Science.gov

Sample records for partial gdh gene

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

    PubMed Central

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

    2014-01-01

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

  2. 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.

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

    PubMed

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

    2016-02-15

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

  4. 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.

  5. Mutations That Disrupt Either the pqq or the gdh Gene of Rahnella aquatilis Abolish the Production of an Antibacterial Substance and Result in Reduced Biological Control of Grapevine Crown Gall▿

    PubMed Central

    Guo, Yan Bin; Li, Jinyun; Li, Lei; Chen, Fan; Wu, Wenliang; Wang, Jianhui; Wang, Huimin

    2009-01-01

    Rahnella aquatilis HX2, a biocontrol agent for grapevine crown gall caused by Agrobacterium vitis, produces an antibacterial substance that inhibits the growth of A. vitis in vitro. In this study, we show that MH15 and MH16, two Tn5-induced mutants of HX2, have lost their abilities to inhibit A. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single Tn5 insertions. They are also impaired in producing pyrroloquinoline quinone (PQQ) or glucose dehydrogenase (GDH). Complementation of MH15 and MH16 with cosmid clones of CP465 and CP104 from an HX2 DNA library restored the antibiosis, biocontrol, and PQQ or GDH production phenotypes. A 6.7-kb BamHI fragment from CP465 that fully restored the MH15-affected phenotypes was cloned and sequenced. Sequence analysis of the mutated DNA region resulted in the identification of seven open reading frames (ORFs), six of which share significant homology with PQQ-synthesizing genes in other bacteria, designated pqqA through pqqF. Meanwhile, A 5.5-kb PstI fragment from CP104 fully complemented the MH16 mutant and contained a single ORF highly similar to that of genes coding for GDHs. An in-frame gdh deletion mutant has the same phenotypes as the Tn5 mutant of MH16. Complementation of both deletion and Tn5 gdh mutants restored the affected phenotypes to wild-type levels. Our results suggest that an antibacterial substance plays a role in biocontrol of A. vitis by HX2. PMID:19734331

  6. Differential interaction of hGDH1 and hGDH2 with manganese: Implications for metabolism and toxicity.

    PubMed

    Dimovasili, Christina; Aschner, Michael; Plaitakis, Andreas; Zaganas, Ioannis

    2015-09-01

    Manganese (Mn) is an essential trace element that serves as co-factor for many important mammalian enzymes. In humans, the importance of this cation is highlighted by the fact that low levels of Mn cause developmental and metabolic abnormalities and, on the other hand, chronic exposure to excessive amounts of Mn is characterized by neurotoxicity, possibly mediated by perturbation of astrocytic mitochondrial energy metabolism. Here we sought to study the effect of Mn on the two human glutamate dehydrogenases (hGDH1 and hGDH2, respectively), key mitochondrial enzymes involved in numerous cellular processes, including mitochondrial metabolism, glutamate homeostasis and neurotransmission, and cell signaling. Our studies showed that, compared to magnesium (Mg) and calcium (Ca), Mn exerted a significant inhibitory effect on both human isoenzymes with hGDH2 being more sensitive than hGDH1, especially under conditions of low ADP levels. Specifically, in the presence of 0.25 mM ADP, the Mn IC50 was 1.14 ± 0.02 mM and 1.54 ± 0.08 mM for hGDH2 and for hGDH1, respectively (p = 0.0001). Increasing Mn levels potentiated this differential effect, with 3 mM Mn inhibiting hGDH2 by 96.5% and hGDH1 by 70.2%. At 1 mM ADP, the Mn IC50 was 1.84 ± 0.02 mM and 2.04 ± 0.07 mM (p = 0.01) for hGDH2 and hGDH1, respectively, with 3 mM Mn inhibiting hGDH2 by 93.6% and hGDH1 by 70.9%. These results were due to the sigmoidal inhibitory curve of Mn that was more pronounced for hGDH2 than for hGDH1. Indeed, at 0.25 mM, the Hill coefficient value was higher for hGDH2 (3.42 ± 0.20) than for hGDH1 (1.94 ± 0.25; p = 0.0002) indicating that interaction of Mn with hGDH2 was substantially more co-operative than for hGDH1. These findings, showing an enhanced sensitivity of the hGDH2 isoenzyme to Mn, especially at low ADP levels, might be of pathophysiological relevance under conditions of Mn neurotoxicity.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2011-09-01

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

  9. 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.

  10. 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

  11. Partial characterization of nif genes from the bacterium Azospirillum amazonense.

    PubMed

    Potrich, D P; Passaglia, L M; Schrank, I S

    2001-09-01

    Azospirillum amazonense revealed genomic organization patterns of the nitrogen fixation genes similar to those of the distantly related species A. brasilense. Our work suggests that A. brasilense nifHDK, nifENX, fixABC operons and nifA and glnB genes may be structurally homologous to the counterpart genes of A. amazonense. This is the first analysis revealing homology between A. brasilense nif genes and the A. amazonense genome. Sequence analysis of PCR amplification products revealed similarities between the amino acid sequences of the highly conserved nifD and glnB genes of A. amazonense and related genes of A. brasilense and other bacteria. However, the A. amazonense non-coding regions (the upstream activator sequence region and the region between the nifH and nifD genes) differed from related regions of A. brasilense even in nitrogenase structural genes which are highly conserved among diazotrophic bacteria. The feasibility of the 16S ribosomal RNA gene-based PCR system for specific detection of A. amazonense was shown. Our results indicate that the PCR primers for 16S rDNA defined in this article are highly specific to A. amazonense and can distinguish this species from A. brasilense.

  12. 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.

  13. A partially linear tree-based regression model for assessing complex joint gene-gene and gene-environment effects.

    PubMed

    Chen, Jinbo; Yu, Kai; Hsing, Ann; Therneau, Terry M

    2007-04-01

    The success of genetic dissection of complex diseases may greatly benefit from judicious exploration of joint gene effects, which, in turn, critically depends on the power of statistical tools. Standard regression models are convenient for assessing main effects and low-order gene-gene interactions but not for exploring complex higher-order interactions. Tree-based methodology is an attractive alternative for disentangling possible interactions, but it has difficulty in modeling additive main effects. This work proposes a new class of semiparametric regression models, termed partially linear tree-based regression (PLTR) models, which exhibit the advantages of both generalized linear regression and tree models. A PLTR model quantifies joint effects of genes and other risk factors by a combination of linear main effects and a non-parametric tree -structure. We propose an iterative algorithm to fit the PLTR model, and a unified resampling approach for identifying and testing the significance of the optimal "pruned" tree nested within the tree resultant from the fitting algorithm. Simulation studies showed that the resampling procedure maintained the correct type I error rate. We applied the PLTR model to assess the association between biliary stone risk and 53 single nucleotide polymorphisms (SNPs) in the inflammation pathway in a population-based case-control study. The analysis yielded an interesting parsimonious summary of the joint effect of all SNPs. The proposed model is also useful for exploring gene-environment interactions and has broad implications for applying the tree methodology to genetic epidemiology research.

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

    PubMed Central

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

    2016-01-01

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

  15. Partial mixture model for tight clustering of gene expression time-course

    PubMed Central

    Yuan, Yinyin; Li, Chang-Tsun; Wilson, Roland

    2008-01-01

    Background Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On the other hand, there has been extensive use of maximum likelihood techniques for model parameter estimation. By contrast, the minimum distance estimator has been largely ignored. Results In this paper we show the inherent robustness of the minimum distance estimator that makes it a powerful tool for parameter estimation in model-based time-course clustering. To apply minimum distance estimation, a partial mixture model that can naturally incorporate replicate information and allow scattered genes is formulated. We provide experimental results of simulated data fitting, where the minimum distance estimator demonstrates superior performance to the maximum likelihood estimator. Both biological and statistical validations are conducted on a simulated dataset and two real gene expression datasets. Our proposed partial regression clustering algorithm scores top in Gene Ontology driven evaluation, in comparison with four other popular clustering algorithms. Conclusion For the first time partial mixture model is successfully extended to time-course data analysis. The robustness of our partial regression clustering algorithm proves the suitability of the combination of both partial mixture model and minimum distance estimator in this field. We show that tight clustering not only is capable to generate more profound understanding of the dataset under study well in accordance to established biological knowledge, but also presents interesting new hypotheses during interpretation of clustering results. In particular, we provide biological evidences that scattered genes can be relevant and are interesting subjects for study, in contrast to prevailing opinion

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

    PubMed

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

    2013-08-01

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

  17. 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.

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

    PubMed

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

    2008-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2016-02-01

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

  1. 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.

  2. 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; Lu, Hai -Jiang; Zhu, Peng -Jia; Jiang, Feng -Jian

    2015-07-17

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

  3. Mutants of Streptomyces roseosporus that express enhanced recombination within partially homologous genes.

    PubMed

    Hosted, T J; Baltz, R H

    1996-10-01

    Streptomyces roseosporus mutants that express enhanced recombination between partially homologous (homeologous) sequences were isolated by selection for recombination between the bacteriophage phi C31 derivative KC570 containing the Streptomyces coelicolor glucose kinase (glk) gene and the S. roseosporus chromosome. The frequencies of homeologous recombination in the ehr mutants were determined by measuring the chromosomal insertion frequencies of plasmids containing S. coelicolor glnA or whiG genes. S. roseosporus ehr mutants showed 10(2)- to 10(4)-fold increases in homeologous recombination relative to Ehr+ strains, but no increase in homologous recombination. Southern hybridization analysis revealed single unique sites for the insertion of each of the plasmids, and the crossovers occurred in frame and in proper translational register, yielding functional chimeric glnA and whiG genes.

  4. Characterization of Lr46, a gene conferring partial resistance to wheat leaf rust.

    PubMed

    Martínez, F; Niks, R E; Singh, R P; Rubiales, D

    2001-01-01

    Components of resistance conferred by the Lr46 gene, reported as causing "slow rusting" resistance to leaf rust in wheat, were studied and compared with the effects of Lr34 and genes for quantitative resistance in cv. Akabozu. Lr34 is a gene that confers non-hypersensitive type of resistance. The effect of Lr46 resembles that of Lr34 and other wheats reported with partial resistance. At macroscopic level, Lr46 produced a longer latency period than observed on the susceptible recurrent parent Lalbahadur, and a reduction of the infection frequency not associated with hypersensitivity. Microscopically, Lr46 increased the percentage of early aborted infection units not associated with host cell necrosis and decreased the colony size. The effect of Lr46 is comparable to that of Lr34 in adult plant stage, but in seedling stage its effect is weaker than that of Lr34.

  5. Breakpoint analysis of Turner patients with partial Xp deletions: implications for the lymphoedema gene location

    PubMed Central

    Boucher, C.; Sargent, C.; Ogata, T.; Affara, N.

    2001-01-01

    BACKGROUND—Turner syndrome is characterised by a 45,X karyotype and a variety of skeletal, lymphoedemic, and gonadal anomalies. Genes involved in the Turner phenotype are thought to be X/Y homologous with the X genes escaping X inactivation. Haploinsufficiency of the SHOX gene has been reported to cause the short stature seen in Turner syndrome patients. More recently, mutations of this gene have been shown to be associated with other skeletal abnormalities, suggesting that haploinsufficiency of SHOX causes all the Turner skeletal anomalies. No such gene has yet been identified for the lymphoedemic features.
METHODS—Fluorescence in situ hybridisation (FISH) analysis with PAC clones on nine patients with partially deleted X chromosomes was performed.
RESULTS/DISCUSSION—The Turner syndrome stigmata for each patient are described and correlation between the breakpoint and the phenotype discussed. A lymphoedema critical region in Xp11.4 is proposed and its gene content discussed with respect to that in the previously reported Yp11.2 lymphoedema critical region.


Keywords: Turner syndrome; lymphoedema; Xp11.4 PMID:11546827

  6. 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.

  7. 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

  8. Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences.

    PubMed

    Kuzmin, I V; Hughes, G J; Rupprecht, C E

    2006-08-01

    Partial nucleoprotein (N) gene sequences of the rhabdoviruses Obodhiang (OBOV), Kotonkon (KOTV), Rochambeau (RBUV), Kern canyon (KCV), Mount Elgon bat (MEBV), Kolongo (KOLV) and Sandjimba (SJAV) were generated and their phylogenetic positions within the family Rhabdoviridae were determined. Both OBOV and KOTV were placed within the genus Ephemerovirus. RBUV was joined to the same cluster, but more distantly. MEBV and KCV were grouped into a monophyletic cluster (putative genus) with Oita virus (OITAV). These three viruses, originating from different regions of the world, were all isolated from insectivorous bats and may be specific for these mammals. African avian viruses KOLV and SJAV were joined to each other and formed another clade at the genus level. Further, they were grouped with the recently characterized rhabdovirus Tupaia virus (TRV). Although the genetic distance was great, the grouping was supported by consistent bootstrap values. This observation suggests that viruses of this group may be distributed widely in the Old World. Non-synonymous/synonymous substitution ratio estimations (dN/dS) using a partial N gene fragment (241 codons) for the three rhabdovirus genera revealed contrasting patterns of evolution, where dN/dS values follow the pattern Ephemerovirus > Vesiculovirus > Lyssavirus. The magnitude of this ratio corresponds well with the number of negatively selected codons. The accumulation of dS appears evenly distributed along the gene fragment for all three genera. These estimations demonstrated clearly that lyssaviruses are subjected to the strongest constraints against amino acid substitutions, probably related to their particular niche and unique pathobiology.

  9. Changes in nitrogen assimilation, metabolism, and growth in transgenic rice plants expressing a fungal NADP(H)-dependent glutamate dehydrogenase (gdhA).

    PubMed

    Abiko, Tomomi; Wakayama, Masataka; Kawakami, Akira; Obara, Mitsuhiro; Kisaka, Hiroaki; Miwa, Tetsuya; Aoki, Naohiro; Ohsugi, Ryu

    2010-07-01

    In plants, glutamine synthetase (GS) is the enzyme that is mainly responsible for the assimilation of ammonium. Conversely, in microorganisms such as bacteria and Ascomycota, NADP(H)-dependent glutamate dehydrogenase (GDH) and GS both have important roles in ammonium assimilation. Here, we report the changes in nitrogen assimilation, metabolism, growth, and grain yield of rice plants caused by an ectopic expression of NADP(H)-GDH (gdhA) from the fungus Aspergillus niger in the cytoplasm. An investigation of the kinetic properties of purified recombinant protein showed that the fungal gdhA had 5.4-10.2 times higher V(max) value and 15.9-43.1 times higher K(m) value for NH(4)(+), compared with corresponding values for rice cytosolic GS as reported in the literature. These results suggested that the introduction of fungal GDH into rice could modify its ammonium assimilation pathway. We therefore expressed gdhA in the cytoplasm of rice plants. NADP(H)-GDH activities in the gdhA-transgenic lines were markedly higher than those in a control line. Tracer experiments by feeding with (15)NH(4)(+) showed that the introduced gdhA, together with the endogenous GS, directly assimilated NH(4)(+) absorbed from the roots. Furthermore, in comparison with the control line, the transgenic lines showed an increase in dry weight and nitrogen content when sufficient nitrogen was present, but did not do so under low-nitrogen conditions. Under field condition, the transgenic line examined showed a significant increase in grain yield in comparison with the control line. These results suggest that the introduction of fungal gdhA into rice plants could lead to better growth and higher grain yield by enhancing the assimilation of ammonium.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

    Kameda, K; Goodridge, A G

    1991-01-01

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

  15. 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)

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

    PubMed Central

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

    2015-01-01

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

  17. Function of Partially Duplicated Human α7 Nicotinic Receptor Subunit CHRFAM7A Gene

    PubMed Central

    de Lucas-Cerrillo, Ana M.; Maldifassi, M. Constanza; Arnalich, Francisco; Renart, Jaime; Atienza, Gema; Serantes, Rocío; Cruces, Jesús; Sánchez-Pacheco, Aurora; Andrés-Mateos, Eva; Montiel, Carmen

    2011-01-01

    The neuronal α7 nicotinic receptor subunit gene (CHRNA7) is partially duplicated in the human genome forming a hybrid gene (CHRFAM7A) with the novel FAM7A gene. The hybrid gene transcript, dupα7, has been identified in brain, immune cells, and the HL-60 cell line, although its translation and function are still unknown. In this study, dupα7 cDNA has been cloned and expressed in GH4C1 cells and Xenopus oocytes to study the pattern and functional role of the expressed protein. Our results reveal that dupα7 transcript was natively translated in HL-60 cells and heterologously expressed in GH4C1 cells and oocytes. Injection of dupα7 mRNA into oocytes failed to generate functional receptors, but when co-injected with α7 mRNA at α7/dupα7 ratios of 5:1, 2:1, 1:1, 1:5, and 1:10, it reduced the nicotine-elicited α7 current generated in control oocytes (α7 alone) by 26, 53, 75, 93, and 94%, respectively. This effect is mainly due to a reduction in the number of functional α7 receptors reaching the oocyte membrane, as deduced from α-bungarotoxin binding and fluorescent confocal assays. Two additional findings open the possibility that the dominant negative effect of dupα7 on α7 receptor activity observed in vitro could be extrapolated to in vivo situations. (i) Compared with α7 mRNA, basal dupα7 mRNA levels are substantial in human cerebral cortex and higher in macrophages. (ii) dupα7 mRNA levels in macrophages are down-regulated by IL-1β, LPS, and nicotine. Thus, dupα7 could modulate α7 receptor-mediated synaptic transmission and cholinergic anti-inflammatory response. PMID:21047781

  18. 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.

  19. SLC25A22 is a Novel Gene for Migrating Partial Seizures in Infancy

    PubMed Central

    Poduri, Annapurna; Heinzen, Erin L.; Chitsazzadeh, Vida; Lasorsa, Francesco Massimo; Elhosary, P. Christina; LaCoursiere, Christopher M.; Martin, Emilie; Yuskaitis, Christopher J.; Hill, Robert Sean; Atabay, Kutay Deniz; Barry, Brenda; Partlow, Jennifer N.; Bashiri, Fahad A.; Zeidan, Radwan M.; Elmalik, Salah A.; Kabiraj, Mohammad M.U.; Kothare, Sanjeev; Stödberg, Tommy; Scheffer, Ingrid E.; Barkovich, A. James; Palmieri, Ferdinando; Salih, Mustafa A.; Walsh, Christopher A.

    2014-01-01

    Objective To identify a genetic cause for migrating partial seizures in infancy (MPSI). Methods We characterized a consanguineous pedigree with MPSI and obtained DNA from affected and unaffected family members. We analyzed single nucleotide polymorphism (SNP) 500K data to identify regions with evidence for linkage. We performed whole exome sequencing and analyzed homozygous variants in regions of linkage to identify a candidate gene and performed functional studies of the candidate gene SLC25A22. Results In a consanguineous pedigree with two individuals with MPSI, we identified two regions of linkage, chromosome 4p16.1-p16.3 and chromosome 11p15.4-pter. Using whole exome sequencing, we identified 8 novel homozygous variants in genes in these regions. Only one variant, SLC25A22 c.G328C, results in a change of a highly conserved amino acid (p.G110R) and was not present in control samples. SLC25A22 encodes a glutamate transporter with strong expression in the developing brain. We show that the specific G110R mutation, located in a transmembraine domain of the protein, disrupts mitochondrial glutamate transport. Interpretation We have shown that MPSI can be inherited and have identified a novel homozygous mutation in SLC25A22 in the affected individuals. Our data strongly suggest that SLC25A22 is responsible for MPSI, a severe condition with few known etiologies. We have demonstrated that a combination of linkage analysis and whole exome sequencing can be used for disease gene discovery. Finally, as SLC25A22 had been implicated in the distinct syndrome neonatal epilepsy with suppression bursts on EEG, we have expanded the phenotypic spectrum associated with SLC25A22. PMID:24596948

  20. Chicken liver glutamate dehydrogenase (GDH) demonstrates a histone H3 specific protease (H3ase) activity in vitro.

    PubMed

    Purohit, Jogeswar S; Tomar, Raghuvir S; Panigrahi, Anil K; Pandey, Shashibhal M; Singh, Divya; Chaturvedi, Madan M

    2013-11-01

    Site-specific proteolysis of the N or C-terminus of histone tails has emerged as a novel form of irreversible post-translational modifications assigned to histones. Though there are many reports describing histone specific proteolysis, there are very few studies on purification of a histone specific protease. Here, we demonstrate a histone H3 specific protease (H3ase) activity in chicken liver nuclear extract. H3ase was purified to homogeneity and identified as glutamate dehydrogenase (GDH) by sequencing. A series of biochemical experiments further confirmed that the H3ase activity was due to GDH. The H3ase clipped histone H3 products were sequenced by N-terminal sequencing and the precise clipping sites of H3ase were mapped. H3ase activity was only specific to chicken liver as it was not demonstrated in other tissues like heart, muscle and brain of chicken. We assign a novel serine like protease activity to GDH which is specific to histone H3. PMID:23856561

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

    PubMed

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

    2016-01-01

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

  2. 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

  3. 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.

  4. Chromosomal localization and partial sequencing of the 18S and 28S ribosomal genes from Bradysia hygida (Diptera: Sciaridae).

    PubMed

    Gaspar, V P; Shimauti, E L T; Fernandez, M A

    2014-03-26

    In insects, ribosomal genes are usually detected in sex chromosomes, but have also or only been detected in autosomal chromosomes in some cases. Previous results from our research group indicated that in Bradysia hygida, nucleolus organizer regions were associated with heterochromatic regions of the autosomal C chromosome, using the silver impregnation technique. The present study confirmed this location of the ribosomal genes using fluorescence in situ hybridization analysis. This analysis also revealed the partial sequences of the 18S and 28S genes for this sciarid. The sequence alignment showed that the 18S gene has 98% identity to Corydalus armatus and 91% identity to Drosophila persimilis and Drosophila melanogaster. The partial sequence analysis of the 28S gene showed 95% identity with Bradysia amoena and 93% identity with Schwenckfeldina sp. These results confirmed the location of ribosomal genes of B. hygida in an autosomal chromosome, and the partial sequence analysis of the 18S and 28S genes demonstrated a high percentage of identity among several insect ribosomal genes.

  5. Partial duplication and point mutations of the ornithine carbamoyl transferase (OCT) gene in congenital hyperammonaemia

    SciTech Connect

    Gilbert-Dussardier, B.; Rozet, J.M.; Seques, B.; Munnich, A.

    1994-09-01

    ACT deficiency is an enzymopathy of the urea cycle inherited as a partially dominant X-linked trait. Affected males often die during the neonatal period with untractable hyperammonaemic coma but may sometimes present with a late onset disease. Heterozygous females are sometimes symptomatic. Twenty-two unrelated patients (18 males and 4 females) were studied by single strand conformational polymorphism (SSCP) analysis followed by direct sequencing of the OCT exons. Nine of them were found to carry point mutations already reported by others (G50Z, E87K, L88N, R827, R141Z, P225L) or by our group (R277W, 2 patients). A duplication (4 bp) in exon 5 (nt177-XTCACTCAC Xnt178) was found in a male patient with a severe neonatal OCT deficiency. This change led to a frameshift mutation with no in-frame stop codon. To our knowledge, this is the first duplication reported in OCT deficiency. Eight novel missense mutations were found in 12 additional patients: R40H (exon 2, 3 patients), C109S (exon 4, 1 patient), T125M (exon 5, 1 patient), R129Q (exon 5, 3 patients), G188R (exon 6, 1 patient), A209V (exon 6, 1 patient), H302L (exon 9, 2 patients). Four of these mutations occurred in CpG doublets and all of them involved conserved regions of the gene. No such alterations were found in 70 control genes. Phenotype-genotype correlations will be discussed.

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2016-05-01

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

  8. 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.

  9. [Molecular phylogenetic relationships among species in the genus Sorghum based on partial Adh1 gene].

    PubMed

    Liao, Fang; Liu, Yong; Yang, Xiu-Li; Huang, Guo-Ming; Niu, Chun-Jing

    2009-05-01

    The genus Sorghum contains some important grain crops and economically important forage grasses as well as agricultural weeds. The goals of this study were to elucidate the phylogenetic relationships between Sorghum species and ascertain the taxonomy status of the quarantine weeds which provide bases for effective utilization of its germ resources on molecular breeding and improvement of crop qualities and thus provide important guidance for port detection. In the present study, total DNA from the seeds of 8 Sorghum species (four S. almum, two S. halepense, one S. silk and one S. sudanense)were extracted, and the partial Adh1 gene of about 2,000 bp in length were amplified by PCR using specific primers designed from conserved regions of Adh1 gene reported in the GenBank (AF050456) and sequenced. Based on these sequences and other 24 Adh1 sequences registered in the GenBank, the phylogenetic trees constructed by multiple methods (MP, ML, and NJ) with the corresponding Adh1 sequence of Cleistachne sorghoides as the outgroup shared almost the same topology. The results showed that: (1) there were obviously three lineages for the genus Sorghum. One included two subgenera Chaetosorghum and Heterosorghum, and another included subgenus Eusorghum, both of which consisted of 2n=20 and 2n=40 species with small chromosomes. Still another lineage contained the two subgenera Parasorghum and Stiposorghum with 2n=10 species and their polyploid relatives with relatively large chromosomes; (2) geographical divergence clearly existed in the S. almum; (3) S. purpureosericeum, S. versicolor, S. nitidum and S. leiocladum of subgenus Parasorghum clustered together, but S. matarankense, S. grande, and S. timorense of the same subgenus clustered with the species of subgenus Stiposorghum, showing closer relationship with subgenus Stiposorghum; (4) S. macrospermum was more closely related to S. laxiflorum than the other species of the genus Sorghum.

  10. 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

    2006-06-01

    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.

  11. 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

  12. Phylogenetic analysis of canine parvovirus partial VP2 gene in India.

    PubMed

    Mukhopadhyay, H K; Matta, Samyukta Lakshmi; Amsaveni, S; Antony, P X; Thanislass, J; Pillai, R M

    2014-02-01

    A total of 85 samples (58.0 %) were found to be positive for Canine parvovirus (CPV) by PCR assay (Hfor/Hrev primers) out of 158 suspected faecal samples of dogs collected from various states/union territories of India. Nine CPV isolates could be obtained in A-72 cell line. The sequencing of the partial VP2 gene of CPV identified the predominant CPV strain as CPV-2a (Ser297Ala) with one CPV-2b (Ser297Ala) and another CPV-2a variant strain (Ser297Gly). Several non-synonymous and synonymous mutations were also recorded in this study. The phylogenetic tree revealed that most of the CPV sequences from Tamil Nadu (Southern India) and Maharashtra (Western India) obtained during 2011 and few sequences from Northern India obtained during 2012 were grouped together along with CPV-2a (Ser297Ala) strains from China and India and followed the same evolution; although there was definitive indication of separate lineages too by few other sequences.

  13. 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

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

    PubMed Central

    2012-01-01

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

  15. 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.

  16. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  19. 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.

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

    PubMed Central

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

    2015-01-01

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

  1. 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.

  2. Partial duplications of the ATRX gene cause the ATR-X syndrome.

    PubMed

    Thienpont, Bernard; de Ravel, Thomy; Van Esch, Hilde; Van Schoubroeck, Dominique; Moerman, Philippe; Vermeesch, Joris Robert; Fryns, Jean-Pierre; Froyen, Guy; Lacoste, Caroline; Badens, Catherine; Devriendt, Koen

    2007-10-01

    ATR-X syndrome is a rare syndromic X-linked mental retardation disorder. We report that some of the patients suspected of ATR-X carry large intragenic duplications in the ATRX gene, leading to an absence of ATRX mRNA and of the protein. These findings underscore the need for including quantitative analyses to mutation analysis of the ATRX gene.

  3. Transcription of metabolic enzyme genes during the excystation of Giardia lamblia.

    PubMed

    Niño, Carlos A; Wasserman, Moises

    2003-12-01

    The present study evaluates the expression of genes of Giardia lamblia, one of the most simple and most early diverging eukaryotes, that encode the metabolic enzymes pyruvate: ferredoxin oxidoreductase (PFOR), acetyl-CoA synthetase (ACS), alcohol dehydrogenase E (ADHE) and glutamate dehydrogenase (GDH) and the cyst wall protein (CWP1) gene in trophozoites, cysts and during the excystation process. Primers were designed to amplify mRNA fragments through quantitative reverse-transcriptase-polymerase-chain-reaction. In trophozoites, all transcripts of the enzymes studied were present. In cysts, three of the transcripts were detected: CWP1, GDH and ACS; but the relative levels of the mRNA of GDH and ACS were very different between trophozoites and cysts. During excystation, PFOR and ADHE transcripts appeared after the first induction phase, and the mRNAs of ACS and GDH increased throughout the process. PMID:14665385

  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. PMID:25229839

  5. Identification and partial characterization of the enzyme of omega: one of five putative DPP IV genes in Drosophila melanogaster

    PubMed Central

    Chihara, Carol J.; Song, Chunyan; LaMonte, Greg; Fetalvero, Kristina; Hinchman, Kristy; Phan, Helen; Pineda, Mario; Robinson, Kelly; Schneider, Gregory P.

    2005-01-01

    The omega (ome) gene product is a modifier of larval cuticle protein 5 and its alleles (and duplicates) in the third instar of Drosophila melanogaster. Using deletion mapping the locus mapped to 70F-71A on the left arm of chromosome 3. A homozygote null mutant (ome 1) shows a pleiotropic phenotype that affected the size, developmental time of the flies, and the fertility (or perhaps the behavior) of homozygous mutant males. The omega gene was verified as producing a dipeptidyl peptidase IV (DPPIV) by genetic analysis, substrate specificity and pH optimum. The identity of the gene was confirmed as CG32145 (cytology 70F4) in the Celera Database (Berkeley Drosophila Genome Project), which is consistent with its deletion map position. The genomic structure of the gene is described and the decrease in DPPIV activity in the mutant ome1 is shown to be due to the gene CG32145 (omega). The D. melanogaster omega DPPIV enzyme was partially purified and characterized. The exons of the ome1 mutant were sequenced and a base substitution mutation in exon 4 was identified that would yield a truncated protein caused by a stop codon. A preliminary study of the compartmentalization of the omega DPPIV enzyme in several organs is also reported. Abbreviations: DPPIV dipeptidyl peptidase IV LCP5 & LCP6 third instar larval cuticle proteins 5 & 6 ome & ome1 omega locus name (CG32145) and mutant allele in D. melanogaster pNA paranotroanilide PMID:17119608

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

    PubMed Central

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

    2015-01-01

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

  7. 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.

  8. 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.

  9. Association and expression analysis of single nucleotide polymorphisms of partial tumor necrosis factor alpha gene with mastitis in crossbred cattle.

