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Sample records for affect highly conserved

  1. Golgi Anti-apoptotic Proteins Are Highly Conserved Ion Channels That Affect Apoptosis and Cell Migration*

    PubMed Central

    Carrara, Guia; Saraiva, Nuno; Parsons, Maddy; Byrne, Bernadette; Prole, David L.; Taylor, Colin W.; Smith, Geoffrey L.

    2015-01-01

    Golgi anti-apoptotic proteins (GAAPs) are multitransmembrane proteins that are expressed in the Golgi apparatus and are able to homo-oligomerize. They are highly conserved throughout eukaryotes and are present in some prokaryotes and orthopoxviruses. Within eukaryotes, GAAPs regulate the Ca2+ content of intracellular stores, inhibit apoptosis, and promote cell adhesion and migration. Data presented here demonstrate that purified viral GAAPs (vGAAPs) and human Bax inhibitor 1 form ion channels and that vGAAP from camelpox virus is selective for cations. Mutagenesis of vGAAP, including some residues conserved in the recently solved structure of a related bacterial protein, BsYetJ, altered the conductance (E207Q and D219N) and ion selectivity (E207Q) of the channel. Mutation of residue Glu-207 or -178 reduced the effects of GAAP on cell migration and adhesion without affecting protection from apoptosis. In contrast, mutation of Asp-219 abrogated the anti-apoptotic activity of GAAP but not its effects on cell migration and adhesion. These results demonstrate that GAAPs are ion channels and define residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion, and migration independently. PMID:25713081

  2. 7 CFR Exhibit M to Subpart G of... - Implementation Procedures for the Conservation of Wetlands and Highly Erodible Land Affecting...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 1981 to 1985 crop years was planted in alfalfa in a crop rotation determined by SCS to be adequate for... and 1985 crop years in a crop rotation determined by SCS to be adequate for the protection of highly... operational or material costs such as fuel, seed, fertilizer, and pesticide costs; (7) Within the crop year...

  3. How research-prioritization exercises affect conservation policy.

    PubMed

    Rudd, Murray A

    2011-10-01

    Conservation scientists are concerned about the apparent lack of impact their research is having on policy. By better aligning research with policy needs, conservation science might become more relevant to policy and increase its real-world salience in the conservation of biological diversity. Consequently, some conservation scientists have embarked on a variety of exercises to identify research questions that, if answered, would provide the evidence base with which to develop and implement effective conservation policies. I synthesized two existing approaches to conceptualizing research impacts. One widely used approach classifies the impacts of research as conceptual, instrumental, and symbolic. Conceptual impacts occur when policy makers are sensitized to new issues and change their beliefs or thinking. Instrumental impacts arise when scientific research has a direct effect on policy decisions. The use of scientific research results to support established policy positions are symbolic impacts. The second approach classifies research issues according to whether scientific knowledge is developed fully and whether the policy issue has been articulated clearly. I believe exercises to identify important research questions have objectives of increasing the clarity of policy issues while strengthening science-policy interactions. This may facilitate the transmission of scientific knowledge to policy makers and, potentially, accelerate the development and implementation of effective conservation policy. Other, similar types of exercises might also be useful. For example, identification of visionary science questions independent of current policy needs, prioritization of best practices for transferring scientific knowledge to policy makers, and identification of questions about human values and their role in political processes could all help advance real-world conservation science. It is crucial for conservation scientists to understand the wide variety of ways in which

  4. 77 FR 74167 - Information Collection Request: Highly Erodible Land Conservation and Wetland Conservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-13

    ... Farm Service Agency Information Collection Request: Highly Erodible Land Conservation and Wetland Conservation AGENCIES: Farm Service Agency, USDA. ACTION: Notice; request for comments. SUMMARY: In accordance... associated with Highly Erodible Land Conservation and Wetland Conservation certification requirements....

  5. Energy Conservation Featured in Illinois High School

    ERIC Educational Resources Information Center

    Modern Schools, 1976

    1976-01-01

    The William Fremd High School in Palatine, Illinois, scheduled to open in 1977, is being built with energy conservation uppermost in mind. In this system, 70 heat pumps will heat and cool 300,000 square feet of educational facilities. (Author/MLF)

  6. High-bay Lighting Energy Conservation Measures

    SciTech Connect

    Ian Metzger, Jesse Dean

    2010-12-31

    This software requires inputs of simple high-bay lighting system inventory information and calculates the energy and cost benefits of various retrofit opportunities. This tool includes energy conservation measures for: 1000 Watt to 750 Watt High-pressure Sodium lighting retrofit, 400 Watt to 360 Watt High Pressure Sodium lighting retrofit, High Intensity Discharge to T5 lighting retrofit, High Intensity Discharge to T8 lighting retrofit, and Daylighting. This tool calculates energy savings, demand reduction, cost savings, building life cycle costs including: simple payback, discounted payback, net-present value, and savings to investment ratio. In addition this tool also displays the environmental benefits of a project.

  7. High resolution schemes for hyperbolic conservation laws

    NASA Technical Reports Server (NTRS)

    Harten, A.

    1983-01-01

    A class of new explicit second order accurate finite difference schemes for the computation of weak solutions of hyperbolic conservation laws is presented. These highly nonlinear schemes are obtained by applying a nonoscillatory first order accurate scheme to an appropriately modified flux function. The so-derived second order accurate schemes achieve high resolution while preserving the robustness of the original nonoscillatory first order accurate scheme. Numerical experiments are presented to demonstrate the performance of these new schemes.

  8. Forest conservation delivers highly variable coral reef conservation outcomes.

    PubMed

    Klein, Carissa J; Jupiter, Stacy D; Selig, Elizabeth R; Watts, Matthew E; Halpern, Benjamin S; Kamal, Muhammad; Roelfsema, Chris; Possingham, Hugh P

    2012-06-01

    Coral reefs are threatened by human activities on both the land (e.g., deforestation) and the sea (e.g., overfishing). Most conservation planning for coral reefs focuses on removing threats in the sea, neglecting management actions on the land. A more integrated approach to coral reef conservation, inclusive of land-sea connections, requires an understanding of how and where terrestrial conservation actions influence reefs. We address this by developing a land-sea planning approach to inform fine-scale spatial management decisions and test it in Fiji. Our aim is to determine where the protection of forest can deliver the greatest return on investment for coral reef ecosystems. To assess the benefits of conservation to coral reefs, we estimate their relative condition as influenced by watershed-based pollution and fishing. We calculate the cost-effectiveness of protecting forest and find that investments deliver rapidly diminishing returns for improvements to relative reef condition. For example, protecting 2% of forest in one area is almost 500 times more beneficial than protecting 2% in another area, making prioritization essential. For the scenarios evaluated, relative coral reef condition could be improved by 8-58% if all remnant forest in Fiji were protected rather than deforested. Finally, we determine the priority of each coral reef for implementing a marine protected area when all remnant forest is protected for conservation. The general results will support decisions made by the Fiji Protected Area Committee as they establish a national protected area network that aims to protect 20% of the land and 30% of the inshore waters by 2020. Although challenges remain, we can inform conservation decisions around the globe by tackling the complex issues relevant to integrated land-sea planning.

  9. Readings in Wildlife and Fish Conservation, High School Conservation Curriculum Project.

    ERIC Educational Resources Information Center

    Ensminger, Jack

    This publication is a tentative edition of readings on Wildlife and Fish Conservation in Louisiana, and as such it forms part of one of the four units of study designed for an experimental high school course, the "High School Conservation Curriculum Project." The other three units are concerned with Forest Conervation, Soil and Water…

  10. Saving the superstar: a review of the social factors affecting tiger conservation in India.

    PubMed

    Rastogi, Archi; Hickey, Gordon M; Badola, Ruchi; Hussain, Syed Ainul

    2012-12-30

    Tiger conservation in India represents an excellent case study of the many challenges facing conservation programs internationally. It is well understood that tigers are sensitive to human disturbances and large areas of habitat need to be protected for their conservation. Such protected areas in India are managed by the governments using an exclusionary approach. However, this approach is known to create several issues with local communities, including historical, legal, livelihood and management issues; with a volume of literature suggesting the inclusion of local communities in management. Yet, other evidence suggests that inclusion of communities in tiger conservation may lead to anthropogenic disturbances that can jeopardize tigers. The gravity of the situation is reflected in the recent disappearance of tigers from two key protected areas in India, the Sariska and Panna Tiger Reserves. This review paper connects the key literature from conservation biology, environmental history, management sciences, policy and political sciences to underline the gridlock of tiger conservation: it needs exclusive protected areas that antagonize communities, and it depends on the support of the same communities for success. We examine the possibility of reconciliation between these disciplines, and assert that research on tiger conservation needs to allow for an increasingly interdisciplinary approach. We call for a more integrated approach to tiger conservation, to examine the values inherent in conservation and to shed more light on the social factors that affect tiger conservation schemes.

  11. Taking high conservation value from forests to freshwaters.

    PubMed

    Abell, Robin; Morgan, Siân K; Morgan, Alexis J

    2015-07-01

    The high conservation value (HCV) concept, originally developed by the Forest Stewardship Council, has been widely incorporated outside the forestry sector into companies' supply chain assessments and responsible purchasing policies, financial institutions' investment policies, and numerous voluntary commodity standards. Many, if not most, of these newer applications relate to production practices that are likely to affect freshwater systems directly or indirectly, yet there is little guidance as to whether or how HCV can be applied to water bodies. We focus this paper on commodity standards and begin by exploring how prominent standards currently address both HCVs and freshwaters. We then highlight freshwater features of high conservation importance and examine how well those features are captured by the existing HCV framework. We propose a new set of freshwater 'elements' for each of the six values and suggest an approach for identifying HCV Areas that takes out-of-fence line impacts into account, thereby spatially extending the scope of existing methods to define HCVs. We argue that virtually any non-marine HCV assessment, regardless of the production sector, should be expanded to include freshwater values, and we suggest how to put those recommendations into practice.

  12. Taking High Conservation Value from Forests to Freshwaters

    NASA Astrophysics Data System (ADS)

    Abell, Robin; Morgan, Siân K.; Morgan, Alexis J.

    2015-07-01

    The high conservation value (HCV) concept, originally developed by the Forest Stewardship Council, has been widely incorporated outside the forestry sector into companies' supply chain assessments and responsible purchasing policies, financial institutions' investment policies, and numerous voluntary commodity standards. Many, if not most, of these newer applications relate to production practices that are likely to affect freshwater systems directly or indirectly, yet there is little guidance as to whether or how HCV can be applied to water bodies. We focus this paper on commodity standards and begin by exploring how prominent standards currently address both HCVs and freshwaters. We then highlight freshwater features of high conservation importance and examine how well those features are captured by the existing HCV framework. We propose a new set of freshwater `elements' for each of the six values and suggest an approach for identifying HCV Areas that takes out-of-fence line impacts into account, thereby spatially extending the scope of existing methods to define HCVs. We argue that virtually any non-marine HCV assessment, regardless of the production sector, should be expanded to include freshwater values, and we suggest how to put those recommendations into practice.

  13. Highly conserved small subunit residues influence rubisco large subunit catalysis.

    PubMed

    Genkov, Todor; Spreitzer, Robert J

    2009-10-30

    The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

  14. Both Direct and Vicarious Experiences of Nature Affect Children’s Willingness to Conserve Biodiversity

    PubMed Central

    Soga, Masashi; Gaston, Kevin J.; Yamaura, Yuichi; Kurisu, Kiyo; Hanaki, Keisuke

    2016-01-01

    Children are becoming less likely to have direct contact with nature. This ongoing loss of human interactions with nature, the extinction of experience, is viewed as one of the most fundamental obstacles to addressing global environmental challenges. However, the consequences for biodiversity conservation have been examined very little. Here, we conducted a questionnaire survey of elementary schoolchildren and investigated effects of the frequency of direct (participating in nature-based activities) and vicarious experiences of nature (reading books or watching TV programs about nature and talking about nature with parents or friends) on their affective attitudes (individuals’ emotional feelings) toward and willingness to conserve biodiversity. A total of 397 children participated in the surveys in Tokyo. Children’s affective attitudes and willingness to conserve biodiversity were positively associated with the frequency of both direct and vicarious experiences of nature. Path analysis showed that effects of direct and vicarious experiences on children’s willingness to conserve biodiversity were mediated by their affective attitudes. This study demonstrates that children who frequently experience nature are likely to develop greater emotional affinity to and support for protecting biodiversity. We suggest that children should be encouraged to experience nature and be provided with various types of these experiences. PMID:27231925

  15. Socio-economic factors affecting the conservation of natural woodlands in Central Riyadh Area - Saudi Arabia.

    PubMed

    Al-Subaiee, Faisal Sultan

    2016-05-01

    This study aimed to identify some socioeconomic factors affecting local people in central Riyadh area for the utilization of wood and other energy sources in cooking and heating in order to develop some recommendations for conserving woodlands. The study results revealed that gas is the most common energy source used for cooking with a mean usage level of 2.79 (SD = 0.58). On the other hand, wood ranked first for heating with the highest mean, usage level of 1.90 (SD = 1.06). However, electricity and gas as sources of energy for heating ranked second and third with mean usage level of 1.81 and 0.80 respectively. The study revealed that local people with the university education were significantly making higher use of electricity for both cooking and heating and those with no formal education ranked the highest on wood use for both cooking and heating. In addition, those living in traditional houses significantly used more wood for cooking than those living in villas and apartments. Also, local people with high income levels significantly were using more electricity for heating than others. The study recommended conducting extension and environmental awareness raising programs to enhance local residents' adoption of wood substitutes, promoting employment opportunities for unemployed locals, and subsidizing prices of alternative energy sources.

  16. 76 FR 82075 - Highly Erodible Land and Wetland Conservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-30

    ... Secretary 7 CFR Part 12 RIN 0560-AH97 Highly Erodible Land and Wetland Conservation AGENCY: Office of the... agricultural commodities are planted on highly erodible land or a converted wetland, or the production of... ``good faith'' provisions in the USDA regulations allow violators of highly erodible land...

  17. Understanding the Local Socio-political Processes Affecting Conservation Management Outcomes in Corbett Tiger Reserve, India

    NASA Astrophysics Data System (ADS)

    Rastogi, Archi; Hickey, Gordon M.; Badola, Ruchi; Hussain, Syed Ainul

    2014-05-01

    Several measures have been recommended to guarantee a sustainable population of tigers: sufficient inviolate spaces for a viable population, sufficient prey populations, trained and skilled manpower to guard against poaching and intrusion, banning trade in tiger products to reduce poaching, and importantly, the political will to precipitate these recommendations into implementation. Of these, the creation of sufficient inviolate spaces (generally in the form of protected areas) has created the most issues with local resource-dependent communities, often resulting in significant challenges for tiger conservation policy and management. Very little empirical research has, however, been done to understand and contextualize the local-level socio-political interactions that may influence the efficacy of tiger conservation in India. In this paper, we present the results of exploratory research into the ways in which local-stakeholder groups affect the management of Corbett Tiger Reserve (CTR). Using a combined grounded theory-case study research design, and the Institutional Analysis and Development framework for analysis, we identify the socio-political processes through which local-stakeholder groups are able to articulate their issues and elicit desirable actions from the management of CTR. Increasing our awareness of these processes can help inform the design and implementation of more effective tiger conservation management and policy strategies that have the potential to create more supportive coalitions of tiger conservation stakeholders at the local level.

  18. Understanding the local socio-political processes affecting conservation management outcomes in Corbett Tiger Reserve, India.

    PubMed

    Rastogi, Archi; Hickey, Gordon M; Badola, Ruchi; Hussain, Syed Ainul

    2014-05-01

    Several measures have been recommended to guarantee a sustainable population of tigers: sufficient inviolate spaces for a viable population, sufficient prey populations, trained and skilled manpower to guard against poaching and intrusion, banning trade in tiger products to reduce poaching, and importantly, the political will to precipitate these recommendations into implementation. Of these, the creation of sufficient inviolate spaces (generally in the form of protected areas) has created the most issues with local resource-dependent communities, often resulting in significant challenges for tiger conservation policy and management. Very little empirical research has, however, been done to understand and contextualize the local-level socio-political interactions that may influence the efficacy of tiger conservation in India. In this paper, we present the results of exploratory research into the ways in which local-stakeholder groups affect the management of Corbett Tiger Reserve (CTR). Using a combined grounded theory-case study research design, and the Institutional Analysis and Development framework for analysis, we identify the socio-political processes through which local-stakeholder groups are able to articulate their issues and elicit desirable actions from the management of CTR. Increasing our awareness of these processes can help inform the design and implementation of more effective tiger conservation management and policy strategies that have the potential to create more supportive coalitions of tiger conservation stakeholders at the local level.

  19. Conservation.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  20. Substitution of a highly conserved histidine in the Escherichia coli heat shock transcription factor, sigma32, affects promoter utilization in vitro and leads to overexpression of the biofilm-associated flu protein in vivo.

    PubMed

    Kourennaia, Olga V; Dehaseth, Pieter L

    2007-12-01

    The heat shock sigma factor (sigma(32) in Escherichia coli) directs the bacterial RNA polymerase to promoters of a specific sequence to form a stable complex, competent to initiate transcription of genes whose products mitigate the effects of exposure of the cell to high temperatures. The histidine at position 107 of sigma(32) is at the homologous position of a tryptophan residue at position 433 of the main sigma factor of E. coli, sigma(70). This tryptophan is essential for the strand separation step leading to the formation of the initiation-competent RNA polymerase-promoter complex. The heat shock sigma factors of all gammaproteobacteria sequenced have a histidine at this position, while in the alpha- and deltaproteobacteria, it is a tryptophan. In vitro the alanine-for-histidine substitution at position 107 (H107A) destabilizes complexes between the GroE promoter and RNA polymerase containing sigma(32), implying that H107 plays a role in formation or maintenance of the strand-separated complex. In vivo, the H107A substitution in sigma(32) impedes recovery from heat shock (exposure to 42 degrees C), and it also leads to overexpression at lower temperatures (30 degrees C) of the Flu protein, which is associated with biofilm formation.

  1. Robust high-order space-time conservative schemes for solving conservation laws on hybrid meshes

    NASA Astrophysics Data System (ADS)

    Shen, Hua; Wen, Chih-Yung; Liu, Kaixin; Zhang, Deliang

    2015-01-01

    In this paper, the second-order space-time conservation element and solution element (CE/SE) method proposed by Chang (1995) [3] is implemented on hybrid meshes for solving conservation laws. In addition, the present scheme has been extended to high-order versions including third and fourth order. Most methodologies of proposed schemes are consistent with that of the original CE/SE method, including: (i) a unified treatment of space and time (thereby ensuring good conservation in both space and time); (ii) a highly compact node stencil (the solution node is calculated using only the neighboring mesh nodes) regardless of the order of accuracy at the cost of storing all derivatives. A staggered time marching strategy is adopted and the solutions are updated alternatively between cell centers and vertexes. To construct explicit high-order schemes, second- and third-order derivatives are calculated by a modified finite-difference/weighted-average procedure which is different from that used to calculate the first-order derivatives. The present schemes can be implemented on a wide variety of meshes, including triangular, quadrilateral and hybrid (consisting of both triangular and quadrilateral elements). Beyond that, it can be easily extended to arbitrary-order schemes and arbitrary shape of polygonal elements by using the present methodologies. A series of common benchmark examples are used to confirm the accuracy and robustness of the proposed schemes.

  2. High-resolution schemes for hyperbolic conservation laws

    NASA Technical Reports Server (NTRS)

    Harten, A.

    1982-01-01

    A class of new explicit second order accurate finite difference schemes for the computation of weak solutions of hyperbolic conservation laws is presented. These highly nonlinear schemes are obtained by applying a nonoscillatory first order accurae scheme to an appropriately modified flux function. The so derived second order accurate schemes achieve high resolution while preserving the robustness of the original nonoscillatory first order accurate scheme.

  3. Highly conserved repetitive DNA sequences are present at human centromeres.

    PubMed Central

    Grady, D L; Ratliff, R L; Robinson, D L; McCanlies, E C; Meyne, J; Moyzis, R K

    1992-01-01

    Highly conserved repetitive DNA sequence clones, largely consisting of (GGAAT)n repeats, have been isolated from a human recombinant repetitive DNA library by high-stringency hybridization with rodent repetitive DNA. This sequence, the predominant repetitive sequence in human satellites II and III, is similar to the essential core DNA of the Saccharomyces cerevisiae centromere, centromere DNA element (CDE) III. In situ hybridization to human telophase and Drosophila polytene chromosomes shows localization of the (GGAAT)n sequence to centromeric regions. Hyperchromicity studies indicate that the (GGAAT)n sequence exhibits unusual hydrogen bonding properties. The purine-rich strand alone has the same thermal stability as the duplex. Hyperchromicity studies of synthetic DNA variants indicate that all sequences with the composition (AATGN)n exhibit this unusual thermal stability. DNA-mobility-shift assays indicate that specific HeLa-cell nuclear proteins recognize this sequence with a relative affinity greater than 10(5). The extreme evolutionary conservation of this DNA sequence, its centromeric location, its unusual hydrogen bonding properties, its high affinity for specific nuclear proteins, and its similarity to functional centromeres isolated from yeast suggest that this sequence may be a component of the functional human centromere. Images PMID:1542662

  4. Cdc14: a highly conserved family of phosphatases with non-conserved functions?

    PubMed

    Mocciaro, Annamaria; Schiebel, Elmar

    2010-09-01

    CDC14 was originally identified by L. Hartwell in his famous screen for genes that regulate the budding yeast cell cycle. Subsequent work showed that Cdc14 belongs to a family of highly conserved dual-specificity phosphatases that are present in a wide range of organisms from yeast to human. Human CDC14B is even able to fulfill the essential functions of budding yeast Cdc14. In budding yeast, Cdc14 counteracts the activity of cyclin dependent kinase (Cdk1) at the end of mitosis and thus has important roles in the regulation of anaphase, mitotic exit and cytokinesis. On the basis of the functional conservation of other cell-cycle genes it seemed obvious to assume that Cdc14 phosphatases also have roles in late mitosis in mammalian cells and regulate similar targets to those found in yeast. However, analysis of the human Cdc14 proteins (CDC14A, CDC14B and CDC14C) by overexpression or by depletion using small interfering RNA (siRNA) has suggested functions that are quite different from those of ScCdc14. Recent studies in avian and human somatic cell lines in which the gene encoding either Cdc14A or Cdc14B had been deleted, have shown - surprisingly - that neither of the two phosphatases on its own is essential for viability, cell-cycle progression and checkpoint control. In this Commentary, we critically review the available data on the functions of yeast and vertebrate Cdc14 phosphatases, and discuss whether they indeed share common functions as generally assumed.

  5. Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

    PubMed

    Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

    2015-01-01

    Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal

  6. Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

    PubMed Central

    Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

    2015-01-01

    Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal

  7. Factors Affecting Diet Variation in the Pyrenean Rock Ptarmigan (Lagopus muta pyrenaica): Conservation Implications

    PubMed Central

    García-González, Ricardo; Aldezabal, Arantza; Laskurain, Nere Amaia; Margalida, Antoni; Novoa, Claude

    2016-01-01

    The Pyrenean rock ptarmigan (Lagopus muta pyrenaica) lives at one of the southernmost limits of the ptarmigan range. Their small population sizes and the impacts of global changes are limiting factors in the conservation of this threatened subspecies. An effective conservation policy requires precise basic knowledge of a species' food and habitat requirements, information that is practically non-existent for this Pyrenean population. Here, we describe the diet of a ptarmigan population in the Eastern Pyrenees, the environmental factors influencing its variability and the relationship between diet floristic composition and quality. Diet composition was determined by microhistological analysis of faeces and diet quality was estimated from free-urate faecal N content. Our results show that grouse diet is based mainly on arctic-alpine shrubs of the Ericaceae family, as well as dwarf willows (Salix spp.) and Dryas octopetala. The most frequently consumed plant species was Rhododendron ferrugineum, but its abundance in the diet was negatively related to the diet nitrogen content. Conversely, the abundance of Salix spp., grass leaves and arthropods increased the nitrogen content of the diet. Seasonality associated with snow-melting contributed the most to variability in the Pyrenean ptarmigan diet, differentiating winter from spring/summer diets. The latter was characterised by a high consumption of dwarf willows, flowers, arthropods and tender forb leaves. Geographic area and sex-age class influenced diet variability to a lesser extent. Current temperature increases in the Pyrenees due to global warming may reduce the persistence and surface area of snow-packs where preferred plants for rock ptarmigan usually grow, thus reducing food availability. The high consumption of Rh. ferrugineum characterised the diet of the Pyrenean population. Given the toxicity of this plant for most herbivores, its potential negative effect on Pyrenean ptarmigan populations should be

  8. Factors Affecting Diet Variation in the Pyrenean Rock Ptarmigan (Lagopus muta pyrenaica): Conservation Implications.

    PubMed

    García-González, Ricardo; Aldezabal, Arantza; Laskurain, Nere Amaia; Margalida, Antoni; Novoa, Claude

    2016-01-01

    The Pyrenean rock ptarmigan (Lagopus muta pyrenaica) lives at one of the southernmost limits of the ptarmigan range. Their small population sizes and the impacts of global changes are limiting factors in the conservation of this threatened subspecies. An effective conservation policy requires precise basic knowledge of a species' food and habitat requirements, information that is practically non-existent for this Pyrenean population. Here, we describe the diet of a ptarmigan population in the Eastern Pyrenees, the environmental factors influencing its variability and the relationship between diet floristic composition and quality. Diet composition was determined by microhistological analysis of faeces and diet quality was estimated from free-urate faecal N content. Our results show that grouse diet is based mainly on arctic-alpine shrubs of the Ericaceae family, as well as dwarf willows (Salix spp.) and Dryas octopetala. The most frequently consumed plant species was Rhododendron ferrugineum, but its abundance in the diet was negatively related to the diet nitrogen content. Conversely, the abundance of Salix spp., grass leaves and arthropods increased the nitrogen content of the diet. Seasonality associated with snow-melting contributed the most to variability in the Pyrenean ptarmigan diet, differentiating winter from spring/summer diets. The latter was characterised by a high consumption of dwarf willows, flowers, arthropods and tender forb leaves. Geographic area and sex-age class influenced diet variability to a lesser extent. Current temperature increases in the Pyrenees due to global warming may reduce the persistence and surface area of snow-packs where preferred plants for rock ptarmigan usually grow, thus reducing food availability. The high consumption of Rh. ferrugineum characterised the diet of the Pyrenean population. Given the toxicity of this plant for most herbivores, its potential negative effect on Pyrenean ptarmigan populations should be

  9. A highly conserved pericentromeric domain in human and gorilla chromosomes.

    PubMed

    Pita, M; Gosálvez, J; Gosálvez, A; Nieddu, M; López-Fernández, C; Mezzanotte, R

    2009-01-01

    Significant similarity between human and gorilla genomes has been found in all chromosome arms, but not in centromeres, using whole-comparative genomic hybridization (W-CGH). In human chromosomes, centromeric regions, generally containing highly repetitive DNAs, are characterized by the presence of specific human DNA sequences and an absence of homology with gorilla DNA sequences. The only exception is the pericentromeric area of human chromosome 9, which, in addition to a large block of human DNA, also contains a region of homology with gorilla DNA sequences; the localization of these sequences coincides with that of human satellite III. Since highly repetitive DNAs are known for their high mutation frequency, we hypothesized that the chromosome 9 pericentromeric DNA conserved in human chromosomes and deriving from the gorilla genome may thus play some important functional role.

  10. Antibody Recognition of a Highly Conserved Influenza Virus Epitope

    SciTech Connect

    Ekiert, Damian C.; Bhabha, Gira; Elsliger, Marc-André; Friesen, Robert H.E.; Jongeneelen, Mandy; Throsby, Mark; Goudsmit, Jaap; Wilson, Ian A.; Scripps; Crucell

    2009-05-21

    Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes a highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.

  11. High performance computing with a conservative spectral Boltzmann solver

    NASA Astrophysics Data System (ADS)

    Haack, Jeffrey R.; Gamba, Irene M.

    2012-11-01

    We present new results building on the conservative deterministic spectral method for the space inhomogeneous Boltzmann equation developed by Gamba and Tharkabhushaman. This approach is a two-step process that acts on the weak form of the Boltzmann equation, and uses the machinery of the Fourier transform to reformulate the collisional integral into a weighted convolution in Fourier space. A constrained optimization problem is solved to preserve the mass, momentum, and energy of the resulting distribution. We extend this method to second order accuracy in space and time, and explore how to leverage the structure of the collisional formulation for high performance computing environments. The locality in space of the collisional term provides a straightforward memory decomposition, and we perform some initial scaling tests on high performance computing resources. We also use the improved computational power of this method to investigate a boundary-layer generated shock problem that cannot be described by classical hydrodynamics.

  12. Dissimilatory nitrate reduction to ammonium conserves nitrogen in anthropogenically affected subtropical mangrove sediments in Southeast China.

    PubMed

    Cao, Wenzhi; Yang, Jingxin; Li, Ying; Liu, Baoli; Wang, Feifei; Chang, Changtang

    2016-09-15

    In this study, basic sediment properties, nutrient flux, and nitrogen cycle (including denitrification, anaerobic ammonium oxidation [anammox], nitrification, and dissimilatory nitrate reduction to ammonium [DNRA]) were investigated at two sampling sites with different tree ages in the mangrove region of the Jiulong River Estuary, China. The results show that sediments at mangrove flat area have relatively strong capability to reduce NO3(-), in which the DNRA rate is relatively high (204.53±48.32μmolNm(-2)h(-1)), which is approximately 75.7-85.9% of the total NO3(-) reduction, while the denitrification and anammox rates are relatively low - only approximately 5.6-9.5% and 8.5-14.8% of the total NO3(-) reduction, respectively. Thus, in the nitrogen-enriched subtropical mangrove system, DNRA is the main pathway to reduce NO3(-), and most of the input nitrogen is conserved as NH4(+) in the system, which assures high productivity of the mangrove system.

  13. High velocity formability and factors affecting it

    NASA Astrophysics Data System (ADS)

    Dehra, Mala Seth

    High velocity forming methods successfully address problems faced in conventional forming techniques. They can be effectively used for forming metals with low formability like aluminum alloys and high strength steel. They can be instrumental is manufacturing of lighter vehicles with higher fuel efficiency. Electromagnetic forming (EMF) is an HVF method that is gaining wide acceptance due to its advantages and scope for commercialization. A number of experimental studies were carried out with EMF with the main goal of exploring fundamentals about material formability at high velocities, which can be used to establish practical design guidelines and to make models of high velocity formability. Thus the main factors that influence high velocity formability-inertia/size effects; changes in constitutive behavior; impact; and dynamic failure modes, were studied mainly with experiments. The role of changes in constitutive behavior in improving formability was studied from existing studies and new theoretical studies involving High velocity Forming Limit Diagram (FLD) and through solving an inverse problem of ring expansion. Tube free-expansion experiments were carried out to demonstrate enhanced metal formability even in the absence of die impact. To further establish the significance of inertia, electromagnetic ring free-expansion experiments with rings of different aspect ratios were carried out. A higher aspect ratio sample had better formability in terms of uniform and total elongation and also had fewer necks than a low aspect ratio (more slender) ring at the same velocity. The results clearly demonstrated the influence of sample aspect ratio (dimensions) and hence inertia on high velocity formability. Die impact experiments were carried out with tubes and rings to show the beneficial influence of die arrest of a moving sample. It was revealed that die impact in an appropriate range of velocities can significantly suppress failure and reduce the number of tears and

  14. Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

    PubMed

    Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

    2017-05-15

    Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results

  15. Molar incisor hypomineralization (MIH): conservative treatment management to restore affected teeth.

    PubMed

    Fragelli, Camila Maria Bullio; Souza, Juliana Feltrin de; Jeremias, Fabiano; Cordeiro, Rita de Cássia Loiola; Santos-Pinto, Lourdes

    2015-01-01

    The purpose of this study was to evaluate the 12-month clinical performance of glass ionomer restorations in teeth with MIH. First permanent molars affected by MIH (48) were restored with glass ionomer cement (GIC) and evaluated at baseline, at 6 and at 12 months, by assessing tooth enamel breakdown, GIC breakdown and caries lesion associations. The data were analyzed using the chi-square test and actuarial survival analysis. The likelihood of a restored tooth remaining unchanged at the end of 12 months was 78%. No statistically significant difference was observed in the association between increased MIH severity and caries at baseline (p > 0.05) for a 6-month period, or between increased MIH severity and previous unsatisfactory treatment at baseline (p > 0.05) for both a 6- and 12-month period. A statistically significant difference was observed in the association between increased MIH severity and extension of the restoration, involving 2 or more surfaces (p < 0.05) at both periods, and between increased MIH severity and caries at baseline (p < 0.05) at a 12-month period. Because the likelihood of maintaining the tooth structures with GIC restorations is high, invasive treatment should be postponed until the child is sufficiently mature to cooperate with the treatment, mainly of teeth affected on just one face.

  16. Socio-economic factors affecting the conservation of natural woodlands in Central Riyadh Area – Saudi Arabia

    PubMed Central

    Al-Subaiee, Faisal Sultan

    2015-01-01

    This study aimed to identify some socioeconomic factors affecting local people in central Riyadh area for the utilization of wood and other energy sources in cooking and heating in order to develop some recommendations for conserving woodlands. The study results revealed that gas is the most common energy source used for cooking with a mean usage level of 2.79 (SD = 0.58). On the other hand, wood ranked first for heating with the highest mean, usage level of 1.90 (SD = 1.06). However, electricity and gas as sources of energy for heating ranked second and third with mean usage level of 1.81 and 0.80 respectively. The study revealed that local people with the university education were significantly making higher use of electricity for both cooking and heating and those with no formal education ranked the highest on wood use for both cooking and heating. In addition, those living in traditional houses significantly used more wood for cooking than those living in villas and apartments. Also, local people with high income levels significantly were using more electricity for heating than others. The study recommended conducting extension and environmental awareness raising programs to enhance local residents’ adoption of wood substitutes, promoting employment opportunities for unemployed locals, and subsidizing prices of alternative energy sources. PMID:27081355

  17. Nitrogen dynamics affected by management practices in croplands transitioning from Conservation Reserve Program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil N may be lost through mineralization, leaching, and other processes when land under the Conservation Reserve Program (CRP) is converted into croplands. Improved management practices are needed to restore soil N levels and reduce N losses. We evaluated the effects of irrigation, tillage, croppin...

