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Sample records for investigate strain variation

  1. Use of Restriction Fragment Length Polymorphisms to Investigate Strain Variation Within Neisseria Meningitidis.

    NASA Astrophysics Data System (ADS)

    Williams, Shelley Diane

    Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty -six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P ^{32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analysed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population. This analysis demonstrates the lack of structure within Neisseria meningitidis due primarily to a heterogenous population and the lack of geographic segregation. The potential utility of this technique as a

  2. Strain variation in corrugated graphene

    NASA Astrophysics Data System (ADS)

    Wang, Xuanye; Tantiwanichapan, Khwanchai; Christopher, Jason; Paiella, Roberto; Swan, Anna

    2015-03-01

    Raman spectroscopy is a powerful non-destructive technique for analyzing strain in graphene. Recently there has been interest in making corrugated graphene devices with varying spatial wavelengths Λ for plasmonic and THz applications. Transferring graphene onto corrugated substrates introduces strain, which if there was perfect clamping (high fraction) would cause a periodic strain variation. However, the strain variation for pattern size smaller than the diffraction limit λ makes it hard to precisely model the strain distribution. Here we present a detailed study on how strain varies in corrugated graphene with sub-diffraction limit periodicity Λ < λ. Mechanically exfoliated graphene was deposited onto sinusoidal shape silicon dioxide gratings with Λ=400 nm period using the pick and place transfer technique. We observed that the graphene is not rigidly clamped, but partially slides to relieve the strain. We model the linewidth variation to extract the local strain variation as well as the sliding in the presence of charge puddling in graphene. The method gives us a better understanding on graphene slippage and strain distribution in graphene on a corrugated substrate with sub-diffraction limit spatial period.

  3. Strain Variation in Mycobacterium marinum Fish Isolates

    PubMed Central

    Ucko, M.; Colorni, A.; Kvitt, H.; Diamant, A.; Zlotkin, A.; Knibb, W. R.

    2002-01-01

    A molecular characterization of two Mycobacterium marinum genes, 16S rRNA and hsp65, was carried out with a total of 21 isolates from various species of fish from both marine and freshwater environments of Israel, Europe, and the Far East. The nucleotide sequences of both genes revealed that all M. marinum isolates from fish in Israel belonged to two different strains, one infecting marine (cultured and wild) fish and the other infecting freshwater (cultured) fish. A restriction enzyme map based on the nucleotide sequences of both genes confirmed the divergence of the Israeli marine isolates from the freshwater isolates and differentiated the Israeli isolates from the foreign isolates, with the exception of one of three Greek isolates from marine fish which was identical to the Israeli marine isolates. The second isolate from Greece exhibited a single base alteration in the 16S rRNA sequence, whereas the third isolate was most likely a new Mycobacterium species. Isolates from Denmark and Thailand shared high sequence homology to complete identity with reference strain ATCC 927. Combined analysis of the two gene sequences increased the detection of intraspecific variations and was thus of importance in studying the taxonomy and epidemiology of this aquatic pathogen. Whether the Israeli M. marinum strain infecting marine fish is endemic to the Red Sea and found extremely susceptible hosts in the exotic species imported for aquaculture or rather was accidentally introduced with occasional imports of fingerlings from the Mediterranean Sea could not be determined. PMID:12406715

  4. Proteome variation among Filifactor alocis strains

    PubMed Central

    Aruni, A. Wilson; Roy, Francis; Sandberg, Lawrence; Fletcher, Hansel M.

    2015-01-01

    Filifactor alocis, a Gram-positive anaerobic rod, is now considered one of the marker organisms associated with periodontal disease. Although there was heterogeneity in its virulence potential, this bacterium was shown to have virulence properties that may enhance its ability to survive and persist in the periodontal pocket. To gain further insight into a possible mechanism(s) of pathogenesis, the proteome of F. alocis strains was evaluated. Proteins including several proteases, neutrophil-activating protein A and calcium-binding acid repeat protein, were identified in F. alocis. During the invasion of HeLa cells, there was increased expression of several of the genes encoding these proteins in the potentially more virulent F. alocis D-62D compared to F. alocis ATCC 35896, the type strain. A comparative protein in silico analysis of the proteome revealed more cell wall anchoring proteins in the F. alocis D-62D compared to F. alocis ATCC 35896. Their expression was enhanced by coinfection with Porphyromonas gingivalis. Taken together, the variation in the pathogenic potential of the F. alocis strains may be related to the differential expression of several putative virulence factors. PMID:23008013

  5. Comparative Investigation of the Genomic Regions Involved in Antigenic Variation of the TprK Antigen among Treponemal Species, Subspecies, and Strains

    PubMed Central

    Brandt, Stephanie L.; Puray-Chavez, Maritza; Reid, Tara Brinck; Godornes, Charmie; Molini, Barbara J.; Benzler, Martin; Hartig, Jörg S.; Lukehart, Sheila A.; Centurion-Lara, Arturo

    2012-01-01

    Although the three Treponema pallidum subspecies (T. pallidum subsp. pallidum, T. pallidum subsp. pertenue, and T. pallidum subsp. endemicum), Treponema paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme cause clinically distinct diseases, these pathogens are genetically and antigenically highly related and are able to cause persistent infection. Recent evidence suggests that the putative surface-exposed variable antigen TprK plays an important role in both treponemal immune evasion and persistence. tprK heterogeneity is generated by nonreciprocal gene conversion between the tprK expression site and donor sites. Although each of the above-mentioned species and subspecies has a functional tprK antigenic variation system, it is still unclear why the level of expression and the rate at which tprK diversifies during infection can differ significantly among isolates. To identify genomic differences that might affect the generation and expression of TprK variants among these pathogens, we performed comparative sequence analysis of the donor sites, as well as the tprK expression sites, among eight T. pallidum subsp. pallidum isolates (Nichols Gen, Nichols Sea, Chicago, Sea81-4, Dal-1, Street14, UW104, and UW126), three T. pallidum subsp. pertenue isolates (Gauthier, CDC2, and Samoa D), one T. pallidum subsp. endemicum isolate (Iraq B), the unclassified Fribourg-Blanc isolate, and the Cuniculi A strain of T. paraluiscuniculi. Synteny and sequence conservation, as well as deletions and insertions, were found in the regions harboring the donor sites. These data suggest that the tprK recombination system is harbored within dynamic genomic regions and that genomic differences might be an important key to explain discrepancies in generation and expression of tprK variants among these Treponema isolates. PMID:22661689

  6. Comparative investigation of the genomic regions involved in antigenic variation of the TprK antigen among treponemal species, subspecies, and strains.

    PubMed

    Giacani, Lorenzo; Brandt, Stephanie L; Puray-Chavez, Maritza; Reid, Tara Brinck; Godornes, Charmie; Molini, Barbara J; Benzler, Martin; Hartig, Jörg S; Lukehart, Sheila A; Centurion-Lara, Arturo

    2012-08-01

    Although the three Treponema pallidum subspecies (T. pallidum subsp. pallidum, T. pallidum subsp. pertenue, and T. pallidum subsp. endemicum), Treponema paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme cause clinically distinct diseases, these pathogens are genetically and antigenically highly related and are able to cause persistent infection. Recent evidence suggests that the putative surface-exposed variable antigen TprK plays an important role in both treponemal immune evasion and persistence. tprK heterogeneity is generated by nonreciprocal gene conversion between the tprK expression site and donor sites. Although each of the above-mentioned species and subspecies has a functional tprK antigenic variation system, it is still unclear why the level of expression and the rate at which tprK diversifies during infection can differ significantly among isolates. To identify genomic differences that might affect the generation and expression of TprK variants among these pathogens, we performed comparative sequence analysis of the donor sites, as well as the tprK expression sites, among eight T. pallidum subsp. pallidum isolates (Nichols Gen, Nichols Sea, Chicago, Sea81-4, Dal-1, Street14, UW104, and UW126), three T. pallidum subsp. pertenue isolates (Gauthier, CDC2, and Samoa D), one T. pallidum subsp. endemicum isolate (Iraq B), the unclassified Fribourg-Blanc isolate, and the Cuniculi A strain of T. paraluiscuniculi. Synteny and sequence conservation, as well as deletions and insertions, were found in the regions harboring the donor sites. These data suggest that the tprK recombination system is harbored within dynamic genomic regions and that genomic differences might be an important key to explain discrepancies in generation and expression of tprK variants among these Treponema isolates. PMID:22661689

  7. Investigation of infectivity of neonates and adults from different rat strains to Toxoplasma gondii Prugniaud shows both variation which correlates with iNOS and Arginase-1 activity and increased susceptibility of neonates to infection.

    PubMed

    Gao, Jiang-Mei; Yi, Si-Qi; Wu, Ming-Shui; Geng, Guo-Qing; Shen, Ji-Long; Lu, Fang-Li; Hide, Geoff; Lai, De-Hua; Lun, Zhao-Rong

    2015-02-01

    Mouse models differ considerably from humans with regard to clinical symptoms of toxoplasmosis caused by Toxoplasma gondii and, by comparison, the rat model is more representative of this disease in humans. In the present study, we found that different strains of adult and newborn rats (Lewis, Wistar, Sprague Dawley, Brown Norway and Fischer 344) exhibited remarkable variation in the number of brain cysts following inoculation with the T.gondii Prugniaud strain. In adult rats, large numbers of cysts (1231 ± 165.6) were observed in Fischer 344, but none in the other four. This situation was different in newborn rats aged from 5 to 20 days old. All Fischer 344 and Brown Norway newborns were cyst-positive while cyst-positive infection in Sprague Dawley neonates ranged from 54.5% to 60% depending on their age at infection. In Wistar and Lewis rat neonates, however, cyst-positivity rates of 0-42.9% and 0-25% were found respectively. To investigate whether rat strain differences in infectivity could be related to inherent strain and genetic differences in the host immune response, we correlated our data with previously reported strain differences in iNOS/Arginase ratio in adult rats and found them to be linked. These results show that interactions between host genetic background and age of rat influence T.gondii infection. PMID:25541383

  8. Investigation of a noncontact strain measurement technique

    SciTech Connect

    Damiano, B.; Talarico, L.J.

    1996-05-01

    The goal of this project was to investigate the feasibility of a new noncontact technique for directly and continuously monitoring peak strain in rotating components. The technique utilizes the unique strain-sensitive magnetic material properties of transformation Induced Plasticity (TRIP) steel alloys to measure strain. These alloys are weakly magnetic when unstrained but become strongly ferromagnetic after mechanical deformation. A computer study was performed to determine whether the strain-induced change in the magnetic material properties of a TRIP steel gage bonded to a rotating component would cause significant perturbations in the magnetic flux of a stationary electromagnet. The effects of strain level, distance between the rotating component and the stationary electromagnet, and motion-induced eddy currents on flux perturbation magnitude were investigated. The calculated results indicate that a TRIP steel strain sensing element can cause a significant perturbation in the magnetic flux of a stationary electromagnet. The magnetic flux perturbation magnitude was found to be inversely proportional to the distance between the magnet face and the TRIP steel element and directly proportional to the TRIP steel strain level. The effect of motion-induced eddy currents on the magnetic flux was found to be negligible. It appears that the technique can be successfully applied to measure peak strain in rotating components; however, the sensitivity of the magnetic flux perturbation magnitude to the distance between the strain sensing element and the electromagnet may require making an independent proximity measurement.

  9. Morphological variation in pathogenic strains of Penicillium marneffei.

    PubMed

    Pracharktam, R; Sriurairatna, S; Jayanetra, P

    1992-01-01

    Penicillium marneffei is a dimorphic fungus known to be pathogenic to animals and man. The natural reservoir of this organism was known to be bamboo rats found in South Vietnam, Thailand and China. The first two human infections were reported in 1959 and 1973 from the United States. Up to 1984, five new cases of human penicillosis were reported from Thailand. Since then several more cases have been reported from different parts of the world mainly from the southern part of China. However, there are very limited mycological descriptions of this fungi. In this report, five Thai strains were studied for colonial morphology in comparison with Reference strain PLM 689. Variation in mycelial pigment was observed ranging from yellowish-green to orange with water soluble red pigment produced in every strain which can be seen early from the reverse side. Ultrastructural study by both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) was compared with that of the reference strain PLM 689. PLM 689 strain had only biverticillate penicilli, but all five strains from Thailand had both monoverticillate and biverticillate penicilli which occasionally appeared on the same branch. The conidia of the Thai isolates were oval in shape and 1.3-2 x 0.7-1.6 microns in size smaller than those of PLM 689 which were 2.5-4 x 2-3 microns. Phialides were also smaller and a little shorter but the number of phialides was similar to those of PLM 689 ranging 4-10 except for one strain which had 3-16 phialides. All Thai strains have stipes smaller and somewhat longer than those of PLM 689.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1402460

  10. Strain-dependent variations in attachment of E. coli to soil particles of different sizes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Attachment of E. coli to soil particles affects the bacteria transport in overland flow and in soil. The objective of this research was to investigate the existence of strain-dependent variations in attachment of manure-borne E. coli to soil particles of different sizes using rep PCR techniques. The...

  11. Strain variation and geographic endemism in Streptococcus iniae.

    PubMed

    Kvitt, H; Colorni, A

    2004-10-21

    Twenty-six Israeli isolates of Streptococcus iniae from both marine and fresh/brackish water sources were compared with each other and with 9 foreign isolates. All the isolates were tentatively identified according to their biochemical profile. Direct sequencing of approximately 600 bp PCR products of the 16S rDNA confirmed their identification as S. iniae at the molecular level and revealed a new (one-nucleotide) variant among Israeli isolates, in addition to 2 variants that had been previously reported. Strain variation was further examined by subjecting the isolates to randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analyses. The RAPD method allowed separation of the isolates into only 2 groups, one including 5 Israeli fresh/brackish water isolates and one including all the other isolates. The AFLP method grouped the Israeli marine isolates into one homogeneous cluster, although they had been obtained in different years (1995 to 2001) from different species of fish, and from wild (Red Sea) as well as cultured (both Mediterranean and Red Sea) sources. The Israeli fresh/brackish water isolates and foreign isolates separated into distinct entities that clustered at generally high degrees of similarity. The distance between the clusters of the Israeli marine and fresh/brackish water isolates indicates that the S. iniae streptococcosis that has been afflicting the aquaculture industries in the 2 environments in recent years was caused by distinct strains. AFLP showed superior discriminative properties over RAPD in detecting intraspecific variation and proved to be an important tool for the characterization of S. iniae. A correlation between strain variation and geographic endemism was established. PMID:15584412

  12. Intragenic tandem repeat variation between Legionella pneumophila strains

    PubMed Central

    Coil, David A; Vandersmissen, Liesbeth; Ginevra, Christophe; Jarraud, Sophie; Lammertyn, Elke; Anné, Jozef

    2008-01-01

    Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects of those found within the coding region of genes are only beginning to be examined. Evidence exists from other organisms that these repeats can be involved in the evolution of new genes, gene regulation, adaptation, resistance to environmental stresses, and avoidance of the immune system. Results In this study, we have investigated the presence and variability in copy number of intragenic tandemly repeated sequences in the genome of Legionella pneumophila, the etiological agent of a severe pneumonia known as Legionnaires' disease. Within the genome of the Philadelphia strain, we have identified 26 intragenic tandem repeat sequences using conservative selection criteria. Of these, seven were "polymorphic" in terms of repeat copy number between a large number of L. pneumophila serogroup 1 strains. These strains were collected from a wide variety of environments and patients in several geographical regions. Within this panel of strains, all but one of these seven genes exhibited statistically different patterns in repeat copy number between samples from different origins (environmental, clinical, and hot springs). Conclusion These results support the hypothesis that intragenic tandem repeats could play a role in virulence and adaptation to different environments. While tandem repeats are an increasingly popular focus of molecular typing studies in prokaryotes, including in L. pneumophila, this study is the first examining the difference in tandem repeat distribution as a function of clinical or environmental origin. PMID:19077205

  13. Molecular Basis for Strain Variation in the Saccharomyces cerevisiae Adhesin Flo11p.

    PubMed

    Barua, Subit; Li, Li; Lipke, Peter N; Dranginis, Anne M

    2016-01-01

    FLO11 encodes a yeast cell wall flocculin that mediates a variety of adhesive phenotypes in Saccharomyces cerevisiae. Flo11p is implicated in many developmental processes, including flocculation, formation of pseudohyphae, agar invasion, and formation of microbial mats and biofilms. However, Flo11p mediates different processes in different yeast strains. To investigate the mechanisms by which FLO11 determines these differences in colony morphology, flocculation, and invasion, we studied gene structure, function, and expression levels. Nonflocculent Saccharomyces cerevisiae Σ1278b cells exhibited significantly higher FLO11 mRNA expression, especially in the stationary phase, than highly flocculent S. cerevisiae var. diastaticus. The two strains varied in cell surface hydrophobicity, and Flo11p contributed significantly to surface hydrophobicity in S. cerevisiae var. diastaticus but not in strain Σ1278b. Sequencing of the FLO11 gene in S. cerevisiae var. diastaticus revealed strain-specific differences, including a 15-amino-acid insertion in the adhesion domain. Flo11p adhesion domains from strain Σ1278b and S. cerevisiae var. diastaticus were expressed and used to coat magnetic beads. The adhesion domain from each strain bound preferentially to homologous cells, and the preferences were independent of the cells in which the adhesion domains were produced. These results are consistent with the idea that strain-specific variations in the amino acid sequences in the adhesion domains cause different Flo11p flocculation activities. The results also imply that strain-specific differences in expression levels, posttranslational modifications, and allelic differences outside the adhesion domains have little effect on flocculation. IMPORTANCE As a nonmotile organism, Saccharomyces cerevisiae employs the cell surface flocculin Flo11/Muc1 as an important means of adapting to environmental change. However, there is a great deal of strain variation in the expression of

  14. Molecular Basis for Strain Variation in the Saccharomyces cerevisiae Adhesin Flo11p

    PubMed Central

    Li, Li; Lipke, Peter N.; Dranginis, Anne M.

    2016-01-01

    ABSTRACT FLO11 encodes a yeast cell wall flocculin that mediates a variety of adhesive phenotypes in Saccharomyces cerevisiae. Flo11p is implicated in many developmental processes, including flocculation, formation of pseudohyphae, agar invasion, and formation of microbial mats and biofilms. However, Flo11p mediates different processes in different yeast strains. To investigate the mechanisms by which FLO11 determines these differences in colony morphology, flocculation, and invasion, we studied gene structure, function, and expression levels. Nonflocculent Saccharomyces cerevisiae Σ1278b cells exhibited significantly higher FLO11 mRNA expression, especially in the stationary phase, than highly flocculent S. cerevisiae var. diastaticus. The two strains varied in cell surface hydrophobicity, and Flo11p contributed significantly to surface hydrophobicity in S. cerevisiae var. diastaticus but not in strain Σ1278b. Sequencing of the FLO11 gene in S. cerevisiae var. diastaticus revealed strain-specific differences, including a 15-amino-acid insertion in the adhesion domain. Flo11p adhesion domains from strain Σ1278b and S. cerevisiae var. diastaticus were expressed and used to coat magnetic beads. The adhesion domain from each strain bound preferentially to homologous cells, and the preferences were independent of the cells in which the adhesion domains were produced. These results are consistent with the idea that strain-specific variations in the amino acid sequences in the adhesion domains cause different Flo11p flocculation activities. The results also imply that strain-specific differences in expression levels, posttranslational modifications, and allelic differences outside the adhesion domains have little effect on flocculation. IMPORTANCE As a nonmotile organism, Saccharomyces cerevisiae employs the cell surface flocculin Flo11/Muc1 as an important means of adapting to environmental change. However, there is a great deal of strain variation in the

  15. Two-dimensional surface strain measurement based on a variation of Yamaguchi's laser-speckle strain gauge

    NASA Technical Reports Server (NTRS)

    Barranger, John P.

    1990-01-01

    A novel optical method of measuring 2-D surface strain is proposed. Two linear strains along orthogonal axes and the shear strain between those axes is determined by a variation of Yamaguchi's laser-speckle strain gage technique. It offers the advantages of shorter data acquisition times, less stringent alignment requirements, and reduced decorrelation effects when compared to a previously implemented optical strain rosette technique. The method automatically cancels the translational and rotational components of rigid body motion while simplifying the optical system and improving the speed of response.

  16. Investigation of a non-contact strain measurement technique

    SciTech Connect

    Talarico, L.J.; Damiano, B.

    1997-03-01

    The goal of this project was to investigate the feasibility of a new non-contact technique for directly and continuously monitoring peak strain in rotating components. The technique utilizes the unique strain-sensitive magnetic material properties of TRansformation Induced Plasticity (TRIP) steel alloys to measure strain. These alloys are weakly magnetic when unstrained but become strongly ferromagnetic after mechanical deformation. A computer study was performed to determine whether the strain-induced change in the magnetic material properties of a TRIP steel gage bonded to a rotating component would cause significant perturbations in the magnetic flux of a stationary electromagnet. The effects of strain level, distance between the rotating component and the stationary electromagnet, and motion-induced eddy currents on flux perturbation magnitude were investigated. The calculated results indicate that a TRIP steel strain sensing element can cause a significant perturbation in the magnetic flux of a stationary electromagnet. The magnetic flux perturbation magnitude was found to be inversely proportional to the distance between the magnet face and the TRIP steel element and directly proportional to the TRIP steel strain level. The effect of motion-induced eddy currents on the magnetic flux was found to be negligible. It appears that the technique can be successfully applied to measure peak strain in rotating components, however, the sensitivity of the magnetic flux perturbation magnitude to the distance between the strain sensing element and the electromagnet may require making an independent proximity measurement.

  17. Gene-related strain variation of Staphylococcus aureus for homologous resistance response to acid stress.

    PubMed

    Lee, Soomin; Ahn, Sooyeon; Lee, Heeyoung; Kim, Won-Il; Kim, Hwang-Yong; Ryu, Jae-Gee; Kim, Se-Ri; Choi, Kyoung-Hee; Yoon, Yohan

    2014-10-01

    This study investigated the effect of adaptation of Staphylococcus aureus strains to the acidic condition of tomato in response to environmental stresses, such as heat and acid. S. aureus ATCC 13565, ATCC 14458, ATCC 23235, ATCC 27664, and NCCP10826 habituated in tomato extract at 35°C for 24 h were inoculated in tryptic soy broth. The culture suspensions were then subjected to heat challenge or acid challenge at 60°C and pH 3.0, respectively, for 60 min. In addition, transcriptional analysis using quantitative real-time PCR was performed to evaluate the expression level of acid-shock genes, such as clpB, zwf, nuoF, and gnd, from five S. aureus strains after the acid habituation of strains in tomato at 35°C for 15 min and 60 min in comparison with that of the nonhabituated strains. In comparison with the nonhabituated strains, the five tomato-habituated S. aureus strains did not show cross protection to heat, but tomato-habituated S. aureus ATCC 23235 showed acid resistance. In quantitative real-time-PCR analysis, the relative expression levels of acid-shock genes (clpB, zwf, nuoF, and gnd) were increased the most in S. aureus ATCC 23235 after 60 min of tomato habituation, but there was little difference in the expression levels among the five S. aureus strains after 15 min of tomato habituation. These results indicate that the variation of acid resistance of S. aureus is related to the expression of acid-shock genes during acid habituation. PMID:25285500

  18. Investigation of high elastoplastic straining of shells of revolution under complex tensile and torque loading

    NASA Astrophysics Data System (ADS)

    Artem'eva, A. A.; Bazhenov, V. G.; Zhegalov, D. V.; Kazakov, D. A.; Nagornykh, E. V.

    2015-11-01

    A method of the numerical solution of nonlinear unsteady problems of axisymmetric elastoplastic straining of shells of revolution with allowance for torque loading at high strains is proposed. The method is based on the geometrically nonlinear theory of the Timoshenko shells and the plasticity theory with due allowance for combined isotropic and kinematic hardening. The problem is solved with the use of the variational difference method. Results of numerical and experimental investigations of elastoplastic straining of cylindrical shells under proportional and sequential kinematic tensile and torque loading are reported.

  19. Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum

    PubMed Central

    Eisen, Michael B.; Pachter, Lior; Brem, Rachel B.

    2014-01-01

    Strain selection and strain improvement are the first, and arguably most important, steps in the industrial production of biological compounds by microorganisms. While traditional methods of mutagenesis and selection have been effective in improving production of compounds at a commercial scale, the genetic changes underpinning the altered phenotypes have remained largely unclear. We utilized high-throughput Illumina short read sequencing of a wild Penicillium chrysogenum strain in order to make whole genome comparisons to a sequenced improved strain (WIS 54–1255). We developed an assembly-free method of identifying chromosomal rearrangements and validated the in silico predictions with a PCR-based assay and Sanger sequencing. Despite many rounds of mutagen treatment and artificial selection, WIS 54–1255 differs from its wild progenitor at only one of the identified rearrangements. We suggest that natural variants predisposed for high penicillin production were instrumental in the success of WIS 54–1255 as an industrial strain. In addition to finding a previously published inversion in the penicillin biosynthesis cluster, we located several genes related to penicillin production associated with these rearrangements. By comparing the configuration of rearrangement events among several historically important strains known to be high penicillin producers to a collection of recently isolated wild strains, we suggest that wild strains with rearrangements similar to those in known high penicillin producers may be viable candidates for further improvement efforts. PMID:24824901

  20. Variation in hemolytic activity of Brachyspira hyodysenteriae strains from pigs.

    PubMed

    Mahu, Maxime; De Pauw, Nele; Vande Maele, Lien; Verlinden, Marc; Boyen, Filip; Ducatelle, Richard; Haesebrouck, Freddy; Martel, An; Pasmans, Frank

    2016-01-01

    Brachyspira hyodysenteriae is the primary cause of swine dysentery, which is responsible for major economic losses to the pig industry worldwide. The hemolytic activity of 10 B. hyodysenteriae strains isolated from stools of pigs with mild to mucohemorrhagic diarrhea was compared and seven hemolysis associated genes were sequenced. Hemolysis induced by these strains varied from strong to near absent. One weakly hemolytic B. hyodysenteriae strain showed sequence changes in five hemolysis associated genes (tlyA, tlyB, hemolysin III, hemolysin activation protein and hemolysin III channel protein) resulting in amino acid substitutions. The occurrence of weakly hemolytic strains identifiable as B. hyodysenteriae should be taken into account in swine dysentery diagnostics. The presence of these strains may affect herd dysentery status, with great impact on a farms trading opportunities. PMID:27338265

  1. Variation in Biofilm Formation among Strains of Listeria monocytogenes

    PubMed Central

    Borucki, Monica K.; Peppin, Jason D.; White, David; Loge, Frank; Call, Douglas R.

    2003-01-01

    Contamination of food by Listeria monocytogenes is thought to occur most frequently in food-processing environments where cells persist due to their ability to attach to stainless steel and other surfaces. Once attached these cells may produce multicellular biofilms that are resistant to disinfection and from which cells can become detached and contaminate food products. Because there is a correlation between virulence and serotype (and thus phylogenetic division) of L. monocytogenes, it is important to determine if there is a link between biofilm formation and disease incidence for L. monocytogenes. Eighty L. monocytogenes isolates were screened for biofilm formation to determine if there is a robust relationship between biofilm formation, phylogenic division, and persistence in the environment. Statistically significant differences were detected between phylogenetic divisions. Increased biofilm formation was observed in Division II strains (serotypes 1/2a and 1/2c), which are not normally associated with food-borne outbreaks. Differences in biofilm formation were also detected between persistent and nonpersistent strains isolated from bulk milk samples, with persistent strains showing increased biofilm formation relative to nonpersistent strains. There were no significant differences detected among serotypes. Exopolysaccharide production correlated with cell adherence for high-biofilm-producing strains. Scanning electron microscopy showed that a high-biofilm-forming strain produced a dense, three-dimensional structure, whereas a low-biofilm-forming strain produced a thin, patchy biofilm. These data are consistent with data on persistent strains forming biofilms but do not support a consistent relationship between enhanced biofilm formation and disease incidence. PMID:14660383

  2. A variational justification of the assumed natural strain formulation of finite elements

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1991-01-01

    The objective is to study the assumed natural strain (ANS) formulation of finite elements from a variational standpoint. The study is based on two hybrid extensions of the Reissner-type functional that uses strains and displacements as independent fields. One of the forms is a genuine variational principle that contains an independent boundary traction field, whereas the other one represents a restricted variational principle. Two procedures for element level elimination of the strain field are discussed, and one of them is shown to be equivalent to the inclusion of incompatible displacement modes. Also, the 4-node C(exp 0) plate bending quadrilateral element is used to illustrate applications of this theory.

  3. A damage detection model for unbonded post-tensioning tendons based on relative strain variation in multi-strand anchors

    NASA Astrophysics Data System (ADS)

    Abdullah, A. B. M.; Rice, Jennifer A.; Hamilton, H. R.

    2014-03-01

    Post-tensioned segmental bridges are common throughout the US; however, in recent years, the incidence of tendon failure in bonded post-tensioned bridges has raised questions regarding their design, construction, and maintenance. These failures have led to the investigation of the applicability of using replaceable unbonded tendons in segmental construction and new methods for monitoring their condition. This paper presents a damage detection algorithm to identify strand breakage in unbonded tendons based on the relative variation of strains in the anchorage. In unbonded construction, the anchorage assembly usually undergoes a severe stress-state condition as the entire prestressing force only passes through the deviator and end anchorage locations. The strain distribution in the anchorage mechanism, therefore, goes through significant changes in response to the breakage of an individual wire or an entire strand in a multi-strand arrangement. In this way, breakage of a post-tensioning strand can be identified by observing a non-uniform variation of the strain field over the anchorage region in contrast to a uniform variation of strains due to environmental or traffic loading. A reduced scale laboratory experiment is performed followed by an extensive finite element simulation to conduct a parametric study with wire/strand breakages at different locations on multi-strand anchorages commonly used in industry. Based on the observed strain variations from simulation, a damage detection model is proposed that enables the adoption of an automated monitoring strategy to characterize the breakage programmatically.

  4. (90377) SEDNA: INVESTIGATION OF SURFACE COMPOSITIONAL VARIATION

    SciTech Connect

    Barucci, M. A.; De Bergh, C.; Merlin, F.; Morea Dalle Ore, C.; Cruikshank, D.; Alvarez-Candal, A.; Dumas, C.

    2010-12-15

    The dwarf planet (90377) Sedna is one of the most remote solar system objects accessible to investigations. To better constrain its surface composition and to investigate the possible heterogeneity of the surface of Sedna, several observations have been carried out at ESO-VLT with the powerful spectrometer SINFONI observing simultaneously the H and K bands. The analyzed spectra (obtained in 2005, 2007, and 2008) show a non-uniform spectral signature, particularly in the K band. Spectral modeling using the Shkuratov radiative transfer code for surface scattering has been performed using the various sets of data, including previous observations at visible wavelengths and photometry at 3.6 and 4.5 {mu}m by the Spitzer Space Telescope. The visible and near-infrared spectra can be modeled with organic materials (triton and titan tholin), serpentine, and H{sub 2}O ice in fairly significant amounts, and CH{sub 4}, N{sub 2}, and C{sub 2}H{sub 6} in varying trace amounts. One of the spectra obtained in 2005 October shows a different signature in the K band and is best modeled with CH{sub 3}OH in place of CH{sub 4}, with reduced amounts of serpentine and with the addition of olivine. The compositional surface heterogeneity can give input on the past history as well clues to the origin of this peculiar, distant object.

  5. Utilization of Genomic Variations Among Xylella fastidiosa Strains for Improved Diagnostic Design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa causes economically important diseases in grapevine, citrus and many other plant species. Our recent whole genome comparative analysis of the four sequenced strains has identified genomic variation among these strains. The...

  6. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.

    PubMed

    Hackett, Jennifer L; Wang, Xiaofei; Smith, Brittny R; Macdonald, Stuart J

    2016-01-01

    Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those

  7. Genetic Variation among Staphylococcus aureus Strains from Norwegian Bulk Milk

    PubMed Central

    Jørgensen, H. J.; Mørk, T.; Caugant, D. A.; Kearns, A.; Rørvik, L. M.

    2005-01-01

    Strains of Staphylococcus aureus obtained from bovine (n = 117) and caprine (n = 114) bulk milk were characterized and compared with S. aureus strains from raw-milk products (n = 27), bovine mastitis specimens (n = 9), and human blood cultures (n = 39). All isolates were typed by pulsed-field gel electrophoresis (PFGE). In addition, subsets of isolates were characterized using multilocus sequence typing (MLST), multiplex PCR (m-PCR) for genes encoding nine of the staphylococcal enterotoxins (SE), and the cloverleaf method for penicillin resistance. A variety of genotypes were observed, and greater genetic diversity was found among bovine than caprine bulk milk isolates. Certain genotypes, with a wide geographic distribution, were common to bovine and caprine bulk milk and may represent ruminant-specialized S. aureus. Isolates with genotypes indistinguishable from those of strains from ruminant mastitis were frequently found in bulk milk, and strains with genotypes indistinguishable from those from bulk milk were observed in raw-milk products. This indicates that S. aureus from infected udders may contaminate bulk milk and, subsequently, raw-milk products. Human blood culture isolates were diverse and differed from isolates from other sources. Genotyping by PFGE, MLST, and m-PCR for SE genes largely corresponded. In general, isolates with indistinguishable PFGE banding patterns had the same SE gene profile and isolates with identical SE gene profiles were placed together in PFGE clusters. Phylogenetic analyses agreed with the division of MLST sequence types into clonal complexes, and isolates within the same clonal complex had the same SE gene profile. Furthermore, isolates within PFGE clusters generally belonged to the same clonal complex. PMID:16332822

  8. Plasticity in bulk metallic glasses investigated via the strain distribution

    SciTech Connect

    Das, Jayanta; Mattern, Norbert; Eckert, Juergen; Bostroem, Magnus; Kvick, Aake; Yavari, Alain Reza; Greer, Alan Lindsay

    2007-09-01

    We measured the atomic-scale elastic strain in order to investigate the yielding of Zr{sub 55}Cu{sub 20}Ni{sub 10}Al{sub 10}Ti{sub 5} and Cu{sub 47.5}Zr{sub 47.5}Al{sub 5} bulk metallic glasses (BMGs) by x-ray synchrotron radiation at room temperature. High resolution strain scanning reveals a deviation from the linear stress-strain relationship at the onset of macroplastic flow. Similar to polycrystalline metals, a saturation of the elastic strain components has been revealed in the case of the ''plastic'' Cu{sub 47.5}Zr{sub 47.5}Al{sub 5} BMG. The results show that the atomic-level elastic strains of the plastic Cu{sub 47.5}Zr{sub 47.5}Al{sub 5} BMG are more homogeneous compared to the 'brittle' Zr{sub 55}Cu{sub 20}Ni{sub 10}Al{sub 10}Ti{sub 5} glass.

  9. Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains.

    PubMed

    Lange, Claudia; Weld, Richard J; Cox, Murray P; Bradshaw, Rosie E; McLean, Kirstin L; Stewart, Alison; Steyaert, Johanna M

    2016-01-01

    Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared to T. cf. atroviride strain LU140 but these strains were found to be highly similar at the DNA sequence level. This unusual combination of phenotypic variability and high DNA sequence similarity between separately isolated strains prompted us to undertake a genome comparison study in order to identify DNA polymorphisms. We further investigated if the polymorphisms had functional effects on the phenotypes. The two strains were clearly identified as individuals, exhibiting different growth rates, conidiation and metabolism. Superior pathogen control demonstrated by LU132 depended on its faster growth, which is a prerequisite for successful distribution and competition. Genome sequencing identified only one non-synonymous single nucleotide polymorphism (SNP) between the strains. Based on this SNP, we successfully designed and validated an RFLP protocol that can be used to differentiate LU132 from LU140 and other Trichoderma strains. This SNP changed the amino acid sequence of SERF, encoded by the previously undescribed single copy gene "small EDRK-rich factor" (serf). A deletion of serf in the two strains did not lead to identical phenotypes, suggesting that, in addition to the single functional SNP between the nearly clonal Trichoderma cf. atroviride strains, other non-genomic factors contribute to their phenotypic variation. This finding is significant as it shows that genomics is an extremely useful but not exhaustive tool for the study of biocontrol complexity and for strain typing. PMID:27190719

  10. Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains

    PubMed Central

    Weld, Richard J.; Cox, Murray P.; Bradshaw, Rosie E.; McLean, Kirstin L.; Stewart, Alison; Steyaert, Johanna M.

    2016-01-01

    Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared to T. cf. atroviride strain LU140 but these strains were found to be highly similar at the DNA sequence level. This unusual combination of phenotypic variability and high DNA sequence similarity between separately isolated strains prompted us to undertake a genome comparison study in order to identify DNA polymorphisms. We further investigated if the polymorphisms had functional effects on the phenotypes. The two strains were clearly identified as individuals, exhibiting different growth rates, conidiation and metabolism. Superior pathogen control demonstrated by LU132 depended on its faster growth, which is a prerequisite for successful distribution and competition. Genome sequencing identified only one non-synonymous single nucleotide polymorphism (SNP) between the strains. Based on this SNP, we successfully designed and validated an RFLP protocol that can be used to differentiate LU132 from LU140 and other Trichoderma strains. This SNP changed the amino acid sequence of SERF, encoded by the previously undescribed single copy gene “small EDRK-rich factor” (serf). A deletion of serf in the two strains did not lead to identical phenotypes, suggesting that, in addition to the single functional SNP between the nearly clonal Trichoderma cf. atroviride strains, other non-genomic factors contribute to their phenotypic variation. This finding is significant as it shows that genomics is an extremely useful but not exhaustive tool for the study of biocontrol complexity and for strain typing. PMID:27190719

  11. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

    PubMed Central

    Zhu, Yuan O.; Sherlock, Gavin; Petrov, Dmitri A.

    2016-01-01

    Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker’s/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation. PMID:27317778

  12. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation.

    PubMed

    Zhu, Yuan O; Sherlock, Gavin; Petrov, Dmitri A

    2016-01-01

    Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker's/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation. PMID:27317778

  13. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.

    PubMed

    van den Broek, M; Bolat, I; Nijkamp, J F; Ramos, E; Luttik, M A H; Koopman, F; Geertman, J M; de Ridder, D; Pronk, J T; Daran, J-M

    2015-09-01

    Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. PMID:26150454

  14. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

    PubMed Central

    van den Broek, M.; Bolat, I.; Nijkamp, J. F.; Ramos, E.; Luttik, M. A. H.; Koopman, F.; Geertman, J. M.; de Ridder, D.; Pronk, J. T.

    2015-01-01

    Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. PMID:26150454

  15. Peculiar Features of Microstructure Formation and Microhardness Variations During Torsional Straining of Tantalum Specimens in Bridgman Anvils

    NASA Astrophysics Data System (ADS)

    Ditenberg, I. A.; Tymentsev, A. N.; Korznikov, A. V.

    2015-04-01

    Using the method of transmission electron microscopy, peculiar features of evolution of microstructure and variations in microhardness of Та are investigated under torsional loading in the Bridgman anvil as a function of plastic deformation at room temperature. A quantitative examination of grain and defect's structure of the material under study and the values of local internal stresses is performed in different loading stages. The mechanisms of formation of submicrocrystalline and nanostructured states are analyzed and so is the microstructure variation as a function of the defect-structure characteristics, strain level, and spacing from the axis of torsion.

  16. Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations

    PubMed Central

    Zheng, Yan-Lin; Wang, Shi-An

    2015-01-01

    The budding yeast Saccharomyces cerevisiae is a platform organism for bioethanol production from various feedstocks and robust strains are desirable for efficient fermentation because yeast cells inevitably encounter stressors during the process. Recently, diverse S. cerevisiae lineages were identified, which provided novel resources for understanding stress tolerance variations and related shaping factors in the yeast. This study characterized the tolerance of diverse S. cerevisiae strains to the stressors of high ethanol concentrations, temperature shocks, and osmotic stress. The results showed that the isolates from human-associated environments overall presented a higher level of stress tolerance compared with those from forests spared anthropogenic influences. Statistical analyses indicated that the variations of stress tolerance were significantly correlated with both ecological sources and geographical locations of the strains. This study provides guidelines for selection of robust S. cerevisiae strains for bioethanol production from nature. PMID:26244846

  17. Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations.

    PubMed

    Zheng, Yan-Lin; Wang, Shi-An

    2015-01-01

    The budding yeast Saccharomyces cerevisiae is a platform organism for bioethanol production from various feedstocks and robust strains are desirable for efficient fermentation because yeast cells inevitably encounter stressors during the process. Recently, diverse S. cerevisiae lineages were identified, which provided novel resources for understanding stress tolerance variations and related shaping factors in the yeast. This study characterized the tolerance of diverse S. cerevisiae strains to the stressors of high ethanol concentrations, temperature shocks, and osmotic stress. The results showed that the isolates from human-associated environments overall presented a higher level of stress tolerance compared with those from forests spared anthropogenic influences. Statistical analyses indicated that the variations of stress tolerance were significantly correlated with both ecological sources and geographical locations of the strains. This study provides guidelines for selection of robust S. cerevisiae strains for bioethanol production from nature. PMID:26244846

  18. Investigation of spatial variations in collection efficiency of solar cells

    NASA Astrophysics Data System (ADS)

    Hiltner, Jason Fredrick

    2001-11-01

    In an effort to investigate spatial variations in solar cells, an apparatus which is capable of mapping collection efficiency with micron resolution and near- solar intensity has been developed. Local reductions in collection are observed in CdTe- and Cu(In1- xGax)Se2- based devices, and are characterized by measuring the response as a function of cell bias and incident laser intensity. By modeling this data with an equivalent circuit, it is clear that the majority of local variations in the response are due to series resistance variations. Further, direct evidence is given for bandgap variations in CdTe solar cells, which are correlated with high resistance regions in some devices. The bandgap variation is attributed to diffusion of S into CdTe, forming the lower bandgap CdTe1- xSx, during the post-deposition CdCl2 treatment commonly used to improve performance. Investigation of the impact of CdCl2 on a CdTe solar cell indicates that the treatment reduces the number of variations seen with above-bandgap photon energies, but also increases local variations in bandgap. The latter effect has been attributed to non-uniform penetration of CdCl2 to the device interface. Finally, elevated-temperature stress on CdTe devices is shown to preferentially degrade regions which exhibit decreases in bandgap, and hence increased S alloying.

  19. Expression and strain variation of the novel “small open reading frame” (smorf) multigene family in Babesia bovis

    PubMed Central

    Ferreri, Lucas M.; Brayton, Kelly A.; Sondgeroth, Kerry S.; Lau, Audrey O.T.; Suarez, Carlos E.; McElwain, Terry F.

    2012-01-01

    Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characterised the general topology of smorf genes and investigated the gene repertoire, transcriptional profile and SMORF expression in two distinct strains, T2Bo and Mo7. Sequence analysis using degenerate primers identified additional smorf genes in each strain and demonstrated that the smorf gene repertoire varies between strains, with conserved and unique genes in both. Smorf genes have multiple semi-conserved and variable blocks, and a large hypervariable insertion in 20 of the 44 genes defines two major branches of the family, termed smorf A and smorf B. A total of 32 smorf genes are simultaneously transcribed in T2Bo strain B. bovis merozoites obtained from deep brain tissue of an acutely infected animal. SMORF peptide-specific antiserum bound in immunoblots to multiple proteins with a range of sizes predicted by smorf genes, confirming translation of smorf gene products from these transcripts. These results indicate that the smorf multigene family is larger than previously described and demonstrate that smorf genes are expressed and are undergoing variation, both within strains and in a lineage-specific pattern independent of strain specificity. The function of these novel proteins is unknown. PMID:22138017

  20. The generation gap: Proteome changes and strain variation during encystation in Giardia duodenalis.

    PubMed

    Emery, Samantha J; Pascovi, Dana; Lacey, Ernest; Haynes, Paul A

    2015-05-01

    The prevalence of Giardia duodenalis in humans is partly owed to its direct and simple life cycle, as well as the formation of the environmentally resistant and infective cysts. Proteomic and transcriptomic studies have previously analysed the encystation process using the well-characterised laboratory genomic strain, WB C6. This study presents the first quantitative study of encystation using pathogenically relevant and alternative assemblage A strains: the human-derived BRIS/82/HEPU/106 (H-106)and avian-derived BRIS/95/HEPU/2041 (B-2041). We utilised tandem MS/MS with a label-free quantitative approach to compare cysts and trophozoite life stages for strain variation, as well as confirm universal encystation markers of assemblage A. A total of 1061 non-redundant proteins were identified from both strains, including trophozoite- and cyst-specific proteomes and life-stage differentially expressed proteins. Additionally, 24 proteins previously classified in the literature as encystation-specific were confirmed as strain-independent markers of encystation. Functional cluster analysis of differentially expressed proteins saw significant overlap between strains, including protein trafficking and localisation in cysts, NEK kinase function, and carbohydrate metabolism in trophozoites. Two significant points of strain specific adaptations in cysts were also identified. B-2041 possessed major up-regulation of the ankyrin repeat protein 21.1 family compared to H-106. Furthermore, cysts of B-2041 retained near-complete VSP variant diversity between cysts and trophozoites, while H-106 lost 45% of its VSP variant diversity between life cycle stages, a constriction previously observed in studies of WB C6. This is the first report of strain variation in the cyst stage in G. duodenalis, and highlights cyst variation and its impacts on reinfection and life cycle success. PMID:26045354

  1. Investigation into the strain tolerance of BSCCO composite tapes

    SciTech Connect

    Gherardi, L.; Caracino, P.; Metra, P.; Vellego, G.

    1994-12-31

    Intense research activity carried out worldwide has led to the development of high {Tc} superconducting tapes with electrical performances closer and closer to those required for power cables applications. In this perspective, the mechanical behavior of these tapes, which is known to be intrinsically rather poor, can turn out to be a critical factor. Mono and multifilamentary composite (silver sheathed) BSCCO tapes have been tested using a specially designed apparatus. The dependence of critical current on stress and strain has been investigated for different configurations, and possible models have been considered taking into account the structural parameters as well as the thermal history of the composite tapes. In particular, the effect of the pre-compression which is assumed to be imposed to the superconductor by the silver sheath during cool down has been analyzed. The comparison between experimentally determined maximum tolerable stress and strain of present tapes, and values typically required during cable manufacturing, handling and service conditions, is discussed. Possible ways to improve the strain tolerance of superconducting tapes are analyzed.

  2. Kinetic Monte Carlo investigation of tetragonal strain on Onsager matrices

    NASA Astrophysics Data System (ADS)

    Li, Zebo; Trinkle, Dallas R.

    2016-05-01

    We use three different methods to compute the derivatives of Onsager matrices with respect to strain for vacancy-mediated multicomponent diffusion from kinetic Monte Carlo simulations. We consider a finite difference method, a correlated finite difference method to reduce the relative statistical errors, and a perturbation theory approach to compute the derivatives. We investigate the statistical error behavior of the three methods for uncorrelated single vacancy diffusion in fcc Ni and for correlated vacancy-mediated diffusion of Si in Ni. While perturbation theory performs best for uncorrelated systems, the correlated finite difference method performs best for the vacancy-mediated Si diffusion in Ni, where longer trajectories are required.

  3. GENETIC VARIATION MEASURED BY MICROSATELLITES AMONG THREE STRAINS OF DOMESTICATED RAINBOW TROUT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement the degree of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Here three strains of rainbow tro...

  4. Measurements of Local Strain Variation in Si(1-x)Ge(x)/Si Heterostructures

    NASA Technical Reports Server (NTRS)

    Bell, L. D.; Kaiser, W. J.; Manion, S. J.; Milliken, S. J.; Pike, W. T.; Fathauer, R. W.

    1995-01-01

    The energy splitting of the conduction-band minimum of Si(1-x), Ge(x), due to strain has been directly measured by the application of ballistic-electron-emission microscope (BEEM) spectroscopy to Ag/Si(1-x), Ge(x) structures. Experimental values for this conduction-band splitting agree well with calculations. For Au/Si(1-x), Ge(x), however, heterogeneity in the strain of the Si(1-x), Ge(x) layer is introduced by deposition of the Au. This variation is attributed to species interdiffusion, which produces a rough Si(1-x)Ge(x) surface. Preliminary modeling indicates that the observed roughness is consistent with the strain variation measured by BEEM.

  5. Investigation on strain sensing properties of carbon-based nanocomposites for structural aircraft applications

    NASA Astrophysics Data System (ADS)

    Lamberti, Patrizia; Spinelli, Giovanni; Tucci, Vincenzo; Guadagno, Liberata; Vertuccio, Luigi; Russo, Salvatore

    2016-05-01

    The mechanical and electrical properties of a thermosetting epoxy resin particularly indicated for the realization of structural aeronautic components and reinforced with multiwalled carbon nanotubes (MWCNTs, at 0.3 wt%) are investigated for specimens subjected to cycles and different levels of applied strain (i.e. ɛ) loaded both in axial tension and flexural mode. It is found that the piezoresistive behavior of the resulting nanocomposite evaluated in terms of variation of the electrical resistance is strongly affected by the applied mechanical stress mainly due to the high sensibility and consequent rearrangement of the electrical percolating network formed by MWCNTs in the composite at rest or even under a small strain. In fact, the variations in electrical resistance that occur during the mechanical stress are correlated to the deformation exhibited by the nanocomposites. In particular, the overall response of electrical resistance of the composite is characterized by a linear increase with the strain at least in the region of elastic deformation of the material in which the gauge factor (i.e. G.F.) of the sensor is usually evaluated. Therefore, the present study aims at investigating the possible use of the nanotechnology for application of embedded sensor systems in composite structures thus having capability of self-sensing and of responding to the surrounding environmental changes, which are some fundamental requirements especially for structural aircraft monitoring applications.

  6. A Quantitative Investigation of Stakeholder Variation in Training Program Evaluation.

    ERIC Educational Resources Information Center

    Michalski, Greg V.

    A survey was conducted to investigate variation in stakeholder perceptions of training results and evaluation within the context of a high-technology product development firm (the case organization). A scannable questionnaire survey booklet was developed and scanned data were exported and analyzed. Based on an achieved sample of 280 (70% response…

  7. Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains.

    PubMed

    Lewis, Jeffrey A; Broman, Aimee T; Will, Jessica; Gasch, Audrey P

    2014-09-01

    Natural variation in gene expression is pervasive within and between species, and it likely explains a significant fraction of phenotypic variation between individuals. Phenotypic variation in acute systemic responses can also be leveraged to reveal physiological differences in how individuals perceive and respond to environmental perturbations. We previously found extensive variation in the transcriptomic response to acute ethanol exposure in two wild isolates and a common laboratory strain of Saccharomyces cerevisiae. Many expression differences persisted across several modules of coregulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. Here, we conducted expression QTL mapping of the ethanol response in two strain crosses to identify the genetic basis for these differences. To understand systemic differences, we focused on "hotspot" loci that affect many transcripts in trans. Candidate causal regulators contained within hotspots implicate upstream regulators as well as downstream effectors of the ethanol response. Overlap in hotspot targets revealed additive genetic effects of trans-acting loci as well as "epi-hotspots," in which epistatic interactions between two loci affected the same suites of downstream targets. One epi-hotspot implicated interactions between Mkt1p and proteins linked to translational regulation, prompting us to show that Mkt1p localizes to P bodies upon ethanol stress in a strain-specific manner. Our results provide a glimpse into the genetic architecture underlying natural variation in a stress response and present new details on how yeast respond to ethanol stress. PMID:24970865

  8. The variation of the yield stress of Ti alloys with strain rate at high temperatures

    SciTech Connect

    Rosen, R.S.; Paddon, S.P.; Kassner, M.E.

    1999-06-01

    This study extended investigation on the elevated-temperature yield-strength dependence of beta-phase titanium alloys on strain rate and temperature. Yield stresses were found to increase substantially with increasing strain rate at elevated temperatures due to the high strain-rate sensitivity of titanium at high temperatures. Above 1000 C, the strain-rate sensitivities were found to increase substantially with increasing temperature and/or decreasing strain rate. The six alloys examined were TIMETAL 21S, Ti-15-3-, Ti-6-4, Ti-13-11-3, Beta C, and Beta III. There was particular interest in determining the strain-rate sensitivity of these alloys through strain-rate change tests above 1000 C. The yield stresses of all the titanium alloys at temperatures above 1093 C were less than 1% of their ambient temperature values. strain hardening was negligible in the alloys tested at these high temperatures. Extended tensile ductilities of 100 to 200% were observed due to the pronounced strain-rare sensitivity. The rate controlling mechanism for plasticity, based on activation energy and the strain-rate sensitivity measurements, is discussed.

  9. Strain variation in microalgal lipid production during mixotrophic growth with glycerol.

    PubMed

    Paranjape, Kiran; Leite, Gustavo B; Hallenbeck, Patrick C

    2016-03-01

    Algal cultivation at high latitudes is challenged by the relatively low annual solar flux. One possible scenario to overcome this limitation is the use of mixotrophic growth to potentially boost biomass and lipid production. Here the effect of glycerol addition on the growth and lipid production by twelve indigenous microalgae was examined. The results show that there is considerable strain dependent variation in the maximum growth rate under mixotrophic conditions with the addition of glycerol causing in some cases up to a 2.4-fold increase in growth rate and a up to a 1.9-fold increase in biomass. In addition, glycerol increased total lipid production 40-60% in some strains. These results also show the value in screening culture collections for desired traits independent of strain identification since here one (PCH02) of the five Chlorella strains showed a large increase in lipid with glycerol. PMID:26773947

  10. Genomic variations associated with attenuation in Mycobacterium avium subsp. paratuberculosis vaccine strains

    PubMed Central

    2013-01-01

    Background Mycobacterium avium subspecies paratuberculosis (MAP) whole cell vaccines have been widely used tools in the control of Johne’s disease in animals despite being unable to provide complete protection. Current vaccine strains derive from stocks created many decades ago; however their genotypes, underlying mechanisms and relative degree of their attenuation are largely unknown. Results Using mouse virulence studies we confirm that MAP vaccine strains 316 F, II and 2e have diverse but clearly attenuated survival and persistence characteristics compared with wild type strains. Using a pan genomic microarray we characterise the genomic variations in a panel of vaccine strains sourced from stocks spanning over 40 years of maintenance. We describe multiple genomic variations specific for individual vaccine stocks in both deletion (26–32 Kbp) and tandem duplicated (11–40 Kbp) large variable genomic islands and insertion sequence copy numbers. We show individual differences suitable for diagnostic differentiation between vaccine and wild type genotypes and provide evidence for functionality of some of the deleted MAP-specific genes and their possible relation to attenuation. Conclusions This study shows how culture environments have influenced MAP genome diversity resulting in large tandem genomic duplications, deletions and transposable element activity. In combination with classical selective systematic subculture this has led to fixation of specific MAP genomic alterations in some vaccine strain lineages which link the resulting attenuated phenotypes with deficiencies in high reactive oxygen species handling. PMID:23339684

  11. Durability investigation of a group of strain gage pressure transducers

    NASA Technical Reports Server (NTRS)

    Lederer, P. S.; Hilten, J. S.

    1972-01-01

    A durability investigation was conducted on a group of eighteen bonded-wire strain gage pressure transducers with ranges of 0 to 15 psig and 0 to 100 psig using an improved version of a previously developed technique. Some of the transducers were subjected to 40 million pressure cycles at a 5-Hz rate at laboratory ambient conditions, others were cycled at a temperature of 150 F (65.6 C). The largest change in sensitivity observed was 0.22% for a 100-psig transducer subjected to 40 million pressure cycles at 150 F. The largest change in zero pressure output observed was 0.91% FS for the same transducer. None of the transducers failed completely as a result of cycling at or below full scale pressure.

  12. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains.

    PubMed

    Mostafavi, Sara; Ortiz-Lopez, Adriana; Bogue, Molly A; Hattori, Kimie; Pop, Cristina; Koller, Daphne; Mathis, Diane; Benoist, Christophe

    2014-11-01

    To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others. PMID:25267973

  13. Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium

    PubMed Central

    Parkinson, John E.; Baumgarten, Sebastian; Michell, Craig T.; Baums, Iliana B.; LaJeunesse, Todd C.; Voolstra, Christian R.

    2016-01-01

    Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages (“Clades A–I”) and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades—the equivalent of contrasting genera or families in other dinoflagellate groups—making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host–symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms. PMID:26868597

  14. Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium.

    PubMed

    Parkinson, John E; Baumgarten, Sebastian; Michell, Craig T; Baums, Iliana B; LaJeunesse, Todd C; Voolstra, Christian R

    2016-03-01

    Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages ("Clades A-I") and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades-the equivalent of contrasting genera or families in other dinoflagellate groups-making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host-symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms. PMID:26868597

  15. Vertical AMS variation within basalt flow profiles from the Xitle volcano (Mexico) as indicator of heterogeneous strain in lava flows

    NASA Astrophysics Data System (ADS)

    Caballero-Miranda, C. I.; Alva-Valdivia, L. M.; González-Rangel, J. A.; Gogitchaishvili, A.; Urrutia-Fucugauchi, J.; Kontny, A.

    2016-02-01

    The within-flow vertical variation of anisotropy of the magnetic susceptibility (AMS) of three basaltic flow profiles from the Xitle volcano were investigated in relation to the lava flow-induced shear strain. Rock magnetic properties and opaque microscopy studies have shown that the magnetic mineralogy is dominated by Ti-poor magnetite with subtle vertical variations in grain size distribution: PSD grains dominate in a thin bottommost zone, and from base to top from PSD-MD to PSD-SD grains are found. The vertical variation of AMS principal direction patterns permitted identification of two to three main lava zones, some subdivided into subzones. The lower zone is very similar in all profiles with the magnetic foliation dipping toward the flow source, whereas the upper zone has magnetic foliation dipping toward the flow direction or alternates between dipping against and toward the flow direction. The K1 (maximum AMS axis) directions tend to be mostly parallel to the flow direction in both zones. The middle zone shows AMS axes diverging among profiles. We present heterogeneous strain ellipse distribution models for different flow velocities assuming similar viscosity to explain the AMS directions and related parameters of each zone. Irregular vertical foliations and transverse to flow lineation of a few samples at the bottommost and topmost part of profiles suggest SD inverse fabric, levels of intense friction, or degassing effects in AMS orientations.

  16. Analysis of transverse shear strains in pre-twisted thick beams using variational asymptotic method

    SciTech Connect

    Ameen, Maqsood M.; Harursampath, Dineshkumar E-mail: dinesh@aero.iisc.ernet.in

    2015-03-10

    The cross-sectional stiffness matrix is derived for a pre-twisted, moderately thick beam made of transversely isotropic materials and having rectangular cross sections. An asymptotically-exact methodology is used to model the anisotropic beam from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy is computed making use of the beam constitutive law and kinematical relations derived with the inclusion of geometrical nonlinearities and an initial twist. The energy functional is minimized making use of the Variational Asymptotic Method (VAM), thereby reducing the cross section to a point on the beam reference line with appropriate properties, forming a 1-D constitutive law. VAM is a mathematical technique employed in the current problem to rigorously split the 3-D analysis of beams into two: a 2-D analysis over the beam cross-sectional domain, which provides a compact semi-analytical form of the properties of the cross sections, and a nonlinear 1-D analysis of the beam ref-erence curve. In this method, as applied herein, the cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged in orders of the small parameters. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that render the 1-D strain measures well-defined. The zeroth-order 3-D warping field thus yielded is then used to integrate the 3-D strain energy density over the cross section, resulting in the 1-D strain energy density, which in turn helps identify the corresponding cross-sectional stiffness matrix. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

  17. End-point disease investigation for virus strains of intermediate virulence as illustrated by flavivirus infections.

    PubMed

    Suen, Willy W; Prow, Natalie A; Setoh, Yin X; Hall, Roy A; Bielefeldt-Ohmann, Helle

    2016-02-01

    Viruses of intermediate virulence are defined as isolates causing an intermediate morbidity/mortality rate in a specific animal model system, involving specific host and inoculation parameters (e.g. dose and route). Therefore, variable disease phenotype may exist between animals that develop severe disease or die and those that are asymptomatic or survive after infection with these isolates. There may also be variability amongst animals within each of these subsets. Such potential variability may confound the use of time-point sacrifice experiments to investigate pathogenesis of this subset of virus strains, as uniformity in disease outcome is a fundamental assumption for time-course sacrifice experiments. In the current study, we examined the disease phenotype, neuropathology, neural infection and glial cell activity in moribund/dead and surviving Swiss white (CD-1) mice after intraperitoneal infection with various Australian flaviviruses, including West Nile virus (WNV) strains of intermediate virulence (WNVNSW2011 and WNVNSW2012), and highly virulent Murray Valley encephalitis virus (MVEV) isolates. We identified notable intragroup variation in the end-point disease in mice infected with either WNVNSW strain, but to a lesser extent in mice infected with MVEV strains. The variable outcomes associated with WNVNSW infection suggest that pathogenesis investigations using time-point sacrifice of WNVNSW-infected mice may not be the best approach, as the assumption of uniformity in outcomes is violated. Our study has therefore highlighted a previously unacknowledged challenge to investigating pathogenesis of virus isolates of intermediate virulence. We have also set a precedent for routine examination of the disease phenotype in moribund/dead and surviving mice during survival challenge experiments. PMID:26614392

  18. A variational justification of the assumed natural strain formulation of finite elements. I - Variational principles. II - The C(0) four-node plate element

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1990-01-01

    The assumed natural strain formulation of finite elements is interpreted from a variational standpoint. The approach is based on hybrid extensions of the Reissner-type functional which uses the strains and displacements as independent fields. Consideration is restricted to linear elasticity. The four-node C(0) plate-bending quadrilateral is used as a specific example to illustrate the application of the present interpretation. A key finding is that any change in the strain-displacement interpolation from the variationally consistent interpolation must be associated in some way to the addition of incompatible displacement modes.

  19. Additional Investigations of Ice Shape Sensitivity to Parameter Variations

    NASA Technical Reports Server (NTRS)

    Miller, Dean R.; Potapczuk, Mark G.; Langhals, Tammy J.

    2006-01-01

    A second parameter sensitivity study was conducted at the NASA Glenn Research Center's Icing Research Tunnel (IRT) using a 36 in. chord (0.91 m) NACA-0012 airfoil. The objective of this work was to further investigate the feasibility of using ice shape feature changes to define requirements for the simulation and measurement of SLD and appendix C icing conditions. A previous study concluded that it was feasible to use changes in ice shape features (e.g., ice horn angle, ice horn thickness, and ice shape mass) to detect relatively small variations in icing spray condition parameters (LWC, MVD, and temperature). The subject of this current investigation extends the scope of this previous work, by also examining the effect of icing tunnel spray-bar parameter variations (water pressure, air pressure) on ice shape feature changes. The approach was to vary spray-bar water pressure and air pressure, and then evaluate the effects of these parameter changes on the resulting ice shapes. This paper will provide a description of the experimental method, present selected experimental results, and conclude with an evaluation of these results.

  20. The Use of High-Throughput DNA Sequencing in the Investigation of Antigenic Variation: Application to Neisseria Species

    PubMed Central

    Davies, John K.; Harrison, Paul F.; Lin, Ya-Hsun; Bartley, Stephanie; Khoo, Chen Ai; Seemann, Torsten; Ryan, Catherine S.; Kahler, Charlene M.; Hill, Stuart A.

    2014-01-01

    Antigenic variation occurs in a broad range of species. This process resembles gene conversion in that variant DNA is unidirectionally transferred from partial gene copies (or silent loci) into an expression locus. Previous studies of antigenic variation have involved the amplification and sequencing of individual genes from hundreds of colonies. Using the pilE gene from Neisseria gonorrhoeae we have demonstrated that it is possible to use PCR amplification, followed by high-throughput DNA sequencing and a novel assembly process, to detect individual antigenic variation events. The ability to detect these events was much greater than has previously been possible. In N. gonorrhoeae most silent loci contain multiple partial gene copies. Here we show that there is a bias towards using the copy at the 3′ end of the silent loci (copy 1) as the donor sequence. The pilE gene of N. gonorrhoeae and some strains of Neisseria meningitidis encode class I pilin, but strains of N. meningitidis from clonal complexes 8 and 11 encode a class II pilin. We have confirmed that the class II pili of meningococcal strain FAM18 (clonal complex 11) are non-variable, and this is also true for the class II pili of strain NMB from clonal complex 8. In addition when a gene encoding class I pilin was moved into the meningococcal strain NMB background there was no evidence of antigenic variation. Finally we investigated several members of the opa gene family of N. gonorrhoeae, where it has been suggested that limited variation occurs. Variation was detected in the opaK gene that is located close to pilE, but not at the opaJ gene located elsewhere on the genome. The approach described here promises to dramatically improve studies of the extent and nature of antigenic variation systems in a variety of species. PMID:24466206

  1. Strain-dependent variations in visceral sensitivity: relationship to stress, anxiety and spinal glutamate transporter expression.

    PubMed

    Moloney, R D; Dinan, T G; Cryan, J F

    2015-04-01

    Responses to painful stimuli differ between populations, ethnic groups, sexes and even among individuals of a family. However, data regarding visceral pain are still lacking. Thus, we investigated differences in visceral nociception across inbred and outbred mouse strains using colorectal distension. Anxiety and depression-like behaviour were assessed using the open field and forced swim test as well as the corticosterone stress response. Possible mechanistic targets [excitatory amino acid transporter (EAAT-1), brain-derived neurotrophic factor (BDNF) and 5HT1A receptor] were also assessed using quantitative real-time polymerase chain reaction. Adult, male, inbred and outbred mouse strains were used in all assays (inbred strains; CBA/J Hsd, C3H/HeNHsd, BALB/c OlaHsd, C57 BL/6JOlaHsd, DBA/2J RccHsd, CAST/EiJ, SM/J, A/J OlaHsd, 129P2/OlaHsd, FVB/NHan Hsd and outbred strains: Swiss Webster, CD-1). mRNA expression levels of EAAT-1, BDNF and 5HT1A receptor (HTR1A) were quantified in the lumbosacral spinal cord, amygdala and hippocampus. A significant effect of strain was found in visceral sensitivity, anxiety and depressive-like behaviours. Strain differences were also seen in both baseline and stress-induced corticosterone levels. CBA/J mice consistently exhibited heightened visceral sensitivity, anxiety behaviour and depression-like behaviour which were associated with decreased spinal EAAT-1 and hippocampal BDNF and HTR1A. Our results show the CBA/J mouse strain as a novel mouse model to unravel the complex mechanisms of brain-gut axis disorders such as irritable bowel syndrome, in particular the underlying mechanisms of visceral hypersensitivity, for which there is great need. Furthermore, this study highlights the importance of genotype and the consequences for future development of transgenic strains in pain research. PMID:25851919

  2. Spatial and Temporal Variations in Strain Rates in the Western Transverse Ranges, California

    NASA Astrophysics Data System (ADS)

    Marshall, S. T.; Funning, G. J.; Owen, S. E.

    2012-12-01

    We determine the spatial and temporal variations in strain rates in the Transverse Ranges of southern California by combing data from 52 continuous GPS sites in the Plate Boundary Observatory network with InSAR time series. To characterize periodic seasonal motions in the GPS time series, phases and amplitudes of annual and semiannual motions are estimated for each GPS station. We remove these seasonal terms, and then perform Principal Component Analysis on the residual time series to remove common-mode errors. We find that seasonal GPS motions are not strongly dependent on local substrate geology. To quantify the spatial patterns of deformation in greater detail than GPS can provide, we use a persistent scatterer InSAR (PSI) data set comprised of 23 ENVISAT ASAR scenes. The PSI data were derived using the software package, StaMPS [Hooper et al. 2004]. The PSI data show potential anthropogenic subsidence in the Oxnard/Ventura area as well as at a location just south of the Oak Ridge. A highly localized zone of subsidence is also present along the Ventura Avenue anticline, where ongoing petroleum extraction is occurring. Comparison of the InSAR and the GPS projected into the InSAR line of sight, shows general agreement. The relative lack of significant non-tectonic motions in the western Transverse Ranges is in stark contrast to the nearby Los Angeles basin where anthropogenic motions dominate many InSAR scenes. To determine the local tectonic deformation rates, we remove strain associated with the nearby San Andreas fault using a rectangular dislocation model. Direct inversion of the GPS velocities into a triangulated network with variable strain/rotation rates produces a generalized map of variations in tectonic strain rates. The strain rate map shows the largest strain rates to be near the central Ventura basin with rates generally decreasing westward towards the Santa Barbara Channel. To determine compatible regional fault slip rates, we use a forward mechanical

  3. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

    PubMed

    Brunk, Elizabeth; George, Kevin W; Alonso-Gutierrez, Jorge; Thompson, Mitchell; Baidoo, Edward; Wang, George; Petzold, Christopher J; McCloskey, Douglas; Monk, Jonathan; Yang, Laurence; O'Brien, Edward J; Batth, Tanveer S; Martin, Hector Garcia; Feist, Adam; Adams, Paul D; Keasling, Jay D; Palsson, Bernhard O; Lee, Taek Soon

    2016-05-25

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks. PMID:27211860

  4. Phenotypic variation amongst genotypically homogeneous Legionella pneumophila serogroup 1 isolates: implications for the investigation of outbreaks of Legionnaires' disease.

    PubMed Central

    Harrison, T. G.; Saunders, N. A.; Haththotuwa, A.; Hallas, G.; Birtles, R. J.; Taylor, A. G.

    1990-01-01

    One hundred and seventy-nine isolates of Legionella pneumophila serogroup 1, obtained from a site associated with an outbreak of Legionnaires' disease, were examined by monoclonal antibody subgrouping, restriction fragment length polymorphism typing, restriction endonuclease analysis and plasmid content. Nine distinct phenotypes were detected but at the genotypic level all strains were closely related. The data presented indicate that phenotypic variation of a single parent strain can occur within an environmental site. The implications of these findings are discussed in relation to the investigation of outbreaks of Legionnaires' disease. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:1969803

  5. The influence of climatically-driven surface loading variations on continental strain and seismicity

    NASA Astrophysics Data System (ADS)

    Craig, Tim; Calais, Eric; Fleitout, Luce; Bollinger, Laurent; Scotti, Oona

    2016-04-01

    In slowly deforming regions of plate interiors, secondary sources of stress and strain can result in transient deformation rates comparable to, or greater than, the background tectonic rates. Highly variable in space and time, these transients have the potential to influence the spatio-temporal distribution of seismicity, interfering with any background tectonic effects to either promote or inhibit the failure of pre-existing faults, and potentially leading to a clustered, or 'pulse-like', seismic history. Here, we investigate the ways in which the large-scale deformation field resulting from climatically-controlled changes in surface ice mass over the Pleistocene and Holocene may have influenced not only the seismicity of glaciated regions, but also the wider seismicity around the ice periphery. We first use a set of geodynamic models to demonstrate that a major pulse of seismic activity occurring in Fennoscandia, coincident with the time of end-glaciation, occurred in a setting where the contemporaneous horizontal strain-rate resulting from the changing ice mass, was extensional - opposite to the reverse sense of coseismic displacement accommodated on these faults. Therefore, faulting did not release extensional elastic strain that was building up at the time of failure, but compressional elastic strain that had accumulated in the lithosphere on timescales longer than the glacial cycle, illustrating the potential for a non-tectonic trigger to tap in to the background tectonic stress-state. We then move on to investigate the more distal influence that changing ice (and ocean) volumes may have had on the evolving strain field across intraplate Europe, how this is reflected in the seismicity across intraplate Europe, and what impact this might have on the paleoseismic record.

  6. Investigations on color variations of Morpho rhetenor butterfly wing scales

    NASA Astrophysics Data System (ADS)

    Liao, Guanglan; Zuo, Haibo; Jiang, Xuan; Yang, Xuefeng; Shi, Tielin

    2012-12-01

    Experiments and simulations are carried out to investigate the optical properties of Morpho rhetenor butterfly wing scales. The upper surface of a male Morpho rhetenor butterfly wing presents a single-layer of scales, the microstructures of which are responsible for the brilliant blue color. The color varies from cyan blue to yellow green and soon afterwards returns back to cyan blue when some ethanol is dropped on the upper surface. At the start of the ethanol volatilization process, the reflection spectrum remains stable. As the ethanol further volatilizes, the peak reflectance decreases slightly, then increases dramatically. Meanwhile, the peak wavelength keeps approximately constant, then decreases, and keeps almost stable at the end of the process. Therefore, the optical properties depend strongly on the varying ambient conditions, including the refractive index and the thickness of the packing medium. Moreover, the possible causes for the scales in dark green region after several dropping ethanol experiments are clarified. This research benefits our understanding of the color variation mechanisms of the wing scales, and provides inspiration for further studies and applications.

  7. Age- and Strain- Dependent Influences of Morphine on Mouse Social Investigation Behavior

    PubMed Central

    Kennedy, Bruce C.; Panksepp, Jules B.; Wong, Jenny C.; Krause, Emily J.; Lahvis, Garet P.

    2011-01-01

    Opioid-coded neural circuits play a substantial role in how individuals respond to drugs of abuse, and most individuals begin using such drugs during adolescence and within a social context. Several studies indicate that adolescent mice exhibit a heightened sensitivity to the effects of morphine, the prototypical opiate drug, when compared with adults, but it is unclear whether these developmental differences are related to aspects of motivated behavior. Moreover, exposure to opioids within the rodent brain can alter the expression of social behavior, yet little is known about whether this relationship changes as a function of development or genetic variation. In this study, we conducted a series of experiments to characterize the relationship between genetic background, adolescent development and morphine-induced changes in mouse social investigation (SI). At two time-points during adolescent development (postnatal day [PD] 25 and 45), social interactions of test mice of the gregarious C57BL/6J (B6) strain were more tolerant to the suppressive effects of morphine (ED50 = 0.97 and 2.17 mg/kg morphine, respectively) than test mice from the less social BALB/cJ (BALB) strain (ED50 = 0.61 and 0.91 mg/kg morphine, respectively). By contrast, this strain-dependent difference was not evident among adult mice on PD 90 (ED50 = 1.07 and 1.41 mg/kg morphine for BALB and B6 mice, respectively). An additional experiment demonstrated that the ability of morphine to alter social responsiveness was not directly related to drug-induced changes in locomotor behavior. Finally, administration of morphine to stimulus mice on PD 25 reduced social interaction of test mice only when individuals were from the B6 genetic background. Overall, these results indicate that alterations in endogenous opioid systems are related to changes in SI that occur during adolescence and that morphine administration may mimic the rewarding nature of SI. PMID:21358324

  8. Strain in Hydrogen-Implanted Si Investigated Using Dark-Field Electron Holography

    NASA Astrophysics Data System (ADS)

    Cherkashin, Nikolay; Reboh, Shay; Lubk, Axel; Hÿtch, Martin J.; Claverie, Alain

    2013-09-01

    The microstructure of ion-implanted crystals is profoundly dictated by mechanical strain developing in interplay with structural defects. Understanding the origin of strain during the early stages of development is challenging and requires accurate measurements and modeling. Here, we investigate the mechanical strain in H-implanted Si. X-ray diffraction analysis is performed to measure the mesoscopic out-of-plane strain and dark-field electron holography to map strain in two-dimensions (2D) with nanometer spatial resolution. Supported by finite element method modeling, we propose that the mean strain field is explained by overlapping and averaging discrete strain fields generated by sub-nanoscopic defects that are intimately related to the H depth concentration.

  9. Experimental Investigations of Woven Textile Tape as Strain Sensor

    NASA Astrophysics Data System (ADS)

    Kannaian, T.; Naveen, V. S.; Muthukumar, N.; Thilagavathi, G.

    2015-10-01

    In this article, a strain sensitive textile based elastomeric tape sensor has been developed and process parameters for sensor development are optimized. Polyester yarns are used as base threads and rubber threads are used as elastomer for the sensor development. The sensor has been developed with the help of narrow width tape loom by introducing the silver coated nylon yarn in the middle of the tape structure. The influence of weave structure, number of conductive threads and rubber thread tension on sensor development has been optimized by using the Box-Behnken method and the results are analyzed using the Design expert software. From the results, it is found that six numbers of conductive threads in a plain weave structure with rubber thread tension of 750 g is suitable for the sensor to give high gauge factor of 1.626.

  10. The response of polymethyl methacrylate (PMMA) subjected to large strains, high strain rates, high pressures, a range in temperatures, and variations in the intermediate principal stress

    NASA Astrophysics Data System (ADS)

    Holmquist, T. J.; Bradley, J.; Dwivedi, A.; Casem, D.

    2016-05-01

    This article presents the response of polymethyl methacrylate (PMMA) subjected to large strains, high strain rates, high pressures, a range in temperatures, and variations in the intermediate principal stress. Laboratory data from the literature, and new test data provided here, are used in the evaluation. The new data include uniaxial stress compression tests (at various strain rates and temperatures) and uniaxial stress tension tests (at low strain rates and ambient temperatures). The compression tests include experiments at ˙ɛ = 13,000 s-1, significantly extending the range of known strain rate data. The observed behavior of PMMA includes the following: it is brittle in compression at high rates, and brittle in tension at all rates; strength is dependent on the pressure, strain, strain rate, temperature, and the intermediate principal stress; the shear modulus increases as the pressure increases; and it is highly compressible. Also presented are novel, high velocity impact tests (using high-speed imaging) that provide insight into the initiation and evolution of damage. Lastly, computational constitutive models for pressure, strength, and failure are presented that provide responses that are in good agreement with the laboratory data. The models are used to compute several ballistic impact events for which experimental data are available.

  11. Cellular basis of morphological variation and temperature-related plasticity in Drosophila melanogaster strains with divergent wing shapes.

    PubMed

    Torquato, Libéria Souza; Mattos, Daniel; Matta, Bruna Palma; Bitner-Mathé, Blanche Christine

    2014-12-01

    Organ shape evolves through cross-generational changes in developmental patterns at cellular and/or tissue levels that ultimately alter tissue dimensions and final adult proportions. Here, we investigated the cellular basis of an artificially selected divergence in the outline shape of Drosophila melanogaster wings, by comparing flies with elongated or rounded wing shapes but with remarkably similar wing sizes. We also tested whether cellular plasticity in response to developmental temperature was altered by such selection. Results show that variation in cellular traits is associated with wing shape differences, and that cell number may play an important role in wing shape response to selection. Regarding the effects of developmental temperature, a size-related plastic response was observed, in that flies reared at 16 °C developed larger wings with larger and more numerous cells across all intervein regions relative to flies reared at 25 °C. Nevertheless, no conclusive indication of altered phenotypic plasticity was found between selection strains for any wing or cellular trait. We also described how cell area is distributed across different intervein regions. It follows that cell area tends to decrease along the anterior wing compartment and increase along the posterior one. Remarkably, such pattern was observed not only in the selected strains but also in the natural baseline population, suggesting that it might be canalized during development and was not altered by the intense program of artificial selection for divergent wing shapes. PMID:25326715

  12. In vitro investigation of Debaryomyces hansenii strains for potential probiotic properties.

    PubMed

    Ochangco, Honeylet Sabas; Gamero, Amparo; Smith, Ida M; Christensen, Jeffrey E; Jespersen, Lene; Arneborg, Nils

    2016-09-01

    In this study, 23 Debaryomyces hansenii strains, isolated from cheese and fish gut, were investigated in vitro for potential probiotic properties i.e. (1) survival under in vitro GI (gastrointestinal) conditions with different oxygen levels, (2) adhesion to Caco-2 intestinal epithelial cells and mucin, and (3) modulation of pro- and anti-inflammatory cytokine secretion by human monocyte-derived dendritic cells. As references two commercially available probiotic Saccharomyces cerevisiae var. boulardii (S. boulardii) strains were included in the study. Our results demonstrate that the different D. hansenii yeast strains had very diverse properties which could potentially lead to different probiotic effects. One strain of D. hansenii (DI 09) was capable of surviving GI stress conditions, although not to the same degree as the S. boulardii strains. This DI 09 strain, however, adhered more strongly to Caco-2 cells and mucin than the S. boulardii strains. Additionally, two D. hansenii strains (DI 10 and DI 15) elicited a higher IL-10/IL-12 ratio than the S. boulardii strains, indicating a higher anti-inflammatory effects on human dendritic cells. Finally, one strain of D. hansenii (DI 02) was evaluated as the best probiotic candidate because of its outstanding ability to survive the GI stresses, to adhere to Caco-2 cells and mucin and to induce a high IL-10/IL-12 ratio. In conclusion, this study shows that strains of D. hansenii may offer promising probiotic traits relevant for further study. PMID:27430508

  13. Deformation Along the Rio Grande Rift: Investigating the Spatial and Temporal Distribution of Strain Using GPS

    NASA Astrophysics Data System (ADS)

    Murray, K. D.; Murray, M. H.; Sheehan, A. F.; Nerem, R. S.

    2014-12-01

    Low velocity (<1 mm/yr) extensional environments, such as the Rio Grande rift (RGR) in Colorado and New Mexico, are complex but can provide insights into continental dynamics, tectonic processes, and seismic hazards. We use eight years of measurements from 26 continuous GPS stations across the RGR installed as part of a collaborative EarthScope experiment. We combine this data with regional Plate Boundary Observatory (PBO) and National Geodetic Survey (NGS) CORS GPS stations, and survey-mode data collected on NGS benchmarks to investigate how deformation is distributed across a broad area from the Great Plains to the Colorado Plateau. The data from over 150 stations are processed using GAMIT/GLOBK, and time series, velocities, strain rates are estimated with respect to realizations of a stable North America reference frame, such as NA12. This study extends our previous analysis, based on 4 years of data, which found an approximately uniform 1.2 nanostrain/yr east-west extensional strain rate across the entire region that was not concentrated on the narrow surface expression of the rift. We expand on this previous work by using a denser network of GPS stations and analyzing longer time series, which reduce horizontal velocity uncertainties to approximately 0.15 mm/yr. We also improve the accuracy of the estimated velocity uncertainties by robustly characterizing time-correlated noise. The noise models indicate that both power-law and flicker noise are present in the time series along with white noise. On average, power law noise constitutes about 90% of the total noise in the vertical component and 60% in the horizontal components for the RGR sites. We use the time series, and velocity and strain-rate estimates to constrain spatial and temporal variations in the deformation field in order to locate possible regions of strain localization and detect transient deformation signals, and to address some of the kinematic and dynamic issues raised by the observation that a

  14. Intraspecific Phenotypic Variation and Morphological Divergence of Strains of Folsomia candida (Willem) (Collembola: Isotomidae), the "Standard" Test Springtaill

    PubMed Central

    Tully, Thomas; Potapov, Mikhail

    2015-01-01

    We describe and compare the external morphology of eleven clonal strains and one sexual lineage of the globally distributed Folsomia candida, known as “standard” test Collembola. Of the 18 morphological characters studied, we measured 14 to have significant between-strains genetic variations, 9 of these had high heritabilities (>78%). The quantified morphological polymorphism was used to analyse the within-species relationships between strains by using both a parsimony analysis and a distance tree. These two detailed morphological phylogenies have revealed that the parthenogenetic strains grouped themselves into two major clades. However the exact position of the sexual strain remains unclear and further analysis is needed to confirm its exact relationship with the parthenogenetic ones. The two morphologically based clades were found to be the same as the ones previously described using molecular analysis. This shows that despite large within-strain variations, morphological characters can be used to differentiate some strains that have diverged within a single morphospecies. We discuss the potential evolutionary interpretations and consequences of these different levels of phenotypic variability. PMID:26355293

  15. Investigation of the mechanical behavior of kangaroo humeral head cartilage tissue by a porohyperelastic model based on the strain-rate-dependent permeability.

    PubMed

    Thibbotuwawa, Namal; Oloyede, Adekunle; Senadeera, Wijitha; Li, Tong; Gu, YuanTong

    2015-11-01

    Solid-interstitial fluid interaction, which depends on tissue permeability, is significant to the strain-rate-dependent mechanical behavior of humeral head (shoulder) cartilage. Due to anatomical and biomechanical similarities to that of the human shoulder, kangaroos present a suitable animal model. Therefore, indentation experiments were conducted on kangaroo shoulder cartilage tissues from low (10(-4)/s) to moderately high (10(-2)/s) strain-rates. A porohyperelastic model was developed based on the experimental characterization; and a permeability function that takes into account the effect of strain-rate on permeability (strain-rate-dependent permeability) was introduced into the model to investigate the effect of rate-dependent fluid flow on tissue response. The prediction of the model with the strain-rate-dependent permeability was compared with those of the models using constant permeability and strain-dependent permeability. Compared to the model with constant permeability, the models with strain-dependent and strain-rate-dependent permeability were able to better capture the experimental variation at all strain-rates (p < 0.05). Significant differences were not identified between models with strain-dependent and strain-rate-dependent permeability at strain-rate of 5 × 10(-3)/s (p = 0.179). However, at strain-rate of 10(-2)/s, the model with strain-rate-dependent permeability was significantly better at capturing the experimental results (p < 0.005). The findings thus revealed the significance of rate-dependent fluid flow on tissue behavior at large strain-rates, which provides insights into the mechanical deformation mechanisms of cartilage tissues. PMID:26275487

  16. Investigating causes of regional variations in atmospheric carbon dioxide concentrations

    NASA Astrophysics Data System (ADS)

    Corbin, Katherine D.

    Atmospheric CO2 concentrations are rapidly increasing due to anthropogenic activities; however, only about half of the emissions have accumulated in the atmosphere, and the fate of the remaining half remains uncertain. Since atmospheric CO2 concentrations contain information regarding carbon sources and sinks, it is important to understand CO 2 variability. This study investigated causes of atmospheric CO 2 variability, focusing on the relationship between CO2 concentrations and clouds, the impact of heterogeneous land cover and agricultural production, and the effect of redistributing fossil fuel emissions. Due to global coverage and sheer data volume, satellite CO2 concentrations will be used in inverse models to improve carbon source and sink estimates. Satellite concentrations will only retrieve CO2 measurements in clear conditions, and it is important to understand how CO 2 concentrations vary with cloud cover in order to optimally utilize these data. This study evaluated differences between clear-sky and mean concentrations on local, regional, and global scales. Analyses of in situ data, regional model simulations, and global model output all revealed clear-sky differences that were regionally coherent on sub-continental scales and that varied both with time and location. In the mid-latitudes, clear-sky CO2 concentrations were systematically lower than on average, and these differences were not due to biology, but rather to frontal convergence of large-scale gradients that were covered by clouds. Instead of using satellite data to represent temporal averages, inverse models and data assimilation systems that use satellite data to calculate carbon sources and sinks must be sampled consistently with the observations, including precise modeling of winds, clouds, fronts, and frontal timing. Just as CO2 concentrations vary with cloud cover, variability in atmospheric CO2 concentrations is also caused by heterogeneity in land cover and surface fluxes. This study

  17. CHARACTERIZATION OF AN AXENIC STRAIN OF HARTMANNELLA VERIFORMIS OBTAINED FROM AN INVESTIGATION OF NOSOCOMIAL LEGIONELLOSIS

    EPA Science Inventory

    A free living amoeba identified as Hartmannella vermiformis was isolated from a water sample obtained during an investigation of nosocomial legionellosis. artmannella vermiformis are known to support the intracellular multiplication of Legionella pneumonhila. This strain of H.ver...

  18. Tracing genomic variations in two highly virulent Yersinia enterocolitica strains with unequal ability to compete for host colonization

    PubMed Central

    2012-01-01

    . Conclusions Our study emphasizes that the virulence of pathogens can be increased, by acquiring new genes and/or improving the function of essential virulence proteins, resulting in permanently hyper-virulent strains. This work also highlights the importance of addressing genetic and phenotypic variations among closely related bacterial strains, even those belonging to the same bioserotype. PMID:22963272

  19. Investigation of the Dynamic Strain Aging and Mechanical Properties in Alloy-625 with Different Microstructures

    NASA Astrophysics Data System (ADS)

    Chatterjee, Arnomitra; Sharma, Garima; Tewari, R.; Chakravartty, J. K.

    2015-03-01

    Tensile tests were carried out on service exposed Alloy 625 ammonia cracker tube used at heavy water production plant to study the effect of microstructure on the serrated yielding and mechanical properties of the material. Owing to temperature gradient during service exposure, the microstructure was different in top, middle, and bottom sections of the tube. Variation of flow stress, ductility, and average work hardening were monitored with temperature. In the present work, emphasis was given on the study of serrated yielding in the service exposed Alloy 625. Detail investigations were made to study the effect of microstructure on the underlying mechanism of dynamic strain aging of the material. The study revealed that both the normal and the inverse Portevin-Le Chatelier effect (PLC) occured in the material at lower and higher temperature regime, respectively. While the normal PLC dynamics was associated with locking of dislocations by interstitial carbon atoms, the inverse one was accomplished by the dislocation pinning by substitutional Mo atoms. Further analyses identified that the basic deformation mechanism was different in middle and bottom samples as that in the top samples which was reflected in the difference in their respective activation energy and stress drop magnitude.

  20. Bovine herpesvirus-1: comparison and differentiation of vaccine and field strains based on genomic sequence variation.

    PubMed

    Fulton, R W; d'Offay, J M; Eberle, R

    2013-03-01

    Bovine herpesvirus-1 (BoHV-1) causes significant disease in cattle including respiratory, fetal diseases, and reproductive tract infections. Control programs usually include vaccination with a modified live viral (MLV) vaccine. On occasion BoHV-1 strains are isolated from diseased animals or fetuses postvaccination. Currently there are no markers for differentiating MLV strains from field strains of BoHV-1. In this study several BoHV-1 strains were sequenced using whole-genome sequencing technologies and the data analyzed to identify single nucleotide polymorphisms (SNPs). Strains sequenced included the reference BoHV-1 Cooper strain (GenBank Accession JX898220), eight commercial MLV vaccine strains, and 14 field strains from cases presented for diagnosis. Based on SNP analyses, the viruses could be classified into groups having similar SNP patterns. The eight MLV strains could be differentiated from one another although some were closely related to each other. A number of field strains isolated from animals with a history of prior vaccination had SNP patterns similar to specific MLV viruses, while other field isolates were very distinct from all vaccine strains. The results indicate that some BoHV-1 isolates from clinically ill cattle/fetuses can be associated with a prior MLV vaccination history, but more information is needed on the rate of BoHV-1 genome sequence change before irrefutable associations can be drawn. PMID:23333211

  1. [Investigation of variation of the production of biological and chemical compounds of Hyssopus officinalis L].

    PubMed

    Varga, E; Hajdú, Z; Veres, K; Máthé, I; Németh, E; Pluhár, Z; Bernáth, J

    1998-05-01

    Hyssopus officinalis L. (Lamiaceae family) has been cultivated in Central Europe for a long time. This essential oil containing species serves not only as spice but in many countries including Hungary, it is used as a folk medicine against certain respiratory diseases. Despite this fact, little is known about the variation of its productivity under Central European climatic conditions. The cultivated populations of hyssop can be characterised by a significant heterogenity. In the course of its breeding the uniformity of flower colour (e.g. blue form), and increase in the oil content are the main achievable purposes. The purpose of this work was to investigate both the variability of strains of different crigin and the time-dependent variations of its production parameters. The optimum of phytomass was obtained at the beginning of July. The essential oil content as well as compounds of the non volatile fractions were also investigated. The non volatile fractions for rosmarinic, caffeic acids were analysed mainly by TLC and densitometry. Both compounds were present in all samples and they are suitable for the characterisation of the plant. The essential oils were gained with Water Steam Distillation (WSD) and Supercritical Fluid Extraction (SFE) with CO2. The oils were analysed by GC, GC-MS techniques. In the essential oil composition of the populations studied significant heterogenity could be observed. In the case of applying SFE extraction the oil composition is more uniform, similarly to the obtained by WSD adding hexane. The heterogenity can be experienced in the offsprings, too. If only the main four components (beta-pinene, limonene, pinocamphone, isopinocamphone) are regarded, among the offsprings clear and mixed lines alike can be found. Results of these experiments justify the necessity and usefulness of selection which is going on. PMID:9703705

  2. Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

    PubMed Central

    2011-01-01

    Background Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date the genotypic diversity of T. cruzi and its relationship, if any, to biological diversity have not been studied at the whole genome level. Results In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate T. cruzi strains by comparative genomic hybridization (CGH). We observed that T. cruzi strains display widespread and focal copy number variations (CNV) and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods. As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes. Gene groups that showed little variation in copy numbers among the strains tested included those encoding protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV. Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent T. cruzi strains. Conclusions The large number of CNV, over 4,000, reported here uphold at a whole genome level the long held paradigm of extraordinary genome plasticity among T. cruzi strains. Moreover, the fact that these heritable markers do not parse T. cruzi strains along the same lines as traditional typing methods is strongly suggestive of genetic exchange playing a major role in T. cruzi population structure and biology. PMID:21385342

  3. Variation in M protein production among Streptococcus pyogenes strains according to emm genotype.

    PubMed

    Matsumoto, Masakado; Suzuki, Masahiro; Hirose, Kaoru; Hiramatsu, Reiji; Minagawa, Hiroko; Minami, Masaaki; Tatsuno, Ichiro; Okamoto, Akira; Ohta, Michio; Hasegawa, Tadao

    2011-06-01

    M protein is an important virulence determinant in Streptococcus pyogenes, but the amounts of M protein in various strains of the species remain to be elucidated. To assess the amount of M protein in strains of each emm genotype, dot blot analysis was performed on 141 clinically isolated strains. Among the cell membrane-associated proteins, M protein was present in greater quantities in the emm1, 3, and 6 strains than in the other emm strains. In addition three strains, one each of the emm1, 3, and 6 types, showed prolific M protein production (M protein-high producers). These three emm genotypes are frequently isolated in clinical practice. Sequencing of the csrRS gene, one of the two-component signal transduction systems implicated in virulence, was performed on 25 strains bearing different amounts of M protein. CsrS mutations, in contrast to CsrR protein, were detected in 11 strains. The M protein-high producer strain of emm1 type carried two amino acid substitutions, whereas the other three emm1 strains carried only one substitution each. The M protein-high producer expressed its emm gene more strongly than the corresponding M protein-low producer did according to TaqMan RT-PCR. These observations suggest that the accumulation of amino acid substitutions in CsrS protein may contribute, at least in part, to the large amount of M protein production seen in several emm genotypes. PMID:21371090

  4. Investigation of Metallo Beta Lactamases and Oxacilinases in Carbapenem Resistant Acinetobacter baumannii Strains Isolated from Inpatients

    PubMed Central

    Aksoy, M. Duygu; Çavuşlu, Şaban; Tuğrul, H. Murat

    2015-01-01

    Background: Resistance to beta-lactam antibiotics is widespread among Acinetobacter strains. Plasmid-mediated metallo beta lactamases (MBL) are responsible for carbapenem resistance, as are oxacillinases (OXA). In recent years, MBL producing carbapenem-resistant strains have been reported in the world and in Turkey in increasing rates. In our country, besides the OXA 51-like enzyme which is inherent in A. baumannii strains, OXA 58-like and OXA 23-like carbapenemases producing strains have also been widely detected. In addition, Verona Imipenemase (VIM) and (IMP)-type MBL have been reported in some centers. Aims: The aim of our study was to investigate the presence of carbapenemases in Acinetobacter strains isolated from hospitalized patients in Edirne. Study Design: Cross-sectional study. Methods: A total of 52 imipenem-resistant A. baumannii strains isolated between January and March 2013 were investigated. The presence of MBL was described phenotypically by the combined disk diffusion test (CDDT), double disk synergy test (DDST), MBL E-test (only performed in 28 strains) and modified Hodge test. blaIMP, blaVIM, blaGIM, blaSIM, blaSPM genes and blaOXA-23, blaOXA-51, blaOXA-40, blaOXA-58 genes were investigated by multiplex polymerase chain reaction (PCR). The blaNDM-1 gene was determined by PCR. Results: By modified Hodge test, 50 strains (96%) were found to be MBL positive. Positivity of MBL was 21% by both CDDT (0.1 M EDTA) and DDST. Twenty-four of 28 strains (85.7%) were positive by MBL E-test. OXA 23-like and OXA 51-like carbapenemases were detected in all strains, but OXA 58-like and OXA 40-like carbapenemases-producing A. baumannii were not detected. Also, MBL genes were not detected by genotypic methods. Conclusion: Only OXA 23-like carbapenemase was responsible for carbapenem resistance in carbapenem-resistant Acinetobacter strains in Edirne. The MBL-producing Acinetobacter strain is not yet a problem in our hospital. MBL resistance was found by

  5. DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies

    PubMed Central

    Hovatta, Iiris; Zapala, Matthew A; Broide, Ron S; Schadt, Eric E; Libiger, Ondrej; Schork, Nicholas J; Lockhart, David J; Barlow, Carrolee

    2007-01-01

    Background Expression quantitative trait locus (eQTL) mapping is used to find loci that are responsible for the transcriptional activity of a particular gene. In recent eQTL studies, expression profiles were derived from either homogenized whole brain or collections of large brain regions. However, the brain is a very heterogeneous organ, and expression profiles of different brain regions vary significantly. Because of the importance and potential power of eQTL studies in identifying regulatory networks, we analyzed gene expression patterns in different brain regions from multiple inbred mouse strains and investigated the implications for the design and analysis of eQTL studies. Results Gene expression profiles of five brain regions in six inbred mouse strains were studied. Few genes exhibited a significant strain-specific expression pattern, whereas a large number of genes exhibited brain region-specific patterns. We constructed phylogenetic trees based on the expression relationships between the strains and compared them with a DNA-level relationship tree. The trees based on the expression of strain-specific genes were constant across brain regions and mirrored DNA-level variation. However, the trees based on region-specific genes exhibited a different set of strain relationships, depending on the brain region. An eQTL analysis showed enrichment of cis-acting regulators among strain-specific genes, whereas brain region-specific genes appear to be mainly regulated by trans-acting elements. Conclusion Our results suggest that many regulatory networks are highly brain region specific and indicate the importance of conducting eQTL mapping studies using data from brain regions or tissues that are physiologically and phenotypically relevant to the trait of interest. PMID:17324278

  6. Investigation of Genetic Variation Underlying Central Obesity amongst South Asians

    PubMed Central

    Scott, William R.; Zhang, Weihua; Loh, Marie; Tan, Sian-Tsung; Lehne, Benjamin; Afzal, Uzma; Peralta, Juan; Saxena, Richa; Ralhan, Sarju; Wander, Gurpreet S.; Bozaoglu, Kiymet; Sanghera, Dharambir K.; Elliott, Paul; Scott, James; Chambers, John C.; Kooner, Jaspal S.

    2016-01-01

    South Asians are 1/4 of the world’s population and have increased susceptibility to central obesity and related cardiometabolic disease. Knowledge of genetic variants affecting risk of central obesity is largely based on genome-wide association studies of common SNPs in Europeans. To evaluate the contribution of DNA sequence variation to the higher levels of central obesity (defined as waist hip ratio adjusted for body mass index, WHR) among South Asians compared to Europeans we carried out: i) a genome-wide association analysis of >6M genetic variants in 10,318 South Asians with focused analysis of population-specific SNPs; ii) an exome-wide association analysis of ~250K SNPs in protein-coding regions in 2,637 South Asians; iii) a comparison of risk allele frequencies and effect sizes of 48 known WHR SNPs in 12,240 South Asians compared to Europeans. In genome-wide analyses, we found no novel associations between common genetic variants and WHR in South Asians at P<5x10-8; variants showing equivocal association with WHR (P<1x10-5) did not replicate at P<0.05 in an independent cohort of South Asians (N = 1,922) or in published, predominantly European meta-analysis data. In the targeted analyses of 122,391 population-specific SNPs we also found no associations with WHR in South Asians at P<0.05 after multiple testing correction. Exome-wide analyses showed no new associations between genetic variants and WHR in South Asians, either individually at P<1.5x10-6 or grouped by gene locus at P<2.5x10−6. At known WHR loci, risk allele frequencies were not higher in South Asians compared to Europeans (P = 0.77), while effect sizes were unexpectedly smaller in South Asians than Europeans (P<5.0x10-8). Our findings argue against an important contribution for population-specific or cosmopolitan genetic variants underlying the increased risk of central obesity in South Asians compared to Europeans. PMID:27195708

  7. VARIATION OF PSPB (PD1208) LOCUS AMONG CLOSELY RELATED XYLELLA FASTIDIOSA STRAINS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa is a Gram negative plant pathogenic bacterium causing grape Pierce’s disease (PD) and almond leaf scorch disease (ALSD). Two distinct genotypes are associated with ALSD. A-genotype strains cause ALSD but not PD. G-genotype strains cause both ALSD and PD. However, little is known a...

  8. Variations of whole genome sequences of Xylella fastidiosa strains within the same pathotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa is a Gram negative and nutritionally fastidious plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce's disease (PD) of grapevine. X. fastidiosa strains from almond can be divided into two pathotypes: ALSD-PD, represented by strain M23, and ALSD-only,...

  9. Genetic variations alter production and behavioral responses following heat stress in two strains of laying hens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heat stress is a problem for both egg production and hen well-being. Given a stressor, genetic differences alter the type and degree of hens’ responses and their adaptation. This study examined heat stress responses of two strains of White Leghorns: Dekalb XL (DXL), a commercial strain individually ...

  10. Strain variations in behavioral traits under heat stress in laying hens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heat stress is a problem for welfare of animals including laying hens. This study examined whether hens’ responses and adaptation to heat stress are affected by their genetic strain. Ninety 28-week-old White Leghorns from two strains were used: DeKalb XL (DXL), a line of hens individually selected ...

  11. Investigations of paleoclimate variations using accelerator mass spectrometry

    SciTech Connect

    Southon, J R; Kashgarian, M; Brown, T A

    2000-08-24

    This project has used Accelerator Mass Spectrometry (AMS) {sup 14}C measurements to study climate and carbon cycle variations on time scales from decades to millennia over the past 30,000 years, primarily in the western US and the North Pacific. {sup 14}C dates provide a temporal framework for records of climate change, and natural radiocarbon acts as a carbon cycle tracer in independently dated records. The overall basis for the study is the observation that attempts to model future climate and carbon cycle changes cannot be taken seriously if the models have not been adequately tested. Paleoclimate studies are unique because they provide realistic test data under climate conditions significantly different from those of the present, whereas instrumental results can only sample the system as it is today. The aim of this project has been to better establish the extent, timing, and causes of past climate perturbations, and the carbon cycle changes with which they are linked. This provides real-world data for model testing, both for the development of individual models and also for inter-model diagnosis and comparison activities such as those of LLNL's PCMDI program; it helps us achieve a better basic understanding of how the climate system works so that models can be improved; and it gives an indication of the natural variability in the climate system underlying any anthropogenically-driven changes. The research has involved four projects which test hypotheses concerning the overall behavior of the North Pacific climate system. All are aspects of an overall theme that climate linkages are strong and direct, so that regional climate records are correlated, details of fine structure are important, and accurate and precise dating is critical for establishing correlations and even causality. An important requirement for such studies is the requirement for an accurate and precise radiocarbon calibration, to allow better correlation of radiocarbon-dated records with

  12. Variations in rupture site and surface strains at failure in the maturing rabbit medial collateral ligament.

    PubMed

    Lam, T C; Shrive, N G; Frank, C B

    1995-11-01

    The relationship between the pattern of surface strain and the site of failure in maturing rabbit ligaments was studied in vitro. Bone-medial collateral ligament (MCL)-bone complexes of 24 female New Zealand White rabbits at 3, 6, 9 and 12 months of age (n = 6 rabbits, 12 MCLs per group) were tested in tension to failure. A video dimension analysis (VDA) system was used to map the surface strain at failure across the width and along the length of the medial side of each MCL during testing. Results showed that the highest strains were consistently located at the femoral insertion decreasing towards the midsubstance, with the highest strain occurring in the anterior portion of the MCL immediately adjacent to the femoral insertion. Strains of the complex at failure increased with rabbit maturation. The strain distribution however, did not change dramatically, even though the locations of MCL failure changed from exclusively tibial avulsion in the three month old rabbits to predominantly midsubstance failures in the 12 month old rabbits. In the six month old rabbits, there was a particular dissociation with all MCLs failing near the tibial insertion while femoral strains were apparently the highest. These results suggest two possibilities beyond that of some unknown artifacts of optical strain measurement. First, since failure sites rarely correlated with areas of maximum surface strain in this study, it seems possible that higher strains could exist deeper in the tissue, particularly at the bone-ligament interface of the tibial insertion in immature animals and somewhere within the midsubstance of the MCL in the adult. Secondly, it is possible that the ligament material may be heterogeneous. PMID:8748528

  13. Strain-specific variations in Toxoplasma gondii GRA1, GRA5, GRA6, GRA8, and GRA14

    NASA Astrophysics Data System (ADS)

    Haryati, S.; Sari, Y.; Prasetyo, A. A.; Sariyatun, R.

    2016-02-01

    Diagnosis and identification of the genetic group of T. gondii (Toxoplasma gondii) are important to control better the T. gondii infection, particularly in immunocompromised people as HIV patients. This study aimed to identify strain-specific variations in T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 in order to help design such diagnostic tool to detect and characterize the parasite. Forty-three T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 sequences deposited in GenBank were aligned. A number of positions in the gene sequences were highly conserved. All GRA sequences had strain-specific positions, however, only GRA1, GRA5, and GRA6, which contained specific variations for each T. gondii lineage. In conclusion, T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 are predicted to contain highly conserved regions and positions with strain-specific variation, which might be useful for the design of diagnostic tools detecting and distinguishing T. gondiistrains.

  14. Latitudinal and Seasonal Investigations of Storm-Time TEC Variation

    NASA Astrophysics Data System (ADS)

    Adimula, I. A.; Oladipo, O. A.; Adebiyi, S. J.

    2016-07-01

    The ionosphere responds markedly and unpredictably to varying magnetospheric energy inputs caused by solar disturbances on the geospace. Knowledge of the impact of the space weather events on the ionosphere is important to assess the environmental effect on the operations of ground- and space-based technologies. Thus, global positioning system (GPS) measurements from the international GNSS service (IGS) database were used to investigate the ionospheric response to 56 geomagnetic storm events at six different latitudes comprising the northern and southern hemispheres in the Afro-European sector. Statistical distributions of total electron content (TEC) response show that during the main phase of the storms, enhancement of TEC is more pronounced in most of the seasons, regardless of the latitude and hemisphere. However, a strong seasonal dependence appears in the TEC response during the recovery phase. Depletion of TEC is majorly observed at the high latitude stations, and its appearance at lower latitudes is seasonally dependent. In summer hemisphere, the depletion of TEC is more pronounced in nearly all the latitudinal bands. In winter hemisphere, enhancement as well as depletion of TEC is observed over the high latitude, while enhancement is majorly observed over the mid and low latitudes. In equinoxes, the storm-time TEC distribution shows a fairly consistent characteristic with the summer distribution, particularly in the northern hemisphere.

  15. Preliminary Investigation of Ice Shape Sensitivity to Parameter Variations

    NASA Technical Reports Server (NTRS)

    Miller, Dean R.; Potapczuk, Mark G.; Langhals, Tammy J.

    2005-01-01

    A parameter sensitivity study was conducted at the NASA Glenn Research Center's Icing Research Tunnel (IRT) using a 36 in. chord (0.91 m) NACA-0012 airfoil. The objective of this preliminary work was to investigate the feasibility of using ice shape feature changes to define requirements for the simulation and measurement of SLD icing conditions. It was desired to identify the minimum change (threshold) in a parameter value, which yielded an observable change in the ice shape. Liquid Water Content (LWC), drop size distribution (MVD), and tunnel static temperature were varied about a nominal value, and the effects of these parameter changes on the resulting ice shapes were documented. The resulting differences in ice shapes were compared on the basis of qualitative and quantitative criteria (e.g., mass, ice horn thickness, ice horn angle, icing limits, and iced area). This paper will provide a description of the experimental method, present selected experimental results, and conclude with an evaluation of these results, followed by a discussion of recommendations for future research.

  16. Experimental investigation of crustacean swimming with variation of limb structures

    NASA Astrophysics Data System (ADS)

    Lai, Hong Kuan; Samaee, Milad; Donnell, Geoffrey; Santhanakrishnan, Arvind; Guy, Robert; Lewis, Timothy

    2015-11-01

    Crustaceans such as crayfish and krill swim by rhythmically paddling a set of four to five limbs (known as swimmerets or pleopods) originating from their abdomen. The limb motion in these animals has been observed to follow tail-to-head metachronal wave pattern with an approximate quarter-period inter-limb phase difference. The goal of this study is to investigate the hydrodynamics of this swimming mechanism as a function of inter-limb phase difference, inclusion of hinges in the limbs, and Reynolds number (Re). 2D PIV measurements were conducted on a scaled robotic model of metachronal paddling, consisting of a rectangular tank fitted with stepper motors coupled to a four-bar linkage that actuated four paddles immersed in water-glycerin fluid medium. The inter-limb phase difference was varied from 0% (synchronous paddling) through 50% across Re range of O(10-1000). Two types of limb models were used, including a simple flat plate and a `split-paddle' structure with two flat plates connected halfway with hinges. The results of the study show that limb models with hinges generated increased horizontal (thrust-producing direction) fluid velocity compared to the simple flat plate paddles, suggesting that asymmetry between power and return strokes is important to augment thrust.

  17. Latitudinal and Seasonal Investigations of Storm-Time TEC Variation

    NASA Astrophysics Data System (ADS)

    Adimula, I. A.; Oladipo, O. A.; Adebiyi, S. J.

    2016-04-01

    The ionosphere responds markedly and unpredictably to varying magnetospheric energy inputs caused by solar disturbances on the geospace. Knowledge of the impact of the space weather events on the ionosphere is important to assess the environmental effect on the operations of ground- and space-based technologies. Thus, global positioning system (GPS) measurements from the international GNSS service (IGS) database were used to investigate the ionospheric response to 56 geomagnetic storm events at six different latitudes comprising the northern and southern hemispheres in the Afro-European sector. Statistical distributions of total electron content (TEC) response show that during the main phase of the storms, enhancement of TEC is more pronounced in most of the seasons, regardless of the latitude and hemisphere. However, a strong seasonal dependence appears in the TEC response during the recovery phase. Depletion of TEC is majorly observed at the high latitude stations, and its appearance at lower latitudes is seasonally dependent. In summer hemisphere, the depletion of TEC is more pronounced in nearly all the latitudinal bands. In winter hemisphere, enhancement as well as depletion of TEC is observed over the high latitude, while enhancement is majorly observed over the mid and low latitudes. In equinoxes, the storm-time TEC distribution shows a fairly consistent characteristic with the summer distribution, particularly in the northern hemisphere.

  18. Investigation of the dominance behavior of Saccharomyces cerevisiae strains during wine fermentation.

    PubMed

    Perrone, Benedetta; Giacosa, Simone; Rolle, Luca; Cocolin, Luca; Rantsiou, Kalliopi

    2013-07-15

    During wine fermentation, different strains of Saccharomyces cerevisiae compete in the same fermenting must and dominance takes place when one strain overcomes all the others. The purpose of this study was to investigate this phenomenon by identifying S. cerevisiae strains endowed with this feature and to test them in laboratory fermentations. First, autochthonous S. cerevisiae from Nebbiolo fermentations were isolated, molecularly identified and characterized. Genetically diverse S. cerevisiae strains were subsequently subjected to physiological characterization and to micro-scale fermentation, the weight loss kinetics was measured and HPLC analysis was performed at the end of the fermentation. Then, the strains that presented good fermentation characteristics were chosen for further analysis and to determine the dominance feature. For this purpose, couples of strains were co-inoculated in Nebbiolo must and the fermentations were monitored by microbiological and chemical analysis. Two different inoculation approaches were used: co-fermentations in flasks with mixed cells and reactor co-fermentations, in which the cells from the two different strains were kept separate by means of a 0.45 μm filter membrane, which allowed the fermenting must to move freely between the two compartments. During the flask co-fermentations, a minisatellite PCR protocol was applied, in order to differentiate the two strains and determine which one was able to dominate. The protocol included a culture-dependent approach and an independent one. In the first case, DNA extraction was performed on all the colonies scraped off the plates after sampling. In the second case, DNA extraction was performed directly on the fermenting must. The strains that were able to dominate were tested against several S. cerevisiae in order to confirm this dominance behavior. Dominance was observed in the early stages of fermentation, as early as 3days. Combinations of dominant and not-dominant strains were

  19. Inter-Individual and Inter-Strain Variations in Zebrafish Locomotor Ontogeny

    PubMed Central

    Lange, Merlin; Neuzeret, Frederic; Fabreges, Benoit; Froc, Cynthia; Bedu, Sebastien; Bally-Cuif, Laure; Norton, William H. J.