    PubMed

    Ranjan, Sanjeev; Bhushan, Bharat; Panigrahi, Manjit; Kumar, Amit; Deb, Rajib; Kumar, Pushpendra; Sharma, Deepak

    2015-01-01

    A total of 129 crossbred cows were selected to explore the genotypic and expression profiling of partial TNF-α gene and its association with mastitis susceptibility. Two exon spanning region of TNF-α gene (221 bp and 239 bp) were amplified by Polymerase Chain Reaction (PCR). The different genotypic analysis by SSCP revealed that 221 bp fragment was monomorphic, whereas 239 bp was polymorphic. Association studies revealed that AA genotypes of 239 bp were more prevalent in mastitis group and the mRNA expression of TNF-α was significantly (P < 0.05) higher in AA genotypic animals compare to AB and BB. This suggested that genotypes AB and BB may be used as candidate markers for mastitis resistance selection in dairy cattle.

  10. Tomato plants transformed with the inhibitor-of-virus-replication gene are partially resistant to Botrytis cinerea.

    PubMed

    Loebenstein, Gad; David, Dalia Rav; Leibman, Diana; Gal-On, Amit; Vunsh, Ron; Czosnek, Henryk; Elad, Yigal

    2010-03-01

    Tomato plants transformed with a cDNA clone encoding the inhibitor-of-virus-replication (IVR) gene were partially resistant to Botrytis cinerea. This resistance was observed as a significant reduction in the size of lesions induced by the fungus in transgenic plants compared with the lesions on the nontransgenic control plants. This resistance was weakened when plants were kept at an elevated temperature, 32 degrees C, before inoculation with B. cinerea compared with plants kept at 17 to 22 degrees C prior to inoculation. Resistance correlated with the presence of IVR transcripts, as detected by reverse transcription-polymerase chain reaction. This is one of the few cases in which a gene associated with resistance to a virus also seems to be involved in resistance to a fungal disease.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    1997-01-01

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

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

    PubMed Central

    Brower, A V

    2000-01-01

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

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

    PubMed Central

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

    1987-01-01

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

  15. Resistance to gemcitabine in a human follicular lymphoma cell line is due to partial deletion of the deoxycytidine kinase gene

    PubMed Central

    Galmarini, Carlos María; Clarke, Marilyn L; Jordheim, Lars; Santos, Cheryl L; Cros, Emeline; Mackey, John R; Dumontet, Charles

    2004-01-01

    Background Gemcitabine is an analogue of deoxycytidine with activity against several solid tumors. In order to elucidate the mechanisms by which tumor cells become resistant to gemcitabine, we developed the resistant subline RL-G from the human follicular lymphoma cell line RL-7 by prolonged exposure of parental cells to increasing concentrations of gemcitabine. Results In vitro, the IC50 increased from 0.015 μM in parental RL-7 cells to 25 μM in the resistant variant, RL-G. Xenografts of both cell lines developed in nude mice were treated with repeated injections of gemcitabine. Under conditions of gemcitabine treatment which totally inhibited the development of RL-7 tumors, RL-G derived tumors grew similarly to those of untreated animals, demonstrating the in vivo resistance of RL-G cells to gemcitabine. HPLC experiments showed that RL-G cells accumulated and incorporated less gemcitabine metabolites into DNA and RNA than RL-7 cells. Gemcitabine induced an S-phase arrest in RL-7 cells but not in RL-G cells. Exposure to gemcitabine induced a higher degree of apoptosis in RL-7 than in RL-G cells, with poly-(ADP-ribose) polymerase cleavage in RL-7 cells. No modifications of Bcl-2 nor of Bax expression were observed in RL-7 or RL-G cells exposed to gemcitabine. These alterations were associated with the absence of the deoxycytidine kinase mRNA expression observed by quantitative RT-PCR in RL-G cells. PCR amplification of désoxycytidine kinase gene exons showed a partial deletion of the dCK gene in RL-G cells. Conclusions These results suggest that partial deletion of the dCK gene observed after selection in the presence of gemcitabine is involved with resistance to this agent both in vitro and in vivo. PMID:15157282

  16. Identification of high-stringency DNA hairpin probes by partial gene folding.

    PubMed

    Strohsahl, Christopher M; Krauss, Todd D; Miller, Benjamin L

    2007-09-30

    Hairpin DNA sequences are widely used as probes for oligonucleotides in a broad range of assays, often as "molecular beacons". A potential disadvantage of the standard methodology for molecular beacon design is the need to add several self-complementary bases to each end of the probe, since these do not correspond to the target sequence. We describe a conceptually new method of hairpin DNA probe identification, in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within an expressed gene having the requisite hairpin structure. Intuitively, such probes should have significantly improved performance over "traditional" hairpin probes, because they are fully complementary with the target. We present experimental evidence verifying this hypothesis for a series of hairpin probes targeting the pag gene of Bacillus anthracis.

  17. 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

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

    PubMed

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

    2015-01-01

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

  19. 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.

  20. Genetic diversity of Mycoplasma gallisepticum field isolates using partial sequencing of the pvpA gene fragment in Russia.

    PubMed

    Sprygin, A V; Andreychuk, D B; Elatkin, N P; Zinyakov, N G; Kolosov, S N; Mudrak, N S; Irza, V N; Drygin, V V; Borisov, A V; Perevozchikova, N A

    2010-06-01

    The genetic diversity of the pvpA gene of Mycoplasma gallisepticum (MG) samples originating from commercial chickens was investigated. In the present study, we evaluated the genetic variability of 26 field samples of MG detected in commercial chickens and turkeys from 18 regions of Russia and compared them to the reference strains of MG available in GenBank. Genetic variability was evaluated by partial nucleotide sequencing of the pvpA gene, which encodes a putative cytadhesin protein. Comparisons with MG strains and isolates from the United States, Australia, China, and Iran using sequence analysis of PCR products showed that Russian MG field samples clustered more closely to each other than to the international reference MG strains. The MG pvpA sequences were found to be highly variable with a discrimination index of 0.975 for Russian field samples. No apparent cluster was found using the criteria of year or location of detection. DNA sequence polymorphism and size variation in the pvpA gene were shown among the Russian MG field samples and could be used for MG typing. These findings might help better understand the relationship among MG isolates from Russia and other countries.

  1. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Feiss, M; Frackman, S; Momany, T

    1988-11-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-07-01

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

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

    PubMed

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

    2011-07-01

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

  8. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    PubMed

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

    2012-05-25

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

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

    PubMed

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

    2016-05-01

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

  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. 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.

  12. Protective efficacies and immune responses induced by recombinant HCD, atpD and gdhA against bacterial cold-water disease in ayu (Plecoglossus altivelis).

    PubMed

    Kato, Goshi; Sakai, Takamitsu; Suzuki, Kyuma; Sano, Natsumi; Takano, Tomokazu; Matsuyama, Tomomasa; Nakayasu, Chihaya

    2014-08-01

    Protective efficacies of three antigenic proteins (3-hydroxyacyl-CoA dehydrogenase (HCD), ATP synthase beta subunit (atpD), and glutamate dehydrogenase (gdhA)) against Flavobacterium psychrophilum were investigated in ayu (Plecoglossus altivelis). Recombinant proteins of HCD, atpD, and gdhA were expressed in Escherichia coli BL21 cells. Ayu were then vaccinated with inactivated cells via the intraperitoneal route. Compared with the empty BL21- and PBS-injected groups, the vaccinated group had a significantly longer survival time after challenge with F. psychrophilum. The antibody titers against each recombinant protein were significantly higher in serum from vaccinated fish, compared with serum from control fish. Results of indirect immunofluorescence assays using serum indicated that the HCD, atpD, and gdhA proteins are located on the surface of F. psychrophilum. These results suggest that these three surface proteins are protective antigens and are good candidates for development of vaccines against bacterial cold-water disease in ayu.

  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. Loss of an Igκ gene enhancer in mature B cells results in rapid gene silencing and partial reversible dedifferentiation.

    PubMed

    Zhou, Xiaorong; Xiang, Yougui; Ding, Xiaoling; Garrard, William T

    2013-05-01

    We address here whether there is cellular memory of a transcriptional enhancer once it has served its purpose to establish an active chromatin state. We have previously shown that the mouse Igκ gene's downstream enhancers, E3' and Ed, are essential but play redundant roles for establishing transcriptional activity in the locus during B cell development. To determine whether these enhancers are also necessary for the maintenance of transcriptional activity, we conditionally deleted E3' in mature B cells that possessed Ed(-/-) alleles. Upon E3' deletion, the locus became rapidly silenced and lost positive histone epigenetic marks, and the mature B cells partially dedifferentiated, induced RAG-1 and -2 along with certain other pro-B cell makers, and then redifferentiated after triggering Igλ gene rearrangements. We conclude that the Igκ gene's downstream enhancers are essential for both the establishment and maintenance of transcriptional activity and that there is no cellular memory of previous transcriptional activity in this locus. Furthermore, upon enhancer loss, the mature B cells unexpectedly underwent reversible retrograde differentiation. This result establishes that receptor editing can occur in mature B cells and raises the possibility that this may provide a tolerance mechanism for eliminating autoreactive B cells in the periphery.

  15. Integrative Analysis of Gene-Environment Interactions under a Multi-response Partially Linear Varying Coefficient Model

    PubMed Central

    Wu, Cen; Cui, Yuehua; Ma, Shuangge

    2014-01-01

    Consider the integrative analysis of genetic data with multiple correlated response variables. The goal is to identify important gene-environment (G×E) interactions along with main gene and environment effects that are associated with the responses. The homogeneity and heterogeneity models can be adopted to describe the genetic basis of multiple responses. To accommodate possible nonlinear effects of some environment effects, a multi-response partially linear varying coefficient (MPLVC) model is assumed. Penalization is adopted for marker selection. The proposed penalization method can select genetic variants with G×E interactions, no G×E interactions, and no main effects simultaneously. It adopts different penalties to accommodate the homogeneity and heterogeneity models. The proposed method can be effectively computed using a coordinate descent algorithm. Simulation study and the analysis of Health Professional’s Follow-up Study (HPFS), which has two correlated continuous traits, SNP measurements, and multiple environment effects, show superior performance of the proposed method over its competitors. PMID:25146388

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

    PubMed

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

    2001-12-01

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

  17. 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

  18. Novel gene mutations in patients with 1alpha-hydroxylase deficiency that confer partial enzyme activity in vitro.

    PubMed

    Wang, Xuemei; Zhang, Martin Y H; Miller, Walter L; Portale, Anthony A

    2002-06-01

    The rate-limiting, hormonally regulated step in the biological activation of vitamin D is its 1alpha-hydroxylation to 1,25-dihydroxyvitamin D [1,25-(OH)(2)D] in the kidney, catalyzed by the mitochondrial cytochrome P450 enzyme, P450c1alpha. We previously cloned the human P450c1alpha cDNA and gene, and identified 14 different mutations, including 7 missense, in 19 patients with 1alpha-hydroxylase deficiency, also known as vitamin D-dependent rickets type 1. None of the missense mutations encoded a protein with detectable enzymatic activity in vitro. Although there is phenotypic variation among such patients, the molecular basis of this variation is unknown. We analyzed 6 additional patients with clinical and radiographic features of rickets; in 4 patients the laboratory abnormalities were typical of 1alpha-hydroxylase deficiency, but in 2 they were unusually mild [mild hypocalcemia and normal serum 1,25-(OH)(2)D concentration]. Direct sequencing revealed that all patients had P450c1alpha mutations on both alleles. Five new and 2 known mutations were identified. The new mutations included a 5-bp deletion with a 6-bp novel insertion causing a frameshift in exon 2, and a G to A change at +1 of intron 2; a minigene experiment proved that this intronic mutation prevented proper splicing. Three new missense mutations were found and tested by expressing the mutant cDNA in mouse Leydig MA-10 cells. The R389G mutant was totally inactive, but mutant L343F retained 2.3% of wild-type activity, and mutant E189G retained 22% of wild-type activity. The two mutations that confer partial enzyme activity in vitro were found in the 2 patents with mild laboratory abnormalities, suggesting that such mutations contribute to the phenotypic variation observed in patients with 1alpha-hydroxylase deficiency.

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

    PubMed

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

    1999-03-01

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

  20. Partial sequence analysis of the L1 gene of bovine papillomavirus type 1 detected by PCR with MY09/MY11 primers in equine sarcoids in Poland.

    PubMed

    Szczerba-Turek, A; Siemionek, J; Wasowicz, K; Szweda, W; Raś, A; Platt-Samoraj, A

    2010-01-01

    BPV-1 is now recognized as a main etiological agent of equine sarcoids. The etiopathogenesis of the equine sarcoids is equivocal and is not yet fully understood. The aim of the present study was to analyse a partial sequence of the L1 gene of BPV associated with equine sarcoids in Polish horses. After clinical diagnosis, 40 skin lesions obtained from 29 horses were collected. The amplicons of a fragment of BPV L1 DNA were detected using PCR with MY09/MY11 primers in 31 specimens. All of them were recognized as BPV-1. Phylogenetic analysis has allowed the amplicons of partial L1 gene to be divided into 3 phylogenetic groups (A, B, C) and one separate isolate (20c). Sequence variants from phylogenetic groups B, C and isolate 20c represented new genetic variants of BPV-1 L1. Sequence variants from groups B and C were submitted to GenBank NCBI. PMID:20731177

  1. Characterization of Hafnia alvei by biochemical tests, random amplified polymorphic DNA PCR, and partial sequencing of 16S rRNA gene.

    PubMed Central

    Ridell, J; Siitonen, A; Paulin, L; Lindroos, O; Korkeala, H; Albert, M J

    1995-01-01

    Hafnia alvei strains which possess the attachment-effacement gene (eaeA) may have clinical importance as new diarrhea-causing pathogens and should therefore be differentiated from other H. alvei strains. We characterized diarrheal H. alvei strains, which were positive in the PCR test for the eaeA gene, using biochemical tests not routinely used for identification of members of the family Enterobacteriaceae, and compared them with eaeA-negative strains isolated from different clinical and nonclinical sources to find characteristics useful for identification. Random amplified polymorphic DNA (RAPD)-PCR and partial sequencing of the 16S rRNA gene were utilized to study the genetic diversity of the isolates. The eaeA-positive strains were found to have many characteristic biochemical properties. Negative reactions in the 2-ketogluconate and histidine assimilation tests and a positive reaction in the 3-hydroxybenzoate assimilation test may be useful in routine diagnostics. Nearly identical RAPD-PCR profiles and identical 353-bp fragments of the 16S rRNA genes indicated little genetic diversity among the eaeA-positive strains. The low level of homology (92%) in the partial 16S rRNA genes of eaeA-positive and -negative H. alvei strains raises questions about the taxonomic positioning of eaeA-positive H. alvei. PMID:7494030

  2. 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.

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

    PubMed Central

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

    1994-01-01

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

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

    PubMed

    Rodríguez, Cristina; Sanz, Pascual; Gancedo, Carlos

    2003-03-01

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

  5. 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

  6. 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.

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

    PubMed Central

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

    2015-01-01

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

  8. AIRE variations in Addison's disease and autoimmune polyendocrine syndromes (APS): partial gene deletions contribute to APS I.

    PubMed

    Bøe Wolff, A S; Oftedal, B; Johansson, S; Bruland, O; Løvås, K; Meager, A; Pedersen, C; Husebye, E S; Knappskog, P M

    2008-03-01

    Autoimmune Addison's disease (AAD) is often associated with other components in autoimmune polyendocrine syndromes (APS). Whereas APS I is caused by mutations in the AIRE gene, the susceptibility genes for AAD and APS II are unclear. In the present study, we investigated whether polymorphisms or copy number variations in the AIRE gene were associated with AAD and APS II. First, nine SNPs in the AIRE gene were analyzed in 311 patients with AAD and APS II and 521 healthy controls, identifying no associated risk. Second, in a subgroup of 25 of these patients, AIRE sequencing revealed three novel polymorphisms. Finally, the AIRE copy number was determined by duplex quantitative PCR in 14 patients with APS I, 161 patients with AAD and APS II and in 39 healthy subjects. In two Scandinavian APS I patients previously reported to be homozygous for common AIRE mutations, we identified large deletions of the AIRE gene covering at least exon 2 to exon 8. We conclude that polymorphisms in the AIRE gene are not associated with AAD and APS II. We further suggest that DNA analysis of the parents of patients found to be homozygous for mutations in AIRE, always should be performed.

  9. Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory.

    PubMed

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

    2006-12-01

    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.

  10. 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.

  11. Phylogenetic analysis of Histoplasma capsulatum based on partial sequence of the D1/D2 region of the 28S rRNA gene.

    PubMed

    Komori, Takashi; Sano, Ayako; Yarita, Kyoko; Kitagawa, Teruyuki; Kamei, Katsuhiko; Nishimura, Kazuko

    2005-01-01

    In order to confirm the phylogenetic relationships of Histoplasma capsulatum, the partial sequences of large subunit (28S) ribosomal gene (D1/D2 region) of 49 isolates were studied. The similarity values of the 49 isolates were more than 99.0% across 617 base pairs, however, the 49 isolates were divided into 9 groups. These 9 groups were independent of 3 varieties, var. capsulatum, var. farciminosum and var. duboisii. These results showed that analysis of the nucleotide sequence of the 28S rRNA gene was very effective for identification of H. capsulatum and that three varieties of H. capsulatum should be reclassified according to the phylogenetic relationship established from analysis of the D1/D2 region sequences. PMID:16282973

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

    PubMed

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

    2009-02-01

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

  13. Nine genes that may contribute to partial trisomy (6)(p22→pter) and unique presentation of persistent hyperplastic primary vitreous with retinal detachment.

    PubMed

    Su, Pen-Hua; Lee, Inn-Chi; Yang, Shun-Fa; Ng, Yan-Yan; Liu, Chan-Sheng; Chen, Jia-Yuh

    2012-04-01

    We report on a newborn girl with facial anomalies, a congenital heart defect, severe pre- and postnatal growth retardation, feeding problems, and persistent hyperplastic primary vitreous. Cytogenetic analysis by high resolution GTG banding showed extra chromosomal material on the short arm of one chromosome 1 of the patient, but neither parent. SKY and CGH analysis demonstrated that the patient had a de novo 46,XX, der(1)t(1;6)(p36.3; p22). Compared with previously reported cases of partial trisomy 6p22 syndrome, this patient exhibited a unique condition for this syndrome: persistent hyperplastic primary vitreous (PHPV) with retinal detachment. The human genome database was searched for candidate genes and we propose the following nine genes located in the 6p22→6pter region for their potential contribution to the phenotype of partial trisomy 6p22→pter and persistent hyperplastic primary vitreous (PHPV) with retinal detachment: Forkhead box Q1 (FOXQ1), FOXF2, FOXC1, NRN1, EDN1, ATXN1, DEK oncogene, E2F3, and NRNS1. PMID:22407547

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

    PubMed

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

    2016-06-01

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

  15. Identification of a streptomycin resistance gene and a partial Tn3 transposon coding for a beta-lactamase in a periodontal strain of Eikenella corrodens.

    PubMed Central

    Lacroix, J M; Walker, C B

    1992-01-01

    The beta-lactamase gene from a periodontal strain of Eikenella corrodens, resistant to penicillins and streptomycin, was inserted into pBGS9 and transformed into Escherichia coli DH5 alpha. A 4.7-kb insert of pJML1, one of the transformants, was partially sequenced and found to contain the right section of transposon Tn3 from the middle of the TnpR resolvase gene to the right inverted repeat RI(R), including the TEM-1 gene. Sequences identical to RSF1010 were found on either side of the Tn3 sequence. pJML1 also contained a streptomycin resistance gene, probably identical to that of RSF1010. A portion of the pJML1 insert was not homologous to either Tn3 or RSF1010 but was homologous to the chromosomal DNA of E. corrodens ATCC 23834. It is assumed that the insert of pJML1 was derived from the chromosomal DNA of E. corrodens EC-38. PMID:1323951

  16. 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.

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

    PubMed

    Panigrahi, Manjit; Sharma, Arjava; Bhushan, Bharat

    2014-01-01

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

  18. Inversin, a novel gene in the vertebrate left-right axis pathway, is partially deleted in the inv mouse.

    PubMed

    Morgan, D; Turnpenny, L; Goodship, J; Dai, W; Majumder, K; Matthews, L; Gardner, A; Schuster, G; Vien, L; Harrison, W; Elder, F F; Penman-Splitt, M; Overbeek, P; Strachan, T

    1998-10-01

    Visceral left-right asymmetry occurs in all vertebrates, but the inversion of embryo turning (inv) mouse, which resulted following a random transgene insertion, is the only model in which these asymmetries are consistently reversed. We report positional cloning of the gene underlying this recessive phenotype. Although transgene insertion was accompanied by neighbouring deletion and duplication events, our YAC phenotype rescue studies indicate that the mutant phenotype results from the deletion. After extensively characterizing the 47-kb deleted region and flanking sequences from the wild-type mouse genome, we found evidence for only one gene sequence in the deleted region. We determined the full-length 5.5-kb cDNA sequence and identified 16 exons, of which exons 3-11 were eliminated by the deletion, causing a frameshift. The novel gene specifies a 1062-aa product with tandem ankyrin-like repeat sequences. Characterization of complementing and non-complementing YAC transgenic families revealed that correction of the inv mutant phenotype was concordant with integration and intact expression of this novel gene, which we have named inversin (Invs). PMID:9771707

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

    PubMed

    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.

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

    PubMed

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

    2011-12-01

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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. Mapping of a Gene Determining Familial Partial Epilepsy with Variable Foci to Chromosome 22q11-q12

    PubMed Central

    Xiong, Lan; Labuda, Malgorzata; Li, Dong-Sheng; Hudson, Thomas J.; Desbiens, Richard; Patry, Georges; Verret, Simon; Langevin, Pierre; Mercho, Suha; Seni, Marie-Hélène; Scheffer, Ingrid; Dubeau, François; Berkovic, Samuel F.; Andermann, Frederick; Andermann, Eva; Pandolfo, Massimo

    1999-01-01

    Summary We identified two large French-Canadian families segregating a familial partial epilepsy syndrome with variable foci (FPEVF) characterized by mostly nocturnal seizures arising from frontal, temporal, and occasionally occipital epileptic foci. There is no evidence for structural brain damage or permanent neurological dysfunction. The syndrome is inherited as an autosomal dominant trait with incomplete penetrance. We mapped the disease locus to a 3.8-cM interval on chromosome 22q11-q12, between markers D22S1144 and D22S685. Using the most conservative diagnostic scheme, the maximum cumulative LOD score was 6.53 at recombination fraction (θ) 0 with D22S689. The LOD score in the larger family was 5.34 at θ=0 with the same marker. The two families share an identical linked haplotype for ⩾10 cM, including the candidate interval, indicating a recent founder effect. A severe phenotype in one of the probands may be caused by homozygosity for the causative mutation, as suggested by extensive homozygosity for the linked haplotype and a bilineal family history of epilepsy. An Australian family with a similar phenotype was not found to link to chromosome 22, indicating genetic heterogeneity of FPEVF. PMID:10577924

  6. Molecular systematics of the Amphisphaeriaceae based on cladistic analyses of partial LSU rDNA gene sequences.

    PubMed

    Jeewon, Rajesh; Liew, Edward C Y; Hyde, Kevin D

    2003-12-01

    The Amphisphaeriaceae is an important family of ascomycetes within the Xylariales. There has been, however, disagreement regarding the taxonomic placement of many genera within this family and whether it should be confined to ascomycetes producing Pestalotiopsis-like anamorphs. In this study, phylogenetic relationships among members of the Amphisphaeriaceae are investigated using partial sequences of the 28S rDNA. Molecular data provided further evidence to support the association of several coelomycetous genera with the ascomycetous Amphisphaeriaceae. Phylogenetic analyses also show that all ascomycetous genera possessing Pestalotiopsis-like anamorphs are monophyletic and confirm the anamorphic-teleomorphic connections of some. There is, however, insufficient evidence to support the restriction of Amphisphaeriaceae to genera, which produce Pestalotiopsis-like anamorphs, because the phylogenetic placement of Amphisphaeria umbrina is not fully resolved and its affinities with other members received low bootstrap support. The results also indicate that Iodosphaeria and Arecophila should be excluded from the Amphisphaeriaceae. The placement of Lanceispora in the Amphisphaeriaceae is doubtful. A broad concept of the family Amphisphaeriaceae is advocated until further data are available.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  11. 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.

  12. Gene transcript accumulation and in situ mRNA hybridization of two putative glutamate dehydrogenase genes in etiolated Glycine max seedlings.

    PubMed

    Dimou, M; Tsaniklidis, G; Aivalakis, G; Katinakis, P

    2015-01-01

    Glutamate dehydrogenase (EC 1.4.1.2) is a multimeric enzyme that catalyzes the reversible amination of α-ketoglutarate to form glutamate. We characterized cDNA clones of two Glycine max sequences, GmGDH1 and GmGDH2, that code for putative α- and β-subunits, respectively, of the NADH dependent enzyme. Temporal and spatial gene transcript accumulation studies using semiquantitative RT-PCR and in situ hybridization have shown an overlapping gene transcript accumulation pattern with differences in relative gene transcript accumulation in the organs examined. Detection of NADH-dependent glutamate dehydrogenase activity in situ using a histochemical method showed concordance with the spatial gene transcript accumulation patterns. Our findings suggest that although the two gene transcripts are co-localized in roots of etiolated soybean seedlings, the ratio of the two subunits of the active holoenzyme may vary among tissues.

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

    PubMed

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

    2016-08-01

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

  14. 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

  15. Phylogenetic analysis of different breeds of domestic chickens in selected area of Peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers.

    PubMed

    Yap, Fook Choy; Yan, Yap Jin; Loon, Kiung Teh; Zhen, Justina Lee Ning; Kamau, Nelly Warau; Kumaran, Jayaraj Vijaya

    2010-10-01

    The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.

  16. Sequence analysis in partial genes of five isolates of Angiostrongylus cantonensis from Taiwan and biological comparison in infectivity and pathogenicity between two strains.

    PubMed

    Lee, June-Der; Chung, Li-Yu; Wang, Lian-Chen; Lin, Rong-Jyh; Wang, Jiun-Jye; Tu, Hung-Pin; Wu, Zhong-Dao; Yen, Chuan-Min

    2014-05-01

    Angiostrongylus cantonensis is the most common infectious agent causing eosinophilic meningitis and is present in Taiwan, Thailand and the Pacific islands. Clinical symptoms vary within different endemic regions, and their severity is probably dependent on the number of ingested parasites and the diversity among strains. The experimentally definitive host is the rat, and non-permissive hosts are certain mammals such as humans and mice. In this study, the partial gene sequences of two A. cantonensis strains isolated from five different regions in Taiwan were selected and molecularly analyzed. The internal transcribed spacer gene and cytochrome-c oxidase subunit I gene sequences of the Hualien (H) strain of A. cantonensis differed from those of the Pingtung (P) strain and the other three strains by 19% and 11%, respectively. We analyzed the infectivity, fecundity, and development of the H and P strain in rats and host pathogenicity in mice inoculated with both strains. The number of the emerged first-stage larvae, adult recovery, and average length of adults in Sprague-Dawley rats significantly differed between rats inoculated with the H and P strain. Young adult recovery, average length of young adults, eosinophil counts in the cerebrospinal fluid (CSF), glutathione peroxidase concentration, levels of reactive oxygen species as well as malondialdehyde concentration in the CSF, and the survival of mice significantly differed between BALB/c mice inoculated with the H and P strain. The H strain of A. cantonensis had lower infectivity, delayed fecundity, and poor development in rats, and caused milder pathology and lower mortality in mice than the P strain. These data clearly indicate that the H strain of A. cantonensis is a pathogenically distinct strain with lower infectivity to its definitive host, and causing mild pathogenic symptoms to its non-permissive host.

  17. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2010-03-01

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

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

    PubMed

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

    2010-03-01

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

  1. 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.

  2. 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

  3. Selection-driven accumulation of suppressor mutants in bacillus subtilis: the apparent high mutation frequency of the cryptic gudB gene and the rapid clonal expansion of gudB(+) suppressors are due to growth under selection.

    PubMed

    Gunka, Katrin; Stannek, Lorena; Care, Rachel A; Commichau, Fabian M

    2013-01-01

    Soil bacteria like Bacillus subtilis can cope with many growth conditions by adjusting gene expression and metabolic pathways. Alternatively, bacteria can spontaneously accumulate beneficial mutations or shape their genomes in response to stress. Recently, it has been observed that a B. subtilis mutant lacking the catabolically active glutamate dehydrogenase (GDH), RocG, mutates the cryptic gudB(CR) gene at a high frequency. The suppressor mutants express the active GDH GudB, which can fully replace the function of RocG. Interestingly, the cryptic gudB(CR) allele is stably inherited as long as the bacteria synthesize the functional GDH RocG. Competition experiments revealed that the presence of the cryptic gudB(CR) allele provides the bacteria with a selective growth advantage when glutamate is scarce. Moreover, the lack of exogenous glutamate is the driving force for the selection of mutants that have inactivated the active gudB gene. In contrast, two functional GDHs are beneficial for the cells when glutamate was available. Thus, the amount of GDH activity strongly affects fitness of the bacteria depending on the availability of exogenous glutamate. At a first glance the high mutation frequency of the cryptic gudB(CR) allele might be attributed to stress-induced adaptive mutagenesis. However, other loci on the chromosome that could be potentially mutated during growth under the selective pressure that is exerted on a GDH-deficient mutant remained unaffected. Moreover, we show that a GDH-proficient B. subtilis strain has a strong selective growth advantage in a glutamate-dependent manner. Thus, the emergence and rapid clonal expansion of the active gudB allele can be in fact explained by spontaneous mutation and growth under selection without an increase of the mutation rate. Moreover, this study shows that the selective pressure that is exerted on a maladapted bacterium strongly affects the apparent mutation frequency of mutational hot spots.

  4. Epilepsy (partial)

    PubMed Central

    2011-01-01

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

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

    PubMed Central

    Manoli, Martha; Driever, Wolfgang

    2014-01-01

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

  6. Cloning, Sequences, and Characterization of Two Chitinase Genes from the Antarctic Arthrobacter sp. Strain TAD20: Isolation and Partial Characterization of the Enzymes

    PubMed Central

    Lonhienne, Thierry; Mavromatis, Konstantinos; Vorgias, Constantin E.; Buchon, Laurent; Gerday, Charles; Bouriotis, Vassilis

    2001-01-01

    Arthrobacter sp. strain TAD20, a chitinolytic gram-positive organism, was isolated from the sea bottom along the Antarctic ice shell. Arthrobacter sp. strain TAD20 secretes two major chitinases, ChiA and ChiB (ArChiA and ArChiB), in response to chitin induction. A single chromosomal DNA fragment containing the genes coding for both chitinases was cloned in Escherichia coli. DNA sequencing analysis of this fragment revealed two contiguous open reading frames coding for the precursors of ArChiA (881 amino acids [aa]) and ArChiB (578 aa). ArChiA and ArChiB are modular enzymes consisting of a glycosyl-hydrolase family 18 catalytic domain as well as two and one chitin-binding domains, respectively. The catalytic domain of ArChiA exhibits 55% identity with a chitodextrinase from Vibrio furnissii. The ArChiB catalytic domain exhibits 33% identity with chitinase A of Bacillus circulans. The ArChiA chitin-binding domains are homologous to the chitin-binding domain of ArChiB. ArChiA and ArChiB were purified to homogeneity from the native Arthrobacter strain and partially characterized. Thermal unfolding of ArChiA, ArChiB, and chitinase A of Serratia marcescens was studied using differential scanning calorimetry. ArChiA and ArChiB, compared to their mesophilic counterpart, exhibited increased heat lability, similar to other cold-adapted enzymes. PMID:11160110

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

    PubMed

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

    2008-03-01

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

  8. Compatibility and Conjugacy on Partial Arrays

    PubMed Central

    Sasikala, K.

    2016-01-01

    Research in combinatorics on words goes back a century. Berstel and Boasson introduced the partial words in the context of gene comparison. Alignment of two genes can be viewed as a construction of two partial words that are said to be compatible. In this paper, we examine to which extent the fundamental properties of partial words such as compatbility and conjugacy remain true for partial arrays. This paper studies a relaxation of the compatibility relation called k-compability. It also studies k-conjugacy of partial arrays. PMID:27774111

  9. 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.

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

    PubMed

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

    2015-03-01

    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

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

    PubMed Central

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

    2009-01-01

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

  12. Localization of the gene (LAMA4) to chromosome 6q21 and isolation of a partial cDNA encoding a variant laminin A chain

    SciTech Connect

    Richards, A.J.; Al-Imara, L.; Carter, N.P.

    1994-07-01

    Laminin is a basement membrane glycoprotein composed of three nonidentical chains, A, B1, and B2. Variant chains such as merosin and S-laminin have been found in different tissues. The authors have isolated a cDNA encoding a novel laminin A variant that hybridizes to a 6.45-kb mRNA. Using amplification of genomic DNA and flow-sorted chromosomes they have assigned the gene (LAMA4) for this new laminin A variant to chromosome 6. Fluorescence in situ hybridization of a YAC clone further localized the gene to 6q21. 19 refs., 2 figs.

  13. 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.

  14. Differential control by IHF and cAMP of two oppositely oriented genes, hpt and gcd, in Escherichia coli: significance of their partially overlapping regulatory elements.

    PubMed

    Izu, H; Ito, S; Elias, M D; Yamada, M

    2002-01-01

    The hpt gene, which encodes hypoxanthine phosphoribosyltransferase, is located next to, but transcribed in the opposite direction to, the gcd gene, which codes for a membrane-bound glucose dehydrogenase, at 3.1 min on the Escherichia coli genome. In their promoter-operator region, putative regulatory elements for integration host factor (IHF) and for the complex comprising 3', 5'-cyclic AMP (cAMP) and its receptor protein (CRP) are present, and they overlap the promoters for hpt and gcd, respectively. The involvement of IHF and cAMP-CRP, as well as the corresponding putative cis-acting elements, in the expression of the two genes was investigated by using lacZ operon fusions. In an adenylate cyclase-deficient strain, addition of cAMP increased the expression of hpt and reduced the expression of gcd. In agreement with this observation, the introduction of mutations into the putative binding element for the cAMP-CRP complex enhanced the expression of gcd. In contrast, mutations introduced into the putative IHF-binding elements increased the level of hpt expression. Similar results were obtained with IHF-defective strains. Thus, the expression of the two genes is regulated in a mutually exclusive manner. Additional experiments with mutations at the -10 sequence of the gcd promoter suggest that the binding of RNA polymerase to the hpt promoter interferes with the interaction of RNA polymerase with the gcd promoter, and vice versa.

  15. A cytomegalovirus protein with properties of herpes simplex virus ICP8: partial purification of the polypeptide and map position of the gene.

    PubMed Central

    Kemble, G W; McCormick, A L; Pereira, L; Mocarski, E S

    1987-01-01

    We demonstrated the presence of a single-stranded DNA-binding protein in human cytomegalovirus (CMV)-infected cells with properties analogous to those of herpes simplex virus (HSV) ICP8. Using monoclonal antibody specific for the CMV protein, we analyzed its fluorescence pattern and time of synthesis, mapped the gene encoding it by using a lambda gt11 library of CMV DNA fragments, and monitored its purification by phosphocellulose and DNA-Sepharose chromatography. In all characteristics we examined, the CMV protein behaved analogously to HSV ICP8. Our results are consistent with a functional role of CMV ICP8 in viral replication that is similar to that of HSV ICP8 and with the evolutionary conservation of the gene of interest in two divergent herpesviruses. Images PMID:3041036

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

    PubMed Central

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

    2010-01-01

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

  17. A frameshift mutation in the human apolipoprotein A-I gene causes high density lipoprotein deficiency, partial lecithin: cholesterol-acyltransferase deficiency, and corneal opacities.

    PubMed Central

    Funke, H; von Eckardstein, A; Pritchard, P H; Karas, M; Albers, J J; Assmann, G

    1991-01-01

    Epidemiologic data of recent years have identified an important role of HDL deficiency in the etiology of atherosclerosis. Biochemical data suggest that some of these deficiencies may be a consequence of defects in the structural genes of HDL apolipoproteins or of plasma enzymes that modify HDL. We analyzed the genetic defect in a 42-yr-old patient suffering from corneal opacities and complete absence of HDL cholesterol but not of coronary artery disease, thus clinically resembling fish eye disease. The observation of an abnormal immunoblot banding pattern of apolipoprotein A-I (apo A-I) and of reduced lecithin: cholesterol acyltransferase (LCAT) activity in plasma led to sequence analysis of the genes for apo A-I and LCAT in this patient and his family. Direct sequencing of polymerase chain reaction amplified DNA segments containing the exons of the candidate genes, resulted in the identification of a frameshift mutation in apo A-I while the LCAT sequence was identical to the wild type. The apo A-I mutation was predictive for an extensive alteration of the COOH-terminal sequence of the encoded protein. Evidence for the release of this mutant protein into the plasma compartment and for the absence of normal apo A-I was derived from ultraviolet laser desorption/ionization mass spectrometry analysis. Our results suggest that a defective apo A-I is the causative defect in this case of HDL deficiency with corneal opacities. Images PMID:1898657

  18. 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

  19. Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene.

    PubMed

    Lynch, T; Gregson, D; Church, D L

    2016-03-01

    Actinomyces species are uncommon but important causes of invasive infections. The ability of our regional clinical microbiology laboratory to report species-level identification of Actinomyces relied on molecular identification by partial sequencing of the 16S ribosomal gene prior to the implementation of the Vitek MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS]) system. We compared the use of the Vitek MS to that of 16S rRNA gene sequencing for reliable species-level identification of invasive infections caused by Actinomyces spp. because limited data had been published for this important genera. A total of 115 cases of Actinomyces spp., either alone or as part of a polymicrobial infection, were diagnosed between 2011 and 2014. Actinomyces spp. were considered the principal pathogen in bloodstream infections (n = 17, 15%), in skin and soft tissue abscesses (n = 25, 22%), and in pulmonary (n = 26, 23%), bone (n = 27, 23%), intraabdominal (n = 16, 14%), and central nervous system (n = 4, 3%) infections. Compared to sequencing and identification from the SmartGene Integrated Database Network System (IDNS), Vitek MS identified 47/115 (41%) isolates to the correct species and 10 (9%) isolates to the correct genus. However, the Vitek MS was unable to provide identification for 43 (37%) isolates while 15 (13%) had discordant results. Phylogenetic analyses of the 16S rRNA sequences demonstrate high diversity in recovered Actinomyces spp. and provide additional information to compare/confirm discordant identifications between MALDI-TOF and 16S rRNA gene sequences. This study highlights the diversity of clinically relevant Actinomyces spp. and provides an important typing comparison. Based on our analysis, 16S rRNA gene sequencing should be used to rapidly identify Actinomyces spp. until MALDI-TOF databases are optimized.

  20. 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

  1. 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

  2. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5.

    PubMed

    Park, J Y; Koo, D H; Hong, C P; Lee, S J; Jeon, J W; Lee, S H; Yun, P Y; Park, B S; Kim, H R; Bang, J W; Plaha, P; Bancroft, I; Lim, Y P

    2005-12-01

    We constructed a bacterial artificial chromosome (BAC) library, designated as KBrH, from high molecular weight genomic DNA of Brassica rapa ssp. pekinensis (Chinese cabbage). This library, which was constructed using HindIII-cleaved genomic DNA, consists of 56,592 clones with average insert size of 115 kbp. Using a partially duplicated DNA sequence of Arabidopsis, represented by 19 and 9 predicted genes on chromosome 4 and 5, respectively, and BAC clones from the KBrH library, we studied conservation and microsynteny corresponding to the Arabidopsis regions in B. rapa ssp. pekinensis. The BAC contigs assembled according to the Arabidopsis homoeologues revealed triplication and rearrangements in the Chinese cabbage. In general, collinearity of genes in the paralogous segments was maintained, but gene contents were highly variable with interstitial losses. We also used representative BAC clones, from the assembled contigs, as probes and hybridized them on mitotic (metaphase) and/or meiotic (leptotene/pachytene/metaphase I) chromosomes of Chinese cabbage using bicolor fluorescence in situ hybridization. The hybridization pattern physically identified the paralogous segments of the Arabidopsis homoeologues on B. rapa ssp. pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis.

  3. Identification of a short interspersed repetitive element in partially spliced transcripts of the bell pepper (Capsicum annuum) PAP gene: new evolutionary and regulatory aspects on plant tRNA-related SINEs.

    PubMed

    Pozueta-Romero, J; Houlné, G; Schantz, R

    1998-07-01

    In bell pepper, a gene encoding a major plastid-lipid associated protein is expressed as both partially and totally spliced transcripts (respectively PAP2 and PAP1). Although PAP is present as a single-copy gene in the bell pepper genome, Southern blots using PAP2 as a probe revealed multiple homologous copies. Analyses of the intronic sequence of PAP2 showed the existence of a 206bp short interspersed repetitive element (SINE) belonging to the Ts family of retrotransposons (Yoshioka et al., 1993). Comparison with PAP sequences in other Solanaceae species suggested that the structure of the gene is highly conserved: the two introns are inserted at the same position. However, the Ts insertion found in bell pepper is absent in tobacco and tomato. Studies using RT-PCR showed that in these latter species only totally spliced transcripts of PAP are present. On the other hand, RNA analyses of tobacco plants transformed with the bell pepper PAP revealed the presence of both totally and incompletely spliced transcripts. Altogether our results support the hypothesis that the Ts insertion into the first intron of PAP results in a splicing defect of the corresponding pre-mRNA. Based on the presence of peculiar, previously unidentified Ts elements, a possible horizontal transmission of Ts elements from animals to plants is discussed.

  4. 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.

  5. Molecular analysis of enterovirus in Cameroon by partial 5'UTR-VP4 gene sequencing reveals a high genetic diversity and frequency of infections.

    PubMed

    Ayukekbong, James Ayukepi; Fobisong, Cajetan; Lindh, Magnus; Nkuo-Akenji, Theresia; Bergström, Tomas; Norder, Helene

    2014-12-01

    Enteroviruses (EVs) often infect humans, presenting as endemic or epidemic infections. In this study, the diversity of infecting EVs was studied among 146 children and 137 adults in a small community in Cameroon. The participants provided 2,458 fecal samples during 1-year monthly collection; 10 or more samples were obtained from 55%. Partial 5'UTR-VP4 region could be sequenced in 393/547 PCR positive samples obtained from 119 children and 85 adults. EV-RNA was detected in at least one sample from 235 participants (83%) during the study period. A total of 121 different strains were identified, 66 infected only children, 29 only adults, and 26 infected both children and adults. There were children with up to five episodes with different strains, and adults with up to four such episodes. Infants aged <5 years were significantly more often EV infected compared to older participants. Infections with species EV-C constituted two third of all cases, and overall EV infections were more common during the rainy season. Species EV-B more often infected children than adults. Most strains were detected only for certain months of the year; however five strains were observed during the time spans of 5-10 months. Two strains were excreted up to eight months in three children and one adult. In 11 of the 128 families with paired samples the child and the adult were infected simultaneously by the same strain, indicating common source of infection. The study revealed a surprising complexity of EV ecosystem in a single community.

  6. Mutation analysis of the HOX paralogous 4-13 genes in children with acute lymphoid malignancies: identification of a novel germline mutation of HOXD4 leading to a partial loss-of-function.

    PubMed

    van Scherpenzeel Thim, Virginie; Remacle, Sophie; Picard, Jacques; Cornu, Guy; Gofflot, Françoise; Rezsohazy, René; Verellen-Dumoulin, Christine

    2005-04-01

    The molecular basis of susceptibility to childhood malignant hemopathy remains largely unknown. An excess of skeletal congenital anomalies has been reported among children with hematological malignancy and points towards involvement of developmental genes, like those belonging to the HOX gene family. In addition to their role in embryogenesis, HOX transcription factors are known to be regulators of proliferation and differentiation of hematopoietic cells. We aimed to explore the possibility that germline alterations of HOX genes might be involved in childhood acute lymphoid malignancies. A cohort of 86 children diagnosed with acute lymphoid malignancy was studied, 20 of them concurrently presenting a congenital anomaly of the skeleton. First, we screened for nucleotide changes throughout the HOX genes of paralogous groups 4 to 13 in the 20 patients with skeletal defects, following a skeletal phenotype-based strategy. Subsequently, we extended the HOX mutation screening to the other 66 children having a malignant lymphoproliferative disorder, but without skeletal defects. In total, 16 germline mutations were identified. While 13 changes were also observed in healthy controls, three variants were exclusively found in acute lymphoid malignancy cases. These comprised the germline c.242A>T (p.Glu81Val) missense mutation of HOXD4, detected in two children diagnosed with acute lymphoblastic leukemia (ALL). Furthermore, this mutation was found in association with other specific HOX variants of cluster D (2q31-q37), defining a unique haplotype. Functional analysis of the murine Hoxd4 homolog revealed that mutant Hoxd4 protein had lower transcriptional activity than wild-type protein in vitro. The p.Glu81Val mutation of HOXD4 thus results in a partial loss-of-function, which might be involved in childhood ALL.

  7. 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

  8. Partial (focal) seizure

    MedlinePlus

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

  9. 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.

  10. Comparison of eukaryotic phytobenthic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing.

    PubMed

    Dorigo, U; Bérard, A; Humbert, J F

    2002-11-01

    We compared the species composition in phytobenthic communities at different sampling sites in a small French river presenting polluted and unpolluted areas. For each sampling point, the total DNA was extracted and used to construct an 18S rRNA gene clone library after PCR amplification of a ca 400 bp fragment. Phytobenthic community composition was estimated by random sequencing of several clones per library. Most of the sequences corresponded to the Bacillariophyceae and Chlorophyceae groups. By combining phylogenetic and correspondence analyses, we showed that our molecular approach is able to estimate and compare the species composition at different sampling sites in order to assess the environmental impact of xenobiotics on phytobenthic communities. Changes in species composition of these communities were found, but no evident decrease in the diversity. We discuss the significance of these changes with regard to the existing level of pollution and their impact on the functionality of the ecosystem. Our findings suggest that it is now possible to use faster molecular methods (DGGE, ARISA.) to test large numbers of samples in the context of ecotoxicological studies, and thus to assess the impact of pollution in an aquatic ecosystem.

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

    PubMed

    Turina, Massimo; Rossi, Marika; Moretti, Marino

    2016-07-01

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

  12. Novel mutation p.A64D in the Serpina7 gene as a cause of partial thyroxine-binding globulin deficiency associated with increases affinity in transthyretin by a known p.A109T mutation in the TTR gene.

    PubMed

    Sklate, R T; Olcese, M C; Maccallini, G C; Sarmiento, R G; Targovnik, H M; Rivolta, C M

    2014-02-01

    Partial thyroxine-binding globulin deficiency (TBG-PD) is an endocrine defect with a prevalence of 1:4 000 in newborns. Due to the presence of a single TBG gene on the X chromosome, most familial TBG defects follow an X-linked inheritance pattern. Abnormal T4 binding to T4-binding prealbumin (TTR) is a rare cause of euthyroid hyperthyroxinemia, which is transmitted by autosomal dominant inheritance. The purpose of the present study was to identify and characterize new mutations in the Serpina7 and TTR genes in a complete family with typical TBG-PD. All patients underwent clinical and biochemical evaluation. Sequencing of DNA, population screening by (SSCP) analysis, and bioinformatics studies were performed. Molecular studies revealed a novel p.A64D mutation in the exon 1 of Serpina7 gene associated with the previously reported p.A109T mutation in the exon 4 of TTR gene. To our knowledge, this is the first report of a patient with a TBG-PD by a mutation in Serpina7 that was coincident with a mutation in TTR gene that increased affinity of TTR for T4. This work contributes to elucidate the molecular basis of the defects of thyroid hormone transport in serum and the improvement of the diagnosis avoiding unnecessary therapy.

  13. 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

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

    PubMed

    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

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

    PubMed

    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.

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

    PubMed

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

    2016-08-01

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

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

    PubMed

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

    2016-08-01

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

  18. GDH Integral on the Proton from Asymmetries

    SciTech Connect

    Yelena Prok

    2004-05-01

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

  19. Transient myeloproliferative disorder with partial trisomy 21.

    PubMed

    Takahashi, Takahide; Inoue, Akira; Yoshimoto, Junko; Kanamitsu, Kiichiro; Taki, Tomohiko; Imada, Masahide; Yamada, Mutsuko; Ninomiya, Shinsuke; Toki, Tsutomu; Terui, Kiminori; Ito, Etsuro; Shimada, Akira

    2015-11-01

    Myeloid malignancy with Down syndrome (ML-DS) is estimated to have a step-wise leukemogenesis including GATA1 mutation. Trisomy 21 is essential for ML-DS; however, we do not know exactly which gene or genes located on chromosome 21 are necessary for the ML-DS. We report a female infant with transient myeloproliferative disorder (TMD) and partial trisomy 21. SNP array analysis showed 10 Mb amplification of 21q22.12-21q22.3, which included DYRK1A, ERG, and ETS but not the RUNX1 gene. With two other reported TMD cases having partial trisomy 21, DYRK1A, ERG, and ETS were the most likely genes involved in collaboration with the GATA1 mutation. PMID:26138905

  20. 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.

  1. 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

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

    PubMed

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

    2014-01-01

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

  3. Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes.

    PubMed

    Pérez-Losada, Marcos; Viscidi, Raphael P; Demma, James C; Zenilman, Jonathan; Crandall, Keith A

    2005-09-01

    Baltimore, Md., is an urban community with a high prevalence of Neisseria gonorrhoeae. Due to partially protective immune responses, introduction of new strains from other host populations, and exposure of N. gonorrhoeae to antibiotics, the phenotypic and genotypic characteristics of the circulating strains can fluctuate over time. Understanding the overall genetic diversity and population structure of N. gonorrhoeae is essential for informing public health interventions to eliminate this pathogen. We studied gonococci population genetics in Baltimore by analyzing a hypervariable and strongly selected outer membrane porB gene and 13 slowly evolving and presumably neutral housekeeping genes (abcZ, adk, aroE, fumC, gdh, glnA, gnd, pdhC, pgm, pilA, ppk, pyrD, and serC) in 204 isolates collected in 1991, 1996, and 2001 from male and female patients of two public sexually transmitted diseases clinics. Genetic diversity (), recombination (C), growth (g), population structure, and adaptive selection under codon-substitution and amino acid property models were estimated and compared between these two gene classes. Estimates of the F(ST) fixation index and the chi(2) test of sequence absolute frequencies revealed significant temporal substructuring for both gene types. Baltimore's N. gonorrhoeae populations have increased since 1991 as indicated by consistent positive values of g. Female patients showed similar or lower levels of and C than male patients. Within the MLST housekeeping genes, levels of and C ranged from 0.001-0.013 and 0.000-0.018, respectively. Overall recombination seems to be the dominant force driving evolution in these populations. All loci showed amino acid sites and physicochemical properties under adaptive (or positive-destabilizing) selection, rejecting the generally assumed hypothesis of stabilizing selection for these MLST genes. Within the porB gene, protein I B showed higher and C values than protein I A. Directional positive selection possibly

  4. Variance Components: Partialled vs. Common.

    ERIC Educational Resources Information Center

    Curtis, Ervin W.

    1985-01-01

    A new approach to partialling components is used. Like conventional partialling, this approach orthogonalizes variables by partitioning the scores or observations. Unlike conventional partialling, it yields a common component and two unique components. (Author/GDC)

  5. 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.

  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, 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.

  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. 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.

  10. 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.

  11. Dynamics of partial control.

    PubMed

    Sabuco, Juan; Sanjuán, Miguel A F; Yorke, James A

    2012-12-01

    Safe sets are a basic ingredient in the strategy of partial control of chaotic systems. Recently we have found an algorithm, the sculpting algorithm, which allows us to construct them, when they exist. Here we define another type of set, an asymptotic safe set, to which trajectories are attracted asymptotically when the partial control strategy is applied. We apply all these ideas to a specific example of a Duffing oscillator showing the geometry of these sets in phase space. The software for creating all the figures appearing in this paper is available as supplementary material. PMID:23278093

  12. 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 Central

    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.

    2014-01-01

    Abstract 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 Cln3Δex7/8 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 Cln3Δex7/8 mice were administered 3×1010 genome copies of AAVrh.10hCLN3 to the brain, with control groups including untreated Cln3Δex7/8 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, Cln3Δex7/8 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 Cln3Δex7/8 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

  13. Partial amino acid sequence and mRNA analysis of cytosolic pyridoxine-beta-D-glucoside hydrolase from porcine intestinal mucosa: proposed derivation from the lactase-phlorizin hydrolase gene.

    PubMed

    Tseung, Chi-Wah; McMahon, Laura G; Vázquez, Jorge; Pohl, Jan; Gregory, Jesse F

    2004-05-15

    We have previously identified and purified a novel beta-glucosidase, designated PNGH (pyridoxine-5'-beta-D-glucoside hydrolase), from the cytosolic fraction of pig intestinal mucosal. PNGH catalyses the hydrolysis of PNG (pyridoxine-5'-beta-D-glucoside), a plant derivative of vitamin B6 that exhibits partial nutritional bioavailability in humans and animals. Preliminary amino acid sequence analysis indicated regions of close similarity of PNGH to the precursor form of LPH (lactase-phlorizin hydrolase), the beta-glucosidase localized to the brush-border membrane. We report in the present study amino acid sequence data for PNGH and results of Northern blot analyses, upon which we propose a common genomic origin of PNGH and LPH. Internal Edman sequencing of the PNGH band isolated by SDS/PAGE yielded data for 16 peptides, averaging 10.8 amino acids in length. These peptides from PNGH (approx. 140 kDa) were highly similar to sequences existing over most of the length of the >200 kDa precursor of rabbit LPH; however, we found no PNGH sequences that corresponded to approx. 350 amino acids between positions 463 and 812 of the LPH precursor, a region encoded by exon 7 of the LPH precursor gene (amino acids 568-784), and no sequences that corresponded to regions near the N-terminus. MS analysis of tryptic peptides yielded 25 peptides, averaging 15 amino acids, with masses that matched segments of the rabbit LPH precursor. Northern blot analysis of pig and human small intestinal polyadenylated mRNA using a non-specific LPH cDNA probe showed an expected approx. 6 kb transcript of the LPH precursor, but also an approx. 4 kb transcript that was consistent with the size predicted from the PNGH protein mass. Using a probe specific to the region encoded by exon 7, hybridization occurred only with the 6 kb transcript. Based on these observations, we propose that both PNGH and LPH enzymes have the same genomic origin, but differ in transcriptional and, possibly, post

  14. Partial amino acid sequence and mRNA analysis of cytosolic pyridoxine-beta-D-glucoside hydrolase from porcine intestinal mucosa: proposed derivation from the lactase-phlorizin hydrolase gene.

    PubMed

    Tseung, Chi-Wah; McMahon, Laura G; Vázquez, Jorge; Pohl, Jan; Gregory, Jesse F

    2004-05-15

    We have previously identified and purified a novel beta-glucosidase, designated PNGH (pyridoxine-5'-beta-D-glucoside hydrolase), from the cytosolic fraction of pig intestinal mucosal. PNGH catalyses the hydrolysis of PNG (pyridoxine-5'-beta-D-glucoside), a plant derivative of vitamin B6 that exhibits partial nutritional bioavailability in humans and animals. Preliminary amino acid sequence analysis indicated regions of close similarity of PNGH to the precursor form of LPH (lactase-phlorizin hydrolase), the beta-glucosidase localized to the brush-border membrane. We report in the present study amino acid sequence data for PNGH and results of Northern blot analyses, upon which we propose a common genomic origin of PNGH and LPH. Internal Edman sequencing of the PNGH band isolated by SDS/PAGE yielded data for 16 peptides, averaging 10.8 amino acids in length. These peptides from PNGH (approx. 140 kDa) were highly similar to sequences existing over most of the length of the >200 kDa precursor of rabbit LPH; however, we found no PNGH sequences that corresponded to approx. 350 amino acids between positions 463 and 812 of the LPH precursor, a region encoded by exon 7 of the LPH precursor gene (amino acids 568-784), and no sequences that corresponded to regions near the N-terminus. MS analysis of tryptic peptides yielded 25 peptides, averaging 15 amino acids, with masses that matched segments of the rabbit LPH precursor. Northern blot analysis of pig and human small intestinal polyadenylated mRNA using a non-specific LPH cDNA probe showed an expected approx. 6 kb transcript of the LPH precursor, but also an approx. 4 kb transcript that was consistent with the size predicted from the PNGH protein mass. Using a probe specific to the region encoded by exon 7, hybridization occurred only with the 6 kb transcript. Based on these observations, we propose that both PNGH and LPH enzymes have the same genomic origin, but differ in transcriptional and, possibly, post

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

    PubMed

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

    2014-06-01

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

  16. Partial hue-matching.

    PubMed

    Logvinenko, Alexander D; Beattie, Lesley L

    2011-01-01

    It is widely believed that color can be decomposed into a small number of component colors. Particularly, each hue can be described as a combination of a restricted set of component hues. Methods, such as color naming and hue scaling, aim at describing color in terms of the relative amount of the component hues. However, there is no consensus on the nomenclature of component hues. Moreover, the very notion of hue (not to mention component hue) is usually defined verbally rather than perceptually. In this paper, we make an attempt to operationalize such a fundamental attribute of color as hue without the use of verbal terms. Specifically, we put forth a new method--partial hue-matching--that is based on judgments of whether two colors have some hue in common. It allows a set of component hues to be established objectively, without resorting to verbal definitions. Specifically, the largest sets of color stimuli, all of which partially match each other (referred to as chromaticity classes), can be derived from the observer's partial hue-matches. A chromaticity class proves to consist of all color stimuli that contain a particular component hue. Thus, the chromaticity classes fully define the set of component hues. Using samples of Munsell papers, a few experiments on partial hue-matching were carried out with twelve inexperienced normal trichromatic observers. The results reinforce the classical notion of four component hues (yellow, blue, red, and green). Black and white (but not gray) were also found to be component colors. PMID:21742961

  17. Partial knee replacement

    MedlinePlus

    ... You will need to understand what surgery and recovery will be like. Partial knee arthroplasty may be a good choice if you have arthritis in only one side or part of the knee and: You are older, thin, and not very active. You do not ...

  18. 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.

  19. Partially coherent ultrafast spectrography

    PubMed Central

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

    2015-01-01

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

  20. 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.

  1. 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.

  2. Partial Androgen Insensitivity Syndrome Presenting with Gynecomastia

    PubMed Central

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

    2015-01-01

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

  3. Melancholia and partial insanity.

    PubMed

    Jackson, S W

    1983-04-01

    In the medical literature of the eighteenth century melancholia came to be defined as partial insanity. Seventeenth-century English law introduced the term and influenced later forensic concerns about the concept. But the history of melancholia reveals a gradual development of such a concept of limited derangement associated with the delusions usually cited in accounts of this disease. In the early nineteenth century the relationship of melancholia and this concept weakened and was gradually abandoned, the content of the syndrome of melancholia was reduced, and out of this complex process emerged the notion of monomania.

  4. Esthetic removable partial dentures.

    PubMed

    Ancowitz, Stephen

    2004-01-01

    This article provides information regarding the many ways that removable partial dentures (RPDs) may be used to solve restorative problems in the esthetic zone without displaying metal components or conspicuous acrylic resin flanges. The esthetic zone is defined and described, as are methods for recording it. Six dental categories are presented that assist the dentist in choosing a variety of RPD design concepts that may be used to avoid metal display while still satisfying basic principles of RPDs. New materials that may be utilized for optimal esthetics are presented and techniques for contouring acrylic resin bases and tinting denture bases are described.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  6. 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.

  7. Partial Triceps Disruption

    PubMed Central

    Foulk, David M.; Galloway, Marc T.

    2011-01-01

    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. PMID:23016005

  8. 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.

  9. 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.

  10. Partial oxidation catalyst

    DOEpatents

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

    2000-01-01

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

  11. 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

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

    PubMed Central

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

    2014-01-01

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

  13. 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

  14. 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

  15. 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.

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

    PubMed Central

    Floková, Kristýna; Miersch, Otto; Strnad, Miroslav; Novák, Ondřej; Wasternack, Claus; Hause, Bettina

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  18. 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.

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

    PubMed

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

    2014-06-01

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

  20. 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.

  1. 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

  2. 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

  3. 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

    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

  4. The partial characterization of tumor necrosis factor-[alpha] resistance, and differential interferon-[alpha] and -[gamma] regulation of the indoleamine 2,3-dioxygenase gene in a human cell line

    SciTech Connect

    Kimbro, K.S.

    1993-01-01

    In order to understand the mechanisms of action of Tumor Necrosis Factor(TNF) on human tumor cells, the author has analyzed a TNF-resistant (TNFr) cell variant of ME180. Studies of the resistant clone showed an increase in in vitro generated free radical resistance, superoxide dismutase, and catalase mRNAs. The analysis of a TNFr clone and its karyotype compared to the parental line, suggest that TNFr could be due to an increase in free radical scavenger proteins and/or chromosomal aberrations. The second component of the thesis involves the analysis of another cytotoxic cytokine, interferon-[gamma], and its ability to induce indoleamine 2,3-dioxygenase (IDO). IDO is the rate limiting enzyme in the catabolism of tryptophan in most cell types. It is predominantly induced following treatment with IFN-[gamma], at a low level or not at all by IFN-[alpha] or-[beta]. The author has determined that the differential regulation of the IDO gene by IFNs may be the result of different interactions of proteins with the regulatory sequences of the IDO gene. The IDO gene has been mapped to chromosome 8.

  5. 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

  6. Partial nucleotide and amino acid sequences of the envelope and the envelope/nonstructural protein-1 gene junction of four dengue-2 virus strains isolated during the 1981 Cuban epidemic.

    PubMed

    Guzman, M G; Deubel, V; Pelegrino, J L; Rosario, D; Marrero, M; Sariol, C; Kouri, G

    1995-03-01

    In 1981, an epidemic of dengue hemorrhagic fever (DHF) caused by dengue-2 virus occurred in Cuba. This was the first DHF epidemic reported in the Western Hemisphere. In this study, we have analyzed four dengue-2 Cuban strains for two short genomic fragments: one on the envelope (E) glycoprotein and one at the E/nonstructural protein-1 (NS1) gene junction. The E segment of these 1981 Cuban isolates were more closely related to older dengue-2 virus strains such as New Guinea C 1944, Thailand 1964, Sri Lanka 1968, and Burma 1976 than to more recent isolates of this virus from Jamaica and Vietnam. More than 9% of the divergence with strains isolated from Jamaica and Vietnam was observed at the E/NS1 gene junction. One nucleotide change was observed between the first strain isolated during the epidemic and the rest of the Cuban strains. This mutation induced a nonconserved amino acid change from phenylalanine to leucine at position 43 that was not observed in any of the other strains with which it was compared.

  7. Partial confinement photonic crystal waveguides

    SciTech Connect

    Saini, S.; Hong, C.-Y.; Pfaff, N.; Kimerling, L. C.; Michel, J.

    2008-12-29

    One-dimensional photonic crystal waveguides with an incomplete photonic band gap are modeled and proposed for an integration application that exploits their property of partial angular confinement. Planar apodized photonic crystal structures are deposited by plasma enhanced chemical vapor deposition and characterized by reflectivity as a function of angle and polarization, validating a partial confinement design for light at 850 nm wavelength. Partial confinement identifies an approach for tailoring waveguide properties by the exploitation of conformal film deposition over a substrate with angularly dependent topology. An application for an optoelectronic transceiver is demonstrated.

  8. Coexpression of the pyrroloquinoline quinone and glucose dehydrogenase genes from Serratia marcescens CTM 50650 conferred high mineral phosphate-solubilizing ability to Escherichia coli.

    PubMed

    Ben Farhat, Mounira; Fourati, Amin; Chouayekh, Hichem

    2013-08-01

    The genes gdh and pqqABCDE encoding glucose dehydrogenase and its pyrroloquinoline quinone cofactor were cloned from the mineral phosphate-solubilizing (MPS) bacterium Serratia marcescens CTM 50650. We investigated, for the first time, the impact of their coexpression in Escherichia coli on MPS ability. The production of recombinant PQQGDH conferred high MPS activity to the engineered E. coli. In fact, the amounts of soluble phosphorus (P) produced from tricalcium phosphate, hydroxyapatite, and Gafsa rock phosphate (GRP) were 574, 426, and 217 mg/L, respectively. In an attempt to increase the soluble P concentration, the E. coli strain coexpressing the gdh and pqqABCDE genes was immobilized in agar, calcium alginate, and k-carrageenan and was then further applied in a repeated batch (six batches) fermentation process to solubilize GRP. Compared to other encapsulated systems, alginate cell beads were noted to yield the highest concentration of soluble P, which attained 300 mg/L/batch. MPS efficiency was maximal in the presence of 5 and 40 g/L of GRP and glucose, respectively. PMID:23737304

  9. 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.

  10. Complex partial status and schizophrenia.

    PubMed

    Ardila, A; Gómez, J

    1988-04-01

    Three cases of complex partial status which were diagnosed as psychotic episodes are presented. The scans of two of these cases show structural abnormalities in the left temporal lobe. It is proposed that there are similar neurophysiological mechanisms in primary schizophrenia and in the perceptual, affective and cognitive phenomena apparent is some complex and psychic partial seizures. The hippocampal-amygdaline system plays a central role in both cases.

  11. [Acrylic resin removable partial dentures].

    PubMed

    de Baat, C; Witter, D J; Creugers, N H J

    2011-01-01

    An acrylic resin removable partial denture is distinguished from other types of removable partial dentures by an all-acrylic resin base which is, in principle, solely supported by the edentulous regions of the tooth arch and in the maxilla also by the hard palate. When compared to the other types of removable partial dentures, the acrylic resin removable partial denture has 3 favourable aspects: the economic aspect, its aesthetic quality and the ease with which it can be extended and adjusted. Disadvantages are an increased risk of caries developing, gingivitis, periodontal disease, denture stomatitis, alveolar bone reduction, tooth migration, triggering of the gag reflex and damage to the acrylic resin base. Present-day indications are ofa temporary or palliative nature or are motivated by economic factors. Special varieties of the acrylic resin removable partial denture are the spoon denture, the flexible denture fabricated of non-rigid acrylic resin, and the two-piece sectional denture. Furthermore, acrylic resin removable partial dentures can be supplied with clasps or reinforced by fibers or metal wires.

  12. 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.

  13. 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.

  14. 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

    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.

  15. 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

  16. Reasonable partiality in professional relationships.

    PubMed

    Almond, Brenda

    2005-04-01

    First, two aspects of the partiality issue are identified: (1) Is it right/reasonable for professionals to favour their clients' interests over either those of other individuals or those of society in general? (2) Are special non-universalisable obligations attached to certain professional roles? Second, some comments are made on the notions of partiality and reasonableness. On partiality, the assumption that only two positions are possible--a detached universalism or a partialist egoism--is challenged and it is suggested that partiality, e.g. to family members, lies between these two positions, being neither a form of egoism, nor of impersonal detachment. On reasonableness, it is pointed out that 'reasonable' is an ambiguous concept, eliding the notions of the 'morally right' and the 'rational.' Third, a series of practical examples are taken from counselling, medicine, law, education and religious practice and some common principles are abstracted from the cases and discussed. These include truth-telling, confidentiality, conflicts of interest between clients and particular others and between clients and society. It is concluded that while partiality can be justified as a useful tool in standard cases, particular circumstances can affect the final verdict.

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2016-05-01

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

  19. Landsliding in partially saturated materials

    NASA Astrophysics Data System (ADS)

    Godt, Jonathan W.; Baum, Rex L.; Lu, Ning

    2009-01-01

    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.

  20. 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.

  1. Sm10.3, a Member of the Micro-Exon Gene 4 (MEG-4) Family, Induces Erythrocyte Agglutination In Vitro and Partially Protects Vaccinated Mice against Schistosoma mansoni Infection

    PubMed Central

    Martins, Vicente P.; Morais, Suellen B.; Pinheiro, Carina S.; Assis, Natan R. G.; Figueiredo, Barbara C. P.; Ricci, Natasha D.; Alves-Silva, Juliana; Caliari, Marcelo V.; Oliveira, Sergio C.

    2014-01-01

    Background The parasitic flatworm Schistosoma mansoni is a blood fluke that causes schistosomiasis. Current schistosomiasis control strategies are mainly based on chemotherapy, but many researchers believe that the best long-term strategy to control disease is a combination of drug treatment and immunization with an anti-schistosome vaccine. Numerous antigens that are expressed at the interface between the parasite and the mammalian host have been assessed. Among the most promising molecules are the proteins present in the tegument and digestive tract of the parasite. Methodology/Principal Findings In this study, we evaluated the potential of Sm10.3, a member of the micro-exon gene 4 (MEG-4) family, for use as part of a recombinant vaccine. We confirmed by real-time PCR that Sm10.3 was expressed at all stages of the parasite life cycle. The localization of Sm10.3 on the surface and lumen of the esophageal and intestinal tract in adult worms and lung-stage schistosomula was confirmed by confocal microscopy. We also show preliminary evidence that rSm10.3 induces erythrocyte agglutination in vitro. Immunization of mice with rSm10.3 induced a mixed Th1/Th2-type response, as IFN-γ, TNF-α, and low levels of IL-5 were detected in the supernatant of cultured splenocytes. The protective effect conferred by vaccination with rSm10.3 was demonstrated by 25.5–32% reduction in the worm burden, 32.9–43.6% reduction in the number of eggs per gram of hepatic tissue, a 23.8% reduction in the number of granulomas, an 11.8% reduction in the area of the granulomas and a 39.8% reduction in granuloma fibrosis. Conclusions/Significance Our data suggest that Sm10.3 is a potential candidate for use in developing a multi-antigen vaccine to control schistosomiasis and provide the first evidence for a possible role for Sm10.3 in the blood feeding process. PMID:24651069

  2. 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.

  3. Partial pressure analysis of plasmas

    SciTech Connect

    Dylla, H.F.

    1984-11-01

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

  4. Full and partial gauge fixing

    SciTech Connect

    Shirzad, A.

    2007-08-15

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

  5. 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.

  6. Partial recovery of microbiomes after antibiotic treatment.

    PubMed

    Raymond, Frédéric; Déraspe, Maxime; Boissinot, Maurice; Bergeron, Michel G; Corbeil, Jacques

    2016-09-01

    Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted. PMID:27494088

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

    PubMed

    Cox, Devin M; Butler, Merlin G

    2015-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  9. Partially Opened Oven on Phoenix

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This view from the Robotic Arm Camera on NASA's Phoenix Mars Lander shows partial opening of doors to one of the tiny ovens of the Thermal and Evolved-Gas Analyzer.

    Each oven has a pair of spring-loaded doors. Near the center of the image, the partial opening of a pair of doors reveals screen over the opening where a soil sample will be delivered. The door to the right is fully opened and the one to the left is partially deployed. The doors are 10 centimeters (4 inches) long. The opening is 4 centimeters (1.5 inches) wide.

    Tests on the Phoenix testbed at the University of Arizona, Tucson, indicate that a soil sample could be delivered into the oven through the partially opened doors. Engineers are also exploring possibilities for opening the doors more completely.This image was taken during Phoenix's eighth Martian day, or sol (June 2, 2008).

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  10. Assessing Partial Knowledge in Vocabulary.

    ERIC Educational Resources Information Center

    Smith, Richard M.

    1987-01-01

    Partial knowledge was assessed in a multiple choice vocabulary test. Test reliability and concurrent validity were compared using Rasch-based dichotomous and polychotomous scoring models. Results supported the polychtomous scoring model, and moderately supported J. O'Connor's theory of vocabulary acquisition. (Author/GDC)

  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. 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.

  13. 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…

  14. Gene expression of regulatory enzymes involved in the intermediate metabolism of sheep subjected to feed restriction.

    PubMed

    van Harten, S; Brito, R; Almeida, A M; Scanlon, T; Kilminster, T; Milton, J; Greeff, J; Oldham, C; Cardoso, L A

    2013-03-01

    The effect of feed restriction on gene expression of regulatory enzymes of intermediary metabolism was studied in two sheep breeds (Australian Merino and Dorper) subjected to two nutritional treatments: feed restriction (85% of daily maintenance requirements) and control (ad libitum feeding), during 42 days. The experimental animals (ram lambs) were divided into four groups, n = 5 (Australian Merino control (MC), Australian Merino Restriction (MR), Dorper control (DC) and Dorper Restriction (DR)). After the trial, animals were sacrificed and samples were taken from liver tissue to quantify glucose levels and gene expression of relevant intermediary metabolism enzymes (phosphofructokinase (PFK), pyruvate kinase (PK), phosphoenolpyruvate carboxykinase, fructose 1,6-bisphosphatase, glucose-6-phosphatase, glycogen synthase (GS), fatty acid synthase (FAS), glutamate dehydrogenase (GDH) and carbamoyl phosphate synthase (CPS)) through real-time PCR. During the experimental period, the MR animals lost 12.6% in BW compared with 5.3% lost by the Dorper lambs. MC and DC rams gained, respectively, 8.8% and 14% during the same period. Within the Dorper breed, restricted feed animals revealed a significant decrease over controls in the transcription of PFK (1.95-fold) and PK (2.26-fold), both glycolytic enzymes. The gluconeogenesis showed no change in the feed restricted animals of both breeds. DR feed group presented a significant decrease over the homologous Merino sheep group on GS. In both experimental breeds, FAS mRNA expression was decreased in restricted feed groups. GDH expression was decreased only in the DR animals (1.84-fold) indicating a reduced catabolism of amino acids in these animals. Finally, CPS was significantly (P < 0.05) higher in the Dorper sheep, indicating a facilitated urea synthesis in this breed. These results indicate a better adaptation of metabolic intermediate regulatory enzymes and hepatic glucose production of Dorper sheep to feed restriction

  15. The partial-birth stratagem.

    PubMed

    1998-06-01

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

  16. 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 ...

  17. 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

  18. Partial stabilization-based guidance.

    PubMed

    Shafiei, M H; Binazadeh, T

    2012-01-01

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

  19. Wettability of partially suspended graphene

    DOE PAGES

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

    2016-04-13

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

  20. GDH Integral on the Proton from Cross Section Differences

    SciTech Connect

    Alexander Skabelin

    2002-02-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. 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

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

    PubMed Central

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

    2011-01-01

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

  10. Genes in sweeping competition.

    PubMed

    Nurminsky, D I

    2001-01-01

    Analysis of DNA variation is a powerful tool for detecting adaptation at the genomic level. The contribution of adaptive evolution is evident from examples of rapidly evolving genes, which represent the likely targets for strong selection. More subtle adaptation is also an integral component of routine maintenance of gene performance, continuously applied to every gene. Adaptive changes in the population are accomplished through selective sweeps, i.e. complete or partial fixation of beneficial alleles. The evidence is accumulating that selective sweeps are quite frequent events which, together with associated genetic hitchhiking, represent dominant forces that influence molecular evolution by shaping the variability pattern in the genome.

  11. Intersexual partial diploids of phycomyces.

    PubMed Central

    Mehta, B J; Cerdá-Olmedo, E

    2001-01-01

    Sexual interaction between strains of opposite sex in many fungi of the order Mucorales modifies hyphal morphology and increases the carotene content. The progeny of crosses of Phycomyces blakesleeanus usually include a small proportion of anomalous segregants that show these signs of sexual stimulation without a partner. We have analyzed the genetic constitution of such segregants from crosses that involved a carF mutation for overaccumulation of beta-carotene and other markers. The new strains were diploids or partial diploids heterozygous for the sex markers. Diploidy was unknown in this fungus and in the Zygomycetes. Random chromosome losses during the vegetative growth of the diploid led to heterokaryosis in the coenocytic mycelia and eventually to sectors of various tints and mating behavior. The changes in the nuclear composition of the mycelia could be followed by selecting for individual nuclei. The results impose a reinterpretation of the sexual cycle of Phycomyces. Some of the intersexual strains that carried the carF mutation contained 25 mg beta-carotene per gram of dry mass and were sufficiently stable for practical use in carotene production. PMID:11404328

  12. GLSMs for partial flag manifolds

    NASA Astrophysics Data System (ADS)

    Donagi, Ron; Sharpe, Eric

    2008-12-01

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

  13. Cloning of an Erwinia herbicola gene necessary for gluconic acid production and enhanced mineral phosphate solubilization in Escherichia coli HB101: nucleotide sequence and probable involvement in biosynthesis of the coenzyme pyrroloquinoline quinone.

    PubMed

    Liu, S T; Lee, L Y; Tai, C Y; Hung, C H; Chang, Y S; Wolfram, J H; Rogers, R; Goldstein, A H

    1992-09-01

    Escherichia coli is capable of synthesizing the apo-glucose dehydrogenase enzyme (GDH) but not the cofactor pyrroloquinoline quinone (PQQ), which is essential for formation of the holoenzyme. Therefore, in the absence of exogenous PQQ, E. coli does not produce gluconic acid. Evidence is presented to show that the expression of an Erwinia herbicola gene in E. coli HB101(pMCG898) resulted in the production of gluconic acid, which, in turn, implied PQQ biosynthesis. Transposon mutagenesis showed that the essential gene or locus was within a 1.8-kb region of a 4.5-kb insert of the plasmid pMCG898. This 1.8-kb region contained only one apparent open reading frame. In this paper, we present the nucleotide sequence of this open reading frame, a 1,134-bp DNA fragment coding for a protein with an M(r) of 42,160. The deduced sequence of this protein had a high degree of homology with that of gene III (M(r), 43,600) of a PQQ synthase gene complex from Acinetobacter calcoaceticus previously identified by Goosen et al. (J. Bacteriol. 171:447-455, 1989). In minicell analysis, pMCG898 encoded a protein with an M(r) of 41,000. These data indicate that E. coli HB101(pMCG898) produced the GDH-PQQ holoenzyme, which, in turn, catalyzed the oxidation of glucose to gluconic acid in the periplasmic space. As a result of the gluconic acid production, E. coli HB101(pMCG898) showed an enhanced mineral phosphate-solubilizing phenotype due to acid dissolution of the hydroxyapatite substrate.

  14. 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.

  15. 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.

  16. Partially entangled states bridge in quantum teleportation

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  17. [The insula in partial epilepsy].

    PubMed

    Isnard, J; Mauguière, F

    2005-01-01

    The role of the insular lobe in temporal lobe epilepsy (TLE) has often been suggested but never directly demonstrated. In this article, we review data from recent literature and from our stereo-electroencephalographic (SEEG) recordings in patients referred for temporal lobe epilepsy surgery (TLE). Our description of the clinical features of insular lobe seizures is based on data from video and SEEG ictal recordings and direct electric cortical stimulation in a population of 50 consecutive patients whose seizures, on the basis of scalp video EEG recordings, were suspected to originate from, or to rapidly propagate to, the peri-sylvian cortex. A total of 144 intra-insular electrodes have been implanted in this series of patients. In six patients a stereotyped sequence of ictal symptoms could be identified on the basis of electro-clinical correlations. The clinical presentation of insular lobe seizures was that of simple partial seizures occurring in full consciousness, beginning with a sensation of laryngeal constriction followed by paresthesiae that were often unpleasant affecting large cutaneous territories. These initial symptoms were eventually followed by dysarthric speech and/or elementary auditory hallucinations, and seizures often ended with focal dystonic postures. The insular origin of these symptoms was supported by the data from functional cortical mapping of the insula using direct cortical stimulations. We were able to reproduce several of the spontaneous ictal symptoms in the six patients with insular seizures. Moreover, from the whole set of insular stimulations that we performed it could be concluded that the insular cortex is involved in somatic, vegetative and visceral functions to which spontaneous ictal insular symptoms are related. The observation of the insular symptoms sequence at the onset of seizures in patients who are candidates for TLE surgery strongly suggests that the epileptic focus is located in the insular lobe. It entails the risk

  18. [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.

  19. 49 CFR 234.106 - Partial activation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., DEPARTMENT OF TRANSPORTATION GRADE CROSSING SAFETY, INCLUDING SIGNAL SYSTEMS, STATE ACTION PLANS, AND... Grade Crossings § 234.106 Partial activation. Upon receipt of a credible report of a partial activation... to warn highway users and railroad employees at the subject crossing in the same manner as...

  20. 49 CFR 234.106 - Partial activation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., DEPARTMENT OF TRANSPORTATION GRADE CROSSING SAFETY, INCLUDING SIGNAL SYSTEMS, STATE ACTION PLANS, AND... Grade Crossings § 234.106 Partial activation. Upon receipt of a credible report of a partial activation... to warn highway users and railroad employees at the subject crossing in the same manner as...

  1. 49 CFR 234.106 - Partial activation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., DEPARTMENT OF TRANSPORTATION GRADE CROSSING SAFETY, INCLUDING SIGNAL SYSTEMS, STATE ACTION PLANS, AND... Grade Crossings § 234.106 Partial activation. Upon receipt of a credible report of a partial activation... to warn highway users and railroad employees at the subject crossing in the same manner as...

  2. 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...

  3. Evaluating Models for Partially Clustered Designs

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  4. Exploring Partial Order of European Countries

    ERIC Educational Resources Information Center

    Annoni, Paola; Bruggemann, Rainer

    2009-01-01

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

  5. Theory of partial agonist activity of steroid hormones

    PubMed Central

    Chow, Carson C.; Ong, Karen M.; Kagan, Benjamin; Simons, S. Stoney

    2015-01-01

    The different amounts of residual partial agonist activity (PAA) of antisteroids under assorted conditions have long been useful in clinical applications but remain largely unexplained. Not only does a given antagonist often afford unequal induction for multiple genes in the same cell but also the activity of the same antisteroid with the same gene changes with variations in concentration of numerous cofactors. Using glucocorticoid receptors as a model system, we have recently succeeded in constructing from first principles a theory that accurately describes how cofactors can modulate the ability of agonist steroids to regulate both gene induction and gene repression. We now extend this framework to the actions of antisteroids in gene induction. The theory shows why changes in PAA cannot be explained simply by differences in ligand affinity for receptor and requires action at a second step or site in the overall sequence of reactions. The theory also provides a method for locating the position of this second site, relative to a concentration limited step (CLS), which is a previously identified step in glucocorticoid-regulated transactivation that always occurs at the same position in the overall sequence of events of gene induction. Finally, the theory predicts that classes of antagonist ligands may be grouped on the basis of their maximal PAA with excess added cofactor and that the members of each class differ by how they act at the same step in the overall gene induction process. Thus, this theory now makes it possible to predict how different cofactors modulate antisteroid PAA, which should be invaluable in developing more selective antagonists. PMID:25984562

  6. 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…

  7. Recombination, transcription, and diversity of a partially germline-joined VH in a mammal.

    PubMed

    Wang, Xinxin; Miller, Robert D

    2012-09-01

    Full or partially germline-joined V genes have been described in a number of different vertebrate lineages where they can contribute to the expressed antibody repertoire through different mechanisms. Here we demonstrate that VH3.1, a partially germline-joined VH gene in the opossum Monodelphis domestica, can undergo V(D)J recombination to generate productive IgH transcripts. VH3.1 is fused to a DH gene segment in the germline DNA and is the only known example of a germline-joined VH in a mammal. B cells that have recombined VH3.1 were not detected until nearly 2 months of age, around the time of weaning, and much later than B cells using the conventional VH. Compared to opossum IgH transcripts using the conventional VH genes, those with VH3.1 have unusually long CDR3 due to the length of the germline-joined DH.

  8. Genes and gene regulation

    SciTech Connect

    MacLean, N.

    1988-01-01

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

  9. 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.

  10. Partial nephrectomy: an option in calculus disease?

    PubMed

    Timoney, A G; Payne, S R; Walmsley, B H; Vinnicombe, J; Abercrombie, G F

    1988-12-01

    Thirty-seven patients treated by partial nephrectomy for calculus disease between 1971 and 1986 were reviewed retrospectively. Of the 25 patients available for analysis, 20% developed immediate surgical complications, 20% had residual post-operative stone and 33% developed true ipsilateral stone recurrence during the period of follow-up. Our results from partial nephrectomy for calculus disease are compared with the results of treatment by percutaneous nephrolithotomy and extracorporeal shockwave lithotripsy. It was concluded that partial nephrectomy should be reserved for situations where stone disease is associated with anatomical abnormalities which cannot be treated by the newer modalities of stone management.

  11. Method for partially coating laser diode facets

    NASA Technical Reports Server (NTRS)

    Dholakia, Anil R. (Inventor)

    1990-01-01

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

  12. Partially coherent contrast-transfer-function approximation.

    PubMed

    Nesterets, Yakov I; Gureyev, Timur E

    2016-04-01

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

  13. Fluctuation theorem for partially masked nonequilibrium dynamics.

    PubMed

    Shiraishi, Naoto; Sagawa, Takahiro

    2015-01-01

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

  14. 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.

  15. 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

  16. Manifest duality for partially massless higher spins

    NASA Astrophysics Data System (ADS)

    Hinterbichler, Kurt; Joyce, Austin

    2016-09-01

    In four dimensions, partially massless fields of all spins and depths possess a duality invariance akin to electric-magnetic duality. We construct metric-like gauge invariant curvature tensors for partially massless fields of all integer spins and depths, and show how the partially massless equations of motion can be recovered from first order field equations and Bianchi identities for these curvatures. This formulation displays duality in its manifestly local and covariant form, in which it acts to interchange the field equations and Bianchi identities.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Electrogenerative partial oxidation of organic compounds

    SciTech Connect

    Stafford, G.R.

    1984-05-22

    This invention provides an electrochemical process for electrogenerative partial oxidation of methyl-substituted hydrocarbons such as ethane, propylene and toluene. Ethane is oxidized to products such as acetaldehyde and acetic acid, and propylene converts to acrolein and acrylic acid.

  2. Partial nephrectomy in a patient with dwarfism.

    PubMed

    Farber, Nicholas J; Dubin, Justin; Parihar, Jaspreet; Han, Chris; Lasser, Michael S

    2016-08-01

    We describe the case of a 50-year-old male with achondroplastic dwarfism who presents with a renal mass in his left kidney concerning for renal cell carcinoma. The patient successfully underwent a robotic partial nephrectomy, which revealed a T1a renal cell carcinoma. The tumor was excised successfully without any intraoperative complications demonstrating that a robotic partial nephrectomy is technically both safe and effective in patients with achondroplastic dwarfism. PMID:27544562

  3. Coherent diffractive imaging and partial coherence

    NASA Astrophysics Data System (ADS)

    Williams, Garth J.; Quiney, Harry M.; Peele, Andrew G.; Nugent, Keith A.

    2007-03-01

    We formulate coherent diffractive imaging in the framework of partially spatially coherent diffraction. We find that the reconstruction can be critically dependent on the degree of coherence in the illuminating field and that even a small departure from full coherence may invalidate the conventional assumption that a mapping exists between an exit surface wave of finite support and a far field diffraction pattern. We demonstrate that the introduction of sufficient phase curvature in the illumination can overcome the adverse effects of partial coherence.

  4. Free fall - A partial unique motion environment

    NASA Technical Reports Server (NTRS)

    Graybiel, A.

    1980-01-01

    Conditions leading to the elicitation of motion sickness have been divided into two main categories: partial motion environments, in which head movements are required to elicit motion sickness, and complete motion environments, in which independent movements of the head are not required for the production of symptoms. It is postulated that, according to this categorization, free fall constitutes a partial motion environment. In support of this hypothesis evidence is reviewed from Skylab missions, experiments in parabolic flight, and ground-based studies.

  5. Gingival enlargement in partial hemifacial hyperplasia.

    PubMed

    Jagtap, Rasika Ravindra; Deshpande, Gaurav Shekhar

    2014-01-01

    Hemifacial hypertrophy is a rare developmental disorder, characterized by unilateral enlargement of facial tissues. The hemifacial hyperplasia is classified as true hemifacial hypertrophy and partial hemifacial hypertrophy. It is unilateral enlargement of viscerocranial condition in which not all structures are enlarged. We present a rare case of gingival enlargement in partial hemifacial hyperplasia highlighting the clinical and radiological findings with the corrective treatment offered for gingival enlargement.

  6. 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...

  7. 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...

  8. Combatting the "partial-birth abortion" myth.

    PubMed

    1998-11-01

    Despite the efforts of pro-choice activists in the US to point out the critical differences between so-called "partial-birth abortions" and late-term abortions, the public remains confused about the issue. Proposed federal legislation banning "partial-birth abortions" excludes any language defining late-term abortions (time period or fetal viability). Thus, such a ban would apply to any abortion at any stage of pregnancy. Only the states of Kansas and Utah have passed legislation that limit the ban to late-term abortions. The term "partial-birth abortion" also has no independent meaning: it is not a medical term nor does it refer to a medical procedure. The correct term, "intact dilation and extraction," is never mentioned in most proposed legislation, much of which is written in broad enough language to outlaw all abortions. Most states that passed bans on "partial-birth abortions," in fact, had previously banned late-term abortions. In Georgia, a court order revised a "partial-birth abortion" law by limiting it to post-viability dilation and extraction and insisting on exceptions to protect the pregnant women's life and health. The courts have severely limited or enjoined "partial-birth abortion" legislation in 19 of the 20 states where challenges were mounted. Because an educated public overwhelmingly rejects the bans, reproductive rights activists are attempting to educate the public despite the inability or unwillingness of the media to make the crucial distinction. PMID:12294330

  9. Combatting the "partial-birth abortion" myth.

    PubMed

    1998-11-01

    Despite the efforts of pro-choice activists in the US to point out the critical differences between so-called "partial-birth abortions" and late-term abortions, the public remains confused about the issue. Proposed federal legislation banning "partial-birth abortions" excludes any language defining late-term abortions (time period or fetal viability). Thus, such a ban would apply to any abortion at any stage of pregnancy. Only the states of Kansas and Utah have passed legislation that limit the ban to late-term abortions. The term "partial-birth abortion" also has no independent meaning: it is not a medical term nor does it refer to a medical procedure. The correct term, "intact dilation and extraction," is never mentioned in most proposed legislation, much of which is written in broad enough language to outlaw all abortions. Most states that passed bans on "partial-birth abortions," in fact, had previously banned late-term abortions. In Georgia, a court order revised a "partial-birth abortion" law by limiting it to post-viability dilation and extraction and insisting on exceptions to protect the pregnant women's life and health. The courts have severely limited or enjoined "partial-birth abortion" legislation in 19 of the 20 states where challenges were mounted. Because an educated public overwhelmingly rejects the bans, reproductive rights activists are attempting to educate the public despite the inability or unwillingness of the media to make the crucial distinction.

  10. Spreading paths in partially observed social networks

    NASA Astrophysics Data System (ADS)

    Onnela, Jukka-Pekka; Christakis, Nicholas A.

    2012-03-01

    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 static, structurally realistic social networks as platforms 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.

  11. 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 ...

  12. Gene conversion in human rearranged immunoglobulin genes.

    PubMed

    Darlow, John M; Stott, David I

    2006-07-01

    Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V(H) segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V(H) replacements with no addition of untemplated nucleotides at the V(H)-V(H) joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V(H) replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion.

  13. Incremental fusion of partial biometric information

    NASA Astrophysics Data System (ADS)

    Abboud, Ali J.; Jassim, Sabah A.

    2012-06-01

    Existing face recognition schemes are mostly based on extracting biometric feature vectors either from whole face images, or from a fixed facial region (e.g., eyes, nose, and mouth). Extreme variation in quality conditions between biometric enrolment and verification stages badly affects the performance of face recognition systems. Such problems have partly motivated several investigations into the use of partial facial features for face recognition. Nevertheless, partial face recognition is potentially useful in several applications, for instance, it used in forensics for detectives to identify individuals after some accidents such as fire or explosion. In this paper, we propose a scheme to fuse the biometric information of partial face images incrementally based on their recognition accuracy (or discriminative power) ranks. Such fusion scheme uses the optimal ratio of full/partial face images in each different quality condition. We found that such scheme is also useful for full face images to enhance authentication accuracy significantly. Nevertheless, it reduces the required storage requirements and processing time of the biometric system. Our experiments show that the required ratio of full/partial facial images to achieve optimal performance varies from (5%) to (80%) according to the quality conditions whereas the authentication accuracy improves significantly for low quality biometric samples.

  14. A compilation of partial sequences of randomly selected cDNA clones from the rat incisor.

    PubMed

    Matsuki, Y; Nakashima, M; Amizuka, N; Warshawsky, H; Goltzman, D; Yamada, K M; Yamada, Y

    1995-01-01

    The formation of tooth organs is regulated by a series of developmental programs. We have initiated a genome project with the ultimate goal of identifying novel genes important for tooth development. As an initial approach, we constructed a unidirectional cDNA library from the non-calcified portion of incisors of 3- to 4-week-old rats, sequenced cDNA clones, and classified their sequences by homology search through the GenBank data base and the PIR protein data base. Here, we report partial DNA sequences obtained by automated DNA sequencing on 400 cDNA clones randomly selected from the library. Of the sequences determined, 51% represented sequences of new genes that were not related to any previously reported gene. Twenty-six percent of the clones strongly matched genes and proteins in the data bases, including amelogenin, alpha 1(I) and alpha 2(I) collagen chains, osteonectin, and decorin. Nine percent of clones revealed partial sequence homology to known genes such as transcription factors and cell surface receptors. A significant number of the previously identified genes were expressed redundantly and were found to encode extracellular matrix proteins. Identification and cataloging of cDNA clones in these tissues are the first step toward identification of markers expressed in a tissue- or stage-specific manner, as well as the genetic linkage study of tooth anomalies. Further characterization of the clones described in this paper should lead to the discovery of novel genes important for tooth development. PMID:7876422

  15. Telecloning of qudits via partially entangled states

    NASA Astrophysics Data System (ADS)

    Araneda, Gabriel; Cisternas, Nataly; Delgado, Aldo

    2016-08-01

    We study the process of quantum telecloning of d-dimensional pure quantum states using partially entangled pure states as quantum channel. This process efficiently mixes optimal universal symmetric cloning with quantum teleportation. It is shown that it is possible to implement universal symmetric telecloning in a probabilistic way using unambiguous state discrimination and quantum state separation schemes. It is also shown that other strategies, such as minimum error discrimination, lead to a decrease in the fidelity of the copies and that certain partially entangled pure states with maximal Schmidt rank lead to an average telecloning fidelity which is always above the optimal fidelity of measuring and preparation of quantum states. We also discuss the case of partially entangled pure states with non-maximal Schmidt rank. The results presented here are valid for arbitrary numbers of copies of a single-input qudit state of any dimension.

  16. 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.

  17. Partial connectivity increases cultural accumulation within groups.

    PubMed

    Derex, Maxime; Boyd, Robert

    2016-03-15

    Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population's ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups. PMID:26929364

  18. Robotic partial nephrectomy: current technique and outcomes.

    PubMed

    Wang, Liang; Lee, Benjamin R

    2013-09-01

    Over the past decade, management of the T1 renal mass has focused on nephron-sparing surgery. Robotic partial nephrectomy has played an increasing role in the technique of preserving renal function by decreasing warm ischemia time, as well as optimizing outcomes of hemorrhage and fistula. Robot-assisted partial nephrectomy is designed to provide a minimally-invasive nephron-sparing surgical option utilizing reconstructive capability, decreasing intracorporeal suturing time, technical feasibility and safety. Ultimately, its benefits are resulting in its dissemination across institutions. Articulated instrumentation and three-dimensional vision facilitate resection, collecting system reconstruction and renorrhaphy, leading to decreased warm ischemia time while preserving oncological outcomes. The aim of the present review was to present our surgical sequence and technique, as well as review the current status of robot-assisted partial nephrectomy.

  19. 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

  20. Diffraction imaging: The limits of partial coherence

    NASA Astrophysics Data System (ADS)

    Chen, Bo; Abbey, Brian; Dilanian, Ruben; Balaur, Eugeniu; van Riessen, Grant; Junker, Mark; Tran, Chanh Q.; Jones, Michael W. M.; Peele, Andrew G.; McNulty, Ian; Vine, David J.; Putkunz, Corey T.; Quiney, Harry M.; Nugent, Keith A.

    2012-12-01

    Coherent diffraction imaging (CDI) typically requires that the source should be highly coherent both laterally and longitudinally. In this paper, we demonstrate that lateral and longitudinal partial coherence can be successfully included in a CDI reconstruction algorithm simultaneously using experimental x-ray data. We study the interplay between lateral partial coherence and longitudinal partial coherence and their relative influence on CDI. We compare our results against the coherence criteria published by Spence [Spence , UltramicroscopyULTRD60304-399110.1016/j.ultramic.2004.05.005 101, 149 (2004)] and show that for iterative ab initio phase-recovery algorithms based on those typically used in CDI and in cases where the coherence properties are known, we are able to relax the minimal coherence requirements by a factor of 2 both laterally and longitudinally, potentially yielding significant reduction in exposure time.

  1. Scintillations of partially coherent Laguerre Gaussian beams

    NASA Astrophysics Data System (ADS)

    Yüceer, M.; Eyyuboğlu, H. T.; Lukin, I. P.

    2010-12-01

    Scintillations of Laguerre-Gaussian (LG) beams for weak atmospheric turbulence conditions are derived for on-axis receiver positions by using Huygens-Fresnel (HF) method in semi-analytic fashion. Numerical evaluations indicate that at the fully coherent limit, higher values of radial mode numbers will give rise to more scintillations, at medium and low partial coherence levels, particularly at longer propagation distances, scintillations will fall against rises in radial mode numbers. At small source sizes, the scintillations of LG beams having full coherence will initially rise, reaching saturation at large source sizes. For LG beams with low partial coherence levels, a steady fall toward the larger source sizes is observed. Partially coherent beams of medium levels generally exhibit a rising trend toward the large source sizes, also changing the respective positions of the related curves. Beams of low coherence levels will be less affected by the variations in the refractive index structure constant.

  2. Partial connectivity increases cultural accumulation within groups.

    PubMed

    Derex, Maxime; Boyd, Robert

    2016-03-15

    Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population's ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups.

  3. 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

  4. 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.

  5. [Fiber-reinforced adhesive partial dentures].

    PubMed

    Kreulen, C M

    2003-06-01

    Dental applications of fiber-reinforced polymers include adhesive partial dentures. Dental resin composite materials can be reinforced by several types of fibres. Fiber orientation, proper wetting of the fibers by the resin and fiber volume are important. An application of fiber reinforced composites is the composite inlay bridge. This paper deals with some aspects of this type of adhesive partial denture. Advantages include the satisfactory esthetics and the minimally invasive character. Not clear yet is the long-term survival. The adhesive properties of fiber-reinforced adhesive partial dentures require an adaptation of the current dental philosophy, in which direct and indirect restorative techniques can be combined. An increase in knowledge and experience is needed to determine the dental applications. PMID:12852063

  6. 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.

  7. 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

  8. Digital generation of partially coherent vortex beams.

    PubMed

    Perez-Garcia, Benjamin; Yepiz, Adad; Hernandez-Aranda, Raul I; Forbes, Andrew; Swartzlander, Grover A

    2016-08-01

    We present an experimental technique to generate partially coherent vortex beams with an arbitrary azimuthal index using only a spatial light modulator. Our approach is based on digitally simulating the intrinsic randomness of broadband light passing through a spiral phase plate. We illustrate the versatility of the technique by generating partially coherent beams with different coherence lengths and orbital angular momentum content, without any moving optical device. Consequently, we study its cross-correlation function in a wavefront folding interferometer. The comparison with theoretical predictions yields excellent agreement. PMID:27472596

  9. Partial gravity - Human impacts on facility design

    NASA Technical Reports Server (NTRS)

    Capps, Stephen; Moore, Nathan

    1990-01-01

    Partial gravity affects the body differently than earth gravity and microgravity environments. The main difference from earth gravity is human locomotion; while the main dfference from microgravity is the specific updown orientation and reach envelopes which increase volume requirements. Much data are available on earth gravity and microgravity design; however, very little information is available on human reactions to reduced gravity levels in IVA situations (without pressure suits). Therefore, if humans commit to permanent lunar habitation, much research should be conducted in the area of partial gravity effects on habitat design.

  10. Pheochromocytoma Presenting as Partial HELLP Syndrome.

    PubMed

    Daaboul, Yazan; Korjian, Serge; Khalil, Lamis; Nemr, Rita

    2015-01-01

    Diagnosis of pheochromocytoma in partial HELLP syndrome is extremely rare. We report a case of a 25-year-old multigravida woman at 30 weeks of gestation who presented with clinical features consistent with partial HELLP syndrome. Her symptoms were not controlled by pharmacologic therapy, and the patient underwent urgent cesarean section. The patient gave birth to a viable baby, but she sustained an episode of ventricular fibrillation intraoperatively that did not result in any long-term sequelae. The patient's symptoms persisted postoperatively and work-up for secondary etiologies of hypertension demonstrated a right adrenal pheochromocytoma. Following resection, the patient's signs and symptoms resolved, and her lab tests normalized. PMID:26351602

  11. 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.

  12. 77 FR 1417 - Partial Approval and Partial Disapproval of Air Quality Implementation Plans; California; San...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-10

    .... Proposed Action On September 9, 2011 (76 FR 55842), EPA proposed to partially approve and partially... approval/disapproval October 1, 2010 (75 FR 60623). SJVUAPCD is scheduled to adopt amendments to Rule 4352.../disapproval January 26, 2010, (75 FR 3996). SJVUAPCD submitted amendments to EPA on July 28, 2011 and...

  13. Partial characterization of a major autolysin from Mycobacterium phlei.

    PubMed

    Li, Z S; Beveridge, T J; Betts, J; Clarke, A J

    1999-01-01

    Autolytic enzyme profiles of fast- and slow-growing mycobacteria were examined using SDS-PAGE zymography with incorporated mycobacterial peptidoglycan sacculi as substrate. Each species tested (Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium aurum, Mycobacterium fortuitum and Mycobacterium kansasii) appeared to produce a different set of enzymes on the basis of differing number and molecular masses. A major autolysin from M. phlei was purified to apparent homogeneity by DEAE-cellulose chromatography, preparative gel electrophoresis and Mono Q FPLC. This enzyme had an estimated molecular mass of 38 kDa, an isoelectric point of 5.5 and a pH optimum of pH 7.5. Digestion of purified peptidoglycan by the enzyme resulted in the appearance of reducing sugars, suggesting that the 38 kDa autolysin is a beta-glycosidase. Partial internal amino acid sequence of the autolysin was determined and should facilitate identification, cloning and overexpression of the encoding gene. PMID:10206696

  14. 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.

  15. Partial dosage compensation in Strepsiptera, a sister group of beetles.

    PubMed

    Mahajan, Shivani; Bachtrog, Doris

    2015-02-01

    Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species.

  16. Partial dosage compensation in Strepsiptera, a sister group of beetles.

    PubMed

    Mahajan, Shivani; Bachtrog, Doris

    2015-02-01

    Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species. PMID:25601100

  17. Partial Dosage Compensation in Strepsiptera, a Sister Group of Beetles

    PubMed Central

    Mahajan, Shivani; Bachtrog, Doris

    2015-01-01

    Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X’s in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species. PMID:25601100

  18. 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,…

  19. Partial spectral analysis of hydrological time series

    NASA Astrophysics Data System (ADS)

    Jukić, D.; Denić-Jukić, V.

    2011-03-01

    SummaryHydrological time series comprise the influences of numerous processes involved in the transfer of water in hydrological cycle. It implies that an ambiguity with respect to the processes encoded in spectral and cross-spectral density functions exists. Previous studies have not paid attention adequately to this issue. Spectral and cross-spectral density functions represent the Fourier transforms of auto-covariance and cross-covariance functions. Using this basic property, the ambiguity is resolved by applying a novel approach based on the spectral representation of partial correlation. Mathematical background for partial spectral density, partial amplitude and partial phase functions is presented. The proposed functions yield the estimates of spectral density, amplitude and phase that are not affected by a controlling process. If an input-output relation is the subject of interest, antecedent and subsequent influences of the controlling process can be distinguished considering the input event as a referent point. The method is used for analyses of the relations between the rainfall, air temperature and relative humidity, as well as the influences of air temperature and relative humidity on the discharge from karst spring. Time series are collected in the catchment of the Jadro Spring located in the Dinaric karst area of Croatia.

  20. Absolute partial photoionization cross sections of ozone.

    SciTech Connect

    Berkowitz, J.; Chemistry

    2008-04-01

    Despite the current concerns about ozone, absolute partial photoionization cross sections for this molecule in the vacuum ultraviolet (valence) region have been unavailable. By eclectic re-evaluation of old/new data and plausible assumptions, such cross sections have been assembled to fill this void.

  1. Partial Hospitalization Programs: A Current Perspective.

    ERIC Educational Resources Information Center

    Whitelaw, Carolyn A.; Perez, Edgardo L.

    1987-01-01

    Reviews the historical background, standards, the issue of day treatment versus day care, functional issues, specialization, efficacy and cost effectiveness, utilization issues, and alternative models of care of partial hospitalization programs in North America. Emphasizes issues of relevance when planning alternative programs to inpatient…

  2. 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…

  3. 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.

  4. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment.

  5. 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…

  6. Dopamine receptor partial agonists and addiction.

    PubMed

    Moreira, Fabricio A; Dalley, Jeffrey W

    2015-04-01

    Many drugs abused by humans acutely facilitate, either directly or indirectly, dopamine neurotransmission in the mesolimbic pathway. As a consequence dopamine receptor agonists and antagonists have been widely investigated as putative pharmacological therapies for addiction. This general strategy, however, has had only limited success due in part to poor treatment adherence and efficacy and the significant adverse effects of dopaminergic medications. In this perspective, we discuss the potential therapeutic use of dopamine receptor partial agonists in addiction, developed initially as antipsychotic agents. Recent research indicates that the dopamine D2 receptor partial agonists, such as aripiprazole, also shows useful ancillary efficacy in several animal models of psychostimulant and opioid addiction. Notably, these findings suggest that unlike full dopamine receptor agonists and antagonists these compounds have low abuse liability and are generally well tolerated. Indeed, partial dopamine agonists attenuate the rewarding properties of opioids without interfering with their analgesic effects. Herein we discuss the utility and potential of dopamine receptor partial agonists as treatments for both stimulant and non-stimulant drug addiction.

  7. PARTIALLY SEEING PROGRAM, 1966-1967.

    ERIC Educational Resources Information Center

    Lake County Special Education District, Gurnee, IL.

    THIS ADMINISTRATIVE OUTLINE OF THE PARTIALLY SEEING PROGRAM IN LAKE COUNTY, ILLINOIS, PRESENTS THE DUTIES AND RESPONSIBILITIES OF THE TWO ITINERANT TEACHERS AND THEIR IMMEDIATE SUPERVISORS. THE PROGRAM'S PHILOSOPHY, GOALS, HISTORY AND PLACEMENT IN THE COUNTY'S ORGANIZATIONAL STRUCTURE IS PRESENTED. THE ITINERANT TEACHER'S ADMINISTRATIVE…

  8. 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.

  9. 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.

  10. 31 CFR 315.41 - Partial redemption.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Partial redemption. 315.41 Section 315.41 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) FISCAL..., SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES General Provisions for Payment §...

  11. 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…

  12. Canonical coordinates for partial differential equations

    NASA Technical Reports Server (NTRS)

    Hunt, L. R.; Villarreal, Ramiro

    1988-01-01

    Necessary and sufficient conditions are found under which operators of the form Sigma (m, j=1) x (2) sub j + X sub O can be made constant coefficient. In addition, necessary and sufficient conditions are derived which classify those linear partial differential operators that can be moved to the Kolmogorov type.

  13. 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.

  14. 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…

  15. 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.

  16. Accommodating blind and partially sighted clients

    PubMed Central

    England, Gary; Gebbels, Tim; Whelan, Chantelle; Freeman, Sarah

    2014-01-01

    Veterinary surgeons provide an important service to blind and partially sighted guide dog owners. By adopting basic disability awareness and visual impairment training, practices can ensure that the assistance needs of those clients are met, facilitating access to veterinary care. PMID:25642013

  17. 24 CFR 203.371 - 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 FAMILY MORTGAGE INSURANCE Contract Rights and Obligations Claim Procedure § 203.371 Partial claim. (a... not exceeded the equivalent of 12 monthly mortgage payments; (3) The mortgagor is able to...

  18. 44 CFR 295.6 - Partial payments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Partial payments. 295.6 Section 295.6 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY CERRO GRANDE FIRE ASSISTANCE CERRO GRANDE FIRE ASSISTANCE General § 295.6...

  19. 44 CFR 295.6 - Partial payments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Partial payments. 295.6 Section 295.6 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY CERRO GRANDE FIRE ASSISTANCE CERRO GRANDE FIRE ASSISTANCE General § 295.6...

  20. Headborne illuminator for the partially sighted.

    PubMed

    Goodlaw, E I; Genensky, S M

    1978-12-01

    An inexpensive, headborne device is described that provides a bright spot of light on reading material even when the material is brought within 1 or 2 cm of the viewing eye. This aid has been used with great success by one of the authors for about 2 yr. This illuminator, or modifications of it, should prove valuable to other partially sighted people.

  1. 32 CFR 751.13 - Partial payments.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... can demonstrate a need for immediate funds to replace some of those items (e.g., food, clothes, baby... shall be taken to ensure the amount of the partial payment is deducted from the adjudicated value of the... payments are to be subtracted from the adjudicated value of the claim before payment of the balance...

  2. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  3. 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

  4. 40 CFR Table 7 to Subpart Vvvvvv... - Partially Soluble HAP

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 15 2014-07-01 2014-07-01 false Partially Soluble HAP 7 Table 7 to... Pt. 63, Subpt. VVVVVV, Table 7 Table 7 to Subpart VVVVVV of Part 63—Partially Soluble HAP As required... partially soluble HAP listed in the following table. Partially soluble HAP name CAS No. 1....

  5. 40 CFR Table 7 to Subpart Vvvvvv... - Partially Soluble HAP

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 15 2013-07-01 2013-07-01 false Partially Soluble HAP 7 Table 7 to... Pt. 63, Subpt. VVVVVV, Table 7 Table 7 to Subpart VVVVVV of Part 63—Partially Soluble HAP As required... partially soluble HAP listed in the following table. Partially soluble HAP name CAS No. 1....

  6. 40 CFR Table 7 to Subpart Vvvvvv... - Partially Soluble HAP

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 15 2012-07-01 2012-07-01 false Partially Soluble HAP 7 Table 7 to... Pt. 63, Subpt. VVVVVV, Table 7 Table 7 to Subpart VVVVVV of Part 63—Partially Soluble HAP As required... partially soluble HAP listed in the following table. Partially soluble HAP name CAS No. 1....

  7. 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

  8. Partial purification and characterization of an aminopeptidase from Eimeria tenella.

    PubMed

    Fetterer, R H; Miska, K B; Barfield, R C

    2005-12-01

    Our previous investigation demonstrated the expression in Eimeria tenella sporulated oocysts of an aminopeptidase (AP) with strong homology to AP N. To further understand the role of proteases during development, we investigated the molecular and biochemical properties of E. tenella AP. Greater than 95% AP activity was present in a soluble extract during sporulation of oocysts with highest activity in fully sporulated oocysts. The AP activity was inhibited by the AP inhibitors bestatin and 1,6-phenanthroline, but not by serine protease inhibitors. The AP had specificity for synthetic endopeptidase substrates that contain arginine, alanine, or glycine at the N terminus. Partial purification of the enzyme yielded a major protein band with an Mr of about 106 kDa and an isoelectric point (Ip) of 5.1. Reverse transcription-polymerase chain reaction indicated that the gene for AP is expressed during sporulation, but expression is absent or greatly reduced in the sporozoites and merozoites. On the basis of the deduced gene structure, the predicted Mr is 110 kDa with a pI of 5.59. Database search indicates that the E. tenella AP shares significant homology with the AP from Apicomplexan taxa: Toxoplasma gondii, Cryptosporidium parvum, and Cryptosporidium hominis. Together, these results confirm the presence of a cytosolic AP related to AP N, which is expressed and active during sporulation of E. tenella oocysts. PMID:16539006

  9. Keratin dressings speed epithelialization of deep partial-thickness wounds.

    PubMed

    Pechter, Patricia M; Gil, Joel; Valdes, Jose; Tomic-Canic, Marjana; Pastar, Irena; Stojadinovic, Olivera; Kirsner, Robert S; Davis, Stephen C

    2012-01-01

    Keratin gene expression is regarded as a hallmark of epidermal biology. It demarcates the three keratinocyte phenotypes: basal (expressing KRT5 and KRT14), differentiating (expressing KRT1 and KRT10), and activated (wound healing), which is characterized by expression of KRT6, KRT16, and KRT17. Activated keratinocytes are among the first signals of epidermal wound healing. In addition, they are found deregulated in nonhealing chronic wounds. To examine keratins as a potential modality for wound-healing disorders, we evaluated two different keratin dressings, liquid or solid, and assessed their effects of epithelialization and closure using porcine partial-thickness wound-healing model in vivo. We found that both forms of keratin dressings accelerated closure and epithelialization, achieving statistically significant differences on day 5. Evidence suggesting early onset of epithelialization was corroborated further by gene expression analyses revealing induction of KRT6A, KRT16, and KRT17 by day 2 postwounding. The data suggest that keratin dressings may stimulate epithelialization by enhancing the activation of keratinocytes. We conclude that keratin-containing dressings can accelerate wound healing and closure. Further studies are needed to determine the molecular mechanisms of this activation.

  10. Retinal pigment epithelial change and partial lipodystrophy.

    PubMed Central

    Davis, T. M.; Holdright, D. R.; Schulenberg, W. E.; Turner, R. C.; Joplin, G. F.

    1988-01-01

    Cuticular drusen and retinal pigment epithelial changes were found incidentally in a 27 year old Lebanese woman during assessment of partial lipodystrophy. Her vision was normal despite involvement of both maculae. The patient had hypocomplementaemia, but serum C3 nephritic factor was absent and renal function was normal. She had impaired glucose tolerance and a continuous infusion of glucose with model assessment (CIGMA) test revealed low normal tissue insulin sensitivity and high normal pancreatic beta cell function. Mild fasting hypertriglyceridaemia (2.0 mmol/l) may have been secondary to impaired insulin sensitivity. Endocrine function was otherwise normal apart from a completely absent growth hormone response to adequate hypoglycaemia. The simultaneous occurrence of partial lipodystrophy and retinal pigmentary epithelial and basement membrane changes appears to be a newly recognized syndrome. Images Figure 1 Figure 2 PMID:3255937

  11. Wear mechanisms of partially stabilized zirconia

    SciTech Connect

    Aronov, V.

    1987-01-01

    This paper is devoted to an investigation of the wear mechanisms of magnesia and yttria partially-stabilized zirconia in ceramic/ceramic and ceramic/metal sliding-contact tribological systems at high temperature. It was found that the wear of ceramics rubbed against ceramics at room temperature may be attributed to intensive plastic deformation of surfaces resulting in low cycle fatigue. The wear mechanism of ceramics rubbed against metals was by polishing and surface fracture, while that of metals was adhesive transfer of material on to ceramic surfaces. Investigation of the wear behavior of magnesia partially-stabilized zirconia rubbed against itself showed that up to three orders of magnitude increase in wear resistance can be achieved in a particular temperature range, depending on both sliding speed and the ambient temperature. XRD analysis revealed that a thermally-induced phase transformation takes place on the frictional interface.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Dynamic partial FPGA reconfiguration in space applications

    NASA Astrophysics Data System (ADS)

    Graczyk, Rafal; Stolarski, Marcin; Palau, Marie-Catherine; Orleanski, Piotr

    2012-05-01

    Design and implementation of hardware mock-up of high performance system for general avionics testing in reconfigurable FPGAs. Strong emphasis is put on exploiting dynamic partial reconfiguration capability as a method for functionality multiplexing and fault mitigation. Additionally, dynamic reconfiguration can be used for fault injection which makes Single Event Upset in configuration memory simulation possible. LEON3 processors are used to create an avionic systems test-bed, for testing the mock-ups of real system flight software and testing dynamic full and partial reconfiguration. Experiments with different means of reconfiguration are performed to measure reconfiguration times and stability of software. Several solutions for whole system reconfiguration controller have been implemented and tested.

  17. 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}

  18. Deterministic dense coding with partially entangled states

    SciTech Connect

    Mozes, Shay; Reznik, Benni; Oppenheim, Jonathan

    2005-01-01

    The utilization of a d-level partially entangled state, shared by two parties wishing to communicate classical information without errors over a noiseless quantum channel, is discussed. We analytically construct deterministic dense coding schemes for certain classes of nonmaximally entangled states, and numerically obtain schemes in the general case. We study the dependency of the maximal alphabet size of such schemes on the partially entangled state shared by the two parties. Surprisingly, for d>2 it is possible to have deterministic dense coding with less than one ebit. In this case the number of alphabet letters that can be communicated by a single particle is between d and 2d. In general, we numerically find that the maximal alphabet size is any integer in the range [d,d{sup 2}] with the possible exception of d{sup 2}-1. We also find that states with less entanglement can have a greater deterministic communication capacity than other more entangled states.

  19. 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.

  20. 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.

  1. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population.

    PubMed

    Allard, Alix; Bink, Marco C A M; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean-Michel; di Guardo, Mario; Di Pierro, Erica A; Laurens, François; van de Weg, Eric W; Costes, Evelyne

    2016-04-01

    In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6-21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase.

  2. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

    PubMed Central

    Allard, Alix; Bink, Marco C.A.M.; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean-Michel; di Guardo, Mario; Di Pierro, Erica A.; Laurens, François; van de Weg, Eric W.; Costes, Evelyne

    2016-01-01

    In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase. PMID:27034326

  3. Partial Conservation of Seniority and Nuclear Isomerism

    SciTech Connect

    Van Isacker, P.; Heinze, S.

    2008-02-08

    We point out the possibility of the partial conservation of the seniority quantum number when most eigenstates are mixed in seniority but some remain pure. This situation occurs in nuclei for the g{sub 9/2} and h{sub 9/2} shells where it is at the origin of the existence of seniority isomers in the ruthenium and palladium isotopes. It also occurs for f bosons.

  4. Partial reinforcement in human biofeedback learning.

    PubMed

    Morley, S

    1979-09-01

    This paper reviews the evidence for the efficacy of partial reinforcement in producing resistance to extinction in human biofeedback experiments. The methodological criteria necessary to demonstrate such effects are discussed, as is the status of the analogy of reinforcement and information feedback. It is suggested that the problem of maintaining responding in the absence of feedback should be tackled empirically rather than assuming the validity of findings from other areas of learning theory.

  5. Lifted Partially Premixed Flames in Microgravity

    NASA Technical Reports Server (NTRS)

    Lock, Andrew J.; Ganguly, Ranjan; Puri, Ishwar K.; Aggarwal, Suesh K.; Hegde, Uday

    2004-01-01

    Lifted Double and Triple flames are established in the UIC-NASA Partially Premixed microgravity rig. The flames examined in this paper are established above a coannular burner because its axisymmetric geometry allows for future implementation of other non-intrusive optical diagnostic techniques easily. Both burner-attached stable flames and lifted flames are established at normal and microgravity conditions in the drop tower facility.

  6. Partial Dynamical Symmetry in Nuclear Systems

    SciTech Connect

    Escher, J E

    2003-06-02

    Partial dynamical symmetry (PDS) extends and complements the concepts of exact and dynamical symmetry. It allows one to remove undesired constraints from an algebraic theory, while preserving some of the useful aspects of a dynamical symmetry, and to study the effects of symmetry breaking in a controlled manner. An example of a PDS in an interacting fermion system is presented. The associated PDS Hamiltonians are closely related with a realistic quadrupole-quadrupole interaction and provide new insights into this important interaction.

  7. Nonphotosensitive video game-induced partial seizures.

    PubMed

    Takahashi, Y; Shigematsu, H; Kubota, H; Inoue, Y; Fujiwara, T; Yagi, K; Seino, M

    1995-08-01

    We report a 9-year-old boy with a ring 20 chromosome anomaly whose complex partial seizures (CPS), presumably of frontal lobe origin, were often induced by playing video games. Neither photosensitivity nor pattern sensitivity was observed. An intensive video-EEG investigation showed that video games as well as mental calculation elicited rhythmic runs of bilateral high-voltage slow waves, which eventually evolved into ictal discharges. This case suggests that higher brain functions can be involved in seizure induction.

  8. 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.

  9. Partial intravenous anesthesia in cats and dogs

    PubMed Central

    Duke, Tanya

    2013-01-01

    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. PMID:23997266

  10. 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.

  11. The partially filled viscous ring damper.

    NASA Technical Reports Server (NTRS)

    Alfriend, K. T.

    1973-01-01

    The problem of a spinning satellite with a partially filled viscous ring damper is investigated. It is shown that there are two distinct modes of motion, the nutation-synchronous mode and spin-synchronous mode. From an approximate solution of the equations of motion a time constant is obtained for each mode. From a consideration of the fluid dynamics several methods are developed for determining the damping constant.

  12. Underdetermined systems of partial differential equations

    SciTech Connect

    Bender, Carl M.; Dunne, Gerald V.; Mead, Lawrence R.

    2000-09-01

    This paper examines underdetermined systems of partial differential equations in which the independent variables may be classical c-numbers or even quantum operators. One can view an underdetermined system as expressing the kinematic constraints on a set of dynamical variables that generate a Lie algebra. The arbitrariness in the general solution reflects the freedom to specify the dynamics of such a system. (c) 2000 American Institute of Physics.

  13. 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.

  14. 75 FR 68093 - Partial Grant and Partial Denial of Clean Air Act Waiver Application Submitted by Growth Energy...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-04

    ... Protection Agency Partial Grant and Partial Denial of Clean Air Act Waiver Application Submitted by Growth Energy To Increase the Allowable Ethanol Content of Gasoline to 15 Percent; Decision of the Administrator...; ] ENVIRONMENTAL PROTECTION AGENCY Partial Grant and Partial Denial of Clean Air Act Waiver Application...

  15. Viscous fingering with partial miscible fluids

    NASA Astrophysics Data System (ADS)

    Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

    2015-11-01

    When a less viscous fluid displaces a more viscous fluid, the contrast in viscosity destabilizes the interface between the two fluids, leading to the formation of fingers. Studies of viscous fingering have focused on fluids that are either fully miscible or perfectly immiscible. In practice, however, the miscibility of two fluids can change appreciably with temperature and pressure, and often falls into the case of partial miscibility, where two fluids have limited solubility in each other. Following our recent work for miscible (Jha et al., PRL 2011, 2013) and immiscible systems (Cueto-Felgueroso and Juanes, PRL 2012, JFM 2014), here we propose a phase-field model for fluid-fluid displacements in a Hele-Shaw cell, when the two fluids have limited (but nonzero) solubility in one another. Partial miscibility is characterized through the design of thermodynamic free energy of the two-fluid system. We elucidate the key dimensionless groups that control the behavior of the system. We present high-resolution numerical simulations of the model applied to the viscous fingering problem. On one hand, we demonstrate the effect of partial miscibility on the hydrodynamic instability. On the other, we elucidate the role of the degree of fingering on the rate of mutual fluid dissolution.

  16. Multichannel cochlear implants in partially ossified cochleas.

    PubMed

    Balkany, T; Gantz, B; Nadol, J B

    1988-01-01

    Deposition of bone within the fluid spaces of the cochlea is encountered commonly in cochlear implant candidates and previously has been considered a relative contraindication to the use of multichannel intracochlear electrodes. This contraindication has been based on possible mechanical difficulty with electrode insertion as well as uncertainty about the potential benefit of the multichannel device in the patient. Fifteen profoundly deaf patients with partial ossification of the basal turn of the cochlea received implants with long intracochlear electrodes (11, Nucleus; 1, University of California at San Francisco/Storz; and 3, Symbion/Inneraid). In 11 cases, ossification had been predicted preoperatively by computed tomographic scan. Electrodes were completely inserted in 14 patients, and partial insertion was accomplished in one patient. All patients currently are using their devices and nine of 12 postlingually deaf patients have achieved some degree of open-set speech discrimination. This series demonstrates that in experienced hands, insertion of long multichannel electrodes into partially ossified cochleas is possible and that results are similar to those achieved in patients who have nonossified cochleas. PMID:3140705

  17. 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

  18. 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.

  19. Acute renal injury after partial hepatectomy.

    PubMed

    Peres, Luis Alberto Batista; Bredt, Luis Cesar; Cipriani, Raphael Flavio Fachini

    2016-07-28

    Currently, partial hepatectomy is the treatment of choice for a wide variety of liver and biliary conditions. Among the possible complications of partial hepatectomy, acute kidney injury (AKI) should be considered as an important cause of increased morbidity and postoperative mortality. Difficulties in the data analysis related to postoperative AKI after liver resections are mainly due to the multiplicity of factors to be considered in the surgical patients, moreover, there is no consensus of the exact definition of AKI after liver resection in the literature, which hampers comparison and analysis of the scarce data published on the subject. Despite this multiplicity of risk factors for postoperative AKI after partial hepatectomy, there are main factors that clearly contribute to its occurrence. First factor relates to large blood losses with renal hypoperfusion during the operation, second factor relates to the occurrence of post-hepatectomy liver failure with consequent distributive circulatory changes and hepatorenal syndrome. Eventually, patients can have more than one factor contributing to post-operative AKI, and frequently these combinations of acute insults can be aggravated by sepsis or exposure to nephrotoxic drugs. PMID:27478539

  20. Partially ordered sets in complex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Du, Fang; Wu, Tie-Jun

    2010-05-01

    In this paper, a partial-order relation is defined among vertices of a network to describe which vertex is more important than another on its contribution to the connectivity of the network. A maximum linearly ordered subset of vertices is defined as a chain and the chains sharing the same end-vertex are grouped as a family. Through combining the same vertices appearing in different chains, a directed chain graph is obtained. Based on these definitions, a series of new network measurements, such as chain length distribution, family diversity distribution, as well as the centrality of families, are proposed. By studying the partially ordered sets in three kinds of real-world networks, many interesting results are revealed. For instance, the similar approximately power-law chain length distribution may be attributed to a chain-based positive feedback mechanism, i.e. new vertices prefer to participate in longer chains, which can be inferred by combining the notable preferential attachment rule with a well-ordered recommendation manner. Moreover, the relatively large average incoming degree of the chain graphs may indicate an efficient substitution mechanism in these networks. Most of the partially ordered set-based properties cannot be explained by the current well-known scale-free network models; therefore, we are required to propose more appropriate network models in the future.

  1. Full and Partial Cloaking in Electromagnetic Scattering

    NASA Astrophysics Data System (ADS)

    Deng, Youjun; Liu, Hongyu; Uhlmann, Gunther

    2016-08-01

    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.

  2. 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

  3. 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.

  4. Energy considerations in the partial space elevator

    NASA Astrophysics Data System (ADS)

    Woo, Pamela; Misra, Arun K.

    2014-06-01

    The space elevator has been proposed as an alternate method for space transportation. A partial elevator is composed of a tether of several hundreds of kilometres, held vertically in tension between two end masses, with its centre of orbit placed at the geosynchronous orbit. A spacecraft can dock at the lower end, and then use the climber on the elevator to ascend to higher altitudes. In this paper, energy calculations are performed, to determine whether a partial elevator can provide sufficient savings in operational costs, compared to the traditional rocket-powered launch. The energy required to launch a spacecraft from a Low Earth Orbit (LEO) to the geostationary orbit (GEO) is calculated for two trajectories. In the first trajectory, the spacecraft travels from LEO to GEO via a Hohmann transfer. In the second trajectory, the spacecraft travels from LEO to the lower end of the partial space elevator with a Hohmann transfer, and then uses the elevator to climb to GEO. The total energy required is compared between the two trajectories. The effects of tether length, spacecraft-to-climber mass ratio, altitude of LEO, and tether material are investigated.

  5. Cloning and overexpression of an NADH-dependent alcohol dehydrogenase gene from Candida maris involved in (R)-selective reduction of 5-acetylfuro[2,3-c]pyridine.

    PubMed

    Kawano, Shigeru; Yano, Miho; Hasegawa, Junzo; Yasohara, Yoshihiko

    2011-01-01

    5-((R)-1-Hydroxyethyl)-furo[2,3-c]pyridine ((R)-FPH) is a useful chiral building block in the synthesis of pharmaceuticals. An NADH-dependent alcohol dehydrogenase (AFPDH) isolated from Candida maris catalyzed the reduction of 5-acetylfuro[2,3-c]pyridine (AFP) to (R)-FPH with 100% enantiomeric excess. The gene encoding AFPDH was cloned and sequenced. The AFPDH gene comprises 762 bp and encodes a polypeptide of 27,230 Da. The deduced amino acid sequence showed a high degree of similarity to those of other members of the short-chain alcohol dehydrogenase superfamily. The AFPDH gene was overexpressed in Escherichia coli under the control of the lac promoter. One L of the cultured broth of an E. coli transformant coexpressing AFPDH and the glucose dehydrogenase (GDH) gene reduced 250 g of AFP to (R)-FPH in an organic solvent two-phase system. Under coupling with NADH regeneration using 2-propanol, 1 L of the cultured broth of an E. coli transformant expressing the AFPDH gene reduced 150 g of AFP to (R)-FPH. The optical purity of the (R)-FPH formed was 100% enantiomeric excess under both reaction conditions.

  6. In vitro resistance to 5-nitroimidazoles and benzimidazoles in Giardia duodenalis: variability and variation in gene expression.

    PubMed

    Argüello-García, Raúl; Cruz-Soto, Maricela; Romero-Montoya, Lydia; Ortega-Pierres, Guadalupe

    2009-12-01

    The susceptibility of Giardia duodenalis trophozoites exposed in vitro to sublethal concentrations of metronidazole (MTZ) and albendazole (ABZ) may exhibit inter-culture (variability) and intra-culture (variation) differences in drug susceptibility. It was previously reported that MTZ-resistant trophozoites may display changes in pyruvate:ferredoxin oxidoreductase (PFOR) expression while changes at the beta-tubulin molecule are apparently absent in ABZ-resistant cultures. To assess the levels of gene expression of these molecules, we obtained cloned cultures growing at concentrations up to 23 microM MTZ (WBRM23) and up to 8muM ABZ (WBRA8) and gene sequence and expression of pfor and beta-tubulin loci were compared with these of drug-susceptible clone WB1. Neither the pfor nor the beta-tubulin genes showed changes at sequence level but the MTZ-resistant clones WBRM21 and WBRM23 showed up-regulation of the pfor RNA using the gdh gene as reference. By using WB1 and WBRA8 clones in representational difference analyses of gene expression (RDA) an insert referred to as ARR-VSP was selected and sequenced. It showed the highest homology to one VSP molecule in the Giardia Genome Database (orf GL50803_101765). This isogene was up-regulated in five ABZ-resistant clones and the clone WBRA8 exhibited the highest RNA expression level. When successive progenies of clones WB1, WBRM23 and WBRA8 were analyzed in Northern blot assays to detect pfor and ARR-VSP RNAs respectively, the expression patterns showed variation for both genes but it was much lower in the clone WBRA8. These results suggest that G. duodenalis cultures either susceptible or resistant to MTZ and ABZ may display variability and variation at RNA expression levels albeit these were more marked in the MTZ-resistant parasites. These data might have further implications defining major mechanisms involved in drug resistance of Giardia. PMID:19481175

  7. 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

  8. Liquid spreading under partial wetting conditions

    NASA Astrophysics Data System (ADS)

    Chen, M.; Pahlavan, A. A.; Cueto-Felgueroso, L.; McKinley, G. H.; Juanes, R.

    2013-12-01

    Traditional mathematical descriptions of multiphase flow in porous media rely on a multiphase extension of Darcy's law, and lead to nonlinear second-order (advection-diffusion) partial differential equations for fluid saturations. Here, we study horizontal redistribution of immiscible fluids. The traditional Darcy-flow model predicts that the spreading of a finite amount of liquid in a horizontal porous medium never stops; a prediction that is not substantiated by observation. To help guide the development of new models of multiphase flow in porous media [1], we draw an analogy with the flow of thin films. The flow of thin films over flat surfaces has been the subject of much theoretical, experimental and computational research [2]. Under the lubrication approximation, the classical mathematical model for these flows takes the form of a nonlinear fourth-order PDE, where the fourth-order term models the effect of surface tension [3]. This classical model, however, effectively assumes that the film is perfectly wetting to the substrate and, therefore, does not capture the partial wetting regime. Partial wetting is responsible for stopping the spread of a liquid puddle. Here, we present experiments of (large-volume) liquid spreading over a flat horizontal substrate in the partial wetting regime, and characterize the four spreading regimes that we observe. We extend our previous theoretical work of two-phase flow in a capillary tube [4], and develop a macroscopic phase-field modeling of thin-film flows with partial wetting. Our model naturally accounts for the dynamic contact angle at the contact line, and therefore permits modeling thin-film flows without invoking a precursor film, leading to compactly-supported solutions that reproduce the spreading dynamics and the static equilibrium configuration observed in the experiments. We anticipate that this modeling approach will provide a natural mathematical framework to describe spreading and redistribution of immiscible

  9. 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.

  10. 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.

  11. 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.

  12. Linear partial difference equations of hypergeometric type

    NASA Astrophysics Data System (ADS)

    Rodal, J.; Area, I.; Godoy, E.

    2007-03-01

    In this paper a systematic study of the orthogonal polynomial solutions of a second order partial difference equation of hypergeometric type of two variables is done. The Pearson's systems for the orthogonality weight of the solutions and also for the difference derivatives of the solutions are presented. The orthogonality property in subspaces is treated in detail, which leads to an analog of the Rodrigues-type formula for orthogonal polynomials of two discrete variables. A classification of the admissible equations as well as some examples related with bivariate Hahn, Kravchuk, Meixner, and Charlier families, and their algebraic and difference properties are explicitly given.

  13. Average characteristics of partially coherent electromagnetic beams.

    PubMed

    Seshadri, S R

    2000-04-01

    Average characteristics of partially coherent electromagnetic beams are treated with the paraxial approximation. Azimuthally or radially polarized, azimuthally symmetric beams and linearly polarized dipolar beams are used as examples. The change in the mean squared width of the beam from its value at the location of the beam waist is found to be proportional to the square of the distance in the propagation direction. The proportionality constant is obtained in terms of the cross-spectral density as well as its spatial spectrum. The use of the cross-spectral density has advantages over the use of its spatial spectrum.

  14. 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.

  15. [Partial lease squares approach to functional analysis].

    PubMed

    Preda, C

    2006-01-01

    We extend the partial least squares (PLS) approach to functional data represented in our models by sample paths of stochastic process with continuous time. Due to the infinite dimension, when functional data are used as a predictor for linear regression and classification models, the estimation problem is an ill-posed one. In this context, PLS offers a simple and efficient alternative to the methods based on the principal components of the stochastic process. We compare the results given by the PLS approach and other linear models using several datasets from economy, industry and medical fields. PMID:17124795

  16. Computing Partial Transposes and Related Entanglement Functions

    NASA Astrophysics Data System (ADS)

    Maziero, Jonas

    2016-10-01

    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.

  17. The geometry of the partial realization problem

    NASA Technical Reports Server (NTRS)

    Brockett, R. W.; Hall, P.

    1979-01-01

    It is shown that the space of sequences of length n which have an extrapolation of McMillan degree k, and no extrapolations of lower McMillan degree can be given the structure of a differentiable manifold. This approach makes the proof of certain known results on the partial realization problem quite straightforward and makes it possible to establish some important new results as well. A key tool is the fact, proven here, that the set of n by a real Hankel matrices of rank r is a manifold with r+1 connected components.

  18. 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.

  19. Laparoscopic partial nephrectomy in a horseshoe kidney.

    PubMed

    Molina, Wilson R; Gill, Inderbir S

    2003-12-01

    A 68-year-old man with an incidentally found 2-cm complex enhancing cystic right renal mass in the right moiety of a horseshoe kidney was treated with a three-port retroperitoneal laparoscopic approach. The tumor was completely excised with cold Endoshears, and Surgicel bolsters were tightly buttressed into the resection bed with 0 Vicryl sutures. The warm ischemia time was 31 minutes. To our knowledge, this is the initial case of retroperitoneal laparoscopic partial nephrectomy in a horseshoe kidney. Three-dimensional CT with volume rendering in a video format provides the necessary information about the number, location, and extrarenal anatomy of the renal artery and vein.

  20. 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.

  1. 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.

  2. 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. PMID:4029302

  3. PARTIAL TRISOMY 4p AND PARTIAL MONOSOMY 13q: CASE REPORT AND A LITERATURE REVIEW.

    PubMed

    Puvabanditsin, S; Herrera-Garcia, G; Gengel, N; Hussein, K; February, M; Mayne, J; Mehta, R

    2016-01-01

    We report on a term first born dichorionic-diamniotic twin with deletion of the distal long arm of chromosome 13, partial trisomy of the short arm of chromosome 4, intrauterine growth retardation, and multiple anomalies including microcephaly, colpocephaly, absent corpus callosum, bulbous tip of the nose, large and low set ears, macroglossia, thin upper lip, double outlet right ventricle, atria/ventricular septal defect, cleft mitral valve, pulmonary stenosis, single umbilical artery, multicystic dysplastic left kidney, sacral dimple, anterior displacement of anus, simian creases, abnormal thumb (congenital clasped thumb), overlapping toes, and congenital hypothyroidism. This is the first report of a patient with partial trisomy 4p and partial monosomy 13q. PMID:27192890

  4. Partial spatial coherence and partial polarization in random evanescent fields on lossless interfaces.

    PubMed

    Norrman, Andreas; Setälä, Tero; Friberg, Ari T

    2011-03-01

    We consider partial spatial coherence and partial polarization of purely evanescent optical fields generated in total internal reflection at an interface of two dielectric (lossless) media. Making use of the electromagnetic degree of coherence, we show that, in such fields, the coherence length can be notably shorter than the light's vacuum wavelength, especially at a high-index-contrast interface. Physical explanation for this behavior, analogous to the generation of incoherent light in a multimode laser, is provided. We also analyze the degree of polarization by using a recent three-dimensional formulation and show that the field may be partially polarized at a subwavelength distance from the surface even though it is fully polarized farther away. The degree of polarization can assume values unattainable by beamlike fields, indicating that electromagnetic evanescent waves generally are genuine three-dimensional fields. The results can find applications in near-field optics and nanophotonics.

  5. Preparation of partially decaffeinated instant green tea.

    PubMed

    Ye, Jian-Hui; Liang, Yue-Rong; Jin, Jing; Liang, Hue-Ling; Du, Ying-Ying; Lu, Jian-Liang; Ye, Qian; Lin, Chen

    2007-05-01

    The caffeine level of instant tea extracted from decaffeinated leaf tea with 4.0 mg g-1 caffeine is commonly above 10.0 mg g-1, the maximum limit of caffeine for decaffeinated instant tea. Further removal of caffeine by active carbon (AC) from the green tea extract was investigated. It showed that the removal of caffeine from the tea extract solutions depended on the treatment time and tea extract concentration while the ethanol concentration and pH had little effect on the removal of caffeine. According to the removal of caffeine and the ratio of total catechins to caffeine in the tested samples, the optimum decaffeination conditions were determined to be as follows: tea extract concentration 15-30 g L-1 for common tea extract but higher for partially decaffeinated tea leaf extract; ratio of tea solution to AC, 100 mL:4 g; treatment time, 4 h; and natural tea extract pH. Instant tea powder extracted from partially decaffeinated leaf tea with a caffeine level of 4.03 mg g-1 and further decaffeinated by AC had a caffeine level of 7.81 mg g-1, which was 31% lower than that without AC treatment.

  6. Alcalase rapeseed inhibitors: purification and partial characterization.

    PubMed

    Vioque, J; Sánchez-Vioque, R; Clemente, A; Pedroche, J; Mar Yust, M; Millán, F

    2001-01-01

    Extensive rapeseed protein hydrolysate obtained sequentially with Alcalase and Flavourzyme showed inhibitory activity towards Alcalase. Inhibitory activity decreased as the hydrolytic process progressed probably by heat denaturation and/or partial protease degradation. Alcalase rapeseed inhibitors were purified by gel filtration and subsequent ion exchange chromatography. They are composed of peptides of 8.4 and 6.1 kDa linked by interchain disulphide bonds, as observed by reducing SDS-PAGE, with a native molecular weight of 18 kDa. Aminoacid composition of the inhibitors was characterized by the high proportion of methionine (4.2%) and cysteine (4.6%). Alcalase inhibitors were partially resistant to heat treatment; after heating at 70 degrees C for 45 minutes more than 50% of the original inhibitory activity remained in the purified protein but after heating at 90 degrees C for 5 minutes, inhibitory activity decreased very fast to a basal level. The possible relation of these protease inhibitors with the 2S albumin storage proteins is discussed.

  7. 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.

  8. Laparoscopic partial nephrectomy and wedge resection.

    PubMed

    Kozlowski, P M; Winfield, H N

    2000-12-01

    Partial nephrectomy is a more challenging operation than radical or simple nephrectomy, primarily because of the risk of complications such as bleeding. This problem is even more troublesome with minimally invasive approaches because of the dearth of effective hemostatic instruments and supplies. The location of the lesion determines whether a transperitoneal or a retroperitoneal route will be employed. Centrally located or anterior renal lesions generally are approached transperitoneally whereas peripheral lateral or posterior lesions are accessed by retroperitoneoscopy. The Harmonic Scalpel with slow cutting and high coagulation settings is useful for incising the renal capsule and parenchyma. The argon beam coagulator is helpful to stop any persistent bleeding. The few reported series of laparoscopic partial nephrectomy indicate considerably longer operative times than are needed for open surgery and hospitalization of upwards of 5 days, largely to monitor drainage and urine leakage. It is hoped that this advanced laparoscopic technique will become more user friendly with further developments in techniques and instrumentation to provide patients with the expected benefits of minimally invasive surgery.

  9. A NUCLEAR MEMBRANE CHANGE AFTER PARTIAL HEPATECTOMY

    PubMed Central

    Kishimoto, Susumu; Lieberman, Irving

    1964-01-01

    Partial hepatectomy (67 per cent extirpation) of the rat leads to a change in the membrane of liver nuclei (purified with citric acid) detectable as an increase in electrophoretic mobility. No change is detectable 2 hours after the operation, but between 2 and 6 hours about a 1.4-fold increase in mobility occurs after which the mobility becomes constant at the elevated level. Removal of only 10 per cent of the liver causes no detectable change in 6 hours. Bilateral adrenalectomy immediately before partial hepatectomy does not affect the development of the nuclear change. Actinomycin D and p-fluorophenylalanine, but not noradrenalin, ionizing radiation, or EDTA, suppress the increase in electrophoretic mobility. The level of actinomycin D required to block the nuclear membrane change is 6 times greater than that necessary to prevent the rate increase in hepatic RNA metabolism that follows removal of part of the liver. This discrepancy and the difference in the response to noradrenalin indicate that, at least initially, the nuclear membrane change and the change in the rate of RNA synthesis are independent processes. The inability of EDTA to block the nuclear membrane change shows that the Zn++ requirement for DNA replication is not related to the events that lead to the alteration in the electrokinetic properties of liver nuclei. PMID:14245434

  10. Preparation of partially decaffeinated instant green tea.

    PubMed

    Ye, Jian-Hui; Liang, Yue-Rong; Jin, Jing; Liang, Hue-Ling; Du, Ying-Ying; Lu, Jian-Liang; Ye, Qian; Lin, Chen

    2007-05-01

    The caffeine level of instant tea extracted from decaffeinated leaf tea with 4.0 mg g-1 caffeine is commonly above 10.0 mg g-1, the maximum limit of caffeine for decaffeinated instant tea. Further removal of caffeine by active carbon (AC) from the green tea extract was investigated. It showed that the removal of caffeine from the tea extract solutions depended on the treatment time and tea extract concentration while the ethanol concentration and pH had little effect on the removal of caffeine. According to the removal of caffeine and the ratio of total catechins to caffeine in the tested samples, the optimum decaffeination conditions were determined to be as follows: tea extract concentration 15-30 g L-1 for common tea extract but higher for partially decaffeinated tea leaf extract; ratio of tea solution to AC, 100 mL:4 g; treatment time, 4 h; and natural tea extract pH. Instant tea powder extracted from partially decaffeinated leaf tea with a caffeine level of 4.03 mg g-1 and further decaffeinated by AC had a caffeine level of 7.81 mg g-1, which was 31% lower than that without AC treatment. PMID:17407319

  11. Adaptive Estimation with Partially Overlapping Models

    PubMed Central

    Shin, Sunyoung; Fine, Jason; Liu, Yufeng

    2015-01-01

    In many problems, one has several models of interest that capture key parameters describing the distribution of the data. Partially overlapping models are taken as models in which at least one covariate effect is common to the models. A priori knowledge of such structure enables efficient estimation of all model parameters. However, in practice, this structure may be unknown. We propose adaptive composite M-estimation (ACME) for partially overlapping models using a composite loss function, which is a linear combination of loss functions defining the individual models. Penalization is applied to pairwise differences of parameters across models, resulting in data driven identification of the overlap structure. Further penalization is imposed on the individual parameters, enabling sparse estimation in the regression setting. The recovery of the overlap structure enables more efficient parameter estimation. An oracle result is established. Simulation studies illustrate the advantages of ACME over existing methods that fit individual models separately or make strong a priori assumption about the overlap structure. PMID:26917931

  12. 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.

  13. 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.

  14. Partial facetectomy for lumbar foraminal stenosis.

    PubMed

    Kang, Kevin; Rodriguez-Olaverri, Juan Carlos; Schwab, Frank; Hashem, Jenifer; Razi, Afshin; Farcy, Jean Pierre

    2014-01-01

    Background. Several different techniques exist to address the pain and disability caused by isolated nerve root impingement. Failure to adequately decompress the lumbar foramen may lead to failed back surgery syndrome. However, aggressive treatment often causes spinal instability or may require fusion for satisfactory results. We describe a novel technique for decompression of the lumbar nerve root and demonstrate its effectiveness in relief of radicular symptoms. Methods. Partial facetectomy was performed by removal of the medial portion of the superior facet in patients with lumbar foraminal stenosis. 47 patients underwent the procedure from 2001 to 2010. Those who demonstrated neurogenic claudication without spinal instability or central canal stenosis and failed conservative management were eligible for the procedure. Functional level was recorded for each patient. These patients were followed for an average of 3.9 years to evaluate outcomes. Results. 27 of 47 patients (57%) reported no back pain and no functional limitations. Eight of 47 patients (17%) reported moderate pain, but had no limitations. Six of 47 patients (13%) continued to experience degenerative symptoms. Five of 47 patients (11%) required additional surgery. Conclusions. Partial facetectomy is an effective means to decompress the lumbar nerve root foramen without causing spinal instability.

  15. Gestational hyperlipidemia and acute pancreatitis with underlying partial lipoprotein lipase deficiency and apolipoprotein E3/E2 genotype

    PubMed Central

    Han, Dong Hee; Moh, In Ho; Kim, Doo-Man; Ihm, Sung Hee; Choi, Moon-Gi; Yoo, Hyung Joon

    2013-01-01

    We report the case of a patient who experienced extreme recurrent gestational hyperlipidemia. She was diagnosed with partial lipoprotein lipase (LPL) deficiency but without an associated LPL gene mutation in the presence of the apolipoprotein E3/2 genotype. This is the first reported case of extreme gestational hyperlipidemia with a partial LPL deficiency in the absence of an LPL gene mutation and the apolipoprotein E 3/2 genotype. She was managed with strict dietary control and medicated with omega-3 acid ethyl esters. A patient with extreme hyperlipidemia that is limited to the gestational period should be considered partially LPL-deficient. Extreme instances of hyperlipidemia increase the risk of acute pancreatitis, and the effect of parturition on declining plasma lipid levels can be immediate and dramatic. Therefore, decisions regarding the timing and route of delivery with extreme gestational hyperlipidemia are critical and should be made carefully. PMID:24009459

  16. Genetics Home Reference: autosomal dominant partial epilepsy with auditory features

    MedlinePlus

    ... Genetics Home Health Conditions ADPEAF autosomal dominant partial epilepsy with auditory features Enable Javascript to view the ... Open All Close All Description Autosomal dominant partial epilepsy with auditory features ( ADPEAF ) is an uncommon form ...

  17. Partial oxidation power plant with reheating and method thereof

    DOEpatents

    Newby, Richard A.; Yang, Wen-Ching; Bannister, Ronald L.

    1999-01-01

    A system and method for generating power having an air compression/partial oxidation system, a turbine, and a primary combustion system. The air compression/partial oxidation system receives a first air stream and a fuel stream and produces a first partially oxidized fuel stream and a first compressed air stream therefrom. The turbine expands the first partially oxidized fuel stream while being cooled by the first compressed air stream to produce a heated air stream. The heated air stream is injected into the expanding first partially oxidized fuel stream, thereby reheating it in the turbine. A second partially oxidized fuel stream is emitted from the turbine. The primary combustion system receives said second partially oxidized fuel stream and a second air stream, combusts said second partially oxidized fuel stream, and produces rotating shaft power and an emission stream therefrom.

  18. Partial oxidation power plant with reheating and method thereof

    DOEpatents

    Newby, R.A.; Yang, W.C.; Bannister, R.L.

    1999-08-10

    A system and method are disclosed for generating power having an air compression/partial oxidation system, a turbine, and a primary combustion system. The air compression/partial oxidation system receives a first air stream and a fuel stream and produces a first partially oxidized fuel stream and a first compressed air stream therefrom. The turbine expands the first partially oxidized fuel stream while being cooled by the first compressed air stream to produce a heated air stream. The heated air stream is injected into the expanding first partially oxidized fuel stream, thereby reheating it in the turbine. A second partially oxidized fuel stream is emitted from the turbine. The primary combustion system receives said second partially oxidized fuel stream and a second air stream, combusts said second partially oxidized fuel stream, and produces rotating shaft power and an emission stream therefrom. 2 figs.

  19. 48 CFR 819.502-3 - Partial set-asides.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Partial set-asides. 819... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 819.502-3 Partial set-asides. When... particular procurement will be partially set aside for small business participation, the solicitation...

  20. 48 CFR 1319.502-3 - Partial set-asides.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Partial set-asides. 1319... PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 1319.502-3 Partial set-asides. A partial set... and one small) will respond with offers unless the set-aside is authorized by the designee set...

  1. 42 CFR 488.715 - Partial extended surveys.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 5 2014-10-01 2014-10-01 false Partial extended surveys. 488.715 Section 488.715... (CONTINUED) STANDARDS AND CERTIFICATION SURVEY, CERTIFICATION, AND ENFORCEMENT PROCEDURES Survey and Certification of Home Health Agencies § 488.715 Partial extended surveys. A partial extended survey is...

  2. 42 CFR 488.715 - Partial extended surveys.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 5 2013-10-01 2013-10-01 false Partial extended surveys. 488.715 Section 488.715... (CONTINUED) STANDARDS AND CERTIFICATION SURVEY, CERTIFICATION, AND ENFORCEMENT PROCEDURES Survey and Certification of Home Health Agencies § 488.715 Partial extended surveys. A partial extended survey is...

  3. A Potential Cost Effective Liquefaction Mitigation Countermeasure: Induced Partial Saturation

    SciTech Connect

    Bian Hanbing; Jia Yun; Shahrour, Isam

    2008-07-08

    This work is devoted to illustrate the potential liquefaction mitigation countermeasure: Induced Partial Saturation. Firstly the potential liquefaction mitigation method is briefly introduced. Then the numerical model for partially saturated sandy soil is presented. At last the dynamic responses of liquefiable free filed with different water saturation is given. It shows that the induced partial saturation is efficiency for preventing the liquefaction.

  4. Viscous fingering with partially miscible fluids

    NASA Astrophysics Data System (ADS)

    Fu, X.; Cueto-Felgueroso, L.; Juanes, R.

    2015-12-01

    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. Experimental and numerical studies of viscous fingering have focused on fluids that are either fully miscible (e.g. water and glycerol) or perfectly immiscible (e.g. water and oil). 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 (e.g. CO2 and water). Following our recent work for miscible systems (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 porous medium, when the two fluids have limited (but nonzero) solubility in one another. In our model, partial miscibility is characterized through the design of the thermodynamic free energy of the two-fluid system. We express the model in dimensionless form and 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. Figure caption: final snapshots in simulations of viscous fingering with a two-fluid system mimicking that of CO2 and water. The colormap corresponds to the concentration of CO2. A band of less viscous gas phase rich in CO2 (red) displaces through the more viscous liquid phase that is undersaturated with CO2 (blue). At the fluid interface, an exchange of CO2 occurs as a result of local chemical potentials that drives the system towards thermodynamic equilibrium. This results in a shrinkage of gas phase as well as a local increase in

  5. Wave Attenuation in Partially Saturated Porous Solids.

    NASA Astrophysics Data System (ADS)

    Yin, Chuan-Sheng

    1992-01-01

    This thesis consists of three independent papers. Paper 1 studies effects of pulsating gas pockets on wave propagation in partially saturated porous solids containing both liquid and gas phases. On the basis of Biot theory, an analytic solution for the White model for study of the effects of saturation history on wave attenuation is derived. One of the most significant findings of this work is that when the average spacing among the neighboring gas pockets is of the order of the boundary-layer thickness associated with the slow compressional (or P2) wave, the attenuation of the compressional (or P) wave due to local fluid flow reaches its maximum. Results of Paper 1 bear direct applications to seismic and logging responses of partially saturated rocks in prospecting for petroleum, and monitoring of oil and natural gas reservoirs. Paper 2 presents the results of the experimental studies of the effects of partial liquid/gas saturation on extensional wave attenuation in Berea sandstones. Two experimental methods are used; one is the resonant-bar method and the other the forced-deformation method. It is found that the wave attenuation depends on sample-saturation history (drainage or imbibition), as well as boundary-flow conditions, and the degree of saturation. The attenuation caused by "flowable" liquid is sensitive only in the region of low degree of gas saturation. An open-pore boundary tends to induce higher attenuation. The results obtained by the forced-deformation method show that the magnitude of the attenuation decreases substantially with decreasing frequency to the extent that no attenuation peak was apparent at frequencies below 100 Hz. Paper 3 analyzes extensional wave propagation in a porous fluid-saturated hollow-cylinder of infinite extent. Analytic solutions of complex Young's modulus for the long wavelength limit was obtained for a hollow -cylinder with open-pore inner surface. A simplified formula for estimating the frequency at which the

  6. Grain boundary wetness of partially molten dunite

    NASA Astrophysics Data System (ADS)

    Mu, S.; Faul, U.

    2013-12-01

    The grain scale melt distribution plays a key role for physical properties of partially molten regions in Earth's upper mantle, but our current understanding of the distribution of basaltic melt at the grain scale is still incomplete. A recent experimental study shows that wetted two-grain boundaries are a common feature of partially molten dunite at small melt fractions (Garapic et al., G3, 2013). In early ideal models which assume isotropic surface energy, the grain scale melt distribution is uniquely determined by knowing the melt fraction and the dihedral angle between two crystalline grains and the melt (von Bargen and Waff, JGR, 1986). Olivine is anisotropic in surface energy, hence the grain scale melt distribution at given melt fraction cannot be characterized by the dihedral angle alone. The grain boundary wetness, which is defined as the ratio of solid-liquid boundary area over the total interfacial area (Takei, JGR, 1998), is a more objective measure of the grain scale melt distribution. The aim of this study is to quantify the relationship between grain size, melt fraction, temperature and grain boundary wetness of partially molten dunite under dry conditions. We annealed olivine-basalt aggregates with melt fractions from 0.03% to 6% at a range of temperatures and 1 GPa in a piston cylinder for 1 to 336 hours, with resulting mean grain sizes of 10 to 60 μm. The samples were sectioned, polished and imaged at high resolution by using a field emission SEM. Each image had a size of 2048 x 1536 pixels with a resolution of 0.014 to 0.029 μm/pixel, depending on magnification. For each sample, depending on grain sizes, we made mosaics of 3 x 3 or 6 x 6 overlapping images. Measurements of melt fraction, grain boundary wetness and grain size were carried out on these high resolution mosaics by using ImageJ software. Analyses of mosaics show that grain boundary wetness increases with increasing melt fraction at constant grain size to values well above those

  7. Reaction Infiltration Instabilities in Partially Molten Rocks

    NASA Astrophysics Data System (ADS)

    Pec, M.; Holtzman, B. K.; Zimmerman, M. E.; Kohlstedt, D. L.

    2015-12-01

    Tabular dunites in ophiolites are thought to form high-permeability, melt channels due to a positive feedback between melt flow and melt-solid reaction in the upper mantle. Reaction-infiltration instability (RII) theory predicts whether or not channels emerge from background flow. To test the applicability of RII theory to mantle rocks, we sandwiched a partially molten rock between a melt reservoir and a porous sink. Hot-pressed 50:50 mixtures of olivine (Ol) and clinopyroxene (Cpx) with either 4, 10 or 20 vol% alkali basalt formed ~4 mm long cylinders of partially molten rock. Source and sink are disks of alkali basalt and porous alumina. We annealed the melt-rock-sink triplets for up to 5 h at a confining pressure of Pc=300 MPa with effective pressure Pe=0 to 299.9 MPa at T=1200° or 1250°C. The melt fraction in the partially molten rock influences the permeability, which, together with the applied pressure gradient, controls the melt migration velocity. The temperature influences the reaction rate. Melt velocity and reaction rate are fundamental parameters in RII theory. In experiments, two distinct features form due to melt migration, 1) a planar reaction layer (RL) and 2) finger-shaped channels. Both the RL and the channels contain Ol+melt with no Cpx, indicating that the reaction melt1+Cpx→melt2+Ol occurs. The channels develop only if the melt velocity is >5µm/s. Once a channel reaches the porous sink, a large increase in the effective permeability is detected. The morphology and spacing of the channels depends on the initial melt fraction. With 20 vol% melt, multiple, voluminous channels with a spacing of 1.8±0.5 mm develop. At lower melt contents, fewer, thinner channels with a spacing of ~3 mm develop. The channel spacing predicted by theory is about a factor 2-4 smaller than observed. Our results indicate that RII theory provides a solid framework for investigating melt migration in experiments and potentially a basis for extrapolation to mantle

  8. Gene doping.

    PubMed

    Harridge, Stephen D R; Velloso, Cristiana P

    2008-01-01

    Gene doping is the misuse of gene therapy to enhance athletic performance. It has recently been recognised as a potential threat and subsequently been prohibited by the World Anti-Doping Agency. Despite concerns with safety and efficacy of gene therapy, the technology is progressing steadily. Many of the genes/proteins which are involved in determining key components of athletic performance have been identified. Naturally occurring mutations in humans as well as gene-transfer experiments in adult animals have shown that altered expression of these genes does indeed affect physical performance. For athletes, however, the gains in performance must be weighed against the health risks associated with the gene-transfer process, whereas the detection of such practices will provide new challenges for the anti-doping authorities.

  9. 76 FR 25177 - Determinations Concerning Need for Error Correction, Partial Approval and Partial Disapproval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-03

    ... Significant Deterioration and Title V Greenhouse Gas Tailoring Rule; Final Rule. 75 FR 31,514 (June 3, 2010...-National Ambient Air Quality Standard (NAAQS) pollutants, among them greenhouse gases (GHGs). The partial... are able to proceed with plans to construct or expand. DATES: This action is effective on May 1,...

  10. Partial oxidation process with extractant purification

    SciTech Connect

    Stellaccio, R.J.

    1983-09-06

    A partial oxidation process is disclosed with an extractant purifier for removing the particulate carbon entrained in a vaporized stream of normally liquid organic extractant-carbon-water dispersion from a decanter and producing a clean vaporized mixture of liquid organic extractant and water and a separate liquid stream of liquid hydrocarbonaceous fuel-carbon dispersion. The extractant purifier comprises a closed, vertical, cylindrical, thermally insulated vessel with an unobstructed central passage. Supported in the upper section of the vessel is a gas-solids separator for separating the particulate carbon from the vaporized dispersion flowing up the vessel and discharging the particulate carbon into atomized liquid hydrocarbon fuel located within the lower section of the purifier.

  11. Algorithm refinement for stochastic partial differential equations.

    SciTech Connect

    Alexander, F. J.; Garcia, Alejandro L.,; Tartakovsky, D. M.

    2001-01-01

    A hybrid particle/continuum algorithm is formulated for Fickian diffusion in the fluctuating hydrodynamic limit. The particles are taken as independent random walkers; the fluctuating diffusion equation is solved by finite differences with deterministic and white-noise fluxes. At the interface between the particle and continuum computations the coupling is by flux matching, giving exact mass conservation. This methodology is an extension of Adaptive Mesh and Algorithm Refinement to stochastic partial differential equations. A variety of numerical experiments were performed for both steady and time-dependent scenarios. In all cases the mean and variance of density are captured correctly by the stochastic hybrid algorithm. For a non-stochastic version (i.e., using only deterministic continuum fluxes) the mean density is correct, but the variance is reduced except within the particle region, far from the interface. Extensions of the methodology to fluid mechanics applications are discussed.

  12. Development of partially fluorinated resin apex seals

    NASA Technical Reports Server (NTRS)

    Green, H. E.; Chang, G. E. C.; Powell, S. H.; Yates, K.

    1984-01-01

    Partially fluorinated polyimides were prepared and molded in the form of discs and pins for test as potential apex seal materials for advanced rotary combustion engines. The polyimides were formulated from the diamine 2,2-bis 4-(4-aminophenoxy)phenyl hexafluoropropane (4-BDAF) and the dianhydrides of pyromellitic acid (PMDA) and benzophenonetetracarboxylic acid (BTDA). Tribological testing was performed at sliding speeds of 0.31 to 11.6 m/s and at temperatures of from 298K to 573K. It is shown that the carbon fiber filled polyimides, particularly the 80/20 compositions, have an excellent balance of wear/friction at 573K. The unfilled, 80/20 and 60/40 compositions indicate an unusual combination of high friction and low wear which may be advantageous in such applications as brakes and traction drives.

  13. Breakdown and partial discharges in magnetic liquids.

    PubMed

    Herchl, F; Marton, K; Tomčo, L; Kopčanský, P; Timko, M; Koneracká, M; Kolcunová, I

    2008-05-21

    The dielectric properties (permittivity, loss factor, dielectric breakdown strength) of magnetic liquids were investigated. The magnetic liquids were composed of magnetite particles coated with oleic acid as surfactant and dispersed in transformer oil. To determine their dielectric properties they were subjected to a uniform magnetic field at high alternating electric fields up to 14 MV m(-1). Nearly constant permittivity of magnetic liquid with particle volume concentration Φ = 0.0019 as a function of electric field was observed. Magnetic liquids with concentrations Φ = 0.019 and 0.032 showed significant changes of permittivity and loss factor dependent on electric and magnetic fields. The best concentration of magnetic fluid was found at which partial current impulse magnitudes were the lowest. The breakdown strength distribution of the magnetic liquid with Φ = 0.0025 was fitted with the Duxbury-Leath, Weibull and Gauss distribution functions. PMID:21694240

  14. Flame propagation in partially premixed conditions

    NASA Astrophysics Data System (ADS)

    Ruetsch, G.; Poinsot, T.; Veynante, D.; Trouvé, A.

    1996-11-01

    Turbulent flame propagation is studied under inhomogenously premixed conditions via data from direct numerical simulations. Departures from the premixed case are studied using four different configurations, ranging from one dimensional unsteady flames to turbulent three-dimensional simulations. Simulations are performed in these cases with various values of the mean equivalence ratio, fluctuations about the mean equivlalence ratio, correlation length scales, and probability denisty functions of the mixture composition. Propagation characteristics are described in terms of the flamelet approach, where the the main contribution of partial premixing on flame propagation is due to flame wrinkling relative to modification of the mean flamelet structure. This behavior is consistent over a broad range of conditions, with the exception being extreme departures from stoichiometric conditions where flamability limits are exceeded and flame quenching is observed.

  15. Electrowetting of partially wetting thin nanofluid films.

    PubMed

    Chakraborty, Monojit; Chatterjee, Rahul; Ghosh, Udita Uday; DasGupta, Sunando

    2015-04-14

    It is observed that the presence of negatively charged, suspended nanoparticles significantly changes the electric-field-induced spreading and contact line dynamics of partially wetting liquid films. Image-analyzing interferometry is used to accurately measure the meniscus profile, including the spatial change in the meniscus curvature. The nanoparticle-containing meniscus exhibits enhanced spreading with an increase in the particle size and weight fraction. The instantaneous contact line velocities are measured using video microscopy and a frame-by-frame analysis of the extracted images. The effects of electric field polarity reversal on the flow toward the contact line are explored as well. The movement of the meniscus is analyzed taking into account the capillary forces and Maxwell-stress-induced flows. An analytical model based on the Young-Laplace equation is used to analyze the electric-field-induced contact line motion, and the model-predicted velocities are compared to the experiments. PMID:25790194

  16. Partial Differential Algebraic Sensitivity Analysis Code

    1995-05-15

    PDASAC solves stiff, nonlinear initial-boundary-value in a timelike dimension t and a space dimension x. Plane, circular cylindrical or spherical boundaries can be handled. Mixed-order systems of partial differential and algebraic equations can be analyzed with members of order or 0 or 1 in t, 0,1 or 2 in x. Parametric sensitivities of the calculated states are compted simultaneously on request, via the Jacobian of the state equations. Initial and boundary conditions are efficiently reconciled.more » Local error control (in the max-norm or the 2-norm) is provided for the state vector and can include the parametric sensitivites if desired.« less

  17. Extrapolation methods for dynamic partial differential equations

    NASA Technical Reports Server (NTRS)

    Turkel, E.

    1978-01-01

    Several extrapolation procedures are presented for increasing the order of accuracy in time for evolutionary partial differential equations. These formulas are based on finite difference schemes in both the spatial and temporal directions. On practical grounds the methods are restricted to schemes that are fourth order in time and either second, fourth or sixth order in space. For hyperbolic problems the second order in space methods are not useful while the fourth order methods offer no advantage over the Kreiss-Oliger method unless very fine meshes are used. Advantages are first achieved using sixth order methods in space coupled with fourth order accuracy in time. Computational results are presented confirming the analytic discussions.

  18. Lithiation of Silica through Partial Reduction

    SciTech Connect

    Ban, C.; Kappes, B. B.; Xu, Q.; Engtrakul, C.; Ciobanu, C. V.; Dillon, A. C.; Zhao, Y.

    2012-06-11

    We demonstrate the reversible lithiation of SiO{sub 2} up to 2/3 Li per Si, and propose a mechanism for it based on molecular dynamics and density functional theory simulations. Our calculations show that neither interstitial Li (no reduction), nor the formation of Li{sub 2}O clusters and Si-Si bonds (full reduction) are energetically favorable. Rather, two Li effectively break a Si-O bond and become stabilized by oxygen, thus partially reducing the SiO{sub 2} anode: this leads to increased anode capacity when the reduction occurs at the Si/SiO{sub 2} interface. The resulting Li{sub x}SiO{sub 2} (x < 2/3) compounds have band-gaps in the range of 2.0-3.4 eV.

  19. NEUTRINO PROCESSES IN PARTIALLY DEGENERATE NEUTRON MATTER

    SciTech Connect

    Bacca, S.; Hally, K.; Liebendoerfer, M.; Perego, A.; Pethick, C. J.; Schwenk, A.

    2012-10-10

    We investigate neutrino processes for conditions reached in simulations of core-collapse supernovae. In regions where neutrino-matter interactions play an important role, matter is partially degenerate, and we extend earlier work that addressed the degenerate regime. We derive expressions for the spin structure factor in neutron matter, which is a key quantity required for evaluating rates of neutrino processes. We show that, for essentially all conditions encountered in the post-bounce phase of core-collapse supernovae, it is a very good approximation to calculate the spin relaxation rates in the nondegenerate limit. We calculate spin relaxation rates based on chiral effective field theory interactions and find that they are typically a factor of two smaller than those obtained using the standard one-pion-exchange interaction alone.

  20. Quantitative phase imaging with partially coherent illumination.

    PubMed

    Nguyen, T H; Edwards, C; Goddard, L L; Popescu, G

    2014-10-01

    In this Letter, we formulate a mathematical model for predicting experimental outcomes in quantitative phase imaging (QPI) when the illumination field is partially spatially coherent. We derive formulae that apply to QPI and discuss expected results for two classes of QPI experiments: common path and traditional interferometry, under varying degrees of spatial coherence. In particular, our results describe the physical relationship between the spatial coherence of the illuminating field and the halo effect, which is well known in phase-contrast microscopy. We performed experiments relevant to this common situation and found that our theory is in excellent agreement with the data. With this new understanding of the effects of spatial coherence, our formulae offer an avenue for removing halo artifacts from phase images. PMID:25360915

  1. Partial pressure measurements with an active spectrometer

    SciTech Connect

    Brooks, N.H.; Jensen, T.H.; Colchin, R.J.; Maingi, R.; Wade, M.R.; Finkenthal, D.F.; Naumenko, N.; Tugarinov, S.

    1998-07-01

    Partial pressure neutral ga measurements have been made using a commercial Penning gauge in conjunction with an active spectrometer. In prior work utilizing bandpass filters and conventional spectrometers, trace concentrations of the hydrogen isotopes H, D, T and of the noble gases He, Ne and Ar were determined from characteristic spectral lines in the light emitted by the neutral species of these elements. For all the elements mentioned, the sensitivity was limited by spectral contamination from a pervasive background of molecular hydrogen radiation. The active spectrometer overcomes this limitations by means of a digital lock-in method and correlation with reference spectra. Preliminary measurements of an admixture containing a trace amount of neon in deuterium show better than a factor of 20 improvement in sensitivity over conventional techniques. This can be further improved by correlating the relative intensities of multiple lines to sets of reference spectra.

  2. Partial 1q Duplications and Associated Phenotype

    PubMed Central

    Morris, Marcos L.M.; Baroneza, José E.; Teixeira, Patricia; Medina, Cristina T.N.; Cordoba, Mara S.; Versiani, Beatriz R.; Roese, Liege L.; Freitas, Erika L.; Fonseca, Ana C.S.; dos Santos, Maria C.G.; Pic-Taylor, Aline; Rosenberg, Carla; Oliveira, Silviene F.; Ferrari, Iris; Mazzeu, Juliana F.

    2016-01-01

    Duplications of the long arm of chromosome 1 are rare. Distal duplications are the most common and have been reported as either pure trisomy or unbalanced translocations. The paucity of cases with pure distal 1q duplications has made it difficult to delineate a partial distal trisomy 1q syndrome. Here, we report 2 patients with overlapping 1q duplications detected by G-banding. Array CGH and FISH were performed to characterize the duplicated segments, exclude the involvement of other chromosomes and determine the orientation of the duplication. Patient 1 presents with a mild phenotype and carries a 22.5-Mb 1q41q43 duplication. Patient 2 presents with a pure 1q42.13qter inverted duplication of 21.5 Mb, one of the smallest distal 1q duplications ever described and one of the few cases characterized by array CGH, thus contributing to a better characterization of distal 1q duplication syndrome. PMID:27022331

  3. Partial 1q Duplications and Associated Phenotype.

    PubMed

    Morris, Marcos L M; Baroneza, José E; Teixeira, Patricia; Medina, Cristina T N; Cordoba, Mara S; Versiani, Beatriz R; Roese, Liege L; Freitas, Erika L; Fonseca, Ana C S; Dos Santos, Maria C G; Pic-Taylor, Aline; Rosenberg, Carla; Oliveira, Silviene F; Ferrari, Iris; Mazzeu, Juliana F

    2016-02-01

    Duplications of the long arm of chromosome 1 are rare. Distal duplications are the most common and have been reported as either pure trisomy or unbalanced translocations. The paucity of cases with pure distal 1q duplications has made it difficult to delineate a partial distal trisomy 1q syndrome. Here, we report 2 patients with overlapping 1q duplications detected by G-banding. Array CGH and FISH were performed to characterize the duplicated segments, exclude the involvement of other chromosomes and determine the orientation of the duplication. Patient 1 presents with a mild phenotype and carries a 22.5-Mb 1q41q43 duplication. Patient 2 presents with a pure 1q42.13qter inverted duplication of 21.5 Mb, one of the smallest distal 1q duplications ever described and one of the few cases characterized by array CGH, thus contributing to a better characterization of distal 1q duplication syndrome. PMID:27022331

  4. PARTIAL SLINGSHOT RECONNECTION BETWEEN TWO FILAMENTS

    SciTech Connect

    Jiang, Yunchun; Hong, Junchao; Yang, Jiayan; Bi, Yi; Zheng, Ruisheng; Yang, Bo; Li, Haidong; Yang, Dan

    2013-02-10

    We present a rare observation of an interaction between two filaments around AR 11358 and AR 11361 on 2011 December 3 that is strongly suggestive of the occurrence of slingshot reconnection. A small elbow-shaped active-region filament (F12) underwent a failed eruption that brought it into contact with a nearby larger, thicker filament (F34). Accompanied by the appearance of complicated internal structures below the erupting F12, its two legs separated away from each other and then connected into F34. This process led the filaments to change their connectivity to form two newly linked filaments, and one of them showed a clear inverse {gamma}-shape. However, the alteration in the filament connectivity was imperfect since F34 is discernible after the eruption. These observations can be interpreted as a partial slingshot reconnection between two filaments that had unequal axial magnetic flux.

  5. Partially stabilized zirconia piston bowl reliability

    SciTech Connect

    Hartsock, D.L.

    1987-10-01

    The Weibull based ''Simplified Structural Ceramic Design Technique'' was used to calculate the reliability of a partially stabilized zirconia (PSZ) piston bowl design. The details of the method and a set of sample calculations are presented. Test results of the piston bowl showed cracks in regions which had a high calculated probability of failure. In addition cracks developed in a region of high compressive/shear stress. Since Weibull reliability analysis only uses tensile stresses this area did not have a high calculated probability of failure. Several hypotheses are presented for the mode of failure in this region. The simplified technique was used to predict what the necessary material properties would have to be for successful PSZ insert of the design shown.

  6. Vehicle detection using partial least squares.

    PubMed

    Kembhavi, Aniruddha; Harwood, David; Davis, Larry S

    2011-06-01

    Detecting vehicles in aerial images has a wide range of applications, from urban planning to visual surveillance. We describe a vehicle detector that improves upon previous approaches by incorporating a very large and rich set of image descriptors. A new feature set called Color Probability Maps is used to capture the color statistics of vehicles and their surroundings, along with the Histograms of Oriented Gradients feature and a simple yet powerful image descriptor that captures the structural characteristics of objects named Pairs of Pixels. The combination of these features leads to an extremely high-dimensional feature set (approximately 70,000 elements). Partial Least Squares is first used to project the data onto a much lower dimensional sub-space. Then, a powerful feature selection analysis is employed to improve the performance while vastly reducing the number of features that must be calculated. We compare our system to previous approaches on two challenging data sets and show superior performance.

  7. Solving Partial Differential Equations on Overlapping Grids

    SciTech Connect

    Henshaw, W D

    2008-09-22

    We discuss the solution of partial differential equations (PDEs) on overlapping grids. This is a powerful technique for efficiently solving problems in complex, possibly moving, geometry. An overlapping grid consists of a set of structured grids that overlap and cover the computational domain. By allowing the grids to overlap, grids for complex geometries can be more easily constructed. The overlapping grid approach can also be used to remove coordinate singularities by, for example, covering a sphere with two or more patches. We describe the application of the overlapping grid approach to a variety of different problems. These include the solution of incompressible fluid flows with moving and deforming geometry, the solution of high-speed compressible reactive flow with rigid bodies using adaptive mesh refinement (AMR), and the solution of the time-domain Maxwell's equations of electromagnetism.

  8. Identification of partially occluded firearms through partonomy

    NASA Astrophysics Data System (ADS)

    Arslan, Abdullah N.; Hempelmann, Christian F.; Attardo, Salvatore; Blount, Grady P.; Sirakova, Nona N.; Sirakov, Nikolay M.

    2015-05-01

    In the present paper we study the problem of weapon identification and threat assessment from a single image with a partially occluded weapon. This problem poses very severe restrictions. To successfully identify a weapon from its parts we extend the first firearm ontology with the meronymic (partonomic) principle which lets us distinguish parts of a gun (e.g., lock, barrel, stock, scope). Adding classes of meronymic information provides meta-data (necessary for threat assessment) and allows for fast and accurate search. Searching for a weapon is treated conceptually as searching for the sum of its parts. An expanding active contour and morphological techniques are applied to partition weapons and extract boundaries, and a minimal inscribed complex polygon. Finite numerical sequences are generated, from the extracted geometric features, and are used to label partonomic nodes and perform quick and accurate search. The paper reports experimental results on weapons partitioning and search.

  9. Faithful teleportation with partially entangled states

    SciTech Connect

    Gour, Gilad

    2004-10-01

    We write explicitly a general protocol for faithful teleportation of a d-state particle (qudit) via a partially entangled pair of (pure) n-state particles. The classical communication cost (CCC) of the protocol is log{sub 2}(nd) bits, and it is implemented by a projective measurement performed by Alice, and a unitary operator performed by Bob (after receiving from Alice the measurement result). We prove the optimality of our protocol by a comparison with the concentrate and teleport strategy. We also show that if d>n/2, or if there is no residual entanglement left after the faithful teleportation, the CCC of any protocol is at least log{sub 2}(nd) bits. Furthermore, we find a lower bound on the CCC in the process transforming one bipartite state to another by means of local operation and classical communication.

  10. Partial versus complete autogynephilia and gender dysphoria.

    PubMed

    Blanchard, R

    1993-01-01

    Autogynephilia (sexual arousal in men produced by the thought or image of themselves as women) is often associated with gender dysphoria (the desire to belong to the opposite sex). Previous research has shown that autogynephiles who are principally aroused by images of themselves as nude women are more gender dysphoric than those principally aroused by images of themselves as partially or fully dressed women. This study tested the hypothesis that the feature of the nude self-image most responsible for its correlation with gender dysphoria is the imagined vulva. The subjects were 220 nonhomosexual male outpatients who reported sexual arousal while imagining themselves with one or more features of the female anatomy. Autogynephilia and gender dysphoria were assessed with questionnaires. The findings confirmed that men who are sexually aroused at the thought of having a vulva are more likely to want to be women.

  11. Turbo Equalization Using Partial Gaussian Approximation

    NASA Astrophysics Data System (ADS)

    Zhang, Chuanzong; Wang, Zhongyong; Manchon, Carles Navarro; Sun, Peng; Guo, Qinghua; Fleury, Bernard Henri

    2016-09-01

    This paper deals with turbo-equalization for coded data transmission over intersymbol interference (ISI) channels. We propose a message-passing algorithm that uses the expectation-propagation rule to convert messages passed from the demodulator-decoder to the equalizer and computes messages returned by the equalizer by using a partial Gaussian approximation (PGA). Results from Monte Carlo simulations show that this approach leads to a significant performance improvement compared to state-of-the-art turbo-equalizers and allows for trading performance with complexity. We exploit the specific structure of the ISI channel model to significantly reduce the complexity of the PGA compared to that considered in the initial paper proposing the method.

  12. Grain boundary wetness of partially molten dunite

    NASA Astrophysics Data System (ADS)

    Mu, Shangshang; Faul, Ulrich H.

    2016-05-01

    Samples of Fo90 olivine and basaltic melt were annealed at a range of temperatures and a pressure of 1 GPa in a piston cylinder apparatus from 1 to 336 h. Post-run samples have melt contents from 0.3 to 6.8 % and mean grain sizes from 4.3 to 84.5 μm. Grain boundary wetness, a measure of the intergranular melt distribution, was determined by analyzing scanning electron microscope images with sufficiently high resolution to detect thin layers wetting grain boundaries, as well as small triple junctions. The measurements show that grain boundary wetness increases with increasing melt content to values well above those predicted by the idealized isotropic equilibrium model for a finite dihedral angle. Additionally, the melt geometry changes with grain size, with grain boundary wetness increasing with increasing grain size at fixed melt content. Grain boundary wetness and dihedral angle of samples annealed at a range of temperatures, but constant melt content does not depend on temperature. These observations emphasize that the dihedral angle alone is not adequate to characterize the melt distribution in partially molten rocks, as the idealized isotropic model does not account for the influence of grain growth. Diffusion creep viscosities calculated from the measured wetness reflect the grain size and melt content dependence. Accordingly, experimentally measured viscosities at small grain sizes underestimate the effect of melt to weaken partially molten rocks for coarser grain sizes. The presence of melt in the mantle may therefore enhance diffusion creep relative to dislocation creep.

  13. Partial volume estimation using continuous representations

    NASA Astrophysics Data System (ADS)

    Siadat, Mohammad-Reza; Soltanian-Zadeh, Hamid

    2001-07-01

    This paper presents a new method for partial volume estimation using standard eigenimage method and B-splines. The proposed method is applied on the multi-parameter volumetric images such as MRI. The proposed approach uses the B-spline bases (kernels) to interpolate a continuous 2D surface or 3D density function for a sampled image dataset. It uses the Fourier domain to calculate the interpolation coefficients for each data point. Then, the above interpolation is incorporated into the standard eigenimage method. This incorporation provides a particular mask depending on the B-spline basis used. To estimate the partial volumes, this mask is convolved with the interpolation coefficients and then the eigenimage transformation is applied on the convolution result. To evaluate the method, images scanned from a 3D simulation model are used. The simulation provides images similar to CSF, white matter, and gray matter of the human brain in T1-, T2-, and PD-weighted MRI. The performance of the new method is also compared to that of the polynomial estimators.1 The results show that the new estimators have standard deviations less than that of the eigenimage method (up to 25%) and larger than those of the polynomial estimators (up to 45%). The new estimators have superior capabilities compared to that of the polynomial ones in that they provide an arbitrary degree of continuity at the boundaries of pixels/voxels. As a result, employing the new method, a continuous, smooth, and very accurate contour/surface of the desired object can be generated. The new B-spline estimators are faster than the polynomial estimators but they are slower than the standard eigenimage method.

  14. CRISPR Detection From Short Reads Using Partial Overlap Graphs.

    PubMed

    Ben-Bassat, Ilan; Chor, Benny

    2016-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

  15. Extensive mitochondrial genome rearrangements between Cerithioidea and Hypsogastropoda (Mollusca; Caenogastropoda) as determined from the partial nucleotide sequences of the mitochondrial DNA of Cerithidea djadjariensis and Batillaria cumingi.

    PubMed

    Kojima, Shigeaki

    2010-06-01

    Partial nucleotide sequences ( approximately 8000 bp) of the mitochondrial DNA of two cerithioidean gastropod species-Cerithidea djadjariensis and Batillaria cumingi-were determined. The order of mitochondrial genes (eight protein genes, two ribosomal RNA genes, and nine transfer RNA genes) was identical between these two species. and remarkably different from the previously reported order in other gastropods. The results indicate that the genome structure of the common ancestor of Cerithioidea and its sister group, Hypsogastropoda, is almost identical to that of the common ancestor of Gastropoda; moreover, independent mitochondrial genome rearrangements were identified between the lineages of Cerithioidea and Hypsogastropoda. The rearrangements within Cerithioidea can be explained by the inversion of a single tRNA gene, two translocations of a single tRNA gene, and three translocations of a genome fragment containing a tRNA gene and protein-coding gene(s).

  16. Sucrose controls storage lipid breakdown on gene expression level in germinating yellow lupine (Lupinus luteus L.) seeds.

    PubMed

    Borek, Sławomir; Nuc, Katarzyna

    2011-10-15

    This study revealed that cytosolic aconitase (ACO, EC 4.2.1.3) and isocitrate lyase (ICL, EC 4.1.3.1, marker of the glyoxylate cycle) are active in germinating protein seeds of yellow lupine. The glyoxylate cycle seems to function not only in the storage tissues of food-storage organs, but also in embryonic tissue of growing embryo axes. Sucrose (60mM) added to the medium of in vitro culture of embryo axes and cotyledons decreased activity of lipase (LIP, EC 3.1.1.3) and activity of glutamate dehydrogenase (NADH-GDH, EC 1.4.1.2). The opposite effect was caused by sucrose on activity of cytosolic ACO, ICL as well as NADP(+)-dependent (EC 1.1.1.42) and NAD(+)-dependent (EC 1.1.1.41) isocitrate dehydrogenase (NADP-IDH and NAD-IDH, respectively); activity of these enzymes was clearly stimulated by sucrose. Changes in the activity of LIP, ACO, NADP-IDH, and NAD-IDH caused by sucrose were based on modifications in gene expression because corresponding changes in the enzyme activities and in the mRNA levels were observed. The significance of cytosolic ACO and NADP-IDH in carbon flow from storage lipid to amino acids, as well as the peculiar features of storage lipid breakdown during germination of lupine seeds are discussed.

  17. Genetic dissections of partial resistances to leaf and neck blast in rice (Oryza sativa L.).

    PubMed

    Rao, Zhi-Ming; Wu, Jian-Li; Zhuang, Jie-Yun; Chai, Rong-Yao; Fan, Ye-Yang; Leung, Hei; Zheng, Kang-Le

    2005-06-01

    In a recombinant inbred line (RIL) population of indica rice, two subpopulations composed of susceptible lines were selected for mapping of partial resistance to leaf blast with two isolates of the pathogen. A third subpopulation composed of susceptible lines with similar heading time was used for mapping of partial resistance to neck blast with a third isolate. The traits measured for partial resistance included diseased leaf area (DLA), lesion size (LS) and lesion number (LN) for leaf blast and lesion length (LL) and conidium amount (CA) for neck blast. A linkage map consisting of 168 DNA markers was constructed by using the whole RIL population. Quantitative trait loci (QTLs) conditioning these traits were determined at one-locus and two-locus levels. Eleven main-effect QTLs and 28 digenic interactions were detected by QTLMapper 1.01 b. Only three QTLs showing main effects were also involved in digenic interactions for the same trait. General contributions of epistatic QTLs of each trait ranged from 16.0% to 51.7%, while those of main-effect QTLs of each trait ranged from 4.7% to 38.8%. The general contributions of main-effect QTLs of most traits were smaller than those of epistatic QTLs, confirming the importance of epistasis as the genetic basis for complex traits. The general contributions of the main and epistatic effects of all QTLs detected for the two traits LL and CA of the partial resistance to neck blast reached 70.6% and 82.6% respectively, which obviously represented a major part of the genetic basis controlling partial resistance to neck blast. The results indicated the necessity for partial resistance mapping to use susceptible subpopulations where the interference of major resistance genes is avoided. PMID:16018181

  18. A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa

    DOE PAGES

    Dalal, Jyoti; Lopez, Harry; Vasani, Naresh B.; Hu, Zhaohui; Swift, Jennifer E.; Yalamanchili, Roopa; Dvora, Mia; Lin, Xiuli; Xie, Deyu; Qu, Rongda; et al

    2015-10-29

    Camelina sativa is an oilseed crop with great potential for biofuel production on marginal land. The seed oil from camelina has been converted to jet fuel and improved fuel efficiency in commercial and military test flights. Hydrogenation-derived renewable diesel from camelina is environmentally superior to that from canola due to lower agricultural inputs, and the seed meal is FDA approved for animal consumption. However, relatively low yield makes its farming less profitable. Our study is aimed at increasing camelina seed yield by reducing carbon loss from photorespiration via a photorespiratory bypass. Genes encoding three enzymes of the Escherichia coli glycolatemore » catabolic pathway were introduced: glycolate dehydrogenase (GDH), glyoxylate carboxyligase (GCL) and tartronic semialdehyde reductase (TSR). These enzymes compete for the photorespiratory substrate, glycolate, convert it to glycerate within the chloroplasts, and reduce photorespiration. As a by-product of the reaction, CO2 is released in the chloroplast, which increases photosynthesis. Camelina plants were transformed with either partial bypass (GDH), or full bypass (GDH, GCL and TSR) genes. Furthermore, transgenic plants were evaluated for physiological and metabolic traits.« less

  19. A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa

    SciTech Connect

    Dalal, Jyoti; Lopez, Harry; Vasani, Naresh B.; Hu, Zhaohui; Swift, Jennifer E.; Yalamanchili, Roopa; Dvora, Mia; Lin, Xiuli; Xie, Deyu; Qu, Rongda; Sederoff, Heike W.

    2015-10-29

    Camelina sativa is an oilseed crop with great potential for biofuel production on marginal land. The seed oil from camelina has been converted to jet fuel and improved fuel efficiency in commercial and military test flights. Hydrogenation-derived renewable diesel from camelina is environmentally superior to that from canola due to lower agricultural inputs, and the seed meal is FDA approved for animal consumption. However, relatively low yield makes its farming less profitable. Our study is aimed at increasing camelina seed yield by reducing carbon loss from photorespiration via a photorespiratory bypass. Genes encoding three enzymes of the Escherichia coli glycolate catabolic pathway were introduced: glycolate dehydrogenase (GDH), glyoxylate carboxyligase (GCL) and tartronic semialdehyde reductase (TSR). These enzymes compete for the photorespiratory substrate, glycolate, convert it to glycerate within the chloroplasts, and reduce photorespiration. As a by-product of the reaction, CO2 is released in the chloroplast, which increases photosynthesis. Camelina plants were transformed with either partial bypass (GDH), or full bypass (GDH, GCL and TSR) genes. Furthermore, transgenic plants were evaluated for physiological and metabolic traits.

  20. Effects of methyl mercury on the activity and gene expression of mouse Langerhans islets and glucose metabolism.

    PubMed

    Maqbool, Faheem; Bahadar, Haji; Niaz, Kamal; Baeeri, Maryam; Rahimifard, Mahban; Navaei-Nigjeh, Mona; Ghasemi-Niri, Seyedeh Farnaz; Abdollahi, Mohammad

    2016-07-01

    Mercury (Hg) is a well-known heavy metal and causes various toxic effects. It is abundantly present in fish in the form of methyl mercury (MeHg). Also, various other forms of mercury can enter human body either from environment like inhalation or through dental amalgams. The present study was designed to assess MeHg induced toxicity in mouse plasma and pancreatic islets with respect to insulin secretion, oxidative balance, glucose tolerance, gene expression, caspases 3 and 9 activities. MeHg was dissolved in tap water and administered at doses 2.5, 5 and 10 mg/kg/day, for 4 weeks. In mice, MeHg significantly caused increase in plasma insulin as well as C-peptides. Glucose intolerance, insulin resistance and hyperglycemia are main consequences of our study that correlate with the gene expression changes of glucose homeostasis as well. MeHg caused increase lipid peroxidation in a dose-dependent manner in plasma as well as pancreatic islets. In addition, total thiol molecules and ferrous reducing antioxidant power in MeHg treated group was decreased in plasma as well as pancreatic islets. Caspases 3 and 9 activities of pancreatic islets were upregulated in MeHg exposed animals. Reactive oxygen species were extremely high in pancreatic islets of MeHg treated groups. MeHg disrupted gluconeogenesis/glycogenolysis pathways and insulin secretory functions of islets by targeting GDH, GLUT2 and GCK genes of pancreatic islets. In conclusion, the current study revealed that insulin pathways, oxidative balance and glucose metabolism encoded genetic makeup are susceptible to MeHg toxicity and the subsequent oxidative stress and alternations in gene expression could lead toward functional abnormalities in other organs. PMID:27178136

  1. A powerful latent variable method for detecting and characterizing gene-based gene-gene interaction on multiple quantitative traits

    PubMed Central

    2013-01-01

    Background On thinking quantitatively of complex diseases, there are at least three statistical strategies for analyzing the gene-gene interaction: SNP by SNP interaction on single trait, gene-gene (each can involve multiple SNPs) interaction on single trait and gene-gene interaction on multiple traits. The third one is the most general in dissecting the genetic mechanism underlying complex diseases underpinning multiple quantitative traits. In this paper, we developed a novel statistic for this strategy through modifying the Partial Least Squares Path Modeling (PLSPM), called mPLSPM statistic. Results Simulation studies indicated that mPLSPM statistic was powerful and outperformed the principal component analysis (PCA) based linear regression method. Application to real data in the EPIC-Norfolk GWAS sub-cohort showed suggestive interaction (γ) between TMEM18 gene and BDNF gene on two composite body shape scores (γ = 0.047 and γ = 0.058, with P = 0.021, P = 0.005), and BMI (γ = 0.043, P = 0.034). This suggested these scores (synthetically latent traits) were more suitable to capture the obesity related genetic interaction effect between genes compared to single trait. Conclusions The proposed novel mPLSPM statistic is a valid and powerful gene-based method for detecting gene-gene interaction on multiple quantitative phenotypes. PMID:24059907

  2. Saline intrusion in partially mixed estuaries

    NASA Astrophysics Data System (ADS)

    Prandle, D.

    2004-03-01

    Restricting interest to partially mixed estuaries, earlier studies of tidally averaged linearised theories relating to the vertical structure of salinity and velocities (accompanying saline intrusion) are extended to take account of tidal straining and associated convective overturning. The applicability of these theories is evaluated by reference to a 'single-point' numerical model in which the time-varying cycle of depth-averaged tidal current amplitude, Û, and a (temporally and vertically) constant saline gradient, S x, are specified. This model highlights the importance of convective overturning in counteracting unstable density structures introduced by tidal straining. By omitting overturning in the model, results agree closely with linearised theoretical derivations. However, incorporating overturning substantially increases tidally averaged surface-to-bed differences for both residual currents, δ u, and salinity, δ s. The vertical structure of tidal currents is a maximum, and hence the effect of tidal straining, in shallow macro-tidal estuaries. The propagation of tidal elevations and currents remains insensitive to saline intrusion in partially mixed estuaries. The applicability of the model was evaluated by simulation of recent measurements by Rippeth et al. (J. Phys. Oceanogr. 31 (2001) 2458). To explore the generality of estuarine responses, the model was run for a wide range of values of saline intrusion lengths, L, and water depths, D. Additional sensitivity analyses were made for changes in Û and bed stress coefficient, k. Response frameworks are shown for: δ u, δ s, potential energy anomaly φ, work done by bed friction and internal shear, rates and efficiency of saline mixing and ratios of relative mixing by diffusion to overturning. By equating the rate of mixing associated with vertical diffusion with river flow, Q, an expression for saline intrusion length L∝D 2/k ÛU o ( Uo river flow velocity) was derived. This formulation agrees with

  3. Compatible Spatial Discretizations for Partial Differential Equations

    SciTech Connect

    Arnold, Douglas, N, ed.

    2004-11-25

    From May 11--15, 2004, the Institute for Mathematics and its Applications held a hot topics workshop on Compatible Spatial Discretizations for Partial Differential Equations. The numerical solution of partial differential equations (PDE) is a fundamental task in science and engineering. The goal of the workshop was to bring together a spectrum of scientists at the forefront of the research in the numerical solution of PDEs to discuss compatible spatial discretizations. We define compatible spatial discretizations as those that inherit or mimic fundamental properties of the PDE such as topology, conservation, symmetries, and positivity structures and maximum principles. A wide variety of discretization methods applied across a wide range of scientific and engineering applications have been designed to or found to inherit or mimic intrinsic spatial structure and reproduce fundamental properties of the solution of the continuous PDE model at the finite dimensional level. A profusion of such methods and concepts relevant to understanding them have been developed and explored: mixed finite element methods, mimetic finite differences, support operator methods, control volume methods, discrete differential forms, Whitney forms, conservative differencing, discrete Hodge operators, discrete Helmholtz decomposition, finite integration techniques, staggered grid and dual grid methods, etc. This workshop seeks to foster communication among the diverse groups of researchers designing, applying, and studying such methods as well as researchers involved in practical solution of large scale problems that may benefit from advancements in such discretizations; to help elucidate the relations between the different methods and concepts; and to generally advance our understanding in the area of compatible spatial discretization methods for PDE. Particular points of emphasis included: + Identification of intrinsic properties of PDE models that are critical for the fidelity of numerical

  4. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    PubMed Central

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  5. Sigma-G RNA polymerase controls forespore-specific expression of the glucose dehydrogenase operon in Bacillus subtilis.

    PubMed Central

    Nakatani, Y; Nicholson, W L; Neitzke, K D; Setlow, P; Freese, E

    1989-01-01

    The gene encoding glucose dehydrogenase (gdh) is part of an operon whose expression is transcriptionally activated specifically in the developing forespore of Bacillus subtilis at stage III of sporulation. The in vivo startpoint of gdh transcription was determined using primer extension analysis. Deletion mapping and site-specific mutagenesis experiments indicated that the region responsible for regulated expression of gdh in vivo was limited to the "-35" and "-10" regions preceding the transcriptional start site. RNA polymerase containing omega G (E omega G) transcribed gdh in vitro with a start site identical to that found in vivo, and transcription of gdh by E omega G in vitro also did not require any specific sequences upstream from "-35" region. These results suggest that the appearance of E omega G in the forespore at stage III of sporulation is sufficient to cause temporal and compartment-specific expression of the gdh operon. Images PMID:2493633

  6. Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes.

    PubMed

    Zhang, Yucheng; Qiu, Sai

    2016-01-01

    The genus Ralstonia contains species that are devastating plant pathogens, opportunistic human pathogens, and/or important degraders of xenobiotic and recalcitrant compounds. However, significant nomenclature problems exist, especially for the Ralstonia solanacearum species complex which consists of four phylotypes. Phylogenomics of the Ralstonia genus was investigated via a comprehensive analysis of 39 Ralstonia genomes as well as four genomes of Cupriavidus necator (more commonly known by its previous name Ralstonia eutropha). These data revealed 686 single-copy orthologs that could be extracted from the Ralstonia core-genome and used to reconstruct the phylogeny of the genus Ralstonia. The generated tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome. Our data confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia, e.g. strains of Ralstonia solanacearum phylotype IIA and IIB may represent two subspecies of R. solanacearum, and strains of R. solanacearum phylotype I and III may be classified into two subspecies of Ralstonia pseudosolanacearum. Recently, strains of R. solanacearum phylotype IV were proposed to be reclassified into different subspecies of Ralstonia syzygii; our study, however, showed that phylotype IV strains had high isDDH values (83.8-96.1 %), indicating it may be not appropriate to classify these closely related strains into different subspecies. We also evaluated the performance of six chromosomal housekeeping genes (gdhA, mutS, adk, leuS, rplB and gyrB) used in Ralstonia phylogenetic inference. The multilocus sequence analysis of these six marker genes was able to reliably infer the phylogenetic relationships of the genus Ralstonia. PMID:26494208

  7. Multimedia document retrieval system using partially ordered/partially reliable transport service

    NASA Astrophysics Data System (ADS)

    Conrad, Phillip T.; Golden, Edward; Amer, Paul D.; Marasli, Rahmi

    1996-03-01

    We investigate the benefits of using a partially-ordered/partially-reliable (PO/PR) transport service for multimedia document retrieval over the Internet by implementing a prototype system. We introduce PMSL, a document specification language combining aspects of Little and Ghafoor's OCPN with features for graceful degradation. We then show that for retrieval of PMSL documents, our PO/PR transport protocol (POCv2) provides several benefits over traditional protocols such as TCP or UDP. First, POCv2 provides mechanisms to achieve the reliability and order requirements of individual multimedia objects as specified by a document author. Second, when network conditions are poor (e.g., high loss rates), POCv2 provides for graceful degradation. Finally, POCv2 simplifies application development by providing appropriate mechanisms for synchronization.

  8. New approach to breast cancer CAD using partial least squares and kernel-partial least squares

    NASA Astrophysics Data System (ADS)

    Land, Walker H., Jr.; Heine, John; Embrechts, Mark; Smith, Tom; Choma, Robert; Wong, Lut

    2005-04-01

    Breast cancer is second only to lung cancer as a tumor-related cause of death in women. Currently, the method of choice for the early detection of breast cancer is mammography. While sensitive to the detection of breast cancer, its positive predictive value (PPV) is low, resulting in biopsies that are only 15-34% likely to reveal malignancy. This paper explores the use of two novel approaches called Partial Least Squares (PLS) and Kernel-PLS (K-PLS) to the diagnosis of breast cancer. The approach is based on optimization for the partial least squares (PLS) algorithm for linear regression and the K-PLS algorithm for non-linear regression. Preliminary results show that both the PLS and K-PLS paradigms achieved comparable results with three separate support vector learning machines (SVLMs), where these SVLMs were known to have been trained to a global minimum. That is, the average performance of the three separate SVLMs were Az = 0.9167927, with an average partial Az (Az90) = 0.5684283. These results compare favorably with the K-PLS paradigm, which obtained an Az = 0.907 and partial Az = 0.6123. The PLS paradigm provided comparable results. Secondly, both the K-PLS and PLS paradigms out performed the ANN in that the Az index improved by about 14% (Az ~ 0.907 compared to the ANN Az of ~ 0.8). The "Press R squared" value for the PLS and K-PLS machine learning algorithms were 0.89 and 0.9, respectively, which is in good agreement with the other MOP values.

  9. Parameter Estimation of Partial Differential Equation Models.

    PubMed

    Xun, Xiaolei; Cao, Jiguo; Mallick, Bani; Carroll, Raymond J; Maity, Arnab

    2013-01-01

    Partial differential equation (PDE) models are commonly used to model complex dynamic systems in applied sciences such as biology and finance. The forms of these PDE models are usually proposed by experts based on their prior knowledge and understanding of the dynamic system. Parameters in PDE models often have interesting scientific interpretations, but their values are often unknown, and need to be estimated from the measurements of the dynamic system in the present of measurement errors. Most PDEs used in practice have no analytic solutions, and can only be solved with numerical methods. Currently, methods for estimating PDE parameters require repeatedly solving PDEs numerically under thousands of candidate parameter values, and thus the computational load is high. In this article, we propose two methods to estimate parameters in PDE models: a parameter cascading method and a Bayesian approach. In both methods, the underlying dynamic process modeled with the PDE model is represented via basis function expansion. For the parameter cascading method, we develop two nested levels of optimization to estimate the PDE parameters. For the Bayesian method, we develop a joint model for data and the PDE, and develop a novel hierarchical model allowing us to employ Markov chain Monte Carlo (MCMC) techniques to make posterior inference. Simulation studies show that the Bayesian method and parameter cascading method are comparable, and both outperform other available methods in terms of estimation accuracy. The two methods are demonstrated by estimating parameters in a PDE model from LIDAR data. PMID:24363476

  10. Neurotrophic factor - Characterization and partial purification

    NASA Technical Reports Server (NTRS)

    Popiela, H.; Ellis, S.

    1981-01-01

    Recent evidence suggests that neurotrophic activity is required for the normal proliferation and development of muscle cells. The present paper reports a study of the purification and characterization of a neurotrophic factor (NTF) from adult chicken ischiatic-peroneal nerves using two independent quantitative in vitro assay systems. The assays were performed by the measurement of the incorporation of tritiated thymidine or the sizes of single-cell clones by chick muscle cells grown in culture. The greatest amount of neutrotrophic activity is found to be extracted at a pH of 8; aqueous suspensions of the activity are stable to long-term storage at room temperature. The specific activity of the substance is doubled upon precipitation with ammonium sulfate or after gel filtration, and increase 4 to 5 fold after salt gradient elution from DEAE cellulose columns. The active fraction obtained after gel filtration and rechromatography on DEAE cellulose exhibits a 7 to 10-fold increase in specific activity. Electrophoresis of the most highly purified material yields a greatly concentrated band at around 80,000 daltons. Although NTF is purified almost 10-fold as indicated by the increase in specific activity, the maximum activity of the partially purified material is greatly reduced, possibly due to a requirement for a cofactor for the expression of maximum activity.

  11. Partial splenic artery embolization in cirrhotic patients

    PubMed Central

    Hadduck, Tyson A; McWilliams, Justin P

    2014-01-01

    Splenomegaly is a common sequela of cirrhosis, and is frequently associated with decreased hematologic indices including thrombocytopenia and leukopenia. Partial splenic artery embolization (PSE) has been demonstrated to effectively increase hematologic indices in cirrhotic patients with splenomegaly. This is particularly valuable amongst those cirrhotic patients who are not viable candidates for splenectomy. Although PSE was originally developed decades ago, it has recently received increased attention. Presently, PSE is being utilized to address a number of clinical concerns in the setting of cirrhosis, including: decreased hematologic indices, portal hypertension and its associated sequela, and splenic artery steal syndrome. Following PSE patients demonstrate significant increases in platelets and leukocytes. Though progressive decline of hematologic indices occur following PSE, they remain improved as compared to pre-procedural values over long-term follow-up. PSE, however, is not without risk and complications of the procedure may occur. The most common complication of PSE is post-embolization syndrome, which involves a constellation of symptoms including fever, pain, and nausea/vomiting. The rate of complications has been shown to increase as the percent of total splenic volume embolized increases. The purpose of this review is to explore the current literature in regards to PSE in cirrhotic patients and to highlight their techniques, and statistically summarize their results and associated complications. PMID:24876920

  12. Precise Point Positioning with Partial Ambiguity Fixing

    PubMed Central

    Li, Pan; Zhang, Xiaohong

    2015-01-01

    Reliable and rapid ambiguity resolution (AR) is the key to fast precise point positioning (PPP). We propose a modified partial ambiguity resolution (PAR) method, in which an elevation and standard deviation criterion are first used to remove the low-precision ambiguity estimates for AR. Subsequently the success rate and ratio-test are simultaneously used in an iterative process to increase the possibility of finding a subset of decorrelated ambiguities which can be fixed with high confidence. One can apply the proposed PAR method to try to achieve an ambiguity-fixed solution when full ambiguity resolution (FAR) fails. We validate this method using data from 450 stations during DOY 021 to 027, 2012. Results demonstrate the proposed PAR method can significantly shorten the time to first fix (TTFF) and increase the fixing rate. Compared with FAR, the average TTFF for PAR is reduced by 14.9% for static PPP and 15.1% for kinematic PPP. Besides, using the PAR method, the average fixing rate can be increased from 83.5% to 98.2% for static PPP, from 80.1% to 95.2% for kinematic PPP respectively. Kinematic PPP accuracy with PAR can also be significantly improved, compared to that with FAR, due to a higher fixing rate. PMID:26067196

  13. Design of channeled partial Mueller matrix polarimeters.

    PubMed

    Alenin, Andrey S; Scott Tyo, J

    2016-06-01

    In this paper, we introduce a novel class of systems called channeled partial Mueller matrix polarimeters (c-pMMPs). Their analysis benefits greatly by drawing from the concepts of generalized construction of channeled polarimeters as described by the modulation matrix. The modulation matrix resembles that of the data reduction method of a conventional polarimeter, but instead of using Mueller vectors as the bases, attention is focused on the Fourier properties of the measurement conditions. By leveraging the understanding of the measurement's structure, its decomposition can be manipulated to reveal noise resilience and information about the polarimeter's ability to measure the aspect of polarization that are important for any given task. We demonstrate the theory with a numerical optimization that designs c-pMMPs for the task of monitoring the damage state of a material as presented earlier by Hoover and Tyo [Appl. Opt.46, 8364 (2007)APOPAI0003-693510.1364/AO.46.008364]. We select several example systems that produce a fewer-than-full-system number of channels yet retain the ability to discriminate objects of interest. Their respective trade-offs are discussed. PMID:27409432

  14. The new BNL partial wave analysis programs

    SciTech Connect

    Cummings, J.P.; Weygand, D.P.

    1997-07-29

    Experiment E852 at Brookhaven National Laboratory is a meson spectroscopy experiment which took data at the Multi-Particle Spectrometer facility of the Alternating Gradient Syncrotron. Upgrades to the spectrometer`s data acquisition and trigger electronics allowed over 900 million data events, of numerous topologies, to be recorded to tape in 1995 running alone. One of the primary goals of E852 is identification of states beyond the quark model, i.e., states with gluonic degrees of freedom. Identification of such states involves the measurement of a systems spin-parity. Such a measurement is usually done using Partial Wave Analysis. Programs to perform such analyses exist, in fact, one was written at BNL and used in previous experiments by some of this group. This program, however, was optimized for a particular final state, and modification to allow analysis of the broad range of final states in E852 would have been difficult. The authors therefore decided to write a new program, with an eye towards generality that would allow analysis of a large class of reactions.

  15. Clinical application of partial splenic embolization.

    PubMed

    Guan, Yong-Song; Hu, Ying

    2014-01-01

    Partial splenic embolization (PSE) is one of the intra-arterial therapeutic approaches of diseases. With the development of interventional radiology, the applications of PSE in clinical practice are greatly extended, while various materials are developed for embolization use. Common indications of PSE include hypersplenism with portal hypertension, hereditary spherocytosis, thalassemia, autoimmune hemolytic anemia, splenic trauma, idiopathic thrombocytopenic purpura, splenic hemangioma, and liver cancer. It is also performed to exclude splenic artery aneurysms from the parent vessel lumen and prevent aneurysm rupture, to treat splenic artery steal syndrome and improve liver perfusion in liver transplant recipients, and to administer targeted treatment to areas of neoplastic disease in the splenic parenchyma. Indicators of the therapeutic effect evaluation of PSE comprise blood routine test, changes in hemodynamics and in splenic volume. Major complications of PSE include the pulmonary complications, severe infection, damages of renal and liver function, and portal vein thrombosis. The limitations of PSE exist mainly in the difficulties in selecting the arteries to embolize and in evaluating the embolized volume.

  16. Partial oxidation of heavy refinery fractions

    SciTech Connect

    Dille, R.M.; Rhodes, H.A.; Wallon, S.B.

    1984-07-31

    This is a partial oxidation process in which heavy hydrocarbonaceous fractions from a petroleum refinery and light liquid paraffinic hydrocarbon extractants are used in the production of synthesis gas, reducing gas, or fuel gas i.e., gaseous mixtures comprising H/sub 2/ and CO. In the process, substantially all of the particulate carbon and soot that are simultaneously produced are recovered and recycled to the reaction zone. A dispersion of carbon-soot-light paraffinic hydrocarbon extractant from the decanting zone is combined with a heavy refinery fraction in admixture with a liquid aromatic-rich hydrocarbon to produce a pumpable single liquid phase mixture which is introduced into a fractionation zone where the following streams are separated from each other: (a) a stream of light paraffinic hydrocarbon extractant which is recycled to the decanting zone, (b) a stream comprising at least a portion of the aromatic-rich hydrocarbon which is recycled for mixing with the heavy refinery fraction, and (c) a stream of pumpable dispersion of carbon-soot heavy refinery fraction and any remaining aromatic-rich hydrocarbon which may be used as fuel in the system or exported. Troublesome asphaltene precipitation that causes operational problems and increased viscosity is avoided by the subject process. Comparatively low cost heavy refinery fractions which ordinarily are difficult to handle may be now used along with light liquid paraffinic hydrocarbon extractants.

  17. Partially ordered state of ice XV

    PubMed Central

    Komatsu, K.; Noritake, F.; Machida, S.; Sano-Furukawa, A.; Hattori, T.; Yamane, R.; Kagi, H.

    2016-01-01

    Most ice polymorphs have order–disorder “pairs” in terms of hydrogen positions, which contributes to the rich variety of ice polymorphs; in fact, three recently discovered polymorphs— ices XIII, XIV, and XV—are ordered counter forms to already identified disordered phases. Despite the considerable effort to understand order–disorder transition in ice crystals, there is an inconsistency among the various experiments and calculations for ice XV, the ordered counter form of ice VI, i.e., neutron diffraction observations suggest antiferroelectrically ordered structures, which disagree with dielectric measurement and theoretical studies, implying ferroelectrically ordered structures. Here we investigate in-situ neutron diffraction measurements and density functional theory calculations to revisit the structure and stability of ice XV. We find that none of the completely ordered configurations are particular favored; instead, partially ordered states are established as a mixture of ordered domains in disordered ice VI. This scenario in which several kinds of ordered configuration coexist dispels the contradictions in previous studies. It means that the order–disorder pairs in ice polymorphs are not one-to-one correspondent pairs but rather have one-to-n correspondence, where there are n possible configurations at finite temperature. PMID:27375120

  18. Partially ordered state of ice XV

    NASA Astrophysics Data System (ADS)

    Komatsu, K.; Noritake, F.; Machida, S.; Sano-Furukawa, A.; Hattori, T.; Yamane, R.; Kagi, H.

    2016-07-01

    Most ice polymorphs have order–disorder “pairs” in terms of hydrogen positions, which contributes to the rich variety of ice polymorphs; in fact, three recently discovered polymorphs— ices XIII, XIV, and XV—are ordered counter forms to already identified disordered phases. Despite the considerable effort to understand order–disorder transition in ice crystals, there is an inconsistency among the various experiments and calculations for ice XV, the ordered counter form of ice VI, i.e., neutron diffraction observations suggest antiferroelectrically ordered structures, which disagree with dielectric measurement and theoretical studies, implying ferroelectrically ordered structures. Here we investigate in-situ neutron diffraction measurements and density functional theory calculations to revisit the structure and stability of ice XV. We find that none of the completely ordered configurations are particular favored; instead, partially ordered states are established as a mixture of ordered domains in disordered ice VI. This scenario in which several kinds of ordered configuration coexist dispels the contradictions in previous studies. It means that the order–disorder pairs in ice polymorphs are not one-to-one correspondent pairs but rather have one-to-n correspondence, where there are n possible configurations at finite temperature.

  19. Partial squeeze film levitation modulates fingertip friction.

    PubMed

    Wiertlewski, Michaël; Fenton Friesen, Rebecca; Colgate, J Edward

    2016-08-16

    When touched, a glass plate excited with ultrasonic transverse waves feels notably more slippery than it does at rest. To study this phenomenon, we use frustrated total internal reflection to image the asperities of the skin that are in intimate contact with a glass plate. We observed that the load at the interface is shared between the elastic compression of the asperities of the skin and a squeeze film of air. Stroboscopic investigation reveals that the time evolution of the interfacial gap is partially out of phase with the plate vibration. Taken together, these results suggest that the skin bounces against the vibrating plate but that the bounces are cushioned by a squeeze film of air that does not have time to escape the interfacial separation. This behavior results in dynamic levitation, in which the average number of asperities in intimate contact is reduced, thereby reducing friction. This improved understanding of the physics of friction reduction provides key guidelines for designing interfaces that can dynamically modulate friction with soft materials and biological tissues, such as human fingertips. PMID:27482117

  20. Partial Wave Analysis of Coupled Photonic Structures

    NASA Technical Reports Server (NTRS)

    Fuller, Kirk A.; Smith, David D.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    The very high quality factors sustained by microcavity optical resonators are relevant to applications in wavelength filtering, routing, switching, modulation, and multiplexing/demultiplexing. Increases in the density of photonic elements require that attention be paid to how electromagnetic (EM) coupling modifies their optical properties. This is especially true when cavity resonances are involved, in which case, their characteristics may be fundamentally altered. Understanding the optical properties of microcavities that are near or in contact with photonic elements---such as other microcavities, nanostructures, couplers, and substrates---can be expected to advance our understanding of the roles that these structures may play in VLSI photonics, biosensors and similar device technologies. Wc present results from recent theoretical studies of the effects of inter- and intracavity coupling on optical resonances in compound spherical particles. Concentrically stratified spheres and bispheres constituted from homogeneous and stratified spheres are subjects of this investigation. A new formulation is introduced for the absorption of light in an arbitrary layer of a multilayered sphere, which is based on multiple reflections of the spherical partial waves of the Lorenz-Mie solution for scattering by a sphere. Absorption efficiencies, which can be used to profile cavity resonances and to infer fluorescence yields or the onset of nonlinear optical processes in the microcavities, are presented. Splitting of resonances in these multisphere systems is paid particular attention, and consequences for photonic device development and possible performance enhancements through carefully designed architectures that exploit EM coupling are considered.