  18. Use of advanced information technologies for water conservation on salt-affected soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Water conservation on arid and semi-arid soils must be done with constant and careful consideration of the distribution of salinity across the landscape and through the soil profile. Soil salinity can be managed through leaching and the application of various soil amendments. The field-scale manag...

  19. How Conservation Reserve Program Affects Runoff and Nutrients in an Oxbow Lake Watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A case study of Beasley Lake Watershed, located in the Mississippi Delta region of the U.S. was used to evaluate runoff from edge-of-field sites with row crop management practices and Conservation Reserve Program (CRP) sites with trees. Approximately one-third of the Beasley Lake watershed (280 ha)...

  20. High-Order Space-Time Methods for Conservation Laws

    NASA Technical Reports Server (NTRS)

    Huynh, H. T.

    2013-01-01

    Current high-order methods such as discontinuous Galerkin and/or flux reconstruction can provide effective discretization for the spatial derivatives. Together with a time discretization, such methods result in either too small a time step size in the case of an explicit scheme or a very large system in the case of an implicit one. To tackle these problems, two new high-order space-time schemes for conservation laws are introduced: the first is explicit and the second, implicit. The explicit method here, also called the moment scheme, achieves a Courant-Friedrichs-Lewy (CFL) condition of 1 for the case of one-spatial dimension regardless of the degree of the polynomial approximation. (For standard explicit methods, if the spatial approximation is of degree p, then the time step sizes are typically proportional to 1/p(exp 2)). Fourier analyses for the one and two-dimensional cases are carried out. The property of super accuracy (or super convergence) is discussed. The implicit method is a simplified but optimal version of the discontinuous Galerkin scheme applied to time. It reduces to a collocation implicit Runge-Kutta (RK) method for ordinary differential equations (ODE) called Radau IIA. The explicit and implicit schemes are closely related since they employ the same intermediate time levels, and the former can serve as a key building block in an iterative procedure for the latter. A limiting technique for the piecewise linear scheme is also discussed. The technique can suppress oscillations near a discontinuity while preserving accuracy near extrema. Preliminary numerical results are shown

  1. 7 CFR 760.821 - Compliance with highly erodible land and wetland conservation.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 7 2014-01-01 2014-01-01 false Compliance with highly erodible land and wetland... Disaster Program § 760.821 Compliance with highly erodible land and wetland conservation. (a) The highly erodible land and wetland conservation provisions of part 12 of this title apply to the receipt of...

  2. 7 CFR 760.821 - Compliance with highly erodible land and wetland conservation.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 7 2011-01-01 2011-01-01 false Compliance with highly erodible land and wetland... Disaster Program § 760.821 Compliance with highly erodible land and wetland conservation. (a) The highly erodible land and wetland conservation provisions of part 12 of this title apply to the receipt of...

  3. 7 CFR 760.821 - Compliance with highly erodible land and wetland conservation.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 7 2012-01-01 2012-01-01 false Compliance with highly erodible land and wetland... Disaster Program § 760.821 Compliance with highly erodible land and wetland conservation. (a) The highly erodible land and wetland conservation provisions of part 12 of this title apply to the receipt of...

  4. 7 CFR 760.821 - Compliance with highly erodible land and wetland conservation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Compliance with highly erodible land and wetland... Disaster Program § 760.821 Compliance with highly erodible land and wetland conservation. (a) The highly erodible land and wetland conservation provisions of part 12 of this title apply to the receipt of...

  5. 7 CFR 760.821 - Compliance with highly erodible land and wetland conservation.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 7 2013-01-01 2013-01-01 false Compliance with highly erodible land and wetland... Disaster Program § 760.821 Compliance with highly erodible land and wetland conservation. (a) The highly erodible land and wetland conservation provisions of part 12 of this title apply to the receipt of...

  6. Subdivision design and stewardship affect bird and mammal use of conservation developments.

    PubMed

    Farr, Cooper M; Pejchar, Liba; Reed, Sarah E

    2017-02-07

    Developing effective tools for conservation on private lands is increasingly important for global biodiversity conservation; private lands are located in more productive and biologically diverse areas, and they face accelerated rates of land conversion. One strategy is conservation development (CD) subdivisions, which cluster houses in a small portion of a property and preserve the remaining land as protected open space. Despite widespread use, the characteristics that make CD more or less effective at achieving biodiversity conservation are not well understood. We investigated CD's ability to successfully protect animal populations by examining bird and mammal occurrences in 14 CD subdivisions and four undeveloped areas (range: 14-432 ha) in northern Colorado, USA. Using point count and camera trap data in an occupancy modeling framework, we evaluated the relative importance of nine subdivision design factors (e.g., housing density, proportion of CD protected) and 14 stewardship factors (e.g., presence of livestock, percent native vegetation cover) in influencing the overall community composition and the probability of use by 16 birds and six mammals. We found that habitat use by 75% of birds and 83% of mammals was associated with design characteristics that maximized the natural or undisturbed land area both within and near the development (e.g., proportion of CD protected, total area of protected open space, proportion of natural land cover in the surrounding landscape). These factors were also associated with an increasing dominance of human-sensitive bird species, larger-bodied mammals, and mammals with larger home ranges. Habitat use by birds was also influenced by local land use composition and quality, and use by several bird and mammal species decreased with increased localized disturbances. We found few differences in habitat use between sampling sites in undeveloped areas and in CD subdivisions. These similarities indicate that, if CDs are large enough

  7. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing

    PubMed Central

    Davies, Bryan W.; Köhrer, Caroline; Jacob, Asha I.; Simmons, Lyle A.; Zhu, Jianyu; Aleman, Lourdes M.; RajBhandary, Uttam L.; Walker, Graham C.

    2010-01-01

    The UPF0054 protein family is highly conserved with homologs present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic phenotype. Despite detailed structural studies, a cellular role for this protein family has remained unknown. We report here that deletion of the Escherichia coli homolog, YbeY, causes striking defects that affect ribosome activity, translational fidelity and ribosome assembly. Mapping of 16S, 23S and 5S rRNA termini reveals that YbeY influences the maturation of all three rRNAs, with a particularly strong effect on maturation at both the 5′- and 3′-ends of 16S rRNA as well as maturation of the 5′-termini of 23S and 5S rRNAs. Furthermore, we demonstrate strong genetic interactions between ybeY and rnc (encoding RNase III), ybeY and rnr (encoding RNase R), and ybeY and pnp (encoding PNPase), further suggesting a role for YbeY in rRNA maturation. Mutation of highly conserved amino acids in YbeY, allowed the identification of two residues (H114, R59) that were found to have a significant effect in vivo. We discuss the implications of these findings for rRNA maturation and ribosome assembly in bacteria. PMID:20807199

  8. High-Resolution Genuinely Multidimensional Solution of Conservation Laws by the Space-Time Conservation Element and Solution Element Method

    NASA Technical Reports Server (NTRS)

    Himansu, Ananda; Chang, Sin-Chung; Yu, Sheng-Tao; Wang, Xiao-Yen; Loh, Ching-Yuen; Jorgenson, Philip C. E.

    1999-01-01

    In this overview paper, we review the basic principles of the method of space-time conservation element and solution element for solving the conservation laws in one and two spatial dimensions. The present method is developed on the basis of local and global flux conservation in a space-time domain, in which space and time are treated in a unified manner. In contrast to the modern upwind schemes, the approach here does not use the Riemann solver and the reconstruction procedure as the building blocks. The drawbacks of the upwind approach, such as the difficulty of rationally extending the 1D scalar approach to systems of equations and particularly to multiple dimensions is here contrasted with the uniformity and ease of generalization of the Conservation Element and Solution Element (CE/SE) 1D scalar schemes to systems of equations and to multiple spatial dimensions. The assured compatibility with the simplest type of unstructured meshes, and the uniquely simple nonreflecting boundary conditions of the present method are also discussed. The present approach has yielded high-resolution shocks, rarefaction waves, acoustic waves, vortices, ZND detonation waves, and shock/acoustic waves/vortices interactions. Moreover, since no directional splitting is employed, numerical resolution of two-dimensional calculations is comparable to that of the one-dimensional calculations. Some sample applications displaying the strengths and broad applicability of the CE/SE method are reviewed.

  9. Conservation Tillage Affects Species Composition But Not Species Diversity: A Comparative Study in Northern Italy

    NASA Astrophysics Data System (ADS)

    Boscutti, Francesco; Sigura, Maurizia; Gambon, Nadia; Lagazio, Corrado; Krüsi, Bertil O.; Bonfanti, Pierluigi

    2015-02-01

    Conservation tillage (CT) is widely considered to be a practice aimed at preserving several ecosystem functions. In the literature, however, there seems to be no clear pattern with regard to its benefits on species diversity and species composition. In Northern Italy, we compared species composition and diversity of both vascular plants and Carabids under two contrasting tillage systems, i.e., CT and conventional tillage, respectively. We hypothesized a significant positive impact of CT on both species diversity and composition. We also considered the potential influence of crop type. The tillage systems were studied under open field conditions with three types of annual crops (i.e., maize, soybean, and winter cereals), using a split-plot design on pairs of adjacent fields. Linear mixed models were applied to test tillage system, crop, and interaction effects on diversity indices. Plant and Carabids communities were analyzed by multivariate methods (CCA). On the whole, 136 plant and 51 carabid taxa were recorded. The two tillage systems studied did not differ in floristic or carabid diversity. Species composition, by contrast, proved to be characteristic for each combination of tillage system and crop type. In particular, CT fields were characterized by nutrient demanding weeds and the associated Carabids. The differences were especially pronounced in fields with winter cereals. The same was true for the flora and Carabids along the field boundaries. For studying the effects of CT practices on the sustainability of agro-ecosystems, therefore, the focus should be on species composition rather than on diversity measures.

  10. Assessment of selected conservation measures for high-temperature process industries

    SciTech Connect

    Kusik, C L; Parameswaran, K; Nadkarni, R; O'Neill, J K; Malhotra, S; Hyde, R; Kinneberg, D; Fox, L; Rossetti, M

    1981-01-01

    Energy conservation projects involving high-temperature processes in various stages of development are assessed to quantify their energy conservation potential; to determine their present status of development; to identify their research and development needs and estimate the associated costs; and to determine the most effective role for the Federal government in developing these technologies. The program analyzed 25 energy conserving processes in the iron and steel, aluminium, copper, magnesium, cement, and glassmaking industries. A preliminary list of other potential energy conservation projects in these industries is also presented in the appendix. (MCW)

  11. Structure-function studies of nerve growth factor: functional importance of highly conserved amino acid residues.

    PubMed Central

    Ibáñez, C F; Hallböök, F; Ebendal, T; Persson, H

    1990-01-01

    Selected amino acid residues in chicken nerve growth factor (NGF) were replaced by site-directed mutagenesis. Mutated NGF sequences were transiently expressed in COS cells and the yield of NGF protein in conditioned medium was quantified by Western blotting. Binding of each mutant to NGF receptors on PC12 cells was evaluated in a competition assay. The biological activity was determined by measuring stimulation of neurite outgrowth from chick sympathetic ganglia. The residues homologous to the proposed receptor binding site of insulin (Ser18, Met19, Val21, Asp23) were substituted by Ala. Replacement of Ser18, Met19 and Asp23 did not affect NGF activity. Modification of Val21 notably reduced both receptor binding and biological activity, suggesting that this residue is important to retain a fully active NGF. The highly conserved Tyr51 and Arg99 were converted into Phe and Lys respectively, without changing the biological properties of the molecule. However, binding and biological activity were greatly impaired after the simultaneous replacement of both Arg99 and Arg102 by Gly. The three conserved Trp residues at positions 20, 75 and 98 were substituted by Phe. The Trp mutated proteins retained 15-60% of receptor binding and 40-80% of biological activity, indicating that the Trp residues are not essential for NGF activity. However, replacement of Trp20 significantly reduced the amount of NGF in the medium, suggesting that this residue may be important for protein stability. Images Fig. 4. PMID:2328722

  12. Human activities in Natura 2000 sites: a highly diversified conservation network.

    PubMed

    Tsiafouli, Maria A; Apostolopoulou, Evangelia; Mazaris, Antonios D; Kallimanis, Athanasios S; Drakou, Evangelia G; Pantis, John D

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity.

  13. 7 CFR 1430.225 - Violations of highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Violations of highly erodible land and wetland conservation provisions. 1430.225 Section 1430.225 Agriculture Regulations of the Department of Agriculture... wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  14. 7 CFR 1412.68 - Compliance with highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Compliance with highly erodible land and wetland conservation provisions. 1412.68 Section 1412.68 Agriculture Regulations of the Department of Agriculture... and wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  15. 7 CFR 1412.68 - Compliance with highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Compliance with highly erodible land and wetland conservation provisions. 1412.68 Section 1412.68 Agriculture Regulations of the Department of Agriculture... and wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  16. 7 CFR 1430.225 - Violations of highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Violations of highly erodible land and wetland conservation provisions. 1430.225 Section 1430.225 Agriculture Regulations of the Department of Agriculture... wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  17. 7 CFR 1412.68 - Compliance with highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Compliance with highly erodible land and wetland conservation provisions. 1412.68 Section 1412.68 Agriculture Regulations of the Department of Agriculture... and wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  18. 7 CFR 1412.68 - Compliance with highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Compliance with highly erodible land and wetland conservation provisions. 1412.68 Section 1412.68 Agriculture Regulations of the Department of Agriculture... and wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  19. 7 CFR 1412.68 - Compliance with highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Compliance with highly erodible land and wetland conservation provisions. 1412.68 Section 1412.68 Agriculture Regulations of the Department of Agriculture... and wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  20. 7 CFR 1430.225 - Violations of highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Violations of highly erodible land and wetland conservation provisions. 1430.225 Section 1430.225 Agriculture Regulations of the Department of Agriculture... wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  1. 7 CFR 1430.225 - Violations of highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Violations of highly erodible land and wetland conservation provisions. 1430.225 Section 1430.225 Agriculture Regulations of the Department of Agriculture... wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  2. 7 CFR 1430.225 - Violations of highly erodible land and wetland conservation provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Violations of highly erodible land and wetland conservation provisions. 1430.225 Section 1430.225 Agriculture Regulations of the Department of Agriculture... wetland conservation provisions. The provisions of part 12 of this title apply to this part....

  3. 78 FR 20503 - Energy Conservation Program: Availability of the Interim Technical Support Document for High...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-05

    ... CFR Part 431 RIN 1904-AC36 Energy Conservation Program: Availability of the Interim Technical Support... interim technical support document (TSD) for high-intensity discharge (HID) lamps energy conservation... submitting comments on the interim TSD or any other aspect of the rulemaking for HID lamps. The...

  4. Understanding How Domestic Violence Affects Behavior in High School Students

    ERIC Educational Resources Information Center

    Frank, Malika

    2011-01-01

    This paper will provide the reader with an understanding of how domestic violence affects the behavior of high school students. The presentation is designed to provide the reader with a working definition of domestic violence, the rate of occurrence and its effects on high school students. Additionally the paper will summarize the negative effects…

  5. Overland flow generation mechanisms affected by topsoil treatment: Application to soil conservation

    NASA Astrophysics Data System (ADS)

    Hueso-González, P.; Ruiz-Sinoga, J. D.; Martínez-Murillo, J. F.; Lavee, H.

    2015-01-01

    Hortonian overland-flow is responsible for significant amounts of soil loss in Mediterranean geomorphological systems. Restoring the native vegetation is the most effective way to control runoff and sediment yield. During the seeding and plant establishment, vegetation cover may be better sustained if soil is amended with an external source. Four amendments were applied in an experimental set of plots: straw mulching (SM); mulch with chipped branches of Aleppo Pine (Pinus halepensis L.) (PM); TerraCottem hydroabsorbent polymer (HP); and sewage sludge (RU). Plots were afforested following the same spatial pattern, and amendments were mixed with the soil at the rate 10 Mg ha- 1. This research demonstrates the role played by the treatments in overland flow generation mechanism. On one hand, the high macroporosity of SM and PM, together with the fact that soil moisture increased with depth, explains weak overland flow and thus low sediment yield due to saturation conditions. Therefore, regarding overland flow and sediment yield, RU behaves similarly to SM and PM. On the other hand, when HP was applied, overland flow developed quickly with relatively high amounts. This, together with the decrease downward in soil moisture along the soil profile, proved that mechanisms of overland flow are of the Hortonian type.

  6. Overland flow generation mechanisms affected by topsoil treatment: Application to soil conservation

    NASA Astrophysics Data System (ADS)

    González Paloma, Hueso; Juan Francisco, Martinez-Murillo; Damian, Ruiz-Sinoga Jose; Hanoch, Lavee

    2015-04-01

    Hortonian overland-flow is responsible for significant amounts of soil loss in Mediterranean geomorphological systems. Restoring the native vegetation is the most effective way to control runoff and sediment yield. During the seeding and plant establishment, vegetation cover may be better sustained if soil is amended with an external source. Four amendments were applied in an experimental set of plots: straw mulching (SM); mulch with chipped branches of Aleppo Pine (Pinus halepensis L.) (PM); TerraCotten hydroabsobent polymers (HP); sewage sludge (RU); and control (C). Plots were afforested following the same spatial pattern, and amendments were mixed with the soil at the rate 10 Mg ha-1. This research demonstrates the role played by the treatments in overland flow generation mechanism (runoff, overland flow and soil moisture along the soil profile). The general overland flow characteristics showed that in the C plots the average overland flow was 8.0 ± 22.0 l per event, and the HP plots produced a similar mean value (8.1 ± 20.1 l). The average overland flow per event was significantly less for soil amended with SM, PM or RU (2.7 ± 8.3 l; 1.3 ± 3.5 l and 2.2 ± 5.9 l, respectively). There was a similar trend with respect to the maximum overland flow. The mean sediment yield per event was relatively high in the C and HP plots (8.6 ± 27.8 kg and 14.8 ± 43.4 kg, respectively), while significantly lower values were registered in the SM, PM and RU plots (0.4 ± 1.0 kg; 0.2 ± 0.3 kg and 0.2 ± 0.3 kg, respectively). Very similar trends were found for the maximum sediment yield. Regarding to the soil moisture values, there was a difference in the trends between the C and HP plots and the SM, PM and RU plots. In the C and HP plots the general trend was for a decrease in soil moisture downward through the soil profile, while in the SM, PM and RU plots the soil moisture remained relatively constant or increased, except for the RU treatment in which the soil moisture

  7. Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes

    PubMed Central

    Horodysky, Andrij Z.; Cooke, Steven J.; Graves, John E.; Brill, Richard W.

    2016-01-01

    Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time- and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental–applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock

  8. Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes.

    PubMed

    Horodysky, Andrij Z; Cooke, Steven J; Graves, John E; Brill, Richard W

    2016-01-01

    Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time- and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental-applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock

  9. On a consistent high-order finite difference scheme with kinetic energy conservation for simulating turbulent reacting flows

    NASA Astrophysics Data System (ADS)

    Trisjono, Philipp; Kang, Seongwon; Pitsch, Heinz

    2016-12-01

    The main objective of this study is to present an accurate and consistent numerical framework for turbulent reacting flows based on a high-order finite difference (HOFD) scheme. It was shown previously by Desjardins et al. (2008) [4] that a centered finite difference scheme discretely conserving the kinetic energy and an upwind-biased scheme for the scalar transport can be combined into a useful scheme for turbulent reacting flows. With a high-order spatial accuracy, however, an inconsistency among discretization schemes for different conservation laws is identified, which can disturb a scalar field spuriously under non-uniform density distribution. Various theoretical and numerical analyses are performed on the sources of the unphysical error. From this, the derivative of the mass-conserving velocity and the local Péclet number are identified as the primary factors affecting the error. As a solution, an HOFD stencil for the mass conservation is reformulated into a flux-based form that can be used consistently with an upwind-biased scheme for the scalar transport. The effectiveness of the proposed formulation is verified using two-dimensional laminar flows such as a scalar transport problem and a laminar premixed flame, where unphysical oscillations in the scalar fields are removed. The applicability of the proposed scheme is demonstrated in an LES of a turbulent stratified premixed flame.

  10. The cheater's high: the unexpected affective benefits of unethical behavior.

    PubMed

    Ruedy, Nicole E; Moore, Celia; Gino, Francesca; Schweitzer, Maurice E

    2013-10-01

    Many theories of moral behavior assume that unethical behavior triggers negative affect. In this article, we challenge this assumption and demonstrate that unethical behavior can trigger positive affect, which we term a "cheater's high." Across 6 studies, we find that even though individuals predict they will feel guilty and have increased levels of negative affect after engaging in unethical behavior (Studies 1a and 1b), individuals who cheat on different problem-solving tasks consistently experience more positive affect than those who do not (Studies 2-5). We find that this heightened positive affect does not depend on self-selection (Studies 3 and 4), and it is not due to the accrual of undeserved financial rewards (Study 4). Cheating is associated with feelings of self-satisfaction, and the boost in positive affect from cheating persists even when prospects for self-deception about unethical behavior are reduced (Study 5). Our results have important implications for models of ethical decision making, moral behavior, and self-regulatory theory.

  11. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity

    PubMed Central

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-01-01

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser696 and Ser698 in the JM (juxtamembrane) region and probably Ser886 and/or Ser893 in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser717 in the JM, and at Ser733, Thr752, Ser783, Ser864, Ser911, Ser958 and Thr998 in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr890, Ser893 and Thr894) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr890, Ser893, Thr894 and Thr899, differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  12. High sequence conservation among cucumber mosaic virus isolates from lily.

    PubMed

    Chen, Y K; Derks, A F; Langeveld, S; Goldbach, R; Prins, M

    2001-08-01

    For classification of Cucumber mosaic virus (CMV) isolates from ornamental crops of different geographical areas, these were characterized by comparing the nucleotide sequences of RNAs 4 and the encoded coat proteins. Within the ornamental-infecting CMV viruses both subgroups were represented. CMV isolates of Alstroemeria and crocus were classified as subgroup II isolates, whereas 8 other isolates, from lily, gladiolus, amaranthus, larkspur, and lisianthus, were identified as subgroup I members. In general, nucleotide sequence comparisons correlated well with geographic distribution, with one notable exception: the analyzed nucleotide sequences of 5 lily isolates showed remarkably high homology despite different origins.

  13. Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

    PubMed

    Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

    2016-10-01

    Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available.

  14. Lexical and Affective Prosody in Children with High Functioning Autism

    PubMed Central

    Grossman, Ruth B.; Bemis, Rhyannon H.; Skwerer, Daniela Plesa; Tager-Flusberg, Helen

    2012-01-01

    Purpose We investigated perception and production of lexical stress and processing of affective prosody in adolescents with high functioning autism (HFA). We hypothesized preserved processing of lexical and affective prosody, but atypical lexical prosody production. Method 16 children with HFA and 15 typically developing (TD) peers participated in three experiments: 1. Perception of affective prosody, 2. Lexical stress perception, 3. Lexical stress production. In Experiment 1, participants labeled sad, happy, and neutral spoken sentences that were low-pass filtered, to eliminate verbal content. In Experiment 2 participants disambiguated word meanings based on lexical stress (HOTdog, vs. hotDOG). In Experiment 3 participants produced these words in a sentence completion task. Productions were analyzed using acoustic measures. Results Accuracy levels showed no group differences. Participants with HFA could determine affect from filtered sentences and disambiguate words based on lexical stress. They produced appropriately differentiated lexical stress patterns but demonstrated atypically long productions indicating reduced ability in natural prosody production. Conclusions Children with HFA were as capable as their TD peers in receptive tasks of lexical stress and affective prosody. Prosody productions were atypically long, despite accurate differentiation of lexical stress patterns. Future research should use larger samples and spontaneous vs. elicited productions. PMID:20530388

  15. High-Resolution Satellite Imagery Is an Important yet Underutilized Resource in Conservation Biology

    PubMed Central

    Boyle, Sarah A.; Kennedy, Christina M.; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E.; de la Sancha, Noé U.

    2014-01-01

    Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making. PMID:24466287

  16. High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

    PubMed

    Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

    2014-01-01

    Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

  17. Influence of FGD gypsum on the properties of a highly erodible soil under conservation tillage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The performance of conservation tillage practices imposed on highly erodible soils may be improved by the use of amendments with a high solubility rate, and whose dissolution products are translocated at depth in the soil profile faster than normally used agricultural lime and fertilizer products. T...

  18. Potential of high residue conservation tillage to enhance water conservation and water use efficiency in corn production in the Southeast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Following the adoption of its first Comprehensive State-wide Water Management Plan in early February 2008, Georgia is on course to drafting regionally-based water development and conservation plans. Conservation tillage-based crop production can be one of the management tools available for achieving...

  19. Mechanical Properties of Heat Affected Zone of High Strength Steels

    NASA Astrophysics Data System (ADS)

    Sefcikova, K.; Brtnik, T.; Dolejs, J.; Keltamaki, K.; Topilla, R.

    2015-11-01

    High Strength Steels became more popular as a construction material during last decade because of their increased availability and affordability. On the other hand, even though general use of Advanced High Strength Steels (AHSS) is expanding, the wide utilization is limited because of insufficient information about their behaviour in structures. The most widely used technique for joining steels is fusion welding. The welding process has an influence not only on the welded connection but on the area near this connection, the so-called heat affected zone, as well. For that reason it is very important to be able to determine the properties in the heat affected zone (HAZ). This area of investigation is being continuously developed in dependence on significant progress in material production, especially regarding new types of steels available. There are currently several types of AHSS on the world market. Two most widely used processes for AHSS production are Thermo-Mechanically Controlled Processing (TMCP) and Quenching in connection with Tempering. In the presented study, TMCP and QC steels grade S960 were investigated. The study is focused on the changes of strength, ductility, hardness and impact strength in heat affected zone based on the used amount of heat input.

  20. High Salt Diet Affects Renal Sodium Excretion and ERRα Expression.

    PubMed

    Wang, Dan; Wang, Yang; Liu, Fu-Qiang; Yuan, Zu-Yi; Mu, Jian-Jun

    2016-04-01

    Kidneys regulate the balance of water and sodium and therefore are related to blood pressure. It is unclear whether estrogen-related receptor α (ERRα), an orphan nuclear receptor and transcription factor highly expressed in kidneys, affects the reabsorption of water and sodium. The aim of this study was to determine whether changes in the expressions of ERRα, Na⁺/K⁺-ATPase and epithelial sodium channel (ENaC) proteins affected the reabsorption of water and sodium in kidneys of Dahl salt-sensitive (DS) rats. SS.13BN rats, 98% homologous to the DS rats, were used as a normotensive control group. The 24 h urinary sodium excretion of the DS and SS.13BN rats increased after the 6-week high salt diet intervention, while sodium excretion was increased in DS rats with daidzein (agonist of ERRα) treatment. ERRα expression was decreased, while β- and γ-ENaC mRNA expressions were increased upon high sodium diet treatment in the DS rats. In the chromatin immunoprecipitation (CHIP) assay, positive PCR signals were obtained in samples treated with anti-ERRα antibody. The transcriptional activity of ERRα was decreased upon high salt diet intervention. ERRα reduced the expressions of β- and γ-ENaC by binding to the ENaC promoter, thereby increased Na+ reabsorption. Therefore, ERRα might be one of the factors causing salt-sensitive hypertension.

  1. High Salt Diet Affects Renal Sodium Excretion and ERRα Expression

    PubMed Central

    Wang, Dan; Wang, Yang; Liu, Fu-Qiang; Yuan, Zu-Yi; Mu, Jian-Jun

    2016-01-01

    Kidneys regulate the balance of water and sodium and therefore are related to blood pressure. It is unclear whether estrogen-related receptor α (ERRα), an orphan nuclear receptor and transcription factor highly expressed in kidneys, affects the reabsorption of water and sodium. The aim of this study was to determine whether changes in the expressions of ERRα, Na+/K+-ATPase and epithelial sodium channel (ENaC) proteins affected the reabsorption of water and sodium in kidneys of Dahl salt-sensitive (DS) rats. SS.13BN rats, 98% homologous to the DS rats, were used as a normotensive control group. The 24 h urinary sodium excretion of the DS and SS.13BN rats increased after the 6-week high salt diet intervention, while sodium excretion was increased in DS rats with daidzein (agonist of ERRα) treatment. ERRα expression was decreased, while β- and γ-ENaC mRNA expressions were increased upon high sodium diet treatment in the DS rats. In the chromatin immunoprecipitation (CHIP) assay, positive PCR signals were obtained in samples treated with anti-ERRα antibody. The transcriptional activity of ERRα was decreased upon high salt diet intervention. ERRα reduced the expressions of β- and γ-ENaC by binding to the ENaC promoter, thereby increased Na+ reabsorption. Therefore, ERRα might be one of the factors causing salt-sensitive hypertension. PMID:27043552

  2. High-Order Entropy Stable Finite Difference Schemes for Nonlinear Conservation Laws: Finite Domains

    NASA Technical Reports Server (NTRS)

    Fisher, Travis C.; Carpenter, Mark H.

    2013-01-01

    Developing stable and robust high-order finite difference schemes requires mathematical formalism and appropriate methods of analysis. In this work, nonlinear entropy stability is used to derive provably stable high-order finite difference methods with formal boundary closures for conservation laws. Particular emphasis is placed on the entropy stability of the compressible Navier-Stokes equations. A newly derived entropy stable weighted essentially non-oscillatory finite difference method is used to simulate problems with shocks and a conservative, entropy stable, narrow-stencil finite difference approach is used to approximate viscous terms.

  3. Acacia shrubs respond positively to high severity wildfire: Implications for conservation and fuel hazard management.

    PubMed

    Gordon, Christopher E; Price, Owen F; Tasker, Elizabeth M; Denham, Andrew J

    2017-01-01

    High severity wildfires pose threats to human assets, but are also perceived to impact vegetation communities because a small number of species may become dominant immediately after fire. However there are considerable gaps in our knowledge about species-specific responses of plants to different fire severities, and how this influences fuel hazard in the short and long-term. Here we conduct a floristic survey at sites before and two years after a wildfire of unprecedented size and severity in the Warrumbungle National Park (Australia) to explore relationships between post-fire growth of a fire responsive shrub genera (Acacia), total mid-story vegetation cover, fire severity and fuel hazard. We then survey 129 plots surrounding the park to assess relationships between mid-story vegetation cover and time-since-fire. Acacia species richness and cover were 2.3 and 4.3 times greater at plots after than before the fire. However the same common dominant species were present throughout the study. Mid-story vegetation cover was 1.5 times greater after than before the wildfire, and Acacia species contribution to mid-story cover increased from 10 to 40%. Acacia species richness was not affected by fire severity, however strong positive associations were observed between Acacia and total mid-story vegetation cover and severity. Our analysis of mid-story vegetation recovery showed that cover was similarly high between 2 and 30years post-fire, then decreased until 52years. Collectively, our results suggest that Acacia species are extremely resilient to high severity wildfire and drive short to mid-term increases in fuel hazard. Our results are discussed in relation to fire regime management from the twin perspectives of conserving biodiversity and mitigating human losses due to wildfire.

  4. Multiple injected and natural conservative tracers quantify mixing in a stream confluence affected by acid mine drainage near Silverton, Colorado

    USGS Publications Warehouse

    Schemel, L.E.; Cox, M.H.; Runkel, R.L.; Kimball, B.A.

    2006-01-01

    The acidic discharge from Cement Creek, containing elevated concentrations of dissolved metals and sulphate, mixed with the circumneutral-pH Animas River over a several hundred metre reach (mixing zone) near Silverton, CO, during this study. Differences in concentrations of Ca, Mg, Si, Sr, and SO42- between the creek and the river were sufficiently large for these analytes to be used as natural tracers in the mixing zone. In addition, a sodium chloride (NaCl) tracer was injected into Cement Creek, which provided a Cl- 'reference' tracer in the mixing zone. Conservative transport of the dissolved metals and sulphate through the mixing zone was verified by mass balances and by linear mixing plots relative to the injected reference tracer. At each of seven sites in the mixing zone, five samples were collected at evenly spaced increments of the observed across-channel gradients, as determined by specific conductance. This created sets of samples that adequately covered the ranges of mixtures (mixing ratios, in terms of the fraction of Animas River water, %AR). Concentrations measured in each mixing zone sample and in the upstream Animas River and Cement Creek were used to compute %AR for the reference and natural tracers. Values of %AR from natural tracers generally showed good agreement with values from the reference tracer, but variability in discharge and end-member concentrations and analytical errors contributed to unexpected outlier values for both injected and natural tracers. The median value (MV) %AR (calculated from all of the tracers) reduced scatter in the mixing plots for the dissolved metals, indicating that the MV estimate reduced the effects of various potential errors that could affect any tracer.

  5. Multiple injected and natural conservative tracers quantify mixing in a stream confluence affected by acid mine drainage near Silverton, Colorado

    NASA Astrophysics Data System (ADS)

    Schemel, Laurence E.; Cox, Marisa H.; Runkel, Robert L.; Kimball, Briant A.

