 GeV2/c2 to 1 GeV2/c2 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 NH3 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 Q2 region and the region of low Q2 where photons become nearly real.

  3. 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.

  4. SOX genes: architects of development.

    PubMed

    Prior, H M; Walter, M A

    1996-07-01

    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.

  5. Partiality and distributive justice in African bioethics.

    PubMed

    Wareham, Christopher Simon

    2017-04-01

    African ethical theories tend to hold that moral agents ought to be partial, in the sense that they should favour members of their family or close community. This is considered an advantage over the impartiality of many Western moral theories, which are regarded as having counterintuitive implications, such as the idea that it is unethical to save a family member before a stranger. The partiality of African ethics is thought to be particularly valuable in the context of bioethics. Thaddeus Metz, in particular, argues that his African-derived theory best accounts for a number of plausible intuitions, such as the intuition that health care practitioners ought to be biased towards the patients for whom they are directly responsible. In this article, I claim that the plausible intuitions drawn on in favour of partiality can be satisfactorily explained on the basis of impartial moral theories. Moreover, I argue that blanket acceptance of partiality has problematic consequences for distributive justice in resource allocation in biomedical contexts. By contrast, impartial theories can justify plausible instances of partiality whilst avoiding the pitfalls of fully partial moral theories. Although this provides grounds for abandoning partiality in principle, I claim that this finding should not be seen as damaging to African medical ethics. Instead, it prompts investigation of underexplored possibilities of impartial African moral theories. To demonstrate the value of this direction, I sketch some novel and attractive conceptions that combine impartiality with elements of African ethics.

  6. Molecular Delineation of Partial Trisomy 14q and Partial Trisomy 12p in a Patient with Dysmorphic Features, Heart Defect and Developmental Delay.

    PubMed

    Bose, Divya; Krishnamurthy, Venkatesh; Venkatesh, K S; Aiyaz, Mohamed; Shetty, Mitesh; Rao, Sudha N; Kutty, A V M

    2015-01-01

    This study describes a molecular analysis of partial trisomy 14q and partial trisomy 12p in a 5-year-old male child presenting with dysmorphic features, congenital heart disease and global developmental delay. Chromosomal analysis of the patient with GTG bands revealed a 47,XY,+der(14)t(12;14)(p13;q22)mat karyotype; the mother's karyotype was 46,XX,t(12;14)(p13;q22). Further, oligonucleotide array- CGH studies revealed an amplification of 32.3 Mb in the 14q11.1q22.1 region, substantiating partial trisomy 14q and additionally displaying an amplification of ∼1 Mb in the 12p13.3pter region for partial trisomy 12p. This is the first study to demonstrate a novel association of partial trisomies of 14q and 12p due to a 3:1 segregation of a maternal balanced translocation involving chromosomes 12 and 14. Gene ontology studies indicated 5 potential candidate genes in the amplified regions for the observed congenital anomalies.

  7. 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.

  8. 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

  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. 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.

  11. Partial duplication 2p as the sole abnormality in two cases with anencephaly.

    PubMed

    Thangavelu, Maya; Frolich, Gary; Rogers, David

    2004-01-15

    Anencephaly/NTD has been observed in aneuploid and non-aneuploid individuals. We present two cases of anencephaly diagnosed prenatally with partial duplication of the short arm of chromosome 2 as the sole abnormality. The absence of aneuploidy involving other regions of the genome in these cases, further substantiates suggestions of the existence of a gene or genes on the short arm of chromosome 2 critical in the development of the central nervous system.

  12. Partial ASL extensions for stochastic programming.

    SciTech Connect

    Gay, David

    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

  13. Clustering stocks using partial correlation coefficients

    NASA Astrophysics Data System (ADS)

    Jung, Sean S.; Chang, Woojin

    2016-11-01

    A partial correlation analysis is performed on the Korean stock market (KOSPI). The difference between Pearson correlation and the partial correlation is analyzed and it is found that when conditioned on the market return, Pearson correlation coefficients are generally greater than those of the partial correlation, which implies that the market return tends to drive up the correlation between stock returns. A clustering analysis is then performed to study the market structure given by the partial correlation analysis and the members of the clusters are compared with the Global Industry Classification Standard (GICS). The initial hypothesis is that the firms in the same GICS sector are clustered together since they are in a similar business and environment. However, the result is inconsistent with the hypothesis and most clusters are a mix of multiple sectors suggesting that the traditional approach of using sectors to determine the proximity between stocks may not be sufficient enough to diversify a portfolio.

  14. Retroperitoneoscopic partial adrenalectomy for large adrenocortical oncocytoma.

    PubMed

    Modi, Pranjal; Goel, Rajiv; Kadam, Gaurang

    2007-04-01

    A young woman had mild hypertension, and on evaluation, a large tumor arising from the right adrenal gland was found. The tumor was hormonally inactive. Retroperitoneoscopic partial adrenalectomy was carried out. The histopathology report described adrenocortical oncocytoma.

  15. 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.

  16. Partial focusing by indefinite complementary metamaterials

    NASA Astrophysics Data System (ADS)

    Cheng, Qiang; Liu, Ruopeng; Mock, Jack J.; Cui, Tie Jun; Smith, David R.

    2008-09-01

    We have experimentally realized a two-dimensional partial focusing within a planar waveguide using complementary indefinite metamaterials. When the electric fields emitted from the dipole are TE polarized, the focusing condition requires negative magnetic response in the propagation direction of the waveguide, which can be achieved by the complementary electric resonator (CELC) structures. We have carefully designed the experimental configurations and the dimensions for the CELC structures. The experimental result is consistent with the theoretical prediction, which validates the partial focusing phenomenon.

  17. The conversion partial denture: a clinical report.

    PubMed

    Waliszewski, Michael P; Brudvik, James S

    2004-04-01

    The treatment alternative described maximizes the benefit of remaining teeth while allowing simplified alteration of the prosthesis if abutments are lost during the life span of the removable partial denture (RPD). A conversion partial is an RPD whose tooth-frame assembly components are individually fabricated and then joined with an acrylic resin major connector. The conversion RPD optimizes retention and stabilization of a terminal dentition and can be easily converted to an immediate complete denture.

  18. Systems of Nonlinear Hyperbolic Partial Differential Equations

    DTIC Science & Technology

    1997-12-01

    McKinney) Travelling wave solutions of the modified Korteweg - deVries -Burgers Equation . J. Differential Equations , 116 (1995), 448-467. 4. (with D.G...SUBTITLE Systems of Nonlinear Hyperbolic Partial Differential Equations 6. AUTHOR’S) Michael Shearer PERFORMING ORGANIZATION NAMES(S) AND...DISTRIBUTION CODE 13. ABSTRACT (Maximum 200 words) This project concerns properties of wave propagation in partial differential equations that are nonlinear

  19. Partial reinforcement, extinction, and placebo analgesia

    PubMed Central

    Yeung, Siu Tsin Au; Colagiuri, Ben; Lovibond, Peter F.; Colloca, Luana

    2014-01-01

    Numerous studies indicate that placebo analgesia can be established via conditioning procedures. However, these studies have exclusively involved conditioning under continuous reinforcement. Thus, it is currently unknown whether placebo analgesia can be established under partial reinforcement and how durable any such effect would be. We tested this possibility using electro-cutaneous pain in healthy volunteers. Sixty undergraduates received placebo treatment (activation of a sham electrode) under the guise of an analgesic trial. The participants were randomly allocated to different conditioning schedules, namely continuous reinforcement (CRF), partial reinforcement (PRF), or control (no conditioning). Conditioning was achieved by surreptitiously reducing pain intensity during training when the placebo was activated compared with when it was inactive. For the CRF group, the placebo was always followed by a surreptitious reduction in pain during training. For the PRF group, the placebo was followed by a reduction in pain stimulation on 62.5% of trials only. In the test phase, pain stimulation was equivalent across placebo and no placebo trials. Both continuous and partial reinforcement produced placebo analgesia, with the magnitude of initial analgesia being larger following continuous reinforcement. However, while the placebo analgesia established under continuous reinforcement extinguished during test phase, the placebo analgesia established under partial reinforcement did not. These findings indicate that partial reinforcement can induce placebo analgesia and that these effects are more resistant to extinction than those established via continuous reinforcement. Partial reinforcement may, therefore, reflect a novel way of enhancing clinical outcomes via the placebo effect. PMID:24602997

  20. Spreading paths in partially observed social networks

    PubMed Central

    Onnela, Jukka-Pekka; Christakis, Nicholas A.

    2012-01-01

    Understanding how and how far information, behaviors, or pathogens spread in social networks is an important problem, having implications for both predicting the size of epidemics, as well as for planning effective interventions. There are, however, two main challenges for inferring spreading paths in real-world networks. One is the practical difficulty of observing a dynamic process on a network, and the other is the typical constraint of only partially observing a network. Using a static, structurally realistic social network as a platform for simulations, we juxtapose three distinct paths: (1) the stochastic path taken by a simulated spreading process from source to target; (2) the topologically shortest path in the fully observed network, and hence the single most likely stochastic path, between the two nodes; and (3) the topologically shortest path in a partially observed network. In a sampled network, how closely does the partially observed shortest path (3) emulate the unobserved spreading path (1)? Although partial observation inflates the length of the shortest path, the stochastic nature of the spreading process also frequently derails the dynamic path from the shortest path. We find that the partially observed shortest path does not necessarily give an inflated estimate of the length of the process path; in fact, partial observation may, counterintuitively, make the path seem shorter than it actually is. PMID:22587148

  1. 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...