    2013-01-01

    Zebrafish exhibit remarkable alterations in behaviour and morphology as they develop from early larval stages to mature adults. In this study we compare the locomotion parameters of six common zebrafish strains from two different laboratories to determine the stability and repeatability of these behaviours. Our results demonstrate large variability in locomotion and fast swim events between strains and between laboratories across time. These data highlight the necessity for careful, strain-specific controls when analysing locomotor phenotypes and open up the possibility of standardising the quantification of zebrafish behaviour at multiple life stages. PMID:23950910

  20. Preliminary investigation of cycle-to-cycle variations in a nonair-breathing diesel engine

    SciTech Connect

    Zheng, M.; Reader, G.T.

    1995-03-01

    The effect of nonair mixtures on cycle-to-cycle variations of cylinder pressure characteristics was investigated experimentally with an indirect-injected (IDI) diesel engine. The engine intake temperature and pressure were maintained at normal air-breathing conditions when operated with nonair mixtures. Preliminary results indicate that increases in carbon dioxide concentration can cause significant cyclic variations. Moreover, the extent of such cyclic variations is notably influenced by the oxygen concentration and inert gas constitutents of the working fluids.

  1. Mitochondrial DNA and Functional Investigations into the Radiosensitivity of Four Mouse Strains

    PubMed Central

    Zhang, Steven B.; Maguire, David; Zhang, Mei; Tian, Yeping; Yang, Shanmin; Zhang, Amy; Casey-Sawicki, Katherine; Han, Deping; Ma, Jun; Yin, Liangjie; Guo, Yongson; Wang, Xiaohui; Chen, Chun; Litvinchuk, Alexandra; Zhang, Zhenhuan; Swarts, Steven; Vidyasagar, Sadasivan; Zhang, Lurong; Okunieff, Paul

    2014-01-01

    We investigated whether genetic radiosensitivity-related changes in mtDNA/nDNA ratios are significant to mitochondrial function and if a material effect on mtDNA content and function exists. BALB/c (radiosensitive), C57BL/6 (radioresistant), and F1 hybrid mouse strains were exposed to total body irradiation. Hepatic genomic DNA was extracted, and mitochondria were isolated. Mitochondrial oxygen consumption, ROS, and calcium-induced mitochondrial swelling were measured. Radiation influenced strain-specific survival in vivo. F1 hybrid survival was influenced by maternal input. Changes in mitochondrial content corresponded to survival in vivo among the 4 strains. Calcium-induced mitochondrial swelling was strain dependent. Isolated mitochondria from BALB/c mice were significantly more sensitive to calcium overload than mitochondria from C57BL/6 mice. Maternal input partially influenced the recovery effect of radiation on calcium-induced mitochondrial swelling in F1 hybrids; the hybrid with a radiosensitive maternal lineage exhibited a lower rate of recovery. Hybrids had a survival rate that was biased toward maternal input. mtDNA content and mitochondrial permeability transition pores (MPTP) measured in these strains before irradiation reflected a dominant input from the parent. After irradiation, the MPTP opened sooner in radiosensitive and hybrid strains, likely triggering intrinsic apoptotic pathways. These findings have important implications for translation into predictors of radiation sensitivity/resistance. PMID:24688546

  2. Variation of spontaneous and induced mitotic recombination in different Drosophila populations: a pilot study on the effects of polyaromatic hydrocarbons in six newly constructed tester strains.

    PubMed

    Vogel, E W; Nivard, M J; Zijlstra, J A

    1991-01-01

    A set of six Drosophila strains was developed, by inducing by chemical treatment with N-ethyl-N-nitrosourea (ENU) new white and, in some strains, yellow mutations in 3 wild-type (WT) and 3 insecticide-resistant (IR) populations. These strains were previously shown to vary with regard to contents and inducibility of microsomal oxidative enzymes (Zijlstra et al., 1984). In this pilot study results from a first evaluation of these strains in somatic mutation experiments are reported, using as genotoxins an aromatic amine (2-naphthylamine, 2-NA), one substituted (9,10-dimethylanthracene, DA) and one non-substituted (benzo[a]pyrene, BP) polycyclic aromatic hydrocarbon. Developing larvae heterozygous for white were chronically exposed to three different exposure doses of each carcinogen. Adult females were inspected for the occurrence of mosaic light clones in their eyes, using the somatic mutation and recombination test (SMART). Evidence is presented indicating strong genotype-dependent variation in both spontaneous and chemically induced mutational and recombinational events in somatic cells of Drosophila. The spontaneous frequencies varied from 3.5% (Hikone-R), 4.3% (Berlin-K), 6.3% (Oregon-K), 9.1% (91-C), 20.5% (Haag-79) to 49.1% (91-R), corresponding to a 14-fold difference in spot frequencies between the two extremes. BP, DA and 2-NA were readily detectable in both Hikone-R (IR) and Oregon-K (WT), less so in 91-C (WT) and Haag-79 (IR), whereas the performance of strain Berlin-K (WT) was rather poor. The special problem with strain 91-R was the high frequency with which mosaic light spots occur not only in female genotypes heterozygous for white, but also in homozygous condition in the original stock. The up to 20-fold variation in induced spot frequencies between different genotypes poses questions for further investigations with respect to the genetic constitution of the various strains and the role of enzyme induction on somatic cell mutagenicity, which in this

  3. Intraspecies Variation in the Emergence of Hyperinfectious Bacterial Strains in Nature

    PubMed Central

    House, John K.; Xie, Yi; Weimer, Bart C.; Sinsheimer, Robert L.; Mahan, Michael J.

    2012-01-01

    Salmonella is a principal health concern because of its endemic prevalence in food and water supplies, the rise in incidence of multi-drug resistant strains, and the emergence of new strains associated with increased disease severity. Insights into pathogen emergence have come from animal-passage studies wherein virulence is often increased during infection. However, these studies did not address the prospect that a select subset of strains undergo a pronounced increase in virulence during the infective process- a prospect that has significant implications for human and animal health. Our findings indicate that the capacity to become hypervirulent (100-fold decreased LD50) was much more evident in certain S. enterica strains than others. Hyperinfectious salmonellae were among the most virulent of this species; restricted to certain serotypes; and more capable of killing vaccinated animals. Such strains exhibited rapid (and rapidly reversible) switching to a less-virulent state accompanied by more competitive growth ex vivo that may contribute to maintenance in nature. The hypervirulent phenotype was associated with increased microbial pathogenicity (colonization; cytotoxin production; cytocidal activity), coupled with an altered innate immune cytokine response within infected cells (IFN-β; IL-1β; IL-6; IL-10). Gene expression analysis revealed that hyperinfectious strains display altered transcription of genes within the PhoP/PhoQ, PhoR/PhoB and ArgR regulons, conferring changes in the expression of classical virulence functions (e.g., SPI-1; SPI-2 effectors) and those involved in cellular physiology/metabolism (nutrient/acid stress). As hyperinfectious strains pose a potential risk to human and animal health, efforts toward mitigation of these potential food-borne contaminants may avert negative public health impacts and industry-associated losses. PMID:22511871

  4. Investigation of Strain-Induced Martensitic Transformation in Metastable Austenite using Nanoindentation

    SciTech Connect

    Ahn, T.-H.; Oh, C.-S.; Kim, D. H.; Oh, K. H.; Bei, Hongbin; George, Easo P; Han, H. N.

    2010-01-01

    Strain-induced martensitic transformation of metastable austenite was investigated by nanoindentation of individual austenite grains in multi-phase steel. A cross-section prepared through one of these indented regions using focused ion beam milling was examined by transmission electron microscopy. The presence of martensite underneath the indent indicates that the pop-ins observed on the load-displacement curve during nanoindentation correspond to the onset of strain-induced martensitic transformation. The pop-ins can be understood as resulting from the selection of a favorable martensite variant during nanoindentation.

  5. The time variations in the parameters of the volumetric strain response to the tidal and baric impacts

    NASA Astrophysics Data System (ADS)

    Cherepantsev, A. S.

    2016-07-01

    The parameters describing the state of the geological medium include its response to the continuous external impacts, which characterizes the structure of the medium and the stresses accumulated in it. In the present paper, through analyzing the long time series of the volumetric strain monitoring data in the nearsurface crustal layer, which were obtained by the American geophysicists under the Plate Boundary Observatory (PBO) project within the Parkfield segment of the San Andreas fault, the time behavior of the volumetric strain response to the separate components of the tides and the air pressure impacts is considered. The analysis of the response regime at the different observational stations suggests a significant influence of the local structural features and tectonic processes at the considered sites of the volumetric strain observations. The estimate of the variations in the partial information from the individual observations (values) is used for improving the reliability of identifying the amplitude peculiarities of the response when synchronizing the variations of the set of the tidal components. It is established that at the PKDLT observation point, a synchronous increase in the transfer coefficient of the tidal impact of the M 2, O 1, and L 2 components two years before the Parkfield earthquake of 2004 took place.

  6. Variation along ITS markers across strains of Fibrocapsa japonica (Raphidophyceae) suggests hybridisation events and recent range expansion

    NASA Astrophysics Data System (ADS)

    Kooistra, Wiebe H. C. F.; de Boer, M. Karin; Vrieling, Engel G.; Connell, Laurie B.; Gieskes, Winfried W. C.

    2001-12-01

    The flagellate micro-alga Fibrocapsa japonica can form harmful algal blooms along all temperate coastal regions of the world. The species was first observed in coastal waters of Japan and the western US in the 1970s; it has been reported regularly worldwide since. To unravel whether this apparent range expansion can be tracked, we assessed genetic variation among nuclear ribosomal DNA ITS sequences, obtained from sixteen global strains collected over the course of three decades. Ten sequence positions showed polymorphism across the strains. Nine out of these revealed ambiguities in several or most sequences sampled. The oldest strain collected (LB-2161) was the only one without such intra-individual polymorphism. In the others, the proportion of ambiguities at variable sites increased with more recent collection date. The pattern does not result from loss of variation due to sexual reproduction and random drift in culture because sister cultures CS-332 and NIES-136 showed virtually the same ITS-pattern after seven years of separation. Neither are the patterns explained by recent range expansion of a single genotype, because in that case one would expect lowest genetic diversity in the recently invaded North Sea; instead, polymorphism is highest there. Recent ballast-water-mediated mixing of formerly isolated populations and subsequent ongoing sexual reproduction among them can explain the increase in ambiguities. The species' capacity to form harmful blooms may well have been enhanced through increased genetic diversity of regional populations.

  7. Variations in SXT elements in epidemic Vibrio cholerae O1 El Tor strains in China

    PubMed Central

    Wang, Ruibai; Yu, Dong; Yue, Junjie; Kan, Biao

    2016-01-01

    Vibrio cholerae O1 El Tor biotype strains are responsible for three multiyear epidemics of cholera in China during the seventh ongoing pandemic. The presence of the integrative conjugative element SXT is strongly correlated with resistance to nalidixic acid, tetracycline, and trimethoprim-sulfamethoxazole in these strains. Here, we sequenced the conserved genes of the SXT element, including eex, setR, and int, from 59 V. cholerae O1 El Tor strains and extracted and assembled the intact SXT sequences from the 11 genome sequenced strains. These elements had characteristics distinct from those of previously reported integrative conjugative elements (ICEs). They could be clearly divided into two types based on the clustering of conserved genes and gene structures of the elements, showing their possibly independent derivation and evolution. These two types were present before and after 2005, respectively, demonstrating the type substitution that occurred in 2005. Four to six antibiotic-resistant genes were found on the SXT elements, including genes resistant to tetracycline, trimethoprim-sulfamethoxazole, and multiple drugs. In summary, our findings demonstrated the roles of the SXT element in the emergence of multidrug resistance in epidemic O1 El Tor V. cholerae strains in China. PMID:26956038

  8. Cuticular hydrocarbon discrimination/variation among strains of the mosquito, Anopheles (Cellia) stephensi Liston.

    PubMed

    Anyanwu, G I; Davies, D H; Molyneux, D H; Phillips, A; Milligan, P J

    1993-06-01

    Cuticular lipids were removed from adult female Anopheles stephensi Liston and the hydrocarbons present were separated and quantified by gas chromatography. Comparison was made between the hydrocarbons of four An. stephensi strains: Russ, sensitive to DDT and malathion and originally isolated in the former U.S.S.R.; Beech, a DDT-resistant Indian strain with high sensitivity to Plasmodium species; St Mal, a strain from Pakistan shown to be resistant to malathion; and Iraq, a DDT-susceptible strain from Iraq. Discriminant analysis indicated that the four groups were distinct and that, on average, 78% of the population could be separated on the basis of the quantities of some of the cuticular hydrocarbons. The profiles of Beech and Russ or Russ and St Mal could be separated in 98% of the cases. There was reduced segregation between the profiles of St. Mal and Iraq, suggesting greater similarity in the hydrocarbons of these two strains. The usefulness of cuticular hydrocarbon in determining species relationships is discussed. PMID:8257238

  9. Sporadic Distribution and Distinctive Variations of Cylindrospermopsin Genes in Cyanobacterial Strains and Environmental Samples from Chinese Freshwater Bodies

    PubMed Central

    Jiang, Yongguang; Xiao, Peng; Yu, Gongliang; Shao, Jihai; Liu, Deming; Azevedo, Sandra M. F. O.

    2014-01-01

    Increasing reports of cylindrospermopsins (CYNs) in freshwater ecosystems have promoted the demand for identifying all of the potential CYN-producing cyanobacterial species. The present study explored the phylogenetic distribution and evolution of cyr genes in cyanobacterial strains and water samples from China. Four Cylindrospermopsis strains and two Raphidiopsis strains were confirmed to produce CYNs. Mutant cyrI and cyrK genes were observed in these strains. Cloned cyr gene sequences from eight water bodies were clustered with cyr genes from Cylindrospermopsis and Raphidiopsis (C/R group) in the phylogenetic trees with high similarities (99%). Four cyrI sequence types and three cyrJ sequence types were observed to have different sequence insertions and repeats. Phylogenetic analysis of the rpoC1 sequences of the C/R group revealed four conserved clades, namely, clade I, clade II, clade III, and clade V. High sequence similarities (>97%) in each clade and a divergent clade IV were observed. Therefore, CYN producers were sporadically distributed in congeneric and paraphyletic C/R group species in Chinese freshwater ecosystems. In the evolution of cyr genes, intragenomic translocations and intergenomic transfer between local Cylindrospermopsis and Raphidiopsis were emphasized and probably mediated by transposases. This research confirms the existence of CYN-producing Cylindrospermopsis in China and reveals the distinctive variations of cyr genes. PMID:24928879

  10. Experimental insight into the proximate causes of male persistence variation among two strains of the androdioecious Caenorhabditis elegans (Nematoda)

    PubMed Central

    Wegewitz, Viktoria; Schulenburg, Hinrich; Streit, Adrian

    2008-01-01

    Background In the androdioecious nematode Caenorhabditis elegans virtually all progeny produced by hermaphrodite self-fertilization is hermaphrodite while 50% of the progeny that results from cross-fertilization by a male is male. In the standard laboratory wild type strain N2 males disappear rapidly from populations. This is not the case in some other wild type isolates of C. elegans, among them the Hawaiian strain CB4856. Results We determined the kinetics of the loss of males over time for multiple population sizes and wild isolates and found significant differences. We performed systematic inter- and intra-strain crosses with N2 and CB4856 and show that the males and the hermaphrodites contribute to the difference in male maintenance between these two strains. In particular, CB4856 males obtained a higher number of successful copulations than N2 males and sired correspondingly more cross-progeny. On the other hand, N2 hermaphrodites produced a higher number of self-progeny, both when singly mated and when not mated. Conclusion These two differences have the potential to explain the observed variation in male persistence, since they should lead to a predominance of self-progeny (and thus hermaphrodites) in N2 and, at the same time, a high proportion of cross-progeny (and thus the presence of males as well as hermaphrodites) in CB4856. PMID:18620600

  11. Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model

    PubMed Central

    Zampieri, Mattia; Legname, Giuseppe; Altafini, Claudio

    2009-01-01

    Prion proteins are known to misfold into a range of different aggregated forms, showing different phenotypic and pathological states. Understanding strain specificities is an important problem in the field of prion disease. Little is known about which PrPSc structural properties and molecular mechanisms determine prion replication, disease progression and strain phenotype. The aim of this work is to investigate, through a mathematical model, how the structural stability of different aggregated forms can influence the kinetics of prion replication. The model-based results suggest that prion strains with different conformational stability undergoing in vivo replication are characterizable in primis by means of different rates of breakage. A further role seems to be played by the aggregation rate (i.e. the rate at which a prion fibril grows). The kinetic variability introduced in the model by these two parameters allows us to reproduce the different characteristic features of the various strains (e.g., fibrils' mean length) and is coherent with all experimental observations concerning strain-specific behavior. PMID:19578427

  12. Bonding dynamics of compliant microbump during ultrasonic bonding investigated by using Si strain gauge

    NASA Astrophysics Data System (ADS)

    Iwanabe, Keiichiro; Nakadozono, Kenichi; Senda, Yousuke; Asano, Tanemasa

    2016-06-01

    The bonding dynamics of a cone-shaped microbump during ultrasonic bonding are investigated by in situ measurements of the strain generated in a substrate using a piezoresistance strain sensor. The strain sensor is composed of a pair of p- and n-type piezoresistance gauges to extract strain components in the ultrasonic vibration along the plane parallel to the substrate surface and along the direction perpendicular to the surface. Flip-chip bonding is performed at room-temperature. The time evolution of the strain generated in the substrate according to the load-up of pressing force and application of ultrasonic vibration is clearly detected. The softening of the bump metal during the application of ultrasonic vibration is clearly observed. Results of a comparative study between the bonding of a cone-shaped microbump and that of a flat-top microbump suggest mechanical stress concentration near the top end of the cone-shaped microbump, which results in the transformation of the crystal texture of the bump from grains to fine crystallites.

  13. Variation in hormone autonomy and regenerative potential of cells transformed by strain A66 of Agrobacterium tumefaciens

    SciTech Connect

    Binns, A.N.; Sciaky, D.; Wood, H.N.

    1982-12-01

    Mutant Agrobacterium tumefaciens strain A66 is shown to differ from its wild-type progenitor (strain A6) by a spontaneous 2.7 kb DNA insert into the T-DNA region of its Ti plasmid. Tobacco stems transformed by A66 exhibit an attenuated response characterized by slow growth and shoot proliferation. Clonal analysis demonstrates that this response is due to an alteration in the growth and regenerative potential of transformed cells, rather than to variation in the frequency of fully autonomous cells within the primary tumor. Cloned A66 transformed tobacco cells exhibit an auxin requirement for growth that can be overcome by shoot proliferation. Other host species, however, may complement the A66 mutation yielding fully auxin-independent tumors when transformed by this bacterium.

  14. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

    PubMed Central

    Henson, Michael W.; Santo Domingo, Jorge W.; Kourtev, Peter S.; Jensen, Roderick V.; Dunn, James A.

    2015-01-01

    Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates’ phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes. PMID:26587353

  15. Geographic variation in sexual attraction of Spodoptera frugiperda corn- and rice-strain males to pheromone lures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The corn- and rice-strains of Spodoptera frugiperda exhibit several genetic and behavioral differences and appear to be undergoing ecological speciation in sympatry. Previous studies reported conflicting results when investigating male attraction to pheromone lures in different regions, but this cou...

  16. Impact of Strain Variation on the Ability of Biosensor Technology to Detect Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: It is important to develop methods that can quickly and accurately detect the presence of bacteria in the food supply that cause disease. Salmonella enterica is a bacteria that is often associated with contamination of food. Strains vary in their ability to cause illness and to spread...

  17. [Genomic variation of laboratory strains and natural populations of Drosophila melanogaster exposed to X-irradiation].

    PubMed

    Shokhanov, S O; Shcherbata, G R; Chernik, Ia I

    1997-01-01

    The spontaneous and X-ray-induced mutation rates and spectrums were estimated in laboratory strains and natural populations of Drosophila melanogaster from the Chernobyl meltdown area. Laboratory strains Oregon R and y2w alpha 4 were stable. In all natural populations, the spontaneous mutation rate was an order of magnitude higher (10(-3)) than in laboratory strains. Irradiation at a total dose of 3000 R was shown to induce genetic instability in the stable laboratory strain y2w alpha 4 and to increase the mutation rate and spectrum range in the unstable natural population P1. A high level of genetic instability was observed both in the first and second generations. Genetic analysis by means of classical genetic and molecular methods was performed; in crosses, a collection of spontaneous and induced mutants was used. The molecular genetic nature of mutations at the white and cut loci was analyzed by Southern blot-hybridization. Mutations at the white locus were shown to result both from transposition and recombination events; cut mutations were caused by deletions. PMID:9162688

  18. Kinetics and strain variation of phagosome proteins of Entamoeba histolytica by proteomic analysis.

    PubMed

    Okada, Mami; Huston, Christopher D; Oue, Miho; Mann, Barbara J; Petri, William A; Kita, Kiyoshi; Nozaki, Tomoyoshi

    2006-02-01

    The protozoan parasite Entamoeba histolytica ingests and feeds on microorganisms and mammalian cells. Phagocytosis is essential for cell growth and implicated in pathogenesis of E. histolytica. We report here the dynamic changes of phagosome proteins during phagosome maturation by proteomic analysis using reversed-phase capillary liquid chromatography and ion trap tandem mass spectrometry. Phagosomes were isolated at various intervals after internalization of latex beads. Immunoblot analysis and electron microscopy verified successful isolation of phagosomes. A total of 159 proteins were identified from the reference strain HM1 at different stages of phagosome maturation. Approximately 70% of them were detected in a time-dependent fashion, suggesting dynamism of phagosome biogenesis. The kinetics of representative proteins were verified by immunoblots and also by video microscopy of live transgenic amebae expressing green fluorescent protein-fused EhRab7A. Furthermore, we observed significant differences in phagosome profiles between HM1 and two recent clinical isolates. Approximately 60% of 229 proteins detected in at least one of these three strains were identified only in one strain, while approximately 20% of these proteins were detected in all three strains. These data should provide significant insights into molecular characterization of phagosome biogenesis, and help to elucidate the pathogenesis of this important infection. PMID:16290089

  19. Investigation of thermomechanical couplings, strain localization and shape memory properties in a shape memory polymer subjected to loading at various strain rates

    NASA Astrophysics Data System (ADS)

    Pieczyska, E. A.; Staszczak, M.; Maj, M.; Kowalczyk-Gajewska, K.; Golasiński, K.; Cristea, M.; Tobushi, H.; Hayashi, S.

    2016-08-01

    This paper presents experimental and modeling results of the effects of thermomechanical couplings occurring in a polyurethane shape memory polymer (SMP) subjected to tension at various strain rates within large strains. The SMP mechanical curves, recorded using a testing machine, and the related temperature changes, measured in a contactless manner using an IR camera, were used to investigate the polymer deformation process at various loading stages. The effects of thermomechanical couplings allowed the determination of the material yield point in the initial loading stage, the investigation of nucleation and development of the strain localization at larger strains and the estimation of the effects of thermoelastic behavior during the unloading process. The obtained stress–strain and thermal characteristics, the results of the dynamic mechanical analysis and estimated values of the shape fixity and shape recovery parameters confirmed that the shape memory polymer (T g = 45 °C) is characterized by good mechanical and shape memory properties, as well as high sensitivity to the strain rate. The mechanical response of the SMP subjected to tension was simulated using the finite element method and applying the large strain, two-phase model. Strain localization observed in the experiment was well reproduced in simulations and the temperature spots were correlated with the accumulated viscoplastic deformation of the SMP glassy phase.

  20. Strain variation in the adaptation of C57Bl6 and BALBc mice to chronic hypobaric hypoxia.

    PubMed

    Cramer, Nathan P; Xu, Xiufen; Christensen, Christine; Bierman, Alexis; Tankersley, Clarke G; Galdzicki, Zygmunt

    2015-05-01

    The interplay of environmental and genetic factors may lead to a spectrum of physiological and behavioral outcomes. How environmental stress factors interact with the diverse mouse genomes is still poorly understood and elucidating the underlying interactions requires specific stress models that can target integrated physiological systems. Here, we employ behavioral tests and whole-body plethysmography to examine the effects of 12 weeks of simulated high altitude (HA) exposure on two inbred mouse strains, BALBc and C57Bl6. We find that HA induced- weight loss recovers at significantly different rates in these two strains. Even at 12 weeks, however, both strains fail to reach body weight levels of controls. Performance on two motor tasks, rotarod and treadmill, improve with HA exposure but more prominently in BALBc mice. Whole-body plethysmography outcomes indicate that compensation to chronic HA includes increased respiratory frequencies and tidal volumes in both strains. However, the effects on tidal volume are significantly greater in BALBc mice and showed a biphasic course. Whole- body metabolic rates are also increased in both strains with prolonged HA exposure, but were more pronounced in BALBc mice suggestive of less successful adaptation in this strain. These adaptations occur in the absence of gross pathological changes in all major organs. Together these results indicate that chronic HA exposure results in environmental stressors that impact the specific physiological responses of BALBc more than C57Bl6 mice. Thus, these strains provide a promising platform for investigating how genetic backgrounds can differentially reinforce the effects of long-lasting environmental stressors and their potential to interact with psychological stressors. PMID:25647362

  1. Investigation of a relationship between dielectric peak diffuseness and elastic modulus variations in a ferroelectric relaxor

    NASA Astrophysics Data System (ADS)

    Sarasúa, L. G.; Moreno, A.; Favre, S.; Eiras, J. A.

    2014-03-01

    The dependence with temperature of elastic modulus of relaxor ferroelectric ceramics is modeled with a Landau-Devonshire-type cluster theory. The effective elastic modulus obtained from experimental data of ultrasonic longitudinal velocity in PCT and PLZT ferroelectric ceramics are compared with the proposed model. This comparison shows that the model is able to reproduce the dependence with temperature of elastic modulus c very well. We obtained that as impurity concentration increases in both families, the diffuseness of the transition shows important variations, but the strengths of the couplings between the polarization and the strain remain almost unchanged. In contrast, other models assigned a change in the strengths of the couplings between the polarization and the strain to explain the diffuse transition in these compounds.

  2. Morphometric structural diversity of a natural armor assembly investigated by 2D continuum strain analysis.

    PubMed

    Varshney, Swati; Song, Juha; Li, Yaning; Boyce, Mary C; Ortiz, Christine

    2015-12-01

    Many armored fish scale assemblies use geometric heterogeneity of subunits as a design parameter to provide tailored biomechanical flexibility while maintaining protection from external penetrative threats. This study analyzes the spatially varying shape of individual ganoid scales as a structural element in a biological system, the exoskeleton of the armored fish Polypterus senegalus (bichir). X-ray microcomputed tomography is used to generate digital 3D reconstructions of the mineralized scales. Landmark-based geometric morphometrics is used to measure the geometric variation among scales and to define a set of geometric parameters to describe shape variation. A formalism using continuum mechanical strain analysis is developed to quantify the spatial geometry change of the scales and illustrate the mechanisms of shape morphing between scales. Five scale geometry variants are defined (average, anterior, tail, ventral, and pectoral fin) and their functional implications are discussed in terms of the interscale mobility mechanisms that enable flexibility within the exoskeleton. The results suggest that shape variation in materials design, inspired by structural biological materials, can allow for tunable behavior in flexible composites made of segmented scale assemblies to achieve enhanced user mobility, custom fit, and flexibility around joints for a variety of protective applications. PMID:26481418

  3. Systematic investigation on topological properties of layered GaS and GaSe under strain

    NASA Astrophysics Data System (ADS)

    An, Wei; Wu, Feng; Jiang, Hong; Tian, Guang-Shan; Li, Xin-Zheng

    2014-08-01

    The topological properties of layered β-GaS and ɛ-GaSe under strain are systematically investigated by ab initio calculations with the electronic exchange-correlation interactions treated beyond the generalized gradient approximation (GGA). Based on the GW method and the Tran-Blaha modified Becke-Johnson potential approach, we find that while ɛ-GaSe can be strain-engineered to become a topological insulator, β-GaS remains a trivial one even under strong strain, which is different from the prediction based on GGA. The reliability of the fixed volume assumption rooted in nearly all the previous calculations is discussed. By comparing to strain calculations with optimized inter-layer distance, we find that the fixed volume assumption is qualitatively valid for β-GaS and ɛ-GaSe, but there are quantitative differences between the results from the fixed volume treatment and those from more realistic treatments. This work indicates that it is risky to use theoretical approaches like GGA that suffer from the band gap problem to address physical properties, including, in particular, the topological nature of band structures, for which the band gap plays a crucial role. In the latter case, careful calibration against more reliable methods like the GW approach is strongly recommended.

  4. Systematic investigation on topological properties of layered GaS and GaSe under strain

    SciTech Connect

    An, Wei; Tian, Guang-Shan; Wu, Feng; Jiang, Hong; Li, Xin-Zheng

    2014-08-28

    The topological properties of layered β-GaS and ε-GaSe under strain are systematically investigated by ab initio calculations with the electronic exchange-correlation interactions treated beyond the generalized gradient approximation (GGA). Based on the GW method and the Tran-Blaha modified Becke-Johnson potential approach, we find that while ε-GaSe can be strain-engineered to become a topological insulator, β-GaS remains a trivial one even under strong strain, which is different from the prediction based on GGA. The reliability of the fixed volume assumption rooted in nearly all the previous calculations is discussed. By comparing to strain calculations with optimized inter-layer distance, we find that the fixed volume assumption is qualitatively valid for β-GaS and ε-GaSe, but there are quantitative differences between the results from the fixed volume treatment and those from more realistic treatments. This work indicates that it is risky to use theoretical approaches like GGA that suffer from the band gap problem to address physical properties, including, in particular, the topological nature of band structures, for which the band gap plays a crucial role. In the latter case, careful calibration against more reliable methods like the GW approach is strongly recommended.

  5. Sequence Variation and Immunologic Cross-Reactivity among Babesia bovis Merozoite Surface Antigen 1 Proteins from Vaccine Strains and Vaccine Breakthrough Isolates

    PubMed Central

    LeRoith, Tanya; Brayton, Kelly A.; Molloy, John B.; Bock, Russell E.; Hines, Stephen A.; Lew, Ala E.; McElwain, Terry F.

    2005-01-01

    The Babesia bovis merozoite surface antigen 1 (MSA-1) is an immunodominant membrane glycoprotein that is the target of invasion-blocking antibodies. While antigenic variation has been demonstrated in MSA-1 among strains from distinct geographical areas, the extent of sequence variation within a region where it is endemic and the effect of variation on immunologic cross-reactivity have not been assessed. In this study, sequencing of MSA-1 from two Australian B. bovis vaccine strains and 14 breakthrough isolates from vaccinated animals demonstrated low sequence identity in the extracellular region of the molecule, ranging from 19.8 to 46.7% between the T vaccine strain and eight T vaccine breakthrough isolates, and from 18.7 to 99% between the K vaccine strain and six K vaccine breakthrough isolates. Although MSA-1 amino acid sequence varied substantially among strains, overall predicted regions of hydrophilicity and hydrophobicity in the extracellular domain were conserved in all strains examined, suggesting a conserved functional role for MSA-1 despite sequence polymorphism. Importantly, the antigenic variation created by sequence differences resulted in a lack of immunologic cross-reactivity among outbreak strains using sera from animals infected with the B. bovis vaccine strains. Additionally, sera from cattle hyperinfected with the Mexico strain of B. bovis and shown to be clinically immune did not cross-react with MSA-1 from any other isolate tested. The results indicate that isolates of B. bovis capable of evading vaccine-induced immunity contain an msa-1 gene that is significantly different from the msa-1 of the vaccine strain, and that the difference can result in a complete lack of cross-reactivity between MSA-1 from vaccine and breakthrough strains in immunized animals. PMID:16113254

  6. Variation Between Strains of Hamsters in the Lethality of Pichinde Virus Infections

    PubMed Central

    Buchmeier, Michael J.; Rawls, William E.

    1977-01-01

    Infection by Pichinde virus, a member of the arenavirus group, was studied in Golden Syrian hamsters (Mesocricetus auratus) with regard to possible mechanisms of resistance to virus infection in adult hamsters. Two hamster strains were found to differ in their susceptibility to lethal Pichinde virus infection. LVG/Lak randomly bred hamsters were found to be 100% susceptible to low doses of Pichinde virus during the first 6 days of life, but after 8 days of life, mortality was uncommon. Peak virus titers in the serum of animals infected at 3 days of life were 4 logs greater than in animals infected at 12 days. MHA/Lak inbred hamsters, in contrast, were found to be susceptible to lethal virus infection both as newborns and as adults. Peak virus titers of greater than 108 plaque-forming units/ml were observed in serum 8 days after infection of adult MHA hamsters as compared with less than 103 plaque-forming units/ml in the serum of adult LVG hamsters. Cultured primary kidney cells and peritoneal macrophages from either hamster strain supported Pichinde virus replication equally well in vitro. Antibodies to the complement-fixing antigens and to antigens at the surface of virus-infected cells were produced by both strains of hamsters. Cyclophosphamide immunosuppression rendered adult LVG animals susceptible to lethal infections, and virus grew to high titers in the treated animals. These findings suggest that immunological factors that appear early in life in LVG hamsters and are deficient in MHA hamsters limit Pichinde virus infection. Unlike previously reported arenavirus diseases, the observations suggest that death is produced by a direct viral effect and not through immunopathological mechanisms. PMID:193786

  7. Impact of dislocation cell elastic strain variations on line profiles from deformed copper.

    SciTech Connect

    Levine, L. E.; Larson, B. C.; Tischler, J. Z.; Geantil, P.; Kassner, M. E.; Liu, W.; Stoudt, M. R.; NIST; ORNL; Univ. of Southern California

    2008-01-01

    Energy scanned, sub-micrometer X-ray beams were used to obtain diffraction line profiles from individual dislocation cells in copper single crystals deformed in compression. Sub-micrometer depth resolution was provided by translating a wire through the diffracted beams and using triangulation to determine the depths of the diffracting volumes. Connection to classic volume-averaged results was made by adding the line profiles from 52 spatially resolved dislocation cell measurements. The resulting sub profile is smooth and symmetric, in agreement with early assumptions; the mean strain and full width half maximum are consistent with the average of the parameters extracted from the more exact individual dislocation cell measurements.

  8. Lifetime Dependent Variation of Stress Hormone Metabolites in Feces of Two Laboratory Mouse Strains

    PubMed Central

    Kolbe, Thomas; Palme, Rupert; Tichy, Alexander; Rülicke, Thomas

    2015-01-01

    Non-invasive measurement of stress hormone metabolites in feces has become routine practice for the evaluation of distress and pain in animal experiments. Since metabolism and excretion of glucocorticoids may be variable, awareness and adequate consideration of influencing factors are essential for accurate monitoring of adrenocortical activity. Reference values are usually provided by baselines compiled prior to the experiment and by age matched controls. The comparison of stress hormone levels between animals of different ages or between studies looking at hormone levels at the beginning and at the end of a long term study might be biased by age-related effects. In this study we analyzed fecal corticosterone metabolites (FCM) during the lifetime of untreated female mice of the strains C57BL/6NCrl and Crl:CD1. For this purpose feces for each individual mouse were collected every two months over a period of 24 hours, at intervals of four hours, until the age of 26 months. Results of the study revealed that age of the animals had a significant impact on the level and circadian rhythm of stress hormone metabolites. Furthermore, long-term observation of mice revealed a strain specific excretion profile of FCM influenced by strong seasonal variability. PMID:26284365

  9. Chemotactic Preferences and Strain Variation in the Response of Phytophthora sojae Zoospores to Host Isoflavones

    PubMed Central

    Tyler, B. M.; Wu, M.; Wang, J.; Cheung, W.; Morris, P. F.

    1996-01-01

    The zoospores of Phytophthora sojae are chemotactically attracted to the isoflavones genistein and daidzein that are released by soybean roots. In this study we have examined the response of P. sojae zoospores to a wide range of compounds having some structural similarity to genistein and daidzein, including isoflavones, flavones, chalcones, stilbenes, benzoins, benzoates, benzophenones, acetophenones, and coumarins. Of 59 compounds examined, 43 elicited some response. A comparison of the chemotactic responses elicited by the various compounds revealed a primary role for the phenolic 4(prm1)- and 7-hydroxyl groups on the isoflavone structure. A few compounds acted as repellents, notably methylated flavones with a hydrophobic B ring. The chemotactic response to many of the analogs was markedly different among different strains of P. sojae. PMID:16535375

  10. When confidence comes and goes: How variation in self-efficacy moderates stressor-strain relationships.

    PubMed

    Peng, Ann C; Schaubroeck, John M; Xie, Jia Lin

    2015-07-01

    Inconsistent published findings regarding a proposed buffering role of self-efficacy in stress coping led us to develop a model in which within-person variability in self-efficacy over time affects how individuals' mean levels of self-efficacy moderate the relationship between demands and psychological symptoms. Results from two independent samples (manufacturing workers and college students) supported the hypothesized interaction between demands, self-efficacy mean level, and self-efficacy variability. Demands were more positively associated with psychological strain among those with high and stable self-efficacy than those with high and variable self-efficacy. We discuss the implications of intrapersonal variability in self-efficacy for research on stress coping. PMID:25602277

  11. Composition, Variation, and Dynamics of Major Osmotic Solutes in Methanohalophilus Strain FDF1

    PubMed Central

    Robertson, Diane E.; Lai, Mei-Chin; Gunsalus, Robert P.; Roberts, Mary F.