    2006-08-01

    The acidic discharge from Cement Creek, containing elevated concentrations of dissolved metals and sulphate, mixed with the circumneutral-pH Animas River over a several hundred metre reach (mixing zone) near Silverton, CO, during this study. Differences in concentrations of Ca, Mg, Si, Sr, and SO42- between the creek and the river were sufficiently large for these analytes to be used as natural tracers in the mixing zone. In addition, a sodium chloride (NaCl) tracer was injected into Cement Creek, which provided a Cl- reference tracer in the mixing zone. Conservative transport of the dissolved metals and sulphate through the mixing zone was verified by mass balances and by linear mixing plots relative to the injected reference tracer. At each of seven sites in the mixing zone, five samples were collected at evenly spaced increments of the observed across-channel gradients, as determined by specific conductance. This created sets of samples that adequately covered the ranges of mixtures (mixing ratios, in terms of the fraction of Animas River water, %AR). Concentratis measured in each mixing zone sample and in the upstream Animas River and Cement Creek were used to compute %AR for the reference and natural tracers. Values of %AR from natural tracers generally showed good agreement with values from the reference tracer, but variability in discharge and end-member concentrations and analytical errors contributed to unexpected outlier values for both injected and natural tracers. The median value (MV) %AR (calculated from all of the tracers) reduced scatter in the mixing plots for the dissolved metals, indicating that the MV estimate reduced the effects of various potential errors that could affect any tracer.

  6. Is climate change affecting wolf populations in the high Arctic?

    USGS Publications Warehouse

    Mech, L.D.

    2004-01-01

    Gobal climate change may affect wolves in Canada's High Arctic (80?? N) acting through three trophic levels (vegetation, herbivores, and wolves). A wolf pack dependent on muskoxen and arctic hares in the Eureka area of Ellesmere Island denned and produced pups most years from at least 1986 through 1997. However, when summer snow covered vegetation in 1997 and 2000 for the first time since records were kept, halving the herbivore nutrition-replenishment period, muskox and hare numbers dropped drastically, and the area stopped supporting denning wolves through 2003. The unusual weather triggering these events was consistent with global-climate-change phenomena. ?? 2004 Kluwer Academic Publishers.

  7. Is climate change affecting wolf populations in the high Arctic?

    USGS Publications Warehouse

    Mech, L.D.

    2004-01-01

    Global climate change may affect wolves in Canada's High Arctic (80DG N) acting through three trophic levels (vegetation, herbivores, and wolves). A wolf pack dependent on muskoxen and arctic hares in the Eureka area of Ellesmere Island denned and produced pups most years from at least 1986 through 1997. However when summer snow covered vegetation in 1997 and 2000 for the first time since records were kept, halving the herbivore nutrition-replenishment period, muskox and hare numbers dropped drastically, and the area stopped supporting denning wolves through 2003. The unusual weather triggering these events was consistent with global-climate-change phenomena.

  8. Spatial overlap between environmental policy instruments and areas of high conservation value in forest.

    PubMed

    Sverdrup-Thygeson, Anne; Søgaard, Gunnhild; Rusch, Graciela M; Barton, David N

    2014-01-01

    In order to safeguard biodiversity in forest we need to know how forest policy instruments work. Here we use a nationwide network of 9400 plots in productive forest to analyze to what extent large-scale policy instruments, individually and together, target forest of high conservation value in Norway. We studied both instruments working through direct regulation; Strict Protection and Landscape Protection, and instruments working through management planning and voluntary schemes of forest certification; Wilderness Area and Mountain Forest. As forest of high conservation value (HCV-forest) we considered the extent of 12 Biodiversity Habitats and the extent of Old-Age Forest. We found that 22% of productive forest area contained Biodiversity Habitats. More than 70% of this area was not covered by any large-scale instruments. Mountain Forest covered 23%, while Strict Protection and Wilderness both covered 5% of the Biodiversity Habitat area. A total of 9% of productive forest area contained Old-Age Forest, and the relative coverage of the four instruments was similar as for Biodiversity Habitats. For all instruments, except Landscape Protection, the targeted areas contained significantly higher proportions of HCV-forest than areas not targeted by these instruments. Areas targeted by Strict Protection had higher proportions of HCV-forest than areas targeted by other instruments, except for areas targeted by Wilderness Area which showed similar proportions of Biodiversity Habitats. There was a substantial amount of spatial overlap between the policy tools, but no incremental conservation effect of overlapping instruments in terms of contributing to higher percentages of targeted HCV-forest. Our results reveal that although the current policy mix has an above average representation of forest of high conservation value, the targeting efficiency in terms of area overlap is limited. There is a need to improve forest conservation and a potential to cover this need by better

  9. Urban Biodiversity, City-Dwellers and Conservation: How Does an Outdoor Activity Day Affect the Human-Nature Relationship?

    PubMed Central

    Jaillon, Alexandre; Piron, Armony; Julliard, Romain; Raymond, Richard; Simon, Laurent; Prévot-Julliard, Anne-Caroline

    2012-01-01

    Urban conservation education programs aim to increase knowledge and awareness towards biodiversity and to change attitudes and behaviour towards the environment. However, to date, few urban conservation education studies have evaluated to what extent these programs have managed to achieve their goals. In this study, we experimentally explored the influence of an urban conservation activity day on individual knowledge, awareness and actions towards biodiversity, in both the short and longer term. We organised three activity days in Paris (France), during which people were invited to participate in urban conservation efforts. Both quantitative (questionnaire) and qualitative (interviews) methods were employed to investigate the influence of this short urban nature experience on the relationships that city-dwellers develop with nearby biodiversity. We found a strong positive correlation between the levels of participation and an immediate interest towards local urban biodiversity. In the longer term, however, although participants claimed to have gained more knowledge, local awareness and interest for species in their daily environment, they did not seem to extend this interest to participating in other related activities. These results highlight the complexity of validating the effectiveness of this type of education program for achieving conservation goals. Although such a short activity may only have a limited environmental impact, it nevertheless seems to increase people's knowledge, awareness, interest and concern. We therefore believe that when repeated locally, these short conservation education programs could enhance people's experience with nature in cities and achieve conservation goals more fully. PMID:22715403

  10. Urban biodiversity, city-dwellers and conservation: how does an outdoor activity day affect the human-nature relationship?

    PubMed

    Shwartz, Assaf; Cosquer, Alix; Jaillon, Alexandre; Piron, Armony; Julliard, Romain; Raymond, Richard; Simon, Laurent; Prévot-Julliard, Anne-Caroline

    2012-01-01

    Urban conservation education programs aim to increase knowledge and awareness towards biodiversity and to change attitudes and behaviour towards the environment. However, to date, few urban conservation education studies have evaluated to what extent these programs have managed to achieve their goals. In this study, we experimentally explored the influence of an urban conservation activity day on individual knowledge, awareness and actions towards biodiversity, in both the short and longer term.We organised three activity days in Paris (France), during which people were invited to participate in urban conservation efforts. Both quantitative (questionnaire) and qualitative (interviews) methods were employed to investigate the influence of this short urban nature experience on the relationships that city-dwellers develop with nearby biodiversity. We found a strong positive correlation between the levels of participation and an immediate interest towards local urban biodiversity. In the longer term, however, although participants claimed to have gained more knowledge, local awareness and interest for species in their daily environment, they did not seem to extend this interest to participating in other related activities. These results highlight the complexity of validating the effectiveness of this type of education program for achieving conservation goals. Although such a short activity may only have a limited environmental impact, it nevertheless seems to increase people's knowledge, awareness, interest and concern. We therefore believe that when repeated locally, these short conservation education programs could enhance people's experience with nature in cities and achieve conservation goals more fully.

  11. Octreotide for conservative management of intractable high output post operative chylous fistula: a case report.

    PubMed

    Prabhu, Sundararaman; Thomas, Shaji

    2015-03-01

    A case of high output post neck dissection chylous fistula is presented, which was successfully managed conservatively with octreotide; a long acting somatostatin analogue. Routine measures had failed, and secondary complications precluded thoracoscopic ligation. We discuss the spectrum of problems associated with chylous fistula and review the rationale behind the use of octreotide.

  12. The transcription factor Spn1 regulates gene expression via a highly conserved novel structural motif

    PubMed Central

    Pujari, Venugopal; Radebaugh, Catherine A.; Chodaparambil, Jayanth V.; Muthurajan, Uma M.; Almeida, Adam R.; Fischbeck, Julie A.; Luger, Karolin; Stargell, Laurie A.

    2010-01-01

    Spn1 plays essential roles in the regulation of gene expression by RNA Polymerase II (RNAPII), and it is highly conserved in organisms ranging from yeast to humans. Spn1 physically and/or genetically interacts with RNAPII, TBP, TFIIS and a number of chromatin remodeling factors (Swi/Snf and Spt6). The central domain of Spn1 (residues 141-305 out of 410) is necessary and sufficient for performing the essential functions of SPN1 in yeast cells. Here we report the high-resolution (1.85Å) crystal structure of the conserved central domain of Saccharomyces cerevisiae Spn1. The central domain is comprised of eight alpha-helices in a right handed super helical arrangement, and exhibits structural similarity to domain I of TFIIS. A unique structural feature of Spn1 is a highly conserved loop, which defines one side of a pronounced cavity. The loop and the other residues forming the cavity are highly conserved at the amino acid level among all Spn1 family members, suggesting that this is a signature motif for Spn1 orthologs. The locations and the molecular characterization of temperature-sensitive mutations in Spn1 indicate that the cavity is a key attribute of Spn1 that is critical for its regulatory functions during RNAPII-mediated transcriptional activity. PMID:20875428

  13. The transcription factor Spn1 regulates gene expression via a highly conserved novel structural motif.

    PubMed

    Pujari, Venugopal; Radebaugh, Catherine A; Chodaparambil, Jayanth V; Muthurajan, Uma M; Almeida, Adam R; Fischbeck, Julie A; Luger, Karolin; Stargell, Laurie A

    2010-11-19

    Spn1/Iws1 plays essential roles in the regulation of gene expression by RNA polymerase II (RNAPII), and it is highly conserved in organisms ranging from yeast to humans. Spn1 physically and/or genetically interacts with RNAPII, TBP (TATA-binding protein), TFIIS (transcription factor IIS), and a number of chromatin remodeling factors (Swi/Snf and Spt6). The central domain of Spn1 (residues 141-305 out of 410) is necessary and sufficient for performing the essential functions of SPN1 in yeast cells. Here, we report the high-resolution (1.85 Å) crystal structure of the conserved central domain of Saccharomyces cerevisiae Spn1. The central domain is composed of eight α-helices in a right-handed superhelical arrangement and exhibits structural similarity to domain I of TFIIS. A unique structural feature of Spn1 is a highly conserved loop, which defines one side of a pronounced cavity. The loop and the other residues forming the cavity are highly conserved at the amino acid level among all Spn1 family members, suggesting that this is a signature motif for Spn1 orthologs. The locations and the molecular characterization of temperature-sensitive mutations in Spn1 indicate that the cavity is a key attribute of Spn1 that is critical for its regulatory functions during RNAPII-mediated transcriptional activity.

  14. Complex evolution of a highly conserved microsatellite locus in several fish species.

    PubMed

    Liu, J-X; Ely, B

    2009-08-01

    The evolutionary dynamics of a highly conserved microsatellite locus (Dla 11) were studied in several fish species. The data indicated that multiple types of compound microsatellites arose through point mutations that were sometimes followed by expansion of the derived motif. Furthermore, extensive length variation was detected among species in the regions immediately flanking the repeat region.

  15. Protein E of Haemophilus influenzae is a ubiquitous highly conserved adhesin.

    PubMed

    Singh, Birendra; Brant, Marta; Kilian, Mogens; Hallström, Björn; Riesbeck, Kristian

    2010-02-01

    Protein E (PE) of nontypeable Haemophilus influenzae (NTHi) is involved in adhesion and activation of epithelial cells. A total of 186 clinical NTHi isolates, encapsulated H. influenzae, and culture collection strains were analyzed. PE was highly conserved in both NTHi and encapsulated H. influenzae (96.9%-100% identity without the signal peptide). PE also existed in other members of the genus Pasteurellaceae. The epithelial cell binding region (amino acids 84-108) was completely conserved. Phylogenetic analysis of the pe sequence separated Haemophilus species into 2 separate clusters. Importantly, PE was expressed in 98.4% of all NTHi (126 isolates) independently of the growth phase.

  16. Balancing forest-regeneration probabilities and maintenance costs in dry grasslands of high conservation priority

    USGS Publications Warehouse

    Bolliger, Janine; Edwards, Thomas C.; Eggenberg, Stefan; Ismail, Sascha; Seidl, Irmi; Kienast, Felix

    2011-01-01

    Abandonment of agricultural land has resulted in forest regeneration in species-rich dry grasslands across European mountain regions and threatens conservation efforts in this vegetation type. To support national conservation strategies, we used a site-selection algorithm (MARXAN) to find optimum sets of floristic regions (reporting units) that contain grasslands of high conservation priority. We sought optimum sets that would accommodate 136 important dry-grassland species and that would minimize forest regeneration and costs of management needed to forestall predicted forest regeneration. We did not consider other conservation elements of dry grasslands, such as animal species richness, cultural heritage, and changes due to climate change. Optimal sets that included 95–100% of the dry grassland species encompassed an average of 56–59 floristic regions (standard deviation, SD 5). This is about 15% of approximately 400 floristic regions that contain dry-grassland sites and translates to 4800–5300 ha of dry grassland out of a total of approximately 23,000 ha for the entire study area. Projected costs to manage the grasslands in these optimum sets ranged from CHF (Swiss francs) 5.2 to 6.0 million/year. This is only 15–20% of the current total estimated cost of approximately CHF30–45 million/year required if all dry grasslands were to be protected. The grasslands of the optimal sets may be viewed as core sites in a national conservation strategy.

  17. On the freestream preservation of high-order conservative flux-reconstruction schemes

    NASA Astrophysics Data System (ADS)

    Abe, Yoshiaki; Haga, Takanori; Nonomura, Taku; Fujii, Kozo

    2015-01-01

    The appropriate procedure for constructing the symmetric conservative metric is presented with which both the freestream preservation and global conservation properties are satisfied in the high-order conservative flux-reconstruction scheme on a three-dimensional stationary-curvilinear grid. A freestream preservation test is conducted, and the symmetric conservative metric constructed by the appropriate procedure preserves the freestream regardless of the order of shape functions, while other metrics cannot always preserve the freestream. Also a convecting vortex is computed on three-dimensional wavy grids, and the formal order of accuracy is achieved when the symmetric conservative metric is appropriately constructed, while it is not when they are inappropriately constructed. In addition, although the sufficient condition for the freestream preservation with the nonconservative (cross product form) metric was reported in the previous study to be that the order of solution polynomial has to be greater than or equal to the twice of the order of a shape function, a special case is newly found in the present study: when the Radau polynomial is used for the correction function, the freestream is preserved even if the solution order is lower than the known condition. Using the properties of Legendre polynomials, the mechanism for this special case is analytically explained, considering the cancellation of aliasing errors.

  18. Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes

    PubMed Central

    Sun, Hong; Skogerbø, Geir; Wang, Zhen; Liu, Wei; Li, Yixue

    2008-01-01

    Large numbers of sequence elements have been identified to be highly conserved among vertebrate genomes. These highly conserved elements (HCEs) are often located in or around genes that are involved in transcription regulation and early development. They have been shown to be involved in cis-regulatory activities through both in vivo and additional computational studies. We have investigated the structural relationships between such elements and genes in six vertebrate genomes human, mouse, rat, chicken, zebrafish and tetraodon and detected several thousand cases of conserved HCE-gene associations, and also cases of HCEs with no common target genes. A few examples underscore the potential significance of our findings about several individual genes. We found that the conserved association between HCE/HCEs and gene/genes are not restricted to elements by their absolute distance on the genome. Notably, long-range associations were identified and the molecular functions of the associated genes do not show any particular overrepresentation of the functional categories previously reported. HCEs in close proximity are found to be linked with different set of gene/genes. The results reflect the highly complex correlation between HCEs and their putative target genes. PMID:19008958

  19. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

    PubMed Central

    Hsiao, Yun-Hua Esther; Bahn, Jae Hoon; Lin, Xianzhi; Chan, Tak-Ming; Wang, Rena; Xiao, Xinshu

    2016-01-01

    Identification of functional genetic variants and elucidation of their regulatory mechanisms represent significant challenges of the post-genomic era. A poorly understood topic is the involvement of genetic variants in mediating post-transcriptional RNA processing, including alternative splicing. Thus far, little is known about the genomic, evolutionary, and regulatory features of genetically modulated alternative splicing (GMAS). Here, we systematically identified intronic tag variants for genetic modulation of alternative splicing using RNA-seq data specific to cellular compartments. Combined with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons. We observed that GMAS events are highly cell type independent, indicating that splicing-altering genetic variants could have widespread function across cell types. Interestingly, GMAS genes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution in primates. We predicted that GMAS SNVs often alter binding of splicing factors, with SRSF1 affecting the most GMAS events and demonstrating global allelic binding bias. However, in contrast to their GMAS targets, the predicted splicing factors are more conserved than expected, suggesting that cis-regulatory variation is the major driving force of splicing evolution. Moreover, GMAS-related splicing factors had stronger consensus motifs than expected, consistent with their susceptibility to SNV disruption. Intriguingly, GMAS SNVs in general do not alter the strongest consensus position of the splicing factor motif, except the more than 100 GMAS SNVs in linkage disequilibrium with polymorphisms reported by genome-wide association studies. Our study reports many GMAS events and enables a better understanding of the evolutionary and regulatory features of this phenomenon. PMID:26888265

  20. Factors affecting characterization of bulk high-temperature superconductors

    SciTech Connect

    Hull, J.R.

    1997-11-01

    Three major factors affect the characterization of bulk high-temperature superconductors in terms of their levitation properties during interaction with permanent magnets. First, the appropriate parameter for the permanent magnet is internal magnetization, not the value of the magnetic field measured at the magnet`s surface. Second, although levitation force grows with superconductor thickness and surface area, for a given permanent magnet size, comparison of levitation force between samples is meaningful when minimum values are assigned to the superconductor size parameters. Finally, the effect of force creep must be considered when time-averaging the force measurements. In addition to levitational force, the coefficient of friction of a levitated rotating permanent magnet may be used to characterize the superconductor.

  1. Touchdown digital polymerase chain reaction for quantification of highly conserved sequences in the HIV-1 genome.

    PubMed

    De Spiegelaere, Ward; Malatinkova, Eva; Kiselinova, Maja; Bonczkowski, Pawel; Verhofstede, Chris; Vogelaers, Dirk; Vandekerckhove, Linos

    2013-08-15

    Digital polymerase chain reaction (PCR) is an emerging absolute quantification method based on the limiting dilution principle and end-point PCR. This methodology provides high flexibility in assay design without influencing quantitative accuracy. This article describes an assay to quantify HIV DNA that targets a highly conserved region of the HIV-1 genome that hampers optimal probe design. To maintain high specificity and allow probe binding and hydrolysis of a probe with low melting temperature, a two-stage touchdown PCR was designed with a first round of amplification at high temperature and a subsequent round at low temperature to allow accumulation of fluorescence.

  2. Interview-based sighting histories can inform regional conservation prioritization for highly threatened cryptic species

    PubMed Central

    Turvey, Samuel T; Trung, Cao Tien; Quyet, Vo Dai; Nhu, Hoang Van; Thoai, Do Van; Tuan, Vo Cong Anh; Hoa, Dang Thi; Kacha, Kouvang; Sysomphone, Thongsay; Wallate, Sousakhone; Hai, Chau Thi Thanh; Thanh, Nguyen Van; Wilkinson, Nicholas M

    2015-01-01

    The use of robust ecological data to make evidence-based management decisions is frequently prevented by limited data quantity or quality, and local ecological knowledge (LEK) is increasingly seen as an important source of information for conservation. However, there has been little assessment of LEK's usefulness for informing prioritization and management of landscapes for threatened species, or assessing comparative species status across landscapes. A large-scale interview survey in the Annamite Mountains (Vietnam and Lao PDR) compiled the first systematic LEK data set for saola Pseudoryx nghetinhensis, one of the world's rarest mammals, and eight other ungulates. Saola conservation is hindered by uncertainty over continued presence across much of its proposed distribution. We analysed comparative LEK-based last-sighting data across three landscapes to determine whether regional sighting histories support previous suggestions of landscape importance for saola conservation (Hue-Quang Nam: top-priority Vietnamese landscape; Pu Mat: lower priority Vietnamese landscape; Viengthong: high-priority Lao landscape) and whether they constitute an effective spatial prioritization tool for cryptic species management. Wild pig and red muntjac may be the only Annamite ungulates with stable populations; the regional status of all other species appears to be worse. Saola have declined more severely and/or are significantly rarer than most other ungulates and have been seen by relatively few respondents. Saola were also frequently considered locally rarest or declining, and never as species that had not declined. In contrast to other species, there are no regional differences in saola sighting histories, with continued persistence in all landscapes challenging suggestions that regional status differs greatly. Remnant populations persist in Vietnam despite heavy hunting, but even remote landscapes in Lao may be under intense pressure. Synthesis and applications. Our local

  3. A Highly Conserved Residue in HIV-1 Nef Alpha Helix 2 Modulates Protein Expression

    PubMed Central

    Johnson, Aaron L.; Dirk, Brennan S.; Coutu, Mathieu; Haeryfar, S. M. Mansour; Arts, Eric J.; Finzi, Andrés

    2016-01-01

    ABSTRACT Extensive genetic diversity is a defining characteristic of human immunodeficiency virus type 1 (HIV-1) and poses a significant barrier to the development of an effective vaccine. To better understand the impact of this genetic diversity on the HIV-1 pathogenic factor Nef, we compiled a panel of reference strains from the NIH Los Alamos HIV Database. Initial sequence analysis identified point mutations at Nef residues 13, 84, and 92 in subtype C reference strain C.BR92025 from Brazil. Functional analysis revealed impaired major histocompatibility complex class I and CD4 downregulation of strain C.BR92025 Nef, which corresponded to decreased protein expression. Metabolic labeling demonstrated that strain C.BR92025 Nef has a greater rate of protein turnover than subtype B reference strain B.JRFL that, on the basis of mutational analysis, is related to Nef residue A84. An alanine-to-valine substitution at position 84, located in alpha helix 2 of Nef, was sufficient to alter the rate of turnover of an otherwise highly expressed Nef protein. In conclusion, these findings highlight HIV-1 Nef residue A84 as a major determinant of protein expression that may offer an additional avenue to disrupt or mediate the effects of this key HIV-1 pathogenic factor. IMPORTANCE The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution

  4. Camera Trapping: A Contemporary Approach to Monitoring Invasive Rodents in High Conservation Priority Ecosystems

    PubMed Central

    Rendall, Anthony R.; Sutherland, Duncan R.; Cooke, Raylene; White, John

    2014-01-01

    Invasive rodent species have established on 80% of the world's islands causing significant damage to island environments. Insular ecosystems support proportionally more biodiversity than comparative mainland areas, highlighting them as critical for global biodiversity conservation. Few techniques currently exist to adequately detect, with high confidence, species that are trap-adverse such as the black rat, Rattus rattus, in high conservation priority areas where multiple non-target species persist. This study investigates the effectiveness of camera trapping for monitoring invasive rodents in high conservation areas, and the influence of habitat features and density of colonial-nesting seabirds on rodent relative activity levels to provide insights into their potential impacts. A total of 276 camera sites were established and left in situ for 8 days. Identified species were recorded in discrete 15 min intervals, referred to as ‘events’. In total, 19 804 events were recorded. From these, 31 species were identified comprising 25 native species and six introduced. Two introduced rodent species were detected: the black rat (90% of sites), and house mouse Mus musculus (56% of sites). Rodent activity of both black rats and house mice were positively associated with the structural density of habitats. Density of seabird burrows was not strongly associated with relative activity levels of rodents, yet rodents were still present in these areas. Camera trapping enabled a large number of rodents to be detected with confidence in site-specific absences and high resolution to quantify relative activity levels. This method enables detection of multiple species simultaneously with low impact (for both target and non-target individuals); an ideal strategy for monitoring trap-adverse invasive rodents in high conservation areas. PMID:24599307

  5. Assessment of the effects of farming and conservation programs on pesticide deposition in high plains wetlands.

    PubMed

    Belden, Jason B; Hanson, Brittany Rae; McMurry, Scott T; Smith, Loren M; Haukos, David A

    2012-03-20

    We examined pesticide contamination in sediments from depressional playa wetlands embedded in the three dominant land-use types in the western High Plains and Rainwater Basin of the United States including cropland, perennial grassland enrolled in conservation programs (e.g., Conservation Reserve Program [CRP]), and native grassland or reference condition. Two hundred and sixty four playas, selected from the three land-use types, were sampled from Nebraska and Colorado in the north to Texas and New Mexico in the south. Sediments were examined for most of the commonly used agricultural pesticides. Atrazine, acetochlor, metolachlor, and trifluralin were the most commonly detected pesticides in the northern High Plains and Rainwater Basin. Atrazine, metolachlor, trifluralin, and pendimethalin were the most commonly detected pesticides in the southern High Plains. The top 5-10% of playas contained herbicide concentrations that are high enough to pose a hazard for plants. However, insecticides and fungicides were rarely detected. Pesticide occurrence and concentrations were higher in wetlands surrounded by cropland as compared to native grassland and CRP perennial grasses. The CRP, which is the largest conservation program in the U.S., was protective and had lower pesticide concentrations compared to cropland.

  6. Targeted carbon conservation at national scales with high-resolution monitoring

    PubMed Central

    Asner, Gregory P.; Knapp, David E.; Martin, Roberta E.; Tupayachi, Raul; Anderson, Christopher B.; Mascaro, Joseph; Sinca, Felipe; Chadwick, K. Dana; Higgins, Mark; Farfan, William; Llactayo, William; Silman, Miles R.

    2014-01-01

    Terrestrial carbon conservation can provide critical environmental, social, and climate benefits. Yet, the geographically complex mosaic of threats to, and opportunities for, conserving carbon in landscapes remain largely unresolved at national scales. Using a new high-resolution carbon mapping approach applied to Perú, a megadiverse country undergoing rapid land use change, we found that at least 0.8 Pg of aboveground carbon stocks are at imminent risk of emission from land use activities. Map-based information on the natural controls over carbon density, as well as current ecosystem threats and protections, revealed three biogeographically explicit strategies that fully offset forthcoming land-use emissions. High-resolution carbon mapping affords targeted interventions to reduce greenhouse gas emissions in rapidly developing tropical nations. PMID:25385593

  7. Targeted carbon conservation at national scales with high-resolution monitoring.

    PubMed

    Asner, Gregory P; Knapp, David E; Martin, Roberta E; Tupayachi, Raul; Anderson, Christopher B; Mascaro, Joseph; Sinca, Felipe; Chadwick, K Dana; Higgins, Mark; Farfan, William; Llactayo, William; Silman, Miles R

    2014-11-25

    Terrestrial carbon conservation can provide critical environmental, social, and climate benefits. Yet, the geographically complex mosaic of threats to, and opportunities for, conserving carbon in landscapes remain largely unresolved at national scales. Using a new high-resolution carbon mapping approach applied to Perú, a megadiverse country undergoing rapid land use change, we found that at least 0.8 Pg of aboveground carbon stocks are at imminent risk of emission from land use activities. Map-based information on the natural controls over carbon density, as well as current ecosystem threats and protections, revealed three biogeographically explicit strategies that fully offset forthcoming land-use emissions. High-resolution carbon mapping affords targeted interventions to reduce greenhouse gas emissions in rapidly developing tropical nations.

  8. Taxonomic distinctness and conservation of a new high biodiversity subterranean area in Brazil.

    PubMed

    Gallão, Jonas E; Bichuette, Maria Elina

    2015-03-01

    Subterranean environments, even though they do not possess a primary production (photosynthesis), may present high biodiversity, faunistic originality, endemism, phylogenetic isolations and unique ecological and/or evolution events, in addition to rare taxa. Studies investigating the biological diversity in Neotropical caves are relatively rare and recent, and most of them have been conducted in Brazil. We sampled caves from the state of Bahia, northeastern Brazil, and through sampling sufficiency tests and richness estimators, we demonstrate that the normatization for the Brazilian cave laws is not adequate for its conservation and that only α diversity index is not enough to verify faunistic patterns. We suggest that a phylogenetic diversity index be more robust and accurate for conservation purposes, particularly the Taxonomic Distinctness index. Moreover, we propose that the sandstone complex caves from Chapada Diamantina National Park need to be classified as being of high subterranean biodiversity in a global scope.

  9. Conservative high-order-accurate finite-difference methods for curvilinear grids

    NASA Technical Reports Server (NTRS)

    Rai, Man M.; Chakrvarthy, Sukumar

    1993-01-01

    Two fourth-order-accurate finite-difference methods for numerically solving hyperbolic systems of conservation equations on smooth curvilinear grids are presented. The first method uses the differential form of the conservation equations; the second method uses the integral form of the conservation equations. Modifications to these schemes, which are required near boundaries to maintain overall high-order accuracy, are discussed. An analysis that demonstrates the stability of the modified schemes is also provided. Modifications to one of the schemes to make it total variation diminishing (TVD) are also discussed. Results that demonstrate the high-order accuracy of both schemes are included in the paper. In particular, a Ringleb-flow computation demonstrates the high-order accuracy and the stability of the boundary and near-boundary procedures. A second computation of supersonic flow over a cylinder demonstrates the shock-capturing capability of the TVD methodology. An important contribution of this paper is the dear demonstration that higher order accuracy leads to increased computational efficiency.

  10. The Hsp90-Dependent Proteome Is Conserved and Enriched for Hub Proteins with High Levels of Protein–Protein Connectivity

    PubMed Central

    Swamy, Krishna B.S.; Yu, Jau-Song; Schuyler, Scott C.; Leu, Jun-Yi

    2014-01-01

    Hsp90 is one of the most abundant and conserved proteins in the cell. Reduced levels or activity of Hsp90 causes defects in many cellular processes and also reveals genetic and nongenetic variation within a population. Despite information about Hsp90 protein–protein interactions, a global view of the Hsp90-regulated proteome in yeast is unavailable. To investigate the degree of dependency of individual yeast proteins on Hsp90, we used the “stable isotope labeling by amino acids in cell culture” method coupled with mass spectrometry to quantify around 4,000 proteins in low-Hsp90 cells. We observed that 904 proteins changed in their abundance by more than 1.5-fold. When compared with the transcriptome of the same population of cells, two-thirds of the misregulated proteins were observed to be affected posttranscriptionally, of which the majority were downregulated. Further analyses indicated that the downregulated proteins are highly conserved and assume central roles in cellular networks with a high number of protein interacting partners, suggesting that Hsp90 buffers genetic and nongenetic variation through regulating protein network hubs. The downregulated proteins were enriched for essential proteins previously not known to be Hsp90-dependent. Finally, we observed that downregulation of transcription factors and mating pathway components by attenuating Hsp90 function led to decreased target gene expression and pheromone response, respectively, providing a direct link between observed proteome regulation and cellular phenotypes. PMID:25316598

  11. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation.

    PubMed

    Weinert, Brian T; Wagner, Sebastian A; Horn, Heiko; Henriksen, Peter; Liu, Wenshe R; Olsen, Jesper V; Jensen, Lars J; Choudhary, Chunaram

    2011-07-26

    Posttranslational modification of proteins by acetylation and phosphorylation regulates most cellular processes in living organisms. Surprisingly, the evolutionary conservation of phosphorylated serine and threonine residues is only marginally higher than that of unmodified serines and threonines. With high-resolution mass spectrometry, we identified 1981 lysine acetylation sites in the proteome of Drosophila melanogaster. We used data sets of experimentally identified acetylation and phosphorylation sites in Drosophila and humans to analyze the evolutionary conservation of these modification sites between flies and humans. Site-level conservation analysis revealed that acetylation sites are highly conserved, significantly more so than phosphorylation sites. Furthermore, comparison of lysine conservation in Drosophila and humans with that in nematodes and zebrafish revealed that acetylated lysines were significantly more conserved than were nonacetylated lysines. Bioinformatics analysis using Gene Ontology terms suggested that the proteins with conserved acetylation control cellular processes such as protein translation, protein folding, DNA packaging, and mitochondrial metabolism. We found that acetylation of ubiquitin-conjugating E2 enzymes was evolutionarily conserved, and mutation of a conserved acetylation site impaired the function of the human E2 enzyme UBE2D3. This systems-level analysis of comparative posttranslational modification showed that acetylation is an anciently conserved modification and suggests that phosphorylation sites may have evolved faster than acetylation sites.

  12. A High-Order Finite Spectral Volume Method for Conservation Laws on Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Wang, Z. J.; Liu, Yen; Kwak, Dochan (Technical Monitor)

    2001-01-01

    A time accurate, high-order, conservative, yet efficient method named Finite Spectral Volume (FSV) is developed for conservation laws on unstructured grids. The concept of a 'spectral volume' is introduced to achieve high-order accuracy in an efficient manner similar to spectral element and multi-domain spectral methods. In addition, each spectral volume is further sub-divided into control volumes (CVs), and cell-averaged data from these control volumes is used to reconstruct a high-order approximation in the spectral volume. Riemann solvers are used to compute the fluxes at spectral volume boundaries. Then cell-averaged state variables in the control volumes are updated independently. Furthermore, TVD (Total Variation Diminishing) and TVB (Total Variation Bounded) limiters are introduced in the FSV method to remove/reduce spurious oscillations near discontinuities. A very desirable feature of the FSV method is that the reconstruction is carried out only once, and analytically, and is the same for all cells of the same type, and that the reconstruction stencil is always non-singular, in contrast to the memory and CPU-intensive reconstruction in a high-order finite volume (FV) method. Discussions are made concerning why the FSV method is significantly more efficient than high-order finite volume and the Discontinuous Galerkin (DG) methods. Fundamental properties of the FSV method are studied and high-order accuracy is demonstrated for several model problems with and without discontinuities.

  13. High order filtering methods for approximating hyperbolic systems of conservation laws

    NASA Technical Reports Server (NTRS)

    Lafon, F.; Osher, S.

    1991-01-01

    The essentially nonoscillatory (ENO) schemes, while potentially useful in the computation of discontinuous solutions of hyperbolic conservation-law systems, are computationally costly relative to simple central-difference methods. A filtering technique is presented which employs central differencing of arbitrarily high-order accuracy except where a local test detects the presence of spurious oscillations and calls upon the full ENO apparatus to remove them. A factor-of-three speedup is thus obtained over the full-ENO method for a wide range of problems, with high-order accuracy in regions of smooth flow.

  14. Demographic Factors Affecting Internet Using Purposes of High School Students

    ERIC Educational Resources Information Center

    Kilic, Abdullah Faruk; Güzeller, Cem Oktay

    2017-01-01

    This study aimed at determining the impact of demographic factors on the Internet usage purposes of high school students. The population of the study consisted of students between 9th and 12th grades from the Anatolian high schools, science high schools, social sciences high schools, sports high schools and fine arts high schools in Turkey. The…

  15. Forest edges have high conservation value for bird communities in mosaic landscapes.

    PubMed

    Terraube, Julien; Archaux, Frédéric; Deconchat, Marc; van Halder, Inge; Jactel, Hervé; Barbaro, Luc

    2016-08-01

    A major conservation challenge in mosaic landscapes is to understand how trait-specific responses to habitat edges affect bird communities, including potential cascading effects on bird functions providing ecosystem services to forests, such as pest control. Here, we examined how bird species richness, abundance and community composition varied from interior forest habitats and their edges into adjacent open habitats, within a multi-regional sampling scheme. We further analyzed variations in Conservation Value Index (CVI), Community Specialization Index (CSI) and functional traits across the forest-edge-open habitat gradient. Bird species richness, total abundance and CVI were significantly higher at forest edges while CSI peaked at interior open habitats, i.e., furthest from forest edge. In addition, there were important variations in trait- and species-specific responses to forest edges among bird communities. Positive responses to forest edges were found for several forest bird species with unfavorable conservation status. These species were in general insectivores, understorey gleaners, cavity nesters and long-distance migrants, all traits that displayed higher abundance at forest edges than in forest interiors or adjacent open habitats. Furthermore, consistently with predictions, negative edge effects were recorded in some forest specialist birds and in most open-habitat birds, showing increasing densities from edges to interior habitats. We thus suggest that increasing landscape-scale habitat complexity would be beneficial to declining species living in mosaic landscapes combining small woodlands and open habitats. Edge effects between forests and adjacent open habitats may also favor bird functional guilds providing valuable ecosystem services to forests in longstanding fragmented landscapes.

  16. How to Go Green: Creating a Conservation Culture in a Public High School through Education, Modeling, and Communication

    ERIC Educational Resources Information Center

    Schelly, Chelsea; Cross, Jennifer E.; Franzen, William; Hall, Pete; Reeve, Stu

    2012-01-01

    This case study examines how energy conservation efforts in one public high school contributed to both sustainability education and the adoption of sustainable behavior within educational and organizational practice. Individual role models, school facilities, school governance and school culture together support both conservation and environmental…

  17. Water Wisdom: 23 Stand-Alone Activities on Water Supply and Water Conservation for High School Students. 2nd Edition.

    ERIC Educational Resources Information Center

    Massachusetts State Water Resources Authority, Boston.

    This water conservation education program for high schools consists of both stand-alone activities and teacher support materials. Lessons are divided into six broad categories: (1) The Water Cycle; (2) Water and Society; (3) Keeping Water Pure; (4) Visualizing Volumes; (5) The Economics of Water Use; and (6) Domestic Water Conservation. The…

  18. Heterochromatin protein 1, a known suppressor of position-effect variegation, is highly conserved in Drosophila.

    PubMed Central

    Clark, R F; Elgin, S C

    1992-01-01

    The Su(var)205 gene of Drosophila melanogaster encodes heterochromatin protein 1 (HP1), a protein located preferentially within beta-heterochromatin. Mutation of this gene has been associated with dominant suppression of position-effect variegation. We have cloned and sequenced the gene encoding HP1 from Drosophila virilis, a distantly related species. Comparison of the predicted amino acid sequence with Drosophila melanogaster HP1 shows two regions of strong homology, one near the N-terminus (57/61 amino acids identical) and the other near the C-terminus (62/68 amino acids identical) of the protein. Little homology is seen in the 5' and 3' untranslated portions of the gene, as well as in the intronic sequences, although intron/exon boundaries are generally conserved. A comparison of the deduced amino acid sequences of HP1-like proteins from other species shows that the cores of the N-terminal and C-terminal domains have been conserved from insects to mammals. The high degree of conservation suggests that these N- and C-terminal domains could interact with other macromolecules in the formation of the condensed structure of heterochromatin. Images PMID:1461737

  19. [Comparative chromosome painting shows the red panda (Ailurus fulgens) has a highly conserved karyotype].

    PubMed

    Tian, Ying; Nie, Wen-Hui; Wang, Jin-Huan; Yang, Yun-Fei; Yang, Feng-Tang

    2002-02-01

    We have established a comparative chromosome map between red panda (Ailurus fulgens, 2n = 36) and dog by chromosome painting with biotin-labelled chromosome-specific probes of the dog. Dog probes specific for the 38 automates delineated 71 homologous segments in the metaphase chromosomes of red panda. Of the 38 autosomal paints, 18 probes each delineated one homologous segment in red panda genome, while the other 20 ones each detected two to five homologous segments. The dog X chromosome-specific paint delineated the whole X chromosome of the red panda. The results indicate that at least 28 fissions (breaks), 49 fusions and 4 inversions were needed to "convert" the dog karyotype to that of the red panda, suggesting that extensive chromosome rearrangements differentiate the karyotypes of red panda and dog. Based on the established comparative chromosome homologies of dog and domestic cat, we could infer that there were 26 segments of conserved synteny between red panda and domestic cat. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in red panda and domestic cat genomes revealed at least 2 cryptic inversions in two large chromosomal regions of conserved synteny between red panda and domestic cat. The karyotype of red panda shows high degree of homology with that of domestic cat.

  20. Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

    PubMed Central

    Beauchemin, Mathieu; Roy, Sougata; Daoust, Philippe; Dagenais-Bellefeuille, Steve; Bertomeu, Thierry; Letourneau, Louis; Lang, B. Franz; Morse, David

    2012-01-01

    Dinoflagellates are an important component of the marine biota, but a large genome with high–copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae. PMID:23019363

  1. Conservation Tillage

    NASA Astrophysics Data System (ADS)

    Gebhardt, Maurice R.; Daniel, Tommy C.; Schweizer, Edward E.; Allmaras, Raymond R.

    1985-11-01

    Conservation production systems combine tillage and planting practices to reduce soil erosion and loss of water from farmland. Successful conservation tillage practices depend on the ability of farm managers to integrate sound crop production practices with effective pest management systems. More scientific information is needed to determine the relations between tillage practices and physical, chemical, and biological soil factors that affect plant and pest ecology. There is a need to devise improved pest management strategies for conservation tillage and to better understand the impact of conservation tillage on water quality, especially as it is related to use of agricultural chemicals. While savings in fuel, labor, and soil have induced many farmers to adopt conservation tillage, improved methods and equipment should increase adoption even more.

  2. BmPLA2 containing conserved domain WD40 affects the metabolic functions of fat body tissue in silkworm, Bombyx mori.

    PubMed

    Orville Singh, Chabungbam; Xin, Hu-Hu; Chen, Rui-Ting; Wang, Mei-Xian; Liang, Shuang; Lu, Yan; Cai, Zi-Zheng; Miao, Yun-Gen

    2016-02-01

    PLA2 enzyme hydrolyzes arachidonic acid, and other polyunsaturated fatty acids, from the sn-2 position to release free arachidonic acid and a lysophospholipid. Previous studies reported that the PLA2 in invertebrate organisms participates in lipid signaling molecules like arachidonic acid release in immune-associated tissues like hemocytes and fat bodies. In the present study, we cloned the BmPLA2 gene from fat body tissue of silkworm Bombyx mori, which has a total sequence of 1.031 kb with a 31.90 kDa protein. In silico results of BmPLA2 indicated that the protein has a putative WD40 conserved domain and its phylogeny tree clustered with Danaus plexippus species. We investigated the transcriptional expression in development stages and tissues. The highest expression of BmPLA2 was screened in fat body among the studied tissues of third day fifth instar larva, with a high expression on third day fifth instar larva followed by a depression of expression in the wandering stage of the fifth instar larva. The expression of BmPLA2 in female pupa was higher than that of male pupa. Our RNAi-mediated gene silencing results showed highest reduction of BmPLA2 expression in post-24 h followed by post-48 and post-72 h. The BmPLA2-RNAi larvae and pupa could be characterized by pharate adult lethality and underdevelopment. The phenotypic characters of fat body cells in RNAi-induced larva implied that BmPLA2 affects the metabolic functions of fat body tissue in silkworm Bombyx mori.

  3. High order numerical methods for networks of hyperbolic conservation laws coupled with ODEs and lumped parameter models

    NASA Astrophysics Data System (ADS)

    Borsche, Raul; Kall, Jochen

    2016-12-01

    In this paper we construct high order finite volume schemes on networks of hyperbolic conservation laws with coupling conditions involving ODEs. We consider two generalized Riemann solvers at the junction, one of Toro-Castro type and a solver of Harten, Enquist, Osher, Chakravarthy type. The ODE is treated with a Taylor method or an explicit Runge-Kutta scheme, respectively. Both resulting high order methods conserve quantities exactly if the conservation is part of the coupling conditions. Furthermore we present a technique to incorporate lumped parameter models, which arise from simplifying parts of a network. The high order convergence and the robust capturing of shocks are investigated numerically in several test cases.

  4. High Fidelity Images--How They Affect Learning.

    ERIC Educational Resources Information Center

    Kwinn, Ann

    1997-01-01

    Discusses the use of graphics in instruction and concludes that cosmetic and motivational graphics can be more realistic and detailed for affective goals, while schematic graphics may be best for the more cognitive functions of focusing attention and presenting actual content. Domains of learning, mental models, and visualization are examined.…

  5. A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK

    SciTech Connect

    Lennon, E.; Gutman, P.D.; Hanlong Yao; Minton, K.W. )

    1991-03-01

    A DNA fragment containing a portion of a DNA damage-inducible gene from Deinococcus radiodurans SARK hybridized to numerous fragments of SARK genomic DNA because of a highly conserved repetitive chromosomal element. The element is of variable length, ranging from 150 to 192 bp, depending on the absence or presence of one or two 21-bp sequences located internally. A putative translational start site of the damage-inducible gene is within the reiterated element. The element contains dyad symmetries that suggest modes of transcriptional and/or translational control.

  6. Symmetrization of conservation laws with entropy for high-temperature hypersonic computations

    NASA Technical Reports Server (NTRS)

    Chalot, F.; Hughes, T. J. R.; Shakib, F.

    1990-01-01

    Results of Hughes, France, and Mallet are generalized to conservation law systems taking into account high-temperature effects. Symmetric forms of different equation sets are derived in terms of entropy variables. First, the case of a general divariant gas is studied; it can be specialized to the usual Navier-Stokes equations, as well as to situations where the gas is vibrationally excited, and undergoes equilibrium chemical reactions. The case of gas in thermochemical nonequilibrium is considered next. Transport phenomena, and in particular mass diffusion, are examined in the framework of symmetric advective-diffusive systems.

  7. High resolution numerical simulation of the linearized Euler equations in conservation law form

    NASA Technical Reports Server (NTRS)

    Sreenivas, Kidambi; Whitfield, David L.; Huff, Dennis L.

    1993-01-01

    A linearized Euler solver based on a high resolution numerical scheme is presented. The approach is to linearize the flux vector as opposed to carrying through the complete linearization analysis with the dependent variable vector written as a sum of the mean and the perturbed flow. This allows the linearized equations to be maintained in conservation law form. The linearized equations are used to compute unsteady flows in turbomachinery blade rows arising due to blade vibrations. Numerical solutions are compared to theoretical results (where available) and to numerical solutions of the nonlinear Euler equations.

  8. Exploring children's cognitive and affective skills related to conservation of mass using Fischer's dynamic skills model: What goes on in their minds and hearts?

    NASA Astrophysics Data System (ADS)

    Asghar, Anila

    I conducted a mixed method study to examine: How, if at all, does middle school students' understanding of the conservation of mass develop as they engage in two different chemistry curricula (an interactive chemistry curriculum, DESIGNS, aimed at helping them to understand the conservation of mass and another presenting the same concepts from a traditional approach)? How do they feel about participating in the science activities, and how, if at all, do their feelings relate to their learning? I used the framework of the Dynamic Skills theory (Fischer, 1980) as a lens through which to understand their thinking and feelings and any changes in them. The study was conducted in two Massachusetts public schools. In each school, one class followed the DESIGNS curriculum (DESIGNS II, in press), while the other followed a traditional chemistry curriculum. Each teacher in the study taught two science classes and used the DESIGNS curriculum in one class and the traditional curriculum in the other. Seventy three middle school students from the two schools participated in this study. The data was gathered through (a) a concept assessment questionnaire and (b) affective response survey (both were administered before, during, and at the end of the curriculum). Additionally, qualitative interviews were conducted with 16 selected students (four from each class) twice (before and after the curriculum). The quantitative analysis revealed that students in the DESIGNS group demonstrated greater conceptual change, on average, as compared to the traditional group. In addition, pretest score and mother's education were also found to be associated with students' learning. The pretest score was negatively associated with the conceptual gain (the lower the pretest score the higher the gain), whereas mother's education had a positive relationship with conceptual understanding. A comparison of students' affective response to their respective curriculum showed that students felt more positive

  9. High order filtering methods for approximating hyberbolic systems of conservation laws

    NASA Technical Reports Server (NTRS)

    Lafon, F.; Osher, S.

    1990-01-01

    In the computation of discontinuous solutions of hyperbolic systems of conservation laws, the recently developed essentially non-oscillatory (ENO) schemes appear to be very useful. However, they are computationally costly compared to simple central difference methods. A filtering method which is developed uses simple central differencing of arbitrarily high order accuracy, except when a novel local test indicates the development of spurious oscillations. At these points, the full ENO apparatus is used, maintaining the high order of accuracy, but removing spurious oscillations. Numerical results indicate the success of the method. High order of accuracy was obtained in regions of smooth flow without spurious oscillations for a wide range of problems and a significant speed up of generally a factor of almost three over the full ENO method.

  10. Low-intensity agricultural landscapes in Transylvania support high butterfly diversity: implications for conservation.

    PubMed

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  11. Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

    PubMed Central

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  12. Effects of the Conservation Reserve Program on Hydrologic Processes in the Southern High Plains

    NASA Astrophysics Data System (ADS)

    Haacker, E. M.; Smidt, S. J.; Kendall, A. D.; Basso, B.; Hyndman, D. W.

    2015-12-01

    The Southern High Plains Aquifer is a rapidly depleting resource that supports agriculture in parts of New Mexico and the Texas Panhandle. The development of the aquifer has changed the landscape and the water cycle of the region. This study illustrates the evolving patterns of land use and the effects of cultivation, from irrigated to dryland farming to the countermanding influence of the Conservation Reserve Program (CRP). Previous research indicates that greater recharge rates occur under cultivated land in the Southern High Plains than under unbroken soil: the transition to cultivation causes increased recharge, under both dryland and irrigated management, though most recharge still occurs through playa lakes. The Conservation Reserve Program takes land out of crop production, replacing the land cover with something more like the natural ecosystem. This may decrease recharge below fields, and reduce runoff that feeds playa lakes; or, CRP may help stabilize playa lakes, increasing recharge. Changes to the water cycle are investigated at the field scale using the System Approach to Land Use Sustainability (SALUS) crop model, and at the regional scale with the Landscape Hydrology Model (LHM), and compared with historical data and water table elevations.

  13. Highly conserved d-loop sequences in woolly mouse opossums Marmosa (Micoureus).

    PubMed

    Rocha, Rita Gomes; Leite, Yuri Luiz Reis; Ferreira, Eduardo; Justino, Juliana; Costa, Leonora Pires

    2012-04-01

    This study reports the occurrence of highly conserved d-loop sequences in the mitochondrial genome of the woolly mouse opossum genus Marmosa subgenus Micoureus (Mammalia, Didelphimorphia, Didelphidae). Sixty-six sequences of Marmosa (Micoureus) demerarae, Marmosa (Micoureus) constantiae, and Marmosa (Micoureus) paraguayanus were amplified using universal d-loop primers and virtually no genetic differences were detected within and among species. These sequences matched the control region of the mitochondrial marsupial genome. Analyses of qualitative aspects of these sequences revealed that their structural composition is very similar to the d-loop region of other didelphid species. However, the total lack of variability has not been reported from other closely related species. The data analyzed here support the occurrence of highly conserved d-loop sequences, and we found no support for the hypothesis that these sequences are d-loop-like nuclear pseudogenes. Furthermore, the control and flanking regions obtained with different primers corroborate the lack of variability of the d-loop sequences in the mitochondrial genome of Marmosa (Micoureus).

  14. Nosema ceranae alters a highly conserved hormonal stress pathway in honeybees.

    PubMed

    Mayack, C; Natsopoulou, M E; McMahon, D P

    2015-12-01

    Nosema ceranae, an emerging pathogen of the western honeybee (Apis mellifera), is implicated in recent pollinator losses and causes severe energetic stress. However, whether precocious foraging and accelerated behavioural maturation in infected bees are caused by the infection itself or via indirect energetic stress remains unknown. Using a combination of nutritional and infection treatments, we investigated how starvation and infection alters the regulation of adipokinetic hormone (AKH) and octopamine, two highly conserved physiological pathways that respond to energetic stress by mobilizing fat stores and increasing search activity for food. Although there was no response from AKH when bees were experimentally infected with N. ceranae or starved, supporting the notion that honeybees have lost this pathway, there were significant regulatory changes in the octopamine pathway. Significantly, we found no evidence of acute energetic stress being the only cause of symptoms associated with N. ceranae infection. Therefore, the parasite itself appears to alter regulatory components along a highly conserved physiological pathway in an infection-specific manner. This indicates that pathogen-induced behavioural alteration of chronically infected bees should not just be viewed as a coincidental short-term by-product of pathogenesis (acute energetic stress) and may be a result of a generalist manipulation strategy to obtain energy for reproduction.

  15. Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms.

    PubMed

    Zhang, Ning; Zeng, Liping; Shan, Hongyan; Ma, Hong

    2012-09-01

    Organismal phylogeny provides a crucial evolutionary framework for many studies and the angiosperm phylogeny has been greatly improved recently, largely using organellar and rDNA genes. However, low-copy protein-coding nuclear genes have not been widely used on a large scale in spite of the advantages of their biparental inheritance and vast number of choices. Here, we identified 1083 highly conserved low-copy nuclear genes by genome comparison. Furthermore, we demonstrated the use of five nuclear genes in 91 angiosperms representing 46 orders (73% of orders) and three gymnosperms as outgroups for a highly resolved phylogeny. These nuclear genes are easy to clone and align, and more phylogenetically informative than widely used organellar genes. The angiosperm phylogeny reconstructed using these genes was largely congruent with previous ones mainly inferred from organellar genes. Intriguingly, several new placements were uncovered for some groups, including those among the rosids, the asterids, and between the eudicots and several basal angiosperm groups. These conserved universal nuclear genes have several inherent qualities enabling them to be good markers for reconstructing angiosperm phylogeny, even eukaryotic relationships, further providing new insights into the evolutionary history of angiosperms.

  16. Early ipsilateral breast tumor recurrences after breast conservation affect survival: An analysis of the National Cancer Institute randomized trial

    SciTech Connect

    Brooks, Joseph P.; Danforth, David N.; Albert, Paul; Sciuto, Linda C. B.S.N.; Smith, Sharon L.; Camphausen, Kevin A.; Poggi, Matthew M. . E-mail: MMPoggi@Bethesda.med.navy.mil

    2005-07-01

    Purpose: To evaluate the effect of an ipsilateral breast tumor recurrence (IBTR) after breast-conservation therapy (BCT) on survival. Methods and Materials: One hundred twenty-one women were randomized to BCT. Patients with an IBTR were analyzed to determine survival. Analysis was performed with Kaplan-Meier estimates, log-rank tests, and time-dependent covariate Cox models. Results: At a median follow-up of 18.4 years, 27 patients had an IBTR. The median survival time after IBTR was 13.1 years. The 5-year survival rate was 91.8% (95% confidence interval [CI], 81.5-100%). The 10-year survival rate was 54.3% (95% CI, 35.8-82.6%). According to a Cox model with time-dependent covariates, the hazard ratio or relative risk of dying for those with an IBTR at <5.3 years after BCT relative to patients without an IBTR after BCT is 1.47 (95% CI, 1.02-2.12%; p = 0.04). The hazard ratio for those who relapse after 5.3 years is 0.59 (95% CI, 0.22-1.61%; p = 0.31). Age at randomization, original tumor size, and the presence of positive regional nodes at initial presentation were not found to be associated with decreased survival. Conclusions: There seems to be a significant association of early IBTR after BCT with decreased survival. Local control should be maximized.

  17. High-performance teams in wildlife conservation: A species reintroduction and recovery example

    NASA Astrophysics Data System (ADS)

    Clark, Tim W.; Westrum, Ron

    1989-11-01

    Reintroduction of animals to the wild to establish free-ranging viable populations is a valuable conservation tool, but ecological skills alone are not enough to ensure a successful reintroduction; also needed to do the work are effectively designed and managed programs. This article suggests general guidelines for organizing and managing reintroduction programs, reviews some basic organizational issues, and considers ways to develop high-performance teams The need to integrate reintroduction programs into their larger interorganizational context is discussed. The reintroduction program's structure must be appropriate for its function and should be properly staffed, led, and buffered from its political environment It should process information well, learn rapidly from its own mistakes, and be creative A high-performance team devotes most of its energies to solving external rather than internal problems

  18. Developing High Quality Decision-Making Discussions about Biological Conservation in a Normal Classroom Setting

    ERIC Educational Resources Information Center

    Grace, Marcus

    2009-01-01

    The conservation of biodiversity is an important socio-scientific issue that is often regarded as a precondition to sustainable development. The foundation for citizens' understanding of conservation issues can be laid down in formal school education. This research focuses on decision-making discussions about biological conservation issues among…

  19. An Evolutionarily Conserved Switch in Response to GABA Affects Development and Behavior of the Locomotor Circuit of Caenorhabditis elegans

    PubMed Central

    Han, Bingjie; Bellemer, Andrew; Koelle, Michael R.

    2015-01-01

    The neurotransmitter gamma-aminobutyric acid (GABA) is depolarizing in the developing vertebrate brain, but in older animals switches to hyperpolarizing and becomes the major inhibitory neurotransmitter in adults. We discovered a similar developmental switch in GABA response in Caenorhabditis elegans and have genetically analyzed its mechanism and function in a well-defined circuit. Worm GABA neurons innervate body wall muscles to control locomotion. Activation of GABAA receptors with their agonist muscimol in newly hatched first larval (L1) stage animals excites muscle contraction and thus is depolarizing. At the mid-L1 stage, as the GABAergic neurons rewire onto their mature muscle targets, muscimol shifts to relaxing muscles and thus has switched to hyperpolarizing. This muscimol response switch depends on chloride transporters in the muscles analogous to those that control GABA response in mammalian neurons: the chloride accumulator sodium-potassium-chloride-cotransporter-1 (NKCC-1) is required for the early depolarizing muscimol response, while the two chloride extruders potassium-chloride-cotransporter-2 (KCC-2) and anion-bicarbonate-transporter-1 (ABTS-1) are required for the later hyperpolarizing response. Using mutations that disrupt GABA signaling, we found that neural circuit development still proceeds to completion but with an ∼6-hr delay. Using optogenetic activation of GABAergic neurons, we found that endogenous GABAA signaling in early L1 animals, although presumably depolarizing, does not cause an excitatory response. Thus a developmental depolarizing-to-hyperpolarizing shift is an ancient conserved feature of GABA signaling, but existing theories for why this shift occurs appear inadequate to explain its function upon rigorous genetic analysis of a well-defined neural circuit. PMID:25644702

  20. Molecular mediators for raft-dependent endocytosis of syndecan-1, a highly conserved, multifunctional receptor.

    PubMed

    Chen, Keyang; Williams, Kevin Jon

    2013-05-17

    Endocytosis via rafts has attracted considerable recent interest, but the molecular mediators remain incompletely characterized. Here, we focused on the syndecan-1 heparan sulfate proteoglycan, a highly conserved, multifunctional receptor that we previously showed to undergo raft-dependent endocytosis upon clustering. Alanine scanning mutagenesis of three to five consecutive cytoplasmic residues at a time revealed that a conserved juxtamembrane motif, MKKK, was the only region required for efficient endocytosis after clustering. Endocytosis of clustered syndecan-1 occurs in two phases, each requiring a kinase and a corresponding cytoskeletal partner. In the initial phase, ligands trigger rapid MKKK-dependent activation of ERK and the localization of syndecan-1 into rafts. Activation of ERK drives the dissociation of syndecan-1 from α-tubulin, a molecule that may act as an anchor for syndecan-1 at the plasma membrane in the basal state. In the second phase, Src family kinases phosphorylate tyrosyl residues within the transmembrane and cytoplasmic regions of syndecan-1, a process that also requires MKKK. Tyrosine phosphorylation of syndecan-1 triggers the robust recruitment of cortactin, which we found to be an essential mediator of efficient actin-dependent endocytosis. These findings represent the first detailed characterization of the molecular events that drive endocytosis of a raft-dependent receptor and identify a novel endocytic motif, MKKK. Moreover, the results provide new tools to study syndecan function and regulation during uptake of its biologically and medically important ligands, such as HIV-1, atherogenic postprandial remnant lipoproteins, and molecules implicated in Alzheimer disease.

  1. A highly conserved SOX6 double binding site mediates SOX6 gene downregulation in erythroid cells

    PubMed Central

    Cantu', Claudio; Grande, Vito; Alborelli, Ilaria; Cassinelli, Letizia; Cantu’, Ileana; Colzani, Maria Teresa; Ierardi, Rossella; Ronzoni, Luisa; Cappellini, Maria Domenica; Ferrari, Giuliana; Ottolenghi, Sergio; Ronchi, Antonella

    2011-01-01

    The Sox6 transcription factor plays critical roles in various cell types, including erythroid cells. Sox6-deficient mice are anemic due to impaired red cell maturation and show inappropriate globin gene expression in definitive erythrocytes. To identify new Sox6 target genes in erythroid cells, we used the known repressive double Sox6 consensus within the εy-globin promoter to perform a bioinformatic genome-wide search for similar, evolutionarily conserved motifs located within genes whose expression changes during erythropoiesis. We found a highly conserved Sox6 consensus within the Sox6 human gene promoter itself. This sequence is bound by Sox6 in vitro and in vivo, and mediates transcriptional repression in transient transfections in human erythroleukemic K562 cells and in primary erythroblasts. The binding of a lentiviral transduced Sox6FLAG protein to the endogenous Sox6 promoter is accompanied, in erythroid cells, by strong downregulation of the endogenous Sox6 transcript and by decreased in vivo chromatin accessibility of this region to the PstI restriction enzyme. These observations suggest that the negative Sox6 autoregulation, mediated by the double Sox6 binding site within its own promoter, may be relevant to control the Sox6 transcriptional downregulation that we observe in human erythroid cultures and in mouse bone marrow cells in late erythroid maturation. PMID:20852263

  2. The human archain gene, ARCN1, has highly conserved homologs in rice and drosophila

    SciTech Connect

    Radice, P.; Jones, C.; Perry, H.

    1995-03-01

    A novel human gene, ARCN1, has been identified in chromosome band 11q23.3. It maps approximately 50 kb telomeric to MLL, a gene that is disrupted in a number of leukemia-associated translocation chromosomes. cDNA clones representing ARCN1 hybridize to 4-kb mRNA species present in all tissues tested. Sequencing of cDNAs suggests that at least two forms of mRNA with alternative 5 {prime} ends are present within the cell. The mRNA with the longest open reading frame gives rise to a protein of 57 kDa. Although the sequence reported is novel, remarkable similarity is observed with two predicted protein sequences from partial DNA sequences generated by rice (Oryza sativa) and fruit fly (Drosophila melanogaster) genome projects. The degree of sequence conservation is comparable to that observed for highly conserved structural proteins, such as heat shock protein HSP70, and is greater than that of {gamma}-gubulin and heat shock protein HSP60. A more distant relationship to the group of clathrin-associated proteins suggests a possible role in vesicle structure or trafficking. In view of its ancient pedigree and a potential involvement in cellular architecture, the authors propose that the ARCN1 protein be named archain. 20 refs., 5 figs.

  3. A highly conserved program of neuronal microexons is misregulated in autistic brains

    PubMed Central

    Irimia, Manuel; Weatheritt, Robert J.; Ellis, Jonathan; Parikshak, Neelroop N.; Gonatopoulos-Pournatzis, Thomas; Babor, Mariana; Quesnel-Vallières, Mathieu; Tapial, Javier; Raj, Bushra; O’Hanlon, Dave; Barrios-Rodiles, Miriam; Sternberg, Michael J.E.; Cordes, Sabine P.; Roth, Frederick P.; Wrana, Jeffrey L.; Geschwind, Daniel H.; Blencowe, Benjamin J.

    2015-01-01

    Summary Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide ‘microexons’ display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein interaction networks during neurogenesis, the misregulation of which is linked to autism. PMID:25525873

  4. A highly conserved program of neuronal microexons is misregulated in autistic brains.

    PubMed

    Irimia, Manuel; Weatheritt, Robert J; Ellis, Jonathan D; Parikshak, Neelroop N; Gonatopoulos-Pournatzis, Thomas; Babor, Mariana; Quesnel-Vallières, Mathieu; Tapial, Javier; Raj, Bushra; O'Hanlon, Dave; Barrios-Rodiles, Miriam; Sternberg, Michael J E; Cordes, Sabine P; Roth, Frederick P; Wrana, Jeffrey L; Geschwind, Daniel H; Blencowe, Benjamin J

    2014-12-18

    Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide "microexons" display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein-interaction networks during neurogenesis, the misregulation of which is linked to autism.

  5. Zero-tolerance biosecurity protects high-conservation-value island nature reserve.

    PubMed

    Scott, John K; McKirdy, Simon J; van der Merwe, Johann; Green, Roy; Burbidge, Andrew A; Pickles, Greg; Hardie, Darryl C; Morris, Keith; Kendrick, Peter G; Thomas, Melissa L; Horton, Kristin L; O'Connor, Simon M; Downs, Justin; Stoklosa, Richard; Lagdon, Russell; Marks, Barbara; Nairn, Malcolm; Mengersen, Kerrie

    2017-04-10

    Barrow Island, north-west coast of Australia, is one of the world's significant conservation areas, harboring marsupials that have become extinct or threatened on mainland Australia as well as a rich diversity of plants and animals, some endemic. Access to construct a Liquefied Natural Gas (LNG) plant, Australia's largest infrastructure development, on the island was conditional on no non-indigenous species (NIS) becoming established. We developed a comprehensive biosecurity system to protect the island's biodiversity. From 2009 to 2015 more than 0.5 million passengers and 12.2 million tonnes of freight were transported to the island under the biosecurity system, requiring 1.5 million hrs of inspections. No establishments of NIS were detected. We made four observations that will assist development of biosecurity systems. Firstly, the frequency of detections of organisms corresponded best to a mixture log-normal distribution including the high number of zero inspections and extreme values involving rare incursions. Secondly, comprehensive knowledge of the island's biota allowed estimation of false positive detections (62% native species). Thirdly, detections at the border did not predict incursions on the island. Fourthly, the workforce detected more than half post-border incursions (59%). Similar approaches can and should be implemented for all areas of significant conservation value.

  6. Energy conservation potential in low-rise, high-density housing

    SciTech Connect

    Not Available

    1980-09-01

    The result of a year's investigation into the energy conservation potential in new urban residential construction is reported. It was made by a Study Team comprised of Pratt Institute faculty, students, and outside consultants. First, a careful study was made of the energy consumption in eleven existing New York Housing Authority projects. With this background, and with the current New York State Energy Conservation Construction Code as a design parameter, the Team designed and analyzed a row house-type base building. Investigation continued with the analysis - by computer simulation - of the effects of 113 design options, or variances to the base building. The energy use characteristics were further evaluated economically under several funding and inflation-rate assumptions. Then the most cost-effective options were ranked, and four extremely efficient, innovative composite buildings hypothesized. The results of this study should prove useful in the design of urban infill housing, as well as providing a beginning for further investigation in the area of energy-efficient, low-rise, high-density housing.

  7. Highly conserved residues in the helical domain of dengue virus type 1 precursor membrane protein are involved in assembly, precursor membrane (prM) protein cleavage, and entry.

    PubMed

    Hsieh, Szu-Chia; Wu, Yi-Chieh; Zou, Gang; Nerurkar, Vivek R; Shi, Pei-Yong; Wang, Wei-Kung

    2014-11-28

    The envelope and precursor membrane (prM) proteins of dengue virus (DENV) are present on the surface of immature virions. During maturation, prM protein is cleaved by furin protease into pr peptide and membrane (M) protein. Although previous studies mainly focusing on the pr region have identified several residues important for DENV replication, the functional role of M protein, particularly the α-helical domain (MH), which is predicted to undergo a large conformational change during maturation, remains largely unknown. In this study, we investigated the role of nine highly conserved MH domain residues in the replication cycle of DENV by site-directed mutagenesis in a DENV1 prME expression construct and found that alanine substitutions introduced to four highly conserved residues at the C terminus and one at the N terminus of the MH domain greatly affect the production of both virus-like particles and replicon particles. Eight of the nine alanine mutants affected the entry of replicon particles, which correlated with the impairment in prM cleavage. Moreover, seven mutants were found to have reduced prM-E interaction at low pH, which may inhibit the formation of smooth immature particles and exposure of prM cleavage site during maturation, thus contributing to inefficient prM cleavage. Taken together, these results are the first report showing that highly conserved MH domain residues, located at 20-38 amino acids downstream from the prM cleavage site, can modulate the prM cleavage, maturation of particles, and virus entry. The highly conserved nature of these residues suggests potential targets of antiviral strategy.

  8. An assessment of high carbon stock and high conservation value approaches to sustainable oil palm cultivation in Gabon

    NASA Astrophysics Data System (ADS)

    Austin, Kemen G.; Lee, Michelle E.; Clark, Connie; Forester, Brenna R.; Urban, Dean L.; White, Lee; Kasibhatla, Prasad S.; Poulsen, John R.

    2017-01-01

    Industrial-scale oil palm cultivation is rapidly expanding in Gabon, where it has the potential to drive economic growth, but also threatens forest, biodiversity and carbon resources. The Gabonese government is promoting an ambitious agricultural expansion strategy, while simultaneously committing to minimize negative environmental impacts of oil palm agriculture. This study estimates the extent and location of suitable land for oil palm cultivation in Gabon, based on an analysis of recent trends in plantation permitting. We use the resulting suitability map to evaluate two proposed approaches to minimizing negative environmental impacts: a High Carbon Stock (HCS) approach, which emphasizes forest protection and climate change mitigation, and a High Conservation Value (HCV) approach, which focuses on safeguarding biodiversity and ecosystems. We quantify the forest area, carbon stock, and biodiversity resources protected under each approach, using newly developed maps of priority species distributions and forest biomass for Gabon. We find 2.7–3.9 Mha of suitable or moderately suitable land that avoid HCS areas, 4.4 million hectares (Mha) that avoid HCV areas, and 1.2–1.7 Mha that avoid both. This suggests that Gabon’s oil palm production target could likely be met without compromising important ecosystem services, if appropriate safeguards are put in place. Our analysis improves understanding of suitability for oil palm in Gabon, determines how conservation strategies align with national targets for oil palm production, and informs national land use planning.

  9. The first complete plastid genomes of Melastomataceae are highly structurally conserved

    PubMed Central

    Neubig, Kurt M.; Majure, Lucas C.

    2016-01-01

    Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be

  10. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

    PubMed

    Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

    2014-04-01

    Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.

  11. Factors Affecting Computer Anxiety in High School Computer Science Students.

    ERIC Educational Resources Information Center

    Hayek, Linda M.; Stephens, Larry

    1989-01-01

    Examines factors related to computer anxiety measured by the Computer Anxiety Index (CAIN). Achievement in two programing courses was inversely related to computer anxiety. Students who had a home computer and had computer experience before high school had lower computer anxiety than those who had not. Lists 14 references. (YP)

  12. School-Related Factors Affecting High School Seniors' Methamphetamine Use

    ERIC Educational Resources Information Center

    Stanley, Jarrod M.; Lo, Celia C.

    2009-01-01

    Data from the 2005 Monitoring the Future survey were used to examine relationships between school-related factors and high school seniors' lifetime methamphetamine use. The study applied logistic regression techniques to evaluate effects of social bonding variables and social learning variables on likelihood of lifetime methamphetamine use. The…

  13. Affective, Cognitive, and Behavioral Differences Between High and Low Procrastinators.

    ERIC Educational Resources Information Center

    Rothblum, Esther D.; And Others

    1986-01-01

    Examined the relation between procrastination and academically related trait measures. Self-reported procrastination was positively correlated with delay in taking self-paced quizzes and negatively correlated with grade point average. High procrastinators, particularly women, were significantly more likely to report more test anxiety and to…

  14. Factors Affecting the Benefits of High-Frequency Amplification

    ERIC Educational Resources Information Center

    Horwitz, Amy R.; Ahlstrom, Jayne B.; Dubno, Judy R.

    2008-01-01

    Purpose: This study was designed to determine the extent to which high-frequency amplification helped or hindered speech recognition as a function of hearing loss, gain-frequency response, and background noise. Method: Speech recognition was measured monaurally under headphones for nonsense syllables low-pass filtered in one-third-octave steps…

  15. How High Frequency Trading Affects a Market Index

    PubMed Central

    Kenett, Dror Y.; Ben-Jacob, Eshel; Stanley, H. Eugene; gur-Gershgoren, Gitit

    2013-01-01

    The relationship between a market index and its constituent stocks is complicated. While an index is a weighted average of its constituent stocks, when the investigated time scale is one day or longer the index has been found to have a stronger effect on the stocks than vice versa. We explore how this interaction changes in short time scales using high frequency data. Using a correlation-based analysis approach, we find that in short time scales stocks have a stronger influence on the index. These findings have implications for high frequency trading and suggest that the price of an index should be published on shorter time scales, as close as possible to those of the actual transaction time scale. PMID:23817553

  16. Finite element solution for energy conservation using a highly stable explicit integration algorithm

    NASA Technical Reports Server (NTRS)

    Baker, A. J.; Manhardt, P. D.

    1972-01-01

    Theoretical derivation of a finite element solution algorithm for the transient energy conservation equation in multidimensional, stationary multi-media continua with irregular solution domain closure is considered. The complete finite element matrix forms for arbitrarily irregular discretizations are established, using natural coordinate function representations. The algorithm is embodied into a user-oriented computer program (COMOC) which obtains transient temperature distributions at the node points of the finite element discretization using a highly stable explicit integration procedure with automatic error control features. The finite element algorithm is shown to posses convergence with discretization for a transient sample problem. The condensed form for the specific heat element matrix is shown to be preferable to the consistent form. Computed results for diverse problems illustrate the versatility of COMOC, and easily prepared output subroutines are shown to allow quick engineering assessment of solution behavior.

  17. Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates

    PubMed Central

    Gershgorin, Roman A.; Gorbunov, Konstantin Yu.; Zverkov, Oleg A.; Rubanov, Lev I.; Seliverstov, Alexandr V.; Lyubetsky, Vassily A.

    2017-01-01

    Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome. PMID:28264444

  18. A New DNA Binding Protein Highly Conserved in Diverse Crenarchaeal Viruses

    SciTech Connect

    Larson, E.T.; Eilers, B.J.; Reiter, D.; Ortmann, A.C.; Young, M.J.; Lawrence, C.M.; /Montana State U. /Tubingen U.

    2007-07-09

    Sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. Its 37 open reading frames (ORFs) generally lack sequence similarity to other genes. One exception, however, is ORF B116. While its function is unknown, orthologs are found in three additional crenarchaeal viral families. Due to the central importance of this protein family to crenarchaeal viruses, we have undertaken structural and biochemical studies of B116. The structure reveals a previously unobserved fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel. Highly conserved loops rise above the surface of the saddle-shaped protein and suggest an interaction with the major groove of DNA. The predicted B116-DNA interaction is confirmed by electrophoretic mobility shift assays.

  19. Data on electrical energy conservation using high efficiency motors for the confidence bounds using statistical techniques.

    PubMed

    Shaikh, Muhammad Mujtaba; Memon, Abdul Jabbar; Hussain, Manzoor

    2016-09-01

    In this article, we describe details of the data used in the research paper "Confidence bounds for energy conservation in electric motors: An economical solution using statistical techniques" [1]. The data presented in this paper is intended to show benefits of high efficiency electric motors over the standard efficiency motors of similar rating in the industrial sector of Pakistan. We explain how the data was collected and then processed by means of formulas to show cost effectiveness of energy efficient motors in terms of three important parameters: annual energy saving, cost saving and payback periods. This data can be further used to construct confidence bounds for the parameters using statistical techniques as described in [1].

  20. Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora

    PubMed Central

    2011-01-01

    Background Cytasters (cytoplasmic asters) are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes. Presentation of the hypothesis The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria. Testing the hypothesis So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of cytasters. Implications of

  1. CpG methylation differences between neurons and glia are highly conserved from mouse to human.

    PubMed

    Kessler, Noah J; Van Baak, Timothy E; Baker, Maria S; Laritsky, Eleonora; Coarfa, Cristian; Waterland, Robert A

    2016-01-15

    Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study used genome-wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type-specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non-CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type-specific differences in CpG methylation, with a genome-wide tendency for neuronal CpG-hypermethylation punctuated by regions of glia-specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type-specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene-associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome-wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease.

  2. MLST analysis reveals a highly conserved core genome among poultry isolates of Clostridium septicum.

    PubMed

    Neumann, Anthony P; Rehberger, Thomas G

    2009-06-01

    Clostridium septicum is a highly virulent, anaerobic bacterium capable of establishing necrotizing tissue infections and forming heat resistant endospores. Disease is primarily facilitated by secretion of numerous toxic products including a lethal pore-forming cytolysin. Spontaneously occurring clostridial myonecrosis involving C. septicum has recently reemerged as a concern for many poultry producers. However, despite its increasing prevalence, the epidemiology of infection and population structure of C. septicum remains largely unknown. In this study a multilocus sequence typing (MLST) approach was utilized to examine evolutionary relationships within a diverse collection of C. septicum isolates recovered from poultry flocks experiencing episodes of gangrenous dermatitis. The 109 isolates examined represented 42 turkey flocks and 24 different flocks of broiler chickens as well as C. septicum type strain, ATCC 12464. Isolates were recovered predominantly from gangrenous lesions although isolates from livers, gastrointestinal tracts, spleens and blood were included. The loci analyzed were csa, the major lethal toxin produced by C. septicum, and the housekeeping genes gyrA, groEL, dnaK, recA, tpi, ddl, colA and glpK. These loci were included in part because of their previous use in MLST analysis of Clostridium perfringens and Clostridium difficile. Results indicated a high level of conservation present within these housekeeping gene fragments when compared to what has been previously reported for the aforementioned clostridia. Of the 5352 bp of sequence data examined for each isolate, 99.7% (5335/5352) was absolutely conserved among the 109 isolates. Only one of the ten unique sequence types, or allelic profiles, identified among the isolates was recovered from both turkeys and broiler chickens suggesting some host species preference. Phylogenetic analyses identified two unique clusters, or clonal complexes, among these poultry isolates which may have important

  3. Target validation of highly conserved Amblyomma americanum tick saliva serine protease inhibitor 19.

    PubMed

    Kim, Tae K; Radulovic, Zeljko; Mulenga, Albert

    2016-04-01

    Amblyomma americanum tick serine protease inhibitor (serpin, AAS) 19, is a highly conserved protein that is characterized by its functional domain being 100% conserved across tick species. We also reported that AAS19 was an immunogenic tick saliva protein with anti-haemostatic functions and an inhibitor of trypsin-like proteases including five of the eight serine protease factors in the blood clotting cascade. In this study the goal was to validate the importance of AAS19 in A. americanum tick physiology, assess immunogenicity and investigate tick vaccine efficacy of yeast-expressed recombinant (r) AAS19. We confirm that AAS19 is important to A. americanum fitness and blood meal feeding. AAS19 mRNA disruption by RNAi silencing caused ticks to obtain blood meals that were 50% smaller than controls, and treated ticks being morphologically deformed with 100% of the deformed ticks dying in incubation. We show that rAAS19 is highly immunogenic in that two 500 μg inoculations mixed with TiterMax Gold adjuvant provoked antibody titers of more than 1:320,000 that specifically reacted with native AAS19 in unfed and partially fed tick tissue. Since AAS19 is injected into animals during tick feeding, we challenge infested immunized rabbits twice to test if tick infestations of immunized rabbits could act as booster. While in the first infestation significantly smaller tick blood meals were observed on one of the two immunized rabbits, smaller blood meals were observed on both rabbits, but 60% of ticks that engorged on immunized rabbits in the second infestation failed to lay eggs. It is notable that ticks fed faster on immunized animals despite obtaining smaller blood meals. We conclude that rAAS19 is a potential component of cocktail tick vaccine.

  4. The Evolutionarily Conserved Protein PHOTOSYNTHESIS AFFECTED MUTANT71 Is Required for Efficient Manganese Uptake at the Thylakoid Membrane in Arabidopsis

    PubMed Central

    Steinberger, Iris; Herdean, Andrei; Gandini, Chiara; Labs, Mathias; Flügge, Ulf-Ingo; Geimer, Stefan; Schmidt, Sidsel Birkelund; Husted, Søren; Spetea, Cornelia; Leister, Dario

    2016-01-01

    In plants, algae, and cyanobacteria, photosystem II (PSII) catalyzes the light-driven oxidation of water. The oxygen-evolving complex of PSII is a Mn4CaO5 cluster embedded in a well-defined protein environment in the thylakoid membrane. However, transport of manganese and calcium into the thylakoid lumen remains poorly understood. Here, we show that Arabidopsis thaliana PHOTOSYNTHESIS AFFECTED MUTANT71 (PAM71) is an integral thylakoid membrane protein involved in Mn2+ and Ca2+ homeostasis in chloroplasts. This protein is required for normal operation of the oxygen-evolving complex (as evidenced by oxygen evolution rates) and for manganese incorporation. Manganese binding to PSII was severely reduced in pam71 thylakoids, particularly in PSII supercomplexes. In cation partitioning assays with intact chloroplasts, Mn2+ and Ca2+ ions were differently sequestered in pam71, with Ca2+ enriched in pam71 thylakoids relative to the wild type. The changes in Ca2+ homeostasis were accompanied by an increased contribution of the transmembrane electrical potential to the proton motive force across the thylakoid membrane. PSII activity in pam71 plants and the corresponding Chlamydomonas reinhardtii mutant cgld1 was restored by supplementation with Mn2+, but not Ca2+. Furthermore, PAM71 suppressed the Mn2+-sensitive phenotype of the yeast mutant Δpmr1. Therefore, PAM71 presumably functions in Mn2+ uptake into thylakoids to ensure optimal PSII performance. PMID:27020959

  5. Butterflies of the high-altitude Atacama Desert: habitat use and conservation

    PubMed Central

    Despland, Emma

    2014-01-01

    The butterfly fauna of the high-altitude desert of Northern Chile, though depauperate, shows high endemism, is poorly known and is of considerable conservation concern. This study surveys butterflies along the Andean slope between 2400 and 5000 m asl (prepuna, puna and Andean steppe habitats) as well as in high and low-altitude wetlands and in the neoriparian vegetation of agricultural sites. We also include historical sightings from museum records. We compare abundances between altitudes, between natural and impacted sites, as well as between two sampling years with different precipitation regimes. The results confirm high altitudinal turnover and show greatest similarity between wetland and slope faunas at similar altitudes. Results also underscore vulnerability to weather fluctuations, particularly in the more arid low-altitude sites, where abundances were much lower in the low precipitation sampling season and several species were not observed at all. Finally, we show that some species have shifted to the neoriparian vegetation of the agricultural landscape, whereas others were only observed in less impacted habitats dominated by native plants. These results suggest that acclimation to novel habitats depends on larval host plant use. The traditional agricultural environment can provide habitat for many, but not all, native butterfly species, but an estimation of the value of these habitats requires better understanding of butterfly life history strategies and relationships with host plants. PMID:25309583

  6. Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes

    PubMed Central

    Shuey, John A.

    2013-01-01

    Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost. PMID:26462535

  7. Wind resource quality affected by high levels of renewables

    DOE PAGES

    Diakov, Victor

    2015-06-17

    For solar photovoltaic (PV) and wind resources, the capacity factor is an important parameter describing the quality of the resource. As the share of variable renewable resources (such as PV and wind) on the electric system is increasing, so does curtailment (and the fraction of time when it cannot be avoided). At high levels of renewable generation, curtailments effectively change the practical measure of resource quality from capacity factor to the incremental capacity factor. The latter accounts only for generation during hours of no curtailment and is directly connected with the marginal capital cost of renewable generators for a givenmore » level of renewable generation during the year. The Western U.S. wind generation is analyzed hourly for a system with 75% of annual generation from wind, and it is found that the value for the system of resources with equal capacity factors can vary by a factor of 2, which highlights the importance of using the incremental capacity factor instead. Finally, the effect is expected to be more pronounced in smaller geographic areas (or when transmission limitations imposed) and less pronounced at lower levels of renewable energy in the system with less curtailment.« less

  8. Wind resource quality affected by high levels of renewables

    SciTech Connect

    Diakov, Victor

    2015-06-17

    For solar photovoltaic (PV) and wind resources, the capacity factor is an important parameter describing the quality of the resource. As the share of variable renewable resources (such as PV and wind) on the electric system is increasing, so does curtailment (and the fraction of time when it cannot be avoided). At high levels of renewable generation, curtailments effectively change the practical measure of resource quality from capacity factor to the incremental capacity factor. The latter accounts only for generation during hours of no curtailment and is directly connected with the marginal capital cost of renewable generators for a given level of renewable generation during the year. The Western U.S. wind generation is analyzed hourly for a system with 75% of annual generation from wind, and it is found that the value for the system of resources with equal capacity factors can vary by a factor of 2, which highlights the importance of using the incremental capacity factor instead. Finally, the effect is expected to be more pronounced in smaller geographic areas (or when transmission limitations imposed) and less pronounced at lower levels of renewable energy in the system with less curtailment.

  9. Factors affecting the erosion of jets penetrating high explosive

    SciTech Connect

    Haselman, L.C.; Winer, K.A.

    1995-05-01

    It has been observed in various experiments with shaped charge jets penetrating high explosives that the erosion of the jet can be considerably greater than that expected from analytical theory or from two dimensional hydrodynamic computer simulations. In a previous study, we found that the initial penetration of the jet agreed with theory, and that the erosion of the jet happened subsequent to the initial penetration. This additional erosion can be the dominant factor in the total length of jet that is eroded. We also found that in one experiment the jet did not show any excess erosion and that the penetration could be predicted from theory. We also found a rough correlation of the amount of excess erosion with the diameter of the jet, with larger jet diameters giving less erosion. A problem with previous experiments was that a wide variety of shaped charges, target shapes, and target thicknesses were used. This made it difficult to isolate the effect of a particular parameter. For the current study we chose to isolate the effects of scale and target thickness. For this purpose we used well characterized jets and carefully chosen targets. We also did computer calculations to help elucidate the underlying mechanisms of the excess erosion.

  10. A highly conserved tyrosine of Tim-3 is phosphorylated upon stimulation by its ligand galectin-9

    SciTech Connect

    Weyer, Philipp S. van de; Muehlfeit, Michael; Klose, Christoph; Bonventre, Joseph V.; Walz, Gerd; Kuehn, E. Wolfgang . E-mail: wolfgang.kuehn@uniklinik-freiburg.de

    2006-12-15

    Tim-3 is a member of the TIM family of proteins (T-cell immunoglobulin mucin) involved in the regulation of CD4+ T-cells. Tim-3 is a T{sub H}1-specific type 1 membrane protein and regulates T{sub H}1 proliferation and the development of tolerance. Binding of galectin-9 to the extracellular domain of Tim-3 results in apoptosis of T{sub H}1 cells, but the intracellular pathways involved in the regulatory function of Tim-3 are unknown. Unlike Tim-1, which is expressed in renal epithelia and cancer, Tim-3 has not been described in cells other than neuronal or T-cells. Using RT-PCR we demonstrate that Tim-3 is expressed in malignant and non-malignant epithelial tissues. We have cloned Tim-3 from an immortalized liver cell carcinoma line and identified a highly conserved tyrosine in the intracellular tail of Tim-3 (Y265). We demonstrate that Y265 is specifically phosphorylated in vivo by the interleukin inducible T cell kinase (ITK), a kinase which is located in close proximity of the TIM genes on the allergy susceptibility locus 5q33.3. Stimulation of Tim-3 by its ligand galectin-9 results in increased phosphorylation of Y265, suggesting that this tyrosine residue plays an important role in downstream signalling events regulating T-cell fate. Given the role of TIM proteins in autoimmunity and cancer, the conserved SH2 binding domain surrounding Y265 could represent a possible target site for pharmacological intervention.

  11. Efficient construction of high-resolution TVD conservative schemes for equations with source terms: application to shallow water flows

    NASA Astrophysics Data System (ADS)

    Burguete, J.; García-Navarro, P.

    2001-09-01

    High-resolution total variation diminishing (TVD) schemes are widely used for the numerical approximation of hyperbolic conservation laws. Their extension to equations with source terms involving spatial derivatives is not obvious. In this work, efficient ways of constructing conservative schemes from the conservative, non-conservative or characteristic form of the equations are described in detail. An upwind, as opposed to a pointwise, treatment of the source terms is adopted here, and a new technique is proposed in which source terms are included in the flux limiter functions to get a complete second-order compact scheme. A new correction to fix the entropy problem is also presented and a robust treatment of the boundary conditions according to the discretization used is stated. Copyright

  12. A Study on Students' Affective Factors in Junior High School English Teaching

    ERIC Educational Resources Information Center

    Zhu, Biyi; Zhou, Yaping

    2012-01-01

    Affect is considered as aspects of emotion, feeling, mood or attitude which condition behaviors in second language acquisition. Positive affect is good for studying while negative affect will inevitably hinder learners' learning process. As we know, students in junior high school are special groups as they are experiencing great changes both in…

  13. Highly conserved serine residue 40 in HIV-1 p6 regulates capsid processing and virus core assembly

    PubMed Central

    2011-01-01

    Background The HIV-1 p6 Gag protein regulates the final abscission step of nascent virions from the cell membrane by the action of two late assembly (L-) domains. Although p6 is located within one of the most polymorphic regions of the HIV-1 gag gene, the 52 amino acid peptide binds at least to two cellular budding factors (Tsg101 and ALIX), is a substrate for phosphorylation, ubiquitination, and sumoylation, and mediates the incorporation of the HIV-1 accessory protein Vpr into viral particles. As expected, known functional domains mostly overlap with several conserved residues in p6. In this study, we investigated the importance of the highly conserved serine residue at position 40, which until now has not been assigned to any known function of p6. Results Consistently with previous data, we found that mutation of Ser-40 has no effect on ALIX mediated rescue of HIV-1 L-domain mutants. However, the only feasible S40F mutation that preserves the overlapping pol open reading frame (ORF) reduces virus replication in T-cell lines and in human lymphocyte tissue cultivated ex vivo. Most intriguingly, L-domain mediated virus release is not dependent on the integrity of Ser-40. However, the S40F mutation significantly reduces the specific infectivity of released virions. Further, it was observed that mutation of Ser-40 selectively interferes with the cleavage between capsid (CA) and the spacer peptide SP1 in Gag, without affecting cleavage of other Gag products. This deficiency in processing of CA, in consequence, led to an irregular morphology of the virus core and the formation of an electron dense extra core structure. Moreover, the defects induced by the S40F mutation in p6 can be rescued by the A1V mutation in SP1 that generally enhances processing of the CA-SP1 cleavage site. Conclusions Overall, these data support a so far unrecognized function of p6 mediated by Ser-40 that occurs independently of the L-domain function, but selectively affects CA maturation and

  14. High Potential for Using DNA from Ancient Herring Bones to Inform Modern Fisheries Management and Conservation

    PubMed Central

    Speller, Camilla F.; Hauser, Lorenz; Lepofsky, Dana; Moore, Jason; Rodrigues, Antonia T.; Moss, Madonna L.; McKechnie, Iain; Yang, Dongya Y.

    2012-01-01

    Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much

  15. A highly conserved baculovirus gene p48 (ac103) is essential for BV production and ODV envelopment.

    PubMed

    Yuan, Meijin; Wu, Wenbi; Liu, Chao; Wang, Yanjie; Hu, Zhaoyang; Yang, Kai; Pang, Yi

    2008-09-15

    Autographa californica multiple nucleopolyhedrovirus (AcMNPV) p48 (ac103) is a highly conserved baculovirus gene of unknown function. In the present study, we generated a knockout of the p48 gene in an AcMNPV bacmid and investigated the role of P48 in baculovirus life cycle. The p48-null Bacmid vAc(P48-KO-PH-GFP) was unable to propagate in cell culture, while a 'repair' Bacmid vAc(P48-REP-PH-GFP) was able to replicate in a manner similar to a wild-type Bacmid vAc(PH-GFP). Titration assays and Western blotting confirmed that vAc(P48-KO-PH-GFP) was unable to produce budded viruses (BVs). qPCR analysis showed that p48 deletion did not affect viral DNA replication. Electron microscopy indicated that P48 was required for nucleocapsid envelopment to form occlusion-derived viruses (ODVs) and their subsequent occlusion. Confocal analysis showed that P48 prominently condensed in the centre of the nucleus. Our results demonstrate that P48 plays an essential role in BV production and ODV envelopment in the AcMNPV life cycle.

  16. One to rule them all: A highly conserved motif in mariner transposase controls multiple steps of transposition.

    PubMed

    Bouuaert, Corentin Claeys; Tellier, Michael; Chalmers, Ronald

    2014-01-01

    The development of transposon-based genome manipulation tools can benefit greatly from understanding transposons' inherent regulatory mechanisms. The Tc1-mariner transposons, which are being widely used in biotechnological applications, are subject to a self-inhibitory mechanism whereby increasing transposase expression beyond a certain point decreases the rate of transposition. In a recent paper, Liu and Chalmers performed saturating mutagenesis on the highly conserved WVPHEL motif in the mariner-family transposase from the Hsmar1 element. Curiously, they found that the majority of all possible single mutations were hyperactive. Biochemical characterizations of the mutants revealed that the hyperactivity is due to a defect in communication between transposase subunits, which normally regulates transposition by reducing the rate of synapsis. This provides important clues for improving transposon-based tools. However, some WVPHEL mutants also showed features that would be undesirable for most biotechnological applications: they showed uncontrolled DNA cleavage activities and defects in the coordination of cleavage between the two transposon ends. The study illustrates how the knowledge of inhibitory mechanisms can help improve transposon tools but also highlights an important challenge, which is to specifically target a regulatory mechanism without affecting other important functions of the transposase.

  17. A highly conserved baculovirus gene p48 (ac103) is essential for BV production and ODV envelopment

    SciTech Connect

    Yuan Meijin; Wu Wenbi; Liu Chao; Wang Yanjie; Hu Zhaoyang; Yang Kai Pang Yi

    2008-09-15

    Autographa californica multiple nucleopolyhedrovirus (AcMNPV) p48 (ac103) is a highly conserved baculovirus gene of unknown function. In the present study, we generated a knockout of the p48 gene in an AcMNPV bacmid and investigated the role of P48 in baculovirus life cycle. The p48-null Bacmid vAc{sup P48-KO-PH-GFP} was unable to propagate in cell culture, while a 'repair' Bacmid vAc{sup P48-REP-PH-GFP} was able to replicate in a manner similar to a wild-type Bacmid vAc{sup PH-GFP}. Titration assays and Western blotting confirmed that vAc{sup P48-KO-PH-GFP} was unable to produce budded viruses (BVs). qPCR analysis showed that p48 deletion did not affect viral DNA replication. Electron microscopy indicated that P48 was required for nucleocapsid envelopment to form occlusion-derived viruses (ODVs) and their subsequent occlusion. Confocal analysis showed that P48 prominently condensed in the centre of the nucleus. Our results demonstrate that P48 plays an essential role in BV production and ODV envelopment in the AcMNPV life cycle.

  18. A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding.

    PubMed

    Zhou, Zhanping; Zhao, Shuangzhi; Liu, Yang; Chang, Zhengying; Ma, Yanhe; Li, Jian; Song, Jiangning

    2016-11-01

    The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography analysis and site-direct mutagenesis of the chitosanase from Bacillus sp. K17 identified the important residues involved in the catalytic interaction and substrate binding. However, despite progress in understanding the catalytic mechanism of the chitosanase from the family GH8, the functional roles of some residues that are highly conserved throughout this family have not been fully elucidated. This study focused on one of these residues, i.e., the aspartic acid residue at position 318. We found that apart from asparagine, mutation of Asp318 resulted in significant loss of enzyme activity. In-depth investigations showed that mutation of this residue not only impaired enzymatic activity but also affected substrate binding. Taken together, our results showed that Asp318 plays an important role in CsnTS activity.

  19. The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli

    SciTech Connect

    Eraso, Jesus M.; Markillie, Lye Meng; Mitchell, Hugh D.; Taylor, Ronald C.; Orr, Galya; Margolin, William

    2014-05-05

    The mraZ and mraW genes are highly conserved in bacteria, both in sequence and location at the head of the division and cell wall (dcw) gene cluster. Although MraZ has structural similarity to the AbrB transition state regulator and the MazE antitoxin, and MraW is known to methylate ribosomal RNA, mraZ and mraW null mutants have no detectable growth phenotype in any species tested to date, hampering progress in understanding their physiological role. Here we show that overproduction of Escherichia coli MraZ perturbs cell division and the cell envelope, is more lethal at high levels or in minimal growth medium, and that MraW antagonizes these effects. MraZGFP localizes to the nucleoid, suggesting that it binds DNA. Indeed, purified MraZ directly binds a region upstream from its own promoter containing three direct repeats to regulate its own expression and that of downstream cell division and cell wall genes. MraZ-LacZ fusions are repressed by excess MraZ but not when DNA binding by MraZ is inhibited. RNAseq analysis indicates that MraZ is a global transcriptional regulator with numerous targets in addition to dcw genes. One of these targets, mioC, is directly bound by MraZ in a region with three direct repeats.

  20. A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability

    PubMed Central

    Ding, Shilei; Tolbert, William D.; Prévost, Jérémie; Pacheco, Beatriz; Coutu, Mathieu; Debbeche, Olfa; Xiang, Shi-Hua

    2016-01-01

    ABSTRACT Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656–667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549–2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697–709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127–2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the

  1. Streamlining and core genome conservation among highly divergent members of the SAR11 clade.

    PubMed

    Grote, Jana; Thrash, J Cameron; Huggett, Megan J; Landry, Zachary C; Carini, Paul; Giovannoni, Stephen J; Rappé, Michael S

    2012-01-01

    SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world's oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade's origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade. IMPORTANCE The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon

  2. Bioproduction and optimization of rosmarinic acid production in Solenostemon scutellarioides through media manipulation and conservation of high yielding clone via encapsulation.

    PubMed

    Sahu, Ranabir; Dewanjee, Saikat; Gangopadhyay, Moumita

    2013-09-01

    The present study describes the role of different exogenous phytohormones, polyamines and sucrose on growth and rosmarinic acid (RA) production in whole plant culture of Solenostemon scutellarioides. It was further aimed to conserve elite clones via synthetic seed technology. S. scutellarioides was treated either singly or in combination with different phytohormones. Cultures incubated with NAA (0.5 mg L(-1)) yielded the highest RA accumulation (g(-1FW)), but negatively affected the growth. So, overall RA content was insignificant. Cultures incubated with IBA, BAP and GA3 at low concentration significantly improved growth and RA bioaccumulation. In the combinatorial study, IBA+BAP+GA3 (0.5 mg L(-1) each) was found optimum for plant biomass and RA production (65.2% improvement of total RA). Amongst polyamines, putrescine (1 mg L(-1)) exhibited 20.4% improvement of total RA content. The intracellular RA accumulation (g(-1FW)) was significantly higher between 5 and 7% of sucrose concentrations. However, the total increase in RA content was inhibited due to deterioration of the culture with increasing sucrose concentration. Based on the effect of different treatments on growth and RA accumulation, a high yielding and stable plant line was selected for conservation via alginate encapsulation. Uniform shaped alginate coated synthetic seeds conserved up to 6 months exhibited high regeneration potential and RA content.

  3. Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).

    PubMed

    Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong

    2006-08-01

    Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

  4. High Throughput Sequencing of T Cell Antigen Receptors Reveals a Conserved TCR Repertoire.

    PubMed

    Hou, Xianliang; Lu, Chong; Chen, Sisi; Xie, Qian; Cui, Guangying; Chen, Jianing; Chen, Zhi; Wu, Zhongwen; Ding, Yulong; Ye, Ping; Dai, Yong; Diao, Hongyan

    2016-03-01

    The T-cell receptor (TCR) repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next-generation sequencing has become a powerful tool for deep TCR profiling. Herein, we used this technology to study the repertoire features of TCR beta chain in the blood of healthy individuals.Peripheral blood samples were collected from 10 healthy donors. T cells were isolated with anti-human CD3 magnetic beads according to the manufacturer's protocol. We then combined multiplex-PCR, Illumina sequencing, and IMGT/High V-QUEST to analyze the characteristics and polymorphisms of the TCR.Most of the individual T cell clones were present at very low frequencies, suggesting that they had not undergone clonal expansion. The usage frequencies of the TCR beta variable, beta joining, and beta diversity gene segments were similar among T cells from different individuals. Notably, the usage frequency of individual nucleotides and amino acids within complementarity-determining region (CDR3) intervals was remarkably consistent between individuals. Moreover, our data show that terminal deoxynucleotidyl transferase activity was biased toward the insertion of G (31.92%) and C (27.14%) over A (21.82%) and T (19.12%) nucleotides.Some conserved features could be observed in the composition of CDR3, which may inform future studies of human TCR gene recombination.

  5. High Throughput Sequencing of T Cell Antigen Receptors Reveals a Conserved TCR Repertoire

    PubMed Central

    Hou, Xianliang; Lu, Chong; Chen, Sisi; Xie, Qian; Cui, Guangying; Chen, Jianing; Chen, Zhi; Wu, Zhongwen; Ding, Yulong; Ye, Ping; Dai, Yong; Diao, Hongyan

    2016-01-01

    Abstract The T-cell receptor (TCR) repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next-generation sequencing has become a powerful tool for deep TCR profiling. Herein, we used this technology to study the repertoire features of TCR beta chain in the blood of healthy individuals. Peripheral blood samples were collected from 10 healthy donors. T cells were isolated with anti-human CD3 magnetic beads according to the manufacturer's protocol. We then combined multiplex-PCR, Illumina sequencing, and IMGT/High V-QUEST to analyze the characteristics and polymorphisms of the TCR. Most of the individual T cell clones were present at very low frequencies, suggesting that they had not undergone clonal expansion. The usage frequencies of the TCR beta variable, beta joining, and beta diversity gene segments were similar among T cells from different individuals. Notably, the usage frequency of individual nucleotides and amino acids within complementarity-determining region (CDR3) intervals was remarkably consistent between individuals. Moreover, our data show that terminal deoxynucleotidyl transferase activity was biased toward the insertion of G (31.92%) and C (27.14%) over A (21.82%) and T (19.12%) nucleotides. Some conserved features could be observed in the composition of CDR3, which may inform future studies of human TCR gene recombination. PMID:26962778

  6. The Program of Sex Chromosome Pairing in Meiosis Is Highly Conserved Across Marsupial Species

    PubMed Central

    Page, Jesús; Berríos, Soledad; Parra, María Teresa; Viera, Alberto; Suja, José Ángel; Prieto, Ignacio; Barbero, José Luis; Rufas, Julio S.; Fernández-Donoso, Raúl

    2005-01-01

    Marsupials present a series of genetic and chromosomal features that are highly conserved in very distant species. One of these features is the absence of a homologous region between X and Y chromosomes. According to this genetic differentiation, sex chromosomes do not synapse during the first meiotic prophase in males, and a special structure, the dense plate, maintains sex chromosome association. In this report we present results on the process of meiotic sex chromosome pairing obtained from three different species, Thylamys elegans, Dromiciops gliroides, and Rhyncholestes raphanurus, representing the three orders of American marsupials. We have investigated the relationships between the axial structures organized along sex chromosomes and the formation of the dense plate. We found that in the three species the dense plate arises as a modification of sex chromosomal axial elements, but without the involvement of other meiotic axial structures, such as the cohesin axes. Considering the phylogenetic relationships among the marsupials studied here, our data reinforce the idea that the dense plate emerged early in marsupial evolution as an efficient mechanism to ensure the association of the nonhomologous sex chromosomes. This situation could have influenced the further evolution of sex chromosomes in marsupials. PMID:15802509

  7. Mammalian ets-1 and ets-2 genes encode highly conserved proteins.

    PubMed Central

    Watson, D K; McWilliams, M J; Lapis, P; Lautenberger, J A; Schweinfest, C W; Papas, T S

    1988-01-01

    Cellular ets sequences homologous to v-ets of the avian leukemia virus E26 are highly conserved. In mammals the ets sequences are dispersed on two separate chromosomal loci, called ets-1 and ets-2. To determine the structure of these two genes and identify the open reading frames that code for the putative proteins, we have sequenced human ets-1 cDNAs and ets-2 cDNA clones obtained from both human and mouse. The human ETS1 gene is capable of encoding a protein of 441 amino acids. This protein is greater than 95% identical to the chicken c-ets-1 gene product. Thus, the human ETS1 gene is homologous to the chicken c-ets-1 gene, the protooncogene that the E26 virus transduced. Human and mouse ets-2 cDNA clones are closely related and contain open reading frames capable of encoding proteins of 469 and 468 residues, respectively. Direct comparison of these data with previously published findings indicates that ets is a family of genes whose members share distinct domains. PMID:2847145

  8. High-order conservative reconstruction schemes for finite volume methods in cylindrical and spherical coordinates

    NASA Astrophysics Data System (ADS)

    Mignone, A.

    2014-08-01

    High-order reconstruction schemes for the solution of hyperbolic conservation laws in orthogonal curvilinear coordinates are revised in the finite volume approach. The formulation employs a piecewise polynomial approximation to the zone-average values to reconstruct left and right interface states from within a computational zone to arbitrary order of accuracy by inverting a Vandermonde-like linear system of equations with spatially varying coefficients. The approach is general and can be used on uniform and non-uniform meshes although explicit expressions are derived for polynomials from second to fifth degree in cylindrical and spherical geometries with uniform grid spacing. It is shown that, in regions of large curvature, the resulting expressions differ considerably from their Cartesian counterparts and that the lack of such corrections can severely degrade the accuracy of the solution close to the coordinate origin. Limiting techniques and monotonicity constraints are revised for conventional reconstruction schemes, namely, the piecewise linear method (PLM), third-order weighted essentially non-oscillatory (WENO) scheme and the piecewise parabolic method (PPM). The performance of the improved reconstruction schemes is investigated in a number of selected numerical benchmarks involving the solution of both scalar and systems of nonlinear equations (such as the equations of gas dynamics and magnetohydrodynamics) in cylindrical and spherical geometries in one and two dimensions. Results confirm that the proposed approach yields considerably smaller errors, higher convergence rates and it avoid spurious numerical effects at a symmetry axis.

  9. Molecular polymorphisms associated with host range in the highly conserved genomes of burrowing nematodes, Radopholus spp.

    PubMed

    Kaplan, D T; Vanderspool, M C; Garrett, C; Chang, S; Opperman, C H

    1996-01-01

    Six polymorphic bands of DNA were amplified from purified Radopholus citrophilus genomic DNA from one strain of each of the sibling species R. citrophilus and R. similis in random amplified polymorphic DNA analyses involving 380 single 10-base primers. Four of these polymorphic DNA fragments were successfully cloned and amplified through subsequent use of primers designed to complement the terminal sequences of the polymorphic DNA. Results of ensuing studies using mini-prepped DNA from 14 burrowing nematode strains collected from Florida, Hawaii, and Central America, characterized for their ability to parasitize citrus, indicated that a 2.4-kb fragment appeared to be associated with citrus parasitism in burrowing nematode populations from Florida. However, a fragment of comparable size was also detected in R. citrophilus from Hawaii and from burrowing nematode populations collected from Belize and Puerto Rico. Overall, findings suggest that the genome organization of the burrowing nematode sibling species R. citrophilus and R. similis is highly conserved. This remarkable genetic similarity should facilitate identification of genetic sequence related to important phenotypes such as citrus parasitism. Detection of R. citrophilus-specific DNA fragments in burrowing nematodes collected from Belize and Puerto Rico suggests that R. citrophilus is resident in some Central American countries.

  10. The human HNRPD locus maps to 4q21 and encodes a highly conserved protein.

    PubMed

    Dempsey, L A; Li, M J; DePace, A; Bray-Ward, P; Maizels, N

    1998-05-01

    The hnRNP D protein interacts with nucleic acids both in vivo and in vitro. Like many other proteins that interact with RNA, it contains RBD (or "RRM") domains and arg-gly-gly (RGG) motifs. We have examined the organization and localization of the human and murine genes that encode the hnRNP D protein. Comparison of the predicted sequences of the hnRNP D proteins in human and mouse shows that they are 96.9% identical (98.9% similar). This very high level of conservation suggests a critical function for hnRNP D. Sequence analysis of the human HNRPD gene shows that the protein is encoded by eight exons and that two additional exons specify sequences in the 3' UTR. Use of two of the coding exons is determined by alternative splicing of the HNRPD mRNA. The human HNRPD gene maps to 4q21. The mouse Hnrpd gene maps to the F region of chromosome 3, which is syntenic with the human 4q21 region.

  11. High chromosome conservation detected by comparative chromosome painting in chicken, pigeon and passerine birds.

    PubMed

    Derjusheva, Svetlana; Kurganova, Anna; Habermann, Felix; Gaginskaya, Elena

    2004-01-01

    Chicken chromosome paints for macrochromosomes 1-10, Z, and the nine largest microchromosomes (Griffin et al. 1999) were used to analyze chromosome homologies between chicken (Gallus gallus domesticus: Galliformes), domestic pigeon (Columba livia: Columbiformes), chaffinch (Fringilla coelebs Passeriformes), and redwing (Turdus iliacus: Passeriformes). High conservation of syntenies was revealed. In general, both macro- and microchromosomes in these birds showed very low levels of interchromosomal rearrangements. Only two cases of rearrangements were found. Chicken chromosome 1 corresponds to chromosome 1 in pigeon, but to chromosomes 3 and 4 in chaffinch and chromosomes 2 and 5 in redwing. Chicken chromosome 4 was shown to be homologous to two pairs of chromosomes in the karyotypes of pigeon and both passerine species. Comparative analysis of chromosome painting data and the results of FISH with (TTAGGG)n probe did not reveal any correlation between the distribution of interstitial telomere sites (ITSs) and chromosome rearrangements in pigeon, chaffinch and redwing. In chaffinch, ITSs were found to co-localize with a tandem repeat GS (Liangouzov et al. 2002), monomers of which contain an internal TTAGGG motif.

  12. Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans

    PubMed Central

    Freel, Kelle C.; Friedrich, Anne; Hou, Jing; Schacherer, Joseph

    2014-01-01

    The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species. PMID:25212859

  13. Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.

    PubMed

    Uno, Y; Nishida, C; Takagi, C; Ueno, N; Matsuda, Y

    2013-11-01

    It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

  14. Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues.

    PubMed

    Kawakami, Hironori; Ohashi, Eiji; Kanamoto, Shota; Tsurimoto, Toshiki; Katayama, Tsutomu

    2015-10-12

    In eukaryotes, the origin recognition complex (ORC) heterohexamer preferentially binds replication origins to trigger initiation of DNA replication. Crystallographic studies using eubacterial and archaeal ORC orthologs suggested that eukaryotic ORC may bind to origin DNA via putative winged-helix DNA-binding domains and AAA+ ATPase domains. However, the mechanisms how eukaryotic ORC recognizes origin DNA remain elusive. Here, we show in budding yeast that Lys-362 and Arg-367 residues of the largest subunit (Orc1), both outside the aforementioned domains, are crucial for specific binding of ORC to origin DNA. These basic residues, which reside in a putative disordered domain, were dispensable for interaction with ATP and non-specific DNA sequences, suggesting a specific role in recognition. Consistent with this, both residues were required for origin binding of Orc1 in vivo. A truncated Orc1 polypeptide containing these residues solely recognizes ARS sequence with low affinity and Arg-367 residue stimulates sequence specific binding mode of the polypeptide. Lys-362 and Arg-367 residues of Orc1 are highly conserved among eukaryotic ORCs, but not in eubacterial and archaeal orthologs, suggesting a eukaryote-specific mechanism underlying recognition of replication origins by ORC.

  15. High connectivity of the crocodile shark between the Atlantic and Southwest Indian Oceans: highlights for conservation.

    PubMed

    da Silva Ferrette, Bruno Lopes; Mendonça, Fernando Fernandes; Coelho, Rui; de Oliveira, Paulo Guilherme Vasconcelos; Hazin, Fábio Hissa Vieira; Romanov, Evgeny V; Oliveira, Claudio; Santos, Miguel Neves; Foresti, Fausto

    2015-01-01

    Among the various shark species that are captured as bycatch in commercial fishing operations, the group of pelagic sharks is still one of the least studied and known. Within those, the crocodile shark, Pseudocarcharias kamoharai, a small-sized lamnid shark, is occasionally caught by longline vessels in certain regions of the tropical oceans worldwide. However, the population dynamics of this species, as well as the impact of fishing mortality on its stocks, are still unknown, with the crocodile shark currently one of the least studied of all pelagic sharks. Given this, the present study aimed to assess the population structure of P. kamoharai in several regions of the Atlantic and Indian Oceans using genetic molecular markers. The nucleotide composition of the mitochondrial DNA control region of 255 individuals was analyzed, and 31 haplotypes were found, with an estimated diversity Hd = 0.627, and a nucleotide diversity π = 0.00167. An analysis of molecular variance (AMOVA) revealed a fixation index ΦST = -0.01118, representing an absence of population structure among the sampled regions of the Atlantic Ocean, and between the Atlantic and Indian Oceans. These results show a high degree of gene flow between the studied areas, with a single genetic stock and reduced population variability. In panmictic populations, conservation efforts can be concentrated in more restricted areas, being these representative of the total biodiversity of the species. When necessary, this strategy could be applied to the genetic maintenance of P. kamoharai.

  16. High Connectivity of the Crocodile Shark between the Atlantic and Southwest Indian Oceans: Highlights for Conservation

    PubMed Central

    da Silva Ferrette, Bruno Lopes; Mendonça, Fernando Fernandes; Coelho, Rui; de Oliveira, Paulo Guilherme Vasconcelos; Hazin, Fábio Hissa Vieira; Romanov, Evgeny V.; Oliveira, Claudio; Santos, Miguel Neves; Foresti, Fausto

    2015-01-01

    Among the various shark species that are captured as bycatch in commercial fishing operations, the group of pelagic sharks is still one of the least studied and known. Within those, the crocodile shark, Pseudocarcharias kamoharai, a small-sized lamnid shark, is occasionally caught by longline vessels in certain regions of the tropical oceans worldwide. However, the population dynamics of this species, as well as the impact of fishing mortality on its stocks, are still unknown, with the crocodile shark currently one of the least studied of all pelagic sharks. Given this, the present study aimed to assess the population structure of P. kamoharai in several regions of the Atlantic and Indian Oceans using genetic molecular markers. The nucleotide composition of the mitochondrial DNA control region of 255 individuals was analyzed, and 31 haplotypes were found, with an estimated diversity Hd = 0.627, and a nucleotide diversity π = 0.00167. An analysis of molecular variance (AMOVA) revealed a fixation index ΦST = -0.01118, representing an absence of population structure among the sampled regions of the Atlantic Ocean, and between the Atlantic and Indian Oceans. These results show a high degree of gene flow between the studied areas, with a single genetic stock and reduced population variability. In panmictic populations, conservation efforts can be concentrated in more restricted areas, being these representative of the total biodiversity of the species. When necessary, this strategy could be applied to the genetic maintenance of P. kamoharai. PMID:25689742

  17. The role of a conserved tyrosine residue in high-potential iron sulfur proteins.

    PubMed Central

    Iwagami, S. G.; Creagh, A. L.; Haynes, C. A.; Borsari, M.; Felli, I. C.; Piccioli, M.; Eltis, L. D.

    1995-01-01

    Conserved tyrosine-12 of Ectothiorhodospira halophila high-potential iron sulphur protein (HiPIP) iso-I was substituted with phenylalanine (Y12F), histidine (Y12H), tryptophan (Y12W), isoleucine (Y12I), and alanine (Y12A). Variants Y12A and Y12I were expressed to reasonable levels in cells grown at lower temperatures, but decomposed during purification. Variants Y12F, Y12H, and Y12W were substantially destabilized with respect to the recombinant wild-type HiPIP (rcWT) as determined by differential scanning calorimetry over a pH range of 7.0-11.0. Characterization of the Y12F variant by NMR indicates that the principal structural differences between this variant and the rcWT HiPIP result from the loss of the two hydrogen bonds of the Tyr-12 hydroxyl group with Asn-14 O delta 1 and Lys-59 NH, respectively. The effect of the loss of the latter interaction is propagated through the Lys-59/Val-58 peptide bond, thereby perturbing Gly-46. The delta delta GDapp of Y12F of 2.3 kcal/mol with respect to rcWT HiPIP (25 degrees C, pH 7.0) is entirely consistent with the contribution of these two hydrogen bonds to the stability of the latter. CD measurements show that Tyr-12 influences several electronic transitions within the cluster. The midpoint reduction potentials of variants Y12F, Y12H, and Y12W were 17, 19, and 22 mV (20 mM MOPS, 0.2 M sodium chloride, pH 6.98, 25 degrees C), respectively, higher than that of rcWT HiPIP. The current results indicate that, although conserved Tyr-12 modulates the properties of the cluster, its principle function is to stabilize the HiPIP through hydrogen bonds involving its hydroxyl group and electrostatic interactions involving its aromatic ring. PMID:8580847

  18. Design of ecoregional monitoring in conservation areas of high-latitude ecosystems under contemporary climate change

    USGS Publications Warehouse

    Beever, Erik A.; Woodward, Andrea

    2011-01-01

    Land ownership in Alaska includes a mosaic of federally managed units. Within its agency’s context, each unit has its own management strategy, authority, and resources of conservation concern, many of which are migratory animals. Though some units are geographically isolated, many are nevertheless linked by paths of abiotic and biotic flows, such as rivers, air masses, flyways, and terrestrial and aquatic migration routes. Furthermore, individual land units exist within the context of a larger landscape pattern of shifting conditions, requiring managers to understand at larger spatial scales the status and trends in the synchrony and spatial concurrence of species and associated suitable habitats. Results of these changes will determine the ability of Alaska lands to continue to: provide habitat for local and migratory species; absorb species whose ranges are shifting northward; and experience mitigation or exacerbation of climate change through positive and negative atmospheric feedbacks. We discuss the geographic and statutory contexts that influence development of ecological monitoring; argue for the inclusion of significant amounts of broad-scale monitoring; discuss the importance of defining clear programmatic and monitoring objectives; and draw from lessons learned from existing long-term, broad-scale monitoring programs to apply to the specific contexts relevant to high-latitude protected areas such as those in Alaska. Such areas are distinguished by their: marked seasonality; relatively large magnitudes of contemporary change in climatic parameters; and relative inaccessibility due to broad spatial extent, very low (or zero) road density, and steep and glaciated areas. For ecological monitoring to effectively support management decisions in high-latitude areas such as Alaska, a monitoring program ideally would be structured to address the actual spatial and temporal scales of relevant processes, rather than the artificial boundaries of individual land

  19. How landscape scale changes affect ecological processes in conservation areas: external factors influence land use by zebra (Equus burchelli) in the Okavango Delta

    PubMed Central

    Bartlam-Brooks, Hattie L A; Bonyongo, Mpaphi C; Harris, Stephen

    2013-01-01

    Most large-bodied wildlife populations in sub-Saharan Africa only survive in conservation areas, but are continuing to decline because external changes influence ecological processes within reserves, leading to a lack of functionality. However, failure to understand how landscape scale changes influence ecological processes limits our ability to manage protected areas. We used GPS movement data to calculate dry season home ranges for 14 zebra mares in the Okavango Delta and investigated the effects of a range of landscape characteristics (number of habitat patches, mean patch shape, mean index of juxtaposition, and interspersion) on home range size. Resource utilization functions (RUF) were calculated to investigate how specific landscape characteristics affected space use. Space use by all zebra was clustered. In the wetter (Central) parts of the Delta home range size was negatively correlated with the density of habitat patches, more complex patch shapes, low juxtaposition of habitats and an increased availability of floodplain and grassland habitats. In the drier (Peripheral) parts of the Delta, higher use by zebra was also associated with a greater availability of floodplain and grassland habitats, but a lower density of patches and simpler patch shapes. The most important landscape characteristic was not consistent between zebra within the same area of the Delta, suggesting that no single foraging strategy is substantially superior to others, and so animals using different foraging strategies may all thrive. The distribution and complexity of habitat patches are crucial in determining space use by zebra. The extent and duration of seasonal flooding is the principal process affecting habitat patch characteristics in the Okavango Delta, particularly the availability of floodplains, which are the habitat at greatest risk from climate change and anthropogenic disturbance to the Okavango's catchment basin. Understanding how the factors that determine habitat

  20. How landscape scale changes affect ecological processes in conservation areas: external factors influence land use by zebra (Equus burchelli) in the Okavango Delta.

    PubMed

    Bartlam-Brooks, Hattie L A; Bonyongo, Mpaphi C; Harris, Stephen

    2013-09-01

    Most large-bodied wildlife populations in sub-Saharan Africa only survive in conservation areas, but are continuing to decline because external changes influence ecological processes within reserves, leading to a lack of functionality. However, failure to understand how landscape scale changes influence ecological processes limits our ability to manage protected areas. We used GPS movement data to calculate dry season home ranges for 14 zebra mares in the Okavango Delta and investigated the effects of a range of landscape characteristics (number of habitat patches, mean patch shape, mean index of juxtaposition, and interspersion) on home range size. Resource utilization functions (RUF) were calculated to investigate how specific landscape characteristics affected space use. Space use by all zebra was clustered. In the wetter (Central) parts of the Delta home range size was negatively correlated with the density of habitat patches, more complex patch shapes, low juxtaposition of habitats and an increased availability of floodplain and grassland habitats. In the drier (Peripheral) parts of the Delta, higher use by zebra was also associated with a greater availability of floodplain and grassland habitats, but a lower density of patches and simpler patch shapes. The most important landscape characteristic was not consistent between zebra within the same area of the Delta, suggesting that no single foraging strategy is substantially superior to others, and so animals using different foraging strategies may all thrive. The distribution and complexity of habitat patches are crucial in determining space use by zebra. The extent and duration of seasonal flooding is the principal process affecting habitat patch characteristics in the Okavango Delta, particularly the availability of floodplains, which are the habitat at greatest risk from climate change and anthropogenic disturbance to the Okavango's catchment basin. Understanding how the factors that determine habitat

  1. Soil bacterial and fungal community responses across a conservation reserve program chronosequence in Texas high plains region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated changes in soil bacterial and fungal communities with increasing restoration time across a Conservation Reserve Program chronosequence (CRP) on fine sandy loam soils in the Texas high plains region. Soil samples (0-10cm) were collected in 2012 and 2014 from seven dryland croplands (0...

  2. A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection.

    PubMed

    Davies, Bryan W; Walker, Graham C

    2008-02-01

    We report here the first characterization of the Sinorhizobium meliloti open reading frame SMc01113. The SMc01113 protein is a member of a highly conserved protein family, universal among bacteria. We demonstrate that the SMc01113 gene is absolutely required for S. meliloti symbiosis with alfalfa and also for the protection of the bacterium from a wide range of environmental stresses.

  3. Energy Conservation Measures for the Charles E. Shea Senior High School, Pawtucket, Rhode Island. Public Service Report.

    ERIC Educational Resources Information Center

    New England Innovation Group, Providence, RI.

    Presented is a study of energy conservation opportunities in a Rhode Island high school. With the aid of an infrared camera system, researchers documented heat losses that were not evident to the naked eye. Each infrared thermogram obtained showed one or more types of heat loss and identified the specific sections of the building where the…

  4. A high order approximation of hyperbolic conservation laws in networks: Application to one-dimensional blood flow

    NASA Astrophysics Data System (ADS)

    Müller, Lucas O.; Blanco, Pablo J.

    2015-11-01

    We present a methodology for the high order approximation of hyperbolic conservation laws in networks by using the Dumbser-Enaux-Toro solver and exact solvers for the classical Riemann problem at junctions. The proposed strategy can be applied to any hyperbolic system, conservative or non-conservative, and possibly with flux functions containing discontinuous parameters, as long as an exact or approximate Riemann problem solver is available. The methodology is implemented for a one-dimensional blood flow model that considers discontinuous variations of mechanical and geometrical properties of vessels. The achievement of formal order of accuracy, as well as the robustness of the resulting numerical scheme, is verified through the simulation of both, academic tests and physiological flows.

  5. High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation

    PubMed Central

    Buckland, Steeves; Cole, Nik C.; Groombridge, Jim J.; Küpper, Clemens; Burke, Terry; Dawson, Deborah A.; Gallagher, Laura E.; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID

  6. Hunting effects on favourable conservation status of highly inbred Swedish wolves.

    PubMed

    Laikre, Linda; Jansson, Mija; Allendorf, Fred W; Jakobsson, Sven; Ryman, Nils

    2013-04-01

    The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called "favourable conservation status" (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne ) of this population is in the minimum range of Ne = 500-1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.

  7. Conserved-residue mutations in Wzy affect O-antigen polymerization and Wzz-mediated chain-length regulation in Pseudomonas aeruginosa PAO1

    NASA Astrophysics Data System (ADS)

    Islam, Salim T.; Huszczynski, Steven M.; Nugent, Timothy; Gold, Alexander C.; Lam, Joseph S.

    2013-12-01

    O antigen (O-Ag) in many bacteria is synthesized via the Wzx/Wzy-dependent pathway in which Wzy polymerizes lipid-linked O-Ag subunits to modal lengths regulated by Wzz. Characterization of 83 site-directed mutants of Wzy from Pseudomonas aeruginosa PAO1 (WzyPa) in topologically-mapped periplasmic (PL) and cytoplasmic loops (CL) verified the functional importance of PL3 and PL5, with the former shown to require overall cationic properties. Essential Arg residues in the RX10G motifs of PL3 and PL5 were found to be conserved in putative homologues of WzyPa, as was the overall sequence homology between these two periplasmic loops in each protein. Amino acid substitutions in CL6 were found to alter Wzz-mediated O-antigen modality, with evidence suggesting that these changes may perturb the C-terminal WzyPa tertiary structure. Together, these data suggest that the catch-and-release mechanism of O-Ag polymerization is widespread among bacteria and that regulation of polymer length is affected by interaction of Wzz with Wzy.

  8. Identifying Affective Domains That Correlate and Predict Mathematics Performance in High-Performing Students in Singapore

    ERIC Educational Resources Information Center

    Lim, Siew Yee; Chapman, Elaine

    2015-01-01

    Past studies have shown that distinct yet highly correlated sub-constructs of three broad mathematics affective variables: (a) motivation, (b) attitudes and (c) anxiety, have varying degree of correlation with mathematics achievement. The sub-constructs of these three affective constructs are as follows: (a) (i) amotivation, (ii) external…

  9. Lexical and Affective Prosody in Children with High-Functioning Autism

    ERIC Educational Resources Information Center

    Grossman, Ruth B.; Bemis, Rhyannon H.; Skwerer, Daniela Plesa; Tager-Flusberg, Helen

    2010-01-01

    Purpose: To investigate the perception and production of lexical stress and processing of affective prosody in adolescents with high-functioning autism (HFA). We hypothesized preserved processing of lexical and affective prosody but atypical lexical prosody production. Method: Sixteen children with HFA and 15 typically developing (TD) peers…

  10. A monotonicity preserving conservative sharp interface flow solver for high density ratio two-phase flows

    SciTech Connect

    Le Chenadec, Vincent; Pitsch, Heinz

    2013-09-15

    This paper presents a novel approach for solving the conservative form of the incompressible two-phase Navier–Stokes equations. In order to overcome the numerical instability induced by the potentially large density ratio encountered across the interface, the proposed method includes a Volume-of-Fluid type integration of the convective momentum transport, a monotonicity preserving momentum rescaling, and a consistent and conservative Ghost Fluid projection that includes surface tension effects. The numerical dissipation inherent in the Volume-of-Fluid treatment of the convective transport is localized in the interface vicinity, enabling the use of a kinetic energy conserving discretization away from the singularity. Two- and three-dimensional tests are presented, and the solutions shown to remain accurate at arbitrary density ratios. The proposed method is then successfully used to perform the detailed simulation of a round water jet emerging in quiescent air, therefore suggesting the applicability of the proposed algorithm to the computation of realistic turbulent atomization.

  11. Liberals, Conservatives and Romantic Nationalists in Interwar Education Policy in Greece: "The High Mountains" Episode

    ERIC Educational Resources Information Center

    Athanasiades, Harris

    2015-01-01

    Greek historiography of interwar education policy unproblematically accepts the assumption that the bone of contention between the "Liberal demoticists" and the "Conservative purists" was the language issue; particularly whether "demotic" or "katharevousa" should be the language of instruction in schooling.…

  12. Using the Eastern Hellbender Salamander in a High School Genetics & Ecological Conservation Activity

    ERIC Educational Resources Information Center

    Chudyk, Sarah; McMillan, Amy; Lange, Catherine

    2014-01-01

    This article contains an original 5E lesson plan developed from conservation genetics research on the giant North American hellbender salamander, Cryptobranchus alleganiensis alleganiensis. The lesson plan provides background information on the hellbender, reviews basic genetics, and exposes students to the scientific process that is used during…

  13. Conservation planning with multiple organizations and objectives.

    PubMed

    Bode, Michael; Probert, Will; Turner, Will R; Wilson, Kerrie A; Venter, Oscar

    2011-04-01

    There has been a dramatic increase in the number of conservation organizations worldwide. It is now common for multiple organizations to operate in the same landscape in pursuit of different conservation goals. New objectives, such as maintenance of ecosystem services, will attract additional funding and new organizations to conservation. Systematic conservation planning helps in the design of spatially explicit management actions that optimally conserve multiple landscape features (e.g., species, ecosystems, or ecosystem services). But the methods used in its application implicitly assume that a single actor implements the optimal plan. We investigated how organizational behavior and conservation outcomes are affected by the presence of autonomous implementing organizations with different objectives. We used simulation models and game theory to explore how alternative behaviors (e.g., organizations acting independently or explicitly cooperating) affected an organization's ability to protect their feature of interest, and investigated how the distribution of features in the landscape influenced organizations' attitudes toward cooperation. Features with highly correlated spatial distributions, although typically considered an opportunity for mutually beneficial conservation planning, can lead to organizational interactions that result in lower levels of protection. These detrimental outcomes can be avoided by organizations that cooperate when acquiring land. Nevertheless, for cooperative purchases to benefit both organizations' objectives, each must forgo the protection of land parcels that they would consider to be of high conservation value. Transaction costs incurred during cooperation and the sources of conservation funding could facilitate or hinder cooperative behavior.

  14. Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes.

    PubMed

    Antezana, Marcos A; Jordan, I King

    2008-05-14

    loosely contained background transcription. Finally, we show that human coding regions are less mutable under the estimated NBDM regimes than under matched context-independent mutation and that this entails marked differences between the spectra of amino-acid mutations that either mutation regime should generate. In the Discussion we examine the mechanisms likely to underlie NBDM heterogeneity along chromosomes and propose that it reflects how the diversity and activity of lesion-bypass polymerases (LBPs) track the landscapes of scheduled and non-scheduled genome repair, replication, and transcription during the cell cycle. We conclude that the primary structure of vertebrate genic DNA at and below the trinucleotide level has been governed over the long term by highly conserved regimes of NBDM which should be under direct natural selection because they alter drastically missense-mutation rates and hence the somatic and the germline mutational loads. Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes.

  15. Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques

    PubMed Central

    Street, Summer L; Kyes, Randall C; Grant, Richard; Ferguson, Betsy

    2007-01-01

    Background Macaca fascicularis (cynomolgus or longtail macaques) is the most commonly used non-human primate in biomedical research. Little is known about the genomic variation in cynomolgus macaques or how the sequence variants compare to those of the well-studied related species, Macaca mulatta (rhesus macaque). Previously we identified single nucleotide polymorphisms (SNPs) in portions of 94 rhesus macaque genes and reported that Indian and Chinese rhesus had largely different SNPs. Here we identify SNPs from some of the same genomic regions of cynomolgus macaques (from Indochina, Indonesia, Mauritius and the Philippines) and compare them to the SNPs found in rhesus. Results We sequenced a portion of 10 genes in 20 cynomolgus macaques. We identified 69 SNPs in these regions, compared with 71 SNPs found in the same genomic regions of 20 Indian and Chinese rhesus macaques. Thirty six (52%) of the M. fascicularis SNPs were overlapping in both species. The majority (70%) of the SNPs found in both Chinese and Indian rhesus macaque populations were also present in M. fascicularis. Of the SNPs previously found in a single rhesus population, 38% (Indian) and 44% (Chinese) were also identified in cynomolgus macaques. In an alternative approach, we genotyped 100 cynomolgus DNAs using a rhesus macaque SNP array representing 53 genes and found that 51% (29/57) of the rhesus SNPs were present in M. fascicularis. Comparisons of SNP profiles from cynomolgus macaques imported from breeding centers in China (where M. fascicularis are not native) showed they were similar to those from Indochina. Conclusion This study demonstrates a surprisingly high conservation of SNPs between M. fascicularis and M. mulatta, suggesting that the relationship of these two species is closer than that suggested by morphological and mitochondrial DNA analysis alone. These findings indicate that SNP discovery efforts in either species will generate useful resources for both macaque species

  16. Conservation hotspots for the turtles on the high seas of the Atlantic Ocean.

    PubMed

    Huang, Hsiang-Wen

    2015-01-01

    Understanding the distribution of bycaught sea turtles could inform conservation strategies and priorities. This research analyses the distribution of turtles caught as longline fisheries bycatch on the high seas of the Atlantic Ocean. This research collected 18,142 bycatch observations and 47.1 million hooks from large-scale Taiwanese longline vessels in the Atlantic Ocean from June 2002 to December 2013. The coverage rates were ranged from 0.48% to 17.54% by year. Seven hundred and sixty-seven turtles were caught, and the major species were leatherback (59.8%), olive ridley (27.1%) and loggerhead turtles (8.7%). Most olive ridley (81.7%) and loggerhead (82.1%) turtles were hooked, while the leatherbacks were both hooked (44.0%) and entangled (31.8%). Depending on the species, 21.4% to 57.7% were dead when brought onboard. Most of the turtles were caught in tropical areas, especially in the Gulf of Guinea (15°N-10°S, 30°W-10°E), but loggerheads were caught in the south Atlantic Ocean (25°S-35°S, 40°W-10°E and 30°S-40°S, 55°W-45°W). The bycatch rate was the highest at 0.030 per 1000 hooks for leatherbacks in the tropical area. The bycatch rates of olive ridley ranged from 0 to 0.010 per thousand hooks. The loggerhead bycatch rates were higher in the northern and southern Atlantic Ocean and ranged from 0.0128 to 0.0239 per thousand hooks. Due to the characteristics of the Taiwanese deep-set longline fleet, bycatch rates were lower than those of coastal longline fisheries, but mortality rates were higher because of the long hours of operation. Gear and bait modification should be considered to reduce sea turtle bycatch and increase survival rates while reducing the use of shallow hooks would also be helpful.

  17. Conservation Hotspots for the Turtles on the High Seas of the Atlantic Ocean

    PubMed Central

    Huang, Hsiang-Wen

    2015-01-01

    Understanding the distribution of bycaught sea turtles could inform conservation strategies and priorities. This research analyses the distribution of turtles caught as longline fisheries bycatch on the high seas of the Atlantic Ocean. This research collected 18,142 bycatch observations and 47.1 million hooks from large-scale Taiwanese longline vessels in the Atlantic Ocean from June 2002 to December 2013. The coverage rates were ranged from 0.48% to 17.54% by year. Seven hundred and sixty-seven turtles were caught, and the major species were leatherback (59.8%), olive ridley (27.1%) and loggerhead turtles (8.7%). Most olive ridley (81.7%) and loggerhead (82.1%) turtles were hooked, while the leatherbacks were both hooked (44.0%) and entangled (31.8%). Depending on the species, 21.4% to 57.7% were dead when brought onboard. Most of the turtles were caught in tropical areas, especially in the Gulf of Guinea (15°N-10°S, 30°W-10°E), but loggerheads were caught in the south Atlantic Ocean (25°S-35°S, 40°W-10°E and 30°S-40°S, 55°W-45°W). The bycatch rate was the highest at 0.030 per 1000 hooks for leatherbacks in the tropical area. The bycatch rates of olive ridley ranged from 0 to 0.010 per thousand hooks. The loggerhead bycatch rates were higher in the northern and southern Atlantic Ocean and ranged from 0.0128 to 0.0239 per thousand hooks. Due to the characteristics of the Taiwanese deep-set longline fleet, bycatch rates were lower than those of coastal longline fisheries, but mortality rates were higher because of the long hours of operation. Gear and bait modification should be considered to reduce sea turtle bycatch and increase survival rates while reducing the use of shallow hooks would also be helpful. PMID:26267796

  18. Inhibitory control and visuo-spatial reversibility in Piaget's seminal number conservation task: a high-density ERP study

    PubMed Central

    Borst, Grégoire; Simon, Grégory; Vidal, Julie; Houdé, Olivier

    2013-01-01

    The present high-density event-related potential (ERP) study on 13 adults aimed to determine whether number conservation relies on the ability to inhibit the overlearned length-equals-number strategy and then imagine the shortening of the row that was lengthened. Participants performed the number-conservation task and, after the EEG session, the mental imagery task. In the number-conservation task, first two rows with the same number of tokens and the same length were presented on a computer screen (COV condition) and then, the tokens in one of the two rows were spread apart (INT condition). Participants were instructed to determine whether the two rows had an identical number of tokens. In the mental imagery task, two rows with different lengths but the same number of tokens were presented and participants were instructed to imagine the tokens in the longer row aligning with the tokens in the shorter row. In the number-conservation task, we found that the amplitudes of the centro-parietal N2 and fronto-central P3 were higher in the INT than in the COV conditions. In addition, the differences in response times between the two conditions were correlated with the differences in the amplitudes of the fronto-central P3. In light of previous results reported on the number-conservation task in adults, the present results suggest that inhibition might be necessary to succeed the number-conservation task in adults even when the transformation of the length of one of the row is displayed. Finally, we also reported correlations between the speed at which participants could imagine the shortening of one of the row in the mental imagery task, the speed at which participants could determine that the two rows had the same number of tokens after the tokens in one of the row were spread apart and the latency of the late positive parietal component in the number-conservation task. Therefore, performing the number-conservation task might involve mental transformation processes in

  19. Human metapneumovirus G protein is highly conserved within but not between genetic lineages.

    PubMed

    Yang, Chin-Fen; Wang, Chiaoyin K; Tollefson, Sharon J; Lintao, Linda D; Liem, Alexis; Chu, Marla; Williams, John V

    2013-06-01

    Human metapneumovirus (HMPV) is an important cause of acute respiratory illnesses in children. HMPV encodes two major surface glycoproteins, fusion (F) and glycoprotein (G). The function of G has not been fully established, though it is dispensable for in vitro and in vivo replication. We analyzed 87 full-length HMPV G sequences from isolates collected over 20 years. The G sequences fell into four subgroups with a mean 63 % amino acid identity (minimum 29 %). The length of G varied from 217 to 241 residues. Structural features such as proline content and N- and O-glycosylation sites were present in all strains but quite variable between subgroups. There was minimal drift within the subgroups over 20 years. The estimated time to the most recent common ancestor was 215 years. HMPV G was conserved within lineages over 20 years, suggesting functional constraints on diversity. However, G was poorly conserved between subgroups, pointing to potentially distinct roles for G among different viral lineages.

  20. High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

    NASA Technical Reports Server (NTRS)

    Potter, Christopher S.; Li, Shuang

    2014-01-01

    The Desert Renewable Energy Conservation Plan (DRECP), a major component of California's renewable energy planning efforts, is intended to provide effective protection and conservation of desert ecosystems, while allowing for the sensible development of renewable energy projects. This NASA mapping report was developed to support the DRECP and the Bureau of Land Management (BLM). We outline in this document remote sensing image processing methods to deliver new maps of biological soils crusts, sand dune movements, desert pavements, and sub-surface water sources across the DRECP area. We focused data processing first on the largely unmapped areas most likely to be used for energy developments, such as those within Renewable Energy Study Areas (RESA) and Solar Energy Zones (SEZs). We used imagery (multispectral and radar) mainly from the years 2009-2011.

  1. On the Total Variation of High-Order Semi-Discrete Central Schemes for Conservation Laws

    NASA Technical Reports Server (NTRS)

    Bryson, Steve; Levy, Doron

    2004-01-01

    We discuss a new fifth-order, semi-discrete, central-upwind scheme for solving one-dimensional systems of conservation laws. This scheme combines a fifth-order WENO reconstruction, a semi-discrete central-upwind numerical flux, and a strong stability preserving Runge-Kutta method. We test our method with various examples, and give particular attention to the evolution of the total variation of the approximations.

  2. Lax pair, conservation laws and Darboux transformation of the high-order Lax equation in fluid dynamics

    NASA Astrophysics Data System (ADS)

    Zheng, Wenxin; Wei, Guangmei

    2017-03-01

    KdV equation is investigated in fluid dynamics, plasma physics and other fields. By means of poseudopotential procedure, the high-order member of KdV hierarchy, ninth-order Lax's KdV equation in fluid dynamics is studied in this paper. Lax pair in AKNS form are derived from poseudopotential. Based on the Lax pair, an infinite number of conservation laws and Darboux transformation are constructed, and soliton solution is obtained by the Darboux transformation.

  3. Epidermal surface antigen (MS17S1) is highly conserved between mouse and human

    SciTech Connect

    Cho, Y.J.; Chema, D.; Cho, M.

    1995-05-20

    A mouse monoclonal antibody ECS-1 raised to human keratinocytes detects a 35-kDa epidermal surface antigen (ESA) and causes keratinocyte dissociation in vitro. ECS-1 stains skin of 16-day mouse embryo and 8- to 9-week human fetus. Mouse Esa cDNA encodes a 379-amino-acid protein that is 99.2% identical to the human, differing at only 3 amino acids. The gene (M17S1) was mapped to mouse chromosome 11, highlighting the conserved linkage synteny existing between human chromosome 17 and mouse chromosome 11. Although the nude locus has been mapped to the same region of chromosome 11, no abnormalities in protein, mRNA, or cDNA or genomic sequences were detected in nude mice. However, both nude and control mice were found to have a second Esa mRNA transcript that conserves amino acid sequence and molecular weight. The mouse and human 5{prime} and 3{prime} untranslated sequences are conserved. Similar RNA folding patterns of the 5{prime} untranslated region are predicted despite a 91-bp insertion in the mouse. These data suggest that both the function and the regulation of ESA protein are of importance and that Esa (M17S1) is not the nude locus gene. 42 refs., 7 figs., 3 tabs.

  4. Voices of At-Risk Youth: Perceptions of Continuation High School Students regarding Factors Affecting Their Engagement in High School

    ERIC Educational Resources Information Center

    Lock, Stephanie J.

    2010-01-01

    Using a theoretical framework of critical pedagogy and the lens of social justice to focus on engagement and student voice, this research includes both quantitative and qualitative methodologies, in respect to the perceptions of continuation high school students regarding factors affecting their engagement in high school. The purpose of this study…

  5. Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

    PubMed Central

    Gracy, Jérome; Fournier, Elisabeth; Kroj, Thomas; Padilla, André

    2015-01-01

    Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. To get a deeper understanding of fungal effectors, we determined by NMR spectroscopy the 3-dimensional structures of the Magnaporthe oryzae effectors AVR1-CO39 and AVR-Pia. Despite a lack of sequence similarity, both proteins have very similar 6 β-sandwich structures that are stabilized in both cases by a disulfide bridge between 2 conserved cysteins located in similar positions of the proteins. Structural similarity searches revealed that AvrPiz-t, another effector from M. oryzae, and ToxB, an effector of the wheat tan spot pathogen Pyrenophora tritici-repentis have the same structures suggesting the existence of a family of sequence-unrelated but structurally conserved fungal effectors that we named MAX-effectors (Magnaporthe Avrs and ToxB like). Structure-informed pattern searches strengthened this hypothesis by identifying MAX-effector candidates in a broad range of ascomycete phytopathogens. Strong expansion of the MAX-effector family was detected in M. oryzae and M. grisea where they seem to be particularly important since they account for 5–10% of the effector repertoire and 50% of the cloned avirulence effectors. Expression analysis indicated that the majority of M. oryzae MAX-effectors are expressed specifically during early infection suggesting important functions during biotrophic host colonization. We hypothesize that the scenario observed for MAX-effectors can serve as a paradigm for ascomycete effector diversity and that the enormous number of sequence-unrelated ascomycete effectors may in fact belong to a restricted set of structurally conserved effector families. PMID:26506000

  6. Structure of Trypanosoma brucei glutathione synthetase: Domain and loop alterations in the catalytic cycle of a highly conserved enzyme

    PubMed Central

    Fyfe, Paul K.; Alphey, Magnus S.; Hunter, William N.

    2010-01-01

    Glutathione synthetase catalyses the synthesis of the low molecular mass thiol glutathione from l-γ-glutamyl-l-cysteine and glycine. We report the crystal structure of the dimeric enzyme from Trypanosoma brucei in complex with the product glutathione. The enzyme belongs to the ATP-grasp family, a group of enzymes known to undergo conformational changes upon ligand binding. The T. brucei enzyme crystal structure presents two dimers in the asymmetric unit. The structure reveals variability in the order and position of a small domain, which forms a lid for the active site and serves to capture conformations likely to exist during the catalytic cycle. Comparisons with orthologous enzymes, in particular from Homo sapiens and Saccharomyces cerevisae, indicate a high degree of sequence and structure conservation in part of the active site. Structural differences that are observed between the orthologous enzymes are assigned to different ligand binding states since key residues are conserved. This suggests that the molecular determinants of ligand recognition and reactivity are highly conserved across species. We conclude that it would be difficult to target the parasite enzyme in preference to the host enzyme and therefore glutathione synthetase may not be a suitable target for antiparasitic drug discovery. PMID:20045436

  7. High-order finite-volume methods for hyperbolic conservation laws on mapped multiblock grids

    NASA Astrophysics Data System (ADS)

    McCorquodale, P.; Dorr, M. R.; Hittinger, J. A. F.; Colella, P.

    2015-05-01

    We present an approach to solving hyperbolic conservation laws by finite-volume methods on mapped multiblock grids, extending the approach of Colella, Dorr, Hittinger, and Martin (2011) [10] for grids with a single mapping. We consider mapped multiblock domains for mappings that are conforming at inter-block boundaries. By using a smooth continuation of the mapping into ghost cells surrounding a block, we reduce the inter-block communication problem to finding an accurate, robust interpolation into these ghost cells from neighboring blocks. We demonstrate fourth-order accuracy for the advection equation for multiblock coordinate systems in two and three dimensions.

  8. High-order finite-volume methods for hyperbolic conservation laws on mapped multiblock grids

    DOE PAGES

    McCorquodale, P. W.; Colella, P.; Dorr, M. R.; ...

    2015-01-13

    We present an approach to solving hyperbolic conservation laws by finite-volume methods on mapped multiblock grids, extending the approach of Colella, Dorr, Hittinger, and Martin (2011) [10] for grids with a single mapping. We consider mapped multiblock domains for mappings that are conforming at inter-block boundaries. By using a smooth continuation of the mapping into ghost cells surrounding a block, we reduce the inter-block communication problem to finding an accurate, robust interpolation into these ghost cells from neighboring blocks. Lastly, we demonstrate fourth-order accuracy for the advection equation for multiblock coordinate systems in two and three dimensions.

  9. Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data.

    PubMed

    Bandaru, Pradeep; Bansal, Mukesh; Nemenman, Ilya

    2011-02-01

    We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical interactions among the metabolite activities using the ARACNE reverse-engineering algorithm and on constraining possible metabolic transformations to satisfy the conservation of mass. The resulting algorithms are validated on synthetic data from an abridged computational model of Escherichia coli metabolism. Precision rates upwards of 50% are routinely observed for identification of full metabolic reactions, and recalls upwards of 20% are also seen.

  10. A Highly Conserved Kinase Is an Essential Component for Stress Tolerance in Yeast and Plant Cells

    NASA Astrophysics Data System (ADS)

    Lee, Jeong Hee; van Montagu, Marc; Verbruggen, Nathalie

    1999-05-01

    Osmotic stress (drought, salt stress) is a major limiting factor for crop productivity in the world. Because cellular responses to osmotic stress are thought to be conserved in eukaryotes and because yeast is much more amenable than plants to genetic research, a functional strategy has been performed to identify limiting steps in osmotolerance of plants based on the complementation of yeast with a plant library. A new plant cDNA that encodes a functional homologue of the yeast Dbf2 kinase enhances salt, drought, cold, and heat tolerance upon overexpression in yeast as well as in transgenic plant cells.

  11. Conservative method for simulation of a high-order nonlinear Schrödinger equation with a trapped term

    NASA Astrophysics Data System (ADS)

    Cai, Jia-Xiang; Bai, Chuan-Zhi; Qin, Zhi-Lin

    2015-10-01

    We propose a new scheme for simulation of a high-order nonlinear Schrödinger equation with a trapped term by using the mid-point rule and Fourier pseudospectral method to approximate time and space derivatives, respectively. The method is proved to be both charge- and energy-conserved. Various numerical experiments for the equation in different cases are conducted. From the numerical evidence, we see the present method provides an accurate solution and conserves the discrete charge and energy invariants to machine accuracy which are consistent with the theoretical analysis. Project supported by the National Natural Science Foundation of China (Grant Nos. 11201169 and 11271195) and the Qing Lan Project of Jiangsu Province, China.

  12. High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance.

    PubMed

    Bart, Rebecca; Cohn, Megan; Kassen, Andrew; McCallum, Emily J; Shybut, Mikel; Petriello, Annalise; Krasileva, Ksenia; Dahlbeck, Douglas; Medina, Cesar; Alicai, Titus; Kumar, Lava; Moreira, Leandro M; Rodrigues Neto, Júlio; Verdier, Valerie; Santana, María Angélica; Kositcharoenkul, Nuttima; Vanderschuren, Hervé; Gruissem, Wilhelm; Bernal, Adriana; Staskawicz, Brian J

    2012-07-10

    Cassava bacterial blight (CBB), incited by Xanthomonas axonopodis pv. manihotis (Xam), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65 Xam strains and deduce the phylogenetic relatedness of Xam across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.

  13. SOR1, a gene required for photosensitizer and singlet oxygen resistance in Cercospora fungi, is highly conserved in divergent organisms.

    PubMed

    Ehrenshaft, M; Jenns, A E; Chung, K R; Daub, M E

    1998-03-01

    Filamentous Cercospora fungi are resistant to photosensitizing compounds that generate singlet oxygen. C. nicotianae photosensitizer-sensitive mutants were restored to full resistance by transformation with SOR1 (Singlet Oxygen Resistance 1), a gene recovered from a wild-type genomic library. SOR1 null mutants generated via targeted gene replacement confirmed the requirement for SOR1 in photosensitizer resistance. SOR1 RNA is present throughout the growth cycle. Although resistance to singlet oxygen is rare in biological systems, SOR1, a gene with demonstrated activity against singlet-oxygen-generating photosensitizers, is highly conserved in organisms from widely diverse taxa. The characterization of SOR1 provides an additional phenotype to this large group of evolutionarily conserved genes.

  14. The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants.

    PubMed

    Woodcock, Paul; Edwards, David P; Fayle, Tom M; Newton, Rob J; Khen, Chey Vun; Bottrell, Simon H; Hamer, Keith C

    2011-11-27

    South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority.

  15. The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants

    PubMed Central

    Woodcock, Paul; Edwards, David P.; Fayle, Tom M.; Newton, Rob J.; Khen, Chey Vun; Bottrell, Simon H.; Hamer, Keith C.

    2011-01-01

    South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority. PMID:22006966

  16. Affective responses of high and low body satisfied men to viewing physique slides.

    PubMed

    Hausenblas, Heather A; Janelle, Christopher M; Gardner, Rebecca Ellis; Hagan, Amy L

    2003-01-01

    The purpose of this study was to examine the acute affective responses of high and low body satisfied (BS) men who viewed physique slides of the male ideal (model-slides), physique slides of themselves (self-slides), and nonphysique slides (control-slides). During three laboratory visits the participants viewed the slides from one of the three conditions, and they completed pre-, in-, and post-task affective measures. It was found that the: (a) high BS group reported less mood disturbance than the low BS group; (b) participants reported an increase in depression, anger, and body dissatisfaction after viewing the self-slides; (c) participants indicated a decrease in body dissatisfaction after viewing the model-slides; and (d) viewing the control-slides did not result in affective changes. Findings suggest that viewing physique slides results in increased mood disturbance, regardless of BS level.

  17. Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

    SciTech Connect

    Hashem, Anwar M.; Van Domselaar, Gary; Li, Changgui; Wang, Junzhi; She, Yi-Min; Cyr, Terry D.; Sui, Jianhua; He, Runtao; Marasco, Wayne A.; Li, Xuguang

    2010-12-10

    Research highlights: {yields} The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. {yields} Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. {yields} The universal antibodies cross-neutralize different influenza A subtypes. {yields} The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it could be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.

  18. A conserved flagellar pocket exposed high mannose moiety is used by African trypanosomes as a host cytokine binding molecule.

    PubMed

    Magez, S; Radwanska, M; Stijlemans, B; Xong, H V; Pays, E; De Baetselier, P

    2001-09-07

    Trypanosomes use antigenic variation of their variant-specific surface glycoprotein (VSG) coat as defense against the host immune system. However, in order to sustain their growth, they need to expose conserved epitopes, allowing host macromolecule binding and receptor-mediated endocytosis. Here we show that Trypanosoma brucei uses the conserved chitobiose-oligomannose (GlcNAc(2)-Man(5-9)) moieties of its VSG as a binding ligand for tumor necrosis factor (TNF), a host cytokine with lectin-like properties. As endocytosis in trypanosomes is restricted to the flagellar pocket, we show that soluble flagellar pocket extracts, and in particular soluble VSG, inhibit the binding of (125)I-TNF to trypanosomes. The interaction between TNF and VSG is confirmed by affinity chromatography, biosensor, and dot-blot affinity measurements, and soluble VSG inhibition of TNF-mediated trypanolysis. In all approaches, removal of N-linked carbohydrates abrogates the TNF-VSG interaction. In addition, synthetic high mannose oligosaccharides can block TNF-VSG interactions, and a VSG glycopeptide carrying the GlcNAc(2)-Man(5-9) moiety is shown to inhibit TNF-mediated trypanosome killing in mixed parasite/macrophage cell cultures. Together, these results support the observation that TNF plays a role in growth control of trypanosomes and, moreover, suggest that, by the use of conserved VSG carbohydrates as lectin-binding epitopes, trypanosomes can limit the necessity to express large numbers of invariant surface exposed receptors.

  19. Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing.

    PubMed

    Xu, Liang; Wang, Yan; Xu, Yuanyuan; Wang, Liangju; Zhai, Lulu; Zhu, Xianwen; Gong, Yiqin; Ye, Shan; Liu, Liwang

    2013-03-01

    MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.

  20. Identification and analysis of a highly conserved chemotaxis gene cluster in Shewanella species.

    SciTech Connect

    Li, J.; Romine, Margaret F.; Ward, M.

    2007-08-01

    A conserved cluster of chemotaxis genes was identified from the genome sequences of fifteen Shewanella species. An in-frame deletion of the cheA-3 gene, which is located in this cluster, was created in S. oneidensis MR-1 and the gene shown to be essential for chemotactic responses to anaerobic electron acceptors. The CheA-3 protein showed strong similarity to Vibrio cholerae CheA-2 and P. aeruginosa CheA-1, two proteins that are also essential for chemotaxis. The genes encoding these proteins were shown to be located in chemotaxis gene clusters closely related to the cheA-3-containing cluster in Shewanella species. The results of this study suggest that a combination of gene neighborhood and homology analyses may be used to predict which cheA genes are essential for chemotaxis in groups of closely related microorganisms.

  1. Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies

    PubMed Central

    Zhang, Shuxiao; Ross, Kevin D.; Seidner, Glen A.; Gorman, Michael R.; Poon, Tiffany H.; Wang, Xiaobo; Keithley, Elizabeth M.; Lee, Patricia N.; Martindale, Mark Q.; Joiner, William J.; Hamilton, Bruce A.

    2015-01-01

    Many protein-coding genes identified by genome sequencing remain without functional annotation or biological context. Here we define a novel protein-coding gene, Nmf9, based on a forward genetic screen for neurological function. ENU-induced and genome-edited null mutations in mice produce deficits in vestibular function, fear learning and circadian behavior, which correlated with Nmf9 expression in inner ear, amygdala, and suprachiasmatic nuclei. Homologous genes from unicellular organisms and invertebrate animals predict interactions with small GTPases, but the corresponding domains are absent in mammalian Nmf9. Intriguingly, homozygotes for null mutations in the Drosophila homolog, CG45058, show profound locomotor defects and premature death, while heterozygotes show striking effects on sleep and activity phenotypes. These results link a novel gene orthology group to discrete neurological functions, and show conserved requirement across wide phylogenetic distance and domain level structural changes. PMID:26131556

  2. A highly conserved novel family of mammalian developmental transcription factors related to Drosophila grainyhead.

    PubMed

    Wilanowski, Tomasz; Tuckfield, Annabel; Cerruti, Loretta; O'Connell, Sinead; Saint, Robert; Parekh, Vishwas; Tao, Jianning; Cunningham, John M; Jane, Stephen M

    2002-06-01

    The Drosophila transcription factor Grainyhead regulates several key developmental processes. Three mammalian genes, CP2, LBP-1a and LBP-9 have been previously identified as homologues of grainyhead. We now report the cloning of two new mammalian genes (Mammalian grainyhead (MGR) and Brother-of-MGR (BOM)) and one new Drosophila gene (dCP2) that rewrite the phylogeny of this family. We demonstrate that MGR and BOM are more closely related to grh, whereas CP2, LBP-1a and LBP-9 are descendants of the dCP2 gene. MGR shares the greatest sequence homology with grh, is expressed in tissue-restricted patterns more comparable to grh and binds to and transactivates the promoter of the human Engrailed-1 gene, the mammalian homologue of the key grainyhead target gene, engrailed. This sequence and functional conservation indicates that the new mammalian members of this family play important developmental roles.

  3. High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis).

    PubMed

    Wang, Fengde; Li, Libin; Liu, Lifeng; Li, Huayin; Zhang, Yihui; Yao, Yingyin; Ni, Zhongfu; Gao, Jianwei

    2012-07-01

    MicroRNAs (miRNAs) are a class of 21-24 nucleotide non-coding RNAs that down-regulate gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in a few model plant species such as Arabidopsis, rice and Populus, and partially investigated in other non-model plant species. However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.

  4. The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

    PubMed

    Webb, Matthew H; Terauds, Aleks; Tulloch, Ayesha; Bell, Phil; Stojanovic, Dejan; Heinsohn, Robert

    2017-01-28

    The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic, with serious implications for conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. Here we quantify dynamic change in availability and use of key ecological resources required for breeding (i.e. food and nesting sites) for a critically endangered nomadic habitat specialist, the swift parrot (Lathamus discolor). We compare estimates of occupied habitat (km(2) ) derived from dynamic presence-background data climatic models to those derived from dynamic occupancy models that include a direct measure of food availability. We also compare estimates that incorporate fine resolution information on key ecological resources (i.e functional habitats) into distribution maps with more common approaches that typically focus on broader climatic suitability. For all models, both the extent and spatial location of occupied areas varied dramatically over the study period. The occupancy models produced significantly smaller (up to an order of magnitude) and more spatially discrete estimates of occupied habitat than climate-based models. Estimates accounting for the area of functional habitats were also significantly smaller than estimates based only on occupied habitat. Importantly, an increase (or decrease) in one functional habitat did not necessarily correspond to changes in the other, with consequences for overall habitat functionality. We argue that these patterns are typical for mobile resource specialists, but currently go unnoticed due to limited data on (1) species' presence/absence and (2) availability of key resources. Understanding changes in the relative availability of functional habitats is crucial to informing conservation planning and accurately assessing extinction risk for mobile

  5. Some Factors That Affecting the Performance of Mathematics Teachers in Junior High School in Medan

    ERIC Educational Resources Information Center

    Manullang, Martua; Rajagukguk, Waminton

    2016-01-01

    Some Factor's That Affecting The Mathematic Teacher Performance For Junior High School In Medan. This research will examine the effect of direct and indirect of the Organizational Knowledge towards the achievement motivation, decision making, organizational commitment, the performance of mathematics teacher. The research method is a method of…

  6. Factors Affecting University Entrants' Performance in High-Stakes Tests: A Multiple Regression Analysis

    ERIC Educational Resources Information Center

    Uy, Chin; Manalo, Ronaldo A.; Cabauatan, Ronaldo R.

    2015-01-01

    In the Philippines, students seeking admission to a university are usually required to meet certain entrance requirements, including passing the entrance examinations with questions on IQ and English, mathematics, and science. This paper aims to determine the factors that affect the performance of entrants into business programmes in high-stakes…

  7. Factors Affecting Effective Teaching and Learning of Economics in Some Ogbomosho High Schools, Oyo State, Nigeria

    ERIC Educational Resources Information Center

    Ojo, Gbemisola Motunrayo; Nkoyane, Vusy

    2016-01-01

    This study was carried out to examine the present curriculum of Economics as a subject in some Ogbomoso Senior High Schools and to determine factors affecting effective teaching of economics in the schools. Variables such as number of students, teachers' ratio available textbooks were also examined. The study adopted descriptive design since it is…

  8. Applications of very high-resolution imagery in the study and conservation of large predators in the Southern Ocean.

    PubMed

    Larue, Michelle A; Knight, Joseph

    2014-12-01

    The Southern Ocean is one of the most rapidly changing ecosystems on the planet due to the effects of climate change and commercial fishing for ecologically important krill and fish. Because sea ice loss is expected to be accompanied by declines in krill and fish predators, decoupling the effects of climate and anthropogenic changes on these predator populations is crucial for ecosystem-based management of the Southern Ocean. We reviewed research published from 2007 to 2014 that incorporated very high-resolution satellite imagery to assess distribution, abundance, and effects of climate and other anthropogenic changes on populations of predators in polar regions. Very high-resolution imagery has been used to study 7 species of polar animals in 13 papers, many of which provide methods through which further research can be conducted. Use of very high-resolution imagery in the Southern Ocean can provide a broader understanding of climate and anthropogenic forces on populations and inform management and conservation recommendations. We recommend that conservation biologists continue to integrate high-resolution remote sensing into broad-scale biodiversity and population studies in remote areas, where it can provide much needed detail.

  9. High root temperature affects the tolerance to high light intensity in Spathiphyllum plants.

    PubMed

    Soto, Adriana; Hernández, Laura; Quiles, María José

    2014-10-01

    Spathiphyllum wallisii plants were sensitive to temperature stress under high illumination, although the susceptibility of leaves to stress may be modified by root temperature. Leaves showed higher tolerance to high illumination, in both cold and heat conditions, when the roots were cooled, probably because the chloroplast were protected by excess excitation energy dissipation mechanisms such as cyclic electron transport. When the roots were cooled both the activity of electron donation by NADPH and ferredoxin to plastoquinone and the amount of PGR5 polypeptide, an essential component of cyclic electron flow around PSI, increased. However, when the stems were heated or cooled under high illumination, but the roots were heated, the quantum yield of PSII decreased considerably and neither the electron donation activity by NADPH and ferredoxin to plastoquinone nor the amount of PGR5 polypeptide increased. In such conditions, the cyclic electron flow cannot be enhanced by high light and PSII is damaged as a result of insufficient dissipation of excess light energy. Additionally, the damage to PSII induced the increase in both chlororespiratory enzymes, NDH complex and PTOX.

  10. An adjoint method for a high-order discretization of deforming domain conservation laws for optimization of flow problems

    NASA Astrophysics Data System (ADS)

    Zahr, M. J.; Persson, P.-O.

    2016-12-01

    The fully discrete adjoint equations and the corresponding adjoint method are derived for a globally high-order accurate discretization of conservation laws on parametrized, deforming domains. The conservation law on the deforming domain is transformed into one on a fixed reference domain by the introduction of a time-dependent mapping that encapsulates the domain deformation and parametrization, resulting in an Arbitrary Lagrangian-Eulerian form of the governing equations. A high-order discontinuous Galerkin method is used to discretize the transformed equation in space and a high-order diagonally implicit Runge-Kutta scheme is used for the temporal discretization. Quantities of interest that take the form of space-time integrals are discretized in a solver-consistent manner. The corresponding fully discrete adjoint method is used to compute exact gradients of quantities of interest along the manifold of solutions of the fully discrete conservation law. These quantities of interest and their gradients are used in the context of gradient-based PDE-constrained optimization. The adjoint method is used to solve two optimal shape and control problems governed by the isentropic, compressible Navier-Stokes equations. The first optimization problem seeks the energetically optimal trajectory of a 2D airfoil given a required initial and final spatial position. The optimization solver, driven by gradients computed via the adjoint method, reduced the total energy required to complete the specified mission nearly an order of magnitude. The second optimization problem seeks the energetically optimal flapping motion and time-morphed geometry of a 2D airfoil given an equality constraint on the x-directed impulse generated on the airfoil. The optimization solver satisfied the impulse constraint to greater than 8 digits of accuracy and reduced the required energy between a factor of 2 and 10, depending on the value of the impulse constraint, as compared to the nominal configuration.

  11. Long-Term Exposure to High Altitude Affects Conflict Control in the Conflict-Resolving Stage.

    PubMed

    Ma, Hailin; Wang, Yan; Wu, Jianhui; Wang, Baoxi; Guo, Shichun; Luo, Ping; Han, Buxin

    2015-01-01

    The neurocognitive basis of the effect of long-term high altitude exposure on conflict control is unclear. Event related potentials (ERPs) were recorded in a flanker task to investigate the influence of high altitude on conflict control in the high-altitude group (who had lived at high altitude for three years but were born at low altitude) and the low-altitude group (living in low altitude only). Although altitude effect was not significant at the behavioral level, ERPs showed cognitive conflict modulation. The interaction between group and trial type was significant: P3 amplitude was greater in the low-altitude group than in the high-altitude group in the incongruent trial. This result suggests that long-term exposure to high altitude affects conflict control in the conflict-resolving stage, and that attentional resources are decreased to resist the conflict control in the high-altitude group.

  12. Human antibodies reveal a protective epitope that is highly conserved among human and nonhuman influenza A viruses.

    PubMed

    Grandea, Andres G; Olsen, Ole A; Cox, Thomas C; Renshaw, Mark; Hammond, Philip W; Chan-Hui, Po-Ying; Mitcham, Jennifer L; Cieplak, Witold; Stewart, Shaun M; Grantham, Michael L; Pekosz, Andrew; Kiso, Maki; Shinya, Kyoko; Hatta, Masato; Kawaoka, Yoshihiro; Moyle, Matthew

    2010-07-13

    Influenza remains a serious public health threat throughout the world. Vaccines and antivirals are available that can provide protection from infection. However, new viral strains emerge continuously because of the plasticity of the influenza genome, which necessitates annual reformulation of vaccine antigens, and resistance to antivirals can appear rapidly and become entrenched in circulating virus populations. In addition, the spread of new pandemic strains is difficult to contain because of the time required to engineer and manufacture effective vaccines. Monoclonal antibodies that target highly conserved viral epitopes might offer an alternative protection paradigm. Herein we describe the isolation of a panel of monoclonal antibodies derived from the IgG(+) memory B cells of healthy, human subjects that recognize a previously unknown conformational epitope within the ectodomain of the influenza matrix 2 protein, M2e. This antibody binding region is highly conserved in influenza A viruses, being present in nearly all strains detected to date, including highly pathogenic viruses that infect primarily birds and swine, and the current 2009 swine-origin H1N1 pandemic strain (S-OIV). Furthermore, these human anti-M2e monoclonal antibodies protect mice from lethal challenges with either H5N1 or H1N1 influenza viruses. These results suggest that viral M2e can elicit broadly cross-reactive and protective antibodies in humans. Accordingly, recombinant forms of these human antibodies may provide useful therapeutic agents to protect against infection from a broad spectrum of influenza A strains.

  13. Two ancient bacterial-like PPP family phosphatases from Arabidopsis are highly conserved plant proteins that possess unique properties.

    PubMed

    Uhrig, R Glen; Moorhead, Greg B

    2011-12-01

    Protein phosphorylation, catalyzed by the opposing actions of protein kinases and phosphatases, is a cornerstone of cellular signaling and regulation. Since their discovery, protein phosphatases have emerged as highly regulated enzymes with specificity that rivals their counteracting kinase partners. However, despite years of focused characterization in mammalian and yeast systems, many protein phosphatases in plants remain poorly or incompletely characterized. Here, we describe a bioinformatic, biochemical, and cellular examination of an ancient, Bacterial-like subclass of the phosphoprotein phosphatase (PPP) family designated the Shewanella-like protein phosphatases (SLP phosphatases). The SLP phosphatase subcluster is highly conserved in all plants, mosses, and green algae, with members also found in select fungi, protists, and bacteria. As in other plant species, the nucleus-encoded Arabidopsis (Arabidopsis thaliana) SLP phosphatases (AtSLP1 and AtSLP2) lack genetic redundancy and phylogenetically cluster into two distinct groups that maintain different subcellular localizations, with SLP1 being chloroplastic and SLP2 being cytosolic. Using heterologously expressed and purified protein, the enzymatic properties of both AtSLP1 and AtSLP2 were examined, revealing unique metal cation preferences in addition to a complete insensitivity to the classic serine/threonine PPP protein phosphatase inhibitors okadaic acid and microcystin. The unique properties and high conservation of the plant SLP phosphatases, coupled to their exclusion from animals, red algae, cyanobacteria, archaea, and most bacteria, render understanding the function(s) of this new subclass of PPP family protein phosphatases of particular interest.

  14. High diversity of methanotrophic bacteria in geothermal soils affected by high methane fluxes

    NASA Astrophysics Data System (ADS)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2014-05-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas 25 times as potent as CO2. Recently, it has been demonstrated that volcanic/geothermal soils act as source, but also as biological filter for methane release to the atmosphere. For long time, volcanic/geothermal soils has been considered inhospitable for methanotrophic microorganisms, but new extremophile methanotrophs belonging to Verrucomicrobia were identified in three different areas (Pozzuoli, Italy; Hell's Gate, New Zealand; Kamchatka, Russia), explaining anomalous behaviours in methane leakages of several geothermal/volcanic sites. Our aim was to increase the knowledge of the relationship between methane emissions from volcanic/geothermal areas and biological methane oxidation, by investigating a geothermal site of Pantelleria island (Italy). Pantelleria Island hosts a high enthalpy geothermal system characterized by high temperature, high CH4 and very low H2S fluxes. Such characteristics are reflected in potentially great supply of methane for methanotrophs and scarce presence of inhibitors of their activity (H2S and NH3) in the Pantelleria soils. Potential methanotrophic activity within these soils was already evidenced by the CH4/CO2 ratio of the flux measurements which was lower than that of the respective fumarolic manifestations indicating a loss of CH4 during the gas travel towards the earth's surface. In this study laboratory incubation experiments using soils sampled at Favara Grande, the main hydrothermal area of Pantelleria, showed very high methane consumption rates (up to 9500 ng CH4 h-1 g-1). Furthermore, microbiological and culture-independent molecular analyses allowed to detect the presence of methanotrophs affiliated to Gamma- and Alpha-Proteobacteria and to the newly discovered acidothermophilic methanotrophs Verrucomicrobia. Culturable methanotrophic Alpha-proteobacteria of the genus Methylocystis were isolated by

  15. The Highly Conserved Proline at Position 438 in Pseudorabies Virus gH Is Important for Regulation of Membrane Fusion

    PubMed Central

    Schröter, Christina; Klupp, Barbara G.; Fuchs, Walter; Gerhard, Marika; Backovic, Marija; Rey, Felix A.

    2014-01-01

    ABSTRACT Membrane fusion in herpesviruses requires viral glycoproteins (g) gB and gH/gL. While gB is considered the actual fusion protein but is nonfusogenic per se, the function of gH/gL remains enigmatic. Crystal structures for different gH homologs are strikingly similar despite only moderate amino acid sequence conservation. A highly conserved sequence motif comprises the residues serine-proline-cysteine corresponding to positions 437 to 439 in pseudorabies virus (PrV) gH. The PrV-gH structure shows that proline438 induces bending at the end of an alpha-helix, thereby placing cysteine404 and cysteine439 in juxtaposition to allow formation of a strictly conserved disulfide bond. However, PrV vaccine strain Bartha unexpectedly carries a serine at this conserved position. To test the influence of this substitution, we constructed different gH chimeras carrying proline or serine at position 438 in gH derived from either PrV strain Kaplan or strain Bartha. Mutants expressing gH with serine438 showed reduced fusion activity in transient-fusion assays and during infection, with delayed penetration kinetics and a small-plaque phenotype which indicates that proline438 is important for efficient fusion. A more drastic effect was observed when disulfide bond formation was completely blocked by mutation of cysteine404 to serine. Although PrV expressing gHC404S was viable, plaque size and penetration kinetics were drastically reduced. Alteration of serine438 to proline in gH of strain Bartha enhanced cell-to-cell spread and penetration kinetics, but restoration of full activity required additional alteration of aspartic acid to valine at position 59. IMPORTANCE The role of the gH/gL complex in herpesvirus membrane fusion is still unclear. Structural studies predicted a critical role for proline438 in PrV gH to allow the formation of a conserved disulfide bond and correct protein folding. Functional analyses within this study corroborated these structural predictions

  16. Verbal marking of affect by children with Asperger Syndrome and high functioning autism during spontaneous interactions with family members.

    PubMed

    Müller, Eve; Schuler, Adriana

    2006-11-01

    Verbal marking of affect by older children with Asperger Syndrome (AS) and high functioning autism (HFA) during spontaneous interactions is described. Discourse analysis of AS and HFA and typically developing children included frequency of affective utterances, affective initiations, affective labels and affective explanations, attribution of affective responses to self and others, and positive and negative markers of affect. Findings indicate that children with AS and HFA engaged in a higher proportion of affect marking and provided a higher proportion of affective explanations than typically developing children, yet were less likely to initiate affect marking sequences or talk about the affective responses of others. No significant differences were found between groups in terms of the marking of positive and negative affect.

  17. Individual differences in beat perception affect gait responses to low- and high-groove music.

    PubMed

    Leow, Li-Ann; Parrott, Taylor; Grahn, Jessica A

    2014-01-01

    Slowed gait in patients with Parkinson's disease (PD) can be improved when patients synchronize footsteps to isochronous metronome cues, but limited retention of such improvements suggest that permanent cueing regimes are needed for long-term improvements. If so, music might make permanent cueing regimes more pleasant, improving adherence; however, music cueing requires patients to synchronize movements to the "beat," which might be difficult for patients with PD who tend to show weak beat perception. One solution may be to use high-groove music, which has high beat salience that may facilitate synchronization, and affective properties, which may improve motivation to move. As a first step to understanding how beat perception affects gait in complex neurological disorders, we examined how beat perception ability affected gait in neurotypical adults. Synchronization performance and gait parameters were assessed as healthy young adults with strong or weak beat perception synchronized to low-groove music, high-groove music, and metronome cues. High-groove music was predicted to elicit better synchronization than low-groove music, due to its higher beat salience. Two musical tempi, or rates, were used: (1) preferred tempo: beat rate matched to preferred step rate and (2) faster tempo: beat rate adjusted to 22.5% faster than preferred step rate. For both strong and weak beat-perceivers, synchronization performance was best with metronome cues, followed by high-groove music, and worst with low-groove music. In addition, high-groove music elicited longer and faster steps than low-groove music, both at preferred tempo and at faster tempo. Low-groove music was particularly detrimental to gait in weak beat-perceivers, who showed slower and shorter steps compared to uncued walking. The findings show that individual differences in beat perception affect gait when synchronizing footsteps to music, and have implications for using music in gait rehabilitation.

  18. STT3, a highly conserved protein required for yeast oligosaccharyl transferase activity in vivo.

    PubMed Central

    Zufferey, R; Knauer, R; Burda, P; Stagljar, I; te Heesen, S; Lehle, L; Aebi, M

    1995-01-01

    N-linked glycosylation is a ubiquitous protein modification, and is essential for viability in eukaryotic cells. A lipid-linked core-oligosaccharide is assembled at the membrane of the endoplasmic reticulum and transferred to selected asparagine residues of nascent polypeptide chains by the oligosaccharyl transferase (OTase) complex. Based on the synthetic lethal phenotype of double mutations affecting the assembly of the lipid-linked core-oligosaccharide and the OTase activity, we have performed a novel screen for mutants in Saccharomyces cerevisiae with altered N-linked glycosylation. Besides novel mutants deficient in the assembly of the lipid-linked oligosaccharide (alg mutants), we identified the STT3 locus as being required for OTase activity in vivo. The essential STT3 protein is approximately 60% identical in amino acid sequence to its human homologue. A mutation in the STT3 locus affects substrate specificity of the OTase complex in vivo and in vitro. In stt3-3 cells very little glycosyl transfer occurs from incomplete lipid-linked oligosaccharide, whereas the transfer of full-length Glc3Man9GlcNAc2 is hardly affected as compared with wild-type cells. Depletion of the STT3 protein results in loss of transferase activity in vivo and a deficiency in the assembly of OTase complex. Images PMID:7588624

  19. Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase

    PubMed Central

    Sohn, Young-Sik; Lee, Seong-Gyu; Lee, Kwang-Hoon; Ku, Bonsu; Shin, Ho-Chul; Cha, Sun-Shin; Kim, Yeon-Gil; Lee, Hyun Sook; Kang, Sung-Gyun; Oh, Byung-Ha

    2016-01-01

    A hypothetical protein TON_0340 of a Thermococcus species is a protein conserved in a variety of organisms including human. Herein, we present four different crystal structures of TON_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. Biochemical and mutational analyses involving many phosphorous compounds show that TON_0340 is a Mn2+-dependent phosphatase. Mg2+ binds to TON_0340 less tightly and activates the phosphatase activity less efficiently than Mn2+. Whereas Ca2+ and Zn2+ are able to bind to the protein, they are unable to activate its enzymatic activity. Since the active-site cavity is small and largely composed of nearly invariant stretches of 11 or 13 amino acids, the physiological substrates of TON_0340 and its homologues are likely to be a small and the same molecule. The Mn2+-bound TON_0340 structure provides a canonical model for the ubiquitously present TON_0340 homologues and lays a strong foundation for the elucidation of their substrate and biological function. PMID:27907125

  20. Low molecular weight serine protease inhibitors from insects are proteins with highly conserved sequences.

    PubMed

    Boigegrain, R A; Pugnière, M; Paroutaud, P; Castro, B; Brehélin, M

    2000-02-01

    A low molecular weight protease inhibitor peptide found in ovaries of the desert locust Schistocerca gregaria (SGPI-2), was purified from plasma of the same locust and sequenced. It was named SGCI. It was found active towards chymotrypsin and human leukocyte elastase. SGCI was synthesized using a solid-phase procedure and the sequence of its reactive site for chymotrypsin was determined. Compared with an inhibitor purified earlier from another locust species, the total sequence of SGCI showed 88% identity. In particular, the sequence of the reactive site of these inhibitors was identical. Our search for a closely related peptide in an insect species far removed from locusts, the lepidopteran Spodoptera littoralis, was unfruitful but a different chymotrypsin inhibitor, belonging to the Kazal family, was found whose mass is greater than that of SGCI (20 vs 3.6 kDa). Its N-terminal sequence shares 80% identity with that of a chymotrypsin inhibitor purified earlier from the haemolymph of another lepidopteran. Conservation of the amino acid sequence in the reactive site seems to be an exception among protease inhibitors.

  1. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets.

    PubMed

    Abergel, Chantal; Coutard, Bruno; Byrne, Deborah; Chenivesse, Sabine; Claude, Jean-Baptiste; Deregnaucourt, Céline; Fricaux, Thierry; Gianesini-Boutreux, Celine; Jeudy, Sandra; Lebrun, Régine; Maza, Caroline; Notredame, Cédric; Poirot, Olivier; Suhre, Karsten; Varagnol, Majorie; Claverie, Jean-Michel

    2003-01-01

    With more than 100 antibacterial drugs at our disposal in the 1980's, the problem of bacterial infection was considered solved. Today, however, most hospital infections are insensitive to several classes of antibacterial drugs, and deadly strains of Staphylococcus aureus resistant to vancomycin--the last resort antibiotic--have recently begin to appear. Other life-threatening microbes, such as Enterococcus faecalis and Mycobacterium tuberculosis are already able to resist every available antibiotic. There is thus an urgent, and continuous need for new, preferably large-spectrum, antibacterial molecules, ideally targeting new biochemical pathways. Here we report on the progress of our structural genomics program aiming at the discovery of new antibacterial gene targets among evolutionary conserved genes of uncharacterized function. A series of bioinformatic and comparative genomics analyses were used to identify a set of 221 candidate genes common to Gram-positive and Gram-negative bacteria. These genes were split between two laboratories. They are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallization, X-ray diffraction, structure interpretation, and function prediction. We describe here our strategies for the 111 genes processed in our laboratory. Bioinformatics is used at most stages of the production process and out of 111 genes processed--and 17 months into the project--108 have been successfully cloned, 103 have exhibited detectable expression, 84 have led to the production of soluble protein, 46 have been purified, 12 have led to usable crystals, and 7 structures have been determined.

  2. Choristoneura fumiferana Granulovirus p74 protein, a highly conserved baculoviral envelope protein.

    PubMed

    Rashidan, Kianoush Khajeh; Nassoury, Nasha; Tazi, Samia; Giannopoulos, Paresa N; Guertin, Claude

    2003-09-30

    A gene that encodes a homologue to baculoviral p74, an envelope-associated viral structural protein, has been identified and sequenced on the genome of Choristoneura fumiferana granulovirus (ChfuGV). A part of the ChfuGV p74 gene was located on an 8.9 kb BamHI subgenomic fragment using different sets of degenerated primers. These were designed using the results of the protein sequencing of a major 74 kDa structural protein that is associated with the occlusion-derived virus (ODV). The gene has a 1992 nucleotide (nt) open-reading frame (ORF) that encodes a protein with 663 amino acids with a predicted molecular mass of 74,812 Da. Comparative studies revealed the presence of two major conserved regions in the ChfuGV p74 protein. This study also shows that all of the p74 proteins contain two putative transmembrane domains at their C-terminal segments. At the nucleotide sequence level, two late promoter motifs (TAAG and GTAAG) were located upstream of the first ATG of the p74 gene. The gene contained a canonical poly(A) signal, AATAAA, at its 3 non-translated region. A phylogenetic tree for baculoviral p74 was constructed using a maximum parsimony analysis. The phylogenetic estimation demonstrated that ChfuGV p74 is related the closest to those of Cydia pomonella granulovirus (CpGV) and Phthorimaea operculella granulovirus (PhopGV).

  3. Unique genome of dicyemid mesozoan: highly shortened spliceosomal introns in conservative exon/intron structure.

    PubMed

    Ogino, Kazutoyo; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2010-01-01

    Dicyemids are enigmatic endoparasites, or endosymbionts, living in the renal sac of benthic cephalopod molluscs. The body of dicyemids consists of only 9-41 cells, with neither extracellular matrices nor differentiated tissues. Due to the unusually simple body organization, dicyemids have long been the subject of phylogenetic controversy. Molecular evidences suggest dicyemids are lophotrochozoans that have secondarily lost many morphological characters. We studied 40 genes of the dicyemid Dicyema japonicum and found that their spliceosomal introns are very short (mean length=26 bp). This size was shorter than that of introns of animals, such as Fugu rubripes and Oikopleura dioica which possess compact genome and introns. In the intron size, the dicyemid was nearly equal to the chlorarachniophyte Bigelowiella natans nucleomorph (18-21 bp) which has the shortest introns of any known eukaryote. Despite the short introns, the intron density (5.3 introns/gene) of the dicyemid is similar to that in model invertebrates. In addition, the exon/intron structure of the dicyemid is more similar to vertebrates than to the model invertebrates. These results suggest that the positions of the introns are possibly conserved under functional constraints.

  4. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species

    PubMed Central

    2013-01-01

    Background Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient “off-the-shelf” markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions When combined with previously described conserved loci, this new set of conserved markers will not only

  5. Novel urban ecosystems, biodiversity, and conservation.

    PubMed

    Kowarik, Ingo

    2011-01-01

    With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation.

  6. 7 CFR Exhibit M to Subpart G of... - Implementation Procedures for the Conservation of Wetlands and Highly Erodible Land Affecting...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... operational or material costs such as fuel, seed, fertilizer, and pesticide costs; (7) Within the crop year in... any associated operational or materials costs such as fuel, seed, fertilizer and pesticide costs; or... commodity is possible (a) as a result of a natural condition, such as drought, and (b) without action by...

  7. 7 CFR Exhibit M to Subpart G of... - Implementation Procedures for the Conservation of Wetlands and Highly Erodible Land Affecting...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... operational or material costs such as fuel, seed, fertilizer, and pesticide costs; (7) Within the crop year in... any associated operational or materials costs such as fuel, seed, fertilizer and pesticide costs; or... commodity is possible (a) as a result of a natural condition, such as drought, and (b) without action by...

  8. 7 CFR Exhibit M to Subpart G of... - Implementation Procedures for the Conservation of Wetlands and Highly Erodible Land Affecting...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... operational or material costs such as fuel, seed, fertilizer, and pesticide costs; (7) Within the crop year in... any associated operational or materials costs such as fuel, seed, fertilizer and pesticide costs; or... commodity is possible (a) as a result of a natural condition, such as drought, and (b) without action by...

  9. 7 CFR Exhibit M to Subpart G of... - Implementation Procedures for the Conservation of Wetlands and Highly Erodible Land Affecting...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... operational or material costs such as fuel, seed, fertilizer, and pesticide costs; (7) Within the crop year in... any associated operational or materials costs such as fuel, seed, fertilizer and pesticide costs; or... commodity is possible (a) as a result of a natural condition, such as drought, and (b) without action by...

  10. Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system.

    PubMed

    Lean, J; Hammer, M P; Unmack, P J; Adams, M; Beheregaray, L B

    2017-04-01

    Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.

  11. Mechanisms regulating GLUT4 transcription in skeletal muscle cells are highly conserved across vertebrates.

    PubMed

    Marín-Juez, Rubén; Diaz, Mónica; Morata, Jordi; Planas, Josep V

    2013-01-01

    The glucose transporter 4 (GLUT4) plays a key role in glucose uptake in insulin target tissues. This transporter has been extensively studied in many species in terms of its function, expression and cellular traffic and complex mechanisms are involved in its regulation at many different levels. However, studies investigating the transcription of the GLUT4 gene and its regulation are scarce. In this study, we have identified the GLUT4 gene in a teleost fish, the Fugu (Takifugu rubripes), and have cloned and characterized a functional promoter of this gene for the first time in a non-mammalian vertebrate. In silico analysis of the Fugu GLUT4 promoter identified potential binding sites for transcription factors such as SP1, C/EBP, MEF2, KLF, SREBP-1c and GC-boxes, as well as a CpG island, but failed to identify a TATA box. In vitro analysis revealed three transcription start sites, with the main residing 307 bp upstream of the ATG codon. Deletion analysis determined that the core promoter was located between nucleotides -132/+94. By transfecting a variety of 5´deletion constructs into L6 muscle cells we have determined that Fugu GLUT4 promoter transcription is regulated by insulin, PG-J2, a PPARγ agonist, and electrical pulse stimulation. Furthermore, our results suggest the implication of motifs such as PPARγ/RXR and HIF-1α in the regulation of Fugu GLUT4 promoter activity by PPARγ and contractile activity, respectively. These data suggest that the characteristics and regulation of the GLUT4 promoter have been remarkably conserved during the evolution from fish to mammals, further evidencing the important role of GLUT4 in metabolic regulation in vertebrates.

  12. Regulation of photoreceptor gene transcription via a highly conserved transcriptional regulatory element by vsx gene products

    PubMed Central

    Pan, Yi; Comiskey, Daniel F.; Kelly, Lisa E.; Chandler, Dawn S.

    2016-01-01

    Purpose The photoreceptor conserved element-1 (PCE-1) sequence is found in the transcriptional regulatory regions of many genes expressed in photoreceptors. The retinal homeobox (Rx or Rax) gene product functions by binding to PCE-1 sites. However, other transcriptional regulators have also been reported to bind to PCE-1. One of these, vsx2, is expressed in retinal progenitor and bipolar cells. The purpose of this study is to identify Xenopus laevis vsx gene products and characterize vsx gene product expression and function with respect to the PCE-1 site. Methods X. laevis vsx gene products were amplified with PCR. Expression patterns were determined with in situ hybridization using whole or sectioned X. laevis embryos and digoxigenin- or fluorescein-labeled antisense riboprobes. DNA binding characteristics of the vsx gene products were analyzed with electrophoretic mobility shift assays (EMSAs) using in vitro translated proteins and radiolabeled oligonucleotide probes. Gene transactivation assays were performed using luciferase-based reporters and in vitro transcribed effector gene products, injected into X. laevis embryos. Results We identified one vsx1 and two vsx2 gene products. The two vsx2 gene products are generated by alternate mRNA splicing. We verified that these gene products are expressed in the developing retina and that expression resolves into distinct cell types in the mature retina. Finally, we found that vsx gene products can bind the PCE-1 site in vitro and that the two vsx2 isoforms have different gene transactivation activities. Conclusions vsx gene products are expressed in the developing and mature neural retina. vsx gene products can bind the PCE-1 site in vitro and influence the expression of a rhodopsin promoter-luciferase reporter gene. The two isoforms of vsx have different gene transactivation activities in this reporter gene system. PMID:28003732

  13. The blues broaden, but the nasty narrows: attentional consequences of negative affects low and high in motivational intensity.

    PubMed

    Gable, Philip; Harmon-Jones, Eddie

    2010-02-01

    Positive and negative affects high in motivational intensity cause a narrowing of attentional focus. In contrast, positive affects low in motivational intensity cause a broadening of attentional focus. The attentional consequences of negative affects low in motivational intensity have not been experimentally investigated. Experiment 1 compared the attentional consequences of negative affect low in motivational intensity (sadness) relative to a neutral affective state. Results indicated that low-motivation negative affect caused attentional broadening. Experiment 2 found that disgust, a high-motivation negative affect not previously investigated in attentional studies, narrowed attentional focus. These experiments support the conceptual model linking high-motivation affective states to narrowed attention and low-motivation affective states to broadened attention.

  14. The New Zealand District High School: A Case Study of the Conservative Politics of Rural Education

    ERIC Educational Resources Information Center

    Lee, Howard

    2005-01-01

    From the late 1860s, when they were established in New Zealand, the district high (now area) schools have sought to provide academically able rural youth with the opportunity to study a high status, abstract, examination-oriented curriculum. This curriculum enabled them to pursue clerical and professional careers in the towns and cities. However,…

  15. 77 FR 18963 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-29

    ... of the Framework Document for High-Intensity Discharge Lamps AGENCY: Office of Energy Efficiency and...) Lamps. The comment period is extended to April 12, 2012. DATES: The comment period for the HID Lamps... availability of framework document for high-intensity discharge (HID) lamps, initiating the rulemaking and...

  16. Factors affecting frequency and orbit utilization by high power transmission satellite systems

    NASA Technical Reports Server (NTRS)

    Kuhns, P. W.; Miller, E. F.; Malley, T. A.

    1972-01-01

    The factors affecting the sharing of the geostationary orbit by high power (primarily television) satellite systems having the same or adjacent coverage areas and by satellites occupying the same orbit segment are examined and examples using the results of computer computations are given. The factors considered include: required protection ratio, receiver antenna patterns, relative transmitter power, transmitter antenna patterns, satellite grouping, and coverage pattern overlap. The results presented indicated the limits of system characteristics and orbit deployment which can result from mixing systems.

  17. Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins.

    PubMed Central

    Gregory, S L; Kortschak, R D; Kalionis, B; Saint, R

    1996-01-01

    We reported the identification of a new family of DNA-binding proteins from our characterization of the dead ringer (dri) gene of Drosophila melanogaster. We show that dri encodes a nuclear protein that contains a sequence-specific DNA-binding domain that bears no similarity to known DNA-binding domains. A number of proteins were found to contain sequences homologous to this domain. Other proteins containing the conserved motif include yeast SWI1, two human retinoblastoma binding proteins, and other mammalian regulatory proteins. A mouse B-cell-specific regulator exhibits 75% identity with DRI over the 137-amino-acid DNA-binding domains of these proteins, indicating a high degree of conservation of this domain. Gel retardation and optimal binding site screens revealed that the in vitro sequence specificity of DRI is strikingly similar to that of many homeodomain proteins, although the sequence and predicted secondary structure do not resemble a homeodomain. The early general expression of dri and the similarity of DRI and homeodomain in vitro DNA-binding specificity compound the problem of understanding the in vivo specificity of action of these proteins. Maternally derived dri product is found throughout the embryo until germ band extension, when dri is expressed in a developmentally regulated set of tissues, including salivary gland ducts, parts of the gut, and a subset of neural cells. The discovery of this new, conserved DNA-binding domain offers an explanation for the regulatory activity of several important members of this class and predicts significant regulatory roles for the others. PMID:8622680

  18. High conservation of a 5' element required for RNA editing of a C target in chloroplast psbE transcripts.

    PubMed

    Hayes, Michael L; Hanson, Maureen R

    2008-09-01

    C-to-U editing modifies 30-40 distinct nucleotides within higher-plant chloroplast transcripts. Many C targets are located at the same position in homologous genes from different plants; these either could have emerged independently or could share a common origin. The 5' sequence GCCGUU, required for editing of C214 in tobacco psbE in vitro, is one of the few identified editing cis-elements. We investigated psbE sequences from many plant species to determine in what lineage(s) editing of psbE C214 emerged and whether the cis-element identified in tobacco is conserved in plants with a C214. The GCCGUU sequence is present at a high frequency in plants that carry a C214 in psbE. However, Sciadopitys verticillata (Pinophyta) edits C214 despite the presence of nucleotide differences compared to the conserved cis-element. The C214 site in psbE genes is represented in members of four branches of spermatophytes but not in gnetophytes, resulting in the parsimonious prediction that editing of psbE C214 was present in the ancestor of spermatophytes. Extracts from chloroplasts from a species that has a difference in the motif and lacks the C target are incapable of editing tobacco psbE C214 substrates, implying that the critical trans-acting protein factors were not retained without a C target. Because noncoding sequences are less constrained than coding regions, we analyzed sequences 5' to two C editing targets located within coding regions to search for possible editing-related conserved elements. Putative editing cis-elements were uncovered in the 5' UTRs near editing sites psbL C2 and ndhD C2.

  19. Affective profiles in Italian high school students: life satisfaction, psychological well-being, self-esteem, and optimism

    PubMed Central

    Di Fabio, Annamaria; Bucci, Ornella

    2015-01-01

    The affective profiles model distinguishes between individuals who are self-fulfilling (high positive affect, low negative affect), high affective (high positive affect, high negative affect), low affective (low positive affect, low negative affect), and self-destructive (low positive affect, high negative affect). The literature shows that the affective profiles model has been used with Swedish people in particular in order to determine differences among profiles in relation to life satisfaction, psychological well-being, self-esteem, and optimism. The present research investigated these differences in Italian high school students. Two studies were conducted: the first with 156 Italian high school students and the second with 148 Italian high school students. The first study analyzed differences among affective profiles with regard to life satisfaction and psychological well-being while the second study analyzed differences among affective profiles with regard to self-esteem and optimism. In the first study, the Positive and Negative Affect Schedule (PANAS), the Satisfaction with Life Scale, and the Meaningful Life Measure were administered to the participants. In the second study, the PANAS, the Self-Esteem Scale, the Life Orientation Test-revised were administered to the participants. The results of the first study showed that, with respect to the other profiles, the self-fulfilling participants had greater life satisfaction and psychological well-being. The results of the second study showed that, with respect to the other profiles, the self-fulfilling participants had higher self-esteem and optimism. These results revealed differences among affective profiles regarding life satisfaction, psychological well-being, self-esteem, and optimism in the Italian context as well thereby offering new possibilities for cross-cultural research and for enhancing self-fulfilling profiles. PMID:26388814

  20. Affective profiles in Italian high school students: life satisfaction, psychological well-being, self-esteem, and optimism.

    PubMed

    Di Fabio, Annamaria; Bucci, Ornella

    2015-01-01

    The affective profiles model distinguishes between individuals who are self-fulfilling (high positive affect, low negative affect), high affective (high positive affect, high negative affect), low affective (low positive affect, low negative affect), and self-destructive (low positive affect, high negative affect). The literature shows that the affective profiles model has been used with Swedish people in particular in order to determine differences among profiles in relation to life satisfaction, psychological well-being, self-esteem, and optimism. The present research investigated these differences in Italian high school students. Two studies were conducted: the first with 156 Italian high school students and the second with 148 Italian high school students. The first study analyzed differences among affective profiles with regard to life satisfaction and psychological well-being while the second study analyzed differences among affective profiles with regard to self-esteem and optimism. In the first study, the Positive and Negative Affect Schedule (PANAS), the Satisfaction with Life Scale, and the Meaningful Life Measure were administered to the participants. In the second study, the PANAS, the Self-Esteem Scale, the Life Orientation Test-revised were administered to the participants. The results of the first study showed that, with respect to the other profiles, the self-fulfilling participants had greater life satisfaction and psychological well-being. The results of the second study showed that, with respect to the other profiles, the self-fulfilling participants had higher self-esteem and optimism. These results revealed differences among affective profiles regarding life satisfaction, psychological well-being, self-esteem, and optimism in the Italian context as well thereby offering new possibilities for cross-cultural research and for enhancing self-fulfilling profiles.

  1. Electrodeposition of High Quality Nickel Phosphorous Alloys for Pollution Reduction and Energy Conservation

    NASA Technical Reports Server (NTRS)

    Engelhaupt, Darell; Ramsey, Brian

    2003-01-01

    NASA and the University of Alabama in Huntsville have developed ecologically friendly, versatile nickel and nickel cobalt phosphorous electroplating processes. Solutions show excellent performance with high efficiency for vastly extended throughput. Properties include, clean, low temperature operation (40 - 60 C), high Faradaic efficiency, low stress and high hardness. A variety of alloy and plating speed options are easily achieved from the same chemistry using soluble anodes for metal replacement with only 25% of the phosphorous additions required for electroless nickel. Thick deposits are easily achieved unattended, for electroforming freestanding shapes without buildup of excess orthophosphate or stripping of equipment.

  2. Electrodeposition of High Quality Nickel Phosphorous Alloys for Pollution Reduction and Energy Conservation

    NASA Technical Reports Server (NTRS)

    Engelhaupt, Darell; Ramsey, Brian

    2004-01-01

    NASA and the University of Alabama in Huntsville have developed ecologically friendly, versatile nickel and nickel cobalt phosphorous electroplating processes. Solutions show excellent performance with high efficiency for vastly extended throughput. Properties include, clean, low temperature operation (40 - 60 C), high Faradaic efficiency, low stress and high hardness. A variety of alloy and plating speed options are easily achieved from the same chemistry using soluble anodes for metal replacement with only 25% of the phosphorous additions required for electroless nickel. Thick deposits are easily achieved unattended, for electroforming freestanding shapes without buildup of excess orthophosphate or stripping of equipment.

  3. Variables Affecting Smooth Particle Hydrodynamics Simulation of High-Velocity Flyer Plate Impact Experiments

    SciTech Connect

    Somasundaram, Deepak S; Trabia, Mohamed; O'Toole, Brendan; Hixson, Robert S

    2014-01-23

    This paper describes our work to characterize the variables affecting the smoothed particle hydrodynamics (SPH) method in the LS-DYNA package for simulating high-velocity flyer plate impact experiments. LS-DYNA simulations are compared with one-dimensional experimental data of an oxygen-free high-conductivity (OFHC) copper flyer plate impacting another plate of the same material. The comparison is made by measuring the velocity of a point on the back surface of the impact plate using the velocity interferometer system for any reflector (VISAR) technique.

  4. High prevalence of affective disorders among adolescents living in Rural Zimbabwe.

    PubMed

    Langhaug, Lisa F; Pascoe, Sophie J; Mavhu, Webster; Woelk, Godfrey; Sherr, Lorraine; Hayes, Richard J; Cowan, Frances M

    2010-08-01

    Poor mental health accounts for considerable disease burden among young people globally. We investigated the prevalence and determinants of affective disorders among rural Zimbabwean youth in 2006. We undertook a cross-sectional survey among 1495 Zimbabwean youth aged 15-23 (median 18) from 12 rural communities in three provinces in south-eastern Zimbabwe. Mental health was assessed using the Shona Symptom Questionnaire (SSQ), a locally validated 14-item indigenous screening tool for affective disorders, notably depression and anxiety disorders. Participants scoring >or=8/14 were considered at risk of being affected and >or=11 as at risk of being severely affected. Most participants (93.1%) completed the SSQ. Of these, 51.7% (95%CI:49.0-54.3%) scored >or=8/14 and 23.8% (95%CI:21.5-26.0%) scored >or=11. Affective disorders were independently associated with household poverty (adjusted odds ratio (AOR) 1.9, 95%CI:1.4-2.7), living in a female-headed household (AOR 1.3, 95%CI:1.0-1.7), having moved home within last 5 years (AOR 1.4, 95%CI:1.0-1.9) and feeling stigmatized (AOR being shunned by others 3.7, 95%CI:2.5-5.7). There was a strong linear association between risk of affective disorders and sexual risk taking (ever sex AOR 1.5, 95%CI:1.0-2.4, and 2.8, 95%CI:1.9-4.2 for affected and severely affected, respectively, test for trend P < 0.001; >or=2 lifetime partners AOR 2.3, 95%CI:1.1-4.8 and 5.4, 95%CI:2.7-10.7, test for trend P < 0.001). This study indicates high levels of psychological morbidity among rural Zimbabwean youth which was associated with sexual risk taking. Interventions to prevent, identify and treat mental health disorders in this vulnerable population are urgently required. In HIV-endemic countries, such interventions may also help reduce HIV transmission.

  5. High Prevalence of Affective Disorders among Adolescents Living in Rural Zimbabwe

    PubMed Central

    Pascoe, Sophie J.; Mavhu, Webster; Woelk, Godfrey; Sherr, Lorraine; Hