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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. Use of restriction fragment length polymorphisms to investigate strain variation within Neisseria meningitidis

    SciTech Connect

    Williams, S.D.

    1989-01-01

    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{sup 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 analyzed 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.

  3. Epstein-Barr Virus Strain Variation.

    PubMed

    Farrell, Paul J

    2015-01-01

    What is wild-type Epstein-Barr virus and are there genetic differences in EBV strains that contribute to some of the EBV-associated diseases? Recent progress in DNA sequencing has resulted in many new Epstein-Barr virus (EBV) genome sequences becoming available. EBV isolates worldwide can be grouped into type 1 and type 2, a classification based on the EBNA2 gene sequence. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than type 2 EBV and molecular mechanisms that may account for this difference in cell transformation are now becoming understood. Study of geographic variation of EBV strains independent of the type 1/type 2 classification and systematic investigation of the relationship between viral strains, infection and disease are now becoming possible. So we should consider more directly whether viral sequence variation might play a role in the incidence of some EBV-associated diseases.

  4. The epidemiological relevance of trypanosome strain variation.

    PubMed

    Tait, A

    1989-01-01

    The study of strain variation in T.b. rhodesiense has yielded a lot of information which suggests that these trypanosomes are a sub-set of the stocks circulating in tsetse and non human hosts and that each focus constitutes a separate set of human infective stocks. These conclusions remain to be fully established by extensive studies in specific foci. Whether the maintenance of these foci or the expansion of them into epidemics is dependent on variation in the trypanosoma stocks generated by mutation or genetic exchange is unanswered. In order to examine such questions, detailed long-term studies using large numbers of isolates are needed. The analysis of strain variation using existing methods requires considerable manpower and equipment and suffers from the need for growth of trypanosomes in laboratory animals with resultant selection of the stocks under study. The question of whether strain variation in T.b. rhodesiense is epidemiologically relevant remains unanswered, variation certainly occurs but the existing studies are not able to answer this question. It is possible that this question could be answered by detailed studies in two or more foci over a long period using new reagents for the detection of variation (e.g. monoclonal antibodies), large trypanosome stock collections and the measurement of parameters such as virulence, tsetse transmissibility etc.

  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. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. 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.

  8. Strain variation in bacteriocuprein superoxide dismutase from symbiotic Photobacterium leiognathi.

    PubMed

    Dunlap, P V; Steinman, H M

    1986-02-01

    Photobacterium leiognathi ATCC 25521 (the type strain and light-organ symbiont of ponyfish) is one of the few bacteria that produces a copper-zinc superoxide dismutase, termed bacteriocuprein. We enzymologically and immunologically characterized the bacteriocuprein superoxide dismutases in sonicates from the type strain and nine additional strains of P. leiognathi, each isolated from the light organ of a separate ponyfish specimen, representing seven ponyfish species. The results indicate considerable strain variation. (i) The level of bacteriocuprein enzymatic activity varied greatly among strains from different species of ponyfish. In four of the nine strains, activity was low or undetectable, while in five strains it was comparable to that in the type strain. (ii) The bacteriocuprein in one strain had a specific activity much lower than that of the type strain, and in another strain, no bacteriocuprein activity and no cross-reactive polypeptide were detectable. (iii) A new electrophoretic variant, which migrated slower than that of strains from fish captured in Thailand and Japan, was identified in strains from fish captured in the Philippine Islands. (iv) Enzymological and immunological differences were observed in bacteriocupreins of strains from male and female specimens of the same ponyfish species, for the two species in which specimens of both sexes were examined. These observations raise the possibility that specific variations in the bacteriocupreins of P. leiognathi might be characteristic of the species, geographical source, or sex of the ponyfish host. Thus, the data indicate that the possibility of strain variation should be considered when other species are screened for bacteriocupreins.

  9. Phenotypic variation of fluoride responses between inbred strains of mice.

    PubMed

    Yan, Dong; Willett, Thomas L; Gu, Xiao-Mei; Martinez-Mier, E Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T

    2011-01-01

    Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F(-)) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO(4), iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism.

  10. Phenotypic Variation of Fluoride Responses between Inbred Strains of Mice

    PubMed Central

    Yan, Dong; Willett, Thomas L.; Gu, Xiao-Mei; Martinez-Mier, E. Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T.

    2011-01-01

    Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F–) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO4, iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism. PMID:21555858

  11. Variation of Shrinkage Strain within the Depth of Concrete Beams

    PubMed Central

    Jeong, Jong-Hyun; Park, Yeong-Seong; Lee, Yong-Hak

    2015-01-01

    The variation of shrinkage strain within beam depth was examined through four series of time-dependent laboratory experiments on unreinforced concrete beam specimens. Two types of beam specimens, horizontally cast and vertically cast, were tested; shrinkage variation was observed in the horizontally cast specimens. This indicated that the shrinkage variation within the beam depth was due to water bleeding and tamping during the placement of the fresh concrete. Shrinkage strains were measured within the beam depth by two types of strain gages, surface-attached and embedded. The shrinkage strain distribution within the beam depth showed a consistent tendency for the two types of gages. The test beams were cut into four sections after completion of the test, and the cutting planes were divided into four equal sub-areas to measure the aggregate concentration for each sub-area of the cutting plane. The aggregate concentration increased towards the bottom of the beam. The shrinkage strain distribution was estimated by Hobbs’ equation, which accounts for the change of aggregate volume concentration. PMID:28793677

  12. Investigating seasonal variations in rock glacier dynamics

    NASA Astrophysics Data System (ADS)

    Cicoira, Alessandro; Vieli, Andreas; Faillettaz, Jerome; Wirz, Vanessa

    2017-04-01

    Periglacial monitoring has highlighted seasonal and inter-annual variations in rock glacier dynamics. Temperature forcing, through heat conduction, has been proposed as one of the key processes to explain these kinematics variations. But this mechanism has not yet been quantitatively assessed against real-world data. We present a numerical model that couples heat conduction and an empirical creep model for ice-rich frozen soils (Arenson, 2005). We use this model to investigate the dynamic response of alpine permafrost to external temperature variations. We compare the modeling with the PERMOS monitoring network data, which include several years of borehole temperature data and variations in surface velocity. These data allow us to conduct a direct comparison and test our model. We are able to model velocity variations from temperature forcing in the right order of magnitude but, in general, these are underestimated, in particular for thicker rock-glaciers.

  13. Genetic Variation in Virulence among Chalkbrood Strains Infecting Honeybees

    PubMed Central

    Vojvodic, Svjetlana; Jensen, Annette B.; Markussen, Bo; Eilenberg, Jørgen; Boomsma, Jacobus J.

    2011-01-01

    Ascosphaera apis causes chalkbrood in honeybees, a chronic disease that reduces the number of viable offspring in the nest. Although lethal for larvae, the disease normally has relatively low virulence at the colony level. A recent study showed that there is genetic variation for host susceptibility, but whether Ascosphaera apis strains differ in virulence is unknown. We exploited a recently modified in vitro rearing technique to infect honeybee larvae from three colonies with naturally mated queens under strictly controlled laboratory conditions, using four strains from two distinct A. apis clades. We found that both strain and colony of larval origin affected mortality rates. The strains from one clade caused 12–14% mortality while those from the other clade induced 71–92% mortality. Larvae from one colony showed significantly higher susceptibility to chalkbrood infection than larvae from the other two colonies, confirming the existence of genetic variation in susceptibility across colonies. Our results are consistent with antagonistic coevolution between a specialized fungal pathogen and its host, and suggest that beekeeping industries would benefit from more systematic monitoring of this chronic stress factor of their colonies. PMID:21966406

  14. Brain strain uncertainty due to shape variation in and simplification of head angular velocity profiles.

    PubMed

    Zhao, Wei; Ji, Songbai

    2017-04-01

    Head angular velocity, instead of acceleration, is more predictive of brain strains. Surprisingly, no study exists that investigates how shape variation in angular velocity profiles affects brain strains, beyond characteristics such as peak magnitude and impulse duration. In this study, we evaluated brain strain uncertainty due to variation in angular velocity profiles and further compared with that resulting from simplifying the profiles into idealized shapes. To do so, we used reconstructed head impacts from American National Football League for shape extraction and simulated head uniaxial coronal rotations from onset to full stop. The velocity profiles were scaled to maintain an identical peak velocity magnitude and duration in order to isolate the shape for investigation. Element-wise peak maximum principal strains from 44 selected impacts were obtained. We found that the shape of angular velocity profile could significantly affect brain strain magnitude (e.g., percentage difference of 4.29-17.89 % in the whole brain relative to the group average, with cumulative strain damage measure (CSDM) uncertainty range of 23.9 %) but not pattern (correlation coefficient of 0.94-0.99). Strain differences resulting from simplifying angular velocity profiles into idealized shapes were largely within the range due to shape variation, in both percentage difference and CSDM (signed difference of 3.91 % on average, with a typical range of 0-6 %). These findings provide important insight into the uncertainty or confidence in the performance of kinematics-based injury metrics. More importantly, they suggest the feasibility to simplify head angular velocity profiles into idealized shapes, at least within the confinements of the profiles evaluated, to enable real-time strain estimation via pre-computation in the future.

  15. Tectonic strain and paleomagnetism: experimental investigation

    NASA Astrophysics Data System (ADS)

    Borradaile, G.; Mothersill, J.

    1989-09-01

    A porous, clay-rich sandstone with a natural remanent magnetisation shows complex changes in the orientation of the remanence vector when the sandstone is subjected to experimental deformation, at 100 MPa, room temperature and constant natural strain rates of 1 × 10 -5 s -1. The paleomagnetic vector does not simply rotate away from the axis of compression. When the rock is shortened perpendicular to bedding the remanence vector rotates toward the bedding, as expected, but the remanence also rotates toward bedding when the rock is shortened parallel to bedding. Moreover, in some cases the remanence vector changes azimuth within the specimen during experimental deformation. Thus bedding anisotropy and the accompanying mineral-fabric anisotropy are more influential than strain in controlling deflections of the paleomagnetic vector in this study. This anisotropy also influences the post-deformational behaviour of remanence: 4 months after deformation, some cores shortened perpendicular to bedding relaxed their remanence vectors back towards the pre-deformational attitude whereas some other cores continued to show progressive changes. Intragranular, recoverable elastic strains in the magnetic grains may be partly responsible for the experimentally induced deflections of remanence.

  16. 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

  17. Sensing sheet: the response of full-bridge strain sensors to thermal variations for detecting and characterizing cracks

    NASA Astrophysics Data System (ADS)

    Tung, S.-T.; Glisic, B.

    2016-12-01

    Sensing sheets based on large-area electronics consist of a dense array of unit strain sensors. This new technology has potential for becoming an effective and affordable monitoring tool that can identify, localize and quantify surface damage in structures. This research contributes to their development by investigating the response of full-bridge unit strain sensors to thermal variations. Overall, this investigation quantifies the effects of temperature on thin-film full-bridge strain sensors monitoring uncracked and cracked concrete. Additionally, an empirical formula is developed to estimate crack width given an observed strain change and a measured temperature change. This research led to the understanding of the behavior of full-bridge strain sensors installed on cracked concrete and exposed to temperature variations. It proves the concept of the sensing sheet and its suitability for application in environments with variable temperature.

  18. 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.

  19. 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.

  20. Regional Variations in Mechanical Strain in the Posterior Human Sclera

    PubMed Central

    Fazio, Massimo A.; Grytz, Rafael; Bruno, Luigi; Girard, Michael J. A.; Gardiner, Stuart; Girkin, Christopher A.; Downs, J. Crawford

    2012-01-01

    Purpose. The goal of this study was to establish sectorial and regional variability in the mechanical strain of peripapillary and mid-peripheral sclera in normal eyes from elderly human donors. Methods. Ten pairs of normal eyes from human donors aged 57 to 90 years old were mechanically inflation-tested within 48 hours post mortem. The intact posterior scleral shells were pressurized from 5 to 45 mm Hg while the full-field three-dimensional displacements of the scleral surface were measured using laser speckle interferometry. The displacement field was fit to continuous and differentiable analytical functions, from which the full strain tensor of the outer scleral surface was calculated. Mean maximum principal (tensile) strain was computed for eight circumferential sectors (45° wide) within the peripapillary and mid-peripheral regions surrounding the optic nerve head (ONH). Results. Overall, the peripapillary sclera exhibited significantly higher tensile strain (1.2%) than mid-peripheral sclera (0.95%) for a 40 mm Hg IOP elevation (P < 0.00001). In the peripapillary region, the inferotemporal sector exhibited the highest tensile strain (1.45%) while the superior sector had the lowest (1.19%; P < 0.00001). Mid-peripheral scleral strains were lower but exhibited a similar sectorial pattern. Conclusions. Human posterior sclera exhibits complex regional mechanical behavior in response to acute IOP elevations from 5 to 45 mm Hg. Results indicate 1) the peripapillary sclera is subjected to significantly higher tensile strain than the adjacent mid-peripheral sclera, and 2) strains are significantly higher in the temporal and inferior quadrants of the peripapillary sclera, which may contribute to the increased prevalence of glaucomatous damage associated with these regions of the ONH. PMID:22700704

  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. Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

    PubMed

    Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

    2011-12-01

    Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

  3. 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.

  4. (90377) Sedna: Investigation of Surface Compositional Variation

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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 μm by the Spitzer Space Telescope. The visible and near-infrared spectra can be modeled with organic materials (triton and titan tholin), serpentine, and H2O ice in fairly significant amounts, and CH4, N2, and C2H6 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 CH3OH in place of CH4, 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. Based on observations obtained at the VLT Observatory Cerro Paranal of European Southern Observatory, ESO, Chile, in the framework of proposal 275.C-5055 and Large Program 178-C-0036/0867.

  5. (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.

  6. Investigation of the strain transfer for surface-attached optical fiber strain sensors

    NASA Astrophysics Data System (ADS)

    Wan, Kai Tai; Leung, Christopher K. Y.; Olson, Noah G.

    2008-06-01

    The relation between the component strain and the strain on a surface-attached optical fiber is governed by the effectiveness of shear transfer through the adhesive and the polymeric coating(s) on the optical fiber. A classical shear lag model can predict the strain transfer through a soft layer well. However, experiments showed that the results are unsatisfactory for bare fiber with stiff adhesive case. A 3D-FEM is established to model the strain transfer of a surface-mounted strain sensor and it is verified by experiments. Then, it is used to investigate the influence of four geometric parameters of the adhesive: (1) side width, (2) top thickness, (3) bond length, (4) bottom thickness, on the strain transfer. By sensitivity analysis, it is revealed that the bond length and the bottom thickness are dominant factors. Based on finite element results, the parameter of the analytical model is modified to suit stiff layer cases. Important considerations for practical installation of surface-attached optical interferometric and FBG strain sensors will be discussed.

  7. Theoretical Investigation of Biaxially Tensile-Strained Germanium Nanowires

    NASA Astrophysics Data System (ADS)

    Zhu, Zhongyunshen; Song, Yuxin; Chen, Qimiao; Zhang, Zhenpu; Zhang, Liyao; Li, Yaoyao; Wang, Shumin

    2017-07-01

    We theoretically investigate highly tensile-strained Ge nanowires laterally on GaSb. Finite element method has been used to simulate the residual elastic strain in the Ge nanowire. The total energy increment including strain energy, surface energy, and edge energy before and after Ge deposition is calculated in different situations. The result indicates that the Ge nanowire on GaSb is apt to grow along 〈100〉 rather than 〈110〉 in the two situations and prefers to be exposed by {105} facets when deposited a small amount of Ge but to be exposed by {110} when the amount of Ge exceeds a critical value. Furthermore, the conduction band minima in Γ-valley at any position in both situations exhibits lower values than those in L-valley, leading to direct bandgap transition in Ge nanowire. For the valence band, the light hole band maxima at Γ-point is higher than the heavy hole band maxima at any position and even higher than the conduction band minima for the hydrostatic strain more than ˜5.0%, leading to a negative bandgap. In addition, both electron and hole mobility can be enhanced by owing to the decrease of the effective mass under highly tensile strain. The results suggest that biaxially tensile-strained Ge nanowires hold promising properties in device applications.

  8. 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.

  9. Variation of the internal transcribed spacer 1 sequence within individual strains and among different strains of Neospora caninum.

    PubMed

    Gondim, Luis F P; Laski, Paul; Gao, Liying; McAllister, Milton M

    2004-02-01

    Small differences have been reported in the internal transcribed spacer 1 (ITS1) region among strains of Neospora caninum. We compared ITS1 sequences among 6 N. caninum strains analyzed in our laboratory, including 2 strains that have not been examined previously (NC-Illinois and NC-Bahia). Five sequences showed 100% similarity and also were identical to 7 of 11 sequences that were previously reported by others. In contrast, initial attempts to sequence the ITS1 of NC-Bahia generated 12 nucleotide differences compared with the other 5 strains, and several ambiguous bases. However, the single band containing the ITS1 region, as observed after electrophoresis on a 2% agarose gel, became divided into 2 distinct bands when reanalyzed using 5 or 10% polyacrylamide gel electrophoresis (PAGE), and the ITS1 within these separate bands were sequenced without ambiguity. The other 5 N. caninum strains were also reexamined using PAGE, and in each strain 2 distinct bands were discovered. In comparison, 2 strains of Toxoplasma gondii continued to show only 1 band when examined using PAGE. The ITS1 sequence of NC-Bahia, from Brazil, differs in several base pairs from those of North American and European strains of N. caninum. Intrastrain variation of the ITS1 region appears to be common in N. caninum, in contrast to T. gondii.

  10. GENETIC VARIATION AMONG STRAINS OF PSEUDOPFIESTERIA SHUMWAYAE AND PFIESTERIA PISCICIDA (DINOPHYCEAE)(1).

    PubMed

    Small, Hamish J; Shields, Jeffrey D; Haas, Leonard W; Vogelbein, Wolfgang K; Moss, Jessica; Reece, Kimberly S

    2009-12-01

    The putatively toxic dinoflagellates Pseudopfiesteria shumwayae (Glasgow et J. M. Burkh.) Litaker, Steid., P. L. Mason, Shields et P. A. Tester and Pfiesteria piscicida Steid. et J. M. Burkh. have been implicated in massive fish kills and of having negative impacts on human health along the mid-Atlantic seaboard of the USA. Considerable debate still remains as to the mechanisms responsible for fish mortality (toxicity vs. micropredation) caused by these dinoflagellates. Genetic differences among these cultures have not been adequately investigated and may account for or correlate with phenotypic variability among strains within each species. Genetic variation among strains of Ps. shumwayae and P. piscicida was examined by PCR-RFLP analysis using cultures obtained from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP), as well as those from our own and other colleagues' collection efforts. Examination of restriction digest banding profiles for 22 strains of Ps. shumwayae revealed the presence of 10 polymorphic restriction endonuclease sites within the first and second internal transcribed spacers (ITS1 and ITS2) and the 5.8S gene of the rDNA complex, and the cytochrome oxidase subunit I (COI) gene. Three compound genotypes were represented within the 22 Ps. shumwayae strains. Conversely, PCR-RFLP examination of 14 strains of P. piscicida at the same ITS1, 5.8S, and ITS2 regions revealed only one variable restriction endonuclease site, located in the ITS1 region. In addition, a dinoflagellate culture listed as P. piscicida (CCMP 1928) and analyzed as part of this study was identified as closely related to Luciella masanensis P. L. Mason, H. J. Jeong, Litaker, Reece et Steid.

  11. 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

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

    PubMed Central

    Hackett, Jennifer L.; Wang, Xiaofei; Smith, Brittny R.

    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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Investigation of cyanobacteria in a controlled hyperbolic straining flow

    NASA Astrophysics Data System (ADS)

    Akbaridoust, Farzan; Philip, Jimmy; Marusic, Ivan

    2016-11-01

    Here we report a systematic study on the effect of straining flow on cyanobacteria, which are a cause of significant water contamination issues worldwide. We focus on the species Anaebena Circinalis. A micro-cross channel equipped with two online computer-controlled on-chip membrane valves was designed and fabricated using standard soft-lithography. The device produces a hyperbolic straining flow on a micron-scaled region similar to G. I. Taylor's four-roll mill at larger scale. It was used to investigate the behaviour of a single filament of cynobacteria in a crowded medium under an increasing uniform strain rate flow. The velocity field and the resulting uniform strain-rate was measured in the absence of bacteria filaments using micro-PIV. A large number of single filaments of bacteria were trapped and exposed to stain-rates over 2 to 15 s-1. Previous studies have reported anecdotal evidence of suspected mechanical damage to Anaebena Circinalis for strain rates considerably lower than the maximum values studied here. In our case, no mechanical damage was observed. This work was performed in part at the Melbourne Centre for Nanofabrication (MCN) in the Victorian Node of the Australian National Fabrication Facility (ANFF).

  15. Regional Variation in Geniohyoid Muscle Strain During Suckling in the Infant Pig

    PubMed Central

    HOLMAN, SHAINA DEVI; KONOW, NICOLAI; LUKASIK, STACEY L.; GERMAN, REBECCA Z.

    2014-01-01

    The geniohyoid muscle (GH) is a critical suprahyoid muscle in most mammalian oropharyngeal motor activities. We used sonomicrometry to evaluate regional strain (i.e., changes in length) in the muscle origin, belly, and insertion during suckling in infant pigs, and compared the results to existing information on strain heterogeneity in the hyoid musculature. We tested the hypothesis that during rhythmic activity, the GH shows regional variation in muscle strain. We used sonomicrometry transducer pairs to divide the muscle into three regions from anterior to posterior. The results showed differences in strain among the regions within a feeding cycle; however, no region consistently shortened or lengthened over the course of a cycle. Moreover, regional strain patterns were not correlated with timing of the suck cycles, neither (1) relative to a swallow cycle (before or after) nor (2) to the time in feeding sequence (early or late). We also found a tight relationship between muscle activity and muscle strain, however, the relative timing of muscle activity and muscle strain was different in some muscle regions and between individuals. A dissection of the C1 innervations of the geniohyoid showed that there are between one and three branches entering the muscle, possibly explaining the variation seen in regional activity and strain. In combination, our findings suggest that regional heterogeneity in muscle strain during patterned suckling behavior functions to stabilize the hyoid bone, whereas the predictable regional strain differences in reflexive behaviors may be necessary for faster and higher amplitude movements of the hyoid bone. PMID:22549885

  16. 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

  17. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting.

    PubMed

    Meyer, Ben M; Froehlich, Jacob M; Galt, Nicholas J; Biga, Peggy R

    2013-01-01

    Although the zebrafish (Danio rerio) has been widely utilized as a model organism for several decades, there is little information available on physiological variation underlying genetic variation among the most commonly used inbred strains. This study evaluated growth performance using physiological and molecular markers of growth in response to fasting in six commonly used zebrafish strains [AB, TU, TL, SJA, WIK, and petstore (PET) zebrafish]. Fasting resulted in a standard decrease in whole blood glucose levels, a typical vertebrate glucose metabolism pattern, in AB, PET, TL, and TU zebrafish strains. Alternatively, fasting did not affect glucose levels in SJA and WIK zebrafish strains. Similarly, fasting had no effect on myostatin mRNA levels in AB, PET, TU, and WIK zebrafish strains, but decreased myostatin-1 and -2 mRNA levels in SJA zebrafish. Consistent with previous work, fasting increased myostatin-2 mRNA levels in TL zebrafish. These data demonstrate that variation is present in growth performance between commonly used inbred strains of zebrafish. These data can help future research endeavors by highlighting the attributes of each strain with regard to growth performance so that the most fitting strain may be utilized. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting

    PubMed Central

    Meyer, Ben M.; Froehlich, Jacob M.; Galt, Nicholas J.; Biga, Peggy R.

    2012-01-01

    Although the zebrafish (Danio rerio) has been widely utilized as a model organism for several decades, there is little information available on physiological variation underlying genetic variation among the most commonly used inbred strains. This study evaluated growth performance using physiological and molecular markers of growth in response to fasting in six commonly used zebrafish strains [AB, TU, TL, SJA, WIK, and petstore (PET) zebrafish]. Fasting resulted in a standard decrease in whole blood glucose levels, typical vertebrate glucose metabolism pattern, in AB, PET, TL, and TU zebrafish strains. Alternatively, fasting did not affect glucose levels in SJA and WIK zebrafish strains. Similarly, fasting had no effect on myostatin mRNA levels in AB, PET, TU, and WIK zebrafish strains, but decreased myostatin-1 and -2 mRNA levels in SJA zebrafish. Consistent with previous work, fasting increased myostatin-2 mRNA levels in TL zebrafish. These data demonstrate that variation is present in growth performance between commonly used inbred strains of zebrafish. These data can help future research endeavors by highlighting the attributes of each strain with regard to growth performance so that the most fitting strain may be utilized. PMID:23047051

  19. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

    PubMed Central

    2015-01-01

    Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas. PMID:26307380

  20. Strain dependent variation of immune responses to A. fumigatus: definition of pathogenic species.

    PubMed

    Rizzetto, Lisa; Giovannini, Gloria; Bromley, Michael; Bowyer, Paul; Romani, Luigina; Cavalieri, Duccio

    2013-01-01

    For over a century microbiologists and immunologist have categorized microorganisms as pathogenic or non-pathogenic species or genera. This definition, clearly relevant at the strain and species level for most bacteria, where differences in virulence between strains of a particular species are well known, has never been probed at the strain level in fungal species. Here, we tested the immune reactivity and the pathogenic potential of a collection of strains from Aspergillus spp, a fungus that is generally considered pathogenic in immuno-compromised hosts. Our results show a wide strain-dependent variation of the immune response elicited indicating that different isolates possess diverse virulence and infectivity. Thus, the definition of markers of inflammation or pathogenicity cannot be generalized. The profound understanding of the molecular mechanisms subtending the different immune responses will result solely from the comparative study of strains with extremely diverse properties.

  1. Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

    PubMed Central

    Weldatsadik, Rigbe G.; Wang, Jingwen; Puhakainen, Kai; Jiao, Hong; Jalava, Jari; Räisänen, Kati; Datta, Neeta; Skoog, Tiina; Vuopio, Jaana; Jokiranta, T. Sakari; Kere, Juha

    2017-01-01

    Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation. PMID:28361960

  2. 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

  3. 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.

  4. Strain Release Induced Novel Fluorescence Variation in CVD-Grown Monolayer WS2 Crystals.

    PubMed

    Feng, Shanghuai; Yang, Ruilong; Jia, Zhiyan; Xiang, Jianyong; Wen, Fusheng; Mu, Congpu; Nie, Anmin; Zhao, Zhisheng; Xu, Bo; Tao, Chenggang; Tian, Yongjun; Liu, Zhongyuan

    2017-10-04

    Tensile strain is intrinsic to monolayer crystals of transition metal disulfides such as Mo(W)S2 grown on oxidized silicon substrates by chemical vapor deposition (CVD) owing to the much larger thermal expansion coefficient of Mo(W)S2 than that of silica. Here we report fascinating fluorescent variation in intensity with aging time in CVD-grown triangular monolayer WS2 crystals on SiO2 (300 nm)/Si substrates and formation of interesting concentric triangular fluorescence patterns in monolayer crystals of large size. The novel fluorescence aging behavior is recognized to be induced by the partial release of intrinsic tensile strain after CVD growth and the induced localized variations or gradients of strain in the monolayer crystals. The results demonstrate that strain has a dramatic impact on the fluorescence and photoluminescence of monolayer WS2 crystals and thus could potentially be utilized to tune electronic and optoelectronic properties of monolayer transition metal disulfides.

  5. 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.

  6. 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

  7. 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. Copyright © 2015, van den Broek et al.

  8. 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

  9. Dynamics of Dual Infection with Campylobacter jejuni Strains in Chickens Reveals Distinct Strain-to-Strain Variation in Infection Ecology

    PubMed Central

    Wigley, Paul; Humphrey, Suzanne; Kemmett, Kirsty; Lacharme-Lora, Lizeth; Humphrey, Tom; Williams, Nicola

    2014-01-01

    Although multiple genotypes of Campylobacter jejuni may be isolated from the same commercial broiler flock, little is known about the infection dynamics of different genotypes within individuals or their colonization sites within the gut. Single experimental infections with C. jejuni M1 (sequence type 137, clonal complex 45) and C. jejuni 13126 (sequence type 21, clonal complex 21) revealed that 13126 colonized the ceca at significantly higher levels. The dissemination and colonization sites of the two C. jejuni strains then were examined in an experimental broiler flock. Two 33-day-old broiler chickens were infected with M1 and two with 13126, and 15 birds were left unchallenged. Cloacal swabs were taken postinfection to determine the colonization and shedding of each strain. By 2 days postinfection (dpi), 8/19 birds were shedding M1 whereas none were shedding 13126. At 8 dpi, all birds were shedding both strains. At 18 dpi, liver and cecal levels of each isolate were quantified, while in 10 birds they also were quantified at nine sites throughout the gastrointestinal (GI) tract. 13126 was found throughout the GI tract, while M1 was largely restricted to the ceca and colon. The livers of 7/19 birds were culture positive for 13126 only. These data show that 13126 has a distinctly different infection biology than strain M1. It showed slower colonization of the lower GI tract but was more invasive and able to colonize at a high level throughout the GI tract. The finding that C. jejuni strains have markedly different infection ecologies within the chicken has implications for control in the poultry industry and suggests that the contamination risk of edible tissues is dependent on the isolate involved. PMID:25107966

  10. The Early Variation of Left Ventricular Strain after Aortic Valve Replacement by Three-Dimensional Echocardiography

    PubMed Central

    Cheng, Leilei; Fan, Li; Wang, Chunsheng; Shu, Xianhong

    2015-01-01

    Aortic stenosis (AS) and aortic incompetence (AI) are common aortic valve diseases. Both may deteriorate into irreversible myocardial dysfunction and will increase the risk of sudden death. In this study, we aimed to investigate the early variation trend of left ventricular function by three-dimensional speckle tracking echocardiography (3D-STE) in the patients who underwent cardiac surgeries for aortic valve disease. Twenty patients with severe aortic AS and 16 patients with severe AI were enrolled. All of them underwent the aortic valve replacement (AVR) procedures. The patients’ global longitudinal strain (GLS) and global circumferential strain (GCS) were evaluated by 3D-STE before surgery and at 1 week after surgery. In addition, GLS and GCS were followed at 1 month as well as 3 months after AVR. In AS patients, the GCS after AVR altered little both at 1 week (p = 0.562) and at 1 month (p = 0.953) compared with the data before the surgery. And it increased significantly at 3 months of follow-up observation compared to that before AVR (p<0.05). Meanwhile, GLS increased progressively after AVR and improved significantly at 3 months after surgery (p<0.05). For the AI patients, GLS as well as GCS decreased at 1 week after AVR compared to those data at baseline (p<0.05). However, these two parameters recovered at 1 month after AVR. Furthermore, GLS and GCS improved significantly at 3 months after the surgery (p<0.05). Therefore, both GLS and GCS were influenced by AVR and would be improved at 3 months after surgery both in AS patients or AI patients. GLS and GCS can be finely evaluated by 3D-STE, and they are helpful to determine the variation tendency of left ventricular function in patients with AVR. PMID:26473730

  11. Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains.

    PubMed

    Connelly, Caitlin F; Skelly, Daniel A; Dunham, Maitreya J; Akey, Joshua M

    2013-07-01

    Noncoding genetic variation is known to significantly influence gene expression levels in a growing number of specific cases; however, the patterns of genome-wide noncoding variation present within populations, the evolutionary forces acting on noncoding variants, and the relative effects of regulatory polymorphisms on transcript abundance are not well characterized. Here, we address these questions by analyzing patterns of regulatory variation in motifs for 177 DNA binding proteins in 37 strains of Saccharomyces cerevisiae. Between S. cerevisiae strains, we found considerable polymorphism in regulatory motifs across strains (mean π = 0.005) as well as diversity in regulatory motifs (mean 0.91 motifs differences per regulatory region). Population genetics analyses reveal that motifs are under purifying selection, and there is considerable heterogeneity in the magnitude of selection across different motifs. Finally, we obtained RNA-Seq data in 22 strains and identified 49 polymorphic DNA sequence motifs in 30 distinct genes that are significantly associated with transcriptional differences between strains. In 22 of these genes, there was a single polymorphic motif associated with expression in the upstream region. Our results provide comprehensive insights into the evolutionary trajectory of regulatory variation in yeast and the characteristics of a compendium of regulatory alleles.

  12. Population Genomics and Transcriptional Consequences of Regulatory Motif Variation in Globally Diverse Saccharomyces cerevisiae Strains

    PubMed Central

    Connelly, Caitlin F.; Skelly, Daniel A.; Dunham, Maitreya J.; Akey, Joshua M.

    2013-01-01

    Noncoding genetic variation is known to significantly influence gene expression levels in a growing number of specific cases; however, the patterns of genome-wide noncoding variation present within populations, the evolutionary forces acting on noncoding variants, and the relative effects of regulatory polymorphisms on transcript abundance are not well characterized. Here, we address these questions by analyzing patterns of regulatory variation in motifs for 177 DNA binding proteins in 37 strains of Saccharomyces cerevisiae. Between S. cerevisiae strains, we found considerable polymorphism in regulatory motifs across strains (mean π = 0.005) as well as diversity in regulatory motifs (mean 0.91 motifs differences per regulatory region). Population genetics analyses reveal that motifs are under purifying selection, and there is considerable heterogeneity in the magnitude of selection across different motifs. Finally, we obtained RNA-Seq data in 22 strains and identified 49 polymorphic DNA sequence motifs in 30 distinct genes that are significantly associated with transcriptional differences between strains. In 22 of these genes, there was a single polymorphic motif associated with expression in the upstream region. Our results provide comprehensive insights into the evolutionary trajectory of regulatory variation in yeast and the characteristics of a compendium of regulatory alleles. PMID:23619145

  13. High Variation of Fluorescence Protein Maturation Times in Closely Related Escherichia coli Strains

    PubMed Central

    Hebisch, Elke; Knebel, Johannes; Landsberg, Janek; Frey, Erwin; Leisner, Madeleine

    2013-01-01

    Fluorescent proteins (FPs) are widely used in biochemistry, biology and biophysics. For quantitative analysis of gene expression FPs are often used as marking molecules. Therefore, sufficient knowledge of maturation times and their affecting factors is of high interest. Here, we investigate the maturation process of the FPs GFP and mCherry expressed by the three closely related Escherichia coli strains of the Colicin E2 system, a model system for colicinogenic interaction. One strain, the C strain produces Colicin, a toxin to which the S strain is sensitive, and against which the R strain is resistant. Under the growth conditions used in this study, the S and R strain have similar growth rates, as opposed to the C strain whose growth rate is significantly reduced due to the toxin production. In combination with theoretical modelling we studied the maturation kinetics of the two FPs in these strains and could confirm an exponential and sigmoidal maturation kinetic for GFP and mCherry, respectively. Our subsequent quantitative experimental analysis revealed a high variance in maturation times independent of the strain studied. In addition, we determined strain dependent maturation times and maturation behaviour. Firstly, FPs expressed by the S and R strain mature on similar average time-scales as opposed to FPs expressed by the C strain. Secondly, dependencies of maturation time with growth conditions are most pronounced in the GFP expressing C strain: Doubling the growth rate of this C strain results in an increased maturation time by a factor of 1.4. As maturation times can vary even between closely related strains, our data emphasize the importance of profound knowledge of individual strains' maturation times for accurate interpretation of gene expression data. PMID:24155882

  14. Experimental and Computational Investigations of Strain Localization in Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Bharathula, Ashwini

    Metallic glasses are metallic alloy systems with disordered atomic structure. Due to their unique amorphous structure, they exhibit an extraordinary set of properties that are ideal for a wide variety of applications ranging from electrical transformers, armor-piercing projectiles, sporting goods and fuel cells to precision gears for micromotors. In particular, owing to their exceptional mechanical properties like near-theoretical strength (1--3 GPa), large elastic strain range (2--3%), and unusual formability above the glass transition temperature, metallic glasses have tremendous potential in structural applications. Unfortunately, their unique structure also gives rise to significant limitations, such as limited ductility at room temperature due to rapid localization of plastic flow in shear bands. However, when the test volumes approach the size of a shear band nucleus (˜50--500 nm), it is believed that shear band formation and propagation can be constrained, leading to enhanced plasticity and failure strength. This study investigates the phenomenon of strain localization using both experimental and computational techniques. On the experimental front, sample size effects on strength, plasticity and deformation modes were explored in a Zr-based bulk metallic glass via micron- and sub-micron scale compression testing. Specimens with diameters ranging from 200 nm to a few microns were fabricated using Focused Ion Beam technique and were tested under uniaxial compression in a nanoindentation set-up with a flat punch tip. Effect of extrinsic factors like specimen geometry and machine stiffness on deformation behavior was discussed. Shear banding was shown to be more stable at this length scale than in macro-scale testing because of a smaller specimen to load frame stiffness ratio. It was found that as the specimen size is reduced to below 300 nm, the deformation mode changes from being discrete and inhomogeneous to more continuous flow including both localized and

  15. Bond-length variation in InxGa1-xAs/InP strained epitaxial layers

    NASA Astrophysics Data System (ADS)

    Romanato, F.; de Salvador, D.; Berti, M.; Drigo, A.; Natali, M.; Tormen, M.; Rossetto, G.; Pascarelli, S.; Boscherini, F.; Lamberti, C.; Mobilio, S.

    1998-06-01

    Tensile and compressive InxGa1-xAs epilayers grown on [001] InP substrates have been analyzed by fluorescence-detected x-ray-absorption fine structure in order to investigate the length variation suffered by Ga-As and In-As atomic bonds under epitaxial strain. A morphological and structural analysis had previously been performed in order to select only pseudomorphic samples with high lattice quality. A clear variation of the nearest-neighbor distances proportional to the tetragonal distortion of the film has been detected. We discuss the relationship between the long- and short-range descriptions of strain accommodation in the framework of an analytical model.

  16. 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.

  17. Variation in intake of sweet and bitter solutions by inbred strains of golden hamsters.

    PubMed

    Frank, Marion E; Wada, Yumiko; Makino, Junshiro; Mizutani, Makoto; Umezawa, Hidehiko; Katsuie, Yasutomi; Hettinger, Thomas P; Blizard, David A

    2004-07-01

    Variation in intake of sweet and bitter solutions by inbred strains of laboratory mice has helped identify genes related to taste behaviors; but similar information is not available for golden hamsters (Mesocricetus auratus ), a species used much in taste research. Thus, 6-hour, 1-bottle intake by water-replete hamsters of 7 inbred strains was measured for water and 2 concentrations of sucrose, maltose, D-phenylalanine (D-Phe), and sodium saccharin, which are sweet; and quinine.HCl, L-phenylalanine (L-Phe), caffeine, and sucrose octaacetate (SOA), which are bitter to humans. Difference scores (DIF), calculated as solution intake minus mean baseline water intake (mL) for each animal, were evaluated by analysis of variance. Compared to ACN, CN, APA, APG, and CBN, five strains with similar DIF for all compounds, GN, an ancestral strain of ACNT, and ACNT preferred sucrose, caffeine, and SOA more strongly; ACNT also preferred saccharin and maltose more strongly and rejected quinine more strongly. Narrow sense heritabilities for the 6 compounds for which strain differences were revealed ranged from 0.31 to 0.57. Genetic correlations indicated the strain variations in intake of sucrose, saccharin, SOA, and caffeine were coupled; a statistical association with several possible interpretations. Intakes of the two amino acids, preferred D-Phe and aversive L-Phe, did not reveal strain differences, and heritability ranged from 0.13 to 0.23 for the two optical isomers. Thus, although, compared to mice, genetic variation in laboratory hamsters may be small, genetic differences that influence taste behaviors in existing strains may help identify relevant genes.

  18. 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.

  19. Investigating Variation, Teacher's Edition. Probing the Natural World/3.

    ERIC Educational Resources Information Center

    Florida State Univ., Tallahassee. Dept. of Science Education.

    The teacher's edition for the unit entitled "Investigating Variation" in Intermediate Science Curriculum Study Level III, provides numerous suggestions for teaching specific activities included in the unit. The unit is aimed at selected aspects of measurement and analysis. The chapters included are "The Road…

  20. Derivation of a variational principle for plane strain elastic-plastic silk biopolymers

    NASA Astrophysics Data System (ADS)

    He, J. H.; Liu, F. J.; Cao, J. H.; Zhang, L.

    2014-01-01

    Silk biopolymers, such as spider silk and Bombyx mori silk, behave always elastic-plastically. An elastic-plastic model is adopted and a variational principle for the small strain, rate plasticity problem is established by semi-inverse method. A trial Lagrangian is constructed where an unknown function is included which can be identified step by step.

  1. 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.

  2. 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.

  3. Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains.

    PubMed

    Dumas, Laura; Dickens, C Michael; Anderson, Nathan; Davis, Jonathan; Bennett, Beth; Radcliffe, Richard A; Sikela, James M

    2014-06-01

    It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to

  4. Strain variation and morphogenesis of yeast- and mycelial-phase Candida albicans in low-sulfate, synthetic medium.

    PubMed Central

    Manning, M; Mitchell, T G

    1980-01-01

    A low-sulfate synthetic medium was developed in which pure cultures of yeast- and mycelial-phase Candida albicans could be cultivated for investigations of the molecular biology of dimorphism. The medium contained ammonium ions, phosphate buffer, salts, glucose, and biotin. Morphogenesis was found to be dependent upon the strain of C. albicans. Of six strains tested in the low-sulfate medium at 37 degrees C, three formed mixed cultures of yeasts, true mycelium and pseudomycelium, two formed pure cultures of true mycelium, and one maintained yeast growth. All six strains produced pure cultures of yeasts at 24 degrees C. The buffering capacity of the medium maintained the pH at 6.9 even at high-density cell growth. The low concentration of sulfate and the absence of amino acids in the medium provided conditions in which to radiolabel cellular constituents with [35S]sulfate. For molecular investigations, the use of two strains is suggested, one forming yeasts and one forming true mycelium in low-sulfate medium at 37 degrees C, thus providing controls for both strain variation and for molecular changes induced by environmental change but unrelated to morphogenesis. Images PMID:6991484

  5. Immunological variation between inbred laboratory mouse strains: points to consider in phenotyping genetically immunomodified mice.

    PubMed

    Sellers, R S; Clifford, C B; Treuting, P M; Brayton, C

    2012-01-01

    Inbred laboratory mouse strains are highly divergent in their immune response patterns as a result of genetic mutations and polymorphisms. The generation of genetically engineered mice (GEM) has, in the past, used embryonic stem (ES) cells for gene targeting from various 129 substrains followed by backcrossing into more fecund mouse strains. Although common inbred mice are considered "immune competent," many have variations in their immune system-some of which have been described-that may affect the phenotype. Recognition of these immune variations among commonly used inbred mouse strains is essential for the accurate interpretation of expected phenotypes or those that may arise unexpectedly. In GEM developed to study specific components of the immune system, accurate evaluation of immune responses must take into consideration not only the gene of interest but also how the background strain and microbial milieu contribute to the manifestation of findings in these mice. This article discusses points to consider regarding immunological differences between the common inbred laboratory mouse strains, particularly in their use as background strains in GEM.

  6. A regulatory trade-off as a source of strain variation in the species Escherichia coli.

    PubMed

    King, Thea; Ishihama, Akira; Kori, Ayako; Ferenci, Thomas

    2004-09-01

    There are few existing indications that strain variation in prokaryotic gene regulation is common or has evolutionary advantage. In this study, we report on isolates of Escherichia coli with distinct ratios of sigma factors (RpoD, sigmaD, or sigma70 and RpoS or sigmaS) that affect transcription initiated by RNA polymerase. Both laboratory E. coli K-12 lineages and nondomesticated isolates exhibit strain-specific endogenous levels of RpoS protein. We demonstrate that variation in genome usage underpins intraspecific variability in transcription patterns, resistance to external stresses, and the choice of beneficial mutations under nutrient limitation. Most unexpectedly, RpoS also controlled strain variation with respect to the metabolic capability of bacteria with more than a dozen carbon sources. Strains with higher sigmaS levels were more resistant to external stress but metabolized fewer substrates and poorly competed for low concentrations of nutrients. On the other hand, strains with lower sigmaS levels had broader nutritional capabilities and better competitive ability with low nutrient concentrations but low resistance to external stress. In other words, RpoS influenced both r and K strategist functions of bacteria simultaneously. The evolutionary principle driving strain variation is proposed to be a conceptually novel trade-off that we term SPANC (for "self-preservation and nutritional competence"). The availability of multiple SPANC settings potentially broadens the niche occupied by a species consisting of individuals with narrow specialization and reveals an evolutionary advantage offered by polymorphic regulation. Regulatory diversity is likely to be a significant contributor to complexity in a bacterial world in which multiple sigma factors are a universal feature.

  7. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

    PubMed Central

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

    2014-01-01

    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. Extensive strain-level copy-number variation across human gut microbiome species.

    PubMed

    Greenblum, Sharon; Carr, Rogan; Borenstein, Elhanan

    2015-02-12

    Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. 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.

  10. 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.

  11. Strain Variation in the Transcriptome of the Dengue Fever Vector, Aedes aegypti.

    PubMed

    Bonizzoni, Mariangela; Dunn, W Augustine; Campbell, Corey L; Olson, Ken E; Marinotti, Osvaldo; James, Anthony A

    2012-01-01

    Studies of transcriptome dynamics provide a basis for understanding functional elements of the genome and the complexity of gene regulation. The dengue vector mosquito, Aedes aegypti, exhibits great adaptability to diverse ecological conditions, is phenotypically polymorphic, and shows variation in vectorial capacity to arboviruses. Previous genome sequencing showed richness in repetitive DNA and transposable elements that can contribute to genome plasticity. Population genetic studies revealed a varying degree of worldwide genetic polymorphism. However, the extent of functional genetic polymorphism across strains is unknown. The transcriptomes of three Ae. aegypti strains, Chetumal (CTM), Rexville D-Puerto Rico (Rex-D) and Liverpool (LVP), were compared. CTM is more susceptible than Rex- D to infection by dengue virus serotype 2. A total of 4188 transcripts exhibit either no or small variation (<2-fold) among sugar-fed samples of the three strains and between sugar- and blood-fed samples within each strain, corresponding most likely to genes encoding products necessary for vital functions. Transcripts enriched in blood-fed mosquitoes encode proteins associated with catalytic activities, molecular transport, metabolism of lipids, carbohydrates and amino acids, and functions related to blood digestion and the progression of the gonotropic cycle. Significant qualitative and quantitative differences were found in individual transcripts among strains including differential representation of paralogous gene products. The majority of immunity-associated transcripts decreased in accumulation after a bloodmeal and the results are discussed in relation to the different susceptibility of CTM and Rex-D mosquitoes to DENV2 infection.