  2. 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...

  3. Genes associated with long-chain omega-3 fatty acids in bovine skeletal muscle.

    PubMed

    Perez, R; Cañón, J; Dunner, S

    2010-01-01

    Long-chain omega-3 fatty acids (n-3 FAs) influence meat tenderness, juiciness, and flavor, and are beneficial to human health. The percentage of long-chain n-3 FAs in total FAs is termed the omega-3 index (O3I). It is thus of great interest to favor rising this index in bovine skeletal muscle, to obtain healthier, tastier, and more nutritive meat. This study was aimed to detect transcriptomic variations related to O3I in muscles in 15-month-old males of 4 Spanish cattle breeds raised under the same conditions. Through the analysis of extreme O3I phenotypes, 3 genes of interest (AANAT, UCP2 and AHA1) were identified. AANAT and UCP2 were strongly up-regulated, while AHA1 was repressed in animals with a high O3I. Moreover, gene expression differed between GDF8-null animal muscles (tested for nt821del11 and Q204X mutations) and the wild-type muscles for genes GDH1, IGF2R, FADS1, ASPH, and AIM1, all showing down-regulation in Asturiana de los Valles calves with muscle hypertrophy (GDF8-null). This shows that in GDF8-null animals other pathways are used for FA synthesis.

  4. 24 CFR 203.495 - Transfers of partial interests.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Transfers of partial interests. 203... Transfers of partial interests. A partial interest in an insured loan may be transferred under a...) Qualification for holding partial interest. A partial interest in an insured loan shall be issued to and...

  5. Linear algebraic theory of partial coherence: continuous fields and measures of partial coherence.

    PubMed

    Ozaktas, Haldun M; Gulcu, Talha Cihad; Alper Kutay, M

    2016-11-01

    This work presents a linear algebraic theory of partial coherence for optical fields of continuous variables. This approach facilitates use of linear algebraic techniques and makes it possible to precisely define the concepts of incoherence and coherence in a mathematical way. We have proposed five scalar measures for the degree of partial coherence. These measures are zero for incoherent fields, unity for fully coherent fields, and between zero and one for partially coherent fields.

  6. 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 ...

  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. Modeling Covariance Matrices via Partial Autocorrelations

    PubMed Central

    Daniels, M.J.; Pourahmadi, M.

    2009-01-01

    Summary We study the role of partial autocorrelations in the reparameterization and parsimonious modeling of a covariance matrix. The work is motivated by and tries to mimic the phenomenal success of the partial autocorrelations function (PACF) in model formulation, removing the positive-definiteness constraint on the autocorrelation function of a stationary time series and in reparameterizing the stationarity-invertibility domain of ARMA models. It turns out that once an order is fixed among the variables of a general random vector, then the above properties continue to hold and follows from establishing a one-to-one correspondence between a correlation matrix and its associated matrix of partial autocorrelations. Connections between the latter and the parameters of the modified Cholesky decomposition of a covariance matrix are discussed. Graphical tools similar to partial correlograms for model formulation and various priors based on the partial autocorrelations are proposed. We develop frequentist/Bayesian procedures for modelling correlation matrices, illustrate them using a real dataset, and explore their properties via simulations. PMID:20161018

  9. The nucleotide sequence of a 39 kb segment of yeast chromosome IV: 12 new open reading frames, nine known genes and one genes for Gly-tRNA.

    PubMed

    Bahr, A; Möller-Rieker, S; Hankeln, T; Kraemer, C; Protin, U; Schmidt, E R

    1997-02-01

    The complete nucleotide sequence of a 39,090 bp segment from the left arm of yeast chromosome IV was determined. Twenty-one open reading frames (ORFs) longer than 100 amino acids and a Gly-tRNA gene were discovered. Nine of the 21 ORFs (D0892, D1022, D1037, D1045, D1057, D1204, D1209, D1214, D1219) correspond to the previously sequenced Saccharomyces cerevisiae genes for the NAD-dependent glutamate dehydrogenase (GDH), the secretory component (SHR3), the GABA transport protein (UGA4), the high mobility group-like protein (NHP2), the hydroxymethylbilane synthase (HEM3), the methylated DNA protein-cysteine S-methyltransferase (MGT1), a putative sugar transport protein, the Shm1 protein (SHM1) and the anti-silencing protein (ASF2). The inferred amino acid sequences of 11 ORFs show significant similarity with known proteins from various organisms, whereas the remaining ORF does not share any similarity with known proteins.

  10. 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.

  11. 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.

  12. 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.

  13. Partial transpose criteria for symmetric states

    NASA Astrophysics Data System (ADS)

    Bohnet-Waldraff, F.; Braun, D.; Giraud, O.

    2016-10-01

    We express the positive-partial-transpose (PPT) separability criterion for symmetric states of multiqubit systems in terms of matrix inequalities based on the recently introduced tensor representation for spin states. We construct a matrix from the tensor representation of the state and show that it is similar to the partial transpose of the density matrix written in the computational basis. Furthermore, the positivity of this matrix is equivalent to the positivity of a correlation matrix constructed from tensor products of Pauli operators. This allows for a more transparent experimental interpretation of the PPT criteria for an arbitrary spin-j state. The unitary matrices connecting our matrix to the partial transpose of the state generalize the so-called magic basis that plays a central role in Wootters' explicit formula for the concurrence of a two-qubit system and the Bell bases used for the teleportation of a one- or two-qubit state.

  14. 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.

  15. 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.

  16. On partially massless theory in 3 dimensions

    NASA Astrophysics Data System (ADS)

    Alexandrov, Sergei; Deffayet, Cédric

    2015-03-01

    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.

  17. Partial Thickness Rotator Cuff Tears: Current Concepts

    PubMed Central

    Matthewson, Graeme; Beach, Cara J.; Nelson, Atiba A.; Woodmass, Jarret M.; Ono, Yohei; Boorman, Richard S.; Lo, Ian K. Y.; Thornton, Gail M.

    2015-01-01

    Partial thickness rotator cuff tears are a common cause of pain in the adult shoulder. Despite their high prevalence, the diagnosis and treatment of partial thickness rotator cuff tears remains controversial. While recent studies have helped to elucidate the anatomy and natural history of disease progression, the optimal treatment, both nonoperative and operative, is unclear. Although the advent of arthroscopy has improved the accuracy of the diagnosis of partial thickness rotator cuff tears, the number of surgical techniques used to repair these tears has also increased. While multiple repair techniques have been described, there is currently no significant clinical evidence supporting more complex surgical techniques over standard rotator cuff repair. Further research is required to determine the clinical indications for surgical and nonsurgical management, when formal rotator cuff repair is specifically indicated and when biologic adjunctive therapy may be utilized. PMID:26171251

  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. 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

  20. Third Partial and 3.0L Second Partial and 2.0L Partial and Amended Consent Decree

    EPA Pesticide Factsheets

    The settlement partially resolves allegations that Volkswagen violated the Clean Air Act (“CAA”) by the sale of approximately 500,000 model year 2009 to 2015 motor vehicles containing 2.0 liter diesel engines equipped with “defeat devices” (“CAA 2.0 liter.

  1. 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

  2. Self-steering partially coherent beams

    NASA Astrophysics Data System (ADS)

    Chen, Yahong; Ponomarenko, Sergey A.; Cai, Yangjian

    2017-01-01

    We introduce a class of shape-invariant partially coherent beams with a moving guiding center which we term self-steering partially coherent beams. The guiding center of each such beam evolves along a straight line trajectory which can be engineered to make any angle with the x-axis. We show that the straight line trajectory of the guiding center is the only option in free space due to the linear momentum conservation. We experimentally generate a particular subclass of new beams, self-steering Gaussian Schell beams and argue that they can find applications for mobile target tracing and trapped micro- and/or nanoparticle transport.

  3. 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%.

  4. 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.

  5. Partial Kluver-Bucy syndrome: two cases.

    PubMed

    Carroll, B T; Goforth, H W; Raimonde, L A

    2001-04-01

    Kluver-Bucy syndrome (KBS) is a rare neuropsychiatric disorder that may be characterized by visual agnosia, placidity, altered sexual activity, hypermetamorphosis, and hyperorality. Patients with KBS present with a complex behavioral syndrome. KBS is usually associated with lesions of the amygdala or amygdaloid pathways. However, partial KBS may occur in the absence of the classic bilateral temporal lesions. Pharmacologic treatment options have been developed from the results of case reports, which suggest that carbamazepine and antipsychotics may be helpful. We present the cases of two patients with partial KBS who responded favorably to antipsychotic medication.

  6. Self-steering partially coherent beams

    PubMed Central

    Chen, Yahong; Ponomarenko, Sergey A.; Cai, Yangjian

    2017-01-01

    We introduce a class of shape-invariant partially coherent beams with a moving guiding center which we term self-steering partially coherent beams. The guiding center of each such beam evolves along a straight line trajectory which can be engineered to make any angle with the x-axis. We show that the straight line trajectory of the guiding center is the only option in free space due to the linear momentum conservation. We experimentally generate a particular subclass of new beams, self-steering Gaussian Schell beams and argue that they can find applications for mobile target tracing and trapped micro- and/or nanoparticle transport. PMID:28051164

  7. 77 FR 64737 - Partial Approval and Partial Disapproval of Air Quality State Implementation Plans; Nevada...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-23

    ... CFR 52.21 for all regulated NSR pollutants, pursuant to delegation agreements with EPA. See 40 CFR 52... AGENCY 40 CFR Part 52 Partial Approval and Partial Disapproval of Air Quality State Implementation Plans... September 21, 2006.\\3\\ Each of these actions triggered a requirement for states to submit an...

  8. 76 FR 55842 - Partial Approval and Partial Disapproval of Air Quality Implementation Plans; California; San...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-09

    ... AGENCY 40 CFR Part 52 Partial Approval and Partial Disapproval of Air Quality Implementation Plans; California; San Joaquin Valley; Reasonably Available Control Technology for Ozone AGENCY: Environmental... disapprove a revision to the San Joaquin Valley Unified Air Pollution Control District (SJVUAPCD or...

  9. 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.

  10. Delayed puberty from partial 17-alpha hydroxylase enzyme deficiency.

    PubMed

    Croxson, Michael; Ogilvie, C Megan; Milsom, Stella; Lewis, John; Davidson, James; Rumsby, Gill

    2012-05-25

    An 18-year-old woman with primary amenorrhoea and pubertal delay was investigated for mild labile hypertension and secondary hypogonadism. Low renin and normal aldosterone levels combined with evidence of primary adrenal insufficiency suggested partial 17-alpha hydroxylase enzyme deficiency. The diagnosis was confirmed by measurement of 24-hour urine steroid metabolites and whole gene sequencing of CYP17A1 that demonstrated c.160_162delTTC (p.Phe54del) homozygous mutation. Ultrasound showed bilateral small ovaries with multiple cysts. The serum anti-mullerian hormone concentration was unremarkable at 6.6 (normal <12.6 ng/ml) but the outlook for her future ovulatory potential is uncertain. Dexamethasone 0.25 mg pre-bed and hydrocortisone 5 mg on waking normalised her hormonal profile and her blood pressure without side-effects.

  11. 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.

  12. A Rasch Model for Partial Credit Scoring.

    ERIC Educational Resources Information Center

    Masters, Geoff N.

    1982-01-01

    An extension of the Rasch model for partial credit scoring of test items is presented. An unconditional maximum likelihood procedure for estimating the model parameters is developed. The relationship of this model to Andrich's Rating Scale model and Samejima's Graded Response model are discussed. (Author/JKS)

  13. 24 CFR 203.341 - Partial claim.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES SINGLE... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Partial claim. 203.341 Section 203.341 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  14. 24 CFR 203.341 - Partial claim.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES SINGLE... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Partial claim. 203.341 Section 203.341 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  15. 24 CFR 203.341 - Partial claim.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES SINGLE... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Partial claim. 203.341 Section 203.341 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  16. 24 CFR 203.341 - Partial claim.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES SINGLE... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Partial claim. 203.341 Section 203.341 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  17. 24 CFR 203.341 - Partial claim.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES SINGLE... 24 Housing and Urban Development 2 2013-04-01 2013-04-01 false Partial claim. 203.341 Section 203.341 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  18. 20 CFR 655.54 - Partial certification.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 3 2012-04-01 2012-04-01 false Partial certification. 655.54 Section 655.54 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR TEMPORARY EMPLOYMENT OF... Temporary Employment in Occupations Other Than Agriculture or Registered Nursing in the United States...

  19. Abnormal activated partial thromboplastin time and malignancy.

    PubMed

    Delicata, M; Hambley, H

    2011-08-01

    Malignancy often results in clotting abnormalities. The aetiology of haemostasis problems in cancer is complex, and is still not completely understood. We describe a case of a patient with malignant mesothelioma, who was found to have elevated activated partial thromboplastin time, due to lupus anticoagulant. We suggest that patients with malignancy should have their coagulation checked prior to any invasive procedures.

  20. Partial intravenous anesthesia in cats and dogs.

    PubMed

    Duke, Tanya

    2013-03-01

    The partial intravenous anesthesia technique (PIVA) is used to lower the inspired concentration of an inhalational anesthetic by concurrent use of injectable drugs. This technique reduces the incidence of undesirable side-effects and provides superior quality of anesthesia and analgesia. Drugs commonly used for PIVA include opioids, alpha-2 adrenergic agonists, injectable anesthetic agents, and lidocaine. Most are administered by intravenous infusion.

  1. A case of partial trisomy 15

    PubMed Central

    Watson, E. Janet; Gordon, R. R.

    1974-01-01

    A girl with mental retardation but few distinctive physical abnormalities is described. Chromosome analysis revealed an extra small acrocentric chromosome with both long and short arms satellited which was identified as a deleted chromosome No. 15. The origin of this chromosome is discussed and the clinical findings compared with those of previously reported cases of partial trisomy 15. Images PMID:4443991

  2. Partial excision of residual burn lesions.

    PubMed

    Engrav, L H; Gottlieb, J R; Millard, S P; Walkinshaw, M D; Heimbach, D M; Marvin, J A

    1987-01-01

    Most burn victims have unattractive residual lesions, which may include hypertrophic donor sites, unsightly skin grafts, hypertrophic scars, and mature scars with altered pigmentation or texture. Some of these lesions can be treated by total excision in one or more stages or they can be reconstructed utilizing grafts, flaps, Z-plasties, or tissue expansion. But frequently these procedures are either not indicated or not elected by the patient. In such a situation, the only surgical option is partial excision, with the goal of making the lesion less conspicuous and more easily concealed by clothing. Whether or not such partial excisions are worthwhile is the obvious question. We could not find an answer in the literature and therefore decided to review our own experience. Between 6/30/81 and 3/12/86, 92 such procedures were performed and followed in 25 patients. Partial excision of hypertrophic donor sites, unsightly skin grafts, and hypertrophic scars did yield improved appearance in most patients. However, partial excision of mature scars, ie, areas of altered pigmentation or texture, did not have the same success. We continue to treat the first three types of lesions in this fashion but no longer include the latter.

  3. 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.

  4. 20 CFR 655.165 - Partial certification.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... certification. The CO may issue a partial certification, reducing either the period of need or the number of H-2A workers being requested or both for certification, based upon information the CO receives during... the CO. The notice will also state that the employer may submit any legal arguments which the...

  5. 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,…

  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. 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…

  8. 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.

  9. Monotherapy for partial epilepsy: focus on levetiracetam

    PubMed Central

    Gambardella, Antonio; Labate, Angelo; Colosimo, Eleonora; Ambrosio, Roberta; Quattrone, Aldo

    2008-01-01

    Levetiracetam (LEV), the S-enantiomer of alpha-ethyl-2-oxo-1-pyrollidine acetamide, is a recently licensed antiepileptic drug (AED) for adjunctive therapy of partial seizures. Its mechanism of action is uncertain but it exhibits a unique profile of anticonvulsant activity in models of chronic epilepsy. Five randomized, double-blind, placebo-controlled trials enrolling adult or pediatric patients with refractory partial epilepsy have demonstrated the efficacy of LEV as adjunctive therapy, with a responder rate (≥50% reduction in seizure frequency) of 28%–45%. Long-term efficacy studies suggest retention rates of 60% after one year, with 13% of patients seizure-free for 6 months of the study and 8% seizure-free for 1 year. More recent studies illustrated successful conversion to monotherapy in patients with refractory epilepsy, and its effectiveness as a single agent in partial epilepsy. LEV has also efficacy in generalized epilepsies. Adverse effects of LEV, including somnolence, lethargy, and dizziness, are generally mild and their occurrence rate seems to be not significantly different from that observed in placebo groups. LEV also has no clinically significant pharmacokinetic interactions with other AEDs, or with commonly prescribed medications. The combination of effective antiepileptic properties with a relatively mild adverse effect profile makes LEV an attractive therapy for partial seizures. PMID:18728811

  10. 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…

  11. 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…

  12. 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.

  13. A Partially Cavitating Hydrofoil in a Gust.

    DTIC Science & Technology

    1980-11-01

    TECHNOLOGYI DAVIDSON LABORATORY CASTLE POINT STATION H4OBOKEN. NEW JERSEY REPORT SIT-DL-80-21 18 November 1980 A PARTIALLY CA VITA TING HYDROFOIL * IN A...Engineering Building 315 CORNELL UNIVERSITY ARMY MOBILITY EQUIPMENT RESEARCH Ithaca, NY 14851 CENTER Fort Belvoir, VA 22060 1 Dr. D.E. Ordway SAGE ACTION, INC

  14. Partial allelotype of schistosomiasis-associated bladder cancer.

    PubMed

    Shaw, M E; Elder, P A; Abbas, A; Knowles, M A

    1999-03-01

    In Egypt and other regions of the Middle East where the trematode Schistosoma haematobium is endemic, bladder cancer is the most common adult cancer. Unlike bladder cancers in Western countries, which are predominantly transitional-cell carcinoma (TCC), these schistosomiasis-associated bladder cancers are predominantly squamous-cell carcinoma (SCC). Our aim was to assess a large series of schistosomiasis-associated bladder tumours for genetic alterations commonly found in TCC in the United Kingdom and the United States. We have carried out a partial allelotype of 70 tumours from patients with schistosomiasis. LOH was found on all chromosome arms studied (3p, 4p, 4q, 8p, 9p, 9q, 11p, 11q, 13q, 14q, 17p, 18q). The most frequent regions of LOH were 9p (65%), 17p (58%), 3p (40%), 9q (39%) and 8p (37%). LOH on 17p, where the TP53 gene is located, was more common in Egyptian TCC than in SCC. Similarly, 8p LOH was more common in TCC than SCC. The most striking difference between this group of tumours and TCCs from the United Kingdom and the United States was the high frequency of 9p LOH in the region of the CDKN2 gene (65%) and the relatively low frequency of 9q LOH (39%); 15 of 43 tumours with LOH of at least one marker on chromosome 9 showed LOH of 9p only. This suggests that a 9p gene, possibly CDKN2, may contribute to the development of the majority of schistosomiasis-associated bladder tumours but that genes on 9q play a much less important role.

  15. Gene conversion variations generate structurally distinct pilin polypeptides in Neisseria gonorrhoeae.

    PubMed

    Swanson, J; Robbins, K; Barrera, O; Koomey, J M

    1987-04-01

    Pilus+ to pilus- phenotype change occurs in Neisseria gonorrhoeae through gene conversion of the gonococcus' complete, expressed pilin gene by nucleotides homologous to the pilS1 copy 5 partial pilin gene; assembly missense pilin is synthesized but pili are not. Reversion to pilus+ occurs by a subsequent recombinational event that replaces the complete pilin gene's pilS1 copy 5-like sequence with nucleotides from a different partial gene to effect expression of an orthodox (i.e., pilus producing) pilin. Sibling pilus+ revertants of common parentage can carry different sequences in their expressed pilin genes because they have undergone nonidentical gene conversion events such as recombinations with sequences from different partial genes, or recombinations with different length nucleotide stretches of the same partial gene; either can yield structurally and antigenically variant pilin polypeptides.

  16. Molecular cytogenetic characterisation of partial trisomy 9q in a case with pyloric stenosis and a review

    PubMed Central

    Heller, A.; Seidel, J; Hubler, A; Starke, H; Beensen, V; Senger, G; Rocchi, M; Wirth, J; Chudoba, I; Claussen, U; Liehr, T

    2000-01-01

    Partial trisomy 9q represents a rare and heterogeneous group of chromosomal aberrations characterised by various clinical features including pyloric stenosis. Here, we describe the case of a 1 year old female patient with different dysmorphic features including pyloric stenosis and prenatally detected partial trisomy 9q. This partial trisomy 9q has been analysed in detail to determine the size of the duplication and to characterise the chromosomal breakpoints. According to the data gained by different molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) with whole and partial chromosome painting probes, yeast artificial chromosome (YAC) probes, and comparative genomic hybridisation (CGH), the derivative chromosome 9 can be described as dup(9)(pter→q22.1::q31.1→q22.1::q31.1→ q22.1::q31.1→qter). Four breakpoint spanning YACs have been identified (y806f02, y906g6, y945f5, and y747b3) for the proximal breakpoint. According to this new case and previously published data, the recently postulated putative critical region for pyloric stenosis can be narrowed down to the subbands 9q22.1-q31.1 and is the result of either partial trisomy of gene(s) located in this region or a gene disrupted in 9q31.


Keywords: partial trisomy 9q; pyloric stenosis; FISH; CGH PMID:10882757

  17. 24 CFR 203.435 - Transfers of partial interests.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Transfers of partial interests. 203... Insured Mortgage § 203.435 Transfers of partial interests. A partial interest in an insured mortgage may... account a financial interest in the insured mortgage. (c) Qualification for holding partial interest....

  18. 38 CFR 36.4316 - Acceptability of partial payments.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Acceptability of partial... Acceptability of partial payments. A partial payment is a remittance by or on behalf of the borrower on a loan... any partial payment and either apply it to the mortgagor's account or identify it with the...

  19. Partial rectangular metric spaces and fixed point theorems.

    PubMed

    Shukla, Satish

    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.

  20. 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.

  1. Planarian immobilization, partial irradiation, and tissue transplantation.

    PubMed

    Guedelhoefer, Otto C; Sánchez Alvarado, Alejandro

    2012-08-06

    The planarian, a freshwater flatworm, has proven to be a powerful system for dissecting metazoan regeneration and stem cell biology. Planarian regeneration of any missing or damaged tissues is made possible by adult stem cells termed neoblasts. Although these stem cells have been definitively shown to be pluripotent and singularly capable of reconstituting an entire animal, 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 transplantation and partial irradiation 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 cover the

  2. 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

  3. 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.

  4. Pneumatic conveying of materials at partial gravity

    NASA Technical Reports Server (NTRS)

    Sullivan, Thomas A.; Koenig, Elissa; Knudsen, Christian W.; Gibson, Michael A.

    1992-01-01

    The feasibility of pneumatic transfer for the movement of regolith at a lunar base is evaluated. Operation of pneumatic conveying systems at partial (lunar and Mars) gravity on NASA's KC-135 aircraft allowed the determination of some key parameters necessary for the design of an operable system. Both horizontal and vertical transfer is studied. In the vertical experiment, the choking velocity for 150-micron glass spheres was determined to be 1/2 to 1/3 the velocity required at 1 g. Pressure drops were reduced by roughly the same amount. Determination of the saltation velocity in the horizontal run was problematic, but qualitatively similar results were obtained. Comparison of the partial g results to 1-g behavior and theoretical analysis is made.

  5. 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.

  6. 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.

  7. Molecular orbital imaging for partially aligned molecules

    NASA Astrophysics Data System (ADS)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

    We investigate molecular orbital reconstruction using high-order harmonic emissions from partially aligned molecular ensembles. By carrying out the reconstruction procedure using the harmonic sampling with or without the spectral minimum, the roles of the harmonic phase and amplitude modulation due to the partial alignment can be separately studied. It is found that with the prior knowledge of the orbital symmetry, the reconstructed result is very sensitive to the modulation of the harmonic phase for the πg orbital, while in the case of σg orbital, the reconstructed result is mainly determined by the harmonic amplitude. These results can provide an important reference for the future experiment of molecular orbital imaging.

  8. Activated partial thromboplastin time and minor coagulopathies.

    PubMed

    Hathaway, W E; Assmus, S L; Montgomery, R R; Dubansky, A S

    1979-01-01

    Five commercially available activated partial thromboplastin time (APTT) test systems were compared with the kaolin partial thromboplastin time (KPTT) method to determine sensitivity in detecting minor coagulation defects. All reagent systems detected severe factor VIII-, IX-, and XI-deficient hemophilia. Homozygous states of factor XII deficiency, Fletcher factor deficiency, and high-molecular-weight kininogen deficiency (Fitzgerald trait) also showed abnormally long APTTs by all systems. Of 19 samples from patients with deficiencies of factors XII, VIII, IX, XI, and II ranging from 2.5 to 52%, eight had deficiencies that were not detected by reagent A (ellagic acid); two, by reagent B (ellagic acid); two, by reagent C (kaolin); one, by reagent D (silica); one, by the KPTT method. All deficiencies were detected by reagent E (celite). Heparin effect on plasma was less well detected by reagent A (ellagic acid) than with the other test systems. APTT test systems can vary greatly in their abilities to detect minor coagulation abnormalities.

  9. 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.

  10. 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.

  11. 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.

  12. 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}

  13. 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.

  14. Bactericidal activity of partially oxidized nanodiamonds.

    PubMed

    Wehling, Julia; Dringen, Ralf; Zare, Richard N; Maas, Michael; Rezwan, Kurosch

    2014-06-24

    Nanodiamonds are a class of carbon-based nanoparticles that are rapidly gaining attention, particularly for biomedical applications, i.e., as drug carriers, for bioimaging, or as implant coatings. Nanodiamonds have generally been considered biocompatible with a broad variety of eukaryotic cells. We show that, depending on their surface composition, nanodiamonds kill Gram-positive and -negative bacteria rapidly and efficiently. We investigated six different types of nanodiamonds exhibiting diverse oxygen-containing surface groups that were created using standard pretreatment methods for forming nanodiamond dispersions. Our experiments suggest that the antibacterial activity of nanodiamond is linked to the presence of partially oxidized and negatively charged surfaces, specifically those containing acid anhydride groups. Furthermore, proteins were found to control the bactericidal properties of nanodiamonds by covering these surface groups, which explains the previously reported biocompatibility of nanodiamonds. Our findings describe the discovery of an exciting property of partially oxidized nanodiamonds as a potent antibacterial agent.

  15. Transitive Properties of Some Partial Differential Operators

    NASA Astrophysics Data System (ADS)

    Todorov, Vladimir

    2011-12-01

    A partial differential operator L:C∞(Rn)→C∞(Rn) is by definition transitive if one can find a function f∈C∞(Rn) for which the forward orbit OL(f) = {Lp(f)|f∞C∞(Rn)} is a dense subset of C∞Rn). Here the orbit OL(f) consists as usual of the iterations of L:Lp(f) = L∘L∘L∘⋯L∘(f) (p times.) It was shown [1] that if L(u) = bu+ ∑ 0<|α|≤paα∂αu is a partial differential operator with constant coefficients then L is transitive if it does not contains a term of the type bu; in other words if b = 0. In this note we show that it is possible to omit the condition b = 0 for operators of first order as well for some operators of a Dirac type.

  16. Partially orthogonal resonators for magnetic resonance imaging

    PubMed Central

    Chacon-Caldera, Jorge; Malzacher, Matthias; Schad, Lothar R.

    2017-01-01

    Resonators for signal reception in magnetic resonance are traditionally planar to restrict coil material and avoid coil losses. Here, we present a novel concept to model resonators partially in a plane with maximum sensitivity to the magnetic resonance signal and partially in an orthogonal plane with reduced signal sensitivity. Thus, properties of individual elements in coil arrays can be modified to optimize physical planar space and increase the sensitivity of the overall array. A particular case of the concept is implemented to decrease H-field destructive interferences in planar concentric in-phase arrays. An increase in signal to noise ratio of approximately 20% was achieved with two resonators placed over approximately the same planar area compared to common approaches at a target depth of 10 cm at 3 Tesla. Improved parallel imaging performance of this configuration is also demonstrated. The concept can be further used to increase coil density. PMID:28186135

  17. Partially orthogonal resonators for magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Chacon-Caldera, Jorge; Malzacher, Matthias; Schad, Lothar R.

    2017-02-01

    Resonators for signal reception in magnetic resonance are traditionally planar to restrict coil material and avoid coil losses. Here, we present a novel concept to model resonators partially in a plane with maximum sensitivity to the magnetic resonance signal and partially in an orthogonal plane with reduced signal sensitivity. Thus, properties of individual elements in coil arrays can be modified to optimize physical planar space and increase the sensitivity of the overall array. A particular case of the concept is implemented to decrease H-field destructive interferences in planar concentric in-phase arrays. An increase in signal to noise ratio of approximately 20% was achieved with two resonators placed over approximately the same planar area compared to common approaches at a target depth of 10 cm at 3 Tesla. Improved parallel imaging performance of this configuration is also demonstrated. The concept can be further used to increase coil density.

  18. Partial peritoneal alimentation in an infant.

    PubMed

    Merritt, R J; Atkinson, J B; Whalen, T V; Thomas, D W; Sinatra, F R; Roloson, G J

    1988-01-01

    We provided partial peritoneal alimentation to a 1.69-kg 11-month-old premature infant who had no available central venous access, depleted peripheral venous access, and gastrointestinal dysfunction. A cuffed silastic catheter was surgically inserted into the suprahepatic space. An alimentation solution was continuously infused into the peritoneum for 28 days to supplement peripheral venous and nasogastric alimentation and contributed 42 +/- 15% of total calories daily. Weight gain was achieved, but complications included hypoglycemia, hypophosphatemia, intravascular dehydration, catheter site leakage, ascites, and hydrocele. At autopsy 11 months later, lipid accumulation was present in the upper peritoneum and the hilar regions of the lungs secondary to preexisting lymphatic obstruction. Partial peritoneal alimentation may be feasible when other access routes are inadequate, but lymphatic obstruction is a contraindication to the peritoneal administration of lipid emulsions.

  19. Partial atrioventricular canal defect in a dog.

    PubMed

    Santamarina, G; Espino, L; Vila, M; Suarez, M L

    2002-01-01

    A case of a partial atrial canal defect is described in a nine-month-old female English setter. The patient had a large ostium primum atrial septal defect and a concurrent malformation of the mitral valve. Electrocardiographic and radiographic findings were suggestive of marked enlargement of the right heart and pulmonary overcirculation. Definitive diagnosis and assessment of the haemodynamic consequences were made using echocardiography. The magnitude of the left-to-right intracardiac shunt was estimated by measuring the pulmonary to systemic flow ratio (Qp/Qs) from Doppler-derived pulmonary and aortic blood flow. The results of this report suggest that dogs with a partial atrioventricular canal defect and concurrent mild mitral regurgitation may exhibit no clinical signs during the first years of life, even in cases with a Qp/Qs ratio of greater than 2.

  20. 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.

  1. 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.

  2. A partial snake for the AGS

    SciTech Connect

    Ratner, L.G.

    1990-01-01

    Based on snake experiments at the Indian University Cyclotron Facility and computer simulations at Brookhaven National Laboratory, as well as the conclusions of a BNL mini-workshop, we feel that a partial Siberian snake is a practical device for the AGS. It is anticipated that such a device could reduce the polarized beam tune-up time from 2--3 weeks to 2--3 days.

  3. Discrete Surface Modelling Using Partial Differential Equations.

    PubMed

    Xu, Guoliang; Pan, Qing; Bajaj, Chandrajit L

    2006-02-01

    We use various nonlinear partial differential equations to efficiently solve several surface modelling problems, including surface blending, N-sided hole filling and free-form surface fitting. The nonlinear equations used include two second order flows, two fourth order flows and two sixth order flows. These nonlinear equations are discretized based on discrete differential geometry operators. The proposed approach is simple, efficient and gives very desirable results, for a range of surface models, possibly having sharp creases and corners.

  4. 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.

  5. 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.

  6. 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.

  7. Simple technique for generating the partially coherent and partially polarized electromagnetic source

    NASA Astrophysics Data System (ADS)

    Ostrovsky, A. S.; Rodríguez, G.; Meneses, C.; Olvera, M. Á.; Juárez, E.

    2011-01-01

    The technique for generating the partially coherent and partially polarized source starting from the completely coherent and completely polarized laser source is proposed and analyzed. This technique differs from the known ones by the simplicity of its physical realization. An original technique for measuring the cross-spectral density matrix is employed. Experimental results of the characterization the coherence and polarization properties of the generated source are shown.

  8. 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

  9. Full and Partial Cloaking in Electromagnetic Scattering

    NASA Astrophysics Data System (ADS)

    Deng, Youjun; Liu, Hongyu; Uhlmann, Gunther

    2017-01-01

    In this paper, we consider two regularized transformation-optics cloaking schemes for electromagnetic (EM) waves. Both schemes are based on the blowup construction with the generating sets being, respectively, a generic curve and a planar subset. We derive sharp asymptotic estimates in assessing the cloaking performances of the two constructions in terms of the regularization parameters and the geometries of the cloaking devices. The first construction yields an approximate full-cloak, whereas the second construction yields an approximate partial-cloak. Moreover, by incorporating properly chosen conducting layers, both cloaking constructions are capable of nearly cloaking arbitrary EM contents. This work complements the existing results in Ammari et al. (SIAM J Appl Math 73:2055-2076, 2013), Bao and Liu (SIAM J Appl Math 74:724-742, 2014), Bao et al. (J Math Pure Appl (9) 101:716-733, 2014) on approximate EM cloaks with the generating set being a singular point, and it also extends Deng et al. (On regularized full- and partial-cloaks in acoustic scat- tering. Preprint, arXiv:1502.01174, 2015), Li et al. (Commun Math Phys, 335:671-712, 2015) on regularized full and partial cloaks for acoustic waves governed by the Helmholtz system to the more challenging EM case governed by the full Maxwell system.

  10. 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

  11. 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.

  12. Partially massless higher-spin theory

    NASA Astrophysics Data System (ADS)

    Brust, Christopher; Hinterbichler, Kurt

    2017-02-01

    We study a generalization of the D-dimensional Vasiliev theory to include a tower of partially massless fields. This theory is obtained by replacing the usual higher-spin algebra of Killing tensors on (A)dS with a generalization that includes "third-order" Killing tensors. Gauging this algebra with the Vasiliev formalism leads to a fully non-linear theory which is expected to be UV complete, includes gravity, and can live on dS as well as AdS. The linearized spectrum includes three massive particles and an infinite tower of partially massless particles, in addition to the usual spectrum of particles present in the Vasiliev theory, in agreement with predictions from a putative dual CFT with the same symmetry algebra. We compute the masses of the particles which are not fixed by the massless or partially massless gauge symmetry, finding precise agreement with the CFT predictions. This involves computing several dozen of the lowest-lying terms in the expansion of the trilinear form of the enlarged higher-spin algebra. We also discuss nuances in the theory that occur in specific dimensions; in particular, the theory dramatically truncates in bulk dimensions D = 3 , 5 and has non-diagonalizable mixings which occur in D = 4 , 7.

  13. 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.

  14. 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

  15. 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.

  16. 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).

  17. 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.

  18. The partial fission of fast spinning asteroids

    NASA Astrophysics Data System (ADS)

    Tardivel, Simon; Sanchez, Paul; Scheeres, Daniel J.

    2016-10-01

    The spin rates of asteroids systematically change over time due the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect. Above a certain spin rate that depends on the body's density, regions of an asteroid can enter in tension, with components held to the body by cohesive forces. When the body fails, deformation or fission can occur. Catastrophic fission leading to complete disruption has been directly observed in active asteroid P/2013 R3. Partial fission, the loss of only part of the body, has been proposed as a mechanism for the formation of binaries and is explored here.The equatorial cavities of (341843) 2008 EV5 and of (185851) 2000 DP107 (a binary system) are consistent with a localized partial fission of the body (LPSC 2016 #1036). The examination of the gravity field of these bodies reveals that a mass placed within these cavities could be shed. In this mechanism, the outward pull of inertial forces creates an average stress at the cavity interface of ≈1 Pa for 2008 EV5 and ≈3 Pa for 2000 DP107 at spin periods of ≈3.15 h for the assumed densities of 1.3 g/cm3.This work continues the study of this partial, localized fission. Specifically, it addresses the issue of the low cohesion necessary to the mechanism. These cohesion values are typically lower than global strength values inferred on other asteroids (10 - 200 Pa), meaning that partial fission may occur prior to larger-scale deformations. Yet, several processes can explain the discrepancy, as they can naturally segregate particles by size. For instance, landslides or granular convection (Brazil nut effect) could bring larger boulders to the equator of the body, while finer particles are left at higher latitudes or sink to the center. Conversely, failure of the interior could bring boulders to the surface. The peculiar profile shape of these asteroids, shared by many binaries (e.g. 1999 KW4, 1996 FG3) may also be a clue of this heterogeneity, as this "spin top" shape is obtained in simulations with

  19. QTL involved in the partial restoration of male fertility of C-type cytoplasmic male sterility in maize.

    PubMed

    Kohls, Susanne; Stamp, Peter; Knaak, Carsten; Messmer, Rainer

    2011-07-01

    Partial restoration of male fertility limits the use of C-type cytoplasmic male sterility (C-CMS) for the production of hybrid seeds in maize. Nevertheless, the genetic basis of the trait is still unknown. Therefore, the aim to this study was to identify genomic regions that govern partial restoration by means of a QTL analysis carried out in an F(2) population (n = 180). This population was derived from the Corn Belt inbred lines B37C and K55. F(2)BC(1) progenies were phenotyped at three locations in Switzerland. Male fertility was rated according to the quality and number of anthers as well as the anthesis-silking interval. A weak effect of environment on the expression of partial restoration was reflected by high heritabilities of all fertility-related traits. Partial restoration was inherited like an oligogenic trait. Three major QTL regions were found consistently across environments in the chromosomal bins 2.09, 3.06 and 7.03. Therefore, a marker-assisted counter-selection of partial restoration is promising. Minor QTL regions were found on chromosomes 3, 4, 5, 6 and 8. A combination of partial restorer alleles at different QTL can lead to full restoration of fertility. The maternal parent was clearly involved in the partial restoration, because the restorer alleles at QTL in bins 2.09, 6.04 and 7.03 originated from B37. The three major QTL regions collocated with other restorer genes of maize, a phenomenon, which seems to be typical for restorer genes. Therefore, a study of the clusters of restorer genes in maize could lead to a better understanding of their evolution and function. In this respect, the long arm of chromosome 2 is particularly interesting, because it harbors restorer genes for the three major CMS systems (C, T and S) of maize.

  20. Genetic contributions to visuospatial cognition in Williams syndrome: insights from two contrasting partial deletion patients

    PubMed Central

    2014-01-01

    Background Williams syndrome (WS) is a rare neurodevelopmental disorder arising from a hemizygotic deletion of approximately 27 genes on chromosome 7, at locus 7q11.23. WS is characterised by an uneven cognitive profile, with serious deficits in visuospatial tasks in comparison to relatively proficient performance in some other cognitive domains such as language and face processing. Individuals with partial genetic deletions within the WS critical region (WSCR) have provided insights into the contribution of specific genes to this complex phenotype. However, the combinatorial effects of different genes remain elusive. Methods We report on visuospatial cognition in two individuals with contrasting partial deletions in the WSCR: one female (HR), aged 11 years 9 months, with haploinsufficiency for 24 of the WS genes (up to GTF2IRD1), and one male (JB), aged 14 years 2 months, with the three most telomeric genes within the WSCR deleted, or partially deleted. Results Our in-depth phenotyping of the visuospatial domain from table-top psychometric, and small- and large-scale experimental tasks reveal a profile in HR in line with typically developing controls, albeit with some atypical features. These data are contrasted with patient JB’s atypical profile of strengths and weaknesses across the visuospatial domain, as well as with more substantial visuospatial deficits in individuals with the full WS deletion. Conclusions Our findings point to the contribution of specific genes to spatial processing difficulties associated with WS, highlighting the multifaceted nature of spatial cognition and the divergent effects of genetic deletions within the WSCR on different components of visuospatial ability. The importance of general transcription factors at the telomeric end of the WSCR, and their combinatorial effects on the WS visuospatial phenotype are also discussed. PMID:25057328

  1. C601S mutation in the androgen receptor results in partial loss of androgen function.

    PubMed

    Singh, Rajender; Singh, Pooja; Gupta, Nalini J; Chakrabarty, Baidyanath; Singh, Lalji; Thangaraj, Kumarasamy

    2010-11-01

    The present study was undertaken on a case of partial androgen insensitivity syndrome to look at the etiology of the disorder. The patient exhibited a female phenotype despite 46,XY chromosome complement. Direct DNA sequencing of coding region of the androgen receptor gene in this case revealed a 2329G>C substitution (cDNA sequence reference) in exon 3 of the gene. The substitution resulted in replacement of Cys with Ser at codon 601 of the ligand-binding domain of the protein. Analyses on 200 control samples revealed absence of this substitution(s). In vitro assays were done using COS-1 cells. The mutation resulted in partial (∼40%) loss of ligand-binding and significant (∼70%) loss of downstream transactivation function. The mutation was absent in the controls. The findings are particularly interesting since another substitution at the same codon (TGC-TTC) has been reported in association with complete androgen insensitivity syndrome.

  2. Gene Therapy

    MedlinePlus

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

  3. Partially coherent flat-topped beam and its propagation.

    PubMed

    Ge, Di; Cai, Yangjian; Lin, Qiang

    2004-08-20

    A partially coherent beam with flat-topped profile is proposed. The cross-spectral density of this beam can be expressed as a finite series of the cross-spectral density of partially coherent Gaussian-Schell-model beams with different parameters. Analytical propagation formulas for partially coherent flat-topped beams are derived through aligned and misaligned optical systems. The propagation property of partially coherent flat-topped beams in free space is illustrated numerically. The fractional Fourier transform of partially coherent fiat-topped beams is also studied. Our method provides a convenient way to describe partially coherent flat-topped beams and treat their propagation and transformation.

  4. 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

  5. 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.

  6. 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.

  7. Resistance to extinction after schedules of partial delay or partial reinforcement in rats with hippocampal lesions.

    PubMed

    Rawlins, J N; Feldon, J; Ursin, H; Gray, J A

    1985-01-01

    Two experimental procedures were employed to establish the reason why hippocampal lesions apparently block the development of tolerance for aversive events in partial reinforcement experiments, but do not do so in partial punishment experiments. Rats were trained to run in a straight alley following hippocampal lesions (HC), cortical control lesions (CC) or sham operations (SO), and resistance to extinction was assessed following differing acquisition conditions. In Experiment 1 a 4-8 min inter-trial interval (ITI) was used. Either every acquisition trial was rewarded immediately (Continuous Reinforcement, CR), or only a randomly selected half of the trials were immediately rewarded, the reward being delayed for thirty seconds on the other trials (Partial Delay, PD). This delay procedure produced increased resistance to extinction in rats in all lesion groups. In Experiment 2 the ITI was reduced to a few seconds, and rats were trained either on a CR schedule, or on a schedule in which only half the trials were rewarded (Partial Reinforcement, PR). This form of partial reinforcement procedure also produced increased resistance to extinction in rats in all lesion groups. It thus appears that hippocampal lesions only prevent the development of resistance to aversive events when the interval between aversive and subsequent appetitive events exceeds some minimum value.

  8. Elementary functions: propagation of partially coherent light.

    PubMed

    Burvall, Anna; Smith, Arlene; Dainty, Christopher

    2009-07-01

    The theory of propagation of partially coherent light is well known, but performing numerical calculations still presents a difficulty because of the dimensionality of the problem. We propose using a recently introduced method based on the use of elementary functions [Wald et al. Proc. SPIE6040, 59621G (2005)] to reduce the integrals to two dimensions. We formalize the method, describe its inherent assumptions and approximations, and introduce a sampling criterion for adequate interpolation. We present an analysis of some special cases, such as the Gaussian Schell-model beam, and briefly discuss generalized numerical propagation of two-dimensional field distributions.

  9. 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.

  10. Multiple Partial Siberian Snakes in the AGS

    NASA Astrophysics Data System (ADS)

    Takano, J.; Ahrens, L. A.; Bai, M.; Brown, K.; Courant, E. D.; Gardner, C. J.; Glenn, J. W.; Hattori, T.; Huang, H.; Lin, F.; Luccio, A. U.; MacKay, W. W.; Okamura, M.; Roser, T.; Tepikian, S.; Tsoupas, N.; Yip, K.; Zelenski, A.; Zeno, K.

    2007-06-01

    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.

  11. A partial differential equation for pseudocontact shift.

    PubMed

    Charnock, G T P; Kuprov, Ilya

    2014-10-07

    It is demonstrated that pseudocontact shift (PCS), viewed as a scalar or a tensor field in three dimensions, obeys an elliptic partial differential equation with a source term that depends on the Hessian of the unpaired electron probability density. The equation enables straightforward PCS prediction and analysis in systems with delocalized unpaired electrons, particularly for the nuclei located in their immediate vicinity. It is also shown that the probability density of the unpaired electron may be extracted, using a regularization procedure, from PCS data.

  12. Radiation of partially ionized atomic hydrogen

    NASA Technical Reports Server (NTRS)

    Soon, W. H.; Kunc, J. A.

    1990-01-01

    A nonlinear collisional-radiative model for determination of production of electrons, positive and negative ions, excited atoms, and spectral and continuum line intensities in stationary partially ionized atomic hydrogen is presented. Transport of radiation is included by coupling the rate equations for production of the electrons, ions, and excited atoms with the radiation escape factors, which are not constant but depend on plasma conditions. It is found that the contribution of the negative ion emission to the total continuum emission can be important. Comparison of the calculated total continuum emission coefficient, including the negative ion emission, is in good agreement with experimental results.

  13. Visual Distinctness Determined by Partially Invariant Features

    DTIC Science & Technology

    2000-03-01

    DISTINCTNESS DETERMINED BY PARTIALLY INVARIANT FEATURES. J.A. Garcia, J. Fdez-Valdivia Departamento de Ciencias de la Computacion e I.A. Univ. de Granada...E.T.S. de Ingenieria Informatica. 18071 Granada. Spain E-mail: jagsadecsai.ugr.es, J.Fdez-Valdivia@decsai.ugr.es Xose R. Fdez-Vidal Departamento de... Fisica Aplicada. Univ. de Santiago de Compostela. Facultad de Fisica . 15706 Santiago de Compostela. Spain E-mail: faxose@usc.es Rosa Rodriguez-Sanchez

  14. Turning points in removable partial denture philosophy.

    PubMed

    Waliszewski, Michael P

    2010-10-01

    This article discusses key turning points in removable partial denture (RPD) philosophy. Early advancements tended to focus upon improving the technical quality of the prosthesis itself. The beginning of the 20th century brought significant public pressure upon the dental profession due to consequences associated with poor quality fixed prostheses. The result was dramatic improvement and heavy demand for RPDs. Technical and efficiency issues conspired to temper this enthusiasm, eventually resulting in reduced respect for RPDs. By highlighting key writings and technical issues during these periods of change it is hoped the reader will gain a more precise understanding of the current status of RPD philosophy.

  15. Communication modes with partially coherent fields.

    PubMed

    Martinsson, Per; Lajunen, Hanna; Friberg, Ari T

    2007-10-01

    We develop a theory for the description of partially coherent wave fields in linear optical systems in terms of the so-called communication modes. The communication modes are the singular functions and singular values of the appropriate propagation kernels. In particular, we show that optical fields of any state of coherence may be readily propagated through deterministic systems using the modal representation based on the system properties. The relation of the communication modes to the conventional coherent-mode representation is discussed, and expressions for the effective degree of coherence in the optical system are derived. The results are illustrated by numerical examples in optical near-field geometry.

  16. Partial muscle carnitine palmitoyltransferase-A deficiency

    SciTech Connect

    Ross, N.S.; Hoppel, C.L.

    1987-01-02

    After initiation of ibuprofen therapy, a 45-year-old woman developed muscle weakness and tenderness with rhabdomyolysis, culminating in respiratory failure. A muscle biopsy specimen showed a vacuolar myopathy, and markedly decreased muscle carnitine content and carnitine palmitoyltransferase activity. Following recovery, muscle carnitine content was normal but carnitine palmitoyltransferase activity was still abnormally low. The ratio of palmitoyl-coenzyme A plus carnitine to palmitoylcarnitine oxidation by muscle mitochondria isolated from the patient was markedly decreased. The authors conclude that transiently decreased muscle carnitine content interacted with partial deficiency of carnitine palmitoyltransferase-A to produce rhabdomyolysis and respiratory failure and that ibuprofen may have precipitated the clinical event.

  17. Partial restoration of chiral symmetry inside hadrons

    SciTech Connect

    Iritani, Takumi; Cossu, Guido; Hashimoto, Shoji

    2016-01-22

    We investigate the spatial distribution of the chiral condensate around static color sources for both quark-antiquark and three-quark systems. In the QCD vacuum a tube-like structure of chromo fields appears between color sources, which leads to a linearly confining potential. We show that the magnitude of the condensate is reduced inside the flux-tube, which suggests that chiral symmetry is partially restored inside the hadrons. By using a static baryon source in a periodic box as a model of the nuclear matter, we estimate the restoration of chiral symmetry with finite baryon number density.

  18. Lax integrable nonlinear partial difference equations

    NASA Astrophysics Data System (ADS)

    Sahadevan, R.; Nagavigneshwari, G.

    2015-03-01

    A systematic investigation to derive nonlinear lattice equations governed by partial difference equations admitting specific Lax representation is presented. Further whether or not the identified lattice equations possess other characteristics of integrability namely Consistency Around the Cube (CAC) property and linearizability through a global transformation is analyzed. Also it is presented that how to derive higher order ordinary difference equations or mappings from the obtained lattice equations through periodic reduction and investigated whether they are measure preserving or linearizable and admit sufficient number of integrals leading to their integrability.

  19. Robot-assisted adrenalectomy (total, partial, & metastasectomy).

    PubMed

    Ball, Mark W; Allaf, Mohamad E

    2014-11-01

    Robotic-assisted adrenalectomy is an increasingly used intervention for patients with a variety of surgical adrenal lesions, including adenomas, aldosteronomas, pheochromocytomas, and metastases to the adrenal gland. Compared with traditional laparoscopy, robotic adrenalectomy has comparable perioperative outcomes and is associated with improved hospital length of stay and blood loss, though it does come at a cost premium. Emerging literature also supports a role for robotics in partial adrenalectomy and metastasectomy. Ultimately, well-conducted prospective trials are needed to fully define the role of robotics in the surgical management of adrenal disease.

  20. [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.

  1. Benzene partial hydrogenation: advances and perspectives.

    PubMed

    Foppa, Lucas; Dupont, Jairton

    2015-04-07

    The partial hydrogenation of benzene to cyclohexene is an economically interesting and technically challenging reaction. Over the last four decades, a lot of work has been dedicated to the development of an exploitable process and several approaches have been investigated. However, environmental constraints often represent a limit to their industrial application, making further research in this field necessary. The goal of this review is to highlight the main findings of the different disciplines involved in understanding the governing principles of this reaction from a sustainable chemistry standpoint. Special emphasis is given to ruthenium-catalyzed liquid phase batch hydrogenation of benzene.

  2. Computing Partial Transposes and Related Entanglement Functions

    NASA Astrophysics Data System (ADS)

    Maziero, Jonas

    2016-12-01

    The partial transpose (PT) is an important function for entanglement testing and quantification and also for the study of geometrical aspects of the quantum state space. In this article, considering general bipartite and multipartite discrete systems, explicit formulas ready for the numerical implementation of the PT and of related entanglement functions are presented and the Fortran code produced for that purpose is described. What is more, we obtain an analytical expression for the Hilbert-Schmidt entanglement of two-qudit systems and for the associated closest separable state. In contrast to previous works on this matter, we only use the properties of the PT, not applying Lagrange multipliers.

  3. 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.

  4. 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.

  5. Treatment algorithms in refractory partial epilepsy.

    PubMed

    Jobst, Barbara C

    2009-09-01

    An algorithm is a "step-by-step procedure for solving a problem or accomplishing some end....in a finite number of steps." (Merriam-Webster, 2009). Medical algorithms are decision trees to help with diagnostic and therapeutic decisions. For the treatment of epilepsy there is no generally accepted treatment algorithm, as individual epilepsy centers follow different diagnostic and therapeutic guidelines. This article presents two algorithms to guide decisions in the treatment of refractory partial epilepsy. The treatment algorithm describes a stepwise diagnostic and therapeutic approach to intractable medial temporal and neocortical epilepsy. The surgical algorithm guides decisions in the surgical treatment of neocortical epilepsy.

  6. The CCAAT box-binding factor stimulates ammonium assimilation in Saccharomyces cerevisiae, defining a new cross-pathway regulation between nitrogen and carbon metabolisms.

    PubMed

    Dang, V D; Bohn, C; Bolotin-Fukuhara, M; Daignan-Fornier, B

    1996-04-01

    In Saccharomyces cerevisiae, carbon and nitrogen metabolisms are connected via the incorporation of ammonia into glutamate; this reaction is catalyzed by the NADP-dependent glutamate dehydrogenase (NADP-GDH) encoded by the GDH1 gene. In this report, we show that the GDH1 gene requires the CCAAT box-binding activator (HAP complex) for optimal expression. This conclusion is based on several lines of evidence: (1) overexpression of GDH1 can correct the growth defect of hap2 and hap3 mutants on ammonium sulfate as a nitrogen source, (ii) Northern (RNA) blot analysis shows that the steady-state level of GDH1 mRNA is strongly lowered in a hap2 mutant, (iii) expression of a GDH1-lacZ fusion is drastically reduced in hap mutants, (iv) NADP-GDH activity is several times lower in the hap mutants compared with that in the isogenic wild-type strain, and finally, (v) site-directed mutagenesis of two consensual HAP binding sites in the GDH1 promoter strongly reduces expression of GDH1 and makes it HAP independent. Expression of GDH1 is also regulated by the carbon source, i.e., expression is higher on lactate than on ethanol, glycerol, or galactose, with the lowest expression being found on glucose. Finally, we show that a hap2 mutation does not affect expression of other genes involved in nitrogen metabolism (GDH2, GLN1, and GLN3 encoding, respectively, the NAD-GDH, glutamine synthetase, and a general activator of several nitrogen catabolic genes). The HAP complex is known to regulate expression of several genes involved in carbon metabolism; its role in the control of GDH1 gene expression, therefore, provides evidence for a cross-pathway regulation between carbon and nitrogen metabolisms.

  7. Method of detecting oxygen partial pressure and oxygen partial pressure sensor

    SciTech Connect

    Dees, D.W.

    1991-12-31

    This invention is comprised of 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.

  8. Gene therapy for deafness: How close are we?

    PubMed

    Moser, Tobias

    2015-07-08

    Virus-mediated transfer of genes encoding the mechanotransducer channel candidates TMC1 and TMC2 into hair cells of the ear partially restores hearing in animal models of human genetic deafness (Askew et al., this issue).

  9. Functional rehabilitation of partial cortical blindness?

    PubMed

    Stoerig, Petra

    2008-01-01

    The current doctrine regards fields of partial cortical blindness as permanent once a temporally restricted window for spontaneous recovery has passed. Accordingly, neuropsychological rehabilitation mainly applies compensatory procedures that train patients to make better use of their sighted field. The more ambitious goal of functional recovery depends on the survival of pathways that continue to transmit retinal information from the blind field. Although wide-spread antero- and retrograde degeneration follows lesions that destroy or denervate the primary visual cortex and cause partial cortical blindness, several retinofugal pathways survive in cats, monkeys, and humans. In all three species, they subserve a variety of visual functions which develop and improve with practice. Post lesion plasticity is greater when the lesion occurs early in life, but changes in behavioural performance and brain responses have also been demonstrated in late lesion subjects. Although the extent of functional improvement is variable, and the most effective approaches still need to be established across cohorts, the evidence for perceptual learning in fields of cortical blindness indicates that the visual processes mediated by the surviving parts of the visual system can be harnessed to improve functional outcome.

  10. 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.

  11. Superconformal partial waves in Grassmannian field theories

    NASA Astrophysics Data System (ADS)

    Doobary, Reza; Heslop, Paul

    2015-12-01

    We derive superconformal partial waves for all scalar four-point functions on a super Grassmannian space Gr( m| n, 2 m|2 n) for all m, n. This family of four-point functions includes those of all (arbitrary weight) half BPS operators in both N=4 SYM ( m = n = 2) and in N = 2 superconformal field theories in four dimensions ( m = 2 , n = 1) on analytic superspace. It also includes four-point functions of all (arbitrary dimension) scalar fields in non-supersymmetric conformal field theories ( m = 2 , n = 0) on Minkowski space, as well as those of a certain class of representations of the compact SU(2 n) coset spaces. As an application we then specialise to N=4 SYM and use these results to perform a detailed superconformal partial wave analysis of the four-point functions of arbitrary weight half BPS operators. We discuss the non-trivial separation of protected and unprotected sectors for the <2222>, <2233> and <3333> cases in an SU( N) gauge theory at finite N. The <2233> correlator predicts a non-trivial protected twist four sector for <3333> which we can completely determine using the knowledge that there is precisely one such protected twist four operator for each spin.

  12. 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.

  13. Partial accretion regime of accreting millisecond pulsars

    NASA Astrophysics Data System (ADS)

    Eksi, Kazim

    2016-07-01

    The inner parts of the disks around neutron stars in low mass X-ray binaries may become geometrically thick due to inhibition of accretion at the disk mid-plane when the central object is rotating rapidly. In such a case matter inflowing through the disk may keep accreting onto the poles of the neutron star from the parts of the disk away from the disk mid-plane while the matter is propelled at the disk mid-plane. An important ingredient of the evolution of millisecond pulsars is then the fraction of the inflowing matter that can accrete onto the poles in the fast rotation regime depending on the fastness parameter. This ``soft'' propeller regime may be associated with the rapid decay stage observed in the light curves of several accreting millisecond pulsars. To date only a few studies considered the partial accretion regime. By using geometrical arguments we improve the existing studies and test the model by reproducing the lightcurves of millisecond X-ray pulsars via time dependent simulations of disk evolution. We also present analytical solutions that represent disks with partial accretion.

  14. 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.

  15. Partial reinforcement, extinction, and placebo analgesia.

    PubMed

    Au Yeung, Siu Tsin; Colagiuri, Ben; Lovibond, Peter F; Colloca, Luana

    2014-06-01

    Numerous studies indicate that placebo analgesia can be established via conditioning procedures. However, these studies have exclusively involved conditioning under continuous reinforcement. Thus, it is currently unknown whether placebo analgesia can be established under partial reinforcement and how durable any such effect would be. We tested this possibility using electrocutaneous pain in healthy volunteers. Sixty undergraduates received placebo treatment (activation of a sham electrode) under the guise of an analgesic trial. The participants were randomly allocated to different conditioning schedules, namely continuous reinforcement (CRF), partial reinforcement (PRF), or control (no conditioning). Conditioning was achieved by surreptitiously reducing pain intensity during training when the placebo was activated compared with when it was inactive. For the CRF group, the placebo was always followed by a surreptitious reduction in pain during training. For the PRF group, the placebo was followed by a reduction in pain stimulation on 62.5% of trials only. In the test phase, pain stimulation was equivalent across placebo and no placebo trials. Both CRF and PRF produced placebo analgesia, with the magnitude of initial analgesia being larger after CRF. However, although the placebo analgesia established under CRF extinguished during test phase, the placebo analgesia established under PRF did not. These findings indicate that PRF can induce placebo analgesia and that these effects are more resistant to extinction than those established via CRF. PRF may therefore reflect a novel way of enhancing clinical outcomes via the placebo effect.

  16. 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).

  17. Wetting of a partially immersed compliant rod

    NASA Astrophysics Data System (ADS)

    Hui, Chung-Yuen; Jagota, Anand

    2016-11-01

    The force on a solid rod partially immersed in a liquid is commonly used to determine the liquid-vapor surface tension by equating the measured force required to remove the rod from the liquid to the vertical component of the liquid-vapor surface tension. Here, we study how this process is affected when the rod is compliant. For equilibrium, we enforce force and configurational energy balance, including contributions from elastic energy. We show that, in general, the contact angle does not equal that given by Young's equation. If surface stresses are tensile, the strain in the immersed part of the rod is found to be compressive and to depend only on the solid-liquid surface stress. The strain in the dry part of the rod can be either tensile or compressive, depending on a combination of parameters that we identify. We also provide results for compliant plates partially immersed in a liquid under plane strain and plane stress. Our results can be used to extract solid surface stresses from such experiments.

  18. Partial triceps disruption: a case report.

    PubMed

    Foulk, David M; Galloway, Marc T

    2011-03-01

    Partial triceps tendon disruptions are a rare injury that can lead to debilitating outcomes if misdiagnosed or managed inappropriately. The clinician should have a high index of suspicion when the mechanism involves a fall onto an outstretched arm and there is resultant elbow extension weakness along with pain and swelling. The most common location of rupture is at the tendon-osseous junction. This case report illustrates a partial triceps tendon disruption with involvement of, primarily, the medial head and the superficial expansion. Physical examination displayed weakness with resisted elbow extension in a flexed position over 90°. Radiographs revealed a tiny fleck of bone proximal to the olecranon, but this drastically underestimated the extent of injury upon surgical exploration. Magnetic resonance imaging is essential to ascertain the percentage involvement of the tendon; it can be used for patient education and subsequently to determine treatment recommendations. Although excellent at finding associated pathology, it may misjudge the size of the tear. As such, physicians must consider associated comorbidities and patient characteristics when formulating treatment plans.

  19. Junction point on partially singular trajectories

    NASA Astrophysics Data System (ADS)

    Odia, Ameze; Bell, David J.

    2012-12-01

    In recent times, several works have been performed on the design of fuel optimal trajectories for space navigation. These works show the possibility of the existence of partially singular trajectories for systems that are linear analytic (Park et al. 2010). Linear analytic systems may show the existence of partially singular subarcs, and the point where these subarcs meet is called a junction point. Thus, knowledge about junction conditions became necessary when solving the optimal control problem for such systems. This led to the development of two 'theorems' on junction conditions, given by McDanell and Powers (McDanell, J.P. and Powers W.F. (1971), 'Necessary Conditions for Joining Optimal Singular and Nonsingular Sub Arcs', SIAM Journal of Control, 9, 161-173). However, the second 'theorem', which is now known as a conjecture, could not satisfy all classes of linear analytic system. Therefore, the aim of this study was to detect and correct the errors in the derivation of the McDanell and Powers conjecture. The error in their derivations was corrected and then tested on two newly mathematically constructed systems. The results of these tests were found to be satisfactory. This implies that by making the necessary corrections, the conjecture can still be useful in generating a general theorem for all classes of systems.

  20. Simple shear deformation of partially molten aplite

    NASA Astrophysics Data System (ADS)

    Stipp, Michael; Tullis, Jan; Berger, Alfons

    2013-04-01

    The tectonic processes which are important for melt distribution and transport in the intermediate and lower crust and which can result in crustal weakening are not yet well understood. Natural migmatites are usually overprinted by annealing and retrogression during uplift and exhumation, largely obliterating the deformation structures and microstructures of their partially molten history. Deformation experiments on partially molten crustal rocks have so far been conducted in pure shear geometry and mostly under low confining pressures in the brittle deformation field, both of which are not representative of nature. We carried out deformation experiments in simple shear that predominates in the crust and especially crustal shear zones. Undrained experiments were carried out on Enfield aplite at ~1.5 GPa, 900° -1000° C, and ˜ 5*10-6 s-1, conditions which favor crystal plastic deformation of quartz and feldspar (Dell'Angelo and Tullis, 1988). Sample slices 1.0-1.5 mm thick were placed between the shear pistons with the shear plane at a 45° -angle to the compression direction. Maximum shear strain in the experiments is ? ?2.8. Despite difficulties in controlling the melt content by varying the amount of added water, we were able to achieve the full range of brittle to crystal plastic deformation mechanisms. With decreasing melt content Enfield aplite displays a transition from discrete fracturing at a high angle (~70-90° ) to the shear plane (>20 vol.% melt), to cataclastic shearing (10-20 vol.% melt) and to crystal plastic deformation (