    1992-01-01

    Methanohalophilus strain FDF1, a member of the halophilic genus of methanogens, can grow over a range of external NaCl concentrations from 1.2 to 2.9 M and utilize methanol, trimethylamine, and dimethyl sulfide as substrates for methanogenesis. It produces the osmolytes glycine betaine, β-glutamine, and Nε-acetyl-β-lysine with increasing external NaCl, but the relative ratio of these zwitterions depends primarily on the methanogenic substrate and less on the external osmolarity. When the cells are grown on methanol in defined medium, accumulation of glycine betaine predominates over the other zwitterionic solutes. The cells also synthesized a carbohydrate which was not detected in cells grown on trimethylamine. This negatively charged compound, identified as α-glucosylglycerate from the 13C and 1H chemical shifts, does not act as an osmoregulatory solute in the salt range 1.4 to 2.7 M in this methanogen as evidenced by its invariant intracellular concentration. 13CH3OH-pulse/12CH3OH-chase experiments were used to determine half-lifes for these organic solute pools in the cells. l-α-Glutamate showed a rapid loss of heavy isotope, indicating that l-α-glutamate functions as a biosynthetic intermediate in these cells. Measurable turnover rates for both β-glutamine, which acts as an osmolyte, and α-glucosylglycerate suggest that they function as metabolic intermediates as well. Molecules which function solely as osmolytes (glycine betaine and Nε-acetyl-β-lysine) showed a slower turnover consistent with their roles as osmotic solutes in Methanohalophilus strain FDF1. PMID:16348748

  12. Feasibility Study of Ex Ovo Chick Chorioallantoic Artery Model for Investigating Pulsatile Variation of Arterial Geometry.

    PubMed

    Nam, Kweon-Ho; Kim, Juho; Ra, Gicheol; Lee, Chong Hyun; Paeng, Dong-Guk

    2015-01-01

    Despite considerable research efforts on the relationship between arterial geometry and cardiovascular pathology, information is lacking on the pulsatile geometrical variation caused by arterial distensibility and cardiomotility because of the lack of suitable in vivo experimental models and the methodological difficulties in examining the arterial dynamics. We aimed to investigate the feasibility of using a chick embryo system as an experimental model for basic research on the pulsatile variation of arterial geometry. Optical microscope video images of various arterial shapes in chick chorioallantoic circulation were recorded from different locations and different embryo samples. The high optical transparency of the chorioallantoic membrane (CAM) allowed clear observation of tiny vessels and their movements. Systolic and diastolic changes in arterial geometry were visualized by detecting the wall boundaries from binary images. Several to hundreds of microns of wall displacement variations were recognized during a pulsatile cycle. The spatial maps of the wall motion harmonics and magnitude ratio of harmonic components were obtained by analyzing the temporal brightness variation at each pixel in sequential grayscale images using spectral analysis techniques. The local variations in the spectral characteristics of the arterial wall motion were reflected well in the analysis results. In addition, mapping the phase angle of the fundamental frequency identified the regional variations in the wall motion directivity and phase shift. Regional variations in wall motion phase angle and fundamental-to-second harmonic ratio were remarkable near the bifurcation area. In summary, wall motion in various arterial geometry including straight, curved and bifurcated shapes was well observed in the CAM artery model, and their local and cyclic variations could be characterized by Fourier and wavelet transforms of the acquired video images. The CAM artery model with the spectral

  13. Feasibility Study of Ex Ovo Chick Chorioallantoic Artery Model for Investigating Pulsatile Variation of Arterial Geometry

    PubMed Central

    Nam, Kweon-Ho; Kim, Juho; Ra, Gicheol; Lee, Chong Hyun; Paeng, Dong-Guk

    2015-01-01

    Despite considerable research efforts on the relationship between arterial geometry and cardiovascular pathology, information is lacking on the pulsatile geometrical variation caused by arterial distensibility and cardiomotility because of the lack of suitable in vivo experimental models and the methodological difficulties in examining the arterial dynamics. We aimed to investigate the feasibility of using a chick embryo system as an experimental model for basic research on the pulsatile variation of arterial geometry. Optical microscope video images of various arterial shapes in chick chorioallantoic circulation were recorded from different locations and different embryo samples. The high optical transparency of the chorioallantoic membrane (CAM) allowed clear observation of tiny vessels and their movements. Systolic and diastolic changes in arterial geometry were visualized by detecting the wall boundaries from binary images. Several to hundreds of microns of wall displacement variations were recognized during a pulsatile cycle. The spatial maps of the wall motion harmonics and magnitude ratio of harmonic components were obtained by analyzing the temporal brightness variation at each pixel in sequential grayscale images using spectral analysis techniques. The local variations in the spectral characteristics of the arterial wall motion were reflected well in the analysis results. In addition, mapping the phase angle of the fundamental frequency identified the regional variations in the wall motion directivity and phase shift. Regional variations in wall motion phase angle and fundamental-to-second harmonic ratio were remarkable near the bifurcation area. In summary, wall motion in various arterial geometry including straight, curved and bifurcated shapes was well observed in the CAM artery model, and their local and cyclic variations could be characterized by Fourier and wavelet transforms of the acquired video images. The CAM artery model with the spectral

  14. Strain induced variations in band offsets and built-in electric fields in InGaN/GaN multiple quantum wells

    NASA Astrophysics Data System (ADS)

    Dong, L.; Mantese, J. V.; Avrutin, V.; Özgür, Ü.; Morkoç, H.; Alpay, S. P.

    2013-07-01

    The band structure, quantum confinement of charge carriers, and their localization affect the optoelectronic properties of compound semiconductor heterostructures and multiple quantum wells (MQWs). We present here the results of a systematic first-principles based density functional theory (DFT) investigation of the dependence of the valence band offsets and band bending in polar and non-polar strain-free and in-plane strained heteroepitaxial InxGa1-xN(InGaN)/GaN multilayers on the In composition and misfit strain. The results indicate that for non-polar m-plane configurations with [12¯10]InGaN//[12¯10]GaN and [0001]InGaN//[0001]GaN epitaxial alignments, the valence band offset changes linearly from 0 to 0.57 eV as the In composition is varied from 0 (GaN) to 1 (InN). These offsets are relatively insensitive to the misfit strain between InGaN and GaN. On the other hand, for polar c-plane strain-free heterostructures with [101¯0]InGaN//[101¯0]GaN and [12¯10]InGaN//[12¯10]GaN epitaxial alignments, the valence band offset increases nonlinearly from 0 eV (GaN) to 0.90 eV (InN). This is significantly reduced beyond x ≥ 0.5 by the effect of the equi-biaxial misfit strain. Thus, our results affirm that a combination of mechanical boundary conditions, epitaxial orientation, and variation in In concentration can be used as design parameters to rapidly tailor the band offsets in InGaN/GaN MQWs. Typically, calculations of the built-in electric field in complex semiconductor structures often must rely upon sequential optimization via repeated ab initio simulations. Here, we develop a formalism that augments such first-principles computations by including an electrostatic analysis (ESA) using Maxwell and Poisson's relations, thereby converting laborious DFT calculations into finite difference equations that can be rapidly solved. We use these tools to determine the bound sheet charges and built-in electric fields in polar epitaxial InGaN/GaN MQWs on c-plane Ga

  15. Metabonomic investigations of age- and batch-related variations in female NMRI mice using proton nuclear magnetic resonance spectroscopy.

    PubMed

    Li, Jia V; Saric, Jasmina; Yap, Ivan K S; Utzinger, Jürg; Holmes, Elaine

    2013-12-01

    The NMRI outbred mouse model is widely used for studying metabolic disease, toxicity, and infection, yet information regarding baseline metabolism of this murine strain is relatively sparse. Using different batches of female NMRI mice, we assessed the stability of the metabolic phenotype with increasing age and weight, and determined the influence of acclimatization on the metabolic profile of biofluids (urine, plasma, and faecal water). Differences in urinary concentrations of 3-ureidopropionate, 2-oxoisocaproate, trimethylamine, and glycine were detected between three batches of 9-week-old female NMRI mice using proton nuclear magnetic resonance ((1)H NMR) spectroscopy coupled with multivariate statistical analysis. An acclimatization period of 2 weeks was imposed after the mice entered the laboratory environment. Strong differences in the faecal metabolome pre- and post-acclimatization were found (reduction in amino acid concentrations), whilst the urine metabolome showed increased levels of trimethylamine-N-oxide, phenylacetyl glycine, and hippurate with decreased excretion of formate and betaine post-acclimatization. Temporal variation in the metabolite profiles over a 16-week study stabilized around 7-week-old animals. The results from this study strongly argue for inclusion of an acclimatization period prior to starting an investigative procedure, and suggest that the metabolic phenotypes of female NMRI mice are more stable at around 7 weeks of age. We have also identified a set of metabolites that are more susceptible to variation in concentration. This information can serve as a benchmark in order to establish confidence in systematic variation attributable to pathology or therapeutic intervention above the background metabolic variation in the NMRI mouse. PMID:24121299

  16. Computational classification of different wild-type zebrafish strains based on their variation in light-induced locomotor response.

    PubMed

    Gao, Yuan; Zhang, Gaonan; Jelfs, Beth; Carmer, Robert; Venkatraman, Prahatha; Ghadami, Mohammad; Brown, Skye A; Pang, Chi Pui; Leung, Yuk Fai; Chan, Rosa H M; Zhang, Mingzhi

    2016-02-01

    Zebrafish larvae display a rapid and characteristic swimming behaviour after abrupt light onset or offset. This light-induced locomotor response (LLR) has been widely used for behavioural research and drug screening. However, the locomotor responses have long been shown to be different between different wild-type (WT) strains. Thus, it is critical to define the differences in the WT LLR to facilitate accurate interpretation of behavioural data. In this investigation, we used support vector machine (SVM) models to classify LLR data collected from three WT strains: AB, TL and TLAB (a hybrid of AB and TL), during early embryogenesis, from 3 to 9 days post-fertilisation (dpf). We analysed both the complete dataset and a subset of the data during the first 30after light change. This initial period of activity is substantially driven by vision, and is also known as the visual motor response (VMR). The analyses have resulted in three major conclusions: First, the LLR is different between the three WT strains, and at different developmental stages. Second, the distinguishable information in the VMR is comparable to, if not better than, the full dataset for classification purposes. Third, the distinguishable information of WT strains in the light-onset response differs from that in the light-offset response. While the classification accuracies were higher for the light-offset than light-onset response when using the complete LLR dataset, a reverse trend was observed when using a shorter VMR dataset. Together, our results indicate that one should use caution when extrapolating interpretations of LLR/VMR obtained from one WT strain to another. PMID:26688204

  17. Local Strain Evaluation of Strained-SOI Structures

    NASA Astrophysics Data System (ADS)

    Usuda, Koji; Mizuno, Tomohisa; Numata, Toshinori; Tezuka, Tsutomu; Sugiyama, Naoharu; Moriyama, Yoshihiko; Nakaharai, Shu; Takagi, Shin-Ichi

    The strain relaxation within a strained-Si on SiGe on insulator (SGOI) structure might be one of the key issues in development of strained-Si MOSFET devices for high-performance ULSIs. In order to investigate the strain relaxation within the thin strained-Si layers, a new characterization technique to directly evaluate a local strain variation in the layers is required. Hence, we have developed the nano-beam electron diffraction (NBD) method which has a lateral resolution of 10 nm and a strain resolution of 0.1%. In this paper, we discuss a detailed investigation of whether the NBD method could be utilized to clarify a strain in a strained-Si layer on the SGOI structures.

  18. Biochemical analysis of bovine viral diarrhea virus polypeptides and studies of strain variation

    SciTech Connect

    Raisch, K.P.

    1989-01-01

    Intracellular viral-specific polypeptides from the National Animal Disease Laboratory (NADL) strain of bovine viral diarrhea virus were studied by biosynthesis labelling, radioimmunoprecipitation (RIP), hypertonic initiation block (HIB) and polyacrylamide gel electrophoresis (PAGE). Eighteen virus-specific proteins were identified; thirteen were glycosylated (gp170, p135, p130, gp118, gp82, p80, gp74, gp63, gp60, p59, gp53, gp50, gp45, gp42, p37, gp32, gp25 and p22). When glycosylation was inhibited by tunicamycin, five {sup 35}S-methionine labelled proteins displayed increased electrophoretic mobility (gp170 to p165, gp74 to p66, gp53 to p45, gp50 to p42 and gp25 to p20) and four could not be identified. Similar shifts in mobility were observed following in vitro deglycosylation with endoglycosidases H and F indicating that the nine glycoproteins contained N-linked simple or high mannose containing moieties. Biosynthetic labelling in the presence of the ionophore, monensin, or in vitro deglycosylation with the endoglycosidase, O-glycanase, had no effect, which is consistent with the absence of O-linked carbohydrates in BVDV-specific proteins. N-linked glycosylation of BVDV proteins is critical for infectivity, because the virus from cells treated with tunicamycin was devoid of infectivity, whereas the virus from monensin-treated cells was fully infective. Partitioning of p130, p59, gp53-50, and p37 into solutions of Triton X-114 tentatively identified these molecules as partially hydrophobic transmembrane proteins. Biosynthesis in the presence of {sup 3}H-myristate and {sup 3}H-palmitate did not result in specifically labelled viral proteins indicating predominantly noncovalent nature of putative interactions of these proteins with membranes. Partial proteolytic peptide mapping revealed similarities among gp170, p130 and p80 and between gp53 and gp50.

  19. Chlorine inactivation of Salmonella Kentucky isolated from chicken carcasses: Evaluation of strain variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inactivation behavior of antibiotic resistant and non-resistant Salmonella Kentucky recovered from pre- and post-chill whole broiler carcasses in a large poultry plant was investigated by the exposure to 30 ppm chlorine for selected time intervals. The antibiotic resistance profiles were non-res...

  20. Investigation of toxin gene diversity and antimicrobial resistance of Clostridium difficile strains

    PubMed Central

    ZHU, SHANSHAN; ZHANG, HUAPING; ZHANG, XINSHENG; WANG, CHAO; FAN, GUANGMING; ZHANG, WEIFENG; SUN, GANG; CHEN, HUIHONG; ZHANG, LIMING; LI, ZHAOYUN

    2014-01-01

    The incidence of Clostridium difficile infection (CDI) has been previously reported in a number of studies. However, data collected from the Chinese population is limited. In the present study, the diversity of the toxin genes, tcdA and tcdB, of 57 Clostridium difficile (C. difficile) isolates from a Chinese population were investigated by polymerase chain reaction (PCR) (38 A+B+, 14 A-B+ and 5 A-B−). Quantitative PCR was used to check the expression of these two genes and it was found that the genes were not expressed by all the strains. The absence of tcdA or tcdB expression in certain strains could be due to the lower expression of tcdD and the higher expression of tcdC, which are positive and negative regulators for these two toxin genes, respectively. In addition, the antimicrobial susceptibilities of 57 isolates were investigated. Therefore, these data would aid in the future prevention of CDI outbreaks and improve the understanding of the infection. PMID:25054021

  1. Investigation of toxin gene diversity and antimicrobial resistance of Clostridium difficile strains.

    PubMed

    Zhu, Shanshan; Zhang, Huaping; Zhang, Xinsheng; Wang, Chao; Fan, Guangming; Zhang, Weifeng; Sun, Gang; Chen, Huihong; Zhang, Liming; Li, Zhaoyun

    2014-09-01

    The incidence of Clostridium difficile infection (CDI) has been previously reported in a number of studies. However, data collected from the Chinese population is limited. In the present study, the diversity of the toxin genes, tcdA and tcdB, of 57 Clostridium difficile (C. difficile) isolates from a Chinese population were investigated by polymerase chain reaction (PCR) (38 A(+)B(+), 14 A(-)B(+) and 5 A(-)B(-)). Quantitative PCR was used to check the expression of these two genes and it was found that the genes were not expressed by all the strains. The absence of tcdA or tcdB expression in certain strains could be due to the lower expression of tcdD and the higher expression of tcdC, which are positive and negative regulators for these two toxin genes, respectively. In addition, the antimicrobial susceptibilities of 57 isolates were investigated. Therefore, these data would aid in the future prevention of CDI outbreaks and improve the understanding of the infection. PMID:25054021

  2. Prediction of variation in d-orbital occupancy in strain induced tetragonal phase of BiFeO3 thin film

    NASA Astrophysics Data System (ADS)

    Verma, Manish; Ram, Kanik

    2016-05-01

    A theoretical study of the possible variation of d-orbital occupancy while going from the rhombohedral bulk phase to the strain induced tetragonal phase of BiFeO3 thin film has been carried out. A possible existence of an intermediate spin (IS) state, S=3/2 and a low spin (LS) state, S=1/2 in the tetragonal phase has been predicted, thereby clearly establishing the role of strain behind the d-orbital occupancy.

  3. Investigation of mid-infrared second harmonic generation in strained germanium waveguides.

    PubMed

    De Leonardis, Francesco; Troia, Benedetto; Soref, Richard A; Passaro, Vittorio M N

    2016-05-16

    In this paper we present a detailed theoretical investigation of second harmonic generation in strained germanium waveguides operating at the mid infrared pump wavelength of 4 μm. The effective second order susceptibility has been estimated through a multiphysics approach considering the residual stress of the SiNx cladding film. Furthermore, general physical features have been investigated by means of a comparative analysis of SHG performance as a function of input pump power, linear and nonlinear phase mismatching, effective recombination carrier lifetime, and temperature, taking into account both continuous and pulsed regimes. Finally, periodically poled germanium devices have been explored with the aim to improve the SHG efficiency. In the same operative conditions, efficiencies of 0.6% and 0.0018% have been obtained in poled and not-poled waveguides, respectively. PMID:27409935

  4. Topographical variations of the strain-dependent zonal properties of tibial articular cartilage by microscopic MRI.

    PubMed

    Lee, Ji Hyun; Badar, Farid; Kahn, David; Matyas, John; Qu, Xianggui; Chen, Christopher T; Xia, Yang

    2014-06-01

    The topographical variations of the zonal properties of canine articular cartilage over the medial tibia were evaluated as the function of external loading by microscopic magnetic resonance imaging (µMRI). T2 and T1 relaxation maps and GAG (glycosaminoglycan) images from a total of 70 specimens were obtained with and without the mechanical loading at 17.6 µm depth resolution. In addition, mechanical modulus and water content were measured from the tissue. For the bulk without loading, the means of T2 at magic angle (43.6 ± 8.1 ms), absolute thickness (907.6 ± 187.9 µm) and water content (63.3 ± 9.3%) on the meniscus-covered area were significantly lower than the means of T2 at magic angle (51.1 ± 8.5 ms), absolute thickness (1251.6 ± 218.4 µm) and water content (73.2 ± 5.6%) on the meniscus-uncovered area. However GAG (86.0 ± 15.3 mg/ml) on the covered area was significantly higher than GAG (70.0 ± 8.8 mg/ml) on the uncovered area. Complex relationships were found in the tissue properties as the function of external loading. The tissue parameters in the superficial zone changed more profoundly than the same properties in the radial zone. The tissue parameters in the meniscus-covered areas changed differently when comparing with the same parameters in the uncovered areas. This project confirms that the load-induced changes in the molecular distribution and structure of cartilage are both depth-dependent and topographically distributed. Such detailed knowledge of the tibial layer could improve the early detection of the subtle softening of the cartilage that will eventually lead to the clinical diseases such as osteoarthritis. PMID:24559385

  5. Investigating the variation of terrestrial water storage under changing climate and land cover

    NASA Astrophysics Data System (ADS)

    Fang, Y.; Niu, G. Y.; Zhang, X.; Troch, P. A. A.

    2015-12-01

    Terrestrial water storage (TWS) consists of groundwater, soil moisture, snow and ice, lakes and rivers and water contained in biomass. The water storage, especially the subsurface storage, is an essential property of the catchment, which controls climate, hydrological and biogeochemical processes at different scales. During the past decades, climate and land cover change has been proved to exert significant influences on hydrological processes which in turn alters the TWS variation. In order to better understand the interaction and feedback mechanism between TWS and earth system, it is necessary to quantify the effects of climate and land cover change on TWS variation. Direct estimation of total TWS has been made possible by the Gravity Recovery And Climate Experiment (GRACE) satellites that measures the earth gravity field. At present, few efforts were made to explicitly investigate the TWS variation under changing climate and land cover. GRACE data has its own limitations. One is its temporal coverage is short, it's only available since 2002, which is not sufficient to reflect the trend due to climate and land cover change. The other reason is that it cannot distinguish different components contributing to TWS. The limitation of TWS observation data can be overcame by numerical models developed to reproduce or to predict different earth system processes. After calibration and validation, with limited observations, these models can be trusted to extend our knowledge to where observations are not available both in time and space. In this study, based on Noah-MP LSM and satellite and ground data, we aim to: (1) Investigate the variation of total TWS as well as its components over Upper Colorado River Basin from 1990 to 2014. (2) Identify the major factors that control the TWS variation. (3) Quantify how the changing climate and land cover affect TWS variation in the same period.

  6. Occurrence of 20S RNA and 23S RNA replicons in industrial yeast strains and their variation under nutritional stress conditions.

    PubMed

    López, Victoria; Gil, Rosario; Vicente Carbonell, José; Navarro, Alfonso

    2002-04-01

    We have characterized industrial yeast strains used in the brewing, baking, and winemaking industries for the presence or absence of cytoplasmic single-stranded 20S and 23S RNAs. Furthermore, the variation of intracellular concentrations of these replicons in brewing and laboratory strains under nutritional stress conditions was determined. Our results show a correlation between the relative abundance of these replicons and exposure of yeast to nutritionally stressful conditions, indicating that these RNAs could be employed as molecular probes to evaluate the exposure of 20S(+) and/or 23S(+) yeast strains to stress situations during industrial manipulation. During this study, several 20S(-)23S(+) Saccharomyces cerevisiae strains were isolated and identified. This is the first time that a yeast strain containing only 23S RNA has been reported, demonstrating that 20S RNA is not required for 23S RNA replication. PMID:11921103

  7. Six low-strain zinc-blende half metals: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Pask, J. E.; Yang, L. H.; Fong, C. Y.; Pickett, W. E.; Dag, S.

    2003-06-01

    A class of spintronic materials, the zinc-blende (ZB) half metals, has recently been synthesized in thin-film form. We apply all-electron and pseudopotential ab initio methods to investigate the electronic and structural properties of ZB Mn and Cr pnictides and carbides, and find six compounds to be half metallic at or near their respective equilibrium lattice constants, making them excellent candidates for growth at low strain. Based on these findings, we further propose substrates on which the growth may be accomplished with minimum strain. Our findings are supported by the recent successful synthesis of ZB CrAs on GaAs and ZB CrSb on GaSb, where our predicted equilibrium lattice constants are within 0.5% of the lattice constants of the substrates on which the growth was accomplished. We confirm previous theoretical results for ZB MnAs, but find ZB MnSb to be half metallic at its equilibrium lattice constant, whereas previous work has found it to be only nearly so. We report here two low-strain half metallic ZB compounds, CrP and MnC, and suggest appropriate substrates for each. Unlike the other five compounds, we predict ZB MnC to become/remain half metallic with compression rather than expansion, and to exhibit metallicity in the minority- rather than majority-spin channel. These fundamentally different properties of MnC can be connected to substantially greater p-d hybridization and d-d overlap, and correspondingly larger bonding-antibonding splitting and smaller exchange splitting. We examine the relative stability of each of the six ZB compounds against NiAs and MnP structures, and find stabilities for the compounds not yet grown comparable to those already grown.

  8. Uranium dioxide fuel cladding strain investigation with the use of CYGRO-2 computer program

    NASA Technical Reports Server (NTRS)

    Smith, J. R.

    1973-01-01

    Previously irradiated UO2 thermionic fuel pins in which gross fuel-cladding strain occurred were modeled with the use of a computer program to define controlling parameters which may contribute to cladding strain. The computed strain was compared with measured strain, and the computer input data were studied in an attempt to get agreement with measured strain. Because of the limitations of the program and uncertainties in input data, good agreement with measured cladding strain was not attained. A discussion of these limitations is presented.

  9. Investigation of geometric uncertainty introduced dosimetric variation in intensity modulated proton therapy (IMPT) and its intervention

    NASA Astrophysics Data System (ADS)

    Zhang, Miao

    The intensity modulated proton therapy (IMPT) can generate plans with reduced normal tissue toxicity and increased target dose conformity. However, geometric uncertainty associated with the treatment process could introduce large dose variations between the delivered dose distribution and the planned. There are three common types of geometric uncertainty: setup uncertainty, inter-, and intra-fractional organ motion. This thesis work will investigate setup uncertainty and inter-fractional organ motion introduced dose variation and find solutions to minimize such variations. A proton treatment planning system was developed by using Geant4 Monte Carlo toolbox as the dose calculation engine. The setup uncertainty was studied on the head and neck cancer site. Plan delivery simulation shown large dose variation occurred even with small amount of setup uncertainty. Two intervention strategies were investigated: (i) different proton pencil beam sizes, and (ii) the energy margin. By varying proton pencil beam size, we found the larger the beam size the less the dose variation, nevertheless the higher normal tissue dose. The energy margin is a planning strategy incorporating the possible motion effect into the planning stage by assigning proton pencil beams an energy value large enough to guarantee protons will travel to where they are planned. The energy margin solution was tested to be effective to minimize the dose variation in the distal edge tracking (DET) based IMPT. The inter-fractional motion was studied by looking at the daily prostate shift in the prostate cancer treatment. Delivery simulation for prostate cancer IMPT shown large dose variation would result even if the image guidance (IG) technique was used to realign the prostate back to its original location on the planning CT. A novel on-line adaptive image guided IMPT (A-IG-IMPT) technique was proposed to minimize the dose variation. By updating the energy value for individual proton pencil beam from the on

  10. Experimental investigation of stress and strain fields in a ductile matrix surrounding an elastic inclusion

    SciTech Connect

    Nugent, E.E.; Calhoun, R.B.; Mortensen, A.

    2000-04-19

    A method for measuring stress and strain distributions within a ductile material deforming by dislocational slip is developed. The method exploits the transparency and room-temperature ductility of silver chloride, and combines the techniques of photoelasticity and marker tracking. This method is used to investigate the deformation of an elasto-plastic ductile matrix surrounding an isolated stiff fiber, the grain size of the material being slightly smaller than the fiber length. The data are compared to predictions of finite element calculations which take the matrix to be an isotropic elasto-plastic von Mises continuum. It is found that this model does not fully capture all of the features of the experimental data. Data suggest that the cause for observed discrepancies is the strong influence exerted by grain boundaries and grain orientation on the distribution of stress and strain within the matrix. A comparison is also made between the data and predictions of the Eshelby equivalent inclusion calculation, to show that a far higher level of discrepancy results than with the finite element calculations; this is caused by the fact that the Eshelby equivalent inclusion calculation is essentially elastic and thus allows significant stress concentrations.

  11. Quantitative investigation of ligament strains during physical tests for sacroiliac joint pain using finite element analysis.

    PubMed

    Kim, Yoon Hyuk; Yao, Zhidong; Kim, Kyungsoo; Park, Won Man

    2014-06-01

    It may be assumed that the stability is affected when some ligaments are injured or loosened, and this joint instability causes sacroiliac joint pain. Several physical examinations have been used to diagnose sacroiliac pain and to isolate the source of the pain. However, more quantitative and objective information may be necessary to identify unstable or injured ligaments during these tests due to the lack of understanding of the quantitative relationship between the physical tests and the biomechanical parameters that may be related to pains in the sacroiliac joint and the surrounding ligaments. In this study, a three-dimensional finite element model of the sacroiliac joint was developed and the biomechanical conditions for six typical physical tests such as the compression test, distraction test, sacral apex pressure test, thigh thrust test, Patrick's test, and Gaenslen's test were modelled. The sacroiliac joint contact pressure and ligament strain were investigated for each test. The values of contact pressure and the combination of most highly strained ligaments differed markedly among the tests. Therefore, these findings in combination with the physical tests would be helpful to identify the pain source and to understand the pain mechanism. Moreover, the technology provided in this study might be a useful tool to evaluate the physical tests, to improve the present test protocols, or to develop a new physical test protocol. PMID:24378472

  12. Investigation of the Enteric Pathogenic Potential of Oral Campylobacter concisus Strains Isolated from Patients with Inflammatory Bowel Disease

    PubMed Central

    Octavia, Sophie; Day, Andrew S.; Riordan, Stephen M.; Grimm, Michael C.; Lan, Ruiting; Lemberg, Daniel; Tran, Thi Anh Tuyet; Zhang, Li

    2012-01-01

    Background Campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (IBD). This study investigated if patients with IBD are colonized with specific oral C. concisus strains that have potential to cause enteric diseases. Methodology Seventy oral and enteric C. concisus isolates obtained from eight patients with IBD and six controls were examined for housekeeping genes by multilocus sequence typing (MLST), Caco2 cell invasion by gentamicin-protection-assay, protein analysis by mass spectrometry and SDS-PAGE, and morphology by scanning electron microscopy. The whole genome sequenced C. concisus strain 13826 which was isolated from an individual with bloody diarrhea was included in MLST analysis. Principal Findings MLST analysis showed that 87.5% of individuals whose C. concisus belonged to Cluster I had inflammatory enteric diseases (six IBD and one with bloody diarrhea), which was significantly higher than that in the remaining individuals (28.6%) (P<0.05). Enteric invasive C. concisus (EICC) oral strain was detected in 50% of patients with IBD and none of the controls. All EICC strains were in Cluster 1. The C. concisus strain colonizing intestinal tissues of patient No. 1 was closely related to the oral C. concisus strain from patient No. 6 and had gene recombination with the patient’s own oral C. concisus. The oral and intestinal C. concisus strains of patient No. 3 were the same strain. Some individuals were colonized with multiple oral C. concisus strains that have undergone natural recombination. Conclusions This study provides the first evidence that patients with IBD are colonized with specific oral C. concisus strains, with some being EICC strains. C. concisus colonizing intestinal tissues of patients with IBD at least in some instances results from an endogenous colonization of the patient’s oral C. concisus and that C. concisus strains undergo natural recombination. PMID

  13. Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

    PubMed Central

    Wu, Fei; Liu, Fang; Ye, Xun; Mougin, Bruno; Meng, Xia; Du, Xiang

    2011-01-01

    Background Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. Methodology/Principal Findings Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R2 methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. Conclusions By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study. PMID:22046403

  14. Investigation of flaw geometry and loading effects on plane strain fracture in metallic structures

    NASA Technical Reports Server (NTRS)

    Hall, L. R.; Finger, R. W.

    1971-01-01

    The effects on fracture and flaw growth of weld-induced residual stresses, combined bending and tension stresses, and stress fields adjacent to circular holes in 2219-T87 aluminum and 5AI-2.5Sn(ELI) titanium alloys were evaluated. Static fracture tests were conducted in liquid nitrogen; fatigue tests were performed in room air, liquid nitrogen, and liquid hydrogen. Evaluation of results was based on linear elastic fracture mechanics concepts and was directed to improving existing methods of estimating minimum fracture strength and fatigue lives for pressurized structure in spacecraft and booster systems. Effects of specimen design in plane-strain fracture toughness testing were investigated. Four different specimen types were tested in room air, liquid nitrogen and liquid hydrogen environments using the aluminum and titanium alloys. Interferometry and holograph were used to measure crack-opening displacements in surface-flawed plexiglass test specimens. Comparisons were made between stress intensities calculated using displacement measurements, and approximate analytical solutions.

  15. An Evaluation of Constitutive Laws and their Ability to Predict Flow Stress over Large Variations in Temperature, Strain, and Strain Rate Characteristic of Friction Stir Welding

    NASA Astrophysics Data System (ADS)

    Kuykendall, Katherine

    2011-07-01

    Constitutive laws commonly used to model friction stir welding have been evaluated, both qualitatively and quantitatively, and a new application of a constitutive law which can be extended to materials commonly used in FSW is presented. Existing constitutive laws have been classified as path-dependent or path-independent. Path-independent laws have been further classified according to the physical phenomena they capture: strain hardening, strain rate hardening, and/or thermal softening. Path-dependent laws can track gradients in temperature and strain rate characteristic to friction stir welding; however, path-independent laws cannot. None of the path-independent constitutive laws evaluated has been validated over the full range of strain, strain rate, and temperature in friction stir welding. Holding all parameters other than constitutive law constant in a friction stir weld model resulted in temperature differences of up to 21%. Varying locations for maximum temperature difference indicate that the constitutive laws resulted in different temperature profiles. The Sheppard and Wright law is capable of capturing saturation but incapable of capturing strain hardening with errors as large as 57% near yield. The Johnson-Cook law is capable of capturing strain hardening; however, its inability to capture saturation causes over-predictions of stress at large strains with errors as large as 37% near saturation. The Kocks and Mecking model is capable of capturing strain hardening and saturation with errors less than 5% over the entire range of plastic strain. The Sheppard and Wright and Johnson-Cook laws are incapable of capturing transients characteristic of material behavior under interrupted temperature or strain rate. The use of a state variable in the Kocks and Mecking law allows it to predict such transients. Constants for the Kocks and Mecking model for AA 5083, AA 3004, and Inconel 600 were determined from Atlas of Formability data. Constants for AA 5083 and AA

  16. Investigation of Strain Aging in the Ordered Intermetallic Compound beta-NiAl. Ph.D. Thesis Final Contractor Report

    NASA Technical Reports Server (NTRS)

    Weaver, Mark Lovell

    1995-01-01

    The phenomenon of strain aging has been investigated in polycrystalline and single crystal NiAl alloys at temperatures between 300 and 1200 K. Static strain aging studies revealed that after annealing at 1100 K for 7200 s (i.e., 2h) followed by furnace cooling, high purity, nitrogen-doped and titanium-doped polycrystalline alloys exhibited continuous yielding, while conventional-purity and carbon-doped alloys exhibited distinct yield points and Luders strains. Prestraining by hydrostatic pressurization removed the yield points, but they could be reintroduced by further annealing treatments. Yield points could be reintroduced more rapidly if the specimens were prestrained uniaxially rather than hydrostatically, owing to the arrangement of dislocations into cell structures during uniaxial deformation. The time dependence of the strain aging events followed at t(exp 2/3) relationship suggesting that the yield points observed in polycrystalline NiAl were the result of the pinning of mobile dislocations by interstitials, specifically carbon. Between 700 and 800 K, yield stress plateaus, yield stress transients upon a ten-fold increase in strain rate, work hardening peaks, and dips in the strain rate sensitivity (SRS) have been observed in conventional-purity and carbon-doped polycrystals. In single crystals, similar behavior was observed; in conventional-purity single crystals, however, the strain rate sensitivity became negative resulting in serrated yielding, whereas, the strain rate sensitivity stayed positive in high purity and in molybdenum-doped NiAl. These observations are indicative of dynamic strain aging (DSA) and are discussed in terms of conventional strain aging theories. The impact of these phenomena on the composition-structure-property relations are discerned. Finally, a good correlation has been demonstrated between the properties of NiAl alloys and a recently developed model for strain aging in metals and alloys developed by Reed-Hill et al.

  17. Investigation of TEC Variations over Mid-Latitude during Quit and Disturbed Days of March 2015

    NASA Astrophysics Data System (ADS)

    Atıcı, Ramazan; Saǧır, Selçuk; Güzel, Esat

    2016-07-01

    The variations during 09-14-March-2015 quit days and 15-20 March 2015 disturbed days of Total Electron Content (TEC) values (provided by IONOLAB group) obtained by analysis the data from Ankara Global Position System (GPS) station of Turkey located at mid-latitude, IRI -2012 model the and IRI-PLUS model are investigated. Also, the variations of the geomagnetic, interplanetary and solar wind parameters are examined. As a result of investigations, TEC values from all three models are not change too much at quit days. Unlike, at the disturbed days, although IRI-2012 and IRI-PLUS TEC values are not change too much, a noticeable change in GPS-TEC values is occurred. GPS-TEC values are rapidly increased on 17-March 2015 to be severe magnetic storm (Dst = -124 nT). Then, on following days it was observed to significantly decrease. Thus, it is said that GPS-TEC values are more sensitive than IRI-2012 and IRI-PLUS models to variations occurred on disturbed days.

  18. Strain variations in the murine cellular immune response to the phenolic glycolipid I antigen of Mycobacterium leprae.

    PubMed Central

    Koster, F T; Teuscher, C; Matzner, P; Umland, E; Yanagihara, D; Brennan, P J; Tung, K S

    1986-01-01

    The cellular immune response to the Mycobacterium leprae-specific phenolic glycolipid I was examined in inbred mice immunized with M. leprae by in vivo delayed cutaneous hypersensitivity and in vitro lymphocyte proliferation. Whereas all mouse strains responded to M.leprae-induced delayed-type hypersensitivity and lymphocyte proliferation, only BALB.K was responsive in both assays to the glycolipid. Responsiveness was determined in part by non-H-2 genes, while the influence of H-2 genes was not apparent. Among congenic BALB/c mice differing only at Igh-C allotype loci, variations in responsiveness were found in both delayed-type hypersensitivity and lymphocytes proliferation assays, indicating a possible role for Igh-C loci-linked genes. Unresponsiveness in the lymphocyte proliferation assay to the glycolipid was inherited as a dominant trait in one set of responder X nonresponder F1 progeny. We conclude that after immunization with M. leprae organisms, the cell-mediated responses to the glycolipid, endowed with a single carbohydrate epitope, are under polygenic control, predominantly non-H-2-linked genes. PMID:3510979

  19. Investigation of TEC variations over the magnetic equatorial and equatorial anomaly regions of the African sector

    NASA Astrophysics Data System (ADS)

    Oryema, B.; Jurua, E.; D'ujanga, F. M.; Ssebiyonga, N.

    2015-11-01

    This paper presents the annual, seasonal and diurnal variations in ionospheric TEC along the African equatorial region. The study also investigated the effects of a geomagnetic storm on ionospheric TEC values. Dual-frequency GPS derived TEC data obtained from four stations within the African equatorial region for the high solar activity year 2012 were used in this study. Annual variations showed TEC having two peaks in the equinoctial months, while minima values were observed in the summer and winter solstices. The diurnal pattern showed a pre-dawn minimum, a steady increase from about sunrise to an afternoon maximum and then a gradual fall after sunset to attain a minimum just before sunrise. Nighttime enhancements of TEC were observed mostly in the equinoctial months. There was comparably higher percentage TEC variability during nighttime than daytime and highest during equinoxes, moderate in winter and least during summer solstice. TEC was observed to exhibit a good correlation with geomagnetic storm indices.

  20. Investigation of photospheric temperature gradient variations using limb darkening measurements and simulations

    NASA Astrophysics Data System (ADS)

    Criscuoli, Serena; Foukal, Peter V.

    2016-05-01

    The temperature stratifications of magnetic elements and unmagnetized plasma are different, so that changes of the facular and network filling factor over the cycle modify the average temperature gradient in the photosphere.Such variations have been suggested to explain irradiance measurements obtained by the SIM spectrometers in he visible and infrared spectral ranges. On the other hand, limb darkening measurements show no dependence upon activity level. We investigate the sensitivity of limb darkening to changes in network area filling factor using a 3-D MHD model of the magnetized photosphere. We find that the expected limb darkening change due to the measured 11- yr variation in filling factor lies outside the formal 99% confidence limit of the limb darkening measurements. This poses important constraints for observational validation of 3D-MHD simulations.

  1. [Investigation of plasmid-mediated quinolone resistance in Escherichia coli strains].

    PubMed

    Aktepe, Orhan Cem; Aşık, Gülşah; Cetinkol, Yeliz; Biçmen, Meral; Gülay, Zeynep

    2012-01-01

    Quinolones are widely used antimicrobial agents, particularly for the treatment of infections caused by gram-negative bacilli such as E.coli. As a consequence, quinolone resistance has been increasing among this species in recent years. Bacterial resistance to quinolones usually results from mutations in the chromosomal genes which encode topoisomerases and also the expression of efflux pumps and loss of porines contributed to development of quinolone resistance. However, recent studies have shown that the spread and increase of quinolone resistance may be due to the transfer of plasmid-mediated genes. To date, three groups of plasmid-mediated quinolone resistance genes, namely qnr, aac(6')-Ib-cr, and qepA, have been described. The aim of this study was to investigate the presence of plasmid-mediated quinolone resistance genes in E.coli clinical isolates. A total of 112 quinolone-resistant E.coli strains isolated from different clinical specimens (84 urine, 16 blood, 10 wound, 2 bronchoalveolar lavage) of which 78 (69.6%) were extended-spectrum beta-lactamase (ESBL) positive, in Afyon Kocatepe University Hospital, Microbiology Laboratory were included in the study. In the isolates, qnrA, qnrB, qnrS, qnrC, qepA, and aac(6')-1b-cr plasmid genes were analysed by polymerase chain reaction (PCR). After aac(6')- 1b determinant was amplified by PCR, all aac(6')-1b positive amplicons were analyzed by digestion with BseGI restriction enzyme to identify aac(6')-1b-cr variant. It was found that, none of the strains horboured qnrA, qnrB, qnrS, qnrC and qepA genes, however, plasmid-mediated quinolone resistance gene aac(6')-1b-cr was found positive in 59.8% (67/112) of the strains. It was notable that 86.6% (58/67) of those isolates were ESBL producers. The rates of quinolone resistance among E.coli isolates infections were high in our region and an increasing trend has been observed in recent years. Our data indicated that the presence of plasmid- mediated resistance genes

  2. Full-Field Strain Methods for Investigating Failure Mechanisms in Triaxial Braided Composites

    NASA Technical Reports Server (NTRS)

    Littell, Justin D.; Binienda, Wieslaw K.; Goldberg, Robert K.; Roberts, Gary D.

    2008-01-01

    Recent advancements in braiding technology have led to commercially viable manufacturing approaches for making large structures with complex shape out of triaxial braided composite materials. In some cases, the static load capability of structures made using these materials has been higher than expected based on material strength properties measured using standard coupon tests. A more detailed investigation of deformation and failure processes in large-unit-cell-size triaxial braid composites is needed to evaluate the applicability of standard test methods for these materials and to develop alternative testing approaches. This report presents some new techniques that have been developed to investigate local deformation and failure using digital image correlation techniques. The methods were used to measure both local and global strains during standard straight-sided coupon tensile tests on composite materials made with 12- and 24-k yarns and a 0 /+60 /-60 triaxial braid architecture. Local deformation and failure within fiber bundles was observed and correlations were made between these local failures and global composite deformation and strength.

  3. Investigation on vibration of single-walled carbon nanotubes by variational iteration method

    NASA Astrophysics Data System (ADS)

    Ahmadi Asoor, A. A.; Valipour, P.; Ghasemi, S. E.

    2016-02-01

    In this paper, the variational iteration method (VIM) has been used to investigate the non-linear vibration of single-walled carbon nanotubes (SWCNTs) based on the nonlocal Timoshenko beam theory. The accuracy of results is examined by the fourth-order Runge-Kutta numerical method. Comparison between VIM solutions with numerical results leads to highly accurate solutions. Also, the behavior of deflection and frequency in vibrations of SWCNTs are studied. The results show that frequency of single walled carbon nanotube versus amplitude increases by increasing the values of B.

  4. Photomechanical investigations on the stress-strain relationship in dentine macrostructure.

    PubMed

    Kishen, A; Asundi, A

    2005-01-01

    In this study photomechanical experiments were carried out to examine the relationship between macroscopic mechanical stress and strain gradients within the root dentine structure. Three-dimensional digital photoelasticity was used to study the stress distribution patterns in tooth models, while digital moire interferometry was used to study the strain gradients within the natural teeth. The stress analysis showed a distinct bending stress distribution, along faciolingual plane in the coronal and cervical regions of the tooth. There was a reduction in bending towards the apical third of the tooth model. The strain analysis displayed strain gradients in the axial (along the long axis of the tooth) and lateral (perpendicular to the long axis of the tooth) directions in dentine. There was a conspicuous reduction in strains from the cervical to the apical third of the root dentine. The root dentine displayed uniform distribution of normal strains. Although there was a steep increase in stresses from the inner core region to the outer surface of an isotropic tooth model, there were more uniform strain gradients in the natural dentine structure. It is apparent from these observations that complex organization of material properties facilitated distinct strain gradients in dentine structure during mechanical functions. PMID:16229654

  5. Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus

    PubMed Central

    Bullman, Susan; Lucid, Alan; Corcoran, Daniel; Sleator, Roy D.; Lucey, Brigid

    2013-01-01

    The recent detection and isolation of C. ureolyticus from patients with diarrhoeal illness and inflammatory bowel diseases warrants further investigation into its role as an emerging pathogen of the human gastrointestinal tract. Regarding the pathogenic mechanisms employed by this species we provide the first whole genome analysis of two C. ureolyticus isolates including the type strain. Comparative analysis, subtractive hybridisation and gene ontology searches against other Campylobacter species identifies the high degree of heterogenicity between C. ureolyticus isolates, in addition to the identification of 106 putative virulence associated factors, 52 of which are predicted to be secreted. Such factors encompass each of the known virulence tactics of pathogenic Campylobacter spp. including adhesion and colonisation (CadF, PEB1, IcmF and FlpA), invasion (ciaB and 16 virB-virD4 genes) and toxin production (S-layer RTX and ZOT). Herein, we provide the first virulence catalogue for C. ureolyticus, the components of which theoretically provide this emerging species with sufficient arsenal to establish pathology. PMID:24023611

  6. Investigation of mycoviruses in endophytic and phytopathogenic strains of Colletotrichum from different hosts.

    PubMed

    Rosseto, P; Costa, A T; Polonio, J C; da Silva, A A; Pamphile, J A; Azevedo, J L

    2016-01-01

    Fungi belonging to the Colletotrichum genus can be categorized as endophytic or phytopathogenic. These fungi can be infected by viruses, termed mycoviruses, which are know to promote hypovirulence in infected fungi. However, there are few studies that have described mycoviral infections of endophytes. The production of secondary metabolites by endophytes with antimicrobial potential in inhibiting numerous pathogens has gained increasing attention. The aim of the current study was to investigate the presence of mycoviruses in endophytic and phytopathogenic fungi of the Colletotrichum genus, as well as to analyze the antimicrobial activity of crude extracts obtained from these samples. To detect the presence of mycoviruses in the samples, dsRNA was extracted, treated with enzymes, and analyzed following electrophoresis in agarose gel. Furthermore, isometric mycoviral particles were observed by transmission electron microscopy. Serial microdilution methodology was used to test crude extracts of Colletotrichum spp for antibacterial activity against Escherichia coli and Staphylococcus aureus, and antifungal activity against Fusarium solani. The results of the molecular and microscopic analyses indicated that a phytopathogenic strain presented infection by mycovirus. The antibacterial activity analysis revealed that the minimum inhibitory concentrations and minimum bactericidal concentrations were low for the fungal extracts of the two endophytes, indicating that these extracts were effective antibacterial agents. However, their antifungal activity against F. solani was not statistically different compared to that of the negative control. PMID:26985921

  7. Study of µm-scale spatial variations in strain of a compositionally step-graded InxGa1 - xAs/GaAs(001) heterostructure

    NASA Astrophysics Data System (ADS)

    Rammohan, K.; Rich, D. H.; Goldman, R. S.; Chen, J.; Wieder, H. H.; Kavanagh, K. L.

    1995-02-01

    The relaxation of strain in compositionally step-graded InxGa1-xAs layers grown on GaAs(001) has been examined with cathodoluminescence (CL) wavelength and linearly polarized imaging approaches. A polarization anisotropy in CL is found, and this correlates with spectral shifts in the peak positions of excitonic luminescence. Varying asymmetries in misfit dislocation densities from transmission electron microscopy are found to be consistent with the μm-scale spatial variations in strain that is deduced from the CL.

  8. Variation in Indole-3-Acetic Acid Production by Wild Saccharomyces cerevisiae and S. paradoxus Strains from Diverse Ecological Sources and Its Effect on Growth

    PubMed Central

    Liu, Yen-Yu; Chen, Hung-Wei; Chou, Jui-Yu

    2016-01-01

    Phytohormone indole-3-acetic acid (IAA) is the most common naturally occurring and most thoroughly studied plant growth regulator. Microbial synthesis of IAA has long been known. Microbial IAA biosynthesis has been proposed as possibly occurring through multiple pathways, as has been proven in plants. However, the biosynthetic pathways of IAA and the ecological roles of IAA in yeast have not been widely studied. In this study, we investigated the variation in IAA production and its effect on the growth of Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus yeasts from diverse ecological sources. We found that almost all Saccharomyces yeasts produced IAA when cultured in medium supplemented with the primary precursor of IAA, L-tryptophan (L-Trp). However, when cultured in medium without L-Trp, IAA production was only detected in three strains. Furthermore, exogenous added IAA exerted stimulatory and inhibitory effects on yeast growth. Interestingly, a negative correlation was observed between the amount of IAA production in the yeast cultures and the IAA inhibition ratio of their growth. PMID:27483373

  9. Full-field Strain Methods for Investigating Failure Mechanisms in Triaxial Braided Composites

    NASA Technical Reports Server (NTRS)

    Littell, Justin D.; Binienda, Wieslaw K.; Goldberg, Robert K.; Roberts, Gary D.

    2008-01-01

    Composite materials made with triaxial braid architecture and large tow size carbon fibers are beginning to be used in many applications, including composite aircraft and engine structures. Recent advancements in braiding technology have led to commercially viable manufacturing approaches for making large structures with complex shape. Although the large unit cell size of these materials is an advantage for manufacturing efficiency, the fiber architecture presents some challenges for materials characterization, design, and analysis. In some cases, the static load capability of structures made using these materials has been higher than expected based on material strength properties measured using standard coupon tests. A potential problem with using standard tests methods for these materials is that the unit cell size can be an unacceptably large fraction of the specimen dimensions. More detailed investigation of deformation and failure processes in large unit cell size triaxial braid composites is needed to evaluate the applicability of standard test methods for these materials and to develop alternative testing approaches. In recent years, commercial equipment has become available that enables digital image correlation to be used on a more routine basis for investigation of full field 3D deformation in materials and structures. In this paper, some new techniques that have been developed to investigate local deformation and failure using digital image correlation techniques are presented. The methods were used to measure both local and global strains during standard straight-sided coupon tensile tests on composite materials made with 12 and 24 k yarns and a 0/+60/-60 triaxial braid architecture. Local deformation and failure within fiber bundles was observed, and this local failure had a significant effect on global stiffness and strength. The matrix material had a large effect on local damage initiation for the two matrix materials used in this investigation

  10. Investigating strength of materials at very high strain rates using magnetically driven expanding cylinders

    NASA Astrophysics Data System (ADS)

    Lovinger, Zev; Nemirovsky, Ron; Avriel, Eyal; Dorogoy, Avraham; Ashuach, Yehezkel; Rittel, Daniel

    2015-09-01

    Dynamic characterization of strength properties is done, in common practice by the means of a Split-Hopkinson Pressure Bar (also named Kolsky-Bar) apparatus. In such systems, strain rates are limited up to ˜ 5 ṡ 103 sec-1. For higher strain rates, the strain rate hardening is assumed to be the same as that measured at lower rates, with no direct measurement to validate the assumptions used for this extrapolation. In this work we are using a pulsed current generator (PCG) to create electro-magnetic (EM) driving forces on expanding cylinders. Most standard techniques for creating EM driving forces on cylinders or rings, as reported in the literature, reach strain rates of 1e3-1e4. Using our PCG, characterized by a fast rise time, we reach strain rates of ˜1e5, thus paving the way to a standard technique to measure strength at very high strain rates. To establish the experimental technique, we conducted a numerical study of the expanding cylinder set up using 2D hydrodynamic simulations to reach the desired high strain rates.

  11. Evaluation of mosquito densoviruses for controlling Aedes aegypti (Diptera: Culicidae): variation in efficiency due to virus strain and geographic origin of mosquitoes.

    PubMed

    Hirunkanokpun, Supanee; Carlson, Jonathan O; Kittayapong, Pattamaporn

    2008-05-01

    Four mosquito densovirus strains were assayed for mortality and infectivity against Aedes aegypti larvae from different geographic regions. The viral titers were quantified by real-time PCR using TaqMan technology. Firstinstar larvae were exposed to the same titer of each densovirus strain for 48 hours. All strains of densoviruses exhibited larvicidal activity and caused more than 80% mortality and infectivity in the three mosquito strains. AalDNV-exposed larvae had the highest mortality rate. The mean time to death of AalDNV-exposed larvae was shorter than other DNVs-exposed larvae. We can conclude that different densovirus strains exhibit some variations in their pathogenicity to different populations of Ae. aegypti mosquitoes. A few mosquitoes from Chachoengsao and Bangkok exposed to AeDNV and AThDNV survived to the adult stage to lay eggs and showed 22% to 50% vertical transmission in the F1 generation. Phylogenetic analysis of four densovirus strains indicated that mosquito densoviruses are separated into two distinct clades. PMID:18458314

  12. Strain Effects on Enhanced Hydrogen Sulphide Detection Capability of Ag-DECORATED Defective Graphene: a First-Principles Investigation

    NASA Astrophysics Data System (ADS)

    Qin, Xian; Meng, Qingyuan; Feng, Yuan Ping

    2012-10-01

    Strain effects on hydrogen sulphide (H2S) adsorption on Ag-decorated Stone-Wales (SW) defect in graphene were investigated by density functional theory calculations. The results indicate that an Ag adatom is easily pinned chemically on the top of the most stretched C-C bond at the SW defect in graphene without mechanical strains. A modest uniform tensile strain (8%) applied in defective graphene greatly increases the binding energy of Ag by 44%, indicating the strain enhanced stabilization of Ag on SW defect. Using the resulting Ag-decorated defective graphene (Ag-SW-g) composite as a model for H2S molecule detection, we found that the tensile strain has little effects on the interaction between the molecule and the composite, and the adsorption energies of H2S around 1.6 eV which is six times larger than that on pristine graphene are produced. The enhanced H2S adsorption on Ag-SW-g is attributed to charge transfer from the molecule to the graphene through the bridge-like Ag adatom. In addition, the electronic property of the Ag-SW-g under different strains changes from a metallic state to a semiconductor state upon H2S adsorption, which should lead to an observable change in its conductivity. These findings pave the way for future development of graphene-based gas sensor.

  13. The Photoelastic Investigation of Three-dimensional Stress and Strain Conditions

    NASA Technical Reports Server (NTRS)

    Oppel, G

    1937-01-01

    The present report contains the description and typical application of two photoelastic methods which are suitable for the study of stress and strain conditions in three dimensions, namely: the fixation method and the immersion method.

  14. Investigation of dielectric pocket induced variations in tunnel field effect transistor

    NASA Astrophysics Data System (ADS)

    Upasana; Narang, Rakhi; Saxena, Manoj; Gupta, Mridula

    2016-04-01

    The performance of conventional Tunnel FETs struggling from ambipolar issues, insufficient on-current, lower transconductance value, higher delay and lower cut off frequency has been improved by introducing several material and device engineering concepts in past few years. Keeping this in view, another interesting and reliable option i.e. Dielectric Pocket TFET (featuring a dielectric pocket placement near tunneling junction) has been comprehensively and qualitatively demonstrated using ATLAS device simulator. The architecture has been explored in terms of various device electrostatic parameters such as potential, energy band profile, electron and hole concentration, electric field variation and band to band generation rate (GBTB) near the tunneling junction where the Dielectric Pocket (DP) has been introduced. Subsequently, a detailed investigation by changing the position and dielectric constant of pocket at respective junctions has been made where DP induced variations in drain current, transconductance and parasitic capacitance have been examined. The work highlights major improvements over conventional TFET in terms of lower subthreshold swing and threshold voltage, higher drain current and transconductance, improved on-to-off current ratio, suppressed ambipolar conduction and improved dynamic power dissipation issues for low voltage analog and digital applications.

  15. A preliminary investigation into the genetic variation and population structure of Taenia hydatigena from Sardinia, Italy.

    PubMed

    Boufana, Belgees; Scala, Antonio; Lahmar, Samia; Pointing, Steve; Craig, Philip S; Dessì, Giorgia; Zidda, Antonella; Pipia, Anna Paola; Varcasia, Antonio

    2015-11-30

    Cysticercosis caused by the metacestode stage of Taenia hydatigena is endemic in Sardinia. Information on the genetic variation of this parasite is important for epidemiological studies and implementation of control programs. Using two mitochondrial genes, the cytochrome c oxidase subunit 1 (cox1) and the NADH dehydrogenase subunit 1 (ND1) we investigated the genetic variation and population structure of Cysticercus tenuicollis from Sardinian intermediate hosts and compared it to that from other hosts from various geographical regions. The parsimony cox1 network analysis indicated the existence of a common lineage for T. hydatigena and the overall diversity and neutrality indices indicated demographic expansion. Using the cox1 sequences, low pairwise fixation index (Fst) values were recorded for Sardinian, Iranian and Palestinian sheep C. tenuicollis which suggested the absence of genetic differentiation. Using the ND1 sequences, C. tenuicollis from Sardinian sheep appeared to be differentiated from those of goat and pig origin. In addition, goat C. tenuicollis were genetically different from adult T. hydatigena as indicated by the statistically significant Fst value. Our results are consistent with biochemical and morphological studies that suggest the existence of variants of T. hydatigena. PMID:26296591

  16. Impact of variation in acute virulence of BVDV1 strains on design of better vaccine efficacy challenge models

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to antigenic differences between BVDV1 and BVDV2 strains both pestivirus species are included in U.S. vaccines. The efficacy of these vaccines in preventing acute infections is evaluated based on reduction of clinical disease. While high virulence BVDV2 strains are used in U.S. vaccine efficac...

  17. Quantitative Differences in Salivary Pathogen Load during Tick Transmission Underlie Strain-Specific Variation in Transmission Efficiency of Anaplasma marginale

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The relative fitness of arthropod-borne pathogens within the vector can be a major determinant of pathogen prevalence within the mammalian host population. Strains of the tick-borne rickettsia Anaplasma marginale differ markedly in transmission efficiency with consequent impact on pathogen strain st...

  18. XRD investigation of the strain/stress state of ion-irradiated crystals

    NASA Astrophysics Data System (ADS)

    Debelle, Aurélien; Declémy, Alain

    2010-05-01

    In this work, it is demonstrated that XRD is a powerful technique for the study of ion-irradiated materials. For this purpose, XRD experiments have been performed under different configurations on a <1 0 0>-oriented yttria-stabilized zirconia single crystal implanted with 300 keV caesium-ions at 3 × 10 14 cm -2. Initially, it is demonstrated that the depth strain profile can be determined from the refinement of a symmetric θ-2 θ scan. Moreover, in order to explore the whole XRD data, a model that describes the strain/stress state of the damaged layer is proposed. This model takes into account the elastic response of the bulk material (substrate) underneath the irradiated layer. The measured elastic strain is then the sum of a free strain due to the formation of radiation-induced defects and of an additional strain arising from the substrate elastic reaction. Application of this model allowed the calculation of the different strain contributions and the stress experienced by the irradiated layer. It is shown that these parameters may reach large values (respectively 0.7% and -1.9 GPa) despite the low radiation damage level.

  19. A novel platform for in situ investigation of cells and tissues under mechanical strain.

    PubMed

    Ahmed, W W; Kural, M H; Saif, T A

    2010-08-01

    The mechanical micro-environment influences cellular responses such as migration, proliferation, differentiation and apoptosis. Cells are subjected to mechanical stretching in vivo, e.g., epithelial cells during embryogenesis. Current methodologies do not allow high-resolution in situ observation of cells and tissues under applied strain, which may reveal intracellular dynamics and the origin of cell mechanosensitivity. A novel polydimethylsiloxane substrate was developed, capable of applying tensile and compressive strain (up to 45%) to cells and tissues while allowing in situ observation with high-resolution optics. The strain field of the substrate was characterized experimentally using digital image correlation, and the deformation was modeled by the finite element method, using a Mooney-Rivlin hyperelastic constitutive relation. The substrate strain was found to be uniform for >95% of the substrate area. As a demonstration of the system, mechanical strain was applied to single fibroblasts transfected with GFP-actin and whole transgenic Drosophila embryos expressing GFP in all neurons during live imaging. Three observations of biological responses due to applied strain are reported: (1) dynamic rotation of intact actin stress fibers in fibroblasts; (2) lamellipodia activity and actin polymerization in fibroblasts; (3) active axonal contraction in Drosophila embryo motor neurons. The novel platform may serve as an important tool in studying the mechanoresponse of cells and tissues, including whole embryos. PMID:20188869

  20. Investigation of genes involved in nisin production in Enterococcus spp. strains isolated from raw goat milk.

    PubMed

    Perin, Luana Martins; Todorov, Svetoslav Dimitrov; Nero, Luís Augusto

    2016-09-01

    Different strains of Lactococcus lactis are capable of producing the bacteriocin nisin. However, genetic transfer mechanisms allow the natural occurrence of genes involved in nisin production in members of other bacterial genera, such as Enterococcus spp. In a previous study, nisA was identified in eight enterococci capable of producing antimicrobial substances. The aim of this study was to verify the presence of genes involved in nisin production in Enterococcus spp. strains, as well as nisin expression. The nisA genes from eight Enterococcus spp. strains were sequenced and the translated amino acid sequences were compared to nisin amino-acid sequences previously described in databases. Although containing nisin structural and maturation related genes, the enterococci strains tested in the present study did not present the immunity related genes (nisFEG and nisI). The translated sequences of nisA showed some point mutations, identical to those presented by Lactococcus strains isolated from goat milk. All enterococci were inhibited by nisin, indicating the absence of immunity and thus that nisin cannot be expressed. This study demonstrated for the first time the natural occurrence of nisin structural genes in Enterococcus strains and highlights the importance of providing evidence of a link between the presence of bacteriocin genes and their expression. PMID:27255139

  1. CagA C-terminal variations in Helicobacter pylori strains from Colombian patients with gastric precancerous lesions

    PubMed Central

    Sicinschi, L. A.; Correa, P.; Peek, R. M.; Camargo, M. C.; Piazuelo, M. B.; Romero-Gallo, J.; Hobbs, S. S.; Krishna, U.; Delgado, A.; Mera, R.; Bravo, L. E.; Schneider, B. G.

    2010-01-01

    The C-terminus of the Helicobacter pylori CagA protein is polymorphic, bearing different EPIYA sequences (EPIYA-A, B, C or D), and one or more CagA multimerization (CM) motifs. The number of EPIYA-C motifs is associated with precancerous lesions and gastric cancer (GC). The relationship between EPIYA, CM motifs and gastric lesions was examined in H. pylori-infected Colombian patients from areas of high and low risk for GC. Genomic DNA was extracted from H. pylori strains cultured from gastric biopsies from 80 adults with dyspeptic symptoms. Sixty-seven (83.8%) of 80 strains were cagA positive. The 3′ region of cagA was sequenced, and EPIYA and CM motifs were identified. CagA proteins contained one (64.2%), two (34.3%) or three EPIYA-C motifs (1.5%), all with Western type CagA-specific sequences. Strains with one EPIYA-C motif were associated with less severe gastric lesions (non-atrophic and multifocal atrophic gastritis), whereas strains with multiple EPIYA-C motifs were associated with more severe lesions (intestinal metaplasia and dysplasia) (p <0.001). In 54 strains, the CM motifs were identical to those common in Western strains. Thirteen strains from the low-risk area contained two different CM motifs: one of Western type located within the EPIYA-C segment and another following the EPIYA-C segment and resembling the CM motif found in East Asian strains. These strains induced significantly shorter projections in AGS cells and an attenuated reduction in levels of CagA upon immunodepletion of SHP-2 than strains possessing Western/Western motifs. This novel finding may partially explain the difference in GC incidence in these populations. PMID:19456839

  2. Influences of vowel and tone variation on emergent word knowledge: a cross-linguistic investigation.

    PubMed

    Singh, Leher; Hui, Tam Jun; Chan, Calista; Golinkoff, Roberta Michnick

    2014-01-01

    To learn words, infants must be sensitive to native phonological contrast. While lexical tone predominates as a source of phonemic contrast in human languages, there has been little investigation of the influences of lexical tone on word learning. The present study investigates infants' sensitivity to tone mispronunciations in two groups of infants. For one group (Chinese learners), tone is phonemic in their native language, and for the second group (English learners), tone is non-phonemic and constituted suprasegmental variation. In Experiment 1, English learners were trained on novel word-object pairings and tested on their recognition of correct pronunciations, tone and vowel mispronunciations of these words at 18 and 24 months. In Experiment 2a, bilingual English-Chinese learners were tested on a similar task translated into Chinese at the same age intervals. Results demonstrate that non-tonal learners treated tonal and vowel substitutions alike as mispronunciations at 18 months but only treated vowel substitutions as mispronunciations at 24 months. Tonal learners treated both tonal and vowel substitutions as mispronunciations at both ages. In Experiment 2b, bilingual non-tone language learners were tested on the same set of tasks replicating a similar set of results as monolingual non-tone language learners (Experiment 1). Findings point to an early predisposition to treat tone as a defining characteristic of words regardless of its lexical relevance at 18 months. Between 18 and 24 months, learners appear to ascribe lexical relevance to tone in a language-specific manner. The current study identifies the influences of tone variation on memories for newly learned words and the time period during which lexical tone - a highly frequent constituent of human languages - actually becomes lexical for early learners. Findings are contextualized with prevailing models of the developing lexicon. PMID:24118787

  3. Can low-level ethanol exposure during pregnancy influence maternal care? An investigation using two strains of rat across two generations.

    PubMed

    Popoola, Daniel O; Borrow, Amanda P; Sanders, Julia E; Nizhnikov, Michael E; Cameron, Nicole M

    2015-09-01

    Gestational alcohol use is well documented as detrimental to both maternal and fetal health, producing an increase in offspring's tendency for alcoholism, as well as in behavioral and neuropsychological disorders. In both rodents and in humans, parental care can influence the development of offspring physiology and behavior. Animal studies that have investigated gestational alcohol use on parental care and/or their interaction mostly employ heavy alcohol use and single strains. This study aimed at investigating the effects of low gestational ethanol dose on parental behavior and its transgenerational transmission, with comparison between two rat strains. Pregnant Sprague Dawley (SD) and Long Evans (LE) progenitor dams (F0) received 1g/kg ethanol or water through gestational days 17-20 via gavage, or remained untreated in their home cages. At maturity, F1 female offspring were mated with males of the same strain and treatment and were left undisturbed through gestation. Maternal behavior was scored in both generations during the first six postnatal days. Arch-back nursing (ABN) was categorized as: 1, when the dam demonstrated minimal kyphosis; 2, when the dam demonstrated moderate kyphosis; and 3, when the dam displayed maximal kyphosis. Overall, SD showed greater amounts of ABN than LE dams and spent more time in contact with their pups. In the F0 generation, water and ethanol gavage increased ABN1 and contact with pups in SD, behaviors which decreased in treated LE. For ABN2, ethanol-treated SD dams showed more ABN2 than water-treated dams, with no effect of treatment on LE animals. In the F1 generation, prenatal exposure affected retrieval. Transgenerational transmission of LG was observed only in the untreated LE group. Strain-specific differences in maternal behavior were also observed. This study provides evidence that gestational gavage can influence maternal behavior in a strain-specific manner. Our results also suggest that the experimental procedure during

  4. Investigation of the Susceptibility of Various Strains of Mice to Methyllycaconitine Toxicosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the mechanism of action for larkspur alkaloids has been described, there is little information on the variation of the physiological response of individual animals to larkspur alkaloids. Anecdotal observations and pilot studies in cattle indicate that there is animal-to-animal variation in...

  5. Strain and micromotion in intact and resurfaced composite femurs: experimental and numerical investigations.

    PubMed

    Pal, Bidyut; Gupta, Sanjay; New, Andrew M R; Browne, Martin

    2010-07-20

    Understanding the load transfer within a resurfaced femur is necessary to determine the influence of mechanical factors on potential failure mechanisms such as early femoral neck fractures and stress shielding. In this study, an attempt has been made to measure the stem-bone micromotion and implant cup-bone relative displacements (along medial-lateral and anterior-posterior direction), in addition to surface strains at different locations and orientations on the proximal femur and to compare these measurements with those predicted by equivalent FE models. The loading and the support conditions of the experiment were closely replicated in the FE models. A new experimental set-up has been developed, with specially designed fixtures and load application mechanism, which can effectively impose bending and deflection of the tested femurs, almost in any direction. High correlation coefficient (0.92-0.95), low standard error of the estimate (170-379 muepsilon) and low percentage error in regression slope (12.8-17.5%), suggested good agreement between the numerical and measured strains. The effect of strain shielding was observed in two (out of eight) strain gauges located on the posterior side. A pronounced strain increase occurred in strain gauges located on the anterior head and neck regions after implantation. Experimentally measured stem-bone micromotion and implant cup-bone relative displacements (0-13.7 microm) were small and similar in trends predicted by the FE models (0-25 microm). Despite quantitative deviations in the measured and numerical results, it appears that the FE model can be used as a valid predictor of the actual strain and stem-bone micromotion. PMID:20392448

  6. Investigations of segregation phenomena in highly strained Mn-doped Ge wetting layers and Ge quantum dots embedded in silicon

    SciTech Connect

    Prestat, E. Porret, C.; Favre-Nicolin, V.; Tainoff, D.; Boukhari, M.; Bayle-Guillemaud, P.; Jamet, M.; Barski, A.

    2014-03-10

    In this Letter, we investigate manganese diffusion and the formation of Mn precipitates in highly strained, few monolayer thick, Mn-doped Ge wetting layers and nanometric size Ge quantum dot heterostructures embedded in silicon. We show that in this Ge(Mn)/Si system manganese always precipitates and that the size and the position of Mn clusters (precipitates) depend on the growth temperature. At high growth temperature, manganese strongly diffuses from germanium to silicon, whereas decreasing the growth temperature reduces the manganese diffusion. In the germanium quantum dots layers, Mn precipitates are detected, not only in partially relaxed quantum dots but also in fully strained germanium wetting layers between the dots.

  7. Metabonomic Investigation of Single and Multiple Strain Trypanosoma brucei brucei Infections

    PubMed Central

    Li, Jia V.; Saric, Jasmina; Wang, Yulan; Utzinger, Jürg; Holmes, Elaine; Balmer, Oliver

    2011-01-01

    Although co-infections are common and can have important epidemiologic and evolutionary consequences, studies exploring biochemical effects of multiple-strain infections remain scarce. We studied metabolic responses of NMRI mice to Trypanosoma brucei brucei single (STIB777AE-Green1 or STIB246BA-Red1) and co-infections using a 1H nuclear magnetic resonance (NMR) spectroscopy-based metabolic profiling strategy. All T. b. brucei infections caused an alteration in urinary biochemical composition by day 4 postinfection, characterized by increased concentrations of 2-oxoisocaproate, D-3-hydroxybutyrate, lactate, 4-hydroxyphenylacetate, phenylpyruvate, and 4-hydroxyphenylpyruvate, and decreased levels of hippurate. Although there were no marked differences in metabolic signatures observed in the mouse infected with a single or dual strain of T. b. brucei, there was a slower metabolic response in mice infected with T. b. brucei green strain compared with mice infected with either the red strain or both strains concurrently. Pyruvate, phenylpyruvate, and hippurate were correlated with parasitemia, which might be useful in monitoring responses to therapeutic interventions. PMID:21212208

  8. Investigation of composition-induced strain effect in FexPt1-x films grown on different substrates

    NASA Astrophysics Data System (ADS)

    Dong, K. F.; Li, H. H.; Chen, J. S.

    2013-12-01

    Different composition FexPt1-x films were fabricated on three typical single crystal substrates (MgO, KTaO3, and SrTiO3), and the composition-induced strain evolution of FexPt1-x films was systematically investigated. The study showed that different Fe compositions in Fe-Pt films resulted in different strain status and crystallographic textures, and thus influenced the magnetic properties. Under the tensile strain between the Fe-Pt and (MgO, KTaO3, and SrTiO3) substrates, Fe-Pt films preferred to form ordered Fe-Pt (001) texture. Decrease of the Fe atom concentration caused the Fe-Pt films to be further relaxed, and an obvious increase of lattice constant c. Moreover, with reducing the mismatch between Fe-Pt and substrate from MgO to KTaO3 and SrTiO3, the strain status of Fe-Pt films changed from completely strained to partially relaxed. The perpendicular anisotropy of Fe55Pt45 films grown on STO was larger than that grown on MgO and KTO, which was attributed to better epitaxial quality of the FePt (001) texture induced by less lattice mismatch.

  9. [Investigation of the presence of panton-valentin leucocidin (PVL) in Staphylococcus aureus strains isolated from clinical samples].

    PubMed

    Ozkul, Hilal; Oktem, I M Ali; Gülay, Zeynep

    2007-07-01

    Panton-Valentin leucocidin (PVL) is a cytotoxin which causes tissue necrosis by degradating leucocytes and other cell types. PVL has recently become very up to date as it has been shown to be the major virulance factor of community acquired methicillin resistant Staphylococcus aureus strains. In this study, the presence of PVL was investigated in methicillin sensitive and resistant S. aureus (MSSA and MRSA, respectively) strains which were isolated from clinical samples between January 2005-May 2006 at Dokuz Eylul University Hospital, Izmir. Fifty five MRSA and 79 MSSA strains which were isolated from blood, wound and respiratory tract samples were randomly included to the study. The presence of PVL was evaluated by multiplex polymerase chain reaction (PCR) which detects pvl and S. aureus-specific nuc genes. As a result, PVL positivities were detected in two (5%) of 40 MSSA and four (10.3%) of 39 MSSA strains isolated in the years 2005 and 2006, respectively. None of the MRSA isolates had pvl gene. Although this cytotoxin was rarely detected among MSSA isolates, it was interesting to note that the prevalence of PVL was twice more in the year 2006 compared to 2005. It was also worth to notify that four of six (66.7%) PVL positive strains had been isolated from the patients of general surgery inpatient or outpatient clinics. PMID:17933245

  10. Investigation of optimization-based reconstruction with an image-total-variation constraint in PET.

    PubMed

    Zhang, Zheng; Ye, Jinghan; Chen, Buxin; Perkins, Amy E; Rose, Sean; Sidky, Emil Y; Kao, Chien-Min; Xia, Dan; Tung, Chi-Hua; Pan, Xiaochuan

    2016-08-21

    Interest remains in reconstruction-algorithm research and development for possible improvement of image quality in current PET imaging and for enabling innovative PET systems to enhance existing, and facilitate new, preclinical and clinical applications. Optimization-based image reconstruction has been demonstrated in recent years of potential utility for CT imaging applications. In this work, we investigate tailoring the optimization-based techniques to image reconstruction for PET systems with standard and non-standard scan configurations. Specifically, given an image-total-variation (TV) constraint, we investigated how the selection of different data divergences and associated parameters impacts the optimization-based reconstruction of PET images. The reconstruction robustness was explored also with respect to different data conditions and activity up-takes of practical relevance. A study was conducted particularly for image reconstruction from data collected by use of a PET configuration with sparsely populated detectors. Overall, the study demonstrates the robustness of the TV-constrained, optimization-based reconstruction for considerably different data conditions in PET imaging, as well as its potential to enable PET configurations with reduced numbers of detectors. Insights gained in the study may be exploited for developing algorithms for PET-image reconstruction and for enabling PET-configuration design of practical usefulness in preclinical and clinical applications. PMID:27452653

  11. Investigation of optimization-based reconstruction with an image-total-variation constraint in PET

    NASA Astrophysics Data System (ADS)

    Zhang, Zheng; Ye, Jinghan; Chen, Buxin; Perkins, Amy E.; Rose, Sean; Sidky, Emil Y.; Kao, Chien-Min; Xia, Dan; Tung, Chi-Hua; Pan, Xiaochuan

    2016-08-01

    Interest remains in reconstruction-algorithm research and development for possible improvement of image quality in current PET imaging and for enabling innovative PET systems to enhance existing, and facilitate new, preclinical and clinical applications. Optimization-based image reconstruction has been demonstrated in recent years of potential utility for CT imaging applications. In this work, we investigate tailoring the optimization-based techniques to image reconstruction for PET systems with standard and non-standard scan configurations. Specifically, given an image-total-variation (TV) constraint, we investigated how the selection of different data divergences and associated parameters impacts the optimization-based reconstruction of PET images. The reconstruction robustness was explored also with respect to different data conditions and activity up-takes of practical relevance. A study was conducted particularly for image reconstruction from data collected by use of a PET configuration with sparsely populated detectors. Overall, the study demonstrates the robustness of the TV-constrained, optimization-based reconstruction for considerably different data conditions in PET imaging, as well as its potential to enable PET configurations with reduced numbers of detectors. Insights gained in the study may be exploited for developing algorithms for PET-image reconstruction and for enabling PET-configuration design of practical usefulness in preclinical and clinical applications.

  12. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.

    PubMed

    Crauwels, S; Van Assche, A; de Jonge, R; Borneman, A R; Verreth, C; Troels, P; De Samblanx, G; Marchal, K; Van de Peer, Y; Willems, K A; Verstrepen, K J; Curtin, C D; Lievens, B

    2015-11-01

    Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production. PMID:26135985

  13. Investigating Cepheid ℓ Carinae's cycle-to-cycle variations via contemporaneous velocimetry and interferometry★

    NASA Astrophysics Data System (ADS)

    Anderson, R. I.; Mérand, A.; Kervella, P.; Breitfelder, J.; LeBouquin, J.-B.; Eyer, L.; Gallenne, A.; Palaversa, L.; Semaan, T.; Saesen, S.; Mowlavi, N.

    2016-02-01

    Baade-Wesselink-type (BW) techniques enable geometric distance measurements of Cepheid variable stars in the Galaxy and the Magellanic clouds. The leading uncertainties involved concern projection factors required to translate observed radial velocities (RVs) to pulsational velocities and recently discovered modulated variability. We carried out an unprecedented observational campaign involving long-baseline interferometry (VLTI/PIONIER) and spectroscopy (Euler/Coralie) to search for modulated variability in the long-period (P ˜ 35.5 d) Cepheid ℓ Carinae. We determine highly precise angular diameters from squared visibilities and investigate possible differences between two consecutive maximal diameters, ΔmaxΘ. We characterize the modulated variability along the line of sight using 360 high-precision RVs. Here we report tentative evidence for modulated angular variability and confirm cycle-to-cycle differences of ℓ Carinae's RV variability. Two successive maxima yield ΔmaxΘ = 13.1 ± 0.7(stat.) μas for uniform disc models and 22.5 ± 1.4(stat.) μas (4 per cent of the total angular variation) for limb-darkened models. By comparing new RVs with 2014 RVs, we show modulation to vary in strength. Barring confirmation, our results suggest the optical continuum (traced by interferometry) to be differently affected by modulation than gas motions (traced by spectroscopy). This implies a previously unknown time dependence of projection factors, which can vary by 5 per cent between consecutive cycles of expansion and contraction. Additional interferometric data are required to confirm modulated angular diameter variations. By understanding the origin of modulated variability and monitoring its long-term behaviour, we aim to improve the accuracy of BW distances and further the understanding of stellar pulsations.

  14. Investigation of passive blade cyclic pitch variation using an automatic yaw control system. Final report

    SciTech Connect

    Hohenemser, K.H.; Swift, A.H.P.

    1982-08-01

    The investigation of passive cyclic pitch variation using an automatic yaw control system made use of the test equipment and of the results of an earlier study. The atmospheric test equipment consisted of a horizontal axis wind turbine with vane controlled upwind two-bladed rotor of 7.6 m (25 ft) diameter having passive cyclic pitch variation. An automatically triggered electric furl actuator prevented over-speeds and over-torques by furling the rotor which means yawing the rotor out of the winds. The atmospheric test equipment was modified to accept two alternative fully automatic yaw or furl control systems. The first system was of the active type and included a hydraulic single acting constant speed governor as it is used for aircraft propeller controls. Upon reaching the rotor speed limit, the governor delivered pressurized oil to a hydraulic furl actuator which then overcame the unfurling spring force and furled the rotor. When the rotor speed fell below the set value, the governor admitted oil flow from the hydraulic actuator into the oil reservoir and the rotor was unfurled by the spring. The second automatic control system was of a purely mechanical passive type. The rotor thrust, which was laterally off-set from the yaw axis, in combination with a yawing component of the rotor torque due to uptilt of the rotor axis overcame at rated power the unfurling spring and furled the rotor. The analytically predicted and experimentally substantiated negative rotor yaw damping would cause excessive furling rates unless alleviated by a furl damper. The tests were supported by a specially developed dynamic yawing analysis. Both analysis and tests indicated that the two-bladed passive cyclic pitch wind rotor can be effectively torque or speed limited by rotor yaw control systems which are less costly and more reliable than the conventional blade feathering control systems.

  15. Experimental investigation of the behaviour of tungsten and molybdenum alloys at high strain-rate and temperature

    NASA Astrophysics Data System (ADS)

    Scapin, Martina; Fichera, Claudio; Carra, Federico; Peroni, Lorenzo

    2015-09-01

    The introduction in recent years of new, extremely energetic particle accelerators such as the Large Hadron Collider (LHC) gives impulse to the development and testing of refractory metals and alloys based on molybdenum and tungsten to be used as structural materials. In this perspective, in this work the experimental results of a tests campaign on Inermet® IT180 and pure Molybdenum (sintered by two different producers) are presented. The investigation of the mechanical behaviour was performed in tension varying the strain-rates, the temperatures and both of them. Overall six orders of magnitude in strain-rate (between 10-3 and 103 s-1) were covered, starting from quasi-static up to high dynamic loading conditions. The high strain-rate tests were performed using a direct Hopkinson Bar setup. Both in quasi-static and high strain-rate conditions, the heating of the specimens was obtained with an induction coil system, controlled in feedback loop, based on measurements from thermocouples directly welded on the specimen. The temperature range varied between 25 and 1000°C. The experimental data were, finally, used to extract the parameters of the Zerilli-Armstrong model used to reproduce the mechanical behaviour of the investigated materials.

  16. Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses.

    PubMed

    Tang, Yinjie J; Yi, Shan; Zhuang, Wei-Qin; Zinder, Stephen H; Keasling, Jay D; Alvarez-Cohen, Lisa

    2009-08-01

    Members of the genus "Dehalococcoides" are the only known microorganisms that can completely dechlorinate tetrachloroethene and trichloroethene to the innocuous end product, ethene. This study examines the central metabolism in "Dehalococcoides ethenogenes" strain 195 via (13)C-labeled tracer experiments. Supported by the genome annotation and the transcript profile, isotopomer analysis of key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic pathway in strain 195. First, the (13)C-labeling studies revealed that strain 195 contains complete amino acid biosynthesis pathways, even though current genome annotation suggests that several of these pathways are incomplete. Second, the tricarboxylic acid cycle of strain 195 is confirmed to be branched, and the Wood-Ljungdahl carbon fixation pathway is shown to not be functionally active under our experimental conditions; rather, CO(2) is assimilated via two reactions, conversion of acetyl-coenzyme A (acetyl coenzyme A [acetyl-CoA]) to pyruvate catalyzed by pyruvate synthase (DET0724-0727) and pyruvate conversion to oxaloacetate via pyruvate carboxylase (DET0119-0120). Third, the (13)C-labeling studies also suggested that isoleucine is synthesized from acetyl-CoA and pyruvate via citramalate synthase (CimA, EC 2.3.1.182), rather than from the common pathway via threonine ammonia-lyase (EC 4.3.1.19). Finally, evidence is presented that strain 195 may contain an undocumented citrate synthase (>95% Re-type stereospecific), i.e., a novel Re-citrate synthase that is apparently different from the one recently reported in Clostridium kluyveri. PMID:19525347

  17. Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground.

    PubMed

    Guo, Jun; Han, Na; Zhang, Yuanyuan; Wang, Haiyin; Zhang, Xuelin; Su, Longxiang; Liu, Chao; Li, Jia; Chen, Chen; Liu, Changting

    2015-01-01

    nucleotide structure variation of S. aureus strains in a spaceflight environment and also provide a valuable insight for understanding the mutation strategies of MRSA on earth. PMID:25304992

  18. Investigation variation of carbon dioxide based on GOSAT data in peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Sim, C. K.; Lim, H. S.; MatJafri, M. Z.

    2015-10-01

    Carbon dioxide (CO2) is an inodorous and transparent gas, and naturally originates in our atmosphere. Due to its optical characteristics, CO2 is the most important greenhouse gas and play a key role in climate change due to an effective thermal infrared (IR) radiation absorber. Satellite observations of atmospheric carbon dioxide (CO2) can significantly improve our knowledge about the sources and sinks of CO2. The remote sensing satellite, namely Greenhouse Gases Observing Satellite (GOSAT) was employed to investigate the spatial and variations of CO2 column-averaged dry airmole fractions, denoted XCO2 over Peninsular Malaysia from January 2013 to December 2013. The analysis of CO2 in the study area shows the significant differences between northeast monsoon (NEM) and the southwest monsoon (SWM). During NEM season, cold air outbreaks from Siberia spreads to equatorial region in the form of north-easterly cold surge winds and associated with a low-level anticyclone over Southeast Asia. Inversely, air masses from the southwest contribute to long-range air pollution due to transportation of atmospheric CO2 by wind is associated with biomass burning in Sumatra, Indonesia. The GOSAT data and the Satellite measurements are able to measure the increase of the atmosphere CO2 values over different regions.

  19. Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains.

    PubMed

    Baruch, Omer; Kashkush, Khalil

    2012-05-01

    Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number. PMID:22183295

  20. Spatial variation of crustal strain in the Kachchh region, India: Implication on the Bhuj earthquake of 2001

    NASA Astrophysics Data System (ADS)

    Sinha, Sushmita; Mohanty, S.

    2012-10-01

    The Kachchh province of Western India is a major seismic domain in an intraplate set-up. This seismic zone is located in a rift basin, which was developed during the early Jurassic break-up of the Gondwanaland. The crustal strain determined from the GPS velocity data of post-seismic time period following the 2001 Bhuj earthquake indicates a maximum strain rate of ˜266 × 10-9 per year along N013°. Focal mechanism solutions of the main event of 26 January 2001 and the aftershocks show that the maximum principal stress axis is close to this high strain direction. Maximum shear strain rate determined from the GPS data of the area has similar orientation. The unusually high strain rate is comparable in magnitude to the continental rift systems. The partitioning of the regional NE-SW horizontal stress (SHmax) by the pre-existing EW-striking boundary fault developed the strike-slip components parallel to the regional faults, the normal components perpendicular to the faults, NE-striking conjugate Riedel shear fractures and tension fractures. The partitioned normal component of the stress is considered to be the major cause for compression across the regional EW faults and development of the second-order conjugate shear fractures striking NE-SW and NW-SE. The NE-striking transverse faults parallel to the anti-Riedel shear planes have become critical under these conditions. These anti-Riedel planes are interpreted to be critical for the seismicity of the Kachchh region. The high strain rate in this area of low to moderate surface heat flow is responsible for deeper position of the brittle-ductile transition and development of deep seated seismic events in this intraplate region.

  1. A Modeling Investigation of Thermal and Strain Induced Recovery and Nonlinear Hardening in Potential Based Viscoplasticity

    NASA Technical Reports Server (NTRS)

    Arnold, S. M.; Saleeb, A. F.; Wilt, T. E.

    1993-01-01

    Specific forms for both the Gibb's and the complementary dissipation potentials were chosen such that a complete potential based multiaxial, isothermal, viscoplastic model was obtained. This model in general possesses three internal state variables (two scalars associated with dislocation density and one tensor associated with dislocation motion) both thermal and dynamic recovery mechanisms, and nonlinear kinematic hardening. This general model, although possessing associated flow and evolutionary laws, is shown to emulate three distinct classes of theories found in the literature, by modification of the driving threshold function F. A parametric study was performed on a specialized nondimensional multiaxial form containing only a single tensorial internal state variable (i.e., internal stress). The study was conducted with the idea of examining the impact of including a strain-induced recovery mechanism and the compliance operator, derived from the Gibb's potential, on the uniaxial and multiaxial response. One important finding was that inclusion of strain recovery provided the needed flexibility in modeling stress-strain and creep response of metals at low homologous temperatures, without adversely affecting the high temperature response. Furthermore, for nonproportional loading paths, the inclusion of the compliance operator had a significant influence on the multiaxial response, but had no influence on either uniaxial or proportional load histories.

  2. The Influence of Strain Rate Variations on the Appearance of Serrated Yielding in 2024-T3 Al-Clad Aluminium Alloy

    SciTech Connect

    Leacock, Alan G.; McMurray, Robert J.; Brown, D.; Poston, Ken

    2007-04-07

    To avoid failure during the stretch forming process using manual control, machine operators tend to achieve the final form using a stop-start approach. It was observed that when approaching full form, stretcher-strain marks appeared on the surface of the part if the operator stopped and restarted the forming operation. In order to investigate this phenomenon, a series of tensile tests was conducted using two batches of 2024-T3 aluminium alloy. The specimens were tested using several different strain rates, representative of those used on the shop floor. Additional tests were conducted involving a series of pauses under displacement control at differing levels of strain and strain rate. In the uninterrupted tests for the two batches of 2024-T3 material tested, serrated yielding was observed just prior to failure. However for the tests in which there was a pause in displacement, the material consistently exhibited serrated yielding when the crosshead began to move again. These results indicate that the pause provides an opportunity for strain ageing and pinning of the dislocations resulting in serrated yielding of this alloy. In order to avoid serrated yielding, stretch forming operations using 2024-T3 aluminium should be conducted at a constant strain rate without interruption. This also has far reaching implications for those involved in the production and testing of these alloys. The test programme described represents an initial attempt to investigate a phenomenon noted during an industrial forming process and should be extended to analyse the affect of strain path changes on the occurrence of serrated yielding.

  3. Analysis of Bulk and Thin Film Model Samples Intended for Investigating the Strain Sensitivity of Niobium-Tin

    SciTech Connect

    Mentink, M. G. T.; Anders, A.; Dhalle, M. M. J.; Dietderich, D. R.; Godeke, A.; Goldacker, W.; Hellman, F.; Kate, H. H. J. ten; Putnam, D.; Slack, J. L.; Sumption, M. D.; Susner, M. A.

    2010-08-01

    Bulk samples and thin films were fabricated and characterized to determine their suitability for studying the effect of composition and morphology on strain sensitivity. Heat capacity and resistivity data are used to determine the critical temperature distribution. It is found that all bulk samples contain stoichiometric Nb{sub 3}Sn regardless of their nominal Nb to Sn ratio. Furthermore, in bulk samples with Cu additions, a bi-modal distribution of stoichiometric and off-stoichiometric Nb-Sn is found. Thus the nominally off-stoichiometric bulk samples require additional homogenization steps to yield homogeneous off-stoichiometric samples. A binary magnetron-sputtered thin film has the intended off-stoichiometric Nb-Sn phase with a mid-point critical temperature of 16.3 K. This type of sample is a suitable candidate for investigating the strain sensitivity of A15 Nb{sub 1-{beta}}Sn{sub {beta}}, with 0.18 < {beta} < 0.25. The strain sensitivity of Nb-Sn as a function of composition and morphology is important for an in-depth understanding of the strain sensitivity of composite Nb{sub 3}Sn wires.

  4. Variation in the TonB-dependent Outer-Membrane Proteins in Plant-Associated Strains of Pseudomonas fluorescens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nutrient acquisition is key to the ecological fitness of environmental bacteria such as Pseudomonas fluorescens and TonB-dependent outer-membrane proteins are important components of the cellular machinery for the uptake of substrates from the environment. Genomic sequences of ten strains of plant-a...

  5. A Review of the Properties of Nb3Sn and Their Variation with A15Composition, Morphology and Strain State

    SciTech Connect

    Godeke, Arno

    2006-03-27

    Significant efforts can be found throughout the literature to optimize the current carrying capacity of Nb{sub 3}Sn superconducting wires. The achievable transport current density in wires depends on the A15 composition, morphology and strain state. The A15 sections in wires contain, due to compositional inhomogeneities resulting from solid state diffusion A15 formation reactions, a distribution of superconducting properties. The A15 grain size can be different from wire to wire and is also not necessarily homogeneous across the A15 regions. Strain is always present in composite wires, and the strain state changes as a result of thermal contraction differences and Lorentz forces in magnet systems. To optimize the transport properties it is thus required to identify how composition, grain size and strain state influence the superconducting properties. This is not accurately possible in inhomogeneous and spatially complex systems such as wires. This article therefore gives an overview of the available literature on simplified, well defined(quasi--)homogeneous laboratory samples. After more than 50 years of research on superconductivity in Nb{sub 3}Sn, a significant amount of results are available, but these are scattered over a multitude of publications. Two reviews exist on the basic properties of A15 materials in general, but no specific review for Nb{sub 3}Sn is available. This article is intended to provide such an overview. It starts with a basic description of the Niobium--Tin intermetallic. After this it maps the influence of Sn content on the electron--phonon interaction strength and on the field-temperature phase boundary. The literature on the influence of Cu, Ti and Ta additions will then be briefly summarized.This is followed by a review on the effects of grain size and strain. The article is concluded with a summary of the main results.

  6. Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time

    PubMed Central

    Hoy, Yana Emmy; Bik, Elisabeth M.; Lawley, Trevor D.; Holmes, Susan P.; Monack, Denise M.

    2015-01-01

    Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals. PMID:26565698

  7. Investigating the impact of oxygen concentration and blood flow variation on photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Penjweini, Rozhin; Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.

    2016-03-01

    Type II photodynamic therapy (PDT) is used for cancer treatment based on the combined action of a photosensitizer, a special wavelength of light, oxygen (3O2) and generation of singlet oxygen (1O2). Intra-patient and inter-patient variability of oxygen concentration ([3O2]) before and after the treatment as well as photosensitizer concentration and hemodynamic parameters such as blood flow during PDT has been reported. Simulation of these variations is valuable, as it would be a means for the rapid assessment of treatment effect. A mathematical model has been previously developed to incorporate the diffusion equation for light transport in tissue and the macroscopic kinetic equations for simulation of [3O2], photosensitizers in ground and triplet states and concentration of the reacted singlet oxygen ([1O₂]rx) during PDT. In this study, the finite-element based calculation of the macroscopic kinetic equations is done for 2-(1- Hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH)-mediated PDT by incorporating the information of the photosensitizer photochemical parameters as well as the tissue optical properties, photosensitizer concentration, initial oxygen concentration ([3O2]0), blood flow changes and Φ that have been measured in mice bearing radiation-induced fibrosarcoma (RIF) tumors. Then, [1O2]rx calculated by using the measured [3O2] during the PDT is compared with [1O2]rx calculated based on the simulated [3O₂]; both calculations showed a reasonably good agreement. Moreover, the impacts of the blood flow changes and [3O2]0 on [1O2]rx have been investigated, which showed no pronounced effect of the blood flow changes on the long-term 1O2 generation. When [3O2]0 becomes limiting, small changes in [3O₂] have large effects on [1O2]rx.

  8. Metabolomic investigation into variation of endogenous metabolites in professional athletes subject to strength-endurance training.

    PubMed

    Yan, Bei; A, Jiye; Wang, Guangji; Lu, Huali; Huang, Xiaoping; Liu, Yi; Zha, Weibin; Hao, Haiping; Zhang, Ying; Liu, Linsheng; Gu, Shenghua; Huang, Qing; Zheng, Yuanting; Sun, Jianguo

    2009-02-01

    Strength-endurance type of sport can lead to modification of human beings' physiological status. The present study aimed to investigate the alteration of metabolic phenotype or biochemical compositions in professional athletes induced by long-term training by means of a novel systematic tool, metabolomics. Resting venous blood samples of junior and senior male rowers were obtained before and after 1-wk and 2-wk training. Venous blood from healthy male volunteers as control was also sampled at rest. Endogenous metabolites in serum were profiled by GC/TOF-MS and multivariate statistical technique, i.e., principal component analysis (PCA), and partial least squares projection to latent structures and discriminant analysis (PLS-DA) were used to process the data. Significant metabolomic difference was observed between the professional athletes and control subjects. Long-term strength and endurance training induced distinct separation between athletes of different exercise seniority, and training stage-related trajectory of the two groups of athletes was clearly shown along with training time. However, most of these variations were not observed by common biochemical parameters, such as hemoglobin, testosterone, and creatine kinase. The identified metabolites contributing to the classification included alanine, lactate, beta-d-methylglucopyranoside, pyroglutamic acid, cysteine, glutamic acid, citric acid, free fatty acids, valine, glutamine, phenylalanine, tyrosine, and so on, which were involved in glucose metabolism, oxidative stress, energy metabolism, lipid metabolism, amino acid metabolism. These findings suggest that metabolomics is a promising and potential tool to profile serum of professional athletes, make a deep insight into physiological states, and clarify the disorders induced by strength-endurance physical exercise. PMID:19036890

  9. Investigating the impact of oxygen concentration and blood flow variation on photodynamic therapy

    PubMed Central

    Penjweini, Rozhin; Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.

    2016-01-01

    Type II photodynamic therapy (PDT) is used for cancer treatment based on the combined action of a photosensitizer, a special wavelength of light, oxygen (3O2) and generation of singlet oxygen (1O2). Intra-patient and inter-patient variability of oxygen concentration ([3O2]) before and after the treatment as well as photosensitizer concentration and hemodynamic parameters such as blood flow during PDT has been reported. Simulation of these variations is valuable, as it would be a means for the rapid assessment of treatment effect. A mathematical model has been previously developed to incorporate the diffusion equation for light transport in tissue and the macroscopic kinetic equations for simulation of [3O2], photosensitizers in ground and triplet states and concentration of the reacted singlet oxygen ([1O2]rx) during PDT. In this study, the finite-element based calculation of the macroscopic kinetic equations is done for 2-(1-Hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH)-mediated PDT by incorporating the information of the photosensitizer photochemical parameters as well as the tissue optical properties, photosensitizer concentration, initial oxygen concentration ([3O2]0), blood flow changes and ϕ that have been measured in mice bearing radiation-induced fibrosarcoma (RIF) tumors. Then, [1O2]rx calculated by using the measured [3O2] during the PDT is compared with [1O2]rx calculated based on the simulated [3O2]; both calculations showed a reasonably good agreement. Moreover, the impacts of the blood flow changes and [3O2]0 on [1O2]rx have been investigated, which showed no pronounced effect of the blood flow changes on the long-term 1O2 generation. When [3O2]0 becomes limiting, small changes in [3O2] have large effects on [1O2]rx. PMID:27453622

  10. Investigations on residual strains and the cathodoluminescence and electron beam induced current signal of grain boundaries in silicon

    SciTech Connect

    Nacke, M.; Allardt, M.; Hieckmann, E.; Weber, J.; Chekhonin, P.; Skrotzki, W.

    2014-04-28

    Cathodoluminescence (CL) and electron beam induced current (EBIC) measurements were used to investigate the optical behavior and electrical activity of grain boundaries (GBs) in coarsely grained silicon. Electron backscatter diffraction (EBSD) was applied for a comprehensive characterization of the structural properties of the high angle and low angle GBs (HAGBs and LAGBs) in the sample. It was found that not only the EBIC but also the panchromatic (pan) CL contrast of Σ3 HAGBs strongly depends on the hkl-type of the boundary plane. At room temperature coherent Σ3 GBs exhibit no significant contrast in the CL or EBIC images, whereas at low temperatures the pan-CL contrast is strong. For incoherent Σ3 GBs, a strong pan-CL and EBIC contrast was observed in the entire temperature range. Only on a LAGB (misorientation angle 4.5°) CL investigations at low temperatures revealed a line with peak position at about (0.82 ± 0.01) eV, usually related to the dislocation associated D1 transition. Cross-correlation EBSD was applied to analyze the strain fields of Σ3 HAGBs as well as of the LAGB. All the components of the local strain tensors were quantitatively determined. The relationship between the extension of the strain field at the LAGB and the spatial D1 intensity distribution is discussed.

  11. Mycoplasma agassizii strain variation and distinct host antibody responses explain differences between enzyme-linked immunosorbent assays and Western blot assays.

    PubMed

    Wendland, Lori D; Klein, Paul A; Jacobson, Elliott R; Brown, Mary B

    2010-11-01

    The precarious status of desert (Gopherus agassizii) and gopher (G. polyphemus) tortoises has resulted in conservation efforts that now include health assessment as an important component of management decision-making. Mycoplasmal upper respiratory tract disease (URTD) is one of very few diseases in chelonians for which comprehensive and rigorously validated diagnostic tests exist. In this study, serum samples obtained from eight Gopherus tortoises documented at necropsy to (i) be enzyme-linked immunosorbent assay (ELISA) seropositive using the PS6 antigen, (ii) be infected with Mycoplasma agassizii as indicated by direct isolation of the pathogen from the respiratory surfaces, and (iii) have histological lesions of mycoplasmal URTD were used to evaluate four distinct clinical isolates of M. agassizii as antigens for ELISA and Western blot analyses. Each animal sample reacted in the Western blot with its homologous M. agassizii strain, but recognition of heterologous M. agassizii strains was variable. Further, individual animals varied significantly with respect to the specific proteins recognized by the humoral immune response. An additional 114 Gopherus serum samples were evaluated using ELISA antigens prepared from the four distinct M. agassizii strains; A₄₀₅ values were significantly correlated (r² goodness of fit range, 0.708 to 0.771; P < 0.0001) for all antigens tested. The results confirm that strain variation is responsible for the observed differences between Western blot binding patterns. Thus, reliance on a single M. agassizii strain as an antigen in Western blot assays may provide false-negative results. This could have adverse consequences for the well-being of these environmentally sensitive hosts if false-negative animals were relocated to sites consisting of true-negative populations. PMID:20810678

  12. Mycoplasma agassizii Strain Variation and Distinct Host Antibody Responses Explain Differences between Enzyme-Linked Immunosorbent Assays and Western Blot Assays ▿

    PubMed Central

    Wendland, Lori D.; Klein, Paul A.; Jacobson, Elliott R.; Brown, Mary B.

    2010-01-01

    The precarious status of desert (Gopherus agassizii) and gopher (G. polyphemus) tortoises has resulted in conservation efforts that now include health assessment as an important component of management decision-making. Mycoplasmal upper respiratory tract disease (URTD) is one of very few diseases in chelonians for which comprehensive and rigorously validated diagnostic tests exist. In this study, serum samples obtained from eight Gopherus tortoises documented at necropsy to (i) be enzyme-linked immunosorbent assay (ELISA) seropositive using the PS6 antigen, (ii) be infected with Mycoplasma agassizii as indicated by direct isolation of the pathogen from the respiratory surfaces, and (iii) have histological lesions of mycoplasmal URTD were used to evaluate four distinct clinical isolates of M. agassizii as antigens for ELISA and Western blot analyses. Each animal sample reacted in the Western blot with its homologous M. agassizii strain, but recognition of heterologous M. agassizii strains was variable. Further, individual animals varied significantly with respect to the specific proteins recognized by the humoral immune response. An additional 114 Gopherus serum samples were evaluated using ELISA antigens prepared from the four distinct M. agassizii strains; A405 values were significantly correlated (r2 goodness of fit range, 0.708 to 0.771; P < 0.0001) for all antigens tested. The results confirm that strain variation is responsible for the observed differences between Western blot binding patterns. Thus, reliance on a single M. agassizii strain as an antigen in Western blot assays may provide false-negative results. This could have adverse consequences for the well-being of these environmentally sensitive hosts if false-negative animals were relocated to sites consisting of true-negative populations. PMID:20810678

  13. Variation in Direct Access to Tests to Investigate Cancer: A Survey of English General Practitioners

    PubMed Central

    Nicholson, Brian D.; Oke, Jason L.; Rose, Peter W.; Mant, David

    2016-01-01

    Background The 2015 NICE guidelines for suspected cancer recommend that English General Practitioners have direct access to diagnostic tests to investigate symptoms of cancer that do not meet the criteria for urgent referral. We aimed to identify the proportion of GPs in England with direct access to these tests. Methods We recruited 533 English GPs through a national clinical research network to complete an online survey about direct access to laboratory, radiology, and endoscopy tests in the three months leading up to the release of the 2015 NICE guidance. If they had direct access to a diagnostic test, GPs were asked about the time necessary to arrange a test and receive a report. Results are reported by NHS sub-region and, adjusting for sampling, for England as a whole. Results Almost all GPs reported direct access to x-ray and laboratory investigations except faecal occult blood testing (54%, 95% CI 49–59%) and urine protein electrophoresis (89%, 95% CI 84–92%). Fewer GPs had direct access to CT scans (54%, 95% CI 49–59%) or endoscopy (colonoscopy 32%, 95% CI 28–37%; gastroscopy 72%, 95% CI 67–77%). There was significant variation in direct access between NHS regions for the majority of imaging tests—for example, from 20 to 85% to MRI. Apart from x-ray, very few GPs (1–22%) could access radiology and endoscopy within the timescales recommended by NICE. The modal request to test time was 2–4 weeks for routine radiology and 4–6 weeks for routine endoscopy with results taking another 1–2 weeks. Conclusion At the time that the 2015 NICE guideline was released, local investment was required to not only provide direct access but also reduce the interval between request and test and speed up reporting. Further research using our data as a benchmark is now required to identify whether local improvements in direct access have been achieved in response to the NICE targets. If alternative approaches to test access are to be proposed they must be

  14. Sequence variation in CYP51A from the Y strain of Trypanosoma cruzi alters its sensitivity to inhibition.

    PubMed

    Cherkesova, Tatiana S; Hargrove, Tatiana Y; Vanrell, M Cristina; Ges, Igor; Usanov, Sergey A; Romano, Patricia S; Lepesheva, Galina I

    2014-11-01

    CYP51 (sterol 14α-demethylase) is an efficient target for clinical and agricultural antifungals and an emerging target for treatment of Chagas disease, the infection that is caused by multiple strains of a protozoan pathogen Trypanosoma cruzi. Here, we analyze CYP51A from the Y strain T. cruzi. In this protein, proline 355, a residue highly conserved across the CYP51 family, is replaced with serine. The purified enzyme retains its catalytic activity, yet has been found less susceptible to inhibition. These biochemical data are consistent with cellular experiments, both in insect and human stages of the pathogen. Comparative structural analysis of CYP51 complexes with VNI and two derivatives suggests that broad-spectrum CYP51 inhibitors are likely to be preferable as antichagasic drug candidates. PMID:25217832

  15. Sequence variation in CYP51A from the Y strain of Trypanosoma cruzi alters its sensitivity to inhibition

    PubMed Central

    Cherkesova, Tatiana S.; Hargrove, Tatiana Y.; Vanrell, M. Cristina; Ges, Igor; Usanov, Sergey A.; Romano, Patricia S.; Lepesheva, Galina I.

    2014-01-01

    CYP51 (sterol 14α-demethylase) is an efficient target for clinical and agricultural antifungals and an emerging target for treatment of Chagas disease, the infection that is caused by multiple strains of a protozoan pathogen Trypanosoma cruzi. Here, we analyze CYP51A from the Y strain T. cruzi. In this protein, proline 355, a residue highly conserved across the CYP51 family, is replaced with serine. The purified enzyme retains its catalytic activity, yet has been found less susceptible to inhibition. These biochemical data are consistent with cellular experiments, both in insect and human stages of the pathogen. Comparative structural analysis of CYP51 complexes with VNI and two derivatives suggests that broad-spectrum CYP51 inhibitors are likely to be preferable as antichagasic drug candidates. PMID:25217832

  16. Genetic Variation among Staphylococcus aureus Strains from Bovine Milk and Their Relevance to Methicillin-Resistant Isolates from Humans ▿

    PubMed Central

    Hata, Eiji; Katsuda, Ken; Kobayashi, Hideki; Uchida, Ikuo; Tanaka, Kiyoshi; Eguchi, Masashi

    2010-01-01

    In genetic analysis of bovine Staphylococcus aureus isolates that are recognized as an important pathogenic bacterium in bovine mastitis, multilocus sequence typing (MLST) showed strong correlation to the results of pulsed-field gel electrophoresis, coa PCR-restriction fragment length polymorphism (RFLP), spa typing, and the coagulase serotyping method. According to MLST results, strains derived from sequence type 97 (ST97) and ST705 were suggested as not only dominant bovine S. aureus lineages in Japan but also pandemic bovine S. aureus lineages. Although both lineages seem to be distantly related to each other by phylogenetic analysis, both had common characteristics, i.e., lukM/lukF′-PV and coagulase serotype VI. These characteristics were very rare among minor bovine strains and human strains and may contribute to the host specificity of these lineages. Four methicillin-resistant S. aureus (MRSA) isolates were first confirmed from bovine milk in Japan; these isolates showed geno- and serotypes that were identical or similar to those of human MRSA isolates in Japan (ST5, staphylococcal cassette chromosome mec type II [SCCmec II], Spa type t002 or t375, and coagulase serotype II, and ST89, SCCmec IIIa, Spa type t5266, and coagulase serotype I). ST5 and ST89 are uncommon among bovine isolates in the world, whereas these STs are common among human MRSA isolates in Japan. PMID:20392913

  17. Strain controlled systematic variation of metal-insulator transition in epitaxial NdNiO{sub 3} thin films

    SciTech Connect

    Kumar, Yogesh; Choudhary, R. J.; Kumar, Ravi

    2012-10-01

    We report here the strain dependent structural and electrical transport properties of epitaxial NdNiO{sub 3} thin films. Pulsed laser deposition technique was used to grow the NdNiO{sub 3} thin films on c-axis oriented SrTiO{sub 3} single crystals. Deposited films were irradiated using 200 MeV Ag{sup 15+} ion beam at the varying fluence (1 Multiplication-Sign 10{sup 11}, 5 Multiplication-Sign 10{sup 11}, and 1 Multiplication-Sign 10{sup 12} ions/cm{sup 2}). X-ray diffraction studies confirm the epitaxial growth of the deposited films, which is maintained even up to the highest fluence. Rise in the in-plane compressive strain has been observed after the irradiation. All the films exhibit metal-insulator transition, however, a systematic decrease in the transition temperature (T{sub MI}) has been observed after irradiation, which may be attributed to the increase in the in-plane compression. Raman spectroscopy data reveal that this reduction in T{sub MI}, with the irradiation, is related to the decrease in band gap due to the stress generated by the in-plane compressive strain.

  18. Variability among Rhizobium Strains Originating from Nodules of Vicia faba.

    PubMed

    van Berkum, P; Beyene, D; Vera, F T; Keyser, H H

    1995-07-01

    Rhizobium strains from nodules of Vicia faba were diverse in plasmid content and serology. Results of multilocus gel electrophoresis and restriction fragment length polymorphism indicated several deep chromosomal lineages among the strains. Linkage disequilibrium among the chromosomal types was detected and may have reflected variation of Rhizobium strains in the different geographical locations from which the strains originated. An investigation of pea strains with antibodies prepared against fava bean strains and restriction fragment length polymorphism analyses, targeting DNA regions coding for rRNA and nodulation, indicated that Rhizobium strains from V. faba nodules were distinguishable from those from Pisum sativum, V. villosa, and Trifolium spp. PMID:16535075

  19. Defect investigations in InAs/GaSb type-II strained layer superlattice

    NASA Astrophysics Data System (ADS)

    Klein, Brianna

    InAs/GaSb type-II strained layer superlattices are a material used for infrared detection. By adjusting the thickness of the InAs and GaSb layers, the material bandgap can be tuned to absorb photons from 3-30 mum. Compared to competing materials such as HgCdTe and InSb, InAs/GaSb superlattices are more mechanically robust, have reduced tunneling currents, and can use strain to suppress Auger recombination. In spite of these advantages, this material still faces several challenges, including low minority carrier lifetime, resulting from trap levels that cause Schockley-Read-Hall recombination. These low lifetimes lead to reduced signal-to-noise ratio and higher dark current. Therefore, increasing the lifetime is important for improving this material's performance. However, to increase the carrier lifetimes, the origin of the traps must first be understood. In this work, several key suspect causes of the "killer" defect were evaluated. A commonly explored suspect in literature, the interfaces, was studied using time-resolved photoluminescence for three different samples. This characterization method was also used to determine if the doping atom and its layer placement significantly impacted the minority carrier lifetime. There is a substantial amount of evidence that the presence of gallium, or the GaSb layer itself harbors the defect. Thus, the rest of the study focused on aspects of GaSb. Layer intermixing of the In and As atoms into the GaSb layer was studied by intentionally incorporating In and As in bulk GaSb and using photocapacitance characterization to observe any possible defect level formation. In addition, trap level formation for different GaSb growth temperatures was also explored with this characterization technique. Finally, in an attempt to reduce trap densities, GaSb was grown with an increased level of Sb monomers rather than dimers. This material was characterized using dark current density measurements and photoluminescence.

  20. Investigation of a Cross-Correlation Based Optical Strain Measurement Technique for Detecting radial Growth on a Rotating Disk

    NASA Technical Reports Server (NTRS)

    Clem, Michelle M.; Woike, Mark R.

    2013-01-01

    The Aeronautical Sciences Project under NASA`s Fundamental Aeronautics Program is extremely interested in the development of novel measurement technologies, such as optical surface measurements in the internal parts of a flow path, for in situ health monitoring of gas turbine engines. In situ health monitoring has the potential to detect flaws, i.e. cracks in key components, such as engine turbine disks, before the flaws lead to catastrophic failure. In the present study, a cross-correlation imaging technique is investigated in a proof-of-concept study as a possible optical technique to measure the radial growth and strain field on an already cracked sub-scale turbine engine disk under loaded conditions in the NASA Glenn Research Center`s High Precision Rotordynamics Laboratory. The optical strain measurement technique under investigation offers potential fault detection using an applied high-contrast random speckle pattern and imaging the pattern under unloaded and loaded conditions with a CCD camera. Spinning the cracked disk at high speeds induces an external load, resulting in a radial growth of the disk of approximately 50.0-im in the flawed region and hence, a localized strain field. When imaging the cracked disk under static conditions, the disk will be undistorted; however, during rotation the cracked region will grow radially, thus causing the applied particle pattern to be .shifted`. The resulting particle displacements between the two images will then be measured using the two-dimensional cross-correlation algorithms implemented in standard Particle Image Velocimetry (PIV) software to track the disk growth, which facilitates calculation of the localized strain field. In order to develop and validate this optical strain measurement technique an initial proof-of-concept experiment is carried out in a controlled environment. Using PIV optimization principles and guidelines, three potential speckle patterns, for future use on the rotating disk, are developed

  1. Variations in polyoma virus genotype in relation to tumor induction in mice. Characterization of wild type strains with widely differing tumor profiles.

    PubMed Central

    Dawe, C. J.; Freund, R.; Mandel, G.; Ballmer-Hofer, K.; Talmage, D. A.; Benjamin, T. L.

    1987-01-01

    The authors have explored the effects of variations in mouse polyoma virus genotype on patterns of tumor formation in the mouse. Four "wild type" virus strains were surveyed. Two were highly oncogenic, inducing multiple tumors of epithelial and mesenchymal origin, at high frequency and with short latency. The other two strains were weakly oncogenic, inducing fewer tumors, solely of mesenchymal origin, and after a long latency. These sharply contrasting tumor profiles were reproduced with virus stocks derived from molecularly cloned viral genomes. Though vastly different in their oncogenic properties, these cloned viruses proved equally effective in transforming established rat fibroblasts in culture and showed the same patterns of tumor antigen expression in cultured mouse cells. Complexes of polyoma middle T antigen and pp60c-src were demonstrated in extracts of epithelial tumors induced by a highly oncogenic virus strain. It is concluded that polyoma viral genetic determinants for tumor induction in the mouse are more complex than those previously defined by the use of cell transformation systems. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 Figure 15 Figure 16 PMID:2437801

  2. CFD investigation of the influence of volute geometrical variations on hydrodynamic characteristics of circulator pump

    NASA Astrophysics Data System (ADS)

    Wu, Denghao; Yuan, Shouqi; Ren, Yun; Mu, Jiegang; Yang, Youdong; Liu, Jian

    2016-03-01

    Improper design of volute geometry can be the main cause that leads to unsteady pressure pulsation and radial force in pumps. Therefore, it is important to understand the influence of volute geometrical parameters on hydrodynamic characteristics of pump and the mechanism. However, the existing studies are limited to investigate the influence of only one or two volute geometrical parameters each time, and a systematic study of the influence of the combinations of different volute geometrical parameters on the pump's hydrodynamic characteristics is missing. In this paper, a study on the understanding of the influence of volute geometrical variations on hydrodynamic characteristics of a high speed circulator pump by using computational fluid dynamics(CFD) technology is presented. Five main volute geometrical parameters D 3, A 8, α 0, φ 0 and R t are selected and 25 different volute configurations are generated by using design of experiments(DOE) method. The 3D unsteady flow numerical simulations, which are based on the SST k- w turbulence model and sliding mesh technique provided by CFX, are executed on the 25 different volute configurations. The hydraulic performance, pressure pulsation and unsteady radial force inside the pump at design condition are obtained and analyzed. It has been found that volute geometrical parameters D 3 and A 8 are major influence factors on hydrodynamic characteristics of the pump, while α 0, φ 0 and R t are minor influence factors. The minimum contribution from both D 3 and A 8 is 58% on head, and maximum contribution from both D 3 and A 8 is 90% on pressure pulsation. Regarding the pressure pulsation intensity, two peaks can be found. One is in the tongue area and the other is in the diffusor area. The contributions are around 60% from tongue and 25% from diffusor, respectively. The amplitude of pressure pulsation has a quadratic polynomial functional relationship with respect to D 3/ D 2 and A 8/ A 10, and fluctuating level of

  3. Investigation of coastal wave field variations with TerraSAR-X

    NASA Astrophysics Data System (ADS)

    Jacobsen, Sven; Lehner, Susanne; Bruck, Miguel; Gies, Tobias; Pleskachevsky, Andrey; Rosenthal, Wolfgang; Bruns, Thomas

    2014-05-01

    Spaceborne Synthetic Aperture Radar (SAR) is a uniquely powerful sensor providing two-dimensional information of the ocean surface like a broad spectrum of meteo-marine parameters such as windfields, significant wave height, peak wavelength and other seastate characteristics. SAR is particularly suitable for many oceanographic observations due to its high resolution in combination with global coverage and the independence of daylight and cloud conditions. The data has been amongst others used to investigate geophysical processes and for numerical model validation. It has also so been found to be a valuable contribution regarding data assimilation into meteorological, marine and coupled models. The X-band radar of the TerraSAR-X (TS-X) satellite acquires images of the sea surface with a high resolution up to 1m. Due to a lower platform altitude and a higher signal frequency, nonlinear imaging effects of the moving ocean surface are reduced when compared to previous C-band sensors and thus individual ocean waves with wavelengths below 30m are detectable. Minor importance of nonlinear effects in the wave imaging process also gives rise to new empirical model functions to derive sea state parameters directly from the SAR image spectrum properties and thus minimizing data processing time. This is of special interest with regard to the development of near-real-time (NRT) data products often favorable for maritime safety and security applications particularly . The latest generation of the empirical algorithm for TS-X seastate analysis XWAVE has been tuned with hundreds of collocated buoy measurements over the open ocean and subsequent validation exhibits a very good agreement with in-situ data. However, in contrast to the open ocean where seastate parameters do not change significantly on the scale of kilometers, coastal waters exhibit a large spacial variablility owing to ,inter alia, subsurface topography influence. The lateral variation complicates the extraction of

  4. Investigating Charge Transport Mechanisms and Spatially Localized Photocurrent Variation in Organic Photovoltaic Devices

    NASA Astrophysics Data System (ADS)

    Leever, Benjamin Jay

    Although the performance of bulk heterojunction (BHJ) organic photovoltaic (OPV) devices is known to be closely related to the interpenetrating phase-separated network of the photoactive layer nanostructure, much initial work focused on improving relatively simplistic metrics such as efficiency and spectral response. Electron microscopy and tomography have yielded important insights into the nature of device morphology, but these methods are often expensive, time-consuming, and most significantly, do not allow for in situ analysis of operating devices. This dissertation focuses on better understanding the role of interfaces and active layer morphology through approaches that enable the analysis of operating devices. The basic device architecture analyzed here is a glass substrate coated with an indium tin oxide (ITO) anode, a poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) interfacial layer, a poly(3-hexylthiophene):[6,6]-phenyl-C 61-butyric acid methyl ester (P3HT:PCBM) photoactive layer, and an aluminum cathode. The primary analysis techniques include atomic force photovoltaic microscopy (AFPM), developed as part of this work, and impedance spectroscopy with equivalent circuit modeling. Conductive atomic force microscopy and photoelectron spectroscopy techniques are also extensively employed, particularly in the investigation of anode surface properties. AFPM analysis demonstrates spatially localized photocurrent variations in operating micron-scale devices, which are too large to be related to P3HT and PCBM segregation alone. By varying anode surface treatments we show a correlation between the conductive uniformity of the anode surface and the variability observed in the photocurrent, suggesting that electrical inhomogeneities in the anode surface are passed through the active layer film. In situ impedance analysis of P3HT:PCBM devices provides an indirect measure of active layer morphology. We acquire and analyze the impedance response of

  5. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano

    PubMed Central

    Meyer, Julie L; Huber, Julie A

    2014-01-01

    Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea. PMID:24257443

  6. Variation in Growth, Colonization of Maize, and Metabolic Parameters of GFP- and DsRed-Labeled Fusarium verticillioides Strains.

    PubMed

    Wu, Lei; Conner, R L; Wang, Xiaoming; Xu, Rongqi; Li, Hongjie

    2016-08-01

    Autofluorescent proteins are frequently applied as visual markers in the labeling of filamentous fungi. Genes gfp and DsRed were transformed into the genome of Fusarium verticillioides via the Agrobacterium tumefaciens-mediated transformation method. The selected transformants displayed a bright green or red fluorescence in all the organelles of the growing fungal mycelia and spores (except for the vacuoles) both in cultures and in the maize (Zea mays) roots they colonized. The results of gene-specific polymerase chain reaction (PCR) analysis and the thermal asymmetrical interlaced (TAIL)-PCR analysis demonstrated that gfp and DsRed were integrated on different chromosomes of the fungus. Reductions in the colony growth on the plates at pH 4.0 and 5.5 was observed for the green fluorescent protein (GFP)-transformant G3 and the DsRed-transformant R4, but transformants G4 and R1 grew as well as the wild-type strain at pH 4.0. The speed of growth of all the transformants was similar to the wild-type strain at pH ≥ 7. The insertion of gfp and DsRed did not alter the production of extracellular enzymes and fumonisin B by F. verticillioides. The transformants expressing GFP and DsRed proteins were able to colonize maize roots. However, the four transformants examined produced fewer CFU in the root samples than the wild-type strain during a sampling period of 7 to 28 days after inoculation. PMID:27088391

  7. Strain variation, based on the hemagglutinin gene, in Norwegian ISA virus isolates collected from 1987 to 2001: indications of recombination.

    PubMed

    Devold, M; Falk, K; Dale, B; Krossøy, B; Biering, E; Aspehaug, V; Nilsen, F; Nylund, A

    2001-11-01

    Infectious salmon anemia (ISA) is caused by a virus that probably belongs to the Orthomyxoviridae and was first recorded in Norway in 1984. The disease has since spread along the Norwegian coast and has later been found in Canada, Scotland, the Faroe Islands, Chile, and the USA. This study presents sequence variation of the hemagglutinin gene from 37 ISA virus isolates, viz. one isolate from Scotland, one from Canada and 35 from Norway. The hemagglutinin gene contains a highly polymorphic region (HPR), which together with the rest of the gene sequence provides a good tool for studies of epizootics. The gene shows temporal and geographical sequence variation, where certain areas are dominated by distinct groups of isolates. Evidence of transmission of ISA virus isolates within and between regions is given. It is suggested that the hemagglutinin gene from different isolates may recombine. Possible recombination sites are found within the HPR and in the 5'-end flanking region close to the HPR. PMID:11775793

  8. Genetic variation responsible for mouse strain differences in integrin {alpha}{sub 2} expression is associated with altered platelet responses to collagen

    SciTech Connect

    Li, Tong-Tong; Larrucea, Susana; Souza, Shiloe; Leal, Suzanne M.; Lopez, Jose A.; Rubin, Edward M.; Nieswandt, Bernhard; Bray, Paul F.

    2003-11-01

    exert quantitative and qualitative alterations in human platelet adhesive receptors. Polymorphisms of both integrin {alpha}{sub 2} and GPIb have been associated with quantitative differences in receptor levels in healthy individuals. The variation of integrin {alpha}{sub 2} in the normal population is 5-fold, and some portion of this variability has been associated with a C/T polymorphism at nucleotide 807. Individuals homozygous for the 807C or 807T alleles have an average 2-fold difference in platelet {alpha}{sub 2} {beta}{sub 1} levels, and this difference has been linked to increased adhesion to collagen and clinical thrombotic events. Comparable alterations in platelet adhesion receptor expression have not been assessed in different mouse strains. Assessing the functional consequences of subtle genetic variations in humans is challenged by numerous gene-gene and gene environment interactions, and studies in mice can greatly minimize these confounding variables. In addition, comparative sequence analyses between species and between nonhuman primates have proved useful for identifying sequences that affect function and expression. Thus, in the case of platelet adhesion receptors, knowing mouse strain differences in expression levels might be valuable for defining the responsible quantitative trait loci as well as affecting strain choice for particular functional experiments.

  9. Investigation of Genetic and Morphological Variation in the Sago Palm (Metroxylon sagu; Arecaceae) in Papua New Guinea

    PubMed Central

    KJÆR, ANDERS; BARFOD, ANDERS S.; ASMUSSEN, CONNY B.; SEBERG, OLE

    2004-01-01

    • Background and Aims The genetic and morphological variation in the sago palm (Metroxylon sagu, Arecaceae) in Papua New Guinea (PNG) was investigated. • Methods Amplified fragment length polymorphism (AFLP) was used to investigate the genetic structure of 76 accessions of M. sagu, collected in seven wild and semi‐wild stands in PNG. • Key Results An analysis of ten quantitative morphological variables revealed that most of these were mutually correlated. Principal component analyses of the same morphological variables showed that neither armature (presence or absence of spines) nor geographical separation was reflected clearly in the quantitative morphological variation. Similarity matrices of genetic, quantitative morphological, geographical and armature data were tested for pair‐wise correlations, using Mantel’s test. The results only showed a significant correlation between genetic and geographical distances. Visual inspection of principal component analyses plots and a neighbour‐joining dendrogram based on genetic distances supported this trend, whereas armature showed no relation with genetic distances. • Conclusions Geographical distribution defines some weak patterns in the genetic variation, whereas the genetic variation does not reflect any patterns in the morphological variation, including armature. The present study supports the accepted taxonomy of M. sagu, recognizing only one species of M. sagu in PNG. PMID:15155379

  10. Development and Characterization of a Reverse Genetic System for Studying Dengue Virus Serotype 3 Strain Variation and Neutralization

    PubMed Central

    Messer, William B.; Yount, Boyd; Hacker, Kari E.; Donaldson, Eric F.; Huynh, Jeremy P.; de Silva, Aravinda M.; Baric, Ralph S.

    2012-01-01

    Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here

  11. Extensive Variation and Rapid Shift of the MG192 Sequence in Mycoplasma genitalium Strains from Patients with Chronic Infection

    PubMed Central

    Mancuso, Miriam; Williams, James A.; Van Der Pol, Barbara; Fortenberry, J. Dennis; Jia, Qiuyao; Myers, Leann; Martin, David H.

    2014-01-01

    Mycoplasma genitalium causes persistent urogenital tract infection in humans. Antigenic variation of the protein encoded by the MG192 gene has been proposed as one of the mechanisms for persistence. The aims of this study were to determine MG192 sequence variation in patients with chronic M. genitalium infection and to analyze the sequence structural features of the MG192 gene and its encoded protein. Urogenital specimens were obtained from 13 patients who were followed for 10 days to 14 months. The variable region of the MG192 gene was PCR amplified, subcloned into plasmids, and sequenced. Sequence analysis of 220 plasmid clones yielded 97 unique MG192 variant sequences. MG192 sequence shift was identified between sequential specimens from all but one patient. Despite great variation of the MG192 gene among and within clinical specimens from different patients, MG192 sequences were more related within M. genitalium specimens from an individual patient than between patients. The MG192 variable region consisted of 11 discrete subvariable regions with different degrees of variability. Analysis of the two most variable regions (V4 and V6) in five sequential specimens from one patient showed that sequence changes increased over time and that most sequences were present at only one time point, suggesting immune selection. Topology analysis of the deduced MG192 protein predicted a surface-exposed membrane protein. Extensive variation of the MG192 sequence may not only change the antigenicity of the protein to allow immune evasion but also alter the mobility and adhesion ability of the organism to adapt to diverse host microenvironments, thus facilitating persistent infection. PMID:24396043

  12. Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization.

    PubMed

    Messer, William B; Yount, Boyd; Hacker, Kari E; Donaldson, Eric F; Huynh, Jeremy P; de Silva, Aravinda M; Baric, Ralph S

    2012-01-01

    Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here

  13. Biochemical analysis and investigation on the prospective applications of alkaline protease from a Bacillus cereus strain.

    PubMed

    Saleem, Mahjabeen; Rehman, Atiqa; Yasmin, Riffat; Munir, Bushra

    2012-06-01

    Proteases have prospective financial and environment-friendly applications; hence attention is focused currently on the finding of new protease producing microorganism so as to meet the requirements of industry. A thermophilic bacterial strain producing extracellular protease activity was isolated from soil and identified as Bacillus cereus by analysis of 16S rRNA. Protease production by the microorganism was improved by studying the impact of the type of nitrogen and carbon source, fermentation period, growth temperature and initial pH of the culture medium in cultivation optimization experiments. The enzyme was purified to homogeneity in two step procedure involving Sephadex G-75 and Q-Sepharose chromatography. The molecular weight of purified enzyme was found to be 58 kDa by SDS-PAGE. Protease exhibited a pH and temperature optima of 7.5 and 60°, respectively. The enzyme was active in the pH range of 6.0-9.0 and stable up to 70°C. Histological analysis of protease treated goat and cow skin pelts showed complete removal of non leather forming structures such as hair shaft, hair follicles and glandular structures. The protease showed the stain removing property from blood stained cotton cloth and found to be compatible with six commercially available detergents. The protease could release peptides from natural proteins after digestion of coagulated egg albumin and blood clot. PMID:22528469

  14. Investigation of Spatial Variation of Sea States Offshore of Humboldt Bay CA Using a Hindcast Model.

    SciTech Connect

    Dallman, Ann Renee; Neary, Vincent Sinclair

    2014-10-01

    Spatial variability of sea states is an important consideration when performing wave resource assessments and wave resource characterization studies for wave energy converter (WEC) test sites and commercial WEC deployments. This report examines the spatial variation of sea states offshore of Humboldt Bay, CA, using the wave model SWAN . The effect of depth and shoaling on bulk wave parameters is well resolved using the model SWAN with a 200 m grid. At this site, the degree of spatial variation of these bulk wave parameters, with shoaling generally perpendicular to the depth contours, is found to depend on the season. The variation in wave height , for example, was higher in the summer due to the wind and wave sheltering from the protruding land on the coastline north of the model domain. Ho wever, the spatial variation within an area of a potential Tier 1 WEC test site at 45 m depth and 1 square nautical mile is almost negligible; at most about 0.1 m in both winter and summer. The six wave characterization parameters recommended by the IEC 6 2600 - 101 TS were compared at several points along a line perpendicular to shore from the WEC test site . As expected, these parameters varied based on depth , but showed very similar seasonal trends.

  15. Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168.

    PubMed

    Anjum, Awais; Brathwaite, Kelly J; Aidley, Jack; Connerton, Phillippa L; Cummings, Nicola J; Parkhill, Julian; Connerton, Ian; Bayliss, Christopher D

    2016-06-01

    Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5'CCCGA and 5'CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. PMID:26786317

  16. Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168

    PubMed Central

    Anjum, Awais; Brathwaite, Kelly J.; Aidley, Jack; Connerton, Phillippa L.; Cummings, Nicola J.; Parkhill, Julian; Connerton, Ian; Bayliss, Christopher D.

    2016-01-01

    Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5′CCCGA and 5′CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. PMID:26786317

  17. The role of dissipation and defect energy in variational formulations of problems in strain-gradient plasticity. Part 2: single-crystal plasticity

    NASA Astrophysics Data System (ADS)

    Reddy, B. D.

    2011-11-01

    Variational formulations are constructed for rate-independent problems in small-deformation single-crystal strain-gradient plasticity. The framework, based on that of Gurtin (J Mech Phys Solids 50: 5-32, 2002), makes use of the flow rule expressed in terms of the dissipation function. Provision is made for energetic and dissipative microstresses. Both recoverable and non-recoverable defect energies are incorporated into the variational framework. The recoverable energies include those that depend smoothly on the slip gradients, the Burgers tensor, or on the dislocation densities (Gurtin et al. J Mech Phys Solids 55:1853-1878, 2007), as well as an energy proposed by Ohno and Okumura (J Mech Phys Solids 55:1879-1898, 2007), which leads to excellent agreement with experimental results, and which is positively homogeneous and therefore not differentiable at zero slip gradient. Furthermore, the variational formulation accommodates a non-recoverable energy due to Ohno et al. (Int J Mod Phys B 22:5937-5942, 2008), which is also positively homogeneous, and a function of the accumulated dislocation density. Conditions for the existence and uniqueness of solutions are established for the various examples of defect energy, with or without the presence of hardening or slip resistance.

  18. GNSS strain rate patterns and their application to investigate geodynamical credibility of the GNSS velocities

    NASA Astrophysics Data System (ADS)

    Araszkiewicz, Andrzej; Figurski, Mariusz

    2015-04-01

    The potential that lies in the use of GNSS measurements for crustal deformation studies have already noticed in the beginning of the first of such a system (GPS). Today thanks to the development of satellite positioning techniques it is possible to detect displacement on the Earth surface with an accuracy less than 1 cm. With long-term observations we can determine the velocities even more accurately. Growing demand in the last years for GNSS applications, both for scientific and civil use, meant that new networks of the reference stations were created. Such a dense GNSS networks allow to conduct research in the field of crust deformation at a higher spatial resolution than before. In Europe most of the research focuses on Mediterranean regions, where we can monitor events resulting from the tectonic plates collision. But even in Central Europe we can see effect of Africa push. In our research we focused on Polish territory, where in the past 5 years a nearly 300 reference stations were established. With minimal movements that have been observed in Poland, a key issue in this type of research is to determine the geodynamic reliability of the estimated stations velocities. While the long-term observations enable us to determine the very accurate velocities, it hard to indicate how reliably they reflect actual tectonic movements is. In this paper we proposed a method for testing the reliability of stations velocities based on the strain rate field analysis. The method is based on the analysis of the distribution of the rate of deformation tensor components obtained for triangular elements built on the basis of assessed station. The paper presents the results of numerical simulations and initial use of the method for the Polish network of reference stations: ASG-EUPOS

  19. The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes

    PubMed Central

    Steward, Charles A.; Gonzalez, Jose M.; Trevanion, Steve; Sheppard, Dan; Kerry, Giselle; Gilbert, James G. R.; Wicker, Linda S.; Rogers, Jane; Harrow, Jennifer L.

    2013-01-01

    Model organisms are becoming increasingly important for the study of complex diseases such as type 1 diabetes (T1D). The non-obese diabetic (NOD) mouse is an experimental model for T1D having been bred to develop the disease spontaneously in a process that is similar to humans. Genetic analysis of the NOD mouse has identified around 50 disease loci, which have the nomenclature Idd for insulin-dependent diabetes, distributed across at least 11 different chromosomes. In total, 21 Idd regions across 6 chromosomes, that are major contributors to T1D susceptibility or resistance, were selected for finished sequencing and annotation at the Wellcome Trust Sanger Institute. Here we describe the generation of 40.4 mega base-pairs of finished sequence from 289 bacterial artificial chromosomes for the NOD mouse. Manual annotation has identified 738 genes in the diabetes sensitive NOD mouse and 765 genes in homologous regions of the diabetes resistant C57BL/6J reference mouse across 19 candidate Idd regions. This has allowed us to call variation consequences between homologous exonic sequences for all annotated regions in the two mouse strains. We demonstrate the importance of this resource further by illustrating the technical difficulties that regions of inter-strain structural variation between the NOD mouse and the C57BL/6J reference mouse can cause for current next generation sequencing and assembly techniques. Furthermore, we have established that the variation rate in the Idd regions is 2.3 times higher than the mean found for the whole genome assembly for the NOD/ShiLtJ genome, which we suggest reflects the fact that positive selection for functional variation in immune genes is beneficial in regard to host defence. In summary, we provide an important resource, which aids the analysis of potential causative genes involved in T1D susceptibility. Database URLs: http://www.sanger.ac.uk/resources/mouse/nod/; http://vega

  20. Use of multiple molecular subtyping techniques to investigate a Legionnaires' disease outbreak due to identical strains at two tourist lodges.

    PubMed Central

    Mamolen, M; Breiman, R F; Barbaree, J M; Gunn, R A; Stone, K M; Spika, J S; Dennis, D T; Mao, S H; Vogt, R L

    1993-01-01

    A multistate outbreak of Legionnaires' disease occurred among nine tour groups of senior citizens returning from stays at one of two lodges in a Vermont resort in October 1987. Interviews and serologic studies of 383 (85%) of the tour members revealed 17 individuals (attack rate, 4.4%) with radiologically documented pneumonia and laboratory evidence of legionellosis. A survey of tour groups staying at four nearby lodges and of Vermont-area medical facilities revealed no additional cases. Environmental investigation of common tour stops revealed no likely aerosol source of Legionella infection outside the lodges. Legionella pneumophila serogroup 1 was isolated from water sources at both implicated lodges, and the monoclonal antibody subtype matched those of the isolates from six patients from whom clinical isolates were obtained. The cultures reacted with monoclonal antibodies MAB1, MAB2, 33G2, and 144C2 to yield a 1,2,5,7 or a Benidorm 030E pattern. The strains were also identical by alloenzyme electrophoresis and DNA ribotyping techniques. The epidemiologic and laboratory data suggest that concurrent outbreaks occurred following exposures to the same L. pneumophila serogroup 1 strain at two separate lodges. Multiple molecular subtyping techniques can provide essential information for epidemiologic investigations of Legionnaires' disease. PMID:8253953

  1. Peripheral temperature variation in the wall of a noncircular duct - An experimental investigation

    NASA Astrophysics Data System (ADS)

    Barrow, H.; Hassan, A. K. A.; Avgerinos, C.

    1984-07-01

    This paper is concerned with the peripheral variation of the temperature in the wall of a straight noncircular duct, with special reference to the prediction of the temperature in the cladding of the fuel rods of a pressurized water reactor, in the event of a loss of coolant. A simple model of the conjugate heat transfers in the wall and the fluid is used to predict the temperature variation around the wall. To test the theory, experiments have been made to determine wall temperatures in a cusped duct using air as the working fluid for a range of fluid flow rates. Overall pressure drop and heat transfer measurements for friction factor and average heat transfer coefficient indicate the inadequacy of the hydraulic radius concept in the case of the very noncircular geometry used in the experiments, and the effect of asymmetry in heat transfer. It is thought that these heat transfer experiments are the first for this particular geometry.

  2. SU-E-T-636: Investigation of Dose Variation in High Dose Radiation Brachytherapy

    SciTech Connect

    Hyvarinen, M; Leventouri, T; Casey, C; Long, S; Pella, S; Dumitru, N; Herrera, R

    2014-06-15

    Purpose: The purpose of this study is to revise most of the HDR types of treatments with their applicators and their localization challenges. Since every millimeter of misplacement counts the study will look into the necessity of increasing the immobilization for several types of applicators Methods: The study took over 136 plans generated by the treatment planning system (TPS) looking into the applicator's placement in regard to the organs at risk (OR) and simulated the three possible displacements at the hottest dose point on the critical organ for several accessories to evaluate the variation of the delivered dose at the point due to the displacement. Results: Significant dose variation was obtained for the Contura, Savi, MLM and Prostate applicators. Conclusion: This study data indicates that an improvement of the immobilization devices for HDR is absolutely necessary. Better applicator fixation devices are required too. Developing new immobilization devices for all the applicators is recommended. Florida Atlantic University may provide Travel reimbursements.

  3. An investigation of the solar zenith angle variation of D-region ionization

    NASA Technical Reports Server (NTRS)

    Ratnasiri, P. A. J.; Sechrist, C. F., Jr.

    1975-01-01

    Model calculations are carried out with a view to interpreting the solar zenith angle variation of D-region ionization. A model is developed for the neutral chemistry including the transport terms relating to molecular and eddy diffusion. The diurnal behavior is described of the minor neutral constituents formed in an oxygen-hydrogen-nitrogen atmosphere, in the height interval between 30 and 120 km. Computations carried out for two cases of the eddy diffusion coefficients models indicate that the constituents which are important for the D-region positive-ion chemistry do not show a significant variation with zenith angle for values up to 75 deg over the D-region heights. In the ion chemistry model, ion-pair production rates are calculated for solar X-rays between 1 A and 100 A, EUV radiations from 100 A up to the Lyman-alpha line, precipitating electrons, and galactic cosmic rays. The solar zenith angle variation of the positive-ion composition, negative-ion composition, and the electron densities are described up to 75 deg zenith angle, in the height interval between 60 and 100 km.

  4. Investigation of capacitance voltage characteristics of strained Si/SiGe n-channel MODFET varactor

    NASA Astrophysics Data System (ADS)

    Elogail, Y.; Kasper, E.; Gunzer, F.; Shaker, A.; Schulze, J.

    2016-06-01

    This work is concerned with the investigation of Capacitance-Voltage (CV) behavior of n-channel Si/SiGe MODFET varactors. This investigation provides a valuable insight into the high frequency response of the device under test and its dependence on design parameters; especially regarding the modulation layer doping concentration. The heterostructure under consideration is much more complicated than conventional MOS varactor with respect to non-uniform doping, energy band offsets and the pn-junction in series. Subsequently, CV characterization has never been applied to such MODFET varactor structure. Experimental CV measurements have shown a non-monotonic behavior with a transition point minimum and higher saturation levels on both sides, in contradiction to the conventional high frequency MOS characteristics. This behavior was confirmed qualitatively using simulations. Moreover, we explain some fundamental capacitance properties of the structure, which provide already very interesting perceptions of the MODFET varactor operation, modeling and possible applications using the obtained stimulating results.

  5. The investigation of short-term variations of Jupiter's Synchrotron Radiation with the large radio interferometer GMRT

    NASA Astrophysics Data System (ADS)

    Imai, Kota; Misawa, Hiroaki; Bhardwaj, Anil; Tsuchiya, Fuminori; Doi, Akihiro; Kondo, Tetsuro; Morioka, Akira

    The goal of this research is to investigate physical processes of short term variations of Jupiter's Synchrotron Radiation (JSR) which is important for revealing the origin of relativistic electrons at Jupiter's Radiation Belt (JRB). JSR has been frequently observed by radio interferometers and single dish radio telescopes to understand characteristics of the spatial distribution and variations inferring dynamics and energetics of the relativistic electrons. Observations with radio interferometers have showed JSR source structure (Dunn et al., 2003, etc), and contributed to modeling of JRB (Garrett et al., 2005, etc). On the other hand, observations of total intensity of JSR with a single dish radio telescope have revealed characteristics of time variable phenomena. The time variations are indispensable parameters giving clues to understand particle source and/or loss processes which characterize the formation of JRB. Recently, Miyoshi et al. (1999) and Bolton et al. (2002) confirmed the existence of short term (days to weeks) variations in JSR. The detection of short term variations makes a great impact on the study on JRB because it has been believed for a long time that the strong internal magnetic field and rapidly rotating magnetosphere of Jupiter protect the JRB region from solar wind variations and magnetospheric disturbances as theoretically suggested by de Pater and Goertz (1994). So far we have made the JSR observations to investigate the short term variations of mainly several hundreds MHz JSR which is emitted by low energy particles (< 10MeV) and has been observed systematically only few times (Miyoshi et al., 1999, Misawa et al., 2005, etc). The latter observation suggested that the short term variation is a general feature at low frequencies. Therefore, it is essential to study its detailed characteristics and the causalities. Theoretically expected physical processes which are responsible for the short term variation are enhanced radial diffusion

  6. Cellular and Molecular Investigations of the Adhesion and Mechanics of Listeria monocytogenes Lineages’ I and II Environmental and Epidemic Strains

    PubMed Central

    Eskhan, Asma O.; Abu-Lail, Nehal I.

    2013-01-01

    Atomic force microscopy (AFM) was used to probe the mechanical and adherence properties of eight L. monocytogenes’ strains representative of the species’ two phylogenetic lineages I and II. From a functional perspective, lineage’ I strains were characterized by lower overall adhesion forces and higher specific and nonspecific forces compared to lineage’ II strains. From a structural perspective, lineage’ II strains were characterized by higher Young’s moduli and longer and stiffer biopolymers compared to lineage’ I strains. Both lineages’ I and II strains were similar in their grafting densities. Finally, our results indicated that epidemic and environmental strains of L. monocytogenes and irrespective of their lineage group were characterized by similar Young’s moduli of elasticties and adhesion forces at the cellular level. However, at the molecular level, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. PMID:23261349

  7. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes lineages' I and II environmental and epidemic strains.

    PubMed

    Eskhan, Asma O; Abu-Lail, Nehal I

    2013-03-15

    Atomic force microscopy (AFM) was used to probe the mechanical and adherence properties of eight Listeria monocytogenes' strains representative of the species' two phylogenetic lineages I and II. From a functional perspective, lineage' I strains were characterized by lower overall adhesion forces and higher specific and nonspecific forces compared to lineage' II strains. From a structural perspective, lineage' II strains were characterized by higher Young's moduli and longer and stiffer biopolymers compared to lineage' I strains. Both lineages' I and II strains were similar in their grafting densities. Finally, our results indicated that epidemic and environmental strains of L. monocytogenes and irrespective of their lineage group were characterized by similar Young's moduli of elasticities and adhesion forces at the cellular level. However, at the molecular level, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser, and more flexible biopolymers compared to environmental strains. PMID:23261349

  8. Genetic variation of southern hemisphere fur seals (Arctocephalus spp.): investigation of population structure and species identity.

    PubMed

    Lento, G M; Haddon, M; Chambers, G K; Baker, C S

    1997-01-01

    We have examined phylogenetic and geographic patterns of variation in the mitochondrial cytochrome b gene of Southern Hemisphere fur seals (Arctocephalus spp.). Our survey of 106 individuals from four putative species reveals three distinct patterns of variation reflecting ancient, recent historic, and contemporary gene flow. For the combined samples of Subantarctic (Arctocephalus tropicalis) and Antarctic (Arctocephalus gazella) fur seals, we find low levels of sequence diversity and reciprocal paraphyly of hapiotypes (where representative haplotypes of a species are found to occur infrequently in another species and vice versa). For the Australian and Cape fur seal subspecies (Arctocephalus pusillus doriferus and A. p. pusillus, respectively), we find low levels of sequence diversity but significant differences in the regional distribution of haplotypes that are consistent with, but not conclusive of, the current subspecies definition based on nonmolecular data. For the New Zealand fur seal (Arctocephalus forsteri), we find high levels of average sequence diversity because of the survival of two divergent lineages of mitochondrial hapiotypes with differences approaching that found in interspecific comparisons of other mammals. The two divergent clades are distributed sympatrically in some regions, but the overall geographic structure of the variation is significant across the range of this species. These new molecular data are inconsistent with current taxonomic definitions of species within the Southern Hemisphere fur seals and argue for reevaluation of these "species" definitions. For management purposes, the definition of evolutionarily significant units (Ryder 1986) and genetic management units (Moritz 1994) in relation to these species may also be evaluated in light of this molecular genetic information. PMID:9183848

  9. Individual variation in p53 and Cip1 expression profiles in normal human fibroblast strains following exposure to high-let radiation

    SciTech Connect

    Carpenter, T.R.; Johnson, N.F.; Gilliland, F.D.

    1995-12-01

    Exposure to {alpha}-particles emitted by radon progeny appears to be the second-leading cause of lung cancer mortality. However, individual susceptibility to the carcinogenic effects of {alpha}-particles remains poorly characterized. Variation in susceptibility to cancer produced by certian classes of DNA-damaging chemicals is suspected to involve differences in metabolic activation and detoxication. Susceptibility to {alpha}-particle-induced cancer may involve variations in capacity or opportunity to repair DNA damage. Subtle variations in DNA repair capacity would more likely explain radon-related lung cancer susceptibility. The p53 tumor suppressor protein accumulates as a cellular response to DNA damage from ionizing radiation and regulates arrest in the G{sub 1} portion of the cell cycle. Arrest in G{sub 1} portion of the cell cycle. While upstream regulation of p53 protein stability is poorly understood, variations in the ability to accumulate p53 following DNA damage represent potential variations in lung cancer susceptibility related to radon progeny. Further, transcription of the cell-cycle regulatory gene Cip1 is regulated by p53 and increases following ionizing radiation. Therefore, variations in the expression of Cip1 following {alpha}-particle exposure may also be a susceptibility factor in radon-related lung cancers. The purpose of the present investigation was to measure p53 and Cip1 protein induction following {alpha}-particle exposure of fibroblast lines from nine individuals to determine if there were significant variations. The expression of Cip1 protein indicates the differences in response are biologically relevant.

  10. Foundation, analysis, and numerical investigation of a variational network-based model for rubber

    NASA Astrophysics Data System (ADS)

    Gloria, Antoine; Le Tallec, Patrick; Vidrascu, Marina

    2014-01-01

    Since the pioneering work by Treloar, many models based on polymer chain statistics have been proposed to describe rubber elasticity. Recently, Alicandro, Cicalese, and the first author rigorously derived a continuum theory of rubber elasticity from a discrete model by variational convergence. The aim of this paper is twofold. First, we further physically motivate this model and complete the analysis by numerical simulations. Second, in order to compare this model to the literature, we present in a common language two other representative types of models, specify their underlying assumptions, check their mathematical properties, and compare them to Treloar's experiments.