  12. 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

  13. Variations in mineralization affect the stress and strain distributions in cortical and trabecular bone.

    PubMed

    van Ruijven, L J; Mulder, L; van Eijden, T M G J

    2007-01-01

    The mechanical properties of bone depend largely on its degree and distribution of mineralization. The present study analyzes the effect of an inhomogeneous distribution of mineralization on the stress and strain distributions in the human mandibular condyle during static clenching. A condyle was scanned with a micro-CT scanner to create a finite element model. For every voxel the degree of mineralization (DMB) was determined from the micro-CT scan. The Young's moduli of the elements were calculated from the DMB using constant, linear, and cubic relations, respectively. Stresses, strains, and displacements in cortical and trabecular bone, as well as the condylar deformation (extension along the antero-posterion axis) and compliance were compared. Over 90% of the bone mineral was located in the cortical bone. The DMB showed large variations in both cortical bone (mean: 884, SD: 111 mg/cm(3)) and trabecular bone (mean: 738, SD: 101 mg/cm(3)). Variations of the stresses and the strains were small in cortical bone, but large in trabecular bone. In the cortical bone an inhomogeneous mineral distribution increased the stresses and the strains. In the trabecular bone, however, it decreased the stresses and increased the strains. Furthermore, the condylar compliance remained relatively constant, but the condylar deformation doubled. It was concluded that neglect of the inhomogeneity of the mineral distribution results in a large underestimation of the stresses and strains of possibly more than 50%. The stiffness of trabecular bone strongly influences the condylar deformation. Vice versa, the condylar deformation largely determines the magnitude of the strains in the trabecular bone.

  14. Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains.

    PubMed

    Reis-Cunha, João Luís; Rodrigues-Luiz, Gabriela F; Valdivia, Hugo O; Baptista, Rodrigo P; Mendes, Tiago A O; de Morais, Guilherme Loss; Guedes, Rafael; Macedo, Andrea M; Bern, Caryn; Gilman, Robert H; Lopez, Carlos Talavera; Andersson, Björn; Vasconcelos, Ana Tereza; Bartholomeu, Daniella C

    2015-07-04

    Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. CL Brener, the reference strain of the T. cruzi genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in T. cruzi. Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the T. cruzi karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different T. cruzi strains. Despite these studies, the extent of diversity in CCNV among T. cruzi strains based on a read depth coverage analysis has not been determined. We identify the CCNV in T. cruzi strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in T. cruzi than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six T. cruzi samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.

  15. Geoelectrical, strain and tilt investigations of hydrological processes at the broadband Geodynamical Observatory Moxa, Germany

    NASA Astrophysics Data System (ADS)

    Hermann, Tobias; Kroner, Corinna; Jahr, Thomas

    2013-11-01

    The Geodynamic Observatory Moxa, located in Thuringia/Germany, is dedicated to studies of temporal deformations of the earth's crust and of variations of the gravity field. One of the essential issues with respect to these investigations is the reduction of the hydrological impact on the data of the gravimeters, strainmeters and tiltmeters. In order to optimise the reductions, we investigated the changes in the hydrological conditions in the woody mountain slope above the observatory with time-lapse electrical resistivity tomography (ERT), and analysed the strain and tilt measurements for prominent signatures of pore pressure induced subsurface deformations. Here we present the results for two profiles - parallel and perpendicular to the slope - measured with ERT during 33 campaigns between June 2007 and April 2010. Resistivity changes and variations of apparent soil moisture, inferred from ERT sections, were found to primarily occur in the first two metres of the subsurface. These variations can be related to subsurface flow in the upper two metres induced by precipitation events and snowmelts. Trees close to the profiles only show a minimum impact on the resistivity and soil moisture changes. Furthermore, systematic hydrologically induced deformations can be observed in hodographs of strain and tilt measurements for large precipitation events (> 80 mm) and snowmelts. In the strain data a short-term (< 3 days) dilatational signal is found with an amplitude of 20 nstrain to 60 nstrain and a long-term (> 7 days) compressional signal between 40 nstrain and 180 nstrain. The preferential N-S direction of long-term deformational signals (> 1 week) is also observed in the tilt data. The direction of tilt changes (25 nrad-120 nrad) is nearly parallel to the drainage direction of the nearby Silberleite creek indicating variations of pore pressure gradients during hydrological events. The results of these hydrological studies at the Geodynamic Observatory Moxa can be used

  16. Genetic structure and natural variation associated with host of origin in Penicillium expansum strains causing blue mould.

    PubMed

    Sanzani, S M; Montemurro, C; Di Rienzo, V; Solfrizzo, M; Ippolito, A

    2013-07-15

    Blue mould, caused by Penicillium expansum, is one of the most economically damaging postharvest diseases of pome fruits, although it may affect a wider host range, including sweet cherries and table grapes. Several reports on the role of mycotoxins in plant pathogenesis have been published, but few focussed on the influence of mycotoxins on the variation in host preference amongst producing fungi. In the present study the influence of the host on P. expansum pathogenicity/virulence was investigated, focussing mainly on the relationship with patulin production. Three P. expansum strain groups, originating from apples, sweet cherries, and table grapes (7 strains per host) were grown on their hosts of isolation and on artificial media derived from them. Strains within each P. expansum group proved to be more aggressive and produced more patulin than the other two groups under evaluation when grown on the host from which they originated. Table grape strains were the most aggressive (81% disease incidence) and strongest patulin producers (up to 554μg/g). The difference in aggressiveness amongst strains was appreciable only in the presence of a living host, suggesting that the complex pathogen-host interaction significantly influenced the ability of P. expansum to cause the disease. Incidence/severity of the disease and patulin production proved to be positively correlated, supporting the role of patulin as virulence/pathogenicity factor. The existence of genetic variation amongst isolates was confirmed by the High Resolution Melting method that was set up herein, which permitted discrimination of P. expansum from other species (P. chrysogenum and P. crustosum) and, within the same species, amongst the host of origin. Host effect on toxin production appeared to be exerted at a transcriptional level.

  17. Significant gene content variation characterizes the genomes of inbred mouse strains

    PubMed Central

    Cutler, Gene; Marshall, Lisa A.; Chin, Ni; Baribault, Helene; Kassner, Paul D.

    2007-01-01

    The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes. PMID:17989247

  18. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

    PubMed Central

    Akagi, Keiko; Li, Jingfeng; Stephens, Robert M.; Volfovsky, Natalia; Symer, David E.

    2008-01-01

    Numerous inbred mouse strains comprise models for human diseases and diversity, but the molecular differences between them are mostly unknown. Several mammalian genomes have been assembled, providing a framework for identifying structural variations. To identify variants between inbred mouse strains at a single nucleotide resolution, we aligned 26 million individual sequence traces from four laboratory mouse strains to the C57BL/6J reference genome. We discovered and analyzed over 10,000 intermediate-length genomic variants (from 100 nucleotides to 10 kilobases), distinguishing these strains from the C57BL/6J reference. Approximately 85% of such variants are due to recent mobilization of endogenous retrotransposons, predominantly L1 elements, greatly exceeding that reported in humans. Many genes’ structures and expression are altered directly by polymorphic L1 retrotransposons, including Drosha (also called Rnasen), Parp8, Scn1a, Arhgap15, and others, including novel genes. L1 polymorphisms are distributed nonrandomly across the genome, as they are excluded significantly from the X chromosome and from genes associated with the cell cycle, but are enriched in receptor genes. Thus, recent endogenous L1 retrotransposition has diversified genomic structures and transcripts extensively, distinguishing mouse lineages and driving a major portion of natural genetic variation. PMID:18381897

  19. 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. Copyright © 2014 by The American Association of Immunologists, Inc.

  20. 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

  1. 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

    2016-02-11

    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. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. A mechanism to account for mouse strain variation in resistance to the larval cestode, Taenia taeniaeformis.

    PubMed Central

    Mitchell, G F; Rajasekariah, G R; Rickard, M D

    1980-01-01

    Mice of various inbred strains differ markedly in resistance to first infection with Taenia taeniaeformis. Hypothymic nude mice of relatively resistant (e.g. BALB/c) and relatively susceptible (e.g. CBA/H) genotypes are highly susceptible but both can be protected against infection by injection of serum from infected mice. Using differential pH elution of "immune serum" from protein A-Sepharose, evidence was obtained that a combination of the pH 6 eluate (enriched for IgG1 molecules) plus the pH 3 or 4 eluate (enriched for IgG2 molecules) was more effective than either eluate alone at transferring protection to nude mice. By using whole serum transfer techniques, the rate of appearance of "host protective serum activity" (presumably antibody) was shown to be increased in genetically resistant versus susceptible mouse strains. It is suggested that, in relatively resistant mouse strains, host protective antibodies prejudice the establishment (or subsequent survival) of larvae prior to the full expression of protective mechanisms in the establishing larvae. In keeping with a host-protective effect of an accelerated immune response early in infection, a high dose challenge with eggs actually resulted in lower infection levels in genetically resistant mouse strains such as BALB/c and C57B1/6. The proposed mechanism of immunologically mediated, genetically based variation in susceptibility to T. taeniaeformis should not influence the effectiveness of a model vaccine against first infection in all strains of mice. PMID:7380476

  3. Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains

    PubMed Central

    Nachshon, Aharon; Abu-Toamih Atamni, Hanifa J.; Steuerman, Yael; Sheikh-Hamed, Roa'a; Dorman, Alexandra; Mott, Richard; Dohm, Juliane C.; Lehrach, Hans; Sultan, Marc; Shamir, Ron; Sauer, Sascha; Himmelbauer, Heinz; Iraqi, Fuad A.; Gat-Viks, Irit

    2016-01-01

    A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences. PMID:27761138

  4. Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains.

    PubMed

    Nachshon, Aharon; Abu-Toamih Atamni, Hanifa J; Steuerman, Yael; Sheikh-Hamed, Roa'a; Dorman, Alexandra; Mott, Richard; Dohm, Juliane C; Lehrach, Hans; Sultan, Marc; Shamir, Ron; Sauer, Sascha; Himmelbauer, Heinz; Iraqi, Fuad A; Gat-Viks, Irit

    2016-01-01

    A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences.

  5. 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.

  6. Variational Monte Carlo investigation of SU (N ) Heisenberg chains

    NASA Astrophysics Data System (ADS)

    Dufour, Jérôme; Nataf, Pierre; Mila, Frédéric

    2015-05-01

    Motivated by recent experimental progress in the context of ultracold multicolor fermionic atoms in optical lattices, we have investigated the properties of the SU (N) Heisenberg chain with totally antisymmetric irreducible representations, the effective model of Mott phases with m variational Monte Carlo based on Gutzwiller projected fermionic wave functions, we have been able to verify these predictions for a representative number of cases with N ≤10 and m ≤N /2 , and we have shown that the opening of a gap is associated to a spontaneous dimerization or trimerization depending on the value of m and N . We have also investigated the marginal cases where Abelian bosonization did not lead to any prediction. In these cases, variational Monte Carlo predicts that the ground state is critical with exponents consistent with conformal field theory.

  7. Investigation on Characteristic Variation of the FBG Spectrum with Crack Propagation in Aluminum Plate Structures

    PubMed Central

    Jin, Bo; Zhang, Weifang; Zhang, Meng; Ren, Feifei; Dai, Wei; Wang, Yanrong

    2017-01-01

    In order to monitor the crack tip propagation of aluminum alloy, this study investigates the variation of the spectrum characteristics of a fiber Bragg grating (FBG), combined with an analysis of the spectrum simulation. The results identify the location of the subordinate peak as significantly associated with the strain distribution along the grating, corresponding to the different plastic zones ahead of the crack tip with various crack lengths. FBG sensors could observe monotonic and cyclic plastic zones ahead of the crack tip, with the quadratic strain distribution along the grating at the crack tip-FBG distance of 1.2 and 0.7 mm, respectively. FBG sensors could examine the process zones ahead of the crack tip with the cubic strain distribution along the grating at the crack tip-FBG distance of 0.5 mm. The spectrum oscillation occurs as the crack approaches the FBG where the highly heterogeneous strain is distributed. Another idea is to use a finite element method (FEM), together with a T-matrix method, to analyze the reflection intensity spectra of FBG sensors for various crack sizes. The described crack propagation detection system may apply in structural health monitoring. PMID:28772949

  8. Investigation on Characteristic Variation of the FBG Spectrum with Crack Propagation in Aluminum Plate Structures.

    PubMed

    Jin, Bo; Zhang, Weifang; Zhang, Meng; Ren, Feifei; Dai, Wei; Wang, Yanrong

    2017-05-27

    In order to monitor the crack tip propagation of aluminum alloy, this study investigates the variation of the spectrum characteristics of a fiber Bragg grating (FBG), combined with an analysis of the spectrum simulation. The results identify the location of the subordinate peak as significantly associated with the strain distribution along the grating, corresponding to the different plastic zones ahead of the crack tip with various crack lengths. FBG sensors could observe monotonic and cyclic plastic zones ahead of the crack tip, with the quadratic strain distribution along the grating at the crack tip-FBG distance of 1.2 and 0.7 mm, respectively. FBG sensors could examine the process zones ahead of the crack tip with the cubic strain distribution along the grating at the crack tip-FBG distance of 0.5 mm. The spectrum oscillation occurs as the crack approaches the FBG where the highly heterogeneous strain is distributed. Another idea is to use a finite element method (FEM), together with a T-matrix method, to analyze the reflection intensity spectra of FBG sensors for various crack sizes. The described crack propagation detection system may apply in structural health monitoring.

  9. Strain-Dependent Variations in Spatial Learning and in Hippocampal Synaptic Plasticity in the Dentate Gyrus Of Freely Behaving Rats

    PubMed Central

    Manahan-Vaughan, Denise; Schwegler, Herbert

    2011-01-01

    Hippocampal synaptic plasticity is believed to comprise the cellular basis for spatial learning. Strain-dependent differences in synaptic plasticity in the CA1 region have been reported. However, it is not known whether these differences extend to other synapses within the trisynaptic circuit, although there is evidence for morphological variations within that path. We investigated whether Wistar and Hooded Lister (HL) rat strains express differences in synaptic plasticity in the dentate gyrus in vivo. We also explored whether they exhibit differences in the ability to engage in spatial learning in an eight-arm radial maze. Basal synaptic transmission was stable over a 24-h period in both rat strains, and the input–output relationship of both strains was not significantly different. Paired-pulse analysis revealed significantly less paired-pulse facilitation in the HL strain when pulses were given 40–100 ms apart. Low frequency stimulation at 1 Hz evoked long-term depression (>24 h) in Wistar and short-term depression (<2 h) in HL rats; 200 Hz stimulation induced long-term potentiation (>24 h) in Wistar, and a transient, significantly smaller potentiation (<1 h) in HL rats, suggesting that HL rats have higher thresholds for expression of persistent synaptic plasticity. Training for 10 days in an eight-arm radial maze revealed that HL rats master the working memory task faster than Wistar rats, although both strains show an equivalent performance by the end of the trial period. HL rats also perform more efficiently in a double working and reference memory task. On the other hand, Wistar rats show better reference memory performance on the final (8–10) days of training. Wistar rats were less active and more anxious than HL rats. These data suggest that strain-dependent variations in hippocampal synaptic plasticity occur in different hippocampal synapses. A clear correlation with differences in spatial learning is not evident however. PMID:21436876

  10. 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.

  11. Arterial blood gases, electrolytes, and metabolic indices associated with hemorrhagic shock: inter- and intrainbred rat strain variation.

    PubMed

    Rose, Rajiv; Kheirabadi, Bijan S; Klemcke, Harold G

    2013-05-01

    We have previously shown interstrain variation (indicating a genetic basis), and intrastrain variation in survival time after hemorrhage (STaH) among inbred rat strains. To assist in understanding physiological mechanisms associated with STaH, we analyzed various arterial blood measures (ABM; pH, Paco2, oxygen content, sodium, potassium, glucose, bicarbonate, base excess, total CO2, and ionized calcium) in inbred rats. Rats from five inbred strains (n = 8-10/strain) were catheterized and, ≈ 24 h later, subjected to a conscious, controlled, 47% hemorrhage. ABM were measured at the start (initial) and end (final) of hemorrhage. Inter- and intrainbred strain variations of ABM were quantified and compared, and correlations of ABM with STaH were determined. All final ABM values and some initial ABM values were different among strains. Most ABM changed (Δ) during hemorrhage, and these changes differed among strains (P <0.03). Some strain-dependent correlations (r ≥ 0.7; P ≤ 0.05) existed between ΔABM and STaH (e.g., BN/Mcwi, ΔK(+), r = -0.84). Dark Agouti rats (longest STaH) had the smallest ΔPaco2, ΔHCO3(-), and Δbase excess, and the highest final glucose. High coefficients of variation (CVs, >10%), strain-specific CVs, and low intraclass correlation coefficients (rI < 0.5) defined the large intrastrain ABM variation that exceeded interstrain variation for most ABM. These results suggest that some ABM (K(+), Paco2, glucose, oxygen content) could predict subsequent STaH in an inbred rat strain-dependent manner. We speculate that whereas genetic differences may be responsible for interstrain variation, individual-specific epigenetic processes (e.g., DNA methylation) may be partly responsible for both inter- and intrastrain ABM variation.

  12. Variations in life tables of geographically isolated strains of the mosquito Culex quinquefasciatus.

    PubMed

    Suman, D S; Tikar, S N; Mendki, M J; Sukumaran, D; Agrawal, O P; Parashar, B D; Prakash, S

    2011-09-01

    Variations in the life tables and other biological attributes of four strains of Culex quinquefasciatus Say (Diptera: Culicidae) from geographically isolated regions of India that had been reared to the fifth generation in the laboratory were assessed under a standardized rearing regime under constant laboratory conditions. Two strains from arid habitats [Jodhpur (JD) and Bikaner (BKN)], one from a semi-arid inland habitat [Bathinda (BTH)], one from a semi-arid coastal habitat [Jamnagar (JMN)] and a standard laboratory strain (LAB) were compared. Horizontal life-table parameters were measured for each strain. Egg mortality ranged from 4.4% (JD and BTH) to 19.5% (BKN). The lowest rate of adult emergence and highest female : male ratio were found in BKN, and the highest rate of adult emergence and lowest female : male ratio were recorded in BTH. The egg-hatching period was longest in BTH and shortest in LAB. The duration from oviposition to adult emergence was longest in JD and shortest in LAB. Females lived longer than males in all strains. The net reproductive rates (R(0) ) of all field-derived strains (122.9-162.2) differed significantly between strains and were significantly greater than that of LAB (107.6). Similarly, both the intrinsic rate of increase (r(m) ) and finite rate of increase (λ) were found to be lower in LAB than in the field strains, but the mean generation time (T) and doubling time (DT) were longest in LAB. For several life-table attributes, JD and BTH clustered together and were more similar to JMN than to BKN and LAB. The results indicate that BTH, BKN and JD can be characterized as r-strategists, more so than JMN. Overall fecundity increased with age. Differences in annual temperature ranges and mean annual rainfall between locations were positively correlated (r = 0.46-0.97) with egg production, female life expectancy, R(0) , r(m) , λ and T. The results suggest that strains of Cx. quinquefasciatus from different geographical areas with

  13. Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci

    PubMed Central

    Diamant, Eran; Palti, Yniv; Gur-Arie, Riva; Cohen, Helit; Hallerman, Eric M.; Kashi, Yechezkel

    2004-01-01

    Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria. PMID:15066845

  14. The impact of anaerobiosis on strain-dependent phenotypic variations in Pseudomonas aeruginosa.

    PubMed

    Fang, Hao; Toyofuku, Masanori; Kiyokawa, Tatsunori; Ichihashi, Akihiro; Tateda, Kazuhiro; Nomura, Nobuhiko

    2013-01-01

    Bacteria participate in social behaviors by communicating with each other and forming surface-associated biofilms. In Pseudomonas aeruginosa, such social behaviors are affected greatly by the environment. Although P. aeruginosa survive under anaerobic conditions, previous studies indicate that quorum sensing is attenuated under such conditions, and that this leads to decreased activity of extracellular virulence factors as compared to aerobic conditions. Hence it has come into question whether P. aeruginosa are virulent under anaerobic conditions. Here, we compared various phenotypes between PAO1 and clinical isolates under anaerobic conditions. Our data revealed that when grown anaerobically, growth and cell morphology greatly differed among the strains. One of the clinical isolates produced comparable amounts of quorum-sensing signaling molecules and extracellular virulence factors under aerobic and anaerobic conditions, while the other strains showed low production under anaerobic conditions. Biofilm formation also exhibited strain-dependent variations, suggesting that there are several mechanisms that lead to biofilm formation under anaerobic conditions. Taken together, these results indicate that the impact of anaerobiosis on the social interactions of P. aeruginosa is strain dependent, and suggest that multiple regulatory mechanisms are involved in the regulation of quorum sensing and biofilm formation under anaerobic conditions.

  15. Molecular Characterization of Trichomonas vaginalis Strains Based on Identifying Their Probable Variations in Asymptomatic Patients

    PubMed Central

    SPOTIN, Adel; EGHTEDAR, Sanaz TAGHIZADEH; SHAHBAZI, Abbas; SALEHPOUR, Asghar; SARAFRAZ, Seddigheh; SHARIATZADEH, Seyyed Ali; MAHAMI-OSKOUEI, Mahmoud

    2016-01-01

    Background: The aim of this study was to identify the Trichomonas vaginalis strains/haplotypes based on identifying their probable variations in asymptomatic patients referred to Tabriz health centers, northwestern Iran. Methods: Sampling was taken from 50-suspected women to T. vaginalis in northwestern Iran. The obtained samples were smeared and cultured. Fifty DNA samples were extracted, amplified and identified by nested polymerase chain reaction and PCR-RFLP of actin gene using two endonuclease enzymes: MseI and RsaI. To reconfirm, the amplicons of actin gene were directly sequenced in order to identify the strains/haplotypes. Results: PCR-RFLP patterns, sequencing and phylogenetic analyses revealed definitely the presence of the G (n=22; 73.4%) and E (n=8; 26.6%) strains. Multiple alignments findings of genotype G showed five haplotypes and two amino acid substitutions in codons 192 and 211 although, no remarkable unique haplotype was found in genotype E. Conclusion: The accurate identification of T. vaginalis strains based on discrimination of their unknown haplotypes particularly those which are impacted on protein translation should be considered in parasite status, drug resistance, mixed infection with HIV and monitoring of asymptomatic trichomoniasis in the region. PMID:28127362

  16. Variation.

    ERIC Educational Resources Information Center

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

  17. Strain effects on phonon transport in antimonene investigated using a first-principles study.

    PubMed

    Zhang, Ai-Xia; Liu, Jiang-Tao; Guo, San-Dong; Li, Hui-Chao

    2017-06-07

    Strain engineering is a very effective method to continuously tune the electronic, topological, optical and thermoelectric properties of materials. In this work, strain-dependent phonon transport of recently-fabricated antimonene (Sb monolayers) under biaxial strain is investigated using a combination of first-principles calculations and the linearized phonon Boltzmann equation within the single-mode relaxation time approximation (RTA). It is found that the ZA dispersion of antimonene with strain less than -1% gives imaginary frequencies, which suggests that compressive strain can induce structural instability. Experimentally, it is possible to enhance structural stability by tensile strain. The calculated results show that lattice thermal conductivity increases with strain increasing from -1% to 6%, and lattice thermal conductivity at 6% strain is 5.6 times larger than that at -1% strain at room temperature. It is interesting that lattice thermal conductivity is inversely proportional to the buckling parameter h in a considered strain range. Such a strain dependence of lattice thermal conductivity is attributed to enhanced phonon lifetimes caused by increased strain, while group velocities have a decreased effect on lattice thermal conductivity with increasing strain. It is found that acoustic branches dominate the lattice thermal conductivity over the full strain range. The cumulative room-temperature lattice thermal conductivity at -1% strain converges to a maximum with the phonon mean free path (MFP) at 50 nm, while that at 6% strain becomes as large as 44 μm, which suggests that strain can give rise to very strong size effects on lattice thermal conductivity in antimonene. Finally, the increased lattice thermal conductivity caused by increasing strain can be explained by a reduced polarized covalent bond, inducing weak phonon anharmonicity. These results may provide guidance on fabrication techniques of group-VA element (As, Sb, Bi) monolayers, and offer

  18. Theory of bond-length variations in relaxed, strained, and amorphous silicon-germanium alloys

    NASA Astrophysics Data System (ADS)

    Tzoumanekas, C.; Kelires, P. C.

    2002-11-01

    We present a theoretical study of bond-length and angle variations in relaxed, epitaxially strained, and amorphous Si1-xGex alloys. Our approach is based on Monte Carlo simulations, within the semigrand-canonical ensemble utilizing Ising-like identity flips, and in conjuction with energies calculated using the empirical potential of Tersoff [Phys. Rev. B 39, 5566 (1989)]. The method offers great statistical precision enabling us to extract clear variations through the whole composition range and for all types of bonds. Our simulations show that in relaxed crystalline alloys, where the lattice constant takes its natural value, bond lengths depend on composition x and that these variations are type specific, in agreement with recent experimental studies. Similar type-specific variations are found for the angles and the second-nearest-neighbor distances. This analysis also reveals that the negative deviation of the lattice constant from Vegard's law is mainly due to radial, and not angular, relaxations. In the epitaxially strained alloys, bond lengths decrease with x due to the two-dimensional confinement in the growth layers, in good agreement with predictions based on the macroscopic theory of elasticity. The dimer bond lengths at the (100)-(2×1)-reconstructed alloy surface remain nearly constant, and they are elongated with respect to the bulk values. In the amorphous alloys, we unravel a remarkable behavior of bond lengths at the dilute low-x alloy limit, characterized by strong relaxations and elongation. Furthermore, the bond lengths decrease with increasing Ge content. We offer an explanation of this effect based on the analysis of the enthalpy of formation of the amorphous alloy.

  19. Estimation of Myocardial Strain and Contraction Phase From Cine MRI Using Variational Data Assimilation.

    PubMed

    Tuyisenge, Viateur; Sarry, Laurent; Corpetti, Thomas; Innorta-Coupez, Elisabeth; Ouchchane, Lemlih; Cassagnes, Lucie

    2016-02-01

    This paper presents a new method to estimate left ventricle deformations using variational data assimilation that combines image observations from cine MRI and a dynamic evolution model of the heart. The main contribution of the model is that it embeds parameters modeling the contraction / relaxation process. It estimates myocardial motion and contraction parameters simultaneously, providing accurate complementary information for diagnosis. The method was applied to synthetic datasets with known ground truth motion and to 47 patients MRI datasets acquired at three slice locations (base, mid-ventricle and apex). Radial and circumferential strain components were compared to those obtained with a reference tag tracking software, exhibiting good agreement with intraclass correlation coefficients (ICC) above 0.8. Results were also evaluated against wall motion score indices used to assess cardiac kinetics in clinical practice. The assimilation process overcame issues caused by temporal artifacts as a result of the dynamic model, compared to using the observation term alone. Moreover we found that the new dynamic model, consisting of a piecewise transport model acting independently on systole and diastole performed better than the standard continuous transport model, which oversmooths temporal variations. Estimated strain and contraction parameters significantly correlated to clinical scores, making them promising features for diagnosing not only hypokinesia but also dyskinesia.

  20. Laboratory investigation of hospital outbreak caused by two different multiresistant Acinetobacter calcoaceticus subsp. anitratus strains.

    PubMed Central

    Vila, J; Almela, M; Jimenez de Anta, M T

    1989-01-01

    During a 7-month period, from December 1986 to June 1987, multiresistant strains of Acinetobacter calcoaceticus subsp. anitratus were isolated from 25 patients in a respiratory intensive care unit. The biochemical characteristics defined two groups of strains, group 1 (14 strains) and group 2 (11 strains). Both groups had the same biochemical characteristics, but group 2 strains could assimilate adipate and phenyl acetate. Moreover, of 16 antibiotics tested only netilmicin and imipenem had some inhibitory activity for group 1 strains; group 2 strains were susceptible to mezlocillin, piperacillin, and ticarcillin. Plasmid profiles of the groups were also different. The results of a laboratory investigation (biochemical characteristics, antibiotic susceptibility, and plasmid isolation) identified two different A. calcoaceticus subsp. anitratus strains as the causes of the outbreak. Images PMID:2745682

  1. Investigation on critical strain of dynamic recrystallization for SiCp/Al-Cu composite

    NASA Astrophysics Data System (ADS)

    Sun, Yali; Xie, Jingpei; Hao, Shiming; Wang, Aiqin; Liu, Pei; Li, Min

    2015-07-01

    Using Gleeble-1500D simulator, the critical strain of dynamic recrystallization of SiCp/Al-Cu composite were investigated at 623-773 K with strain rate of 0.01-10 s-1. The results show that the main softening mechanism is the dynamic recrystallization through the stress-strain curves of SiCp/Al-Cu composite, the activation energy is 272.831 KJ/mol. lnθ-ε and (-∂(lnθ)/∂ε)-ε) curves were plotted based on the experimental data to further obtain the critical strain and steady strain of DRX. Then the critical strain model and the steady-state strain model of DRX were set up. Furthermore, the dynamic recrystallization volume fraction of SiCp/Al-Cu composite was investigated.

  2. Strain variation amongst clinical and potable water isolates of M. kansasii using automated repetitive unit PCR.

    PubMed

    Thomson, Rachel; Tolson, Carla; Huygens, Flavia; Hargreaves, Megan

    2014-05-01

    Mycobacterium kansasii is a pulmonary pathogen that has been grown readily from municipal water, but rarely isolated from natural waters. A definitive link between water exposure and disease has not been demonstrated and the environmental niche for this organism is poorly understood. Strain typing of clinical isolates has revealed seven subtypes with Type 1 being highly clonal and responsible for most infections worldwide. The prevalence of other subtypes varies geographically. In this study 49 water isolates are compared with 72 patient isolates from the same geographical area (Brisbane, Australia), using automated repetitive unit PCR (Diversilab) and ITS_RFLP. The clonality of the dominant clinical strain type is again demonstrated but with rep-PCR, strain variation within this group is evident comparable with other reported methods. There is significant heterogeneity of water isolates and very few are similar or related to the clinical isolates. This suggests that if water or aerosol transmission is the mode of infection, then point source contamination likely occurs from an alternative environmental source. Copyright © 2014 Elsevier GmbH. All rights reserved.

  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.

  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. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  10. Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation.

    PubMed

    Oosterkamp, Margreet J; Boeren, Sjef; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

    2013-10-01

    Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. Alicycliphilus denitrificans strain BC can use chlorate, nitrate, and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis, and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells are shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. All MS data have been deposited in the ProteomeXchange with identifier PXD000258.

  11. Variations in the multiple tbp genes in different Halobacterium salinarum strains and their expression during growth.

    PubMed

    Teufel, Katharina; Bleiholder, Anne; Griesbach, Tim; Pfeifer, Felicitas

    2008-09-01

    The presence and expression of the multiple tbp genes encoding TATA-box binding proteins (TBPs) was investigated in various strains and mutants of the archaeon Halobacterium salinarum. Six genes, tbpA through tbpF, are present in the genome of Hbt. salinarum NRC-1 and also in the gas vesicle negative mutant strain R1. The only tbp gene located in the chromosome is tbpE, whereas all others are found in the plasmid DNA. Due to the dynamic nature of the plasmids in the Halobacterium strains, the copy numbers of the alternative tbp genes vary significantly. Five tbp genes (tbpA through tbpE) were present in the wild-type strain Hbt. salinarum PHH1. The tbpC gene of Hbt. salinarum PHH1 carried an ISH27-2 insertion element at the start of the reading frame that prevented the expression. All other tbp genes of PHH1 were expressed under aerobic and anaerobic growth conditions and quantitative RT-PCR yielded tbpE as dominant tbp transcript during the exponential growth phase. The plasmid deletion variant Hbt. salinarum PHH4 lacked all of the tbp genes except for tbpE and showed an altered growth behaviour compared to PHH1 wild-type in the stationary growth phase under anaerobic growth conditions.

  12. Sequence variation in the Toxoplasma gondii eIF4A gene among strains from different hosts and geographical locations.

    PubMed

    Chen, J; Fang, S F; Zhou, D H; Li, Z Y; Liu, G H; Zhu, X Q

    2014-04-29

    Toxoplasma gondii is an opportunistic protozoan parasite that infects a wide range of animals, including humans. The T. gondii eukaryotic translation initiation factor 4A (eIF4A) protein is expressed in the tachyzoite, but its expression is markedly downregulated in the bradyzoite, and it is therefore considered to be associated with tachyzoite virulence. The present study examined sequence variation in the eIF4A gene among nine strains of different genotypes from different hosts and geographical localities using polymerase chain reaction amplification, sequence analysis, and phylogenetic reconstruction by Bayesian inference. The complete genomic sequence of the eIF4A gene was 3156 bp in length in the strain TgCgCaI, 3153 bp in the strain MAS, 3152 bp in the strain TgPNY, and 3154 bp in the other six strains. Sequence analysis identified 29 (0-0.8%) variable nucleotide positions among all strains, with 16 of these variations located in the coding region, while the other 12 were distributed between the two introns. Phylogenetic analyses revealed that these eIF4A sequences were not effective molecular markers for intra-species phylogenetic analysis and differential identification of T. gondii strains from different hosts and geographical locations. This study demonstrated the existence of low sequence variation in the eIF4A gene, suggesting that T. gondii eIF4A may represent a suitable candidate vaccine against toxoplasmosis.

  13. 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.

  14. Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

    PubMed Central

    2012-01-01

    Background Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Results Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Conclusions Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons

  15. Linearization of CMOS Hot-Electron Injectors for Self-Powered Monitoring of Biomechanical Strain Variations.

    PubMed

    Zhou, Liang; Chakrabartty, Shantanu

    2017-04-01

    In our previous work we demonstrated that by eliminating regulation and rectification modules from the energy harvesting pathway, the minimum activation power of a piezoelectricity-driven hot-electron injector (p-HEI) can be reduced down to a few nanowatts. As a result the p-HEI device could be used for self-powered, in-vivo recording of biomechanical strain variations. However, for large magnitudes of input strain energy, the response of the modified p-HEI sensor was found to be quasi-linear with respect to the number of loading cycles, which made the calibration of the sensor difficult across a wide variety of biomedical applications. In this paper we propose a compensation circuit that is able to linearize the response of the p-HEI injector over a wide range of input power while maintaining a low activation threshold. The compensation circuit uses a combination of a storage capacitor and a non-linear resistor which produces a compressive input-output response required for linearization. Using prototypes fabricated in a 0.5-μm bulk CMOS process we validate the functionality of the injector and demonstrate that it can achieve a linear injection response for input power ranging from 5 nW to 1.5 μW.

  16. Along-strike Variations in Active Strain Accumulation in the Northwest Himalaya

    NASA Astrophysics Data System (ADS)

    Morell, K. D.; Ahmad, T.; Sandiford, M.; Codilean, A. T.; Fulop, R. H.

    2015-12-01

    The spatial distribution of channel steepness, erosion rate, and physiographic data highlight pronounced along-strike changes in active strain accumulation in the northwest Himalaya. In particular, the data suggest that the mid-crustal ramp of the Main Himalayan Thrust could merge along-strike with an active portion of the Main Boundary Thrust near longitude ~77º E. This along-strike change in active fault geometry also coincides with the lateral termination of both lesser and greater Himalayan sequences, a significant reduction in total shortening within the wedge, and pronounced variations in regional seismicity. Recent activity along extensional structures in the high Himalaya of this same region appears to have led to significant reorganization, modification and capture of the Sutlej River basin, one of the largest Himalayan river systems. Given the recent 2015 Gorkha earthquake along a comparable section ~500-km along strike, these new constraints on active fault architecture could have regional implications for how strain is partitioned along seismogenic faults in the northwest Himalaya.

  17. Virulence variation among strains of the emerging infectious fungus Batrachochytrium dendrobatidis (Bd) in multiple amphibian host species.

    PubMed

    Dang, Trang D; Searle, Catherine L; Blaustein, Andrew R

    2017-05-11

    Emerging infectious diseases have been documented in numerous plant and animal populations. The infectious disease amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is associated with global amphibian population declines. While much Bd-amphibian research has centered on response variation in hosts, a paucity of information exists on how variation in the pathogen, such as strain differences, affects infection dynamics. To examine how different Bd strains may differentially impact multiple hosts, we conducted laboratory experiments to measure 2 infection outcomes, viz. host survival and pathogen load, in 3 amphibian host species (Pacific treefrog, western toad, and Cascades frog) after exposure to 3 different Bd strains (an additional fourth Bd strain was tested in toads only). Our results confirm that the infection response differs among host species. Western toads experienced significant mortality, but Pacific treefrogs and Cascades frogs did not. Interestingly, our experiment also captured strain-dependent virulence variation but only in 1 host species, the western toad. Increased mortality was observed in 2 of the 4 Bd strains tested in this host species. Toads were also the only host species found to have variable pathogen load dependent on strain type; individuals exposed to the Panama strain harbored significantly higher loads compared to all other strains. These findings underscore the dynamic nature of Bd infection, showing that virulence can vary contingent on host and strain type. We highlight the importance of both host- and pathogen-dependent factors in determining overall infection virulence and show the need for in vivo testing to fully assess pathogenicity.

  18. Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae.

    PubMed

    Mezzetti, Francesco; Fay, Justin C; Giudici, Paolo; De Vero, Luciana

    2017-01-01

    Glutathione (GSH) production during wine fermentation is a desirable trait as it can limit must and wine oxidation and protect various aromatic compounds. UMCC 2581 is a Saccharomyces cerevisiae wine strain with enhanced GSH content at the end of wine fermentation. This strain was previously derived by selection for molybdate resistance following a sexual cycle of UMCC 855 using an evolution-based strategy. In this study, we examined genetic and gene expression changes associated with the derivation of UMCC 2581. For genetic analysis we sporulated the diploid UMCC 855 parental strain and found four phenotype classes of segregants related to molybdate resistance, demonstrating the presence of segregating variation from the parental strain. Using bulk segregant analysis we mapped molybdate traits to two loci. By sequencing both the parental and evolved strain genomes we identified candidate mutations within the two regions as well as an extra copy of chromosome 1 in UMCC 2581. Combining the mapped loci with gene expression profiles of the evolved and parental strains we identified a number of candidate genes with genetic and/or gene expression changes that could underlie molybdate resistance and increased GSH levels. Our results provide insight into the genetic basis of GSH production relevant to winemaking and highlight the value of enhancing wine strains using existing variation present in wine strains.

  19. Analysis of Equid Herpesvirus 1 Strain Variation Reveals a Point Mutation of the DNA Polymerase Strongly Associated with Neuropathogenic versus Nonneuropathogenic Disease Outbreaks

    PubMed Central

    Nugent, J.; Birch-Machin, I.; Smith, K. C.; Mumford, J. A.; Swann, Z.; Newton, J. R.; Bowden, R. J.; Allen, G. P.; Davis-Poynter, N.

    2006-01-01

    Equid herpesvirus 1 (EHV-1) can cause a wide spectrum of diseases ranging from inapparent respiratory infection to the induction of abortion and, in extreme cases, neurological disease resulting in paralysis and ultimately death. It has been suggested that distinct strains of EHV-1 that differ in pathogenic capacity circulate in the field. In order to investigate this hypothesis, it was necessary to identify genetic markers that allow subgroups of related strains to be identified. We have determined all of the genetic differences between a neuropathogenic strain (Ab4) and a nonneuropathogenic strain (V592) of EHV-1 and developed PCR/sequencing procedures enabling differentiation of EHV-1 strains circulating in the field. The results indicate the occurrence of several major genetic subgroups of EHV-1 among isolates recovered from outbreaks over the course of 30 years, consistent with the proposal that distinct strains of EHV-1 circulate in the field. Moreover, there is evidence that certain strain groups are geographically restricted, being recovered predominantly from outbreaks occurring in either North America or Europe. Significantly, variation of a single amino acid of the DNA polymerase is strongly associated with neurological versus nonneurological disease outbreaks. Strikingly, this variant amino acid occurs at a highly conserved position for herpesvirus DNA polymerases, suggesting an important functional role. PMID:16571821

  20. Investigation of cosmic-ray variations using the Elbrus spectrograph

    NASA Astrophysics Data System (ADS)

    Baisultanova, L. M.; Daova, S. P.; Dorman, L. I.; Stremoukhov, V. M.; Khamirzov, Kh. M.

    The soft-muon detector and the muon-neutron detector at the Elbrus cosmic-ray-measuring facility are described. The expected contribution of geomagnetic effects to various classes of cosmic-ray variations is estimated. Amplitudes and phases of the first harmonic of the solar-diurnal variation of cosmic rays are determined. Data on cosmic-ray modulation in interplanetary space are interpreted on the basis of a theory of fast-particle propagation in a moving magnetoplasma in the presence of additional scatterers, moving with a velocity that differs significantly from that of the background plasma.

  1. 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.

  2. Numerical investigation of large strains of hyperelastic solids

    NASA Astrophysics Data System (ADS)

    Fakhrutdinov, L. R.; Sultanov, L. U.

    2016-11-01

    The work is concerned with numerical investigation of large deformations of hyperelastic solids. The kinematics of continua is described in terms of the deformation gradient tensor and left Cauchy-Green tensor. The stress state is described by the Cauchy stress tensor. An incremental method is used to solve the nonlinear problems. The linearized physical equations for the Cauchy stresses for Mooney-Rivlin material are given.

  3. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa.

    PubMed

    Doddapaneni, Harshavardhan; Yao, Jiqiang; Lin, Hong; Walker, M Andrew; Civerolo, Edwin L

    2006-09-01

    The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 x 10(-2) per base pair of DNA and the average INDEL frequency was 2.06 x 10(-2) per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. INDELs and strain specific genes have been identified as the main source of variations

  4. 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

  5. The role of dissipation and defect energy in variational formulations of problems in strain-gradient plasticity. Part 1: polycrystalline plasticity

    NASA Astrophysics Data System (ADS)

    Reddy, B. D.

    2011-11-01

    A general set of flow laws and associated variational formulations are constructed for small-deformation rate-independent problems in strain-gradient plasticity. The framework is based on the thermodynamically consistent theory due to Gurtin and Anand (J Mech Phys Solids 53:1624-1649, 2005), and includes as variables a set of microstresses which have both energetic and dissipative components. The flow law is of associative type. It is expressed as a normality law with respect to a convex but otherwise arbitrary yield function, or equivalently in terms of the corresponding dissipation function. Two cases studied are, first, an extension of the classical Hill-Mises or J 2 flow law and second, a form written as a linear sum of the magnitudes of the plastic strain and strain gradient. This latter form is motivated by work of Evans and Hutchinson (Acta Mater 57:1675-1688, 2009) and Nix and Gao (J Mech Phys Solids 46:411-425, 1998), who show that it leads to superior correspondence with experimental results, at least for particular classes of problems. The corresponding yield function is obtained by a duality argument. The variational problem is based on the flow rule expressed in terms of the dissipation function, and the problem is formulated as a variational inequality in the displacement, plastic strain, and hardening parameter. Dissipative components of the microstresses, which are indeterminate, are absent from the formulation. Existence and uniqueness of solutions are investigated for the generalized Hill-Mises and linear-sum dissipation functions, and for various combinations of defect energy. The conditions for well-posedness of the problem depend critically on the choice of dissipation function, and on the presence or otherwise of a defect energy in the plastic strain or plastic strain gradient, and of internal-variable hardening.

  6. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Evidence of horizontal transfer as origin of strain to strain variation of the tyramine production trait in Lactobacillus brevis.

    PubMed

    Coton, Emmanuel; Coton, Monika

    2009-02-01

    Lactobacillus brevis strains with the ability to decarboxylate tyrosine to tyramine have been described and the involvement of several genes constituting a tyrdc operon at the chromosomal level has been demonstrated in this species. In this study, the existence of Lb. brevis strains unable to form tyramine was observed. In order to evaluate if the tyramine-producing ability was strain-dependent or if it could be correlated to the existence of a new species or subspecies, different isolates were analysed. Analysis by M13-RAPD and sequencing of 16S rDNA, 16S-23S ISR and house-keeping gene recA confirmed that all the isolates belonged to the Lb. brevis species. Analysis of the TyrDC pathway encoding operon region in representative strains indicated the existence of a polymorphism. The genetic differences observed showed that the tyrosine decarboxylating ability is not a Lb. brevis species trait but that it is strain-dependent within this species and suggest that the genes encoding the tyramine-producing pathway constitute a genomic island.

  8. Investigating time patterns of variation in radiation cancer associations

    PubMed Central

    Richardson, D; Ashmore, J

    2005-01-01

    Aims: In occupational settings, carcinogenic exposures are often repeated or protracted over time. The time pattern of exposure accrual may influence subsequent temporal patterns of cancer risk. The authors present several simple models that may be used to evaluate the influence of time since exposure or age at exposure on cancer incidence or mortality in an occupational cohort. Methods: A cohort of 40 415 nuclear industry workers was identified via the Canadian National Dose Registry. Vital status and cause of death were ascertained through 1994. Associations between ionising radiation and mortality due to lung cancer, leukaemia, and cancers other than lung and leukaemia were quantified using conditional logistic regression models with risk sets constructed by incidence density sampling. A step function, a bilinear function, and a sigmoid function were used to evaluate temporal variation in exposure effects. Results: Step and sigmoid functions were used to explore latency and morbidity periods. For analyses of lung cancer, leukaemia, and other cancers the best fitting models were obtained when exposure assignment was lagged by 13, 0, and 5 years, respectively. A bilinear function was used to evaluate whether exposure effects diminished with time since exposure. In analyses of lung cancer and leukaemia, there was evidence that radiation effects attenuated with protracted time since exposure. In analyses of age at exposure, there was evidence of variation in radiation mortality associations for analyses of lung cancer and leukaemia; discounting radiation doses accrued at younger ages (for example, 15–35 years) led to significant improvements in model fit. Conclusions: This paper illustrates empirical approaches to evaluating temporal variation in the effect of a protracted exposure on disease risk. PMID:16046608

  9. Strain-specific variation in murine natural killer gene complex contributes to differences in immunosurveillance for urethane-induced lung cancer.

    PubMed

    Kreisel, Daniel; Gelman, Andrew E; Higashikubo, Ryuji; Lin, Xue; Vikis, Haris G; White, J Michael; Toth, Kelsey A; Deshpande, Charuhas; Carreno, Beatriz M; You, Ming; Taffner, Samantha M; Yokoyama, Wayne M; Bui, Jack D; Schreiber, Robert D; Krupnick, Alexander S

    2012-09-01

    Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide and results from a complex interaction between carcinogen exposure and inherent susceptibility. Despite its prevalence, genetic factors that predispose to the development of lung cancer remain elusive. Inbred mouse models offer a unique and clinically relevant tool to study genetic factors that contribute to lung carcinogenesis due to the development of tumors that resemble human adenocarcinoma and broad strain-specific variation in cancer incidence after carcinogen administration. Here, we set out to investigate whether strain-specific variability in tumor immunosurveillance contributes to differences in lung cancer. Using bone marrow transplantation, we determined that hematopoietic cells from lung cancer-resistant mice could significantly impede the development of cancer in a susceptible strain. Furthermore, we show that this is not due to differences in tumor-promoting inflammatory changes or variability in immunosurveillance by the adaptive immune system but results from strain-specific differences in natural killer (NK) cell cytotoxicity. Using a newly discovered congenic strain of mice, we show a previously unrecognized role for strain-specific polymorphisms in the natural killer gene complex (NKC) in immunosurveillance for carcinogen-induced lung cancer. Because polymorphisms in the NKC are highly prevalent in man, our data may explain why certain individuals without obvious risk factors develop lung cancer whereas others remain resistant to the disease despite heavy environmental carcinogen exposure. ©2012 AACR.

  10. 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.

  11. Copy-number variation of housekeeping gene rpl13a in rat strains selected for nervous system excitability.

    PubMed

    Kalendar, Ruslan; Belyayev, Alexander; Zachepilo, Tatiana; Vaido, Alexander; Maidanyuk, Dmitry; Schulman, Alan H; Dyuzhikova, Natalia

    2017-06-01

    We evaluated copy number variation (CNV) for four genes in rat strains differing in nervous system excitability. rpl13a copy number is significantly reduced in hippocampus and bone marrow in rats with a high excitability threshold and stress. The observed phenomenon may be associated with a role for rpl13a in lipid metabolism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse.

    PubMed

    Hartmann, Stefanie; Hasenkamp, Natascha; Mayer, Jens; Michaux, Johan; Morand, Serge; Mazzoni, Camila J; Roca, Alfred L; Greenwood, Alex D

    2015-08-18

    Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.

  13. Experimental Investigations on Anisotropic Evolution of 304 Stainless Sheets under Tensile Pre-Strains

    NASA Astrophysics Data System (ADS)

    Teng, Lai; Guo, Cheng

    2011-08-01

    The anisotropic evolution of cold rolled 304 stainless steel sheets under pre-strains is investigated experimentally. Uni-axial tensile yield stress and r-value are measured in experiments to represent the anisotropy. The tensile pre-strains under plane stress are achieved by cutting large specimens into small one at different angles to rolling direction. Then the uni-axial tensile tests are performed on the small specimens to investigate the anisotropic evolution. It is found that the yield stress increases with the increase of the pre-strains and decreases with the increase of the angles. However, the changes of r-value are hardly affected by the pre-strains, the small changes of r-value show that the material may remember the rolling direction even after the pre-strains. The sigmoidal shape can be observed in the tensile curves, and its shape depends on the pre-strains and angles. The change of hardening rate can be divided into three stages, and is the most significant at 90° to the rolling direction in the three stages, at the same time the pre-strains cause noncoincidence of the hardening rate curves at the same angle. Moreover, the hardening rate depends on the directions of tensile loading. Second derivative of the hardening rate also can be divided into three stages, and the differences of three stages may mainly be controlled by the different volume fraction of martensite.

  14. [Isolation and characterization of wild Sporothrix schenkii strains and investigation of sporototrichin reactors].

    PubMed

    Sánchez-Alemán, Miguel Angel; Araiza, Javier; Bonifaz, Alexandro

    2004-01-01

    We conducted a study in the southern mountains of the Mexican State of Oaxaca that consisted of isolation of wild Sporothrix schenckii strains obtained from soil samples and investigation of positive reactors to skin test reaction with sprotrichin antigen. The study was conducted by means of recollection of soil samples and processing of these with dilution methods and fungal isolation in ordinary culture media Sabouraud simple Agar with and without antibiotics (SS, SA). Suspected strains underwent dimorphism, melanin formation, and virulence confirmation tests. Investigation of positive reactors to sporotrichin Y (yeast) was also conducted. Three supposed strains were identified due to their reproductive characteristics, melanin production, and virulence. In the community, 144 individuals were studied, of whom 6.25% were positive to sporotichin. Isolation of virulent strains of Sporothrix schenkii from nature (soil) and primoinfection of a percentage of the studied population were confirmed.

  15. Investigation of osteogenic activity of primary rabbit periosteal cells stimulated by multi-axial tensile strain.

    PubMed

    Chiu, Chih-Hao; Liu, Jun-Liang; Chang, Chih-Hsuan; Lei, Kin Fong; Chen, Alvin Chao-Yu

    2017-03-01

    Periosteum-derived cells was indicated to respond to mechanical force and have stem cell potential capable of differentiating into multiple tissue. Investigation of osteogenic activity under mechanical stimulation is important to understand the therapeutic conditions of fracture healing. In this work, a cell culture platform was developed for respectively providing isotropic and anisotropic axial strain. Primary rabbit periosteal cells were isolated and cultured in the chamber. Multi-axial tensile strain was received and osteogenic activity was investigated by mRNA expressions of CBFA1 and OPN. The highest mRNA expression was found in moderate strain (5-8%) under anisotropic axial strain. These results provided important foundation for further in vivo studies and development of tailor-made stretching rehabilitation equipment.

  16. Strain variation in the ?100? growth sectors of potash alum single crystals and its relationship to growth rate dispersion

    NASA Astrophysics Data System (ADS)

    Ristić, R. I.; Sherwood, J. N.; Shripathi, T.

    1990-04-01

    X-ray topographic studies of growth sector geometry in {110} sections of large potash alum crystals confirm the occurrence of growth rate dispersion of the {100} growth fronts. Contrary to previous speculations that this variation arises as a consequence of the refraction of screw dislocations in and out of these sectors we show that the dispersion occurs even in the absence of this effect and despite the presence of continuously propagating edge dislocations in the sectors. Strain mapping using double crystal diffractometry yields a strong correlation between increase of lattice strain along the sector and cessation of growth. This leads to the speculation that the potential cause of the growth rate dispersion is the absorption of undetectable amounts of impurities at the growth interface to generate the observed strain which in turn influences the growth rate (or vice versa). This speculation is in agreement with other observations of the influence of lattice strain on crystal growth.

  17. Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates of Saccharomyces cerevisiae sake strains.

    PubMed

    Oba, Takahiro; Kusumoto, Kenichi; Kichise, Yuki; Izumoto, Eiji; Nakayama, Shunichi; Tashiro, Kosuke; Kuhara, Satoru; Kitagaki, Hiroshi

    2014-08-01

    Research on the relationship between mitochondrial membrane potential and fermentation profile is being intensely pursued because of the potential for developing advanced fermentation technologies. In the present study, we isolated naturally occurring strains of yeast from sake mash that produce high levels of malic acid and demonstrate that variations in mitochondrial membrane potential correlate with malic acid production. To define the underlying biochemical mechanism, we determined the activities of enzymes required for malic acid synthesis and found that pyruvate carboxylase and malate dehydrogenase activities in strains that produce high levels of malic acid were elevated compared with the standard sake strain K901. These results inspired us to hypothesize that decreased mitochondrial membrane potential was responsible for increased malic acid synthesis, and we present data supporting this hypothesis. Thus, the mitochondrial membrane potential of high malic acid producers was lower compared with standard strains. We conclude that mitochondrial membrane potential correlates with malic acid production.

  18. [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.

  19. Genotypic Variation and Stability of Four Variable-Number Tandem Repeats and Their Suitability for Discriminating Strains of Mycobacterium leprae

    PubMed Central

    Truman, Richard; Fontes, Amanda B.; de Miranda, Antonio B.; Suffys, Philip; Gillis, Thomas

    2004-01-01

    It has not been possible to distinguish different strains of Mycobacterium leprae according to their genetic sequence. However, the genome contains several variable-number tandem repeats (VNTR), which have been used effectively in strain typing of other bacteria. To determine their suitability for differentiating M. leprae, we developed PCR systems to amplify 5 different VNTR loci and examined a battery of 12 M. leprae strains derived from patients in different regions of the United States, Brazil, Mexico, and the Philippines, as well as from wild armadillos and a sooty mangabey monkey. We found diversity at four VNTR (D = 0.74), but one system (C16G8) failed to yield reproducible results. Alleles for the GAA VNTR varied in length from 10 to 16 copies, those for AT17 varied in length from 10 to 15 copies, those for GTA varied in length from 9 to 12 copies, and those for TA18 varied in length from 13 to 20 copies. Relatively little variation was seen with interspecies transfer of bacilli or during short-term passage of strains in nude mice or armadillos. The TA18 locus was more polymorphic than other VNTR, and genotypic variation was more common after long-term expansion in armadillos. Most strain genotypes remained fairly stable in passage, but strain Thai-53 showed remarkable variability. Statistical cluster analysis segregated strains and passage samples appropriately but did not reveal any particular genotype associable with different regions or hosts of origin. VNTR polymorphisms can be used effectively to discriminate M. leprae strains. Inclusion of additional loci and other elements will likely lead to a robust typing system that can be used in community-based epidemiological studies and select clinical applications. PMID:15184434

  20. Investigation of molecular penetration depth variation with SMBI fluxes

    NASA Astrophysics Data System (ADS)

    Zhou, Yu-Lin; Wang, Zhan-Hui; Xu, Min; Wang, Qi; Nie, Lin; Feng, Hao; Sun, Wei-Guo

    2016-09-01

    We study the molecular penetration depth variation with the SMBI fluxes. The molecular transport process and the penetration depth during SMBI with various injection velocities and densities are simulated and compared. It is found that the penetration depth of molecules strongly depends on the radial convective transport of SMBI and it increases with the increase of the injection velocity. The penetration depth does not vary much once the SMBI injection density is larger than a critical value due to the dramatic increase of the dissociation rate on the fueling path. An effective way to improve the SMBI penetration depth has been predicted, which is SMBI with a large radial injection velocity and a lower molecule injection density than the critical density. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375053, 11575055, 11405022, and 11405112), the Chinese National Fusion Project for ITER (Grant Nos. 2013GB107001 and 2013GB112005), the International S&T Cooperation Program of China (Grant No. 2015DFA61760), and the Funds of the Youth Innovation Team of Science and Technology in Sichuan Province of China (Grant No. 2014TD0023).

  1. First-principles investigation of strain effects on the stacking fault energies, dislocation core structure, and Peierls stress of magnesium and its alloys

    NASA Astrophysics Data System (ADS)

    Zhang, S. H.; Beyerlein, I. J.; Legut, D.; Fu, Z. H.; Zhang, Z.; Shang, S. L.; Liu, Z. K.; Germann, T. C.; Zhang, R. F.

    2017-06-01

    Taking pure Mg, Mg-Al, and Mg-Zn as prototypes, the effects of strain on the stacking fault energies (SFEs), dislocation core structure, and Peierls stress were systematically investigated by means of density functional theory and the semidiscrete variational Peierls-Nabarro model. Our results suggest that volumetric strain may significantly influence the values of SFEs of both pure Mg and its alloys, which will eventually modify the dislocation core structure, Peierls stress, and preferred slip system, in agreement with recent experimental results. The so-called "strain factor" that was previously proposed for the solute strengthening could be justified as a major contribution to the strain effect on SFEs. Based on multivariate regression analysis, we proposed universal exponential relationships between the dislocation core structure, the Peierls stress, and the stable or unstable SFEs. Electronic structure calculations suggest that the variations of these critical parameters controlling strength and ductility under strain can be attributed to the strain-induced electronic polarization and redistribution of valence charge density at hollow sites. These findings provide a fundamental basis for tuning the strain effect to design novel Mg alloys with both high strength and ductility.

  2. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-08

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  3. Infection of Tribolium beetles with a tapeworm: variation in susceptibility within and between beetle species and among genetic strains.

    PubMed

    Yan, G; Norman, S

    1995-02-01

    Host susceptibility and resistance to parasites are often hypothesized to be genetically variable traits. We tested 2 species of Tribolium flour beetles for among-strain variation in susceptibility to the rat tapeworm Hymenolepis diminuta. Twelve genetic strains of Tribolium confusum and 11 strains of Tribolium castaneum were examined. We found T. castaneum was more susceptible to the tapeworm than T. confusum. There was significant among-strain and between-sex variation for both beetle species in infection intensity and prevalence. Among-vial variation was marginally significant. These results add to evidence that host susceptibility to a parasite is a genetically variable trait. We view these results as important findings for understanding natural selection on host-parasite interactions. Traits that are genetically variable can respond to natural selection. Thus, if a beetle's susceptibility to the tapeworm is correlated with fitness and heritable, susceptibility can evolve. Susceptibility is likely to be pleiotropic and have important consequences on issues ranging from parasite transmission to host species interactions and community structure.

  4. Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries.

    PubMed

    Cui, Yujun; Yang, Xianwei; Xiao, Xiao; Anisimov, Andrey P; Li, Dongfang; Yan, Yanfeng; Zhou, Dongsheng; Rajerison, Minoarisoa; Carniel, Elisabeth; Achtman, Mark; Yang, Ruifu; Song, Yajun

    2014-08-01

    Plague, one of the most devastating infectious diseases in human history, is caused by the bacterial species Yersinia pestis. A live attenuated Y. pestis strain (EV76) has been widely used as a plague vaccine in various countries around the world. Here we compared the whole genome sequence of an EV76 strain used in China (EV76-CN) with the genomes of Y. pestis wild isolates to identify genetic variations specific to the EV76 lineage. We identified 6 SNPs and 6 Indels (insertions and deletions) differentiating EV76-CN from its counterparts. Then, we screened these polymorphic sites in 28 other strains of EV76 lineage that were stored in different countries. Based on the profiles of SNPs and Indels, we reconstructed the parsimonious dissemination history of EV76 lineage. This analysis revealed that there have been at least three independent imports of EV76 strains into China. Additionally, we observed that the pyrE gene is a mutation hotspot in EV76 lineages. The fine comparison results based on whole genome sequence in this study provide better understanding of the effects of laboratory passages on the accumulation of genetic polymorphisms in plague vaccine strains. These variations identified here will also be helpful in discriminating different EV76 derivatives. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Investigations on fracture curves in strain and stress space for advanced high strength steel forming

    NASA Astrophysics Data System (ADS)

    Panich, S.; Drotleff, K.; Liewald, M.; Uthaisangsuk, V.

    2016-08-01

    Conventional forming limit curves (FLCs) are inappropriate for describing formability for advanced high strength (AHS) steel sheets, since such steel grades experience fracture without localized necking occurrence. The aim of this work was to develop a fracture curve (FC) for the AHS steel grade DP980. The FC was determined by means of the Nakajima stretch forming test and tensile tests of various sample geometries, by which shear fracture governed. An optical strain measurement system was used to capture strain histories of deformed samples up to failure. From these results, fracture strains were gathered and plotted in a strain space. Subsequently, the strain based curve was transformed to space between stress triaxiality and plastic strain. Hereby, effects of anisotropic yield function, namely, the Hill’48 model on obtained stress fracture loci were investigated. In order to verify applicability of the determined limit curves, a Mini-tunnel part was pressed and simulated. It was found that the stress based FC do predict failure of the DP980 steel sheet more accurately than the strain based F C.

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

    PubMed

    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.

  7. Structural investigation of lipopolysaccharides from nontypeable Haemophilus influenzae: investigation of inner-core phosphoethanolamine addition in NTHi strain 981.

    PubMed

    Tinnert, Ann-Sofie; Månsson, Martin; Yildirim, Håkan H; Hood, Derek W; Schweda, Elke K H

    2005-08-15

    LPS of NTHi comprises a conserved tri-l-glycero-D-manno-heptosyl inner-core moiety (l-alpha-D-Hepp-(1-->2)-[PEtn-->6]-l-alpha-D-Hepp-(1-->3)-[beta-D-Glcp-(1-->4)]-l-alpha-D-Hepp-(1-->5)-alpha-Kdop) in which addition of PEtn to the central heptose (HepII) in strain Rd is controlled by the gene lpt6. It was recently shown that NTHi strain 981 contains an additional PEtn linked to O-3 of the terminal heptose of the inner-core moiety (HepIII). In order to establish whether lpt6 is also involved in adding PEtn to HepIII, lpt6 in strain 981 was inactivated. The structure of the LPS of the resulting mutant strain 98llpt6 was investigated by MS and NMR techniques by which it was confirmed that the lpt6 gene product is responsible for addition of PEtn to O-6 of HepII in strain 981. However, it is not responsible for adding PEtn to O-3 of HepIII since the 981lpt6 mutant still had full substitution with PEtn at HepIII.

  8. Investigation of Staphylococcus strains with heterogeneous resistance to glycopeptides in a Turkish university hospital

    PubMed Central

    Nakipoglu, Yasar; Derbentli, Sengul; Cagatay, Atahan A; Katranci, Handan

    2005-01-01

    Background The hetero-glycopeptide intermediate staphylococci is considered to be the precursor of glycopeptide intermediate staphylococci especially vancomycin intermediate Staphylococcus aureus (VISA). For this purpose, we aimed to investigate the heterogeneous resistance to glycopeptide and their frequencies in 135 Staphylococcus strains. Methods Heterogeneous resistance of Staphylococcus strains was detected by inoculating the strains onto Brain Heart Infusion agar supplemented with 4 mg/L of vancomycin (BHA-V4). Agar dilution method was used for determining MICs of glycopeptides and population analysis profile was performed for detecting frequency of heterogeneous resistance for the parents of selected strains on BHA-4. Results Eight (6%) out of 135 Staphylococcus strains were exhibited heterogeneous resistance to at least one glycopeptide. One (1.2%) out of 81 S. aureus was found intermediate resistance to teicoplanin (MIC 16 mg/L). Other seven strains were Staphylococcus haemolyticus (13%) out of 54 coagulase negative staphylococci (CoNS). Six of the seven strains were detected heterogeneously reducing susceptibility to vancomycin (MICs ranged between 5–8 mg/L) and teicoplanin (MICs ranged between 32–64 mg/L), and one S. haemolyticus was found heterogeneous resistance to teicoplanin (MIC 32 mg/L). Frequencies of heterogeneous resistance were measured being one in 106 – 107 cfu/ml. MICs of vancomycin and teicoplanin for hetero-staphylococci were determined as 2–6 folds and 3–16 folds higher than their parents, respectively. These strains were isolated from six patients (7%) and two (4%) of health care wokers hands. Hetero-VISA strain was not detected. Conclusion Heterogeneous resistance to glycopeptide in CoNS strains was observed to be significantly more emergent than those of S. aureus strains (vancomycin P 0.001, teicoplanin, P 0.007). The increase MICs of glycopeptide resistance for subpopulations of staphylococci comparing with their parents

  9. Reduction of influence of variation in center frequencies of RF echoes on estimation of artery-wall strain.

    PubMed

    Hasegawa, Hideyuki; Kanai, Hiroshi

    2008-09-01

    Atherosclerotic change of the arterial wall leads to a significant change in its elasticity. For assessment of elasticity, measurement of arterial wall deformation is required. For motion estimation, correlation techniques are widely used, and we have developed a phase-sensitive correlation method, namely, the phased-tracking method, to measure the regional strain of the arterial wall due to the heartbeat. Although phase-sensitive methods using demodulated complex signals require less computation in comparison with methods using the correlation between RF signals or iterative methods, the displacement estimated by such phase-sensitive methods are biased when the center frequency of the RF echo apparently varies. One of the reasons for the apparent change in the center frequency would be the interference of echoes from scatterers within the wall. In the present study, a method was introduced to reduce the influence of variation in the center frequencies of RF echoes on the estimation of the artery-wall strain when using the phase-sensitive correlation technique. The improvement in the strain estimation by the proposed method was validated using a phantom. The error from the theoretical strain profile and the standard deviation in strain estimated by the proposed method were 12.0% and 14.1%, respectively, significantly smaller than those (23.7% and 46.2%) obtained by the conventional phase-sensitive correlation method. Furthermore, in the preliminary in vitro experimental results, the strain distribution of the arterial wall well corresponded with pathology, i.e., the region with calcified tissue showed very small strain, and the region almost homogeneously composed of smooth muscle and collagen showed relatively larger strain and clear strain decay with respect to the radial distance from the lumen.

  10. Estimation of Staphylococcus aureus growth parameters from turbidity data: characterization of strain variation and comparison of methods.

    PubMed

    Lindqvist, R

    2006-07-01

    Turbidity methods offer possibilities for generating data required for addressing microorganism variability in risk modeling given that the results of these methods correspond to those of viable count methods. The objectives of this study were to identify the best approach for determining growth parameters based on turbidity data and use of a Bioscreen instrument and to characterize variability in growth parameters of 34 Staphylococcus aureus strains of different biotypes isolated from broiler carcasses. Growth parameters were estimated by fitting primary growth models to turbidity growth curves or to detection times of serially diluted cultures either directly or by using an analysis of variance (ANOVA) approach. The maximum specific growth rates in chicken broth at 17 degrees C estimated by time to detection methods were in good agreement with viable count estimates, whereas growth models (exponential and Richards) underestimated growth rates. Time to detection methods were selected for strain characterization. The variation of growth parameters among strains was best described by either the logistic or lognormal distribution, but definitive conclusions require a larger data set. The distribution of the physiological state parameter ranged from 0.01 to 0.92 and was not significantly different from a normal distribution. Strain variability was important, and the coefficient of variation of growth parameters was up to six times larger among strains than within strains. It is suggested to apply a time to detection (ANOVA) approach using turbidity measurements for convenient and accurate estimation of growth parameters. The results emphasize the need to consider implications of strain variability for predictive modeling and risk assessment.

  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. Seasonal variations in bacterial communities and antibiotic-resistant strains associated with green bottle flies (Diptera: Calliphoridae).

    PubMed

    Wei, Ting; Ishida, Ryuichi; Miyanaga, Kazuhiko; Tanji, Yasunori

    2014-05-01

    Green bottle flies occur frequently around human environments in Japan. Many species of green bottle flies have been studied with regard to their importance in forensic examinations or clinical therapies, but the bacterial communities associated with this group of flies have not been comprehensively investigated. In this research, 454 pyrosequencing was used to reveal the bacterial communities in green bottle flies collected in different seasons. Meanwhile, the bacteria were screened with selective media and tested for antibiotic susceptibility. Samples collected in three different seasons harbored distinctive bacterial communities. The predominant genera associated with green bottles flies were Staphylococcus in spring, Ignatzschineria in summer, and Vagococcus, Dysgonomonas, and an unclassified Acetobacteraceae in autumn. An upward trend in bacterial community diversity was observed from spring to autumn. Changes in climatic conditions could be the cause of these seasonal variations in fly-associated bacterial communities. The species of isolated antibiotic-resistant bacteria also differed across seasons, but it was difficult to correlate seasonal changes in antibiotic-resistant bacteria with changes in whole communities. A number of multiple-antibiotic-resistant bacteria were isolated, and some of these strains were closely affiliated with pathogens such as Enterococcus faecalis and Enterococcus faecium, which could cause serious threats to public health. Overall, this research provided us with information about the composition and seasonality of bacterial communities in green bottle flies, and highlighted the risks of fly-mediated dissemination of antibiotic-resistant pathogens.

  13. Resiliency to social defeat stress relates to the inter-strain social interaction and is influenced by season variation.

    PubMed

    Han, Qiuqin; Yang, Liu; Liu, Yan; Lv, Ning; Yu, Jin; Wu, Gencheng; Zhang, Yuqiu

    2014-02-21

    Exposure to social defeat (SD) stress exerts social avoidance and depressive disorders. Little is known about the relationship between resiliency to stressors and the inter-strain social interaction (SI) level. We hypothesized that SD resiliency is correlated with a high SI between the same strain. C57BL/6J mice experienced a 10-day period of SD stress by repeated CD-1 mice offensive. The susceptible mice exhibited significant social-avoidance behaviors with less time in interaction-zone (IZ) and lower social interaction ratio (SIR) toward the Target (CD-1 mice), while resilient ones exhibited similar social interaction to control mice. When the Target was C57BL/6J mouse, either susceptible or resilient mice spent more time in IZ and the inter-strain SI in the resilient group was significantly higher than the susceptible. Correlation analysis revealed a significantly non-zero slope of the linear relationship between SIRs toward two strains. But different groups had a similar baseline of the inter-strain SI before stress, indicating a SD-induced defect in both types of SI. In addition, in four different seasons, animals exhibited a significant resiliency to the stress in summer. These data suggest that SD resiliency is related to a higher SI toward the same-strain, and may be regulated by seasonal variations.

  14. 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.

  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. 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.

  17. 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

  18. Chlorine inactivation of Salmonella Kentucky isolated from chicken carcasses: evaluation of strain variation.

    PubMed

    Mohamed, T M; Parveen, S; Ludwig, J B; Oscar, T P

    2015-02-01

    The current study was undertaken to evaluate chlorine resistance among strains of Salmonella Kentucky isolated from chicken carcasses. Selected strains (n = 8) were exposed to 30 ppm of chlorine in 10% buffered peptone water (pH 7.4) for 0 to 10 min at 4°C and 150 rpm. The initial level (mean ± SD) of Salmonella Kentucky was 6.18 ± 0.09 log CFU/ml and did not differ (P > 0.05) among strains. A two-way analysis of variance indicated that the level of Salmonella Kentucky in chlorinated water was affected (P < 0.05) by a time by strain interaction. Differences among strains increased as a function of chlorine exposure time. After 10 min of chlorine exposure, the most resistant strain (SK145) was 5.63 ± 0.54 log CFU/ml, whereas the least resistant strain (SK275) was 3.07 ± 0.29 log CFU/ml. Significant differences in chlorine resistance were observed for most strain comparisons. Death of Salmonella Kentucky was nonlinear over time and fitted well to a power law model with a shape parameter of 0.34 (concave upward). Time (minutes) for a 1-log reduction of Salmonella Kentucky differed (P < 0.05) among strains: >10 min for SK145, 6.0 min for SK254, 1.5 min for SK179, and 0.3 to 0.65 min for other strains. Results of this study indicate that strain is an important variable to include in models that predict changes in levels of Salmonella Kentucky in chlorinated water.

  19. The Epstein-Barr virus EBNA-2 gene in oral hairy leukoplakia: strain variation, genetic recombination, and transcriptional expression.

    PubMed Central

    Walling, D M; Perkins, A G; Webster-Cyriaque, J; Resnick, L; Raab-Traub, N

    1994-01-01

    Oral hairy leukoplakia (HLP) lesions frequently contain defective Epstein-Barr virus (EBV) genomes with deletions in the EBNA-2 gene that abundantly replicate and persist within the lesion. To characterize these viral strains and recombinant variants, the EBNA-2 gene in EBV DNA from several different HLP biopsy specimens was analyzed. Amplification of EBNA-2 coding sequences by PCR demonstrated the presence in HLP of intact EBNA-2 genes as well as a variety of internally deleted variants of both EBNA-2A and EBNA-2B. Some of the deletion variants evolved within the HLP lesion from intact EBNA-2 genes, while other variants appeared to be transmissible strains that directly infected the lesion. Intrastrain recombination within the HLP lesion also generated variation within the EBNA-2 polyproline region. Cloning and sequencing of HLP cDNA demonstrated transcription from the internally deleted EBNA-2 open reading frame, indicating that these variant genes are expressed in HLP. Comparative analysis of the HLP EBNA-2 sequences confirmed previous findings of EBV coinfection with multiple types and strains. Sequence variation of these wild-type genes demonstrated that EBNA-2A sequences distinguish at least two separate strains and a variety of substrains of EBV type 1. Two of the HLP EBNA-2A sequences contained amino acid changes in a cytotoxic T-cell epitope within an otherwise highly conserved region of the gene. These data indicate that EBV coinfection, strain variation, and recombination within the EBNA-2 gene are common features of HLP and suggest that the expression of internally deleted EBNA-2 variants could contribute to EBV pathogenesis in permissive infection. Images PMID:7966582

  20. Genetic diversity and host range variation of Ralstonia solanacearum strains entering North America.

    PubMed

    Norman, David J; Zapata, Mildred; Gabriel, Dean W; Duan, Y P; Yuen, Jeanne M F; Mangravita-Novo, Arianna; Donahoo, Ryan S

    2009-09-01

    Each year, large volumes of ornamental and food plant propagative stock are imported into the North America; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 107 new R. solanacearum strains were collected over a 10-year period from imported propagative stock and compared with 32 previously characterized R. solanacearum strains using repetitive polymerase chain reaction (rep-PCR) element (BOX, ERIC, and REP) primers. Additional strain comparisons were made by sequencing the endoglucanase and the cytochrome b561 genes. Using rep-PCR primers, populations could be distinguished by biovar and, to a limited extent, country of origin and original host. Similarity coefficients among rep-PCR clusters within biovars were relatively low in many cases, indicating that disease outbreaks over time may have been caused by different clonal populations. Similar population differentiations of R. solanacearum were obtained when comparing strain sequences using either the endoglucanase or cytochrome b561 genes. We found that most of the new biovar 1 strains of R. solanacearum entering the United States were genetically distinct from the biovar 1 strains currently found infecting vegetable production. These introduced biovar 1 strains also had a broader host range and could infect not only tomato, tobacco, and potato but also anthurium and pothos and cause symptoms on banana. All introductions into North America of race 3, biovar 2 strains in the last few years have been linked to geranium production and appeared to be clonal.

  1. Strain-induced optical band gap variation of SnO2 films

    DOE PAGES

    Rus, Stefania Florina; Ward, Thomas Zac; Herklotz, Andreas

    2016-06-29

    In this paper, thickness dependent strain relaxation effects are utilized to study the impact of crystal anisotropy on the optical band gap of epitaxial SnO2 films grown by pulsed laser deposition on (0001)-oriented sapphire substrates. An X-ray diffraction analysis reveals that all films are under tensile biaxial in-plane strain and that strain relaxation occurs with increasing thickness. Variable angle spectroscopic ellipsometry shows that the optical band gap of the SnO2 films continuously increases with increasing film thickness. This increase in the band gap is linearly related to the strain state of the films, which indicates that the main origin ofmore » the band gap change is strain relaxation. The experimental observation is in excellent agreement with results from density functional theory for biaxial in-plane strain. Our research demonstrates that strain is an effective way to tune the band gap of SnO2 films and suggests that strain engineering is an appealing route to tailor the optical properties of oxide semiconductors.« less

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

    USDA-ARS?s Scientific Manuscript database

    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,...

  3. Strain-induced optical band gap variation of SnO2 films

    SciTech Connect

    Rus, Stefania Florina; Ward, Thomas Zac; Herklotz, Andreas

    2016-06-29

    In this paper, thickness dependent strain relaxation effects are utilized to study the impact of crystal anisotropy on the optical band gap of epitaxial SnO2 films grown by pulsed laser deposition on (0001)-oriented sapphire substrates. An X-ray diffraction analysis reveals that all films are under tensile biaxial in-plane strain and that strain relaxation occurs with increasing thickness. Variable angle spectroscopic ellipsometry shows that the optical band gap of the SnO2 films continuously increases with increasing film thickness. This increase in the band gap is linearly related to the strain state of the films, which indicates that the main origin of the band gap change is strain relaxation. The experimental observation is in excellent agreement with results from density functional theory for biaxial in-plane strain. Our research demonstrates that strain is an effective way to tune the band gap of SnO2 films and suggests that strain engineering is an appealing route to tailor the optical properties of oxide semiconductors.

  4. Strain-induced optical band gap variation of SnO2 films

    SciTech Connect

    Rus, Stefania Florina; Ward, Thomas Zac; Herklotz, Andreas

    2016-06-29

    In this paper, thickness dependent strain relaxation effects are utilized to study the impact of crystal anisotropy on the optical band gap of epitaxial SnO2 films grown by pulsed laser deposition on (0001)-oriented sapphire substrates. An X-ray diffraction analysis reveals that all films are under tensile biaxial in-plane strain and that strain relaxation occurs with increasing thickness. Variable angle spectroscopic ellipsometry shows that the optical band gap of the SnO2 films continuously increases with increasing film thickness. This increase in the band gap is linearly related to the strain state of the films, which indicates that the main origin of the band gap change is strain relaxation. The experimental observation is in excellent agreement with results from density functional theory for biaxial in-plane strain. Our research demonstrates that strain is an effective way to tune the band gap of SnO2 films and suggests that strain engineering is an appealing route to tailor the optical properties of oxide semiconductors.

  5. Variations in Virulence and Molecular Biology among Emerging Strains of Clostridium difficile

    PubMed Central

    Hunt, Jonathan J.

    2013-01-01

    SUMMARY Clostridium difficile is a Gram-positive, spore-forming organism which infects and colonizes the large intestine, produces potent toxins, triggers inflammation, and causes significant systemic complications. Treating C. difficile infection (CDI) has always been difficult, because the disease is both caused and resolved by antibiotic treatment. For three and a half decades, C. difficile has presented a treatment challenge to clinicians, and the situation took a turn for the worse about 10 years ago. An increase in epidemic outbreaks related to CDI was first noticed around 2003, and these outbreaks correlated with a sudden increase in the mortality rate of this illness. Further studies discovered that these changes in CDI epidemiology were associated with the rapid emergence of hypervirulent strains of C. difficile, now collectively referred to as NAP1/BI/027 strains. The discovery of new epidemic strains of C. difficile has provided a unique opportunity for retrospective and prospective studies that have sought to understand how these strains have essentially replaced more historical strains as a major cause of CDI. Moreover, detailed studies on the pathogenesis of NAP1/BI/027 strains are leading to new hypotheses on how this emerging strain causes severe disease and is more commonly associated with epidemics. In this review, we provide an overview of CDI, discuss critical mechanisms of C. difficile virulence, and explain how differences in virulence-associated factors between historical and newly emerging strains might explain the hypervirulence exhibited by this pathogen during the past decade. PMID:24296572

  6. A new look at the drug-resistance investigation of uropathogenic E. coli strains.

    PubMed

    Adamus-Białek, Wioletta; Lechowicz, Łukasz; Kubiak-Szeligowska, Anna B; Wawszczak, Monika; Kamińska, Ewelina; Chrapek, Magdalena

    2017-02-01

    Bacterial drug resistance and uropathogenic tract infections are among the most important issues of current medicine. Uropathogenic Escherichia coli strains are the primary factor of this issue. This article is the continuation of the previous study, where we used Kohonen relations to predict the direction of drug resistance. The characterized collection of uropathogenic E. coli strains was used for microbiological (the disc diffusion method for antimicrobial susceptibility testing), chemical (ATR/FT-IR) and mathematical (artificial neural networks, Ward's hierarchical clustering method, the analysis of distributions of inhibition zone diameters for antibiotics, Cohen's kappa measure of agreement) analysis. This study presents other potential tools for the epidemiological differentiation of E. coli strains. It is noteworthy that ATR/FT-IR technique has turned out to be useful for the quick and simple identification of MDR strains. Also, diameter zones of resistance of this E. coli population were compared to the population of E. coli strains published by EUCAST. We observed the bacterial behaviors toward particular antibiotics in comparison to EUCAST bacterial collections. Additionally, we used Cohen's kappa to show which antibiotics from the same class are closely related to each other and which are not. The presented associations between antibiotics may be helpful in selecting the proper therapy directions. Here we present an adaptation of interdisciplinary studies of drug resistance of E. coli strains for epidemiological and clinical investigations. The obtained results may be some indication in deciding on antibiotic therapy.

  7. Strain relaxation of metastable SiGe/Si: Investigation with two complementary X-ray techniques

    SciTech Connect

    Kasper, E.; Werner, J.; Oehme, M.; Lyutovich, K.; Burle, N.; Escoubas, S.

    2012-03-15

    Metastable and strain relaxed SiGe layers with about 20% Ge content have been grown by molecular beam epitaxy on Si substrates at 550 deg. C. The thickness regime of metastability and the onset of strain relaxation were investigated on dust particle free surfaces obtained by careful chemical cleaning and epitaxy loading under clean room conditions. Compared to earlier results true metastable regime without misfit dislocations was obtained up to 140 nm thickness. The onset of strain relaxation started with heterogeneous nucleation sites of misfit dislocations. X-ray topography proved to be a unique monitoring tool to observe a low density of single dislocations. From these results we suggested to define a critical thickness band with lower bound t{sub cl} from dislocation nucleation to an upper bound t{sub co} (600 nm in our case) defined by the onset of considerable strain relaxation. The strain relief was measured by X-ray diffraction (reciprocal space mapping) and found to be very abrupt (76% strain relaxation at 800 nm thickness).

  8. 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.

  9. Numerical and experimental investigation of FBG strain response at cryogenic temperatures

    NASA Astrophysics Data System (ADS)

    Venkatesan, V. N.; Ramalingam, R.

    2017-02-01

    Strain response of FBG sensors are investigated at various temperatures from 298 K to 4.2 K. Numerical modelling is carried out for acrylate coated, substrate-free fiber Bragg grating (FBG) sensors at room temperature of 298 K and cryogenic temperatures of 77 K, 10 K and 4.2 K. A 1550 nm Bragg wavelength (λB) FBG sensor is modelled and simulated for applied strain (ε) ranging from 0 to 800 µm/m. The Bragg wavelength shifts (ΔλB) thus obtained are compared with the experimentally investigated values obtained by subjecting the FBG sensor to axial strain, with its sensing part not being bonded to any surface. The MTS25 tensile machine with a cryostat under vacuum conditions (10-4 mbar pressure) is used for the experiments and the required temperatures are maintained using liquid Nitrogen (LN2) and compressed Helium gas (He). The Bragg wavelength shift (ΔλB) versus induced strain (ε) is regressed with a linear polynomial function and the strain sensitivity obtained in both the cases are discussed.

  10. Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus.

    PubMed

    Lindsay, Jodi A; Holden, Matthew T G

    2006-07-01

    The bacterium Staphylococcus aureus is a common cause of human infection, and it is becoming increasingly virulent and resistant to antibiotics. Our understanding of the evolution of this species has been greatly enhanced by the recent sequencing of the genomes of seven strains of S. aureus. Comparative genomic analysis allows us to identify variation in the chromosomes and understand the mechanisms by which this versatile bacterium has accumulated diversity within its genome structure.

  11. Models of strain variation in nappes and thrust sheets: A review

    NASA Astrophysics Data System (ADS)

    Sanderson, David J.

    1982-10-01

    Strain within nappes and thrust sheets can be modelled using simple boundary conditions. An original rectangular prism of material resting on a thrust plane is considered to be subject to various pure and simple shear components operating parallel to the thrust. Deformation gradient tensors are determined for the models and solutions found for the principal strains. A two-dimensional model considers heterogeneous simple shear combined with a stretch (α) in the direction of shear. Simple shear zones arise as a special case where α = 1. Recumbent fold nappes, characteristic of gravitational collapse, can be modelled with α > 1, and thrust sheets with layer parallel shortening and folding with α < 1. Differential transport of nappes gives rise to additional wrench-type shears. Solutions for the principal strains in this type of model are found and used to interpret side-wall ramps and steep zones parallel to nappe movements. By including a stretch in the transport direction these differential transport models produce prolate strains ( α > 1) and oblate strains ( α < 1). Finally a brief consideration of bending strains produced in a sheet passing over a ramp indicates reversals in the shear direction during the strain history. These predict possible crenulation of early thrust fabrics at ramps.

  12. 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.

  13. [Investigation of the virulence genes in methicillin-resistant Staphylococcus aureus strains isolated from biomaterial surfaces].

    PubMed

    Sudağidan, Mert; Cavuşoğlu, Cengiz; Bacakoğlu, Feza

    2008-01-01

    Staphylococci are the most important agents of nosocomial infections originating from biomaterials. The aim of this study was to investigate the presence of virulence genes and their phenotypic expressions in 11 methicillin-resistant Staphylococcus aureus strains isolated from the surfaces of clinically used biomaterials of 48 thorasic intensive-care unit patients. By the use of specific primers, the presence of genes encoding the attachment and biofilm production (icaA, icaC, bap), methicillin resistance (mecA), enterotoxins A-E (sea, seb, sec, sed, see), toxic shock syndrome toxin (tst), exfoliative toxins A and B (eta and etb), alpha- and beta-hemolysins (hla and hlb), staphylococcal exotoxin-like protein-1 (set1), proteases (sspA, sspB, aur, serine proteaz gene), lipase (geh) and the regulatory genes (sarA and agrCA) were investigated by polymerase chain reaction (PCR). The phenotypic properties of the isolates such as biofilm formation, antibiotic susceptibility, extracellular protease and lipase production were also evaluated. None of the isolates were found to be biofilm and/or slime producers, however, all strains were found to have icaA gene which is responsible for biofilm formation. Nevertheless the presence of icaC and bap genes that are also responsible for biofilm formation were not detected. All the strains have had mecA gene and were resistant to oxacillin, penicilin G and gentamicin, while 10 were also resistant to erythromycin and nine were also resistant to ofloxacin. The isolates were susceptible to vancomycin, teicoplanin and co-trimoxazole. Screening of toxin and regulatory genes revealed that all the strains harboured sea, set1, hla, hlb and sarA genes. The phenotypic tests for the determination of extracellular protease production revealed that all the strains formed very weak zones on skim milk and milk agar plates, and yielded negative results on casein agar plates. Furthermore, all strains were found to harbour sspA, sspB, aur and serine

  14. An outbreak of mumps with genetic strain variation in a highly vaccinated student population in Scotland.

    PubMed

    Willocks, L J; Guerendiain, D; Austin, H I; Morrison, K E; Cameron, R L; Templeton, K E; DE Lima, V R F; Ewing, R; Donovan, W; Pollock, K G J

    2017-09-14

    An outbreak of mumps within a student population in Scotland was investigated to assess the effect of previous vaccination on infection and clinical presentation, and any genotypic variation. Of the 341 cases, 79% were aged 18-24. Vaccination status was available for 278 cases of whom 84% had received at least one dose of mumps containing vaccine and 62% had received two. The complication rate was 5·3% (mainly orchitis), and 1·2% were admitted to hospital. Genetic sequencing of mumps virus isolated from cases across Scotland classified 97% of the samples as genotype G. Two distinct clusters of genotype G were identified, one circulating before the outbreak and the other thereafter, suggesting the virus that caused this outbreak was genetically different from the previously circulating virus. Whilst the poor vaccine effectiveness we found may be due to waning immunity over time, a contributing factor may be that the current mumps vaccine is less effective against some genotypes. Although the general benefits of the measles-mumps-rubella (MMR) vaccine should continue to be promoted, there may be value in reassessing the UK vaccination schedule and the current mumps component of the MMR vaccine.

  15. [Investigation on strains of Legionella pneumophila, isolated from a hospital of Milano, with three genotyping methods].

    PubMed

    Bianchi, A; Tesauro, M; Consonni, M; Galli, M G

    2009-01-01

    Various techniques have been developed in recent years for the molecular typing of microorganisms. Remains particularly difficult to isolate clinical strains for the low availability of cases and even more problematic matching clinical / environmental strains. We investigated 13 strains of Legionella pneumophila of clinical and environmental origin, isolated in 3 Health Facilities in Milan (2003-2006), using three molecular typing methods: Pulse-Field Gel Electrophoresis, Amplified Fragment Length Polymorphism and Sequence-Based Typing. PFGE and AFLP showed the correlation between a clinical case with only one of the environmental isolates taken from the places frequented by the patient, demonstrating with certainty the nosocomial origin of the case and identifying the source of infection in the shower water (Clin. 1 and Env. 1N). Two clinical samples from patients admitted to different wards presented an identical profile, which suggests that the nosocomial origin assumed an epidemic form, even without having isolated the environmental strain due to the absence of samples drawn during the period under consideration (Clin. 2 and 3). Finally, the comparison between the isolated environmental strains demonstrated a heterogeneous presence of strains, not correlated to each other although they belong to the same serum-group, having profiles that are clearly different regarding number and position of bands (Env. 2 and 4). The profile 2,10,18,10,1,1 had never been isolated and typed previously in Europe. The SBT has proved a better technique for reproducibility and interpretation of results than PFGE and AFLP To complete studies on SBT method, now considered gold standard, is currently being the EWGLI 5th Proficiency Panel, in which we are actively involved with the genotyping of five strains according to the latest version of the protocol (4.1).

  16. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

    PubMed

    Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

    2008-07-22

    Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of

  17. Effects of strain variations on aging response and corrosion properties of third generation Al-Li alloys

    NASA Astrophysics Data System (ADS)

    Wright, Ellen E.

    Due to their high specific strength (strength/density) and specific stiffness (elastic modulus/density), Al-Li alloys are attractive alloys for structural aircraft applications. To produce contoured aircraft components from Al-Li wrought products, stretch forming prior to aging is a common manufacturing technique. The effects of different amounts of tensile straining (0-9%) on the mechanical, microstructural, and corrosion properties of two third generation Al-Li alloys (2099 and 2196) were investigated. In addition to typical characterization techniques, electron backscatter diffraction (EBSD), 2D micro-digital image correlation (DIC), and scanning Kelvin probe force microscopy (SKPFM) were used to examine site-specific effects of orientation, micro-strain evolution during straining, and surface potential on corrosion, respectively. Tapping mode atomic force microscopy (AFM) was also performed to study galvanic corrosion in artificial seawater (3.5% NaCl) as it occurred in-situ. There was evidence of intergranular corrosion for 0% strain conditions, but the dominant form of corrosion was localized pitting for all specimens except Alloy 2196 strained 0%. Pitting initiated at grain boundaries and triple points. In many cases, pitting extended into particular grains and was elongated in the extrusion direction. Regions of high micro-strain preferentially corroded, and large, recrystallized grains in mostly unrecrystallized microstructures were detrimental to corrosion properties. Recommendations for improved thermomechanical processing and/or alloying to promote corrosion resistance of 2XXX series Al-Li alloys were investigated.

  18. 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.

  19. Investigation of the Influence of Tool Geometry on Effective Strain Distribution in Full Forward Extrusion

    NASA Astrophysics Data System (ADS)

    Merklein, Marion; Ndzomssi, Franck; Engel, Ulf

    2011-05-01

    Due to strain hardening of the material, the hardness of cold forged parts is considerably improved. It is well known that the hardness of cold forged parts is closely related to its deformation, and that this relation is not dependent on the deformation process. The effective strain defines the local deformation, and can be determined in simulation of the cold forming process. In order to reach the required or to set specific hardness distribution with cold forging without any heat treatment processes, it is necessary to find out which manufacturing parameters influence the effective strain, and determine the effects of these parameters. The research work covered in this paper investigates the influence of the die geometry (as manufacturing parameter) on the effective strain. For that, a full forward extrusion process was modeled using the FE-software Simufact. Forming and three parameters of the die geometry, namely the deformation ratio, the shoulder radius and the opening angle were varied. The maximum effective strain from each combination is determined, and the effects of each considered parameter as well as the effects of interactions between these factors are checked.

  20. An investigation of the potential causes for the seasonal and annual variations in indoor radon concentrations.

    PubMed

    Barazza, F; Gfeller, W; Palacios, M; Murith, C

    2015-11-01

    Indoor radon concentrations exhibit strong variations on short and long timescales. Besides human influences, meteorological factors significantly affect the radon concentrations indoors as well as outdoors. In this article, long-term measurements showing strong annual variations are presented, which take a very similar course in different buildings located in largely separated regions in Switzerland. Also, seasonal variations can be very significant. In general, variations in indoor radon levels can primarily be attributed to human influences. On the other hand, specific weather conditions can have a significant impact on indoor radon levels. In order to further investigate the connection between indoor radon levels and meteorological factors, a measuring campaign has been started in two buildings located in two different regions in Switzerland exhibiting different climatic characteristics. Preliminary results of these investigations are presented, which provide evidence for correlations between indoor radon levels and in particular outdoor temperatures, contributing to seasonal and annual as well as short-term variations in indoor radon concentrations.

  1. Assessing Autism-like Behavior in Mice: Variations in Social Interactions Among Inbred Strains.

    PubMed Central

    Bolivar, Valerie J.; Walters, Samantha R.; Phoenix, Jennifer L.

    2007-01-01

    Autism is a pervasive developmental disorder, with characteristics including impairments in reciprocal social interaction, impaired communication, and repetitive/stereotyped behaviors. Despite decades of research, the etiology of autism remains elusive. Thus, it is important that we pursue all avenues, in attempting to understand this complicated disorder. One such avenue is the development of animal models. While autism may be uniquely human, there are behavioral characteristics of the disorder that can be established in animal models. Evidence supports a genetic component for this disorder, and over the past few decades the mouse has been a highly valuable tool for the elucidation of pathways involved in many human disorders (e.g., Huntington’s disease). As a first step toward establishing a mouse model of autism, we studied same-sex social behavior in a number of inbred mouse strains. In Study 1, we examined intra-strain social behavior of male pairs after one mouse had 15 minutes prior exposure to the testing chamber. In Study 2, we evaluated intra-strain and inter-strain social behavior when both mice were naive to the testing chamber. The amount and type of social behavior seen differed between these studies, but overall there were general inbred strain differences in social behavior. Some strains were highly social (e.g., FVB/NJ, while others displayed low levels of social behavior (e.g., A/J, BTBR T+ tf/J). These strains may be useful in future genetic studies to determine specific genes involved in mouse social behavior, the findings of which should in turn help us to determine some of the genes involved in human social behavior and its disorders (e.g., autism). PMID:17097158

  2. Genetic Basis of Variations in Nitrogen Source Utilization in Four Wine Commercial Yeast Strains

    PubMed Central

    Gutiérrez, Alicia; Beltran, Gemma; Warringer, Jonas; Guillamón, Jose M.

    2013-01-01

    The capacity of wine yeast to utilize the nitrogen available in grape must directly correlates with the fermentation and growth rates of all wine yeast fermentation stages and is, thus, of critical importance for wine production. Here we precisely quantified the ability of low complexity nitrogen compounds to support fast, efficient and rapidly initiated growth of four commercially important wine strains. Nitrogen substrate abundance in grape must failed to correlate with the rate or the efficiency of nitrogen source utilization, but well predicted lag phase length. Thus, human domestication of yeast for grape must growth has had, at the most, a marginal impact on wine yeast growth rates and efficiencies, but may have left a surprising imprint on the time required to adjust metabolism from non growth to growth. Wine yeast nitrogen source utilization deviated from that of the lab strain experimentation, but also varied between wine strains. Each wine yeast lineage harbored nitrogen source utilization defects that were private to that strain. By a massive hemizygote analysis, we traced the genetic basis of the most glaring of these defects, near inability of the PDM wine strain to utilize methionine, as consequence of mutations in its ARO8, ADE5,7 and VBA3 alleles. We also identified candidate causative mutations in these genes. The methionine defect of PDM is potentially very interesting as the strain can, in some circumstances, overproduce foul tasting H2S, a trait which likely stems from insufficient methionine catabolization. The poor adaptation of wine yeast to the grape must nitrogen environment, and the presence of defects in each lineage, open up wine strain optimization through biotechnological endeavors. PMID:23826223

  3. 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.

  4. 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.

  5. Strain Variation and Disease Severity in Congenital Cytomegalovirus Infection: In Search of a Viral Marker.

    PubMed

    Arav-Boger, Ravit

    2015-09-01

    The wide spectrum of congenital cytomegalovirus (CMV) disease and known differences in the biology and in vitro growth of CMV strains continue to drive studies in search for specific viral genetic determinants that may predict severity of congenital CMV disease. Several CMV genes have been studied in detail in congenitally infected children, but the complexity of the viral genome and differences in the definition of symptomatic disease versus asymptomatic CMV infection continue to raise questions related to what constitutes a pathogenic CMV strain. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. 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

  7. 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

  8. 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. Copyright © 2015. Published by Elsevier Inc.

  9. 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.

  10. 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.

  11. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  13. Genetic diversity and host range variation of Ralstonia solanacearum strains entering the United States

    USDA-ARS?s Scientific Manuscript database

    Each year, large volumes of plant propagative stock are imported into the United States; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 106 R. solanacearum strains were collected over a 10-year period from imported ornamental propagative sto...

  14. Composition, variation, and dynamics of major osmotic solutes in Methanohalophilus strain FDF1

    SciTech Connect

    Robertson, D.E.; Roberts, M.F. ); Meichin Lai; Gunsalus, R.P. )

    1992-08-01

    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, [beta]-glutamine, and N[sup [epsilon

  15. TEMPERATURE-DEPENDENT VARIATION IN THE SYNTHESIS OF GROUP-SPECIFIC CARBOHYDRATE BY STREPTOCOCCAL VARIANT STRAINS

    PubMed Central

    Ayoub, Elia M.; Dudding, Burton A.

    1973-01-01

    A temperature-dependent alteration in the synthesis of the group-specific polysaccharide was found to occur in two "variant" streptococcal strains, A-486-Var and C 121/46/4. These strains synthesize a polysaccharide with variant immunochemical characteristics when grown at 37°C. However, when these organisms are grown at lower temperatures, 22°C, an enhanced synthesis of Group A carbohydrate occurs. Other variant strains show no appreciable alteration of the cell wall carbohydrate composition when grown at lower temperatures. Studies on an intermediate strain show that this organism has a propensity for the synthesis of a polysaccharide with higher glucosamine content and enhanced Group A serological reactivity when grown at 22°C. Immunochemical studies performed on the carbohydrates produced by the A-486-Var at various temperatures revealed that the appearance of Group A serological reactivity at lower temperatures is due to the additional synthesis of a polysaccharide with Group A specificity along with the continued synthesis of a variant carbohydrate. This finding contrasts with data obtained on the carbohydrate produced by the intermediate organisms that appears to consist predominently of one molecule bearing dual A and variant antigenic determinants. PMID:4123827

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

    USDA-ARS?s Scientific Manuscript database

    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...

  17. 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.

  18. Variation of the mineral density in cortical bone may serve to keep strain amplitudes within a physiological range.

    PubMed

    de Jong, W C; van Ruijven, L J; Brugman, P; Langenbach, G E J

    2013-08-01

    Within-bone variation in mineral density could be functional. A heterogeneous mineral-density distribution might serve to maintain habitual amplitudes of bone strain within a non-harmful, i.e., physiological range. Regions of a bone that would be strained the most on the basis of architecture alone might have a higher mineral density to make them more stiff and resistant to strain. We hypothesised that the cortical bone of the rabbit mandible contains such a functional distribution of mineral density. We thereby expected similar mineral-density patterns in the mandibles of different individuals due to the shared masticatory function. Secondly, we hypothesised that the highest mineral densities occur in mandibular regions predicted to be exposed to the largest amplitudes of strain-when taking into account bone architecture only. Mineral-density maps of the cortical bone of rabbit mandibles were obtained using micro-computed tomography (μCT). The μCT scans of two rabbits were converted into finite-element models (FEMs). To predict mandibular deformation during biting, these models were loaded by muscle forces and reaction forces. The forces acted on the condyles and on either the incisal or molar bite point. The FEMs were assigned a homogeneous material stiffness to calculate the strain amplitudes that would occur when only the architecture of the mandibular bone would be of influence. We found the cortical bone-mineral density patterns to be similar in all six mandibles. The mineral density of the corpus was higher than that of the ramus. A second consistent feature of the mandibular mineral-density distribution was that the medial ridge of the temporal-muscle insertion groove contained more mineral than its surrounding regions. The strain amplitudes calculated with the FEMs were variable and did not feature clear corpo-ramal differences. However, specific mandibular bone sites calculated to be exposed to the largest amplitudes of strain, including the medial

  19. Variation in the sensitivity of Callosobruchus (Coleoptera: Bruchidae) acetylcholinesterase to the organophosphate insecticide malaoxon: effect of species, geographical strain and food type.

    PubMed

    Gbaye, Olajire A; Holloway, Graham J; Callaghan, Amanda

    2012-09-01

    Bruchid beetles, Callosobruchus species, are serious pests of economically important grain legumes; their activity in stores is often controlled by the use of synthetic insecticides. Esterases are known to be involved in insecticide resistance in insects. However, there is a dearth of information on esterase activity in the genus Callosobruchus. In this study, the effect of species, geographical strain and food type on the variation in acetylcholinesterase (AChE) activity and its inhibition by malaoxon (malathion metabolite) was investigated using an in vitro spectrophotometric method. AChE activity varied significantly among species and strains and also among legume type used for rearing them. Generally, irrespective of species, strain or food type, the higher the AChE activity of a population, the higher is its inhibition by malaoxon. C. chinensis had the highest AChE activity of the species studied, and in the presence of malaoxon it had the lowest remaining AChE activity, while C. rhodesianus retained the highest activity. A first-hand knowledge of AChE activity in regional Callosobruchus in line with the prevailing food types should be of utmost importance to grain legume breeders, researchers on plant materials for bruchid control and pesticide manufacturer/applicators for a robust integrated management of these bruchids. Copyright © 2012 Society of Chemical Industry.

  20. Investigation on grain size effect in high strain rate ductility of 1100 pure aluminum

    NASA Astrophysics Data System (ADS)

    Bonora, N.; Bourne, N.; Ruggiero, A.; Iannitti, G.; Testa, G.

    2017-01-01

    The effect of the initial grain size on the material ductility at high strain rates in 1100 pure aluminum was investigated. Dynamic tensile extrusion (DTE) tests, at different impact velocities, were performed. Samples have been annealed at 350°C for different exposure times to induce grain growth. Extruded fragments were soft-recovered and the overall length of the extruded jets was used as a measure of material ductility at high strain rates. Numerical simulation of DTE test at different velocity was performed using the modified Rusinek-Klepaczko constitutive model. Results indicates that, as reported for pure copper, the overall ductility of the aluminum increases when grain size decreases. Numerical simulation results were in quite good agreement with experimental data.

  1. Micro-diffraction Investigation of Localized Strain in Mesa-etched HgCdTe Photodiodes

    NASA Astrophysics Data System (ADS)

    Tuaz, Aymeric; Ballet, Philippe; Biquard, Xavier; Rieutord, François

    2017-09-01

    We present an x-ray micro-diffraction investigation of localized strain and lattice disorientation in HgCdTe layers with a submicronic resolution using a synchrotron white beam in Laue configuration. Diffraction peak displacement mapping evidences bending of the crystal planes around mesa-etched photodiodes, with strong dependence upon the processing steps. The etching step by itself does not induce any deformation within the layer, while the passivation step leads to sufficient strain for plastic deformation to occur at the lateral edges of the etching. The annealing step is found to have a healing effect on the layer, which reduces the overall deformation and even re-crystallizes plastically deformed areas of the layer.

  2. Investigation of Strain/Vorticity and Large-Scale Flow Structure in Turbulent Nonpremixed Jet Flames

    NASA Technical Reports Server (NTRS)

    Clemens, N. T.

    1999-01-01

    Our study will use the microgravity environment to investigate the underlying flow structure of turbulent nonpremixed round jet flames. In particular, we aim to investigate the large-scale turbulent structure using planar laser Mie scattering (PLMS), and the strain rate and vorticity fields using particle image velocimetry (PIV). This work is motivated by recent studies in our laboratory that have led to several interesting observations of nominally momentum-driven turbulent nonpremixed planar flames. First of all, the organized large-scale turbulent structures that are observed in nonreacting planar jets may be substantially modified or suppressed in nonpremixed planar jet flames. Furthermore, a recent study using PIV and planar laser-induced fluorescence of OH has shown that in transitional and turbulent nonpremixed planar jet flames the presence of the flame seems to greatly influence the underlying vorticity and strain fields, as compared to nonreacting jets. For example, the reaction zones in the jet flames are strongly correlated with regions of high vorticity. A related study has demonstrated that vorticity is not correlated in the same way with either iso-scalar surfaces or scalar dissipation layers in nonreacting planar jets. Furthermore, the relationship between strain and the reaction zone appears to be modified by the presence of high levels of heat release. In particular, the strain rate field in planar jet flames exhibits a preferred direction of principal compressive strain that apparently is related to strong shear across the reaction zone. This preferred direction of strain was not observed in nonreacting jets. One of the major problems encountered when conducting these types of studies is that it is difficult to know to what extent buoyancy influences the results. Therefore, the microgravity environment provides us with an excellent opportunity to explore these issues without the complicating effects of buoyancy. This is particularly the case when

  3. Electrochemical strain microscopy probes morphology-induced variations in ion uptake and performance in organic electrochemical transistors

    NASA Astrophysics Data System (ADS)

    Giridharagopal, R.; Flagg, L. Q.; Harrison, J. S.; Ziffer, M. E.; Onorato, J.; Luscombe, C. K.; Ginger, D. S.

    2017-07-01

    Ionic transport phenomena in organic semiconductor materials underpin emerging technologies ranging from bioelectronics to energy storage. The performance of these systems is affected by an interplay of film morphology, ionic transport and electronic transport that is unique to organic semiconductors yet poorly understood. Using in situ electrochemical strain microscopy (ESM), we demonstrate that we can directly probe local variations in ion transport in polymer devices by measuring subnanometre volumetric expansion due to ion uptake following electrochemical oxidation of the semiconductor. The ESM data show that poly(3-hexylthiophene) electrochemical devices exhibit voltage-dependent heterogeneous swelling consistent with device operation and electrochromism. Our data show that polymer semiconductors can simultaneously exhibit field-effect and electrochemical operation regimes, with the operation modality and its distribution varying locally as a function of nanoscale film morphology, ion concentration and potential. Importantly, we provide a direct test of structure-function relationships by correlating strain heterogeneity with local stiffness maps. These data indicate that nanoscale variations in ion uptake are associated with local changes in polymer packing that may impede ion transport to different extents within the same macroscopic film and can inform future materials optimization.

  4. Antigenic analysis of classical swine fever virus E2 glycoprotein using pig antibodies identifies residues contributing to antigenic variation of the vaccine C-strain and group 2 strains circulating in China.

    PubMed

    Chen, Ning; Tong, Chao; Li, Dejiang; Wan, Jing; Yuan, Xuemei; Li, Xiaoliang; Peng, Jinrong; Fang, Weihuan

    2010-12-31

    Glycoprotein E2, the immunodominant protein of classical swine fever virus (CSFV), can induce neutralizing antibodies and confer protective immunity in pigs. Our previous phylogenetic analysis showed that subgroup 2.1 viruses branched away from subgroup 1.1, the vaccine C-strain lineage, and became dominant in China. The E2 glycoproteins of CSFV C-strain and recent subgroup 2.1 field isolates are genetically different. However, it has not been clearly demonstrated how this diversity affects antigenicity of the protein. Antigenic variation of glycoprotein E2 was observed not only between CSFV vaccine C-strain and subgroup 2.1 strains, but also among strains of the same subgroup 2.1 as determined by ELISA-based binding assay using pig antisera to the C-strain and a representative subgroup 2.1 strain QZ-07 currently circulating in China. Antigenic incompatibility of E2 proteins markedly reduced neutralization efficiency against heterologous strains. Single amino acid substitutions of D705N, L709P, G713E, N723S, and S779A on C-strain recombinant E2 (rE2) proteins significantly increased heterologous binding to anti-QZ-07 serum, suggesting that these residues may be responsible for the antigenic variation between the C-strain and subgroup 2.1 strains. Notably, a G713E substitution caused the most dramatic enhancement of binding of the variant C-strain rE2 protein to anti-QZ-07 serum. Multiple sequence alignment revealed that the glutamic acid residue at this position is conserved within group 2 strains, while the glycine residue is invariant among the vaccine strains, highlighting the role of the residue at this position as a major determinant of antigenic variation of E2. A variant Simpson's index analysis showed that both codons and amino acids of the residues contributing to antigenic variation have undergone similar diversification. These results demonstrate that CSFV vaccine C-strain and group 2 strains circulating in China differ in the antigenicity of their E2

  5. Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria

    PubMed Central

    Kopf, Matthias; Klähn, Stephan; Scholz, Ingeborg; Hess, Wolfgang R.; Voß, Björn

    2015-01-01

    In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5′UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5′UTR. Such an sRNA/mRNA structure, which we name ‘actuaton’, represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation. PMID:25902393

  6. Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1.

    PubMed

    Lu, Zen H; di Domenico, Alex; Wright, Steven H; Knight, Pamela A; Whitelaw, C Bruce A; Pemberton, Alan D

    2011-02-16

    C57BL/6J mice possess a single intelectin (Itln) gene on chromosome 1. The function of intelectins is not well understood, but roles have been postulated in insulin sensitivity, bacterial recognition, intestinal lactoferrin uptake and response to parasites and allergens. In contrast to C57BL/6J mice, there is evidence for expansion of the Itln locus in other strains and at least one additional mouse Itln gene product has been described. The aim of this study was to sequence and characterise the Itln locus in the 129S7 strain, to determine the nature of the chromosomal expansion and to inform possible future gene deletion strategies. Six 129S7 BAC clones were sequenced and assembled to generate 600 kbp of chromosomal sequence, including the entire Itln locus of approximately 500 kbp. The locus contained six distinct Itln genes, two CD244 genes and several Itln- and CD244-related pseudogenes. It was approximately 433 kbp larger than the corresponding C57BL/6J locus. The expansion of the Itln locus appears to have occurred through multiple duplications of a segment consisting of a full-length Itln gene, a CD244 (pseudo)gene and an Itln pseudogene fragment. Strong evidence for tissue-specific distribution of Itln variants was found, indicating that Itln duplication contributes more than a simple gene dosage effect. We have characterised the Itln locus in 129S7 mice to reveal six Itln genes with distinct sequence and expression characteristics. Since C57BL/6J mice possess only a single Itln gene, this is likely to contribute to functional differences between C57BL/6J and other mouse strains.

  7. Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1

    PubMed Central

    2011-01-01

    Background C57BL/6J mice possess a single intelectin (Itln) gene on chromosome 1. The function of intelectins is not well understood, but roles have been postulated in insulin sensitivity, bacterial recognition, intestinal lactoferrin uptake and response to parasites and allergens. In contrast to C57BL/6J mice, there is evidence for expansion of the Itln locus in other strains and at least one additional mouse Itln gene product has been described. The aim of this study was to sequence and characterise the Itln locus in the 129S7 strain, to determine the nature of the chromosomal expansion and to inform possible future gene deletion strategies. Results Six 129S7 BAC clones were sequenced and assembled to generate 600 kbp of chromosomal sequence, including the entire Itln locus of approximately 500 kbp. The locus contained six distinct Itln genes, two CD244 genes and several Itln- and CD244-related pseudogenes. It was approximately 433 kbp larger than the corresponding C57BL/6J locus. The expansion of the Itln locus appears to have occurred through multiple duplications of a segment consisting of a full-length Itln gene, a CD244 (pseudo)gene and an Itln pseudogene fragment. Strong evidence for tissue-specific distribution of Itln variants was found, indicating that Itln duplication contributes more than a simple gene dosage effect. Conclusions We have characterised the Itln locus in 129S7 mice to reveal six Itln genes with distinct sequence and expression characteristics. Since C57BL/6J mice possess only a single Itln gene, this is likely to contribute to functional differences between C57BL/6J and other mouse strains. PMID:21324158

  8. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania.

    PubMed

    Rogers, Matthew B; Hilley, James D; Dickens, Nicholas J; Wilkes, Jon; Bates, Paul A; Depledge, Daniel P; Harris, David; Her, Yerim; Herzyk, Pawel; Imamura, Hideo; Otto, Thomas D; Sanders, Mandy; Seeger, Kathy; Dujardin, Jean-Claude; Berriman, Matthew; Smith, Deborah F; Hertz-Fowler, Christiane; Mottram, Jeremy C

    2011-12-01

    Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy numbers, identifying large copy number variations between species, with 200 tandem gene arrays in L. major and 132 in L. mexicana. Chromosome copy number also varied significantly between species, with nine supernumerary chromosomes in L. infantum, four in L. mexicana, two in L. braziliensis, and one in L. major. A significant bias against gene arrays on supernumerary chromosomes was shown to exist, indicating that duplication events occur more frequently on disomic chromosomes. Taken together, our data demonstrate that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism.

  9. Regulatory gene mutation: a driving force behind group a Streptococcus strain- and serotype-specific variation.

    PubMed

    Sarkar, Poulomee; Sumby, Paul

    2017-02-01

    Data from multiple bacterial pathogens are consistent with regulator-encoding genes having higher mutation frequencies than the genome average. Such mutations drive both strain- and type- (e.g., serotype, haplotype) specific phenotypic heterogeneity, and may challenge public health due to the potential of variants to circumvent established treatment and/or preventative regimes. Here, using the human bacterial pathogen the group A Streptococcus (GAS; S. pyogenes) as a model organism, we review the types and regulatory-, phenotypic-, and disease-specific consequences of naturally occurring regulatory gene mutations. Strain-specific regulator mutations that will be discussed include examples that transform isolates into hyper-invasive forms by enhancing expression of immunomodulatory virulence factors, and examples that promote asymptomatic carriage of the organism. The discussion of serotype-specific regulator mutations focuses on serotype M3 GAS isolates, and how the identified rewiring of regulatory networks in this serotype may be contributing to a decades old epidemiological association of M3 isolates with particularly severe invasive infections. We conclude that mutation plays an outsized role in GAS pathogenesis and has clinical relevance. Given the phenotypic variability associated with regulatory gene mutations, the rapid examination of these genes in infecting isolates may inform with respect to potential patient complications and treatment options.

  10. Investigation of VIM, IMP, NDM-1, KPC AND OXA-48 enzymes in Enterobacteriaceae strains.

    PubMed

    Demir, Yelda; Zer, Yasemin; Karaoglan, Ilkay

    2015-05-01

    Gram-negative bacteria especially Enterobacteriaceae species have become an increasing etiologic agent of nosocomial infections. The development of resistance to carbapenems have become an increasing problem in the treatment of nosocomial infections. Especially carbapenamases are common for Enterobacteriaceae strains. This study was performed to detect the types of carbapenemases in Enterobacteriaceae strains isolated from various clinical samples. Enterobacteriaceae species were isolated from urine, blood, tracheal aspirates, wound, and other respiratory samples. Susceptibility of isolates to imipenem, meropenem and ertapenem was tested. Carbapenemase genes were studied using HyplexSuperBug ID kit. VIM (1-13), IMP (1-22), NDM-1, KPC(1-10) and OXA-48 genes were investigated. Ninety-five isolates of Enterobacteriaceae spp. were included in the study. Sixty isolates were resistant to imipenem, meropenem and ertapenem and 20 isolates were found resistant to imipenem or ertapenem while 15 were susceptible to all carbapenems. Among the isolates with carbapenem resistance, 57 were positive for one carbapenemase gene and susceptible isolates did not have carbapenemase gene. OXA-48 was found in 49 of the isolates (86%), NDM-1 in 6 (10.5%) isolates, VIM in 2 isolates. IMP and KPC gene loci were not identified. Carbapenemase genes play a crucial role in the development and spread of resistant strains.

  11. Investigation of the Antimicrobial Activity of Bacillus licheniformis Strains Isolated from Retail Powdered Infant Milk Formulae.

    PubMed

    Alvarez-Ordóñez, Avelino; Begley, Máire; Clifford, Tanya; Deasy, Thérèse; Considine, Kiera; O'Connor, Paula; Ross, R Paul; Hill, Colin

    2014-03-01

    This study investigated the potential antimicrobial activity of ten Bacillus licheniformis strains isolated from retail infant milk formulae against a range of indicator (Lactococcus lactis, Lactobacillus bulgaricus and Listeria innocua) and clinically relevant (Listeria monocytogenes, Staphylococcus aureus, Streptococcus agalactiae, Salmonella Typhimurium and Escherichia coli) microorganisms. Deferred antagonism assays confirmed that all B. licheniformis isolates show antimicrobial activity against the Gram-positive target organisms. PCR and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analyses indicated that four of the B. licheniformis isolates produce the bacteriocin lichenicidin. The remaining six isolates demonstrated a higher antimicrobial potency than lichenicidin-producing strains. Further analyses identified a peptide of ~1,422 Da as the most likely bioactive responsible for the antibacterial activity of these six isolates. N-terminal sequencing of the ~1,422 Da peptide from one strain identified it as ILPEITXIFHD. This peptide shows a high homology to the non-ribosomal peptides bacitracin and subpeptin, known to be produced by Bacillus spp. Subsequent PCR analyses demonstrated that the six B. licheniformis isolates may harbor the genetic machinery needed for the synthesis of a non-ribosomal peptide synthetase similar to those involved in production of subpeptin and bacitracin, which suggests that the ~1,422 Da peptide might be a variant of subpeptin and bacitracin.

  12. 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

  13. 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

  14. Micromagnetic and Moessbauer spectroscopic investigation of strain-induced martensite in austenitic stainless steel

    SciTech Connect

    Meszaros, I.; Kaldor, M.; Hidasi, B.; Vertes, A.; Czako-Nagy, I.

    1996-08-01

    Strain-induced martensite in 18/8 austenitic stainless steel was studied. Magnetic measurements and Moessbauer spectroscopic investigations were performed to characterize the amount of {alpha}{prime}-martensite due to room-temperature plastic tensile loading. The effects of cold work and annealing heat treatment were explored using magnetic Barkhausen noise, saturation polarization, coercive force, hardness, and conversion electron Moessbauer spectroscopy. The suggested Barkhausen noise measurement technique proved to be a useful quantitative and nondestructive method for determining the ferromagnetic phase ratio of the studied alloy.

  15. Study of growth rate and composition variations in metalorganic vapour phase selective area epitaxy at atmospheric pressure and application to the growth of strained layer DBR lasers

    NASA Astrophysics Data System (ADS)

    Silvestre, L.; Ougazzaden, A.; Delprat, D.; Ramdane, A.; Daguet, C.; Patriarche, G.

    1997-01-01

    In selective area epitaxy (SAE), a lateral variation of thickness accompanied by a variation of composition occurs because of the presence of dielectric masks on the substrate surface. To take advantage of these behaviours for monolithic integration of electronic devices, a good control of growth rate and composition is necessary. For this aim, different bulk materials InP, InGaAs and InGaAsP have been systematically investigated as a function of the geometry of dielectric masks specially designed for this work. All growths were performed by metalorganic vapour phase epitaxy (MOVPE) at atmospheric pressure. An estimation of growth rate enhancement and composition variation between the open regions in dielectric masks and the unmasked region has been established, allowing the choice of specific mask geometry for each application. Following this study, a strained multiple quantum well (MQW) structure for a distributed Bragg reflector (DBR) laser has been selectively grown. The standard buried ridge structure (BRS) processed presents good characteristics (8 mA threshold current) and we obtained a 7 nm tuning range with a ridge structure, which constitutes the best value reported with SAE.

  16. Variation of strain energy release rate with plate thickness. [fracture mode transition

    NASA Technical Reports Server (NTRS)

    Sih, G. C.; Hartranft, R. J.

    1973-01-01

    An analytical model of a through-thickness crack in a statically stretched plate is presented in which the crack front stress state is permitted to vary in the direction of the plate thickness. The amplitude or intensity of this stress field can be made nearly constant over a major portion of the interior crack front which is in a state of plane strain. The average amount of work available for extending a small segment of the crack across the thickness is associated with an energy release rate quantity in a manner similar to the two-dimensional Griffith crack model. The theoretically calculated energy release rate is shown to increase with increasing plate thickness, indicating that available work for crack extension is higher in a thicker plate.

  17. A Numerical Investigation of the Strain Effect on Saturation Optical Intensity in Electroabsorption Modulators Based on Asymmetric Intra-step-barrier Coupled Double Strained Quantum Wells

    NASA Astrophysics Data System (ADS)

    Abedi, Kambiz

    2011-12-01

    In this paper, the strain effect on saturation optical intensity in electroabsorption modulators (EAMs) based on asymmetric intra-step-barrier coupled double strained quantum well (AICD-SQWs) active region is theoretically investigated and compared with intra-step quantum well (IQW) structure. For this purpose, the thermionic emission and tunneling escape processes are taken into account and the escape times of photogenerated carriers are calculated. Then, the electroabsorption coefficient is calculated for different well strains for TE input light polarization. Finally, the saturation optical intensity of electroabsorption modulators with AICD-SQW structures in comparison with IQW structure is evaluated. Numerical results show that the tensile strain of well has the most significant effect on the saturation optical intensity of electroabsorption modulators with AICD-SQW structures due to reduction in escape times.

  18. Investigation of the use of a cocktail of lux-tagged Cronobacter strains for monitoring growth in infant milk formulae.

    PubMed

    Flaherty, Claire; Begley, Máire; Hill, Colin

    2013-08-01

    The objective of the present study was to create a collection of Lux-tagged Cronobacter strains to determine whether bioluminescence could be used to monitor growth of this pathogen in infant milk formula (IMF). Nine Cronobacter strains (seven C. sakazakii, one C. malonaticus, and one C. muytjensii) were transformed with plasmid p16S lux, and integration of the plasmid at the desired site on the chromosome was confirmed by PCR. The integrated plasmid was stable in the absence of antibiotic selection, and growth of the Lux-tagged strains was similar to that of their nontagged counterparts. Growth of Lux-tagged strains was monitored in real time in 10 commercial brands of IMF by measuring light emission with a luminometer. Although all of the IMF samples tested were able to support the growth of the Cronobacter strains, differences were observed among IMF brands. Variations in the amount of light emitted by individual Cronobacter strains were also noted. Monitoring light emission with a combination of two strains that produced higher and lower than average relative light readings was a good surrogate for evaluating the entire collection of Lux-tagged strains.

  19. Precise measurement of seismic traveltimes-investigation of variation from tidal stress in shallow crust

    SciTech Connect

    Liu, H.; Westerlund, R.E.; Fletcher, J.B.

    1983-05-01

    We have conducted 8 precise seismic surveys near Hollister, CA, over a period of 1 y in an attempt to detect the traveltime variation caused by the solid-earth tidal stress. The surveys were conducted along a 600 m baseline located in quartz monzonite hills 2 km west of the San Andreas fault. A 656 cm/sup 3/ air gun fired in a mud-filled pit 2 m deep provided a repeatable seismic source. The signals from two 2.3 Hz vertical-component geophones 600 m apart were digitized at a nominal rate of 600 samples/s by two cassette recorders modified for precise synchronization of data sampling against a master clock. Each survey consists of approx.100 traveltime measurements over the 12 h period between 6 p.m. and 6 a.m. local time; the time frame of each experiment was limited by daytime cultural noises. Analysis of traveltime variation is done either by timing of amplitude extrema or by cross-correlation of a waveform contructed from the digital data by a cubic-spline interpolation. Fractional error of the repeatablility of traveltime measurement is typically +- 3.3 x 10/sup -4/ for the first high-frequency, large amplitude arrival following the direct body waves. The first survey, conducted at a spring tide in August, 1981, showed a variation of ..delta..t/t -2 x 10/sup -3/ and correlated in time with the extensional tidal strain component along the baseline direction. The next two surveys, conducted at two neap tides, showed variation of ..delta..t/t approx.6 x 10/sup -4/ and also correlated with the same tidal strain component. However, the other 5 surveys conducted after the onset of 1981 rainy season and into the 1982 dry season, 4 at spring tides and 1 between a spring and a neap tide, showed traveltime constant to within 1 standard deviation. These results corroborate only partially the previously reported tidal stress variation of traveltimes in the shallow crust.

  20. Temporal Variation of Strain Field Around the Dedana Fault in NE Japan, Before and After the 2008 Iwate-Miyagi Nairiku Earthquake (M7.2)

    NASA Astrophysics Data System (ADS)

    Ohzono, M.; Miura, S.; Ohta, Y.; Iinuma, T.; Tachibana, K.; Sato, T.; Ueki, S.; Tsushima, H.; Miyao, K.; Takasuka, K.

    2008-12-01

    The Dedana fault (DF) is a southern part of the Kitakami-teichi-seien fault zone (KTSFZ), which consists of some typical active thrust faults along the eastern margin of Ou backbone range (OBR) in northeastern Japan. Based on the recent GPS studies, Miura et al. [EPS04] have found a strain concentration zone with EW contraction along OBR. In order to clarify more detailed strain field around the KTSFZ, we have installed 7 new continuous GPS sites along the EW line crossing the DF to complement the pre-existing sites operated by the Geographical Survey Institute (GSI) and the National Astronomical Observatory (NAO) in October 2007. Ohzono et al. [JPGU08] have pointed out a possibility of abrupt strain rate increase in OBR bounded by the DF from the time series of the site coordinates by March 2008. The Iwate-Miyagi Nairiku (inland) earthquake (M7.2) occurred beneath OBR on 13 June 2008 (UT). Its hypocenter is located at the southwest about 20 km away from the DF. This earthquake caused the large coseismic displacement around the source area. Ohta et al. [in review to EPS] proposed a fault model to explain the coseismic deformation observed by GPS. Soon after the earthquake, additional 14 GPS sites were deployed by the Japanese University Consortium for GPS (JUNCO) to reveal the postseismic deformation, which is distributed in the shallower part of the coseismic fault and the DF [Iinuma et al., submitted to ASC08]. Examining the time series of the site coordinates before and after the earthquake, we can summarize the temporal variation of the strain field around the DF as follows: 1) Before the earthquake, 8 months GPS data provide the clear strain increase in OBR around the west of the DF. However, this may be caused by the long-term strain accumulation as already suggested. We should investigate the data more carefully. 2) During the earthquake, the DF does not seem to be displaced because the EW profile of the coseismic displacement cannot be explained by the

  1. 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

  2. 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.

  3. Investigation of Copy Number Variation in Children with Conotruncal Heart Defects

    PubMed Central

    Campos, Carla Marques Rondon; Zanardo, Evelin Aline; Dutra, Roberta Lelis; Kulikowski, Leslie Domenici; Kim, Chong Ae

    2015-01-01

    Background Congenital heart defects (CHD) are the most prevalent group of structural abnormalities at birth and one of the main causes of infant morbidity and mortality. Studies have shown a contribution of the copy number variation in the genesis of cardiac malformations. Objectives Investigate gene copy number variation (CNV) in children with conotruncal heart defect. Methods Multiplex ligation-dependent probe amplification (MLPA) was performed in 39 patients with conotruncal heart defect. Clinical and laboratory assessments were conducted in all patients. The parents of the probands who presented abnormal findings were also investigated. Results Gene copy number variation was detected in 7/39 patients: 22q11.2 deletion, 22q11.2 duplication, 15q11.2 duplication, 20p12.2 duplication, 19p deletion, 15q and 8p23.2 duplication with 10p12.31 duplication. The clinical characteristics were consistent with those reported in the literature associated with the encountered microdeletion/microduplication. None of these changes was inherited from the parents. Conclusions Our results demonstrate that the technique of MLPA is useful in the investigation of microdeletions and microduplications in conotruncal congenital heart defects. Early diagnosis of the copy number variation in patients with congenital heart defect assists in the prevention of morbidity and decreased mortality in these patients. PMID:25387403

  4. Antigen dose and strain variation as factors in the genetic control of the immune response to sperm whale myoglobin.

    PubMed Central

    Young, C R; Ebringer, A; Archer, J R

    1978-01-01

    The primary and secondary immune response to the antigen sperm whale myoglobin was investigated in DBA/2, 129 and B10.BR mice over a dose range of immunization from 10 to 2000 microgram. Using an antigen excess technique, the quantity of antibody produced after secondary immunization followed a sigmoidal dose-response curve and the maximal plateau level was found to be different for each strain of mice. Furthermore, the genetic control of the immune response was investigated in twelve different inbred strains of mice following secondary immunization with 500 microgram of myoglobin. A continuous distribution for the mean antibody responses was obtained for the twelve different strains of mice. High responsiveness was associated with H-2 haplotypes d, f and k located on chromosome 17, the non-agouti gene 'a' located on chromosome 2 and the chinchilla gene 'c(ch)' located on chromosome 7. It is concluded that either a large number of IR-genes to myoglobin are present in many loci located on different chromosomes or the antibody differences could be explained by a cross-tolerance mechanism requiring no IR-genes at all. PMID:417022

  5. Genomic variations of Oenococcus oeni strains and the potential to impact on malolactic fermentation and aroma compounds in wine.

    PubMed

    Bartowsky, Eveline J; Borneman, Anthony R

    2011-11-01

    Malolactic fermentation (MLF) is the bacterially driven decarboxylation of L-malic acid to L-lactic acid and carbon dioxide, and brings about deacidification, flavour modification and microbial stability of wine. The main objective of MLF is to decrease wine sourness by a small increase in wine pH via the metabolism of L-malic acid. Oenococcus oeni is the main lactic acid bacterium to conduct MLF in virtually all red wine and an increasing number of white and sparkling wine bases. Over the last decade, it is becoming increasingly recognized that O. oeni exhibits a diverse array of secondary metabolic activities during MLF which can modify the sensory properties of wine. These secondary activities include the metabolism of organic acids, carbohydrates, polysaccharides and amino acids, and numerous enzymes such as glycosidases, esterases and proteases, which generate volatile compounds well above their odour detection threshold. Phenotypic variation between O. oeni strains is central for producing different wine styles. Recent studies using array-based comparative genome hybridization and genome sequencing of three O. oeni strains have revealed the large genomic diversity within this species. This review will explore the links between O. oeni metabolism, genomic diversity and wine sensory attributes.

  6. Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance.

    PubMed

    Rodríguez-Castillo, Juan Germán; Pino, Camilo; Niño, Luis Fernando; Rozo, Juan Carlos; Llerena-Polo, Claudia; Parra-López, Carlos A; Tauch, Andreas; Murcia-Aranguren, Martha Isabel

    2017-10-01

    Isolates of the Mycobacterium tuberculosis lineage 2/East-Asian are considered one of the most successful strains due to their increased pathogenicity, hyper-virulence associated with drug resistance, and high transmission. Recent studies in Colombia have shown that the Beijing-like genotype is associated with multidrug-resistance and high prevalence in the southwest of the country, but the genetic basis of its success in dissemination is unknown. In contribution to this matter, we obtained the whole sequences of six genomes of clinical isolates assigned to the Beijing-like genotype. The genomes were compared with the reference genome of M. tuberculosis H37Rv and 53 previously published M. tuberculosis genomes. We found that the six Beijing-like isolates belong to a modern Beijing sub-lineage and share specific genomic variants: i.e. deletion in the PPE8 gene, in Rv3806c (ubiA) responsible of high ethambutol resistance and in Rv3862c (whiB6) which is involved in granuloma formation and virulence, are some of them. Moreover, each isolated has exclusively single nucleotide polymorphisms (SNPs) in genes related with cell wall processes and cell metabolism. We identified polymorphisms in genes related to drug resistance that could explain the drug-resistant phenotypes found in the six isolates from Colombia. We hypothesize that changes due to these genetic variations contribute to the success of these strains. Finally, we analyzed the IS6110 insertion sequences finding very low variance between them, suggesting that SNPs is the major cause of variability found in Beijing-like strains circulating in Colombia. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  9. Local structure of superconducting (La,Sr)2CuO4 under strain: Microscopic mechanism of strain-induced Tc variation

    NASA Astrophysics Data System (ADS)

    Oyanagi, H.; Tsukada, A.; Naito, M.; Saini, N. L.

    2007-01-01

    High-quality polarized x-ray absorption spectroscopy data for (La,Sr)2CuO4 thin-film single crystals reveal strain-dependent local disorder (in the oxygen radial distribution) that correlates with the superconducting critical temperature. The temperature-dependent in-plane oxygen displacement shows that local lattice distortion strongly depends on strain, i.e., the biaxial tensile strain develops domains with the bond-stretching-type local distortion which is weakened by the compressive strain. We suggest that the two-dimensional strain modifies electronic inhomogeneity that influences the superconducting critical temperature through superfluid density, rather than band structure effects.

  10. Investigation of Harper-Dorn creep under the condition of large strains

    NASA Astrophysics Data System (ADS)

    Cheng, Yu-Ching

    The purpose of this investigation is to identify and clarify the perspective of the nature and origin of necessary procedures and requirements for Harper-Dorn creep. Harper-Dorn creep represents to the anomalous high temperature deformation behavior, which is first reported by Harper and Dorn in aluminum under the condition of small strains about 0.01. To accomplish the purpose of this investigation, four types of large grained materials are selected: commercial purity grade lead, high purity grade lead, high purity grade polycrystalline aluminum, and high purity grade single crystalline aluminum. Creep experiments are conducted under 0.98 melting temperature of the selected materials in long term tests. Microstructures are examed by optical microscope, scanning electron microscope and transmission electron microscope. Mechanical results represent that creep curves of commercial purity grade lead are smooth and stress exponents obeys the five-power-law at both high and low stress areas. Micro-structural results show that dynamic recovery is the proper restoration mechanism for commercial purity grade lead. Mechanical results represent that creep curves of high purity grade aluminum and lead show periodic accelerations in strain. The creep results of high purity grade aluminum verify that the present test conditions correspond to the priors. Furthermore, under the condition of large strains about 0.05, it was determined that the stress exponent of Harper-Dorn creep is about 2.6 and does not reveal Newtonian behavior. Micro-structural results indicate that dynamic re-crystallization is a dominate restoration mechanism for Harper-Dorn creep in large grain size, low dislocation density, and high purity grade materials. Therefore, this investigation provides new evidence that dynamic re-crystallization occurs during Harper-Dorn creep. The evidence is proved by the occurrence of periodic accelerations in creep curves and the transition of the stress exponents

  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.

  12. Prediction of variation in d-orbital occupancy in strain induced tetragonal phase of BiFeO{sub 3} thin film

    SciTech Connect

    Verma, Manish; Ram, Kanik

    2016-05-15

    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 BiFeO{sub 3} 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.

  13. 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

  14. Microstructures and strain variation: Evidence of multiple splays in the North Almora Thrust Zone, Kumaun Lesser Himalaya, Uttarakhand, India

    NASA Astrophysics Data System (ADS)

    Joshi, Gaurav; Agarwal, Amar; Agarwal, K. K.; Srivastava, Samriddhi; Alva Valdivia, L. M.

    2017-01-01

    The North Almora Thrust zone (NATZ) marks the boundary of the Almora Crystalline Complex (ACC) against the Lesser Himalayan Sedimentary sequence (LHS) in the north. Its southern counterpart, the South Almora Thrust (SAT), is a sharply marked contact between the ACC and the LHS in the south. Published studies argue various contradictory emplacement modes of the North Almora Thrust. Recent studies have implied splays of smaller back thrusts in the NATZ. The present study investigates meso- and microstructures, and strain distribution in the NATZ and compares it with strain distribution across the SAT. In the NATZ, field evidence reveals repeated sequence of 10-500 m thick slices of proto- to ultra-mylonite, thrust over the Lesser Himalayan Rautgara quartzite. In accordance with the field evidence, the strain analysis reveals effects of splays of smaller thrust in the NATZ. The study therefore, argues that contrary to popular nomenclature the northern contact of the ACC with the LHS is not a single thrust plane, but a thrust zone marked by numerous thrust splays.

  15. 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

  16. Investigating the effect of lateral viscosity variations in the Earth's mantle

    NASA Astrophysics Data System (ADS)

    O'Farrell, K. A.; Lithgow-Bertelloni, C. R.

    2015-12-01

    Seismic tomography can be used to investigate radial viscosity variations on instantaneous flow models by predicting the global geoid and comparing with the observed geoid. This method is one of many that has been used to constrain viscosity structure in the Earth's mantle in the last few decades. Using the 3D mantle convection model, Stag-YY (e.g., Hernlund and Tackley, 2008), we are further able to explore the effect of lateral variations in viscosity in addition to the radial variations. Examining over 50 tomographic models we found notable differences by comparing a synthetically produced geoid with the observed geoid. Comparing S- and P-wave tomographic models, the S-wave models provided a better fit to the observed geoid. Using this large suite of 50 tomographic models, we have been able to constrain the radial viscosity structure of the Earth. We found that two types of viscosity profiles yielded equally good fits. A viscosity profile with a low transition zone viscosity and a lower mantle viscosity equal to the upper mantle, or a profile with a large lower mantle viscosity and a transition zone viscosity similar to the upper mantle. Using the set of radial viscosity profiles that gave the best fit to the observed geoid, we can explore a range of lateral viscosity variations and see how they affect the different types of tomographic models. Improving on previous studies of lateral viscosity variations (e.g. Ghosh, Becker and Zhong, 2010), we systematically explore a large range of tomographic models and density-velocity conversion factors. We explore which type of tomographic model (S- or P- wave) is more strongly affected by lateral viscosity variations, as well as the effect on isotropic and anisotropic models. We constrain the strength of lateral viscosity variations necessary to produce a high correlation between observed and predicted geoid anomalies. We will discuss the wavelength of flow that is most affected by the lateral viscosity variations

  17. Investigation of the stress distribution around a mode 1 crack with a novel strain gradient theory

    NASA Astrophysics Data System (ADS)

    Lederer, M.; Khatibi, G.

    2017-01-01

    Stress concentrations at the tip of a sharp crack have extensively been investigated in the past century. According to the calculations of Inglis, the stress ahead of a mode 1 crack shows the characteristics of a singularity. This solution is exact in the framework of linear elastic fracture mechanics (LEFM). From the viewpoint of multiscale modelling, however, it is evident that the stress at the tip of a stable crack cannot be infinite, because the strengths of atomic bonds are finite. In order to prevent the problem of this singularity, a new version of strain gradient elasticity is employed here. This theory is implemented in the commercial FEM code ABAQUS through user subroutine UEL. Convergence of the model is proved through consecutive mesh refinement. In consequence, the stresses ahead of a mode 1 crack become finite. Furthermore, the model predicts a size effect in the sense “smaller is stronger”.

  18. Thin film’s magnetostriction investigated by strain modulated ferromagnetic resonance at low temperature

    NASA Astrophysics Data System (ADS)

    Nesteruk, K.; Żuberek, R.; Piechota, S.; Gutowski, M. W.; Szymczak, H.

    2014-07-01

    The novel experimental setup for measurements of magnetostriction of thin films in the temperature range starting from 4.2 K up to the room temperature, using the strain modulated ferromagnetic resonance phenomenon, is presented. The sample under investigation is fixed at the anti-node of vibrations of the longitudinal mode sapphire resonator. The resonator is excited by means of a piezoelectric transducer via the mechanical waveguide. The sapphire rod is put into a helium flow cryostat, thus allowing the measurements in the wide temperature range. The temperature gradient along the resonator length is negligible due to the very high thermal conductivity of sapphire. The setup is controlled by specially designed electronic circuit interfaced to a computer. As an illustrative example, the measurements of epitaxial Fe/GaAs(001) films were performed with in-plane magnetic field, in the temperature range between 10 K and the room temperature.

  19. 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.

  20. Investigating variations in implementation fidelity of an organizational-level occupational health intervention.

    PubMed

    Augustsson, Hanna; von Thiele Schwarz, Ulrica; Stenfors-Hayes, Terese; Hasson, Henna

    2015-06-01

    The workplace has been suggested as an important arena for health promotion, but little is known about how the organizational setting influences the implementation of interventions. The aims of this study are to evaluate implementation fidelity in an organizational-level occupational health intervention and to investigate possible explanations for variations in fidelity between intervention units. The intervention consisted of an integration of health promotion, occupational health and safety, and a system for continuous improvements (Kaizen) and was conducted in a quasi-experimental design at a Swedish hospital. Implementation fidelity was evaluated with the Conceptual Framework for Implementation Fidelity and implementation factors used to investigate variations in fidelity with the Framework for Evaluating Organizational-level Interventions. A multi-method approach including interviews, Kaizen notes, and questionnaires was applied. Implementation fidelity differed between units even though the intervention was introduced and supported in the same way. Important differences in all elements proposed in the model for evaluating organizational-level interventions, i.e., context, intervention, and mental models, were found to explain the differences in fidelity. Implementation strategies may need to be adapted depending on the local context. Implementation fidelity, as well as pre-intervention implementation elements, is likely to affect the implementation success and needs to be assessed in intervention research. The high variation in fidelity across the units indicates the need for adjustments to the type of designs used to assess the effects of interventions. Thus, rather than using designs that aim to control variation, it may be necessary to use those that aim at exploring and explaining variation, such as adapted study designs.

  1. A model to investigate postoperative ileus with strain gauge transducers in awake rats.

    PubMed

    Huge, A; Kreis, M E; Jehle, E C; Ehrlein, H J; Starlinger, M; Becker, H D; Zittel, T T

    1998-02-01

    Postoperative ileus influences patients well-being, hospital stay, and health cost, and postoperative inhibition of colonic motility is a major contributor to postoperative ileus. Experimental models for investigating postoperative ileus are needed. In particular, recording of postoperative colonic motility in awake rats has not been described yet. Gastric, small intestinal, and colonic motility were recorded with strain gauge transducers in awake rats, and the effects of anesthesia and abdominal surgery on gastrointestinal motility were investigated. Ether anesthesia increased gastric motility and inhibited small intestinal motility, while enflurane anesthesia had only minor effects on gastrointestinal motility. Abdominal surgery inhibited gastric, small intestinal, and colonic motility, and a detailed analysis of gastrointestinal motility in our postoperative ileus model is given. We established a model to record gastric, small intestinal, and colonic motility in awake rats postoperatively. We could demonstrate that enflurane anesthesia had little effect on gastrointestinal motility, while laparotomy and short manipulation of the cecum produced a prolonged inhibition of gastrointestinal motility. Our model could be used to investigate postoperative ileus, particularly of the colon, in awake rats.

  2. Community Genomic Analysis of Strain Variation of a Novel Archaeon in an Acid Mine Drainage Environment

    NASA Astrophysics Data System (ADS)

    Yelton, P.; Banfield, J.; Wilmes, P.

    2006-12-01

    Microorganisms play a significant role in acid mine drainage (AMD) generation within the Richmond Mine, Iron Mountain, California. To better understand the contributions of individual microbial species to this process, the assemblies of community genomic data from AMD biofilms were manually curated. Not reported previously is detailed analysis of genomic sequence from G-plasma, an archaeal population from a sample collected from the 5-way location in 2002. The G-plasma population exhibits a small number of differing nucleotide sequences at most genomic locations and comprises multiple genome types. Linkage between these sequence types indicates frequent homologous recombination. As the near complete genome is still in many fragments, the current investigation focused on the 25% of the genome in large, confidently linked pieces. Many predicted proteins from this organism were detected via proteomic analysis. In combination, information about genome heterogeneity and protein expression is providing clues to the role of this population in the biofilm community.

  3. 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. Copyright 2002 John Wiley & Sons, Ltd.

  4. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.

    PubMed

    Strope, Pooja K; Skelly, Daniel A; Kozmin, Stanislav G; Mahadevan, Gayathri; Stone, Eric A; Magwene, Paul M; Dietrich, Fred S; McCusker, John H

    2015-05-01

    Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments-one of which is the human body-as an opportunistic pathogen. To aid in the understanding of the S. cerevisiae population and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the "100-genomes" strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5 was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen.

  5. Strain-specific variation of the decorin-binding adhesin DbpA influences the tissue tropism of the lyme disease spirochete.

    PubMed

    Lin, Yi-Pin; Benoit, Vivian; Yang, Xiuli; Martínez-Herranz, Raúl; Pal, Utpal; Leong, John M

    2014-07-01

    Lyme disease spirochetes demonstrate strain- and species-specific differences in tissue tropism. For example, the three major Lyme disease spirochete species, Borrelia burgdorferi sensu stricto, B. garinii, and B. afzelii, are each most commonly associated with overlapping but distinct spectra of clinical manifestations. Borrelia burgdorferi sensu stricto, the most common Lyme spirochete in the U.S., is closely associated with arthritis. The attachment of microbial pathogens to cells or to the extracellular matrix of target tissues may promote colonization and disease, and the Lyme disease spirochete encodes several surface proteins, including the decorin- and dermatan sulfate-binding adhesin DbpA, which vary among strains and have been postulated to contribute to strain-specific differences in tissue tropism. DbpA variants differ in their ability to bind to its host ligands and to cultured mammalian cells. To directly test whether variation in dbpA influences tissue tropism, we analyzed murine infection by isogenic B. burgdorferi strains that encode different dbpA alleles. Compared to dbpA alleles of B. afzelii strain VS461 or B. burgdorferi strain N40-D10/E9, dbpA of B. garinii strain PBr conferred the greatest decorin- and dermatan sulfate-binding activity, promoted the greatest colonization at the inoculation site and heart, and caused the most severe carditis. The dbpA of strain N40-D10/E9 conferred the weakest decorin- and GAG-binding activity, but the most robust joint colonization and was the only dbpA allele capable of conferring significant joint disease. Thus, dbpA mediates colonization and disease by the Lyme disease spirochete in an allele-dependent manner and may contribute to the etiology of distinct clinical manifestations associated with different Lyme disease strains. This study provides important support for the long-postulated model that strain-specific variations of Borrelia surface proteins influence tissue tropism.

  6. In vivo measurement of rotator cuff tendon strain with ultrasound elastography: an investigation using a porcine model.

    PubMed

    Hatta, Taku; Yamamoto, Nobuyuki; Sano, Hirotaka; Itoi, Eiji

    2014-09-01

    To clarify the relationship between the strain ratio measured by ultrasound elastography and the mechanical properties of the tendon measured by a universal testing machine. We also attempted to determine the effect of the type and depth of soft tissue overlying the tendon on the elastographic measurement. Twelve fresh porcine shoulders were prepared. Elastographic measurement was performed on the infraspinatus tendon by manually applying repetitive compressions from an ultrasound probe with an acoustic coupler consisting of an elastomer with definite elasticity as a reference material. The strain ratio, defined as tendon/reference strain, was obtained by 4 different approaches: with the probe placed on the skin, on the subcutaneous fat after removing the skin, on the muscle after removing the subcutaneous fat, and directly on the tendon. The strain ratios measured by these approaches were compared statistically. The relationship between the depth of the tendon measured on elastography and the strain ratio was also investigated. We also attempted to clarify the relationship between the strain ratio of the tendon and its elastic property. The tendon was mounted on a testing machine, and compressive force was applied. Tendon compliance was calculated as the reciprocal of the Young modulus in the range of 5% to 10% strain, which was compared to its strain ratio. The tendon/reference strain ratio significantly correlated with the tendon compliance (r = 0.73; P < .01). The strain ratio was not affected by differences in the measuring approaches (P = .4) or by the depth to the tendon level (P = .8). Our results indicated that the strain ratio of the rotator cuff tendon could be measured with minimal influence by overlying soft tissues if its depth from the skin was less than 22 mm. We believe that ultrasound elastography would be a useful tool for assessment of tendon elasticity in clinical practice. © 2014 by the American Institute of Ultrasound in Medicine.

  7. 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.

  8. [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

  9. Complex investigations of Mt. Elbrus magmatic center from combination of relative gravity and strain data

    NASA Astrophysics Data System (ADS)

    Kopaev, A.; Gurbanov, A.; Milyukov, V.; Yushkin, V.

    2003-04-01

    We have carried out 2 relative gravity surveys on Mt. Elbrus using quartz Sodin gravimeters and portable GPS receivers in extremely hard conditions with precision of 0.1-0.5 mGal. Its processing included common reduction to Bouguer anomalies as well as topographic correction using DTM with 50 m resolution. Resulting Bouguer anomalies reach 150 mGal near the Elbrus summit at the height of 4600 m and could be interpreted together with previous surveys results as a sign of large and shallow magmatic chamber. We plan to do more observations in 2003 and employ modern so-called ”gravity probability tomography” methods to discriminate between magmatic chamber and supposed caldera. Preliminary results of interpretation of regional gravity field from old gravity data imply the presence of the long (some 50 km) magmatic structure associated with the main magma-generating fault system connecting three magmatic centers in region young and sleeping (Mt. Elbrus, last eruption 1700 years ago), old Syltran (10 000 years) and Tchegem (25 000 years). The same magmatic structure is clearly visible from careful analysis of the tidal strain data from large Baksan laser strain meter recorded during 1998-2002 and processed using the combination of PRETERNA, TSOFT and ETERNA programs with careful taking into account for atmospheric and temperature perturbations. After applying the correction for tidal deformations of topography, resulting anomaly reaches 20 % - 25 % and could be explained by reducing the DVp/Vp ratio by 25 %. Future plans include adding of magnetic and resistivity data that are already available for Mt. Elbrus area. Our investigations have been supported by the RFBR grants ## 02-05-65012 and 00-05-64882.

  10. Experimental and Analytical Investigations on Plane Strain Toughness for 7085 Aluminum Alloy

    NASA Astrophysics Data System (ADS)

    Shuey, R. T.; Barlat, F.; Karabin, M. E.; Chakrabarti, D. J.

    2009-02-01

    Data are presented on plane strain fracture toughness, yield strength, and strain hardening for three orientations of samples from quarter-thickness ( t/4) and midthickness ( t/2) locations of alloy 7085 plates with different gages aged past peak strength with different 2nd step aging times (T7X). These data are fit to an expression adapted from Hahn and Rosenfield (1968), in which toughness is proportional to strain hardening, the square root of yield strength, and the square root of a critical strain ɛ c . Strain-hardening exponent n is replaced by an alternative measure, since the stress-strain data do not follow a power law. With increased overaging, the increase of strain hardening dominates the decrease of strength, such that toughness increases. The critical strain, which represents the influence of the microstructure on toughness, has no trend with overaging time. Constituents and grain boundary precipitates, thought to be the microstructural elements most differentiating alloy 7085 from alloy 7050, are quantified at t/4 and at t/2 on one plate. From this the greater critical strain at t/2 than at t/4 is mainly attributed to greater effective spacing of constituents. Critical strain is also greater with longitudinal loading and crack propagating in the long transverse direction, but definite understanding of this will require better anisotropic fracture mechanics and further microstructural characterization.

  11. 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.

  12. In-situ x-ray scattering investigation of strain in thin-film morphological evolution of homoepitaxial Ag(001)

    NASA Astrophysics Data System (ADS)

    Hayden, S. T.; Kim, C.; Conrad, E. H.; Gramlich, M. W.; Miceli, P. F.

    2010-03-01

    Because it escapes detection in most experimental probes of surfaces, the role of strain during film growth has not been widely investigated. However, large strain fields arise from vacancy nano-clusters [C. Kim et al., APL 91, 093131 (2007)] that can be incorporated during film growth at lower temperatures. It has also been suggested that extreme surface morphologies, resulting from a deposition flux at grazing angles, might lead to significant strain [Y. Shim et. al., PRL 101, 11601 (2008)]. Because of its simultaneous sensitivity to both the surface and the subsurface, x-ray scattering is a particularly valuable technique for exploring the role of strain in epitaxial crystal growth. This talk will discuss our recent in-situ x-ray diffuse scattering and reflectivity measurements, performed at the Advanced Photon Source, which investigate the low temperature homoepitaxial growth of Ag(001).

  13. Strain gauge transducer technique for investigation of the pathophysiology of postoperative colonic ileus in awake rats.

    PubMed

    Huge, A; Habermann, F M; Jehle, E C; Zittel, T T

    1998-12-01

    Postoperative inhibition of colonic motility is a major contributor to postoperative ileus, but only limited information is available on its pathophysiology. We developed a model to record perioperative gastrointestinal motility in awake rats and investigated the effect of nitric oxide (NO) synthesis blockade on postoperative colonic ileus in rats. Rats were equipped with an i.v. catheter. Two strain gauge transducers were sutured to the colon, and the effects of NO synthesis blockade on postoperative colonic motility were investigated. NO synthesis blockade slightly increased baseline colonic motility. Abdominal surgery profoundly inhibited colonic motility. Blockade of NO synthesis did not prohibit intraoperative inhibition of colonic motility, but significantly hastened recovery of postoperative colonic ileus compared to vehicle. We established a model to record gastric, small intestinal and colonic motility in awake rats postoperatively. Laparotomy and short manipulation of the cecum produced a prolonged inhibition of colonic motility. Inhibition of NO synthesis improved recovery of postoperative colonic motility, indicating that NO partly mediates postoperative colonic ileus in rats.

  14. 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.

  15. Correlation Investigation of Radio and Optical Variations in a Large Sample of Fermi Blazars

    NASA Astrophysics Data System (ADS)

    Zhang, B. K.; Zhao, X. Y.; Zhang, L.; Dai, B. Z.

    2017-08-01

    We have performed a correlation analysis of radio and optical variations in a large sample of Fermi blazars, of which there are 36 flat spectrum radio quasars and 34 BL Lacertae objects. The discrete cross-correlation function (DCF) method has been employed to investigate the correlation and the possible time lag. A clear correlation has been found in 55 sources (78.6% of the sample sources). It is confirmed that the variations in optical bands lead those in radio bands by several days to several hundred days. In four cases, optical flares are found to occur simultaneously with the radio flares. A jet-in-shock model has been used to explain these results. We estimate that the lag between the radio and optical bands may range from 3 days to 2.4 years. The DCF analysis results are consistent with expectations.

  16. 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.

  17. Investigating Natural Variation in Drosophila Courtship Song by the Evolve and Resequence Approach

    PubMed Central

    Turner, Thomas L.; Miller, Paige M.

    2012-01-01

    A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development. PMID:22466043

  18. 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

  19. An atomistic investigation of the effect of strain on frictional properties of suspended graphene

    SciTech Connect

    Bai, Qingshun; He, Xin; Bai, Jinxuan; Tong, Zhen

    2016-05-15

    We performed molecular dynamics (MD) simulations of a diamond probe scanned on a suspended graphene to reveal the effect of strain on the frictional properties of suspended graphene. The graphene was subjected to some certain strain along the scanning direction. We compared the friction coefficient obtained from different normal loads and strain. The results show that the friction coefficient can be decreased about one order of magnitude with the increase of the strain. And that can be a result of the decreased asymmetry of the contact region which is caused by strain. The synthetic effect of potential energy and the fluctuation of contact region were found to be the main reason accounting for the fluctuation of the friction force. The strain can reduce the fluctuation of the contact region and improve the stability of friction.

  20. Investigation of persistent colonization by Pseudomonas aeruginosa-like strains in a spring water bottling plant.

    PubMed

    Morais, P V; Mesquita, C; Andrade, J L; da Costa, M S

    1997-03-01

    Ninety-seven strains, producing a fluorescent pigment under UV light and/or a green diffusive pigment on cetrimide-naladixic acid agar, were isolated from a spring water bottling plant. These strains were presumptively identified as Pseudomonas aeruginosa, but they could not be confirmed as strains of this species nor identified by the API 20NE identification system. The isolates and reference strains were clustered by computer-assisted whole-cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The numerical analysis of the protein electrophoregrams resulted in the formation of four clusters at a similarity level of 80% and two unclustered type strains. One cluster included strains isolated during a 4-month period and reference strains of several biotypes of P. fluorescens. The remaining isolates formed another cluster with a very high similarity of level, which included two groups of strains based on biochemical characterization by the API 20NE Test System. Strains were typed by random amplified polymorphic DNA (RAPD)-PCR and two different RAPD patterns were obtained, corresponding to each biochemical profile. This persistent colonization seems to be caused by a single species present in the bottling system, with two clonal origins, not related to P. aeruginosa or to any of the other type strains tested. Partial 16S rDNA sequence of a representative strain of one cluster of isolates had a level of similarity of 99.3% with P. alcaligenes. This study shows that characteristics similar to P. aeruginosa on cetrimide-naladixic acid agar can be exhibited by several groups of fluorescent pseudomonads that do not belong to this species, clearly showing that confirmation tests must be performed before a decision regarding the water quality is made.

  1. Investigation of persistent colonization by Pseudomonas aeruginosa-like strains in a spring water bottling plant.

    PubMed Central

    Morais, P V; Mesquita, C; Andrade, J L; da Costa, M S

    1997-01-01

    Ninety-seven strains, producing a fluorescent pigment under UV light and/or a green diffusive pigment on cetrimide-naladixic acid agar, were isolated from a spring water bottling plant. These strains were presumptively identified as Pseudomonas aeruginosa, but they could not be confirmed as strains of this species nor identified by the API 20NE identification system. The isolates and reference strains were clustered by computer-assisted whole-cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The numerical analysis of the protein electrophoregrams resulted in the formation of four clusters at a similarity level of 80% and two unclustered type strains. One cluster included strains isolated during a 4-month period and reference strains of several biotypes of P. fluorescens. The remaining isolates formed another cluster with a very high similarity of level, which included two groups of strains based on biochemical characterization by the API 20NE Test System. Strains were typed by random amplified polymorphic DNA (RAPD)-PCR and two different RAPD patterns were obtained, corresponding to each biochemical profile. This persistent colonization seems to be caused by a single species present in the bottling system, with two clonal origins, not related to P. aeruginosa or to any of the other type strains tested. Partial 16S rDNA sequence of a representative strain of one cluster of isolates had a level of similarity of 99.3% with P. alcaligenes. This study shows that characteristics similar to P. aeruginosa on cetrimide-naladixic acid agar can be exhibited by several groups of fluorescent pseudomonads that do not belong to this species, clearly showing that confirmation tests must be performed before a decision regarding the water quality is made. PMID:9055406

  2. National survey of prevalent HIV strains: limited genetic variation of Korean HIV-1 clade B within the population of Korean men who have sex with men.

    PubMed

    Kim, Gab Jung; Nam, Jeong-Gu; Shin, Bo Gyeong; Kee, Mee Kyeong; Kim, Eun-Jin; Lee, Joo-Shil; Kim, Sung Soon

    2008-06-01

    The evolution of HIV is the result of an explosive combination of factors-a high rate of mutation, replication dynamics, frequent recombination, and natural selection. To understand the evolution of the distinctive Korean HIV-1 B clade, we investigated the characteristics of the genetic variation of the HIV-1 subtype B env gene within the group of Korean men who have sex with men (MSM). From 1985 to 2005, 700 HIV-1-infected Koreans were sequenced at the V1 to V5 region of the HIV-1 env gene. In the phylogenetic analysis, 560 isolates were identified as HIV-1 subtype B, and 489 of the 560 isolates were HIV-1 Korean clade B. Based on epidemiologic investigation, 249 of 700 HIV-1-infected patients were HIV-1 subtype B-infected MSM. Interestingly, the proportion of the GPGS motif in MSM infected by Koreans was 1.6 times higher than in MSM infected by foreigners, and the genetic expansions of diversity and divergence for HIV-1 subtype B in Korean MSM were 2.1% and 2.5%, respectively. This was much lower than those observed in other countries. Therefore, our findings imply that the HIV strains in this group were closely related. This result may be helpful for understanding the evolution of the distinct HIV-1 Korean B clade.

  3. 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

    2016-02-26

    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.

  4. 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

  5. Investigating the non-classical boundary conditions relevant to strain gradient theories

    NASA Astrophysics Data System (ADS)

    Jafari, Akbar; Ezzati, Meysam

    2017-02-01

    In the present study, two classes of non-classical constitutive equations consisting of the first and the second order strain gradients theories (FSG and SSG) were applied in order to develop the governing equations of static and free vibrational behavior of beam structures. The governing equations in orders of six and eight were constructed for FSG and SSG theories, respectively. Therefore, higher order or in other words non-classical boundary conditions (HOBCs or NCBCs) came into play in addition to the classical ones (CBCs). Some explanations were presented about the concept of the non-classical boundary conditions. Analytical and finite element (FE) approaches were employed to solve the governing equations. The analytical solutions were utilized in validation and convergence study of FE results. Comparisons were made with the relevant data reported in the open literature; however, to the best of the authors' knowledge, few references have been published on SSG theory and HOBCs. In the numerical studies, the effects of applying different combinations of CBCs and HOBCs to the static and free vibration behaviors of the beam were investigated. Moreover, the impacts of non-classical elastic constants and the beam size on its behavior were also studied.

  6. A theoretical investigation of the influence of the surface effect on the ferroelectric property of strained barium titanate film

    NASA Astrophysics Data System (ADS)

    Fang, Chao; Liu, Wei Hua

    2017-07-01

    The influence of the surface effect on the ferroelectric property of strained barium titanate film has been investigated. In this study, based on time-dependent Ginsburg-Landau-Devonshire thermodynamic theory, the surface effects have been simulated by introducing a surface constant, which leads to the strained BaTiO3 film consisting of inner tetragonal core and gradient lattice strain layer. Further, surface effects produce a depolarization field which has a dominant effect on the ferroelectric properties of the films. The spontaneous polarization, dielectric properties and ferroelectric hysteresis loop of BaTiO3 film are calculated under different boundary conditions. Theoretical and experimental results for strained BaTiO3 film are compared and discussed.

  7. 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

  8. The Investigation of Strain-Induced Martensite Reverse Transformation in AISI 304 Austenitic Stainless Steel

    NASA Astrophysics Data System (ADS)

    Cios, G.; Tokarski, T.; Żywczak, A.; Dziurka, R.; Stępień, M.; Gondek, Ł.; Marciszko, M.; Pawłowski, B.; Wieczerzak, K.; Bała, P.

    2017-07-01

    This paper presents a comprehensive study on the strain-induced martensitic transformation and reversion transformation of the strain-induced martensite in AISI 304 stainless steel using a number of complementary techniques such as dilatometry, calorimetry, magnetometry, and in-situ X-ray diffraction, coupled with high-resolution microstructural transmission Kikuchi diffraction analysis. Tensile deformation was applied at temperatures between room temperature and 213 K (-60 °C) in order to obtain a different volume fraction of strain-induced martensite (up to 70 pct). The volume fraction of the strain-induced martensite, measured by the magnetometric method, was correlated with the total elongation, hardness, and linear thermal expansion coefficient. The thermal expansion coefficient, as well as the hardness of the strain-induced martensitic phase was evaluated. The in-situ thermal treatment experiments showed unusual changes in the kinetics of the reverse transformation (α' → γ). The X-ray diffraction analysis revealed that the reverse transformation may be stress assisted—strains inherited from the martensitic transformation may increase its kinetics at the lower annealing temperature range. More importantly, the transmission Kikuchi diffraction measurements showed that the reverse transformation of the strain-induced martensite proceeds through a displacive, diffusionless mechanism, maintaining the Kurdjumov-Sachs crystallographic relationship between the martensite and the reverted austenite. This finding is in contradiction to the results reported by other researchers for a similar alloy composition.

  9. 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.

  10. The Investigation of Strain-Induced Martensite Reverse Transformation in AISI 304 Austenitic Stainless Steel

    NASA Astrophysics Data System (ADS)

    Cios, G.; Tokarski, T.; Żywczak, A.; Dziurka, R.; Stępień, M.; Gondek, Ł.; Marciszko, M.; Pawłowski, B.; Wieczerzak, K.; Bała, P.

    2017-10-01

    This paper presents a comprehensive study on the strain-induced martensitic transformation and reversion transformation of the strain-induced martensite in AISI 304 stainless steel using a number of complementary techniques such as dilatometry, calorimetry, magnetometry, and in-situ X-ray diffraction, coupled with high-resolution microstructural transmission Kikuchi diffraction analysis. Tensile deformation was applied at temperatures between room temperature and 213 K (-60 °C) in order to obtain a different volume fraction of strain-induced martensite (up to 70 pct). The volume fraction of the strain-induced martensite, measured by the magnetometric method, was correlated with the total elongation, hardness, and linear thermal expansion coefficient. The thermal expansion coefficient, as well as the hardness of the strain-induced martensitic phase was evaluated. The in-situ thermal treatment experiments showed unusual changes in the kinetics of the reverse transformation (α' → γ). The X-ray diffraction analysis revealed that the reverse transformation may be stress assisted—strains inherited from the martensitic transformation may increase its kinetics at the lower annealing temperature range. More importantly, the transmission Kikuchi diffraction measurements showed that the reverse transformation of the strain-induced martensite proceeds through a displacive, diffusionless mechanism, maintaining the Kurdjumov-Sachs crystallographic relationship between the martensite and the reverted austenite. This finding is in contradiction to the results reported by other researchers for a similar alloy composition.

  11. Investigation of S3-2 satellite data for local time variation of energetic electron precipitation

    NASA Technical Reports Server (NTRS)

    Robbe, S.; Sheldon, W. R.; Benbrook, J. R.; Bering, E. A.; Vampola, A. L.

    1994-01-01

    Data on precipitating electrons from the S3-2 satellite were investigated for local time variation at four L = 4 stations in the southern hemisphere. The equatorial pitch angles of electrons mirroring at 100 km, assumed to be the edge of the bounce loss cone, are calculated for L = 4 using the International Geomagnetic Reference Field for the epoch of the S3-2 data, along with the variation in mirror altitude per degree of equatorial pitch angle. The largest obstacle to the investigation was uneven sampling in terms of local time for all of the stations. However, this situation was improved upon by the use of S3-2 measurements at the conjugate locations of the four stations which provided additional data on electrons in the southern hemisphere bounce loss cone. Evidence for an effect of the dawn-to-dusk geoelectric field was found at two of the stations, Halley Bay and Siple, in the form of a minimum in electron precipitation at dusk. However, the present study does not completely resolve the question of local time modulation of electron precipitation at L = 4 in the southern hemisphere. Furthermore, while the average precipitation was lowest at the Kerguelen site, as would be expected on the basis of drift loss cone (DLC) theories, the intensity at that site exceeds the level that is expected on the basis of these DLC theories.

  12. Quantitative susceptibility mapping for investigating subtle susceptibility variations in the human brain.

    PubMed

    Schweser, Ferdinand; Sommer, Karsten; Deistung, Andreas; Reichenbach, Jürgen Rainer

    2012-09-01

    Quantitative susceptibility mapping (QSM) is a novel magnetic resonance-based technique that determines tissue magnetic susceptibility from measurements of the magnetic field perturbation. Due to the ill-posed nature of this problem, regularization strategies are generally required to reduce streaking artifacts on the computed maps. The present study introduces a new algorithm for calculating the susceptibility distribution utilizing a priori information on its regional homogeneity derived from gradient echo phase images and analyzes the impact of erroneous a priori information on susceptibility map fidelity. The algorithm, Homogeneity Enabled Incremental Dipole Inversion (HEIDI), was investigated with a special focus on the reconstruction of subtle susceptibility variations in a numerical model and in volunteer data and was compared with two recently published approaches, Thresholded K-space Division (TKD) and Morphology Enabled Dipole Inversion (MEDI). HEIDI resulted in susceptibility maps without streaking artifacts and excellent depiction of subtle susceptibility variations in most regions. By investigating HEIDI susceptibility maps acquired with the volunteers' heads in different orientations, it was demonstrated that the apparent magnetic susceptibility distribution of human brain tissue considerably depends on the direction of the main magnetic field.

  13. Investigation of cycle-to-cycle variations in an engine-like geometry

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Frouzakis, C. E.; Wright, Y. M.; Tomboulides, A. G.; Boulouchos, K.

    2014-12-01

    The multiple-cycle direct numerical simulation data of the flow in the valve/piston assembly investigated in Schmitt et al. ["Direct numerical simulation of multiple cycles in a valve/piston assembly," Phys. Fluids 26, 035105 (2014)] is revisited to identify the relevant flow features leading to the observed cyclic variations. These are found to be the radial velocity at top dead center (TDC) remaining from the previous cycle, the location of the center of the hollow jet during intake and the strength and orientation of the vortex ring at bottom dead center. Comparisons between these features showed strong correlations in the flow field within a cycle and between two consecutive cycles. The trajectory of the hollow jet during intake is strongly influenced by the remaining radial velocity from the previous cycle. Subsequently, the hollow jet forms a vortex ring whose orientation and strength influences the radial velocity at TDC of the next cycle. This has in turn an effect on the jet trajectory of the following cycle. The results in this simplified geometry are a first attempt to understand the origin of cause-and-effect relationships of cycle-to-cycle variations (CCVs) in the flow field and can serve as a base for investigating CCVs in more realistic engine geometries. Moreover, the reported correlations are a useful validation platform for large Eddy simulation models.

  14. Super Profile analysis of socioeconomic variations in coronary investigation and revascularisation rates

    PubMed Central

    Manson-Siddle, C. J.; Robinson, M. B.

    1998-01-01

    OBJECTIVES: To investigate socioeconomic variations in the utilisation of tertiary cardiology services. DESIGN: Cross sectional ecological study, using the Super Profile classification of enumeration districts, and ischaemic heart disease standardised mortality ratios as a proxy for needs. SETTING: The former Yorkshire Regional Health Authority area in England and its seven constituent district health authority areas. SUBJECTS: Patients with a primary diagnosis of ischaemic heart disease aged > or = 25 years who underwent investigation by angiography, or treatment by coronary artery bypass grafting (CABG) or percutaneous transluminal coronary angioplasty (PTCA), as a primary procedure between April 1992 and March 1994 in an NHS hospital. MAIN RESULTS: There is an overall increasing trend in investigation and revascularisation rates from the affluent to the deprived in the region suggesting equity. However, the gradient is slight compared with the corresponding mortality gradient. Age specific analysis shows a more appropriate trend in rates for the under 65s, but a downward trend from affluence to deprivation for the elderly. Much of the regional trend is caused by very high rates in one geographically small but densely populated district that has two tertiary cardiology centres. In other districts, with higher heart disease mortality but much lower procedure rates, there is a decreasing trend from the affluent to the deprived suggesting considerable inequity. CONCLUSIONS: This study confirms wide socioeconomic variations in coronary investigation and revascularisation within the former Yorkshire Region, suggesting that in some districts need is not being met and that service utilisation is inequitable. Such inequities are over and above those that result from proximity to tertiary cardiology centres.   PMID:9876362

  15. 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.

  16. 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.

  17. 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. Copyright 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

    PubMed Central

    Ahmed, Wylie W.; Kural, Mehmet H.; Saif, Taher A.

    2010-01-01

    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. We have developed a novel polydimethylsiloxane (PDMS) substrate 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 (DIC) and the deformation was modeled with finite element method (FEM) using a Mooney-Rivlin hyperelastic constitutive relation. The substrate strain was found to be uniform for greater than 95% of the substrate area. As a demonstration of our system, we applied mechanical strain to single fibroblasts transfected with GFP-Actin and whole transgenic Drosophila embryos expressing GFP in all neurons during live imaging. We report three observations of biological responses due to applied strain: (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. Our novel platform may serve as an important tool in studying the mechanoresponse of cells and tissues including whole embryos. PMID:20188869

  19. Variations in GPs' decisions to investigate suspected lung cancer: a factorial experiment using multimedia vignettes.

    PubMed

    Sheringham, Jessica; Sequeira, Rachel; Myles, Jonathan; Hamilton, William; McDonnell, Joe; Offman, Judith; Duffy, Stephen; Raine, Rosalind

    2017-06-01

    Lung cancer survival is low and comparatively poor in the UK. Patients with symptoms suggestive of lung cancer commonly consult primary care, but it is unclear how general practitioners (GPs) distinguish which patients require further investigation. This study examined how patients' clinical and sociodemographic characteristics influence GPs' decisions to initiate lung cancer investigations. A factorial experiment was conducted among a national sample of 227 English GPs using vignettes presented as simulated consultations. A multimedia-interactive website simulated key features of consultations using actors ('patients'). GP participants made management decisions online for six 'patients', whose sociodemographic characteristics systematically varied across three levels of cancer risk. In low-risk vignettes, investigation (ie, chest X-ray ordered, computerised tomography scan or respiratory consultant referral) was not indicated; in medium-risk vignettes, investigation could be appropriate; in high-risk vignettes, investigation was definitely indicated. Each 'patient' had two lung cancer-related symptoms: one volunteered and another elicited if GPs asked. Variations in investigation likelihood were examined using multilevel logistic regression. GPs decided to investigate lung cancer in 74% (1000/1348) of vignettes. Investigation likelihood did not increase with cancer risk. Investigations were more likely when GPs requested information on symptoms that 'patients' had but did not volunteer (adjusted OR (AOR)=3.18; 95% CI 2.27 to 4.70). However, GPs omitted to seek this information in 42% (570/1348) of cases. GPs were less likely to investigate older than younger 'patients' (AOR=0.52; 95% CI 0.39 to 0.7) and black 'patients' than white (AOR=0.68; 95% CI 0.48 to 0.95). GPs were not more likely to investigate 'patients' with high-risk than low-risk cancer symptoms. Furthermore, they did not investigate everyone with the same symptoms equally. Insufficient data gathering

  20. Investigation of strain birefringence and wavefront distortion in 001 plates of KD sub 2 PO sub 4

    SciTech Connect

    De Yoreo, J.J.; Woods, B.W.

    1991-08-26

    When 001 plates of KD{sub 2}PO{sub 4} (KD*P) are used in Pockels cells, strain induced refractive index variations result in beam depolarization and transmitted wavefront distortion. The depolarization is determined by the induced birefringence while the wavefront distortion is controlled by the average index shift. Here we show that the birefringence is determined by the shear stress in the xy-plane of the crystal while the average index shift depends only on the normal stresses. Furthermore, for depolarization losses of 0.1 to 1.0% and wavefront distortion of 0.1 to 1.0{lambda}, the critical range of stress is 10{sup 5} to 10{sup 6} Pa. We also present measured depolarization loss and wavefront distortion profiles for 5, 16 and 27cm, 95% deuterated, KD*P crystals. Using the analysis described above we show that the maximum internal stresses in the crystals are within the critical range, but that the area averaged stresses are substantially lower. We find that crystals from different locations along the length of a boule have similar strain birefringence and wavefront distortion profiles indicating that the growth conditions which generate the internal strain persist throughout much of the growth history of the boule. Finally, we discuss potential sources of strain in KD*P. 8 refs., 3 figs.

  1. Synchrotron X-ray diffraction investigations on strains in the oxide layer of an irradiated Zircaloy fuel cladding

    NASA Astrophysics Data System (ADS)

    Chollet, Mélanie; Valance, Stéphane; Abolhassani, Sousan; Stein, Gene; Grolimund, Daniel; Martin, Matthias; Bertsch, Johannes

    2017-05-01

    For the first time the microstructure of the oxide layer of a Zircaloy-2 cladding after 9 cycles of irradiation in a boiling water reactor has been analyzed with synchrotron micro-X-ray diffraction. Crystallographic strains of the monoclinic and to some extent of the tetragonal ZrO2 are depicted through the thick oxide layer. Thin layers of sub-oxide at the oxide-metal interface as found for autoclave-tested samples and described in the literature, have not been observed in this material maybe resulting from irradiation damage. Shifts of selected diffraction peaks of the monoclinic oxide show that the uniform strain produced during oxidation is orientated in the lattice and displays variations along the oxide layer. Diffraction peaks and their shifts from families of diffracting planes could be translated into a virtual tensor. This virtual tensor exhibits changes through the oxide layer passing by tensile or compressive components.

  2. How does variation in lower anterior face height influence perceived attractiveness? A quantitative investigation.

    PubMed

    Naini, Farhad B; Donaldson, Ana Nora A; McDonald, Fraser; Cobourne, Martyn T

    2013-09-01

    The purpose of this investigation was to undertake an objective and quantitative evaluation of how severity of lower anterior face height (LAFH) variations influences perceived attractiveness. Cross-sectional study St George's Hospital, London, UK PARTICIPANTS AND METHODS: The LAFH of an idealized male and female frontal facial image were altered in 2·5 mm increments from -20 to 20 mm (male images) and from -10 to 20 mm (female images), in order to represent reduction and increase in height of this region. These images were rated by a pre-selected group of pre-treatment orthognathic patients (n = 75), clinicians (n = 35) and laypersons (n = 75). Ratings on a seven-point Likert scale. With an increase in LAFH, desire for surgery became significant at 15-16 mm for male faces and 13-14 mm for female faces. With a reduction in LAFH, desire for surgery became significant at -14 to -17 mm for male faces; a smaller reduction of -6 to -8 mm led to a significant desire for surgery for female faces. The classical vertical facial trisection canon of upper face height as one-third (33·3%), midface height as one-third (33·3%) and LAFH as one-third (33·3%) of total anterior face height may be used as an 'ideal' proportional ratio. Mild LAFH variations were largely acceptable. In terms of the percentage LAFH to total anterior face height (TAFH) and anterior face height (AFH), observers did not desire surgery for LAFH variations of 25-42% of TAFH (40-66% of AFH) for male faces, and 28-42% of TAFH (45-66% of AFH) for female faces.

  3. A qualitative comparative investigation of variation in general practitioners' prescribing patterns.

    PubMed Central

    Jaye, Chrys; Tilyard, Murray

    2002-01-01

    BACKGROUND: In New Zealand there is increasing interest in the variation in the prescribing behaviours of general practitioners (GPs). Research conducted to date hasfocused primarily on the quantifiable aspects of prescribing variation. AIM: To investigate the qualitative aspects that may help explain variations in prescribing behaviour between GPs. DESIGN OF STUDY: Qualitative and comparative interviews. SETTING: Thirty New Zealand GPs. METHOD: A sample of 60 GPs (comprising 20 low, 20 medium, and 20 high-cost prescribers) was selected. Half of this sample (10 GPs in each prescribing category) was recruited to the study. Responders participated in a 60-minute interview. RESULTS: Low-cost prescribers reported more experience in practice and appeared to have a more 'relaxed' attitude towards medicine. They were more comfortable with refusing patients and they responded to patient expectations with education and explanation. In addition, they viewed the prescription as a pragmatic means of delivering health care to patients. Low and medium-cost prescribers did moreformal counselling and emphasised the 'listening' aspects of general practice. High-cost prescribers appeared to be more highly motivated and to have a more 'serious' attitude toward medicine. They tended to view their obligations and responsibilities to the patient in terms of medical competence. They described their roles with patients in terms of service provision and suggested that patients viewed the prescription as a signifier of the GP's service to the patient. CONCLUSION: This study suggests that there are discernible, non-quantifiable differences between low, medium, and high-cost prescribers in the Otago and Southland areas of New Zealand. PMID:12014535

  4. 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

  5. Investigations of the structural stability of highly strained [(Al)GaIn]As/Ga (PAs) multiple quantum wells

    NASA Astrophysics Data System (ADS)

    Marschner, T.; Lutgen, S.; Volk, M.; Stolz, W.; Göbel, E. O.

    1996-10-01

    The structural stability of highly strained [(Al)GaIn]As/Ga (PAs) strained layer superlattice (SLS) structures as a function of the average lattice mismatch is investigated. The SLS structures, grown by metalorganic vapor-phase epitaxy, are studied by using high-resolution x-ray diffraction. The range of stable SLS structures obtained experimentally is compared to a recent theoretical model assuming strain relaxation by formation of misfit dislocations [D. C. Houghton, M. Davies, and M. Dion, Appl. Phys. Lett. 64, 505 (1994)]. In particular, the influence of the surface migration length of the group-III species on the growth surface is investigated by varying the Al concentration in the compressively strained [(Al)GaIn]As layers. Structurally stable [(Al)GaIn]As/Ga(PAs) SLS structures having a total layer thickness of 1 μm and an average lattice mismatch of up to (Δd/d)⊥=1.2×10-2 have been realized. These values exceed by far the values of the misfit dislocation model. This behavior indicates that surface morphology changes rather than misfit dislocation formation are the primary cause for the instability of highly strained SLSs.

  6. Investigation of differences in sensitivity between 3 strains of Daphnia magna (crustacean Cladocera) exposed to malathion (organophosphorous pesticide).

    PubMed

    Toumi, Hela; Boumaiza, Moncef; Millet, Maurice; Radetski, Claudemir M; Camara, Baba I; Felten, Vincent; Ferard, Jean-François

    2015-01-01

    Acute and chronic ecotoxic effects of organophosphorous insecticide malathion (Fyfanon 50 EC 500 g L(-1)) were investigated on three strains of Daphnia magna. The nominal effective concentrations immobilizing 50% (EC50) of Daphnia after 24 and 48 h were 0.53 and 0.36 μg L(-1), 0.70 and 0.44 μg L(-1), and 0.75 and 0.46 μg L(-1) for the strains 1, 2, and 3 respectively. There was an increase in malathion ecotoxicity with time of exposure as confirmed by chronic studies. In fact, after 21 days of exposure, significant effects on survival (lowest observed effect concentration or LOECs) were recorded at malathion concentrations of 22, 220 and 230 ng L(-1) for strains 1, 2 and 3 respectively. Other endpoints were also examined, including reproduction (with different parameters), body length and embryo toxicity. ICs10 and ICs20 were calculated for these different parameters. ICs10 ranged from 4.7 to more than 220 ng L(-1) for the three tested strains. The most sensitive parameter was the number of neonates per adult (ICs10 = 4.7 and 10.8 ng L(-1) for strains 1 and 2 respectively) or the number of broods (IC10 = 10 ng L(-1) for strain 3). Moreover, an increase in embryo development abnormalities was observed at the two highest tested malathion concentrations. Abnormalities comprised undeveloped second antennae, curved or unextended shell spines, and curved post-abdomen spines in live neonates. Results suggest that malathion could act as an endocrine disruptor in D. magna as it interferes with development. It also induces a significant decrease in acetylcholinesterase (AChE) activities for the three strains. Both strains 2 and 3 seemed more sensitive (LOECs = 60 ng L(-1)) than strain 1 (LOEC = 120 ng L(-1)). Our results suggest that the AChE activity response can also be used as a biomarker of inter-strain (or inter-clonal) susceptibility (i.e. strain (or clone)-specific response).

  7. 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.

  8. 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.

  9. Investigations on variation of defects in fused silica with different annealing atmospheres using positron annihilation spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Lijuan; Chen, Jing; Jiang, Yilan; Liu, Jiandang; Gu, Bingchuan; Jiang, Xiaolong; Bai, Yang; Zhang, Chuanchao; Wang, Haijun; Luan, Xiaoyu; Ye, Bangjiao; Yuan, Xiaodong; Liao, Wei

    2017-10-01

    The laser damage resistance properties of the fused silica can be influenced by the microstructure variation of the atom-size intrinsic defects and voids in bulk silica. Two positron annihilation spectroscopy techniques have been used to investigate the microstructure variation of the vacancy clusters and the structure voids in the polishing redeposition layer and the defect layer of fused silica after annealing in different atmospheres. The fused silica samples were isothermally annealed at 1000 K for 3 h in a furnace under an air atmosphere, a vacuum atmosphere and a hydrogen atmosphere, respectively. The positron annihilation results show that ambient oxygen atmosphere only affects the surface of the fused silica (about 300 nm depth) due to the large volume and low diffusion coefficient of the oxygen atom. However, hydrogen atoms can penetrate into the defect layer inside the fused silica and then have an influence on vacancy defects and vacancy clusters, while having no effect on the large voids. Besides, research results indicate that an annealing process can reduce the size and concentration of vacancy clusters. The obtained data can provide important information for understanding the laser damage mechanism and improving laser damage resistance properties of the fused silica optics.

  10. Virulence variation among epidemic and non-epidemic strains of Saint Louis encephalitis virus circulating in Argentina

    PubMed Central

    Rivarola, María Elisa; Tauro, Laura Beatriz; Llinás, Guillermo Albrieu; Contigiani, Marta Silvia

    2014-01-01

    Saint Louis encephalitis virus caused an outbreak of febrile illness and encephalitis cases in Córdoba, Argentina, in 2005. During this outbreak, the strain CbaAr-4005 was isolated from Culex quinquefasciatus mosquitoes. We hypothesised that this epidemic variant would be more virulent in a mouse model than two other non-epidemic strains (78V-6507 and CorAn-9275) isolated under different epidemiological conditions. To test this hypothesis, we performed a biological characterisation in a murine model, including mortality, morbidity and infection percentages and lethal infection indices using the three strains. Mice were separated into age groups (7, 10 and 21-day-old mice) and analysed after infection. The strain CbaAr-4005 was the most infective and lethal of the three variants, whereas the other two strains exhibited a decreasing mortality percentage with increasing animal age. The strain CbaAr-4005 produced the highest morbidity percentages and no significant differences among age groups were observed. The epidemic strain caused signs of illness in all inoculated animals and showed narrower ranges from the onset of symptoms than the other strains. CbaAr-4005 was the most virulent for Swiss albino mice. Our results highlight the importance of performing biological characterisations of arbovirus strains likely to be responsible for emerging or reemerging human diseases. PMID:24810175

  11. 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.

  12. Investigation of short-term variations in term breast milk composition during repeated breast expression sessions.

    PubMed

    Khan, Sadaf; Prime, Danielle K; Hepworth, Anna R; Lai, Ching Tat; Trengove, Naomi J; Hartmann, Peter E

    2013-05-01

    Breast milk composition can be affected by several factors, and it can exhibit short-term (weekly) variations. Investigating variations in breast milk composition is important to accurately estimate nutrient requirements of the infant. To investigate short-term changes in breast milk composition between left and right breasts, over a 3-week period within the first 6 months of lactation. The left and right breasts of the mothers of healthy, term infants (n = 23) were simultaneously expressed with an electric breast pump for 15 minutes, on 3 occasions within 3 weeks. Milk samples (5 mL) were collected from the total expression volume of each breast at each session. The macronutrient contents, total solids, and energy content were determined using a mid-infrared human milk analyzer. Mothers (n = 17) measured their 24-hour milk production, and the average 24-hour fat contents were also determined. Over the 3 weekly sessions, no significant changes were found in macronutrient contents. On average, total solids (P = .04) and energy (P = .04) decreased by week 3 of follow-up sessions from 14 to 13 g/100 mL and from 82 to 76 Kcal/100 mL, respectively; however, these changes became insignificant when expression volume was taken into account. The macronutrient concentration was similar for the left and right breasts; however, milk composition varied markedly between mothers. Furthermore, average 24-hour fat content was significantly lower than the mean fat content from a single expression session (P < .01). Our findings highlight that when determining the nutritional adequacy of a mother's milk, assuming an average concentration requires caution. The study findings illustrate the importance of using average 24-hour fat content of milk to obtain representative measures of infant energy intake.

  13. 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.

  14. The bandgap distribution investigated across the strain-induced bending ZnO nanowire

    NASA Astrophysics Data System (ADS)

    Tse, Geoffrey; Yu, Dapeng

    2016-12-01

    In this work, the strain dependence of electronic and optical properties in wurtzite zinc oxide (ZnO) lattice were explored. Ab initio density functional theory (DFT) was used in evaluating the energy bandgap and the dielectric tensor, respectively. The influence on the bandgap due to the shear distortion was so small that the reducing linear trends on uniaxial compressive/tensile strain were reported, in which the evolution of the absorption curve with uniaxial strain agrees well with the experimental results across the bending section. This study provides a set of useful data in analyzing the evolution of the optical adsorption across the bending ZnO nanowire, and gives a systematic explanation to the available experiments from the electronic structure’s perspective.

  15. Determining horizontal displacement and strains due to subsidence. Rept. of Investigations/1991

    SciTech Connect

    Tandanand, S.; Powell, L.R.

    1991-01-01

    Horizontal displacements and ground strains induced by mine subsidence are significant information needed for calculating damage and developing precautions against subsidence effects on surface structures. To devise a simple method for determining the surface horizontal displacements and strains simultaneously with the subsidence prediction, the U.S. Bureau of Mines examined the significance of the tilt number, which is the proportionality constant in the relationship between the horizontal displacement and the slope of the subsidence profile. The ratio of the tilt number to the critical radius of the subsidence trough is identical to the ratio of the maximum possible horizontal displacement to the full subsidence, which is found to be constant in most European coalfields. If this ratio is known for a particular minesite in the United States, then horizontal displacement and ground strains can be readily obtained from the primary subsidence data.

  16. Investigation of equinoctial asymmetry in the latitudinal variation of zonal scintillation drift

    NASA Astrophysics Data System (ADS)

    Abadi, P.; Otsuka, Y.; Shiokawa, K.; Shinagawa, H.; Liu, H.

    2016-12-01

    We investigate latitudinal variation of zonal scintillation drift for Mar and Sep equinox by using three single-frequency GPS receivers spaced closely with mutual distances 100 m, in Kototabang (0.2°S, 100.3°E; Mag. Lat.: 9.9°S), Indonesia. The zonal drift is estimated from cross-correlation analysis of time series of GPS signal intensity among the three receivers. We have collected the zonal drift data for Mar and Sep during 20-24 LT in 2003-2015. Fig. 1 shows the latitudinal profile of zonal drift velocity both for Mar and Sep which are classified also into high and moderate solar activity levels (F10.7). As shown in Fig. 1, the latitudinal gradient of zonal shear is negative for both Mar and Sept and at both moderate and high F107. The negative gradient indicates that the zonal drift velocity is larger at magnetic equator and that it decreases as increasing the latitude. Our interesting finding is that the latitudinal gradient of the zonal drift velocity in Mar equinox is more negative than that in Sep equinox at both moderate and high F10.7. Because the zonal scintillation drift velocity can be assumed to represent the zonal background plasma drift in the nighttime F-region, we can consider that latitudinal shear of zonal background plasma drift in Mar equinox is more negative than that in Sep equinox. Furthermore, the zonal background plasma drift is caused by zonal neutral wind through the F-region dynamo. We then investigate the latitudinal shear of zonal neutral wind velocity for Mar and Sep equinoxes, obtained by in-situ measurement from CHAMP satellite (altitude of 400 km). Fig. 2 shows the latitudinal variation of the zonal wind velocity. Interestingly, we also find that the latitudinal gradient of the zonal wind is more negative in Mar equinox than that in Sep equinox at both moderate and high F10.7. We find also the equinoctial asymmetry in the latitudinal variation of the zonal wind. We, thus, conclude that the equinoctial asymmetry of zonal drift

  17. Investigation of seasonal Be-7 variation near the Martian Poles using Mars Odyssey GRS data

    NASA Astrophysics Data System (ADS)

    Kim, Kyeong Ja; Boynton, William; Hamara, Dave

    (7) Be variation near the Martian Poles using Mars Odyssey has been investigated for about two Martian years. (7) Be is a cosmogenic nuclide produced via nuclear spallation interaction with carbon and oxygen in the atmosphere of the Mars. Because CO _{2} is main constituent of the atmosphere of the Mars and it condenses during winter season and sublimes in spring, and also it is transferred from the northern hemisphere to southern hemisphere. We assumed that the pattern of air movement could be monitored by the (7) Be production in the atmosphere. Since (7) Be peak is superimposed with (10) B which has a wide peak area and is from the background material of HPGe crystal. For this study, (7) Be peak area is defined using the thick target experiment and the influenced region due to (10) B is eliminated for (7) Be peak analysis. Our results show that the variation of (7) Be activity at 15 degree gives a lot of noise except the time associated with (7) Be spike due to solar particle event. However, the variations of (7) Be activity for 30 degree show that there is a peak rise at L _{s}100 for North Pole and L _{s}180 for South Pole. In the case of (7) Be activities at mid latitudes for L _{s}125 and L _{s}190 are distinctively higher than the rest of the seasonal zones. This implies that (7) Be activity was higher at the summer of northern hemisphere and fall season of southern hemisphere. This could be a significant and real effect associated with air density increase; therefore, the production of (7) Be increases for these seasons. Our results also show that there were two (7) Be spikes due to solar particle events observed. These spikes are distinctively high compared to the effect from the Martian atmospheric density changes. Our result of (7) Be activity of Mars could be less significant in understanding air circulation. However, this result indicated that a possible study where atmospheric density is high could be investigated with this technique including the

  18. 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

  19. Experimental investigation of strains in fabric under biaxial and shear forces.

    NASA Technical Reports Server (NTRS)

    Alley, V. L., Jr.; Faison, R. W.

    1972-01-01

    The paper defines the experimental phase of an objective to obtain the mechanical characteristics and coefficients required by the generalized form of Hooke's law for nylon-polyurethane-coated fabric. Test specimens were cylindrical fabric sleeves and were loaded in axial tension by an Instron, in hoop tension by pressurizing, and in shear by a torquing fixture. An extensive amount of strain data is included for a wide combination of the three membrane loads. The tests indicate highly nonlinear stress-strain characteristics of the fabric and a strong dependency on all three membrane loads.

  20. Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains.

    PubMed

    Hardy, Katherine J; Oppenheim, Beryl A; Gossain, Savita; Gao, Fang; Hawkey, Peter M

    2006-01-01

    Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.

  1. Arterial Blood Gases, Electrolytes and Metabolic Indices Associated with Hemorrhagic Shock: Inter-and Intrainbred Rat Strain Variation

    DTIC Science & Technology

    2013-03-07

    intake postsurgery became a part of the model. Such alterations may result in some baseline changes in a strain-dependent manner. As expected, strain...Lancet 1: 521–527, 1963. 9. Carey LC, Lowery BD, Cloutier CT. Blood sugar and insulin response of humans in shock. Ann Surg 172: 342–350, 1970. 10

  2. Radial oscillations of thin cylindrical and spherical shells: investigation of Lie point symmetries for arbitrary strain-energy functions

    NASA Astrophysics Data System (ADS)

    Roussos, N.; Mason, D. P.

    2005-03-01

    The Lie point symmetry structure of the second order differential equations which describe non-linear radial oscillations of thin-walled hyperelastic cylindrical and spherical shells is investigated. The differential equations depend on the strain-energy function and on the net applied surface pressure. If the net applied surface pressure is time independent, the differential equations admit the Lie point symmetry corresponding to time translational invariance for arbitrary strain-energy functions. Other Lie point symmetries exist for each equation only for special classes of strain-energy function. For the cylindrical shell the special class includes the Mooney-Rivlin strain-energy function and the differential equation reduces to the Ermakov-Pinney equation. A new solution is obtained for a specific time dependent net applied surface pressure. For the spherical shell the special class does not include the Mooney-Rivlin strain-energy function. For free oscillations the differential equation reduces to the Ermakov-Pinney equation but there also exists a special net applied surface pressure and for this pressure the differential equation is more general than the Ermakov-Pinney equation.

  3. An experimental investigation of strain rate, temperature and humidity effects on the mechanical behavior of a perfluorosulfonic acid membrane

    NASA Astrophysics Data System (ADS)

    Lu, Zongwen; Lugo, Melissa; Santare, Michael H.; Karlsson, Anette M.; Busby, F. Colin; Walsh, Peter

    2012-09-01

    The time-dependent hygro-thermal mechanical behavior of a perfluorosulfonic acid (PFSA) membrane (Nafion® 211 membrane) commonly used in Proton Exchange Membrane Fuel Cells (PEMFCs) is investigated at selected strain rates for a broad range of temperatures and humidities. Tensile tests and relaxation tests are conducted to determine Young's modulus and proportional limit stress as functions of strain rate, temperature and humidity. The results show that Young's modulus and proportional limit stress increase as the strain rate increases, and decrease as the temperature or humidity increases. The results also show that the mechanical response of Nafion® 211 membrane is more sensitive to typical changes in strain rate or temperature than to typical changes in humidity. In addition, two temperature/humidity cycles are conducted to determine the steady state swelling behavior of Nafion® 211 membrane as a function of temperature and humidity. The results show that the membrane swells with increasing temperature and humidity, and that there is little or no hygro-thermal history effect for the swelling strains.

  4. [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.

  5. Variation in composition and relative content of accumulated photopigments in a newly isolated Rhodobacter capsulatus strain XJ-1 in response to arsenic.

    PubMed

    Lin, Hua Z; Yue, Ying H; Lü, Jiang C; Zhao, Gui C; Yang, Ping S

    2014-01-01

    This study aimed to isolate and characterize a new arsenic (As)-tolerant bacterial strain (XJ-1) from the Halosol soil, to evaluate its As tolerance, and to examine the variation in composition and relative content of accumulated photosynthetic pigments in response to As. The experiments were performed with high-performance liquid chromatography (HPLC), inductively-coupled plasma mass spectrometry (ICP-MS), liquid chromatography/mass spectrometry (LC/MS), thin-layer chromatography (TLC) and grayscale intensity image analysis using Gel-Pro analyzer software. Strain XJ-1 was identified as Rhodobacter (R.) capsulatus based on 16S rRNA gene sequencing and physiological characteristics. Strain XJ-1 was able to grow when exposed to arsenite [As(III)] and arsenate [As(V)] under anaerobic-light conditions. The median effective concentrations (EC50) of As(III) and As(V) were 0.61 mM and 2.03 mM, respectively. Strain XJ-1 could reduce As(V) to As(III), but As(III) could not be transformed back to As(V) or other organic As compounds. Accumulation of bacteriochlorophylls and carotenoids in strain XJ-1 varied in the presence of 0.2-1.2 mM As(III) and 0-2.5 mM As(V). As exposure resulted in pronounced variation in compositions and contents of photosynthetic pigments, especially hydroxyspheroidene, bacteriophaeophytin, the ratio of tetrahydrogeranylgeranyl to phytylated BChl a, and the ratio of spheroidene to spheroidenone. This research highlights the adaptative response of R. capsulatus strain XJ-1 photosystems to environmental As, and demonstrates the potential of utilizing the sensitivity of its photosynthetic pigments to As(III) and As(V) for the biodetection of As in the environment.

  6. Effect of straining graphene on nanopore creation using Si cluster bombardment: A reactive atomistic investigation

    NASA Astrophysics Data System (ADS)

    Berdiyorov, G. R.; Mortazavi, B.; Ahzi, S.; Peeters, F. M.; Khraisheh, M. K.

    2016-12-01

    Graphene nanosheets have recently received a revival of interest as a new class of ultrathin, high-flux, and energy-efficient sieving membranes because of their unique two-dimensional and atomically thin structure, good flexibility, and outstanding mechanical properties. However, for practical applications of graphene for advanced water purification and desalination technologies, the creation of well controlled, high-density, and subnanometer diameter pores becomes a key factor. Here, we conduct reactive force-field molecular dynamics simulations to study the effect of external strain on nanopore creation in the suspended graphene by bombardment with Si clusters. Depending on the size and energy of the clusters, different kinds of topography were observed in the graphene sheet. In all the considered conditions, tensile strain results in the creation of nanopores with regular shape and smooth edges. On the contrary, compressive strain increases the elastic response of graphene to irradiation that leads to the formation of net-like defective structures with predominantly carbon atom chains. Our findings show the possibility of creating controlled nanopores in strained graphene by bombardment with Si clusters.

  7. Root surface strain during canal shaping and its influence on apical microcrack development: a preliminary investigation.

    PubMed

    Jamleh, A; Komabayashi, T; Ebihara, A; Nassar, M; Watanabe, S; Yoshioka, T; Miyara, K; Suda, H

    2015-12-01

    To determine the root surface strain (RSS) generated during root canal shaping and its effects on apical microcrack development. Twenty-five extracted human mandibular premolars were selected and decoronated. The teeth were instrumented with either the ProTaper (PT) or WaveOne (WO) (Dentsply Maillefer) NiTi rotary systems (n = 10 per group) or used as controls (n = 5). Instrumented root canals were enlarged to ProTaper F4 (size 40, 0.06 taper) or using WaveOne LARGE (size 40, 0.08 taper) instruments according to the manufacturer's instructions. An electrical strain gage (KFG02-120-C1-16, Kyowa Dengyo, Tokyo, Japan) was fixed on the proximal root surface and connected to a strain amplifier via a bridge box in order to measure RSS. During canal shaping, the strain output of the amplifier was recorded. The instantaneous RSS induced by each instrument and the maximum RSSs were determined. All teeth were then stained with contrast media and imaged with micro-computed tomography (micro-CT) at an isotropic resolution of 10 μm to detect microcracks. The mean maximum RSS values (microstrain) and mean number of microcracks recorded for both groups were tested for statistical significance using Mann-Whitney U-test. Presence/absence of microcracks in both groups was compared by chi-square tests. Increased baseline RSS from strain accumulation during canal shaping was observed, with similar maximum RSS (mean ± SD) for PT (416.6 ± 185.1 μstrain) and WO (398.2 ± 163.8 μstrain) (P = 0.94). The interevaluator reliability for microcrack detection using micro-CT had a kappa value of 0.998. Compared to the PT group, there was a trend for fewer samples with microcracks in the WO group (P = 0.051). On the micro-CT images, apical microcracks were detected in 20 PT and 11 WO samples (P = 0.10). The microcracks were observed in the buccolingual direction in all WO and 81% of PT samples. No vertical root fractures were found. The maximum RSS obtained during canal

  8. Investigation of Helium Isotope Variations of Alkaline Volcanic Rocks in Kutahya Region

    NASA Astrophysics Data System (ADS)

    Cesur, Duru; Mutlu, Halim; Aldanmaz, Ercan; Güleç, Nilgün; Stuart, Finlay M.

    2016-04-01

    The noble gases, in particular helium isotopes, provide valuable information on the mantle source of recent basaltic volcanism, especially when linked to trace elements and radiogenic isotopes. Although the alkaline volcanics in the Kütahya region have been studied in detail by several works by means of trace element variations, radiogenic dating and isotope systematics, noble gas isotope compositions that could significantly contribute to dynamics of volcanism have not been investigated yet. In this study which aims to fill the deficiency of such data, helium isotope compositions of olivine-basalts in Kütahya region are measured. In this study we report helium isotope compositions of olivine from basalts. In olivine-basalts in alkaline volcanic rocks from the Kütahya region, western Turkey, are investigated. 3He/4He range from 3.0 to 5.19 Ra. These low helium isotope values are most probably indicative of a lithospheric mantle source. Kütahya alkaline volcanics are enriched in incompatible elements and show prominent negative Ti, Nd and Ta anomaly. Primitive mantle normalized trace element concentration patterns clearly display continental crustal contamination. Chemical compositions and helium isotope systematics imply contribution of a lithospheric mantle source and contamination of continental crust in the genesis of the Kütahya alkaline lavas. Keywords: Kütahya alkaline rocks, olivine, helium isotope, crust-mantle interaction Acknowledgement: This study has been supported by TUBITAK (Project No. 112Y366)

  9. 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.

  10. Investigating precipitation patterns and delta O18 variations in northern Siberia

    NASA Astrophysics Data System (ADS)

    Darvishsefat, Neda; Werner, Martin; Meyer, Hanno; Lohmann, Gerrit

    2017-04-01

    This study is being conducted as part of the PLOT project (Paleolymnological Transect - Quaternary climate gradients in northern Eurasia), which investigates glacial-interglacial changes of the hydrological cycle in the Eurasian Arctic in the late quaternary. The area of interest in this project is along a west-eastern transect in Northern Russia, from Ladoga lake to El gygytgyn lake, where quaternary climate variations in this region will be studied by selected lake sediments which cover the related period of interest. In our study, we focus on variations of the stable isotopes of water (H218O and HDO). They act as tracers of climate processes that influence the hydrological cycle and can be used as a proxy to describe changes in the climate. Changes in the fractionation of both oxygen and hydrogen isotopes, delta 18O and delta D, in precipitation and its relation to changes of both climate variables (e.g. temperature) and the hydrological cycle (e.g. precipitation amount) are the main variables of interest. For this purpose, our study utilizes a set of new simulations with the model ECHAM5-WISO, an atmospheric general circulation model with implemented stable water isotope diagnostics, to study the isotope variations in northern Siberia. For the present-day and last glacial maximum (LGM) climate, ECHAM5-WISO has been run with a high horizontal model resolution of approx. 1°x1° (T106 resolution). Model results are compared both to proxy data as well as simulation results using the fully-coupled Earth system model ECHAM5/MPIOM, which has been run in coarser spatial resolution, only. First analyses compare simulated monthly means of d18O in precipitation, temperature and precipitation amount, as well as interannual values, to observational datasets near the different PLOT lake sites and at further locations (Tiksi, Yakutsk, Irkutsk) in northern Siberia. For the present-day climate, monthly temperatures are well simulated in the ECHAM5-wiso simulation

  11. 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.

  12. Investigating of spatial variations of PM2.5 concentration in Suzhou using remote sensing imagery

    NASA Astrophysics Data System (ADS)

    Zhang, Shanzheng; Li, Bailiang

    2017-04-01

    Suzhou is located at the center of Yangtze Delta, suffering the air pollution from construction of mega city, industrial emission and traffic development. Particulate matter not greater than 2.5 micrometers (PM2.5) is now considered as the most important pollutants in the air in East China. For Suzhou city, some studies on PM2.5 temporal variations based on ground measurements have been conducted. However, until now, there is limited remote sensing based research to investigate the spatial pattern of PM2.5 in Suzhou. MODIS is often used to evaluate the spatial variabiilty of air quality, however, due to its low spatial resolution (250m), we have adopted China launched HJ-1 satellite with 30 m resolution of CCD sensor. Following the solar radiation S6 model and dark object atmospheric correction method (Kaufman,et al., 2000), atmospheric optical depth (AOD) was estimated. A statistical relationship has been built up between AOD and PM2.5. We have retrieved the spatial distribution of PM2.5 across Suzhou city in the winter of 2014. Results indicate that PM2.5 has the highest value in Kunshan (East of Suzhou) and Changshu and Taicang (NE of Suzhou) due to the heavy-polluted industry, while in the island of the Taihu Lake, the PM2.5 is significantly lower than other places maybe because of high deposition rate of PM2.5 over water and forest surfaces. The spatial variation also shows that traffic has less contribution to the PM2.5 generation than the industry. We believe this study will be very useful to identify the causes of local PM2.5 pollution. The findings could also benefit local management and policy making.

  13. Investigation on seasonal variations of Be-7 and H-3 in the rainwater of Korea

    NASA Astrophysics Data System (ADS)

    Kim, K. J.; Choi, Y.; Yoon, Y. Y.; Sohn, J.

    2014-12-01

    Both Beryllium-7 (Be-7) and Tritium (H-3) are produced by cosmic ray interactions in upper atmosphere by spallation reactions. We investigated these nuclides in rainwater along with sodium concentration in the region of Deajeon, Korea (36.32°N, 127.41°E) for 7 months during 2007 and 2008. The results of our study demonstrate that Be-7 in rainwater is inversely propotional to the amount of sodium, proportional to the amount of rainwater and air mixing of the stratosphere in sping. Both isotopes show their peaks during fall and spring seasons. The trend of H-3 variation is shifted about a month compared to that of Be-7. This could be due to the different residence time between H-3 and Be-7 in the atmosphere. The detection efficiency of uncorrected Be-7 concentrations in this area ranged from 0.06 to 14.13 Bq/L which is lower than the reference values of New Zealand (0.5 ~ 4.3 x 107 (atoms/kg rain)) and Japan. The H-3 concentrations of this study ranged from 4.8±0.10 and 18.6±0.3 (TU). This range is well compared to the H-3 concentration of the Northern Hemisphere. Also, sodium variation of the rainwater is found to be inversely proportaional to Be-7 concentrations. This could be associated with air mixing phenomenon involved in the movement of salt in land of Korea. This presentation demonstrates details in both chemistry and data analysis along with other previously published data. This study will provide reference values of Be-7 for the Korean region and will guide a prospective geolgical application associated with atmospheric cosmogenic nuclide production.

  14. 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.

  15. Structural and optical investigation of InAsxP1-x/InP strained superlattices

    NASA Astrophysics Data System (ADS)

    Lamberti, C.; Bordiga, S.; Boscherini, F.; Mobilio, S.; Pascarelli, S.; Gastaldi, L.; Madella, M.; Papuzza, C.; Rigo, C.; Soldani, D.; Ferrari, C.; Lazzarini, L.; Salviati, G.

    1998-01-01

    We report a complete characterization of InAsxP1-x/InP (0.05variations, which accommodate the nearly constant As-In bond length. In our investigation we characterize not only very high quality heterostructures but also samples showing serious interface problems such as nonplanarity and/or a consistent chemical spread along the growth axis. In the study presented here we thus propose a general method, based on

  16. 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.

  17. A theoretical investigation of orientation relationships and transformation strains in steels.

    PubMed

    Koumatos, K; Muehlemann, A

    2017-03-01

    The identification of orientation relationships (ORs) plays a crucial role in the understanding of solid phase transformations. In steels, the most common models of ORs are the ones by Nishiyama-Wassermann (NW) and Kurdjumov-Sachs (KS). The defining feature of these and other OR models is the matching of directions and planes in the parent face-centred cubic γ phase to ones in the product body-centred cubic/tetragonal α/α' phase. In this article a novel method that identifies transformation strains with ORs is introduced and used to develop a new strain-based approach to phase-transformation models in steels. Using this approach, it is shown that the transformation strains that leave a close-packed plane in the γ phase and a close-packed direction within that plane unrotated are precisely those giving rise to the NW and KS ORs when a cubic product phase is considered. Further, it is outlined how, by choosing different pairs of unrotated planes and directions, other common ORs such as the ones by Pitsch and Greninger-Troiano can be derived. One of the advantages of our approach is that it leads to a natural generalization of the NW, KS and other ORs for different ratios of tetragonality r of the product body-centred tetragonal α' phase. These generalized ORs predict a sharpening of the transformation textures with increasing tetragonality and are thus in qualitative agreement with experiments on steels with varying alloy concentration.

  18. Diffusion behavior of Cu/Ta heterogeneous interface under high temperature and high strain: An atomistic investigation

    NASA Astrophysics Data System (ADS)

    Li, Ganglong; Wu, Houya; Luo, Honglong; Chen, Zhuo; Tay, Andrew A. O.; Zhu, Wenhui

    2017-09-01

    Three-dimensional (3D) integration technology using Cu interconnections has emerged as a promising solution to improve the performance of silicon microelectronic devices. However, Cu diffuses into SiO2 and requires a barrier layer such as Ta to ensure acceptable reliability. In this paper, the effects of temperature and strain normal to the interface on the inter-diffusion of Cu and Ta at annealing conditions are investigated using a molecular dynamics (MD) technique with embedded atomic method (EAM) potentials. Under thermal annealing conditions without strain, it is found that a Cu-rich diffusion region approximately 2 nm thick is formed at 1000 K after 10 ns of annealing. Ta is capable of diffusing into the interior of Cu but Cu hardly diffuses into the inner lattice of Ta. At the Cu side near the interface an amorphous structure is formed due to the process of diffusion. The diffusion activation energy of Cu and Ta are found to be 0.9769 and 0.586 eV, respectively. However, when a strain is applied, a large number of crystal defects are generated in the sample. As the strain is increased, extrinsic stacking faults (ESFs) and lots of Shockley partial dislocations appear. The density of the dislocations and the diffusion channels increase, promoting the diffusion of Cu atoms into the inner lattice of Ta. The thickness of the diffusion layer increases to 4 times the value when only a temperature load of 700 K is applied. The MD simulations demonstrated that Ta is very effective as a barrier layer under thermal loading only, and its effectiveness is impaired by tensile strain at the Cu/Ta interface. The simulations also clarified the mechanism that caused the impairment. The methodology and approach described in this paper can be followed further to study the effectiveness of barrier layers under various annealing and strain conditions, and to determine the minimum thickness of barrier layers required for a particular application.

  19. 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.

  20. Numerical Investigation of the Dynamic Compressive Behaviour of Rock Materials at High Strain Rate

    NASA Astrophysics Data System (ADS)

    Hao, Y.; Hao, H.

    2013-03-01

    The dynamic compressive strength of rock materials increases with the strain rate. They are usually obtained by conducting laboratory tests such as split Hopkinson pressure bar (SHPB) test or drop-weight test. It is commonly agreed now that the dynamic increase factor (DIF) obtained from impact test is affected by lateral inertia confinement, friction confinement between the specimen and impact materials and the specimen sizes and geometries. Therefore, those derived directly from testing data do not necessarily reflect the true dynamic material properties. The influences of these parameters, however, are not straightforward to be quantified in laboratory tests. Therefore, the empirical DIF relations of rock materials obtained directly from impact tests consist of contributions from lateral inertia and end friction confinements, which need be eliminated to reflect the true dynamic material properties. Moreover, different rocks, such as granite, limestone and tuff have different material parameters, e.g., equation of state (EOS) and strength, which may also affect the DIF of materials but are not explicitly studied in the open literature. In the present study, numerical models of granite, limestone and tuff materials with different EOS and strength under impact loads are developed to simulate SHPB tests and to study the influences of EOS and strength, lateral inertia confinement and end friction confinement effects on their respective DIFs in the strain rate range between 1 and 1,000 s-1. The commercial software AUTODYN with user-provided subroutines is used to perform the numerical simulations of SHPB tests. Numerical simulation results indicate that the lateral inertia confinement, friction confinement and specimen aspect ( L/ D) ratio significantly influence DIF obtained from impact tests and the inertia confinement effect is different for different rocks. Based on the numerical results, quantifications on the relative contributions from the lateral inertia

  1. Variations in biofilm formation, desiccation resistance and Benzalkonium chloride susceptibility among Listeria monocytogenes strains isolated in Canada.

    PubMed

    Piercey, Marta J; Ells, Timothy C; Macintosh, Andrew J; Truelstrup Hansen, Lisbeth

    2017-09-18

    Listeria monocytogenes is a pathogenic foodborne microorganism noted for its ability to survive in the environment and food processing facilities. Survival may be related to the phenotype of individual strains including the ability to form biofilms and resist desiccation and/or sanitizer exposure. The objectives of this research were to compare 14 L. monocytogenes strains isolated from blood (3), food (6) and water (5) with respect to their benzalkonium chloride (BAC) sensitivity, desiccation resistance, and ability to form biofilm. Correlations were tested between those responses, and the presence of the SSI-1 (Stress Survival Islet) and LGI1/CC8 (Listeria Genomic Island 1 in a clonal complex 8 background) genetic markers. Genetic sequences from four strains representing different phenotypes were also probed for predicted amino acid differences in biofilm, desiccation, and membrane related genes. The water isolates were among the most desiccation susceptible strains, while strains exhibiting desiccation resistance harboured SSI-1 or both the SSI-1 and LGI1/CC8 markers. BAC resistance was greatest in planktonic LGI1/CC8 cells (relative to non-LGI1/CC8 cells), and higher BAC concentrations were also needed to inhibit the formation of biofilm by LGI1/CC8 strains during incubation for 48h and 6days compared to other strains. Formation of biofilm on stainless steel was not significantly (p>0.05) different among the strains. Analysis of genetic sequence data from desiccation and BAC sensitive (CP4 5-1, CP5 2-3, both from water), intermediate (Lm568, food) and desiccation and BAC resistant (08 5578, blood, human outbreak) strains led to the finding of amino acid differences in predicted functional protein domains in several biofilm, desiccation and peptidoglycan related genes (e.g., lmo0263, lmo0433, lmo0434, lmo0771, lmo0973, lmo1080, lmo1224, lmo1370, lmo1744, and lmo2558). Notably, the LGI1/CC8 strain 08-5578 had a frameshift mutation in lmo1370, a gene previously

  2. Nanoindentation of lemur enamel: an ecological investigation of mechanical property variations within and between sympatric species.

    PubMed

    Campbell, Sara E; Cuozzo, Frank P; Sauther, Michelle L; Sponheimer, Matt; Ferguson, Virginia L

    2012-06-01

    The common morphological metrics of size, shape, and enamel thickness of teeth are believed to reflect the functional requirements of a primate's diet. However, the mechanical and material properties of enamel also contribute to tooth function, yet are rarely studied. Substantial wear and tooth loss previously documented in Lemur catta at the Beza Mahafaly Special Reserve suggests that their dental morphology, structure, and possibly their enamel are not adapted for their current fallback food (the mechanically challenging tamarind fruit). In this study, we investigate the nanomechanical properties, mineralization, and microstructure of the enamel of three sympatric lemur species to provide insight into their dietary functional adaptations. Mechanical properties measured by nanoindentation were compared to measurements of mineral content, prism orientation, prism size, and enamel thickness using electron microscopy. Mechanical properties of all species were similar near the enamel dentin junction and variations correlated with changes in microstructure (e.g., prism size) and mineral content. Severe wear and microcracking within L. catta's enamel were associated with up to a 43% reduction in nanomechanical properties in regions of cracking versus intact enamel. The mechanical and material properties of L. catta's enamel are similar to those of sympatric folivores and suggest that they are not uniquely mechanically adapted to consume the physically challenging tamarind fruit. An understanding of the material and mechanical properties of enamel is required to fully elucidate the functional and ecological adaptations of primate teeth. Copyright © 2012 Wiley Periodicals, Inc.

  3. 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.

  4. Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique.

    PubMed

    Salles, N; Richard, N; Mousseau, N; Hemeryck, A

    2017-08-07

    The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth.

  5. Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique

    NASA Astrophysics Data System (ADS)

    Salles, N.; Richard, N.; Mousseau, N.; Hemeryck, A.

    2017-08-01

    The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth.

  6. Serotyping of Brunei pneumococcal clinical strains and the investigation of their capability to adhere and invade a brain endothelium model.

    PubMed

    Rahman, Nurul Adhwa; Sharudin, Aishah; Diah, Suwarni; Muharram, Siti Hanna

    2017-09-01

    Pneumococcal infections have caused morbidity and mortality globally. Streptococcus pneumoniae (pneumococci) are commensal bacteria that colonize the nasopharynx, asymptomatically. From there, pneumococci can spread in the lungs causing pneumonia and disseminate in the bloodstream causing bacteremia (sepsis) and reach the brain leading to meningitis. Endothelial cells are one of the most important components of the blood-brain barrier that separates the blood from the brain and plays the first protective role against pneumococcal entry. Thus this study aimed to investigate on the ability of non-meningitis pneumococcal clinical strains to adhere and invade a brain endothelium model. Two pneumococcal Brunei clinical strains were serotyped by multiplex PCR method using oligonucleotide sequences derived from Centers for Disease Control and Prevention. A validated immortalised mouse brain endothelial cell line (bEnd.3) was used as a brain endothelium model for the study of the pneumococcal breach of the blood-brain barrier using an adherence and invasion assay. Both of the pneumococcal clinical strains were found to be serotype 19F, a common circulating serotype in Southeast Asia and globally and possess the ability to adhere and invade the brain endothelial cells. In addition, this is the first report on the serotype identification of pneumococci in Brunei Darussalam and their application on a brain endothelium model. Further studies are required to understand the virulence capabilities of the clinical strains. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. An Investigation into the Gravity Current Aspects of a Cold Air Outbreak Using Variational Analysis Techniques

    DTIC Science & Technology

    1988-01-01

    temperatures dropped 30 degrees in a matter of hours in central Florida with dramatic drops in dewpoint as well. A method is developed using variational ... calculus to decompose observed gridded radiosonde data from this period into component fields. Three variational filters are used iteratively to extract

  8. Investigating different filter and rescaling methods on simulated GRACE-like TWS variations for hydrological applications

    NASA Astrophysics Data System (ADS)

    Zhang, Liangjing; Dobslaw, Henryk; Dahle, Christoph; Thomas, Maik; Neumayer, Karl-Hans; Flechtner, Frank

    2017-04-01

    By operating for more than one decade now, the GRACE satellite provides valuable information on the total water storage (TWS) for hydrological and hydro-meteorological applications. The increasing interest in use of the GRACE-based TWS requires an in-depth assessment of the reliability of the outputs and also its uncertainties. Through years of development, different post-processing methods have been suggested for TWS estimation. However, since GRACE offers an unique way to provide high spatial and temporal scale TWS, there is no global ground truth data available to fully validate the results. In this contribution, we re-assess a number of commonly used post-processing methods using a simulated GRACE-type gravity field time-series based on realistic orbits and instrument error assumptions as well as background error assumptions out of the updated ESA Earth System Model. Three non-isotropic filter methods from Kusche (2007) and a combined filter from DDK1 and DDK3 based on the ground tracks are tested. Rescaling factors estimated from five different hydrological models and the ensemble median are applied to the post-processed simulated GRACE-type TWS estimates to correct the bias and leakage. Time variant rescaling factors as monthly scaling factors and scaling factors for seasonal and long-term variations separately are investigated as well. Since TWS anomalies out of the post-processed simulation results can be readily compared to the time-variable Earth System Model initially used as "truth" during the forward simulation step, we are able to thoroughly check the plausibility of our error estimation assessment (Zhang et al., 2016) and will subsequently recommend a processing strategy that shall also be applied for planned GRACE and GRACE-FO Level-3 products for terrestrial applications provided by GFZ. Kusche, J., 2007:Approximate decorrelation and non-isotropic smoothing of time-variable GRACE-type gravity field models. J. Geodesy, 81 (11), 733-749, doi:10

  9. Investigation of Seasonal Variation Within the Eastern Equatorial Hydrogen Signal, Mars

    NASA Astrophysics Data System (ADS)

    Clevy, J. R.; Elphic, R. C.; Kattenhorn, S. A.

    2006-12-01

    The Neutron Spectrometer (NS) on board NASA's Mars Odyssey has identified two mid-latitude regions of low epithermal neutron flux, which are predicted to have a high weight percent of hydrogen in the top meter of regolith. In a previous study of the Eastern Equatorial Hydrogen (EEH), centered on Schiaparelli Basin, we draped the NS signal over a digital elevation model to define the spatial extent and topographic placement of the EEH reserve. All of the available records were included in the study, producing a static, time-averaged map. A bimodal relationship between the hydrogen concentration and topography emerged with north-facing slopes and low-lying areas both showing low epithermal counts. To determine the processes driving the hydrogen accumulation it was necessary to ascertain whether these areas represented static deposits of hydrogen or seasonally variable concentrations. Certain hydrogen sources, jarosite for example, would be expected in low-lying, poorly- or slowly-drained areas. Such deposits should map out as fixed areas of low flux with little if any seasonal variation. To best preserve seasonal effects, the Martian year was broken down into eight seasons, each covering 45 degrees of solar latitude (Ls), and grouped into pairs that bracket each solstice and equinox as experienced in the northern hemisphere (e.g. early and late summer are the 45 degrees before and after the summer solstice at 90° Ls). A time sequence was created using each season from each year of atmospherically corrected NS data. Preliminary investigation of the time sequence indicates that in addition to expected areas of stable low flux, there is some seasonal variability across the EEH, hinting at a mobile component in the signal as well. Topographic control of the hydrogen was apparent along the highlands separating the Schiaparelli Basin from Hellas Basin and most evident in a NE--SW trend from -11°S, 49°E down to -21°S, 35°E. While the EEH is roughly circular, the

  10. Variation in the production and distribution of substituted benzoquinone compounds among genetic strains of the confused flour beetle, Tribolium confusum.

    PubMed

    Yezerski, A; Gilmor, T P; Stevens, L

    2000-01-01

    Insects often produce chemicals, such as defensive compounds, whose quantity and distribution can affect their fitness. For evolution to produce adaptations, chemical production must be genetically variable. Here we report the results of a study using high-performance liquid chromatography to quantify two important chemical secretions of the flour beetle Tribolium confusum, methyl-1, 4-benzoquinone (MBQ) and ethyl-1,4-benzoquinone (EBQ). Our results show a distinct difference in the production of the compounds among four genetically distinct strains of T. confusum (b-+, b-I, b-IV, b-Pakistan) with an unusually high amount measured for the b-Pakistan strain. By measuring internal and external benzoquinone levels separately, we were also able to detect differences in production and distribution of the compounds between the strains. Some strains secrete more of the chemicals, whereas other strains appear to sequester the compounds within their bodies. The sexes also differ in total quinone production as well as in their internal to external benzoquinone ratios, suggesting the trait is sex influenced. Finally, a consistent correlation in the amounts of MBQ to EBQ in individual beetles suggests that the substituted benzoquinones share a common precursor or pathway.

  11. On the origin of residual strain in shape memory alloys: experimental investigation on evolutions in the microstructure of CuAlBe during complex thermomechanical loadings

    NASA Astrophysics Data System (ADS)

    Barati, M.; Arbab Chirani, S.; Kadkhodaei, M.; Saint-Sulpice, L.; Calloch, S.

    2017-02-01

    The behaviors of shape memory alloys (SMAs) strongly depend on the presence of different phases: austenite, thermally-induced martensite and stress-induced martensite. Consequently, it is important to know the phase volume fraction of each phases and their evolution during thermomechanical loadings. In this work, a three-phase proportioning method based on electric resistivity variation of a CuAlBe SMA is proposed. Simple thermomechanical loadings (i. e. pseudoplasticity and pseudoelasticity), one-way shape memory effect, recovery stress, assisted two-way memory effect at different level of stress and cyclic pseudoelasticity tests are investigated. Based on the electric resistivity results, during each loading path, evolution of the microstructure is determined. The origin of residual strain observed during the considered thermomechanical loadings is discussed. A special attention is paid to two-way shape memory effect generated after considered cyclic loadings and its relation with the developed residual strain. These results permit to identify and to validate the macroscopic models of SMAs behaviors.

  12. Investigating the Biosynthesis of Membrane-spanning Lipids Using Model Strains of Acidobacteria

    NASA Astrophysics Data System (ADS)

    Bradley, A. S.; Chubiz, L. M.

    2016-12-01

    Glycerol dialkyl glycerol tetraethers (GDGTs), deriving from the membrane-spanning lipids of microbes, are detected in a wide range of environments including marine and lacustrine waters, sediments, and in terrestrial soils. In sediments and soils, ratios of various GDGT structures form the basis of the TEX86 proxy based on isoprenoidal GDGTs derived from archaea, and the MBT/CBT proxy based on bacterial-derived branched GDGTs (brGDGTs), which is influenced by both temperature and pH. While the relationships of the proxy values to environmental variables have been empirically calibrated, much uncertainty remains in understanding genetic and physiological factors that affect the production of these lipid structures by microbes. In this study we compare two model bacterial strains - Edaphobacter aggregans WGB-1 , which has been previously demonstrated to produce brGDGTs (Damsté et al 2011) and Edaphobacter modestus JBG-1 (a non-brGDGT producer) to gain traction into understanding brGDGT production. We have sequenced each genome, facilitating comparisons that can be used to computationally generate hypotheses for genes involved in brGDGT biosynthesis. We will also report the results of initial experiments conducted to understand how the lipid profiles of each strain vary as a function of growth phase. Through a combination of genetic approaches and physiolotical experiments, we aim to bring new understanding to brGDGTs and how proxies derived from these lipids relate to environmental variables. Damsté et al. 2011 AEM 77: 4147

  13. 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.

  14. 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.

  15. Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat.

    PubMed

    Hedh, Jenny; Johansson, Tomas; Tunlid, Anders

    2009-10-01

    Ectomycorrhizal fungi are known to vary in host range. Some fungi can enter into symbiosis with multiple plant species, while others have restricted host ranges. The aim of this study was to examine variation in host specificity among strains from the basidiomycete Paxillus involutus s. lat. Recent studies have shown that this fungus consists of at least four genetically isolated lineages, phylogenetic species (PS) I (which corresponds to the morphological species Paxillus obscurosporus), PS II (P. involutus s. str.), PS III (Paxillus validus), and PS IV (not yet supported by any reference material). Thirty-five Paxillus strains of PS I to IV were examined in microcosms for their capacity to infect birch (Betula pendula) and spruce (Picea abies). Seventeen strains were compatible and formed mycorrhizae with both tree species. Seven strains were incompatible with both birch and spruce. The gene content in three pairs of incompatible and compatible strains PS I, II, and III were compared using microarray-based comparative genomic hybridizations. Of 4,113 P. involutus gene representatives analyzed, 390 varied in copy numbers in at least one of the three pairwise comparisons. Only three reporters showed significant changes in all three pairwise comparisons, and none of these were changed in a similar way in three comparisons. Our data indicate that changes in host range have occurred frequently and independently among strains in P. obscurosporus, P. involutus s. str., and P. validus. No evidence was obtained demonstrating that these changes have been associated with the gain or loss of similar genes in these three species.

  16. Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains.

    PubMed

    Freidlin, Paul Jeffrey; Nissan, Israel; Luria, Anna; Goldblatt, Drora; Schaffer, Lana; Kaidar-Shwartz, Hasia; Chemtob, Daniel; Dveyrin, Zeev; Head, Steven Robert; Rorman, Efrat

    2017-02-15

    CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endogenous roles in the bacterium. Genotyping in the Israel National Mycobacterium Reference Center Tel-Aviv of over 1500 MTBC strains from 2008-2013 showed three strains with validated negative 43-spacer spoligotypes, that is, with putatively deleted direct repeat regions (deleted-DR/CRISPR regions). Two isolates of each of three negative spoligotype MTBC (a total of 6 isolates) were subjected to Next Generation Sequencing (NGS). As positive controls, NGS was performed for three intact-DR isolates belonging to T3_Eth, the largest multiple-drug-resistant (MDR)-containing African-origin cluster in Israel. Other controls consisted of NGS reads and complete whole genome sequences from GenBank for 20 intact-DR MTBC and for 1 deleted-DR MTBC strain recognized as CAS by its defining RD deletion. NGS reads from negative spoligotype MTBC mapped to reference H37Rv NC_000962.3 suggested that the DR/CRISPR regions were completely deleted except for retention of the middle IS6110 mobile element. Clonally specific deletion of CRISPR-flanking genes also was observed, including deletion of at least cas2 and cas1 genes. Genomic RD deletions defined lineages corresponding to the major spoligotype families Beijing, EAI, and Haarlem, consistent with 24 loci MIRU-VNTR profiles. Analysis of NGS reads, and analysis of contigs obtained by manual PCR confirmed that all 43 gold standard DR/CRISPR spacers were missing in the deleted-DR genomes. Although many negative spoligotype strains are recorded as spoligotype-international-type (SIT) 2669 in the SITVIT international database, this is the first time to our knowledge that it has been shown that negative spoligotype strains are found in at least 4 different 24 loci MIRU-VNTR and RD deletion families. We report for the first time

  17. Head impact accelerations for brain strain-related responses in contact sports: a model-based investigation.

    PubMed

    Ji, Songbai; Zhao, Wei; Li, Zhigang; McAllister, Thomas W

    2014-10-01

    Both linear [Formula: see text] and rotational [Formula: see text] accelerations contribute to head impacts on the field in contact sports; however, they are often isolated in injury studies. It is critical to evaluate the feasibility of estimating brain responses using isolated instead of full degrees-of-freedom (DOFs) accelerations. In this study, we investigated the sensitivities of regional brain strain-related responses to resultant [Formula: see text] and [Formula: see text] as well as the relative contributions of these acceleration components to the responses via random sampling and linear regression using parameterized, triangulated head impacts with kinematic variable values based on on-field measurements. Two independently established and validated finite element models of the human head were employed to evaluate model-consistency and dependency in results: the Dartmouth Head Injury Model and Simulated Injury Monitor. For the majority of the brain, volume-weighted regional peak strain, strain rate, and von Mises stress accumulated from the simulation significantly correlated with the product of the magnitude and duration of [Formula: see text], or effectively, the rotational velocity, but not to [Formula: see text]. Responses from [Formula: see text]-only were comparable to the full-DOF counterparts especially when normalized by injury-causing thresholds (e.g., volume fractions of large differences virtually diminished (i.e., [Formula: see text]1 %) at typical difference percentage levels of 1-4 % on average). These model-consistent results support the inclusion of both rotational acceleration magnitude and duration into kinematics-based injury metrics and demonstrate the feasibility of estimating strain-related responses from isolated [Formula: see text] for analyses of strain-induced injury relevant to contact sports without significant loss of accuracy, especially for the cerebrum.

  18. 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.

  19. Investigation of the InAs/GaAs Quantum Dots’ Size: Dependence on the Strain Reducing Layer’s Position

    PubMed Central

    Souaf, Manel; Baira, Mourad; Nasr, Olfa; Hadj Alouane, Mohamed Helmi; Maaref, Hassen; Sfaxi, Larbi; Ilahi, Bouraoui

    2015-01-01

    This work reports on theoretical and experimental investigation of the impact of InAs quantum dots (QDs) position with respect to InGaAs strain reducing layer (SRL). The investigated samples are grown by molecular beam epitaxy and characterized by photoluminescence spectroscopy (PL). The QDs optical transition energies have been calculated by solving the three dimensional Schrödinger equation using the finite element methods and taking into account the strain induced by the lattice mismatch. We have considered a lens shaped InAs QDs in a pure GaAs matrix and either with InGaAs strain reducing cap layer or underlying layer. The correlation between numerical calculation and PL measurements allowed us to track the mean buried QDs size evolution with respect to the surrounding matrix composition. The simulations reveal that the buried QDs’ realistic size is less than that experimentally driven from atomic force microscopy observation. Furthermore, the average size is found to be slightly increased for InGaAs capped QDs and dramatically decreased for QDs with InGaAs under layer. PMID:28793465

  20. 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.

  1. Along-strike variation in deformation style inferred from kinematic reconstruction and strain rate analysis: A case study of the Ethiopian Rift

    NASA Astrophysics Data System (ADS)

    Muluneh, Ameha A.; Cuffaro, Marco; Kidane, Tesfaye

    2017-09-01

    In this paper we combine kinematic reconstruction and seismic strain rate analysis to understand the along-strike variation in strain accommodation in the Ethiopian Rift (ER) evolution. The reconstruction poles close the southern and central ER at 19 and 15 Myr, respectively whereas there is 34 ± 14 km overlap in the northern ER at 11 Myr. Using Kostrov summation, seismic strain rates of 6.81 ×10-9 yr-1 and 0.06 × 10-9 yr-1 are obtained for the south-central and northern ER, respectively. Comparison of the seismic and geodetic strain rates shows that seismic deformation dominates the south and central ER contrary to the northern ER that deforms aseismically. The results obtained indicate that Nubia/Somalia plate reconstructions together with information on the onset of rifting overestimate the kinematics of the northern ER. We argue that magmatic processes play significant role in accommodating the ∼ 2 Myr opening of the rift. Our findings agree well with previous geophysical and geological studies in the Ethiopian Rift.

  2. 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.

  3. Investigation into image quality difference between total variation and nonlinear sparsifying transform based compressed sensing

    NASA Astrophysics Data System (ADS)

    Dong, Jian; Kudo, Hiroyuki

    2017-03-01

    Compressed sensing (CS) is attracting growing concerns in sparse-view computed tomography (CT) image reconstruction. The most standard approach of CS is total variation (TV) minimization. However, images reconstructed by TV usually suffer from distortions, especially in reconstruction of practical CT images, in forms of patchy artifacts, improper serrate edges and loss of image textures. Most existing CS approaches including TV achieve image quality improvement by applying linear transforms to object image, but linear transforms usually fail to take discontinuities into account, such as edges and image textures, which is considered to be the key reason for image distortions. Actually, discussions on nonlinear filter based image processing has a long history, leading us to clarify that the nonlinear filters yield better results compared to linear filters in image processing task such as denoising. Median root prior was first utilized by Alenius as nonlinear transform in CT image reconstruction, with significant gains obtained. Subsequently, Zhang developed the application of nonlocal means-based CS. A fact is gradually becoming clear that the nonlinear transform based CS has superiority in improving image quality compared with the linear transform based CS. However, it has not been clearly concluded in any previous paper within the scope of our knowledge. In this work, we investigated the image quality differences between the conventional TV minimization and nonlinear sparsifying transform based CS, as well as image quality differences among different nonlinear sparisying transform based CSs in sparse-view CT image reconstruction. Additionally, we accelerated the implementation of nonlinear sparsifying transform based CS algorithm.

  4. 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

  5. Investigation of outdoor BTEX: Concentration, variations, sources, spatial distribution, and risk assessment.

    PubMed

    Miri, Mohammad; Rostami Aghdam Shendi, Maryam; Ghaffari, Hamid Reza; Ebrahimi Aval, Hamideh; Ahmadi, Ehsan; Taban, Ebrahim; Gholizadeh, Abdolmajid; Yazdani Aval, Mohsen; Mohammadi, Amir; Azari, Ali

    2016-11-01

    The aim of this study was to measure BTEX (benzene, toluene, ethylbenzene, and xylenes) concentrations in the ambient air of Tehran, the capital of Iran, and investigate their seasonal variations, probable sources, spatial mapping, and risk assessment. The concentrations of BTEX were measured using a continuous monitoring device installed in seven stations around the city. Spatial mapping procedure was conducted using the inverse distance weighting (IDW) method. Monte Carlo simulation was used to assess the carcinogenic and noncarcinogenic risks imposed by BTEX. The highest and lowest annual mean concentrations of toluene and ethylbenzene were recorded as 16.25 and 3.63 μg m(-3), respectively. The maximum (6.434) and minimum (3.209) toluene/benzene (T/B) ratio was observed in summer and winter, respectively. The spatial distribution of BTEX pollution indicated that the highest concentrations were found along the major roads because of heavy traffic. Spearman's rank correlation coefficients and concentration ratios showed that BTEX were produced by the multiemission sources. The mean of inhalation lifetime cancer risk (LTCR) for benzene was 3.93 × 10(-7), which is lower than the limits recommended by the United States Environmental Protection Agency (US EPA) and the World Health Organization (WHO). The hazard quotient (HQ), noncarcinogenic risk index, for all BTEX compounds was <1. The obtained results showed no threat of BTEX concentrations to human health. However, as the concentrations of BTEX will increase due to the rapid growth of vehicles and industrial activities, much effort is required to control and manage the levels of these compounds in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations.

    PubMed

    Zhang, Shan; Song, Weizhi; Yu, Min; Lin, Xuezheng

    2017-03-17

    Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96.78%) and best sequence synteny were identified between strains G and K5. These findings suggest they belong to the same species, despite the long geographic distance between them (Antarctic and Siberia). 4542 gene clusters in total were identified from the five genomes, and of which 1424 were shared by all of them. The number of genes unique to strains G, K5, 273-4, PAMC21119 and PRwf-1 are 183, 188, 300, 637 and 665, respectively. COG assignment revealed their differences in gene content related to stress response. The extensive sequence rearrangements and the large number of genes unique to strain PAMC21119 and PRwf-1 suggest they may have experienced a high level of gene exchanges in the permafrost soil and the surface of fish skin.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  8. Genome sequence variation in the constricta strain dramatically alters the protein interaction and localization map of Potato yellow dwarf virus

    USDA-ARS?s Scientific Manuscript database

    The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12,792 nucleotides long and organized into seven open reading frames with the gene order 3’-N-X-P-Y-M-G-L-5’, which encodes the nucleocapsid, phosphoprotein, movement, matrix, glycoprotein and RNA-d...

  9. 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.

  10. Do variations in mast cell hyperplasia account for differences in radiation-induced lung injury among different mouse strains, rats and nonhuman primates?

    PubMed

    Down, Julian D; Medhora, Meetha; Jackson, Isabel L; Cline, J Mark; Vujaskovic, Zeljko

    2013-08-01

    The role of mast cell infiltrates in the pathology of radiation damage to the lung has been a subject of continuing investigation over the past four decades. This has been accompanied by a number of proposals as to how mast cells and the secretory products thereof participate in the generation of acute inflammation (pneumonitis) and the chronic process of collagen deposition (fibrosis). An additional pathophysiology examines the possible connection between mast cell hyperplasia and pulmonary hypertension through the release of vasoactive mediators. The timing and magnitude of pneumonitis and fibrosis are known to vary tremendously among different genetic mouse strains and animal species. Therefore, we have systematically compared mast cell numbers in lung sections from nine mouse strains, two rat strains and nonhuman primates (NHP) after whole thorax irradiation (WTI) at doses ranging from 10-15 Gy and at the time of entering respiratory distress. Mice of the BALB/c strain had a dramatic increase in interstitial mast cell numbers, similar to WAG/Rij and August rats, while relatively low levels of mast cell infiltrate were observed in other mouse strains (CBA, C3H, B6, C57L, WHT and TO mice). Enumeration of mast cell number in five NHPs (rhesus macaque), exhibiting severe pneumonitis at 17 weeks after 10 Gy WTI, also indicated a low response shared by the majority of mouse strains. There appeared to be no relationship between the mast cell response and the strain-dependent susceptibility towards pneumonitis or fibrosis. Further investigations are required to explore the possible participation of mast cells in mediating specific vascular responses and whether a genetically diverse mast cell response occurs in humans.

  11. Do Variations in Mast Cell Hyperplasia Account for Differences in Radiation-Induced Lung Injury among Different Mouse Strains, Rats and Nonhuman Primates?

    PubMed Central

    Down, Julian D.; Medhora, Meetha; Jackson, Isabel L.; Cline, J. Mark; Vujaskovic, Zeljko

    2013-01-01

    The role of mast cell infiltrates in the pathology of radiation damage to the lung has been a subject of continuing investigation over the past four decades. This has been accompanied by a number of proposals as to how mast cells and the secretory products thereof participate in the generation of acute inflammation (pneumonitis) and the chronic process of collagen deposition (fibrosis). An additional pathophysiology examines the possible connection between mast cell hyperplasia and pulmonary hypertension through the release of vasoactive mediators. The timing and magnitude of pneumonitis and fibrosis are known to vary tremendously among different genetic mouse strains and animal species. Therefore, we have systematically compared mast cell numbers in lung sections from nine mouse strains, two rat strains and nonhuman primates (NHP) after whole thorax irradiation (WTI) at doses ranging from 10–15 Gy and at the time of entering respiratory distress. Mice of the BALB/c strain had a dramatic increase in interstitial mast cell numbers, similar to WAG/Rij and August rats, while relatively low levels of mast cell infiltrate were observed in other mouse strains (CBA, C3H, B6, C57L, WHT and TO mice). Enumeration of mast cell number in five NHPs (rhesus macaque), exhibiting severe pneumonitis at 17 weeks after 10 Gy WTI, also indicated a low response shared by the majority of mouse strains. There appeared to be no relationship between the mast cell response and the strain-dependent susceptibility towards pneumonitis or fibrosis. Further investigations are required to explore the possible participation of mast cells in mediating specific vascular responses and whether a genetically diverse mast cell response occurs in humans. PMID:23819595

  12. An investigation on the chemotactic responses of different entomopathogenic nematode strains to mechanically damaged maize root volatile compounds.

    PubMed

    Laznik, Z; Trdan, S

    2013-07-01

    Entomopathogenic nematodes (EPNs) respond to a variety of stimuli when foraging. In a laboratory investigation, we tested the chemotactic responses of 8 EPN strains (Steinernema and Heterorhabditis) to three mechanically damaged maize root compounds (linalool, α-caryophyllene and β-caryophyllene). We hypothesized that the EPN directional response to the tested volatile compounds would vary among the species and volatile compound and may be related to foraging strategies. The nematodes with an intermediate foraging strategy (Steinernema feltiae) proved to be less active in their movement toward volatile compounds in a comparison with the ambushers (Steinernema carpocapsae) and cruisers (Steinernema kraussei and Heterorhabditis bacteriophora); β-caryophyllene was found to be the most attractive substance in our experiment. The results of our investigation showed that the cruisers were more attracted to β-caryophyllene than the ambushers and intermediates. The foraging strategy did not affect the movement of the IJs toward the other tested volatile compounds or the control. Our results suggest that the response to different volatile cues is more a strain-specific characteristic than a different host-searching strategy. Only S. carpocapsae strain B49 displayed an attraction to linalool, whereas S. kraussei showed a retarded reaction to β-caryophyllene and α-caryophyllene in our experiment. The EPN strains showed only a weak attraction to α-caryophyllene, suggesting that this volatile compound could not have an important role in the orientation of IJs to the damaged roots of maize plants. These results expand our knowledge of volatile compounds as the cues that may be used by EPNs for finding hosts or other aspects of navigation in the soil. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Influence of nociception and stress-induced antinociception on genetic variation in isoflurane anesthetic potency among mouse strains.

    PubMed

    Mogil, Jeffrey S; Smith, Shad B; O'Reilly, Meghan K; Plourde, Gilles

    2005-10-01

    Genetic background influences anesthetic potency to suppress motor response to noxious stimulation (minimum alveolar concentration [MAC]) as well as nociceptive sensitivity in unmedicated animals. However, the influence on MAC of baseline sensitivity to the noxious stimuli used to assess MAC has virtually never been studied. The authors assessed room air nociceptive sensitivity and isoflurane MAC in multiple mouse strains. Isoflurane requirement for loss of righting response (MACLORR) was also measured. One outbred and 10 inbred mouse strains were tested for latency to respond (in room air) to a tail clip (either 500 g or 2,000 g). Naive mice of the same 11 strains were tested for isoflurane MAC and MACLORR. To assess the role of opioid-mediated stress-induced antinociception, mice were also tested for nociceptive sensitivity after injection of naloxone (10 mg/kg) or saline. Robust strain differences were observed for all measures. The authors found that tail-clip latency (using a 500-g or 2,000-g clip, respectively) correlated significantly with MAC (r = -0.76 and -0.58, respectively) but not MACLORR (r = -0.10 and -0.26). Naloxone produced strain-dependent reductions in open air tail-clip latencies, and these reductions were also strongly correlated with MAC (r = -0.67 and -0.71). The authors suggest that genetic variability in isoflurane MAC (but not MACLORR) may reflect genetic variability in the underlying sensitivity to the noxious stimulus being used to measure MAC. This variable sensitivity to nociception in the awake state is at least partially mediated by endogenous antinociceptive mechanisms activated by the tail-clip stimulus itself.

  14. 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.

  15. Lactobacillus kefiri shows inter-strain variations in the amino acid sequence of the S-layer proteins.

    PubMed

    Malamud, Mariano; Carasi, Paula; Bronsoms, Sílvia; Trejo, Sebastián A; Serradell, María de Los Angeles

    2017-04-01

    The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer protein (SLPs) encoding genes expressed by six aggregative and sixteen non-aggregative strains of potentially probiotic Lactobacillus kefiri. Peptide mass fingerprint (PMF) analysis confirmed the identity of SLPs extracted from L. kefiri, and based on the homology with phylogenetically related species, primers located outside and inside the SLP-genes were employed to amplify genomic DNA. The O-glycosylation site SASSAS was found in all L. kefiri SLPs. Ten strains were selected for sequencing of the complete genes. The total length of the mature proteins varies from 492 to 576 amino acids, and all SLPs have a calculated pI between 9.37 and 9.60. The N-terminal region is relatively conserved and shows a high percentage of positively charged amino acids. Major differences among strains are found in the C-terminal region. Different groups could be distinguished regarding the mature SLPs and the similarities observed in the PMF spectra. Interestingly, SLPs of the aggregative strains are 100% homologous, although these strains were isolated from different kefir grains. This knowledge provides relevant data for better understanding of the mechanisms involved in SLPs functionality and could contribute to the development of products of biotechnological interest from potentially probiotic bacteria.

  16. 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

  17. [Investigation of hydrophobicity of Proteus vulgaris strains and ability of Proteus vulgaris and Proteus penneri strains to penetrate bladder membrane HCV T-29 cells ].

    PubMed

    Bartodziejska, Beata; Błaszczyk, Aleksandra; Wykrota, Marianna; Kwil, Iwona; Babicka, Dorota; Rózalski, Antoni

    2002-01-01

    Proteus bacilli play a particularly important role in urinary tract infections (UTI). Fimbriae and adherence ability and hemolysins production (HpmA, HlyA) are one of the factors of pathogenicity of these bacteria. In this paper we describe the invasion of HCV T-29 transitional bladder urothelial cells carcinoma strains of P. penneri, as well as P. vulgaris strains belonging to different serogroups. The cytotoxic effect was observed at 8 hour of incubation of the tested cells with P. vulgaris O21 and the same effect (complete lysis) at 6 hours by P. vulgaris O4 (this strain manifests maximal activity in the production of HlyA hemolysin). P. penneri strains, produce different types of fimbriae, expressed similar bacterial invasiveness. The hydrophobic properties of 25 P. vulgaris strains were also tested and only 3 strains occur to have hydrophobic cell surface.

  18. 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

  19. Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.

    PubMed

    Hayden, Hillary S; Gillett, Will; Saenphimmachak, Channakhone; Lim, Regina; Zhou, Yang; Jacobs, Michael A; Chang, Jean; Rohmer, Laurence; D'Argenio, David A; Palmieri, Anthony; Levy, Ruth; Haugen, Eric; Wong, Gane K S; Brittnacher, Mitch J; Burns, Jane L; Miller, Samuel I; Olson, Maynard V; Kaul, Rajinder

    2008-06-01

    Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.

  20. 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

  1. 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

    2014-11-03

    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. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  2. 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.

  3. Dynamic investigations on the influence of epitaxial strain on the superconducting transition in YBa2Cu3O7-x

    NASA Astrophysics Data System (ADS)

    Hühne, R.; Okai, D.; Dörr, K.; Trommler, S.; Herklotz, A.; Holzapfel, B.; Schultz, L.

    2008-07-01

    YBa2Cu3O7-x (YBCO) films have been prepared on piezoelectric (001) Pb(Mg1/3Nb2/3)0.72Ti0.28O3 (PMN-PT) substrates for dynamic investigations on the influence of strain on the superconducting transition temperature. The YBCO films deposited by off-axis pulsed laser deposition showed a perfect epitaxial growth on the piezocrystals but also significant surface roughness due to the miscut of the substrate. The in-plane lattice constant of the PMN-PT substrate was varied dynamically by the application of an electric field of <=10 kV cm-1. As a result, a reversible shift of the superconducting transition by about 0.1 K was found on an optimally doped YBCO film for an applied strain of 0.05%. The results show for the first time that this approach is suitable for studying the strain dependence of superconducting properties in detail.

  4. Investigation of pre-pubertal sex differences in wheel running and social behavior in three mouse strains

    PubMed Central

    Gordon, Elizabeth A.; Corbitt, Cynthia

    2015-01-01

    Sex differences in social behaviors exist in mammals during adulthood, and further evidence suggests that sex differences in behavior are present before sexual maturity. In order to model behavioral disorders in animals, it is important to assess baseline sex-related behavioral differences, especially when studying disorders for which sex-related behavioral effects are expected. We investigated the effect of sex on behavior in 3 strains of pre-pubertal mice (C57BL/6, CFW, and CF1) using a wheel-running assay. We found no significant sex differences in latency to run on the wheel or total duration of wheel running within each strain. During the social interaction test, there were no differences between sexes in latency or total duration of contact or following between a subject and novel mouse. We also evaluated behavioral patterns of wheel running and stereotypical behaviors, such as burrowing and grooming. Both sexes showed characteristic wheel running behavior, spending the majority of each trial interacting with the wheel when it was free and more time performing other activities (e.g., stereotypical behaviors, general locomotion) when it was jammed. These results provide evidence that, among various strains of pre-pubertal mice, baseline sex-related behavioral differences are not strong enough to influence the measured behaviors. PMID:26316671

  5. 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.

  6. Antimicrobial resistance investigation on Staphylococcus strains in a local hospital in Guangzhou, China, 2001-2010.

    PubMed

    Deng, Yang; Liu, Junyan; Peters, Brian M; Chen, Lei; Miao, Jian; Li, Bing; Li, Lin; Chen, Dingqiang; Yu, Guangchao; Xu, Zhenbo; Shirtliff, Mark E

    2015-02-01

    A retrospective study was conducted on 1,739 Staphylococcus isolates from the First Affiliated Hospital of Jinan University (FAHJU) in Guangzhou during 2001-2010. With the exception of teicoplanin and vancomycin, antimicrobial resistance was commonly observed among the isolates examined, with high resistance rates for β-lactamases (94.0% and 73.7% for penicillin and oxacillin) and resistance percentages for cefoxitin, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, trimethoprim-sulfamethoxazole, and tetracycline ranging from 83.9% to 19.4%. Two hundred sixty-three of the 1,739 isolates were subjected to SCCmec typing and 42 to MLST, spaA, and coa typing. ST239-MRSA-III was prevalently identified along with one distinct coa type HIJKL and 2 spaA types (WGKAOMQ-t037 and WGKAQQ-t030). Class 1 integrons were commonly detected (31.6%), although none of the integron-positive MRSA strains had been isolated since 2009. The widespread detection of integron-based antimicrobial resistance determinants may further contribute to the emergence of superbugs.

  7. 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

  8. 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

  9. Fluconazole susceptibility and strain variation of Candida albicans isolates from HIV-infected patients with oropharyngeal candidosis.

    PubMed

    Barchiesi, F; Arzeni, D; Del Prete, M S; Sinicco, A; Falconi Di Francesco, L; Pasticci, M B; Lamura, L; Nuzzo, M M; Burzacchini, F; Coppola, S; Chiodo, F; Scalise, G

    1998-05-01

    Over a 16 month period we conducted a prospective study in a cohort of 45 HIV-positive patients to detect the development of resistance to fluconazole and to analyse the epidemiology of oropharyngeal candidosis (OPC). Each episode was treated with fluconazole 100 mg/day po for 10 days. All yeast isolates were tested for their in-vitro susceptibility to fluconazole. Multiple strains of Candida albicans simultaneously isolated from a given patient were typed by electrophoretic karyotyping. Overall, 106 episodes of OPC were diagnosed among the 45 patients: 18/45 patients (40%) had only one episode, 11/45 (24%) had two episodes, and the remaining 16/45 (36%) had three or more episodes (range 3-7). Cure (complete resolution of signs and symptoms and negative post-treatment cultures) and improvement (complete resolution of signs and symptoms but positive post-treatment cultures) were observed in 30/106 (28%) and 69/106 (65%) episodes of OPC, respectively. Failure (absence of improvement or exacerbation of signs and symptoms) was observed in seven episodes (7%) from four patients. In two of these four patients a significant and progressive increase in fluconazole MICs was observed: from 0.25 to 16 mg/L in one patient, and from < or = 0.125 to 32 mg/L in the second one. Tests on multiple colonies from individual isolation plates showed that it was not unusual to obtain different fluconazole MICs, indicating that, in order to avoid misleading results, one should perform in-vitro susceptibility testing by using a multiple colony inoculum rather than an inoculum made from a single colony. A total of 213 strains of C. albicans isolated from seven patients who suffered from four or more episodes of OPC through the course of the study were typed by electrophoretic karyotyping. Five individuals (71%) were infected with yeasts with only one DNA type, while the other two patients showed the presence of two or three different DNA types. The simultaneous presence of multiple types

  10. 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

  11. Investigation of the hybrid model with the Killingbeck potential in a variational approach

    NASA Astrophysics Data System (ADS)

    Alimohammadi, M.; Hassanabadi, H.

    2017-10-01

    The energy spectrum and transition rates have been obtained for some nuclei in critical point by employing the hybrid collective model. For this purpose, the corresponding Hamiltonian with β-dependent Killingbeck potential has been solved by the variational method. Our results have been compared with other references and experimental data.

  12. 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.

  13. Variation of lifespan in multiple strains, and effects of dietary restriction and BmFoxO on lifespan in silkworm, Bombyx mori.

    PubMed

    Song, Jiangbo; Tang, Dongmei; Li, Zhiquan; Tong, Xiaoling; Zhang, Jianfei; Han, Minjin; Hu, Hai; Lu, Cheng; Dai, Fangyin

    2017-01-31

    Established animal models have accelerated our understanding of the mechanisms involved in lifespan determination. However, more experimental animals are required to clarify the complex mechanisms behind the phenomena of aging and lifespan. In this study, we reported the variation of lifespan in nine distinct silkworm strains. Lifespan correlated significantly with BmFoxO gene expression in the representative silkworm strains tested (Xiafang, Dazao-N, and N4). In general, the female silkworm was longer lived than the male of the same strain. Dietary restriction extended the silkworm lifespan compared with that of silkworms fed ad libitum. The expression of BmFoxO was significantly elevated in the dietary restriction group on day 3 of the 4th instar and day 3 of the 5th instar, suggesting that BmFoxO contributes to dietary restriction-mediated lifespan extension. The RNA interference and overexpression of the BmFoxO gene significantly shortened and extended the silkworm adulthood, respectively. In conclusion, our findings suggest that the silkworm might serve as a promising experimental animal to explore the complex biological mechanisms of lifespan determination.

  14. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains.

    PubMed

    Giuntini, Elisa; Mengoni, Alessio; De Filippo, Carlotta; Cavalieri, Duccio; Aubin-Horth, Nadia; Landry, Christian R; Becker, Anke; Bazzicalupo, Marco

    2005-11-10

    Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.

  15. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains

    PubMed Central

    Giuntini, Elisa; Mengoni, Alessio; De Filippo, Carlotta; Cavalieri, Duccio; Aubin-Horth, Nadia; Landry, Christian R; Becker, Anke; Bazzicalupo, Marco

    2005-01-01

    Background Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusion The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti. PMID:16283928

  16. Observational investigation of ionospheric turbulent spectral content in relation to geomagnetic field variations and local seismicity

    NASA Astrophysics Data System (ADS)

    Contadakis, M. E.; Arambelos, D.; Asteriadis, G.; Pikridas, Ch.; Spatalas, S.; Chatzinikos, M.

    2006-04-01

    Atmospheric and underground explosions as well as shallow earthquakes producing strong vertical ground displacement, are known to produce pressure waves that propagates at infrasonic speeds in the atmosphere. At ionospheric altitudes these waves are coupled to ionospheric gravity waves and induce variations in the ionospheric electron density. On the other hand local lithospheric density, ion inhalation, temperature or electromagnetic field variations, produced by the local tectonic activity during the earthquake preparation period, induces near surface atmospheric variations and affect the ionospheric density through the Lithospher-Atmosphere- Ionosphere Coupling. That is the lithospheric near surface tectonic activity results to local pre- co- and post seismic disturbances on the ionospheric Total Electron Content (TEC). Nevertheless these disturbances are mixed with disturbances induced to the ionospher by a number of agents such as tropospheric jets, magnetic storms and sub-storms, solar activity, ionosphere-magnetosphere coupling etc, and a major problem is to discriminate the influence of those agents from the influence of the local tectonic activity. In this paper we present the results of the wavelet analysis of TVEC variations over a network of 4 GPS stations, depicted from EUREF-EPN network, covering the whole area of Greece. Our results indicate that 1) Disturbances with period higher than 3 hours have a Universal origin i.e. earth-tides, Aurora or Equatorial anomaly. 2) Disturbances with periods equal or smaller than 3 hours are of local origin. 3) Strong Variations of geomagnetic field affect the disturbances of all periods. 4) Disturbances with period 3 hours present a good coherency in the measurements of more than one GPS stations. In concluding disturbances with period equal or less than 3 hours are suitable for de

  17. An investigation into the relationship between thickness variations and manufacturing techniques of mouthguards.

    PubMed

    Farrington, Timothy; Coward, Trevor; Onambele-Pearson, Gladys; Taylor, Rebecca L; Earl, Philip; Winwood, Keith

    2016-02-01

    The aim of this study was to measure the finished thickness of a single identical 4-mm EVA mouthguard model from a large fabricated sample group and to evaluate the degree of material thinning and variations during the fabrication process. Twenty boxes were distributed to dental technician participants, each containing five duplicated dental models (n = 100), alongside 5 × 4 mm mouthguard blanks and a questionnaire. The mouthguards were measured using electronic callipers (resolution: ±0.01 mm) at three specific points. The five thickest and thinnest mouthguards were examined using a CT scanner to describe the surface typography unique to each mouthguard, highlighting dimensional thinning patterns during the fabrication process. Of the three measurement points, the anterior sulcus point of the mouthguard showed a significant degree of variation (up to 34% coefficient of variation), in finished mouthguard thickness between individuals. The mean thickness of the mouthguards in the anterior region was 1.62 ± 0.38 mm with a range of 0.77-2.80 mm. This variation was also evident in the occlusion and posterior lingual regions but to a lesser extent (up to 12.2% and 9.8% variations, respectively). This study highlights variability in the finished thickness of the mouthguards especially in the anterior sulcus region measurement point, both within and between individuals. At the anterior region measurement point of the mouthguard, the mean thickness was 1.62 mm, equating to an overall material thinning of 59.5% when using a single 4-mm EVA blank. This degree of thinning is comparative to previous single operator research studies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. 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

  19. 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.

  20. Variation in lipid extractability by solvent in microalgae. Additional criterion for selecting species and strains for biofuel production from microalgae.

    PubMed

    Mendoza, Héctor; Carmona, Laura; Assunção, Patricia; Freijanes, Karen; de la Jara, Adelina; Portillo, Eduardo; Torres, Alicia

    2015-12-01

    The lipid extractability of 14 microalgae species and strains was assessed using organic solvents (methanol and chloroform). The high variability detected indicated the potential for applying this parameter as an additional criterion for microalgae screening in industrial processes such as biofuel production from microalgae. Species without cell walls presented higher extractability than species with cell walls. Analysis of cell integrity by flow cytometry and staining with propidium iodide showed a significant correlation between higher resistance to the physical treatments of cell rupture by sonication and the lipid extractability of the microalgae. The results highlight the cell wall as a determining factor in the inter- and intraspecific variability in lipid extraction treatments.

  1. [Investigation of OXA type beta-lactamases and PFGE patterns in Acinetobacter baumannii strains resistant to carbapenems].

    PubMed

    Keyik, Serafettin; Arslan, Uğur; Türk Dağı, Hatice; Seyhan, Tuba; Fındık, Duygu

    2014-10-01

    Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen leading to nosocomial infections. Over the last 10 years, a significant and threatening increase in resistance to carbapenems, mainly due to the dissemination of class D beta-lactamases, has been reported in A.baumannii worldwide. The most common types of beta-lactamases causing carbapenem resistance in A.baumannii are the OXA-23, OXA-24, OXA-40, OXA-58 and OXA-143 type serine beta-lactamases. The aim of this study was to investigate the presence of OXA type beta-lactamases in carbapenem-resistant A.baumannii strains and the clonal relationship between the strains. A total of 105 non-duplicate carbapenem-resistant A.baumannii strains isolated from various clinical samples (68 blood, 18 bronchoalveolar lavage, 13 drainage, 3 urine, 2 cerebrospinal fluid and 1 catheter samples) in the Microbiology Laboratories of Selcuk University, Meram (2009-2012) and Selcuklu (2007-2008) Medical School Hospitals, were included in the study. The isolates were identified by conventional methods and Phoenix 100 BD (BD Diagnostic, USA) and Vitek II (bioMerieux, France) automated systems. Carbapenem susceptibility test was performed by Kirby-Bauer disk diffusion method according to the CLSI standards. bla(OXA 23-like), bla(OXA 24-like), bla(OXA 58-like) and bla(OXA 51-like) genes were amplified by multiplex PCR assay and clonal relatedness was investigated by pulsed-field gel electrophoresis (PFGE) using ApaI enzyme. The bla(OXA 51-like) gene was determined in all carbapenem-resistant A.baumannii isolates, while the bla(OXA 23-like) and bla(OXA 58-like) genes were detected in 46.6% and 53.3% of isolates, respectively. However bla(OXA 24-like) gene was not demonstrated in any isolates. bla(OXA 23-like) gene was determined in both Meram and Selcuklu Medical School hospitals, but bla(OXA 58-like) gene was detected only in Meram Medical School hospital. PFGE analysis of the isolates revealed 32 different

  2. Temporal Variations in the Dynamics of Potentially Microcystin-Producing Strains in a Bloom-Forming Planktothrix agardhii (Cyanobacterium) Population▿ †

    PubMed Central

    Briand, Enora; Gugger, Muriel; François, Jean-Christophe; Bernard, Cécile; Humbert, Jean-François; Quiblier, Catherine

    2008-01-01

    The concentration of microcystins (MCs) produced during blooms depends on variations in both the proportion of strains containing the genes involved in MC production and the MC cell quota (the ratio between the MC concentration and the density of cells with the mcyA genotype) for toxic strains. In order to assess the dynamics of MC-producing and non-MC-producing strains and to identify the impact of environmental factors on the relative proportions of these two subpopulations, we performed a 2-year survey of a perennial bloom of Planktothrix agardhii (cyanobacteria). Applying quantitative real-time PCR to the mcyA and phycocyanin genes, we found that the proportion of cells with the mcyA genotype varied considerably over time (ranging from 30 to 80% of the population). The changes in the proportion of cells with the mcyA genotype appeared to be inversely correlated to changes in the density of P. agardhii cells and also, to a lesser extent, to the availability of certain nutrients and the abundance of cladocerans. Among toxic cells, the MC cell quota varied throughout the survey. However, a negative correlation between the MC cell quota and the mcyA cell number during two short periods characterized by marked changes in the cyanobacterial biomass was found. Finally, only 54% of the variation in the MC concentrations measured in the lake can be explained by the dynamics of the density of cells with the MC producer genotype, suggesting that this measurement is not a satisfactory method for use in monitoring programs intended to predict the toxic risk associated with cyanobacterial proliferation. PMID:18441113

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

    PubMed Central

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

    1995-01-01

    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

  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. 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

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

    PubMed

    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

    1993-10-01

    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.

  7. Intraspecific differentiation of Paramecium novaurelia strains (Ciliophora, Protozoa) inferred from phylogenetic analysis of ribosomal and mitochondrial DNA variation.

    PubMed

    Tarcz, Sebastian

    2013-01-01

    Paramecium novaurelia Beale and Schneller, 1954, was first found in Scotland and is known to occur mainly in Europe, where it is the most common species of the P. aurelia complex. In recent years, two non-European localities have been described: Turkey and the United States of America. This article presents the analysis of intraspecific variability among 25 strains of P. novaurelia with the application of ribosomal and mitochondrial loci (ITS1-5.8S-ITS2, 5' large subunit rDNA (5'LSU rDNA) and cytochrome c oxidase subunit 1 (COI) mtDNA). The mean distance observed for all of the studied P. novaurelia sequence pairs was p=0.008/0.016/0.092 (ITS1-5.8S-ITS2/5'LSU rDNA/COI). Phylogenetic trees (NJ/MP/BI) based on a comparison of all of the analysed sequences show that the studied strains of P. novaurelia form a distinct clade, separate from the P. caudatum outgroup, and are divided into two clusters (A and B) and two branches (C and D). The occurrence of substantial genetic differentiation within P. novaurelia, confirmed by the analysed DNA fragments, indicates a rapid evolution of particular species within the Paramecium genus. Copyright © 2012 Elsevier GmbH. All rights reserved.

  8. Continuous Tuning of Phase Transition Temperature in VO2 Thin Films on c-Cut Sapphire Substrates via Strain Variation.

    PubMed

    Jian, Jie; Wang, Xuejing; Li, Leigang; Fan, Meng; Zhang, Wenrui; Huang, Jijie; Qi, Zhimin; Wang, Haiyan

    2017-02-15

    Vanadium dioxide (VO2) thin films with controlled thicknesses are deposited on c-cut sapphire substrates with Al-doped ZnO (AZO) buffer layers by pulsed laser deposition. The surface roughness of AZO buffer layers is varied by controlling oxygen pressure during growth. The strain in the VO2 lattice is found to be dependent on the VO2 thickness and the VO2/AZO interface roughness. The semiconductor-to-metal transition (SMT) properties of VO2 thin films are characterized and the transition temperature (Tc) is successfully tuned by the VO2 thickness as well as the VO2/AZO interface roughness. It shows that the Tc of VO2 decreases with the decrease of film thickness or VO2/AZO interface roughness. Other SMT properties of the VO2 films are maintained during the Tc tuning. The results suggest that the strain tuning induced by AZO buffer provides an effective approach for tuning Tc of VO2 continuously.

  9. 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.

  10. Contribution of Gag and protease to variation in susceptibility to protease inhibitors between different strains of subtype B human immunodeficiency virus type 1.

    PubMed

    Sutherland, Katherine A; Mbisa, Jean L; Cane, Patricia A; Pillay, Deenan; Parry, Chris M

    2014-01-01

    Recent reports have shown that human immunodeficiency virus type 1 (HIV-1) Gag can directly affect susceptibility to protease inhibitors (PIs) in the absence of known resistance mutations in protease. Inclusion of co-evolved Gag alongside protease in phenotypic drug susceptibility assays can alter PI susceptibility in comparison with protease with a WT Gag. Using a single-replication-cycle assay encompassing full-length Gag together with protease we demonstrated significant variation in PI susceptibility between a number of PI-naïve subtype B viruses. Six publicly available subtype B molecular clones, namely HXB2, NL4-3, SF2, YU2, JRFL and 89.6, displayed up to nine-fold reduced PI susceptibility in comparison with the assay reference strain. For two molecular clones, YU2 and JRFL, Gag contributed solely to the observed reduction in susceptibility, with the N-terminal region of Gag contributing significantly. Gag and protease from treatment-naïve, patient-derived viruses also demonstrated significant variation in susceptibility, with up to a 17-fold reduction to atazanavir in comparison with the assay reference strain. In contrast to the molecular clones, protease was the main determinant of the reduced susceptibility. Common polymorphisms in protease, including I13V, L63P and A71T, were shown to contribute to this reduction in PI susceptibility, in the absence of major resistance mutations. This study demonstrated significant variation in PI susceptibility of treatment-naïve patient viruses, and provided further evidence of the independent role of Gag, the protease substrate and in particular the N-terminus of Gag in PI susceptibility. It also highlighted the importance of considering co-evolved Gag and protease when assessing PI susceptibility.

  11. 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.

  12. Microcosm investigations of stormwater pond sediment toxicity to embryonic and larval amphibians: variation in sensitivity among species.

    PubMed

    Snodgrass, Joel W; Casey, Ryan E; Joseph, Debra; Simon, Judith A

    2008-07-01

    Stormwater ponds have become common features of modern development and often represent significant amounts of open space in urbanized areas. Although stormwater ponds may provide habitat for wildlife, factors responsible for producing variation in wildlife use of ponds have received limited attention. To investigate the role of variation in species tolerances of pollutants in structuring pond-breeding amphibian assemblages, we exposed species tolerant (Bufo americanus) and not tolerant (Rana sylvatica) of urbanization to pond sediments in laboratory microcosms. Pond microcosms had elevated sediment metal levels and chloride water concentrations. Among R. sylvatica embryos, exposure to pond sediments resulted in 100% mortality. In contrast, B. americanus embryos and larvae experienced only sublethal effects (i.e., reduced size at metamorphosis) due to pond sediment exposure. Our results suggest variation in pollutant tolerance among early developmental stages of amphibians may act in concert with terrestrial habitat availability to structure amphibian assemblages associated with stormwater ponds.

  13. Origins of Tropospheric Ozone Interannual Variation (IAV) over Reunion: A Model Investigation

    NASA Technical Reports Server (NTRS)

    Liu, Junhua; Rodriguez, Jose M.; Thompson, Anne M.; Logan, Jennifer A.; Douglass, Anne R.; Olsen, Mark A.; Steenrod, Stephen D.; Posny, Francoise

    2016-01-01

    Observations from long-term ozonesonde measurements show robust variations and trends in the evolution of ozone in the middle and upper troposphere over Reunion Island (21.1 degrees South Latitude, 55.5 degrees East Longitude) in June-August. Here we examine possible causes of the observed ozone variation at Reunion Island using hindcast simulations by the stratosphere-troposphere Global Modeling Initiative chemical transport model for 1992-2014, driven by assimilated Modern-Era Retrospective Analysis for Research and Applications (MERRA) meteorological fields. Reunion Island is at the edge of the subtropical jet, a region of strong stratospheric-tropospheric exchange. Our analysis implies that the large interannual variation (IAV) of upper tropospheric ozone over Reunion is driven by the large IAV of the stratospheric influence. The IAV of the large-scale, quasi-horizontal wind patterns also contributes to the IAV of ozone in the upper troposphere. Comparison to a simulation with constant emissions indicates that increasing emissions do not lead to the maximum trend in the middle and upper troposphere over Reunion during austral winter implied by the sonde data. The effects of increasing emission over southern Africa are limited tothe lower troposphere near the surface in August-September.

  14. 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.

  15. Origins of Tropospheric Ozone Interannual Variation (IAV) over Reunion: A Model Investigation

    NASA Technical Reports Server (NTRS)

    Liu, Junhua; Rodriguez, Jose M.; Thompson, Anne M.; Logan, Jennifer A.; Douglass, Anne R.; Olsen, Mark A.; Steenrod, Stephen D.; Posny, Francoise

    2016-01-01

    Observations from long-term ozonesonde measurements show robust variations and trends in the evolution of ozone in the middle and upper troposphere over Reunion Island (21.1 degrees South Latitude, 55.5 degrees East Longitude) in June-August. Here we examine possible causes of the observed ozone variation at Reunion Island using hindcast simulations by the stratosphere-troposphere Global Modeling Initiative chemical transport model for 1992-2014, driven by assimilated Modern-Era Retrospective Analysis for Research and Applications (MERRA) meteorological fields. Reunion Island is at the edge of the subtropical jet, a region of strong stratospheric-tropospheric exchange. Our analysis implies that the large interannual variation (IAV) of upper tropospheric ozone over Reunion is driven by the large IAV of the stratospheric influence. The IAV of the large-scale, quasi-horizontal wind patterns also contributes to the IAV of ozone in the upper troposphere. Comparison to a simulation with constant emissions indicates that increasing emissions do not lead to the maximum trend in the middle and upper troposphere over Reunion during austral winter implied by the sonde data. The effects of increasing emission over southern Africa are limited tothe lower troposphere near the surface in August-September.

  16. Origins of tropospheric ozone interannual variation over Réunion: A model investigation

    NASA Astrophysics Data System (ADS)

    Liu, Junhua; Rodriguez, Jose M.; Thompson, Anne M.; Logan, Jennifer A.; Douglass, Anne R.; Olsen, Mark A.; Steenrod, Stephen D.; Posny, Françoise

    2016-01-01

    Observations from long-term ozonesonde measurements show robust variations and trends in the evolution of ozone in the middle and upper troposphere over Réunion Island (21.1°S, 55.5°E) in June-August. Here we examine possible causes of the observed ozone variation at Réunion Island using hindcast simulations by the stratosphere-troposphere Global Modeling Initiative chemical transport model for 1992-2014, driven by assimilated Modern-Era Retrospective Analysis for Research and Applications meteorological fields. Réunion Island is at the edge of the subtropical jet, a region of strong stratospheric-tropospheric exchange. Our analysis implies that the large interannual variation (IAV) of upper tropospheric ozone over Réunion is driven by the large IAV of the stratospheric influence. The IAV of the large-scale, quasi-horizontal wind patterns also contributes to the IAV of ozone in the upper troposphere. Comparison to a simulation with constant emissions indicates that increasing emissions do not lead to the maximum trend in the middle and upper troposphere over Réunion during austral winter implied by the sonde data. The effects of increasing emission over southern Africa are limited to the lower troposphere near the surface in August-September.

  17. An investigation on inter-individual variation in perceived discomfort of static posture holding.

    PubMed

    Ogutu, Jack; Park, Woojin; Son, Minseok

    2015-01-01

    Realizing population-level discomfort evaluation and control of common static posture holding tasks requires an understanding of the inter-individual variation in discomfort perception. However, little research is available. This study aimed to determine the types of mathematical probability distribution suitable for modeling population discomfort distributions of various static posture holding tasks and characterize how the magnitude of inter-individual variation in perceived discomfort varies across static posture holding tasks. Ten male and ten female subjects participated. The participants conducted static posture holding for a set of 180 short-duration (20-second-long) static posture holding tasks and subjectively rated the overall perceived discomfort for each task using the Borg CR-10 discomfort scale. Statistical analyses were conducted according to the study objectives. The static posture holding tasks exhibited multifarious discomfort distribution patterns. Probability distribution identification analyses indicated that no single distribution type could represent population discomfort distributions universally across different static posture holding tasks. Sample standard deviation of discomfort ratings data quantifying the magnitude of inter-individual variation in discomfort perception varied considerably across static posture holding tasks. It seemed to have a positive relationship with sample mean within the range of the experimental conditions. Population-level evaluation of discomforts associated with static posture holding tasks must be based on careful examinations of empirical discomfort distributions.

  18. Adipose tissue Mest and Sfrp5 are concomitant with variations of adiposity among inbred mouse strains fed a non-obesogenic diet.

    PubMed

    Anunciado-Koza, Rea P; Higgins, David C; Koza, Robert A

    2016-05-01

    The expression of a subset of genes including mesoderm specific transcript (Mest), secreted frizzled-related protein 5 (Sfrp5) and bone morphogenetic protein 3 (Bmp3) in adipose tissue biopsies of C57BL/6J mice before exposure to an obesogenic diet were shown to be predictive for the development of obesity in mice after feeding a high fat diet for 8 weeks. This observation led to the supposition that adipose tissue expression of this subset of genes within inbred strains of mice could be associated with their susceptibility in the development of adiposity when fed a low fat diet. The analyses of male mice from 5 inbred strains showed average bodyweights ranging from 25.82 to 36.58 g at 16 weeks of age. Bodyweight was highest for AKR/J and adiposity correlated highly with bodyweight for all strains. Analyses of epididymal fat gene expression showed Mest, Sfrp5 and Bmp3 to be highly concomitant with adiposity across all strains of mice. Naked 1 (Nkd1), a gene previously shown to be associated with variations of adiposity in mice fed a high fat diet, but not predictive for the development of adiposity, showed no correlation with adiposity. In addition, the expression of Mest and Sfrp5 were tightly associated across the 5 mouse strains with the highest and lowest expression occurring in DBA/2J and C57BL/6J (B6) respectively suggesting a common mechanism for their regulation. Surprisingly, when independent cohorts for these 2 strains were fed high fat diet for 8 weeks, DBA/2J showed no further increase in Sfrp5 expression whereas expression levels for B6 mice were induced almost 20-fold. Analyses of (B6 x DBA2/J) F1 mice fed a low fat diet for 8 weeks showed intermediate levels of adiposity and gene expression for Sfrp5 and Mest suggesting a strong genetic basis for these differences. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  19. 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

  20. 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

  1. Strain-Dependent Variations in Stress Coping Behavior Are Mediated by a 5-HT/GABA Interaction within the Prefrontal Corticolimbic System

    PubMed Central

    Maran, Dario; Viscomi, Maria Teresa; Puglisi-Allegra, Stefano

    2015-01-01

    Background: Serotonin and γ–aminobutyric acid (GABA) transmission is crucial in coping strategies. Methods: Here, using mice from 2 inbred strains widely exploited in behavioral neurochemistry, we investigated whether serotonin transmission in medial prefrontal cortex and GABA in basolateral amygdala determine strain-dependent liability to stress response and differences in coping. Results: C57BL/6J mice displayed greater immobility in the forced swimming test, higher serotonin outflow in medial prefrontal cortex, higher GABA outflow in basolateral amygdala induced by stress, and higher serotonin 1A receptor levels in medial prefrontal cortex accompanied by lower GABAb receptor levels in basolateral amygdala than DBA/2J mice. In assessing whether serotonin in medial prefrontal cortex determines GABA functioning in response to stress and passive coping behavior in C57BL/6J and DBA/2J mice, we observed that selective prefrontal serotonin depletion in C57BL/6J and DBA/2J reduced stress-induced GABA outflow in basolateral amygdala and immobility in the forced swimming test. Conclusions: These results show that strain-dependent prefrontal corticolimbic serotonin/GABA regulation determines the strain differences in stress-coping behavior in the forced swimming test and point to a role of a specific neuronal system in genetic susceptibility to stress that opens up new prospects for innovative therapies for stress disorders. PMID:25522413

  2. Investigating peptide sequence variations for 'double-click' stapled p53 peptides.

    PubMed

    Lau, Yu Heng; de Andrade, Peterson; Sköld, Niklas; McKenzie, Grahame J; Venkitaraman, Ashok R; Verma, Chandra; Lane, David P; Spring, David R

    2014-06-28

    Stapling peptides for inhibiting the p53/MDM2 interaction is a promising strategy for developing anti-cancer therapeutic leads. We evaluate double-click stapled peptides formed from p53-based diazidopeptides with different staple positions and azido amino acid side-chain lengths, determining the impact of these variations on MDM2 binding and cellular activity. We also demonstrate a K24R mutation, necessary for cellular activity in hydrocarbon-stapled p53 peptides, is not required for analogous 'double-click' peptides.

  3. Investigation of three-layer rectangular panel bending by variation method

    NASA Astrophysics Data System (ADS)

    Osadchiy, N. V.; Malyshev, V. A.; Shepel, V. T.

    2017-04-01

    The task of transverse bending of a rectangular three-layer panel with the lightweight filler is considered. The differential equation system of transverse bending of the panel is generated within the scope of Lagrange variational principle. An explicit solution of the differential equation system in double trigonometric Fourier series is obtained. It is shown that the maximum deflection of the three-layer panel can be compared with the three-layer beam deflection, with a multiple panel width excess over its length.

  4. An investigation of surface albedo variations during the recent sahel drought. [ats 3 observations

    NASA Technical Reports Server (NTRS)

    Norton, C. C.; Mosher, F. R.; Hinton, B.

    1978-01-01

    Applications Technology Satellite 3 green sensor data were used to measure surface reflectance variations in the Sahara/Sahel during the recent drought period; 1967 to 1974. The magnitude of the seasonal reflectance change is shown to be as much as 80% for years of normal precipitation and less than 50% for drought years. Year to year comparisons during both wet and dry seasons reveal the existence of a surface reflectance cycle coincident with the drought intensity. The relationship between the green reflectance and solar albedo is examined and estimated to be about 0.6 times the reflectance change observed by the green channel.

  5. Investigation of factors affecting the calibration of strain gage based transducers ( Goodzeit gages'') for SSC magnets

    SciTech Connect

    Davidson, M.; Gilbertson, A.; Dougherty, M.

    1991-03-01

    These transducers are designed to measure stresses on SSC collared coils. They are individually calibrated with a bonded ten-stack of SSC inner coil cable by applying a known load and reading corresponding output from the gages. The transducer is supported by a notched backing plate'' that allows for bending of the gage beam during calibration or in use with an actual coil. Several factors affecting the calibration and use of the transducers are: the number of times a backing plate'' is used, the similarities or difficulties between bonded ten-stacks, and the differences between the ten-stacks and the coil they represent. The latter is probably the most important because a calibration curve is a model of how a transducer should react within a coil. If the model is wrong, the calibration curve is wrong. Information will be presented regarding differences in calibrations between Brookhaven National Labs (also calibrating these transducers) and Fermilab -- what caused these differences, the investigation into the differences between coils and ten-stacks and how they relate to transducer calibration, and some suggestions for future calibrations.

  6. Coronary stent strut size dependent stress-strain response investigated using micromechanical finite element models.

    PubMed

    Savage, P; O'Donnell, B P; McHugh, P E; Murphy, B P; Quinn, D F

    2004-02-01

    Cardiovascular stents are metal scaffolds that are used in the treatment of atherosclerosis. These devices are typically composed of very thin struts (< or = 100 microm thickness, for coronary applications). At this size-scale the question arises as to the suitability of using bulk material properties in stent design. This paper investigates the use of finite element analysis to predict the mechanical failure of stent struts, typical of the strut size used in coronary stents. 316 L stainless steel in uniaxial loading was considered. To accurately represent the constitutive behavior of the material at this size-scale, a computational micromechanics approach was taken involving an explicit representation of the grain structure in the steel struts, and the use of crystal plasticity theory to represent the constitutive behavior of the individual grains. The development of the finite element models is discussed and results are presented for the predictions of tensile mechanical behavior as a function of strut thickness. The results showed that using this modelling approach, a size effect, already seen experimentally, is produced. This has significant implications for stent design, especially in the context of the desire to produce smaller stents for small bore neurovascular and peripheral artery applications.

  7. Preliminary Investigations of Creep Strain of Neogene Clay from Warsaw in Drained Triaxial Tests Assisted by Computed Microtomography

    NASA Astrophysics Data System (ADS)

    Kaczmarek, Łukasz Dominik; Dobak, Paweł Józef; Kiełbasiński, Kamil

    2017-06-01

    The study concerns soil creep deformation in multistage triaxial stress tests under drained conditions. High resolution X-ray computed microtomography (XμCT) was involved in structure recognition before and after triaxial tests. Undisturbed Neogene clay samples, which are widespread in central Poland, were used in this study. XμCT was used to identify representative sample series and informed the detection and rejection of unreliable ones. Maximum deviatoric stress for in situ stress confining condition was equal 95.1 kPa. This result helped in the design of further multistage investigations. The study identified the rheological strain course, which can be broken down into three characterizations: decreasing creep strain rate, transitional constant creep velocity, and accelerating creep deformation. The study found that due to multistage creep loading, the samples were strengthened. Furthermore, there is a visibly "brittle" character of failure, which may be the consequence of the microstructure transformation as a function of time as well as collapse of voids. Due to the glacial tectonic history of the analyzed samples, the reactivation of microcracks might also serve as an explanation. The number of the various sizes of shear planes after failure is confirmed by XμCT overexposure.

  8. Investigation of the dynamic stress–strain response of compressible polymeric foam using a non-parametric analysis

    SciTech Connect

    Koohbor, Behrad; Kidane, Addis; Lu, Wei -Yang; Sutton, Michael A.

    2016-01-25

    Dynamic stress–strain response of rigid closed-cell polymeric foams is investigated in this work by subjecting high toughness polyurethane foam specimens to direct impact with different projectile velocities and quantifying their deformation response with high speed stereo-photography together with 3D digital image correlation. The measured transient displacement field developed in the specimens during high stain rate loading is used to calculate the transient axial acceleration field throughout the specimen. A simple mathematical formulation based on conservation of mass is also proposed to determine the local change of density in the specimen during deformation. By obtaining the full-field acceleration and density distributions, the inertia stresses at each point in the specimen are determined through a non-parametric analysis and superimposed on the stress magnitudes measured at specimen ends to obtain the full-field stress distribution. Furthermore, the process outlined above overcomes a major challenge in high strain rate experiments with low impedance polymeric foam specimens, i.e. the delayed equilibrium conditions can be quantified.

  9. Investigation of the dynamic stress–strain response of compressible polymeric foam using a non-parametric analysis

    DOE PAGES

    Koohbor, Behrad; Kidane, Addis; Lu, Wei -Yang; ...

    2016-01-25

    Dynamic stress–strain response of rigid closed-cell polymeric foams is investigated in this work by subjecting high toughness polyurethane foam specimens to direct impact with different projectile velocities and quantifying their deformation response with high speed stereo-photography together with 3D digital image correlation. The measured transient displacement field developed in the specimens during high stain rate loading is used to calculate the transient axial acceleration field throughout the specimen. A simple mathematical formulation based on conservation of mass is also proposed to determine the local change of density in the specimen during deformation. By obtaining the full-field acceleration and density distributions,more » the inertia stresses at each point in the specimen are determined through a non-parametric analysis and superimposed on the stress magnitudes measured at specimen ends to obtain the full-field stress distribution. Furthermore, the process outlined above overcomes a major challenge in high strain rate experiments with low impedance polymeric foam specimens, i.e. the delayed equilibrium conditions can be quantified.« less

  10. Convergent beam electron diffraction investigation of strain induced by Ti self-aligned silicides in shallow trench Si isolation structures

    NASA Astrophysics Data System (ADS)

    Armigliato, Aldo; Spessot, Alessio; Balboni, Roberto; Benedetti, Alessandro; Carnevale, Gianpietro; Frabboni, Stefano; Mastracchio, Gianfranco; Pavia, Giuseppe

    2006-03-01

    The deformation induced onto silicon by the formation of Ti self-aligned silicides (salicides) in shallow trench isolation structures has been investigated by the convergent beam electron diffraction technique (CBED) in the transmission electron microscope (TEM). The splitting of the high order Laue zone (HOLZ) lines in the CBED patterns taken in TEM cross sections close to the salicide/silicon interface has been explained assuming that the salicide grains induce a local bending of the lattice planes of the underlying matrix. This bending, which affects in opposite sense the silicon areas below adjacent grains, decreases with the distance from the interface, eventually vanishing at a depth of 300-400 nm. The proposed strain field has been implemented into a fully dynamical simulation of the CBED patterns and has proved to be able to reproduce both the asymmetry of the HOLZ line splitting and the associated subsidiary fringes. This model is confirmed by the shift of a Bragg contour observed in large angle CBED patterns, taken in a cross section cut along a perpendicular direction. The whole experimental results cannot be explained by just a strain relaxation of the TEM cross section, induced by the salicide film onto the underlying silicon.

  11. Outbreak investigation identifies a single Listeria monocytogenes strain in sheep with different clinical manifestations, soil and water.

    PubMed

    Dreyer, M; Thomann, A; Böttcher, S; Frey, J; Oevermann, A

    2015-08-31

    Listeria (L.) monocytogenes causes orally acquired infections and is of major importance in ruminants. Little is known about L. monocytogenes transmission between farm environment and ruminants. In order to determine potential sources of infection, we investigated the distribution of L. monocytogenes genetic subtypes in a sheep farm during a listeriosis outbreak by applying four subtyping methods (MALDI-TOF-MS, MLST, MLVA and PFGE). L. monocytogenes was isolated from a lamb with septicemia and from the brainstem of three sheep with encephalitis. Samples from the farm environment were screened for the presence of L. monocytogenes during the listeriosis outbreak, four weeks and eight months after. L. monocytogenes was found only in soil and water tank swabs during the outbreak. Four weeks later, following thorough cleaning of the barn, as well as eight months later, L. monocytogenes was absent in environmental samples. All environmental and clinical L. monocytogenes isolates were found to be the same strain. Our results show that the outbreak involving two different clinical syndromes was caused by a single L. monocytogenes strain and that soil and water tanks were potential infection sources during this outbreak. However, silage cannot be completely ruled out as the bales fed prior to the outbreak were not available for analysis. Faeces samples were negative, suggesting that sheep did not act as amplification hosts contributing to environmental contamination. In conclusion, farm management appears to be a crucial factor for the limitation of a listeriosis outbreak. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Investigation of H2 Concentration and Combustion Instability Effects on the Kinetics of Strained Syngas Flames

    SciTech Connect

    Ahsan R. Choudhuri

    2006-08-07

    The flame extinction limits of syngas (H{sub 2}-CO) flames were measured using a twin-flame-counter-flow burner. Plots of Extinction limits vs. global stretch rates were generated at different mixture compositions and an extrapolation method was used to calculate the flame extinction limit corresponding to an experimentally unattainable zero-stretch condition. The zero-stretch extinction limit of H{sub 2}-CO mixtures decreases (from rich to lean) with the increase in H{sub 2} concentration in the mixture. The average difference between the measured flame extinction limit and the Le Chatelier's calculation is around {approx} 7%. The measured OH{sup -} chemiluminescent data indicates that regardless of mixture compositions the OH radical concentration reduces (within the experimental uncertainties) to an extinction value prior to the flame extinction. Flame extinction limits of H{sub 2}-CO mixtures measured in a flat-flame burner configuration also show a similar relation. Additionally, the measured laminar flame velocity close to the extinction indicates that regardless of fuel composition the premixed flame of hydrogen fuel blends extinguishes when the mixture laminar flame velocity falls below a critical value. The critical laminar flame velocity at extinction for H{sub 2}-CO premixed flames (measured in the flat flame burner configuration) is found to be 3.77({+-}0.38) cm/s. An externally perturbed H{sub 2}-CO twin flame was not experimentally achievable for the mixture conditions used in the present investigation. A slightest perturbation in the flow-field distorts the H{sub 2}-CO twin-flame. The flame becomes highly unstable with the introduction of an externally excited flow oscillation.

  13. Investigation of heat transfer in 9-layer film blowing process by using variational principles

    NASA Astrophysics Data System (ADS)

    Kolarik, Roman; Zatloukal, Martin

    2013-04-01

    In this work, coextrusion experiments utilizing an industrial 9-layer Brampton Engineering coextrusion film blowing line has been performed under different processing conditions (low/high air cooling intensity) in order to evaluate variational principles based modeling approach using energy equation utilizing variable heat transfer coefficient along the multi-layer bubble. It has been revealed that the variational principle based model can describe the bubble shape and temperature profile reasonably well even if the multi-layer film has been viewed as the static elastic membrane characterized only by one material parameter - bubble compliance J, which was not allow to vary along the bubble. Moreover, it has been found that if the freezeline height becomes long, heat transfer coefficient starts to vary significantly along the bubble which has crucial impact on the temperature profile along the multi-layer bubble. The performed theoretical parametric study revealed that increase in blow-up ratio or decrease in bubble curvature and air temperature causing bubble cooling efficiency increases, which allows to cooled down the multi-layer bubble for the given freezeline height to solidification temperature by smaller amount of the air volume flow rate.

  14. Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis

    PubMed Central

    2013-01-01

    Background Xylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research. By expressing three different fungal pathways in two S. cerevisiae hosts respectively, we found that the xylose utilization efficiency by recombinant S. cerevisiae depends not only on the choice of xylose pathway but also on the choice of host, exhibiting an obvious host or context dependence. To investigate molecular mechanisms of this context dependence, we applied RNA-seq analysis in this study for a systematic characterization of the xylose utilization via different pathways in different S. cerevisiae hosts. Results Based on the RNA-seq analysis, the transcripts that were regulated during xylose utilization have been identified. Three transcription factors involved in regulation of amino acid metabolism, responses to oxidative stresses, and degradation of aggregated proteins, respectively, were found to participate in xylose metabolism regulation regardless of which pathway was expressed and which host the xylose pathway was expressed in. Nine transcription factors, involved in homeostasis, regulation of amino acid metabolism, and stress responses, were identified as the key modules responsible for the host-specific responses to the same xylose pathway. In addition, the transcriptional regulations of xylose utilization in different yeast hosts were compared to two reference regulation patterns, which indicated that diverse regulation strategies were adopted by different hosts for improved xylose utilization. Conclusions This study provides the first transcriptomic study of the host dependence of xylose utilization in S. cerevisiae. Both the conserved regulatory modules for xylose metabolism and the key modules responsible for host dependence were identified. As indicated by the functions of the conserved transcription factors involved in xylose metabolism regulation, the xylose utilization in recombinant S. cerevisiae may be

  15. An exploratory investigation of the flight dynamics effects of rotor rpm variations and rotor state feedback in hover

    NASA Technical Reports Server (NTRS)

    Chen, Robert T. N.

    1992-01-01

    This paper presents the results of an analytical study conducted to investigate airframe/engine interface dynamics, and the influence of rotor speed variations on the flight dynamics of the helicopter in hover, and to explore the potential benefits of using rotor states as additional feedback signals in the flight control system. The analytical investigation required the development of a parametric high-order helicopter hover model, which included heave/yaw body motion, the rotor speed degree of freedom, rotor blade motion in flapping and lead-lag, inflow dynamics, a drive train model with a flexible rotor shaft, and an engine/rpm governor. First, the model was used to gain insight into the engine/drive train/rotor system dynamics and to obtain an improved simple formula for easy estimation of the dominant first torsional mode, which is important in the dynamic integration of the engine and airframe system. Then, a linearized version of the model was used to investigate the effects of rotor speed variations and rotor state feedback on helicopter flight dynamics. Results show that, by including rotor speed variations, the effective vertical damping decreases significantly from that calculated with a constant speed assumption, thereby providing a better correlation with flight test data. Higher closed-loop bandwidths appear to be more readily achievable with rotor state feedback. The results also indicate that both aircraft and rotor flapping responses to gust disturbance are significantly attenuated when rotor state feedback is used.

  16. Variation of the spore population of a natural source strain of Bacillus cereus in the presence of inosine.

    PubMed

    Collado, J; Fernández, A; Rodrigo, M; Martínez, A

    2004-05-01

    The heat resistance of a wild strain of Bacillus cereus spores isolated from liquid egg was characterized, and the effect of the nutritional germinant inosine on the spore population was then studied, considering different factors such as germination temperature, inosine concentration, and age of spore culture. The heat resistance clearly indicates that these spores can survive mild heat treatments such as those used for cooked refrigerated food of extended durability or liquid egg, posing safety problems for these foods with temperature abuse. The germination study indicates that temperature, spore age, and the interaction between the two were the factors affecting the level of spores remaining after the germination process. No significant differences were found for the three inosine concentrations used in the study (1, 5, and 10 mM). The highest reduction in the spore concentration was reached at 30 degrees C after 120 min, although the reduction in the spore counts at germination temperatures of 4 and 8 degrees C was also considerable.

  17. Influences of Vowel and Tone Variation on Emergent Word Knowledge: A Cross-Linguistic Investigation

    ERIC Educational Resources Information Center

    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…

  18. Influences of Vowel and Tone Variation on Emergent Word Knowledge: A Cross-Linguistic Investigation

    ERIC Educational Resources Information Center

    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…

  19. High-pressure resistance variation of Escherichia coli O157:H7 strains and Salmonella serovars in tryptic soy broth, distilled water, and fruit juice.

    PubMed

    Whitney, Brooke M; Williams, Robert C; Eifert, Joseph; Marcy, Joseph

    2007-09-01

    The effect of high pressure on the log reduction of six strains of Escherichia coli O157:H7 and five serovars of Salmonella enterica was investigated in tryptic soy broth, sterile distilled water, and commercially sterile orange juice (for Salmonella) and apple cider (for E. coli). Samples were subjected to high-pressure processing treatment at 300 and 550 MPa for 2 min at 6 degrees C. Samples were plated onto tryptic soy agar directly after pressurization and after being held for 24 h at 4 degrees C. At 300 MPa, little effect was seen on E. coli O157:H7 strains, while Salmonella serovars varied in resistance, showing reductions between 0.26 and 3.95 log CFU/ml. At 550 MPa, E. coli O157:H7 strains exhibited a range of reductions (0.28 to 4.39 log CFU/ml), while most Salmonella populations decreased beyond the detection limit (> 5-log CFU/ml reduction). The most resistant strains tested were E. coli E009 and Salmonella Agona. Generally, bacterial populations in fruit juices showed larger decreases than did populations in tryptic soy broth and distilled water. E. coli O157:H7 cultures held for 24 h at 4 degrees C after treatment at 550 MPa showed a significant log decrease as compared with cultures directly after treatment (P < or = 0.05), while Salmonella serovars did not show this significant decrease (P > 0.05). All Salmonella serovars tested in orange juice treated at 550 MPa for 2 min at 6 degrees C and held for 24 h showed a > 5-log decrease, while E. coli O157:H7 strains require a higher pressure, higher temperature, longer pressurization, or a chemical additive to achieve a 5-log decrease.

  20. Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor

    SciTech Connect

    Hedrick, David B.; Peacock, Aaron; Lovley, Derek; Woodard, Trevor L.; Nevin, Kelly P.; Long, Philip E.; White, David C.

    2009-02-01

    The polar lipid fatty acids, lipopolysaccharide hydroxy-fatty acids, and respiratory quinones of Geobacter metallireducens str. GS-15, Geobacter sulfurreducens str. PCA, and Geobacter bemidjiensis str. Bem are reported. Also, the lipids of G. metallireducens were compared when grown with Fe3+ or nitrate as electron acceptors and G. sulfurreducens with Fe3+ or fumarate. In all experiments, the most abundant polar lipid fatty acids were 14:0, i15:0, 16:1*7c, 16:1*5c, and 16:0; lipopolysaccharide hydroxyfatty acids were dominated by 3oh16:0, 3oh14:0, 9oh16:0, and 10oh16:0; and menaquinone-8 was the most abundant respiratory quinone. Some variation in lipid proWles with strain were observed, but not with electron acceptor.

  1. 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.

  2. Seasonal variation in Campylobacter-contaminated retail chicken products: a year-round investigation in Japan.

    PubMed

    Ishihara, Kanako; Takahashi, Ryuta; Andoh, Masako; Ueno, Hiroshi; Muramatsu, Yasukazu; Tamura, Yutaka

    2012-01-01

    Campylobacter was isolated from retail meat samples collected during the fiscal year 2009 in Japan. The higher percentages of contamination of chicken products were observed from June (39.3%) to November (83.3%). However, the highest number of human campylobacteriosis cases was reported in June in the Infectious Agents Surveillance Report. The chicken isolates with distinct clusters IVb and I, based on the restriction fragment length polymorphism of the flaA gene, were predominantly obtained during the periods between April and November 2009 and between February and March 2010, respectively. Extensive monitoring of Campylobacter contamination in chickens produced in various places is needed to analyse the seasonal variations between contamination of the meat products and the number of human cases with campylobacteriosis.

  3. Investigations of the Response of Swimming Paramecia to Variations in their Apparent Weight

    NASA Astrophysics Data System (ADS)

    Valles, James; Jung, Ilyong; Guevorkian, Karine; Mickalide, Harry; Wagman, Michael

    2011-11-01

    There is a set of micro-organisms that are small enough that they swim at low Reynolds number and large enough that gravity exerts an influence on their behavior Many protists, like paramecia, for example, exhibit negative gravi-taxis by orienting their swimming upward and negative gravi-kinesis by increasing their propulsion when swimming against their apparent weight. It is not clear whether these responses to a very weak force (about 100 pN) are active or passive. We have developed a technique, Magnetic Force Buoyancy Variation, which enables us to vary the apparent weight of the swimmers in situ. We will describe experiments on paramecia conducted at the National High Magnetic Field Laboratory. In particular, we will describe how increasing the apparent weight induces paramecia to accumulate at upper surfaces. A simple force model suggests that this accumulation is a passive response. Supported by NSF-PHY0750360 and a grant to the NHMFL, NSF DMR-0654118.

  4. Investigation of sulphur isotope variation due to different processes applied during uranium ore concentrate production.

    PubMed

    Krajkó, Judit; Varga, Zsolt; Wallenius, Maria; Mayer, Klaus; Konings, Rudy

    The applicability and limitations of sulphur isotope ratio as a nuclear forensic signature have been studied. The typically applied leaching methods in uranium mining processes were simulated for five uranium ore samples and the n((34)S)/n((32)S) ratios were measured. The sulphur isotope ratio variation during uranium ore concentrate (UOC) production was also followed using two real-life sample sets obtained from industrial UOC production facilities. Once the major source of sulphur is revealed, its appropriate application for origin assessment can be established. Our results confirm the previous assumption that process reagents have a significant effect on the n((34)S)/n((32)S) ratio, thus the sulphur isotope ratio is in most cases a process-related signature.

  5. Extensive lava flow fields on Venus: Preliminary investigation of source elevation and regional slope variations

    NASA Technical Reports Server (NTRS)

    Magee-Roberts, K.; Head, James W., III; Lancaster, M. G.

    1992-01-01

    Large-volume lava flow fields have been identified on Venus, the most areally extensive of which are known as fluctus and have been subdivided into six morphologic types. Sheetlike flow fields (Type 1) lack the numerous, closely spaced, discrete lava flow lobes that characterize digitate flow fields. Transitional flow fields (Type 2) are similar to sheetlike flow fields but contain one or more broad flow lobes. Digitate flow fields are divided further into divergent (Types 3-5) and subparallel (Type 6) classes on the basis of variations in the amount of downstream flow divergence. As a result of our previous analysis of the detailed morphology, stratigraphy, and tectonic associations of Mylitta Fluctus, we have formulated a number of questions to apply to all large flow fields on Venus. In particular, we would like to address the following: (1) eruption conditions and style of flow emplacement (effusion rate, eruption duration), (2) the nature of magma storage zones (presence of neutral buoyancy zones, deep or shallow crustal magma chambers), (3) the origin of melt and possible link to mantle plumes, and (4) the importance of large flow fields in plains evolution. To answer these questions we have begun to examine variations in flow field dimension and morphology; the distribution of large flow fields in terms of elevation above the mean planetary radius; links to regional tectonic or volcanic structures (e.g., associations with large shield edifices, coronae, or rift zones); statigraphic relationships between large flow fields, volcanic plains, shields, and coronae; and various models of flow emplacement in order to estimate eruption parameters. In this particular study, we have examined the proximal elevations and topographic slopes of 16 of the most distinctive flow fields that represent each of the 6 morphologic types.

  6. Application of mobile sampling to investigate spatial variation in fine particle composition

    NASA Astrophysics Data System (ADS)

    Li, Hugh Z.; Dallmann, Timothy R.; Gu, Peishi; Presto, Albert A.

    2016-10-01

    Long-term exposure to particulate matter (PM) is a major contributor to air pollution related deaths. Evidence indicates that metals play an important role in harming human health due to their redox potential. We conducted a mobile sampling campaign in 2013 summer and winter in Pittsburgh, PA to characterize spatial variation in PM2.5 mass and composition. Thirty-six sites were chosen based on three stratification variables: traffic density, proximity to point sources, and elevation. We collected filters in three time sessions (morning, afternoon, and overnight) in each season. X-ray fluorescence (XRF) was used to analyze concentrations of 26 elements: Na, Mg, Al, Si, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Rb, Sr, Zr, Cd, Sb, and Pb. Trace elements had a broad range of concentrations from 0 to 300 ng/m3. Comparison of data from mobile sampling filters with stationary monitors suggested that the mobile sampling strategy did not lead to a biased dataset. We developed Land Use Regression (LUR) models to describe spatial variation of PM2.5, Si, S, Cl, K, Ca, Ti, Cr, Fe, Cu, and Zn. Using ArcGIS-10.3 (ESRI, Redlands, CA), we extracted different independent variables related to traffic influence, land-use type, and facility emissions based on the National Emission Inventory (NEI). To validate LUR models, we used regression diagnostics such as leave-one-out cross validation (LOOCV), mean studentized prediction residual (MSPR), and root mean square of studentized residuals (RMS). The number of predictors in final LUR models ranged from 1 to 6. Models had an average R2 of 0.57 (SD = 0.16). Traffic related variables explained the most variability with an average R2 contribution of 0.20 (SD = 0.20). Overall, these results demonstrated significant intra-urban spatial variability of fine particle composition.

  7. Flagellar variation in Serratia marcescens is associated with color variation.

    PubMed Central

    Paruchuri, D K; Harshey, R M

    1987-01-01

    The pigmented enterobacterium Serratia marcescens, an opportunistic pathogen, shows a striking variation of its red color. Different strains differ greatly both in color and in the frequency with which they produce color variants. Within a strain, the variations occur at constant rates and are reversible. During an investigation of this phenomenon we observed that variation of a 39-kilodalton protein in S. marcescens 274 is closely associated with color variation. Using antibodies to this protein we identified it as being a component of the bacterial flagella. Variation of surface proteins often provides an organism with alternate offense-defense strategies for survival in a challenging environment. The pigment, in association with flagella, may provide such a function for S. marcescens. Images PMID:3539927

  8. Effect of Rickettsia felis Strain Variation on Infection, Transmission, and Fitness in the Cat Flea (Siphonaptera: Pulicidae).

    PubMed

    Healy, Sean P; Brown, Lisa D; Hagstrom, Melena R; Foil, Lane D; Macaluso, Kevin R

    2017-03-02

    Rickettsia felis is a human pathogen transmitted by the cat flea, Ctenocephalides felis (Bouché) (str. LSU), as well as an obligate symbiont of the parthenogenic booklouse Liposcelis bostrychophila (Badonnel) (str. LSU-Lb). The influence of genetic variability in these two strains of R. felis on host specialization and fitness and possible resulting differences on infection and transmission kinetics in C. felis is unknown. Utilizing an artificial host system, cat fleas were exposed to a R. felis str. LSU-Lb-infected bloodmeal and monitored for infection at 7-d intervals for 28 d. Quantitative real-time PCR was used to determine rickettsial load and infection density in newly exposed cat fleas, and transmission frequency between cat fleas. The effect of persistent R. felis infection on cat flea F1 progeny was also assessed. At 7 d postexposure 76.7% of the cat fleas successfully acquired R. felis str. LSU-Lb. In R. felis str. LSU-Lb-exposed cat fleas, the mean infection load (6.15 × 106), infection density (0.76), and infection prevalence (91/114) were significantly greater than R. felis str. LSU infection load (3.09 × 106), infection density (0.68), and infection prevalence (76/113). A persistent R. felis str. LSU-Lb infection was detected for 28 d in adult cat fleas but neither female:male ratio distortion nor vertical transmission was observed in F1 progeny. While infection kinetics differed, with higher intensity associated with R. felis str. LSU-Lb, no distinct phenotype was observed in the F1 progeny.

  9. MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

    PubMed Central

    Falush, Daniel

    2016-01-01

    ABSTRACT Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (k = 30, 50) to fit a k-mer “palette” of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample. The method returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date. Tree figures are also returned that quantify the relatedness of novel organisms to reference sequences, and the accuracy of such figures is demonstrated on simulated spike-ins and a metagenomic soil sample. The software implementing MetaPalette is available at: https://github.com/dkoslicki/MetaPalette. Pretrained databases are included for Archaea, Bacteria, Eukaryota, and viruses. IMPORTANCE Taxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-specific markers. The compositions of palettes are easy to model, allowing rapid inference of community composition. In addition to providing strain-level information where applicable, our approach provides taxonomic profiles that are more accurate than those of competing methods. Author Video: An author video summary of this article is available. PMID:27822531

  10. A Computational Icing Effects Study for a Three-Dimensional Wing: Comparison with Experimental Data and Investigation of Spanwise Variation

    NASA Technical Reports Server (NTRS)

    Thompson, D.; Mogili, P.; Chalasani, S.; Addy, H.; Choo, Y.

    2004-01-01

    Steady-state solutions of the Reynolds-averaged Navier-Stokes (RANS) equations were computed using the Colbalt flow solver for a constant-section, rectangular wing based on an extruded two-dimensional glaze ice shape. The one equation Spalart-Allmaras turbulence model was used. The results were compared with data obtained from a recent wind tunnel test. Computed results indicate that the steady RANS solutions do not accurately capture the recirculating region downstream of the ice accretion, even after a mesh refinement. The resulting predicted reattachment is farther downstream than indicated by the experimental data. Additionally, the solutions computed on a relatively coarse baseline mesh had detailed flow characteristics that were different from those computed on the refined mesh or the experimental data. Steady RANS solutions were also computed to investigate the effects of spanwise variation in the ice shape. The spanwise variation was obtained via a bleeding function that merged the ice shape with the clean wing using a sinusoidal spanwise variation. For these configurations, the results predicted for the extruded shape provided conservative estimates for the performance degradation of the wing. Additionally, the spanwise variation in the ice shape and the resulting differences in the flow fields did not significantly change the location of the primary reattachment.

  11. Comparative experimental investigation on the efficacy of mono- and multiprobiotic strains in non-alcoholic fatty liver disease prevention.

    PubMed

    Kobyliak, Nazarii; Falalyeyeva, Tetyana; Virchenko, Oleksandr; Mykhalchyshyn, Galyna; Bodnar, Petro; Spivak, Mykola; Yankovsky, Dmytro; Beregova, Tetyana; Ostapchenko, Lyudmyla

    2016-03-15

    To investigate the efficacy of different probiotic strains, their combinations and forms (alive or lyophilized) in nonalcoholic fatty liver disease (NAFLD) prevention. In this study, 70 rats have been used divided into 7 groups of 10 animals in each: I - intact rats, II-VII - rats with monosodium glutamate (MSG)-induced NAFLD. Rats with NAFLD were untreated (group II, MSG-obesity group) and treated with probiotics (groups III-VII). In order to develop NAFLD, newborn rats of groups II-VII were injected with a solution of monosodium glutamate (MSG) (4 mg/g) subcutaneously (s.c.) at 2nd,4th, 6th, 8th,10th postnatal day. The groups III-V received lyophilized monoprobiotics B. animalis VKL, B. animalis VKB, L.casei IMVB-7280, respectively. The group VI received 2.5 ml/kg of an aqueous solution of a mixture of the three probiotic strains (2:1:1 Lactobacillus casei IMVB-7280, Bifidobacterium animalis VKL, Bifidobacterium animalis VKB) at a dose of 50 mg/kg (5 × 10(9) CFU/kg) (g) (intragastrically). The group VII was treated with multiprobiotic "Symbiter" containing biomass of 14 alive probiotic strains (Lactobacillus + Lactococcus (6 × 10(10) CFU/g), Bifidobacterium (1 × 10(10)/g), Propionibacterium (3 × 10(10)/g), Acetobacter (1 × 10(6)/g)) at a dose of 140 mg/kg (1.4 × 10(10) CFU/kg). The treatment with probiotics was started at the age of 1 month. There were 3 courses of treatment, each included 2-week administration and 2-week break. All parameters were measured in 4-month aged rats. Introduction of MSG during the neonatal period leads to the NAFLD development in the 4-months old rats. For steatosis degree there was no significant difference between MSG-obesity group and lyophilized monocomponent probiotics groups (III-V). The highest manifestation of steatosis was observed for B. animalis VKL group (2.0 ± 0.25) as compared to B. animalis VKB (1.70 ± 0.21) and L. casei IMVB-7280 (1.80 ± 0.20). The steatosis score changes between all monoprobiotics groups (III

  12. Variation in human mate choice: Simultaneously investigating heritability, parental influence, sexual imprinting, and assortative mating

    PubMed Central

    Zietsch, Brendan P.; Verweij, Karin J. H.; Heath, Andrew C.; Martin, Nicholas G.

    2012-01-01

    Human mate choice is central to individuals’ lives and to the evolution of the species, but the basis of variation in mate choice is not well understood. Here we look at a large community-based sample of twins and their partners and parents (N > 20,000 individuals) to test for genetic and family environmental influences on mate choice, with and without controlling for the effects of assortative mating. Key traits are analyzed, including height, body mass index, age, education, income, personality, social attitudes, and religiosity. This revealed near-zero genetic influences on male and female mate choice over all traits and no significant genetic influences on mate choice for any specific trait. A significant family environmental influence was found for the age and income of females’ mate choices, possibly reflecting parental influence over mating decisions. We also tested for evidence of sexual imprinting, where individuals acquire mate-choice criteria during development by using their opposite-sex parent as the template of a desirable mate; there was no such effect for any trait. The main discernable pattern to mate choice was assortative mating; we found that partner similarity was due to initial choice rather than convergence and also due at least in part to phenotypic matching. PMID:21508607

  13. Investigating Müllerian mimicry: predator learning and variation in prey defences.

    PubMed

    Ihalainen, E; Lindström, L; Mappes, J

    2007-03-01

    Inexperienced predators are assumed to select for similarity of warning signals in aposematic species (Müllerian mimicry) when learning to avoid them. Recent theoretical work predicts that if co-mimic species have unequal defences, predators attack them according to their average unpalatability and mimicry may not be beneficial for the better defended co-mimic. In this study, we tested in a laboratory environment whether a uniform warning signal is superior to a variable one in promoting predator learning, and simultaneously whether co-mimics are preyed upon according to their average unpalatability. There was an interaction of signal variation and unpalatability but inexperienced birds did not select for signal similarity in artificial prey; when the prey was moderately defended a variable signal was even learnt faster than a uniform one. Due to slow avoidance learning, moderately defended prey had higher mortality than highly defended prey (although this was not straightforward), but mixing high and moderate unpalatability did not increase predation compared with high unpalatability. This does not support the view that predators are sensitive to varying unpalatability. The results suggest that inexperienced predators may neither strongly select for accurate Müllerian mimicry nor affect the benefits of mimicry when the co-mimics are unequally defended.

  14. Variation in human mate choice: simultaneously investigating heritability, parental influence, sexual imprinting, and assortative mating.

    PubMed

    Zietsch, Brendan P; Verweij, Karin J H; Heath, Andrew C; Martin, Nicholas G

    2011-05-01

    Human mate choice is central to individuals' lives and to the evolution of the species, but the basis of variation in mate choice is not well understood. Here we looked at a large community-based sample of twins and their partners and parents ([Formula: see text] individuals) to test for genetic and family environmental influences on mate choice, while controlling for and not controlling for the effects of assortative mating. Key traits were analyzed, including height, body mass index, age, education, income, personality, social attitudes, and religiosity. This revealed near-zero genetic influences on male and female mate choice over all traits and no significant genetic influences on mate choice for any specific trait. A significant family environmental influence was found for the age and income of females' mate choices, possibly reflecting parental influence over mating decisions. We also tested for evidence of sexual imprinting, where individuals acquire mate-choice criteria during development by using their opposite-sex parent as the template of a desirable mate; there was no such effect for any trait. The main discernible pattern of mate choice was assortative mating; we found that partner similarity was due to initial choice rather than convergence and also at least in part to phenotypic matching.

  15. Theoretical investigation of tensile strained GeSn waveguide with Si₃N₄ liner stressor for mid-infrared detector and modulator applications.

    PubMed

    Zhang, Qingfang; Liu, Yan; Yan, Jing; Zhang, Chunfu; Hao, Yue; Han, Genquan

    2015-03-23

    We theoretically investigate a tensile strained GeSn waveguide integrated with Si₃N₄ liner stressor for the applications in mid-infrared (MIR) detector and modulator. A substantial tensile strain is induced in a 1 × 1 μm² GeSn waveguide by the expansion of 500 nm Si₃N₄ liner stressor and the contour plots of strain are simulated by the finite element simulation. Under the tensile strain, the direct bandgap E(G,Γ) of GeSn is significantly reduced by lowering the Γ conduction valley in energy and lifting of degeneracy of valence bands. Absorption coefficients of tensile strained GeSn waveguides with different Sn compositions are calculated. As the Si₃N₄ liner stressor expands by 1%, the cut-off wavelengths of tensile strained Ge(0.97)Sn(0.03), Ge(0.95)Sn(0.05), and Ge(0.90)Sn(0.10) waveguide photodetectors are extended to 2.32, 2.69, and 4.06 μm, respectively. Tensile strained Ge(0.90)Sn(0.10) waveguide electro-absorption modulator based on Franz-Keldysh (FK) effect is demonstrated in theory. External electric field dependence of cut-off wavelength and propagation loss of tensile strained Ge(0.90)Sn(0.10) waveguide is observed, due to the FK effect.

  16. Impacts of diurnal variation of ultraviolet-B and photosynthetically active radiation on phycobiliproteins of the hot-spring cyanobacterium Nostoc sp. strain HKAR-2.

    PubMed

    Kannaujiya, Vinod K; Sinha, Rajeshwar P

    2017-01-01

    The effects of diurnal variation of photosynthetically active radiation (PAR; 400-700 nm) and ultraviolet-B (UV-B; 280-315 nm) radiation on phycobiliproteins (PBPs) and photosynthetic pigments (PP) have been studied in the hot-spring cyanobacterium Nostoc sp. strain HKAR-2. The variations in PBPs and PP were monitored by alternating light and dark under PAR, UV-B, and PAR + UV-B radiations over a period of 25 h. There was a decline in the amount of Chl a and PBPs during light periods of UV-B and PAR + UV-B and an increase during dark periods showing a circadian rhythm by destruction and resynthesis of pigment-protein complex. However, a marked induction in carotenoids was recorded during light periods of the same radiations. Moreover, the ratio of Chl a/PE and Chl a/PC was increased in dark periods showing the resynthesis of bleached Chl a. The wavelength shift in emission fluorescence of PBPs toward shorter wavelengths further indicated the bleaching and destruction of PBPs during light periods. Oxidative damage upon exposure to PAR, UV-B, and PAR + UV-B was alleviated by induction of antioxidative enzymes such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). The studied cyanobacterium exhibits a significant increase in the activities of SOD, CAT, and APX upon exposure to UV-B and PAR + UV-B radiations. The results indicate that pigment-protein composition of Nostoc sp. stain HKAR-2 was significantly altered during diurnal variation of light/radiation, which might play an important role in optimization for their productivity in a particular cyanobacterium.

  17. A Genre-Based Investigation of Discussion Sections of Research Articles in Dentistry and Disciplinary Variation

    ERIC Educational Resources Information Center

    Basturkmen, Helen

    2012-01-01

    Outwardly the rhetorical organisation of sections of research reports in different disciplines can appear similar. Close examination, however, may reveal subtle differences. Numerous studies have drawn on the genre-based approach developed by Swales (1990, 2004) to investigate the schematic structure of sections of articles in a range of…

  18. A Monte Carlo Investigation of the Analysis of Variance Applied to Non-Independent Bernoulli Variates.

    ERIC Educational Resources Information Center

    Draper, John F., Jr.

    The applicability of the Analysis of Variance, ANOVA, procedures to the analysis of dichotomous repeated measure data is described. The design models for which data were simulated in this investigation were chosen to represent simple cases of two experimental situations: situation one, in which subjects' responses to a single randomly selected set…

  19. A Genre-Based Investigation of Discussion Sections of Research Articles in Dentistry and Disciplinary Variation

    ERIC Educational Resources Information Center

    Basturkmen, Helen

    2012-01-01

    Outwardly the rhetorical organisation of sections of research reports in different disciplines can appear similar. Close examination, however, may reveal subtle differences. Numerous studies have drawn on the genre-based approach developed by Swales (1990, 2004) to investigate the schematic structure of sections of articles in a range of…

  20. Variations Among Inner City Elementary Schools: An Investigation into the Nature and Causes of Their Differences.

    ERIC Educational Resources Information Center

    Doll, Russell C.

    The investigation in this study of inner-city elementary schools identified two main causes for successful learning environments. The strongest influence was thought to be the principal. An analysis of "problem oriented schools" showed that successful principals were prone to act independently of bureaucratic directives, and that they heeded…

  1. High-resolution typing reveals distinct Chlamydia trachomatis strains in an at-risk population in Nanjing, China.

    PubMed

    Bom, Reinier J M; van den Hoek, Anneke; Wang, Qianqiu; Long, Fuquan; de Vries, Henry J C; Bruisten, Sylvia M

    2013-08-01

    We investigated Chlamydia trachomatis strains from Nanjing, China, and whether these strains differed from Amsterdam, the Netherlands. C. trachomatis type was determined with multilocus sequence typing. Most strains were specific to Nanjing, but some clustered with strains from Amsterdam. This demonstrates a geographical variation in C. trachomatis previously left undetected.

  2. Investigation of the phase morphology of bacterial PHA inclusion bodies by contrast variation SANS

    NASA Astrophysics Data System (ADS)

    Russell, R. A.; Holden, P. J.; Garvey, C. J.; Wilde, K. L.; Hammerton, K. M.; Foster, L. J.

    2006-11-01

    Under growth-limiting conditions, many bacteria are able to metabolise excess organic acids into polyhydroxyalkanoates (PHA) and store these polymers as intracellular inclusions until the return of favourable conditions. Various models have been proposed for the macromolecular organisation of the boundary layer surrounding the polymer, and contrast-variation small-angle neutron scattering (SANS) was used to study its organisation. Inclusions formed by Pseudomonas oleovorans under hydrogenating conditions showed lowest scattering intensity at ca. 20% D 2O. The inclusions consist of protein and membrane lipids in the boundary layer and polyhydroxyoctanoate (lipid) in the inclusion body. At 20% D 2O the contributions of lipids were contrast matched with the solvent, indicating that lipids contributed the bulk of the scattering intensity observed at other D 2O/H 2O ratios. These results are inconsistent with a model of the boundary layer which proposed outer and inner layers of crystalline protein lattice sandwiching a membrane lipid membrane layer [E.S. Stuart, R.W. Lenz, R.C. Fuller, Can J Microbiol 41(Suppl 1) (1995) 84-93], and is more consistent with a model consisting of a lipid monolayer containing embedded proteins [U. Pieper-furst, M.H. Madkour, F. Mayer, A. Steinbuchel, J. Bacteriol. 176 (1994) 4328-4337.] By altering the H/D content of the precursors, we were able to collect SANS data from preparations of both deuterated and H/D copolymer inclusions, where initial PHA produced was hydrogenated followed by deuteration. Deuterated inclusions showed minimum intensity above 90% D 2O/H 2O whereas the sequentially produced copolymer (assumed to be in a core/shell arrangement) displayed minimum scattering some 20% lower, which is consistent with the increased hydrogenation of the boundary layer expected from its synthesis during supply of hydrogenated followed by deuterated precursors.

  3. Investigating different filter and rescaling methods on simulated GRACE-like TWS variations for hydrological applications

    NASA Astrophysics Data System (ADS)

    Zhang, Liangjing; Dahle, Christoph; Neumayer, Karl-Hans; Dobslaw, Henryk; Flechtner, Frank; Thomas, Maik

    2016-04-01

    Terrestrial water storage (TWS) variations obtained from GRACE play an increasingly important role in various hydrological and hydro-meteorological applications. Since monthly-mean gravity fields are contaminated by errors caused by a number of sources with distinct spatial correlation structures, filtering is needed to remove in particular high frequency noise. Subsequently, bias and leakage caused by the filtering need to be corrected before the final results are interpreted as GRACE-based observations of TWS. Knowledge about the reliability and performance of different post-processing methods is highly important for the GRACE users. In this contribution, we re-assess a number of commonly used post-processing methods using a simulated GRACE-like gravity field time-series based on realistic orbits and instrument error assumptions as well as background error assumptions out of the updated ESA Earth System Model. Two non-isotropic filter methods from Kusche (2007) and Swenson and Wahr (2006) are tested. Rescaling factors estimated from five different hydrological models and the ensemble median are applied to the post-processed simulated GRACE-like TWS estimates to correct the bias and leakage. Since TWS anomalies out of the post-processed simulation results can be readily compared to the time-variable Earth System Model initially used as "truth" during the forward simulation step, we are able to thoroughly check the plausibility of our error estimation assessment and will subsequently recommend a processing strategy that shall also be applied to planned GRACE and GRACE-FO Level-3 products for hydrological applications provided by GFZ. Kusche, J. (2007): Approximate decorrelation and non-isotropic smoothing of time-variable GRACE-type gravity field models. J. Geodesy, 81 (11), 733-749, doi:10.1007/s00190-007-0143-3. Swenson, S. and Wahr, J. (2006): Post-processing removal of correlated errors in GRACE data. Geophysical Research Letters, 33(8):L08402.

  4. Investigating the genetic basis of fever-associated syndromic epilepsies using copy number variation analysis.

    PubMed

    Hartmann, Corinna; von Spiczak, Sarah; Suls, Arvid; Weckhuysen, Sarah; Buyse, Gunnar; Vilain, Catheline; Van Bogaert, Patrick; De Jonghe, Peter; Cook, Joseph; Muhle, Hiltrud; Stephani, Ulrich; Helbig, Ingo; Mefford, Heather C

    2015-03-01

    Fever-associated syndromic epilepsies ranging from febrile seizures plus (FS+) to Dravet syndrome have a significant genetic component. However, apart from SCN1A mutations in >80% of patients with Dravet syndrome, the genetic underpinnings of these epilepsies remain largely unknown. Therefore, we performed a genome-wide screening for copy number variations (CNVs) in 36 patients with SCN1A-negative fever-associated syndromic epilepsies. Phenotypes included Dravet syndrome (n = 23; 64%), genetic epilepsy with febrile seizures plus (GEFS+) and febrile seizures plus (FS+) (n = 11; 31%) and unclassified fever-associated epilepsies (n = 2; 6%). Array comparative genomic hybridization (CGH) was performed using Agilent 4 × 180K arrays. We identified 13 rare CNVs in 8 (22%) of 36 individuals. These included known pathogenic CNVs in 4 (11%) of 36 patients: a 1q21.1 duplication in a proband with Dravet syndrome, a 14q23.3 deletion in a proband with FS+, and two deletions at 16p11.2 and 1q44 in two individuals with fever-associated epilepsy with concomitant autism and/or intellectual disability. In addition, a 3q13.11 duplication in a patient with FS+ and two de novo duplications at 7p14.2 and 18q12.2 in a patient with atypical Dravet syndrome were classified as likely pathogenic. Six CNVs were of unknown significance. The identified genomic aberrations overlap with known neurodevelopmental disorders, suggesting that fever-associated epilepsy syndromes may be a recurrent clinical presentation of known microdeletion syndromes.

  5. The gene expression profile of resistant and susceptible Bombyx mori strains reveals cypovirus-associated variations in host gene transcript levels.

    PubMed

    Guo, Rui; Wang, Simei; Xue, Renyu; Cao, Guangli; Hu, Xiaolong; Huang, Moli; Zhang, Yangqi; Lu, Yahong; Zhu, Liyuan; Chen, Fei; Liang, Zi; Kuang, Sulan; Gong, Chengliang

    2015-06-01

    High-throughput paired-end RNA sequencing (RNA-Seq) was performed to investigate the gene expression profile of a susceptible Bombyx mori strain, Lan5, and a resistant B. mori strain, Ou17, which were both orally infected with B. mori cypovirus (BmCPV) in the midgut. There were 330 and 218 up-regulated genes, while there were 147 and 260 down-regulated genes in the Lan5 and Ou17 strains, respectively. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment for differentially expressed genes (DEGs) were carried out. Moreover, gene interaction network (STRING) analyses were performed to analyze the relationships among the shared DEGs. Some of these genes were related and formed a large network, in which the genes for B. mori cuticular protein RR-2 motif 123 (BmCPR123) and the gene for B. mori DNA replication licensing factor Mcm2-like (BmMCM2) were key genes among the common up-regulated DEGs, whereas the gene for B. mori heat shock protein 20.1 (Bmhsp20.1) was the central gene among the shared down-regulated DEGs between Lan5 vs Lan5-CPV and Ou17 vs Ou17-CPV. These findings established a comprehensive database of genes that are differentially expressed in response to BmCPV infection between silkworm strains that differed in resistance to BmCPV and implied that these DEGs might be involved in B. mori immune responses against BmCPV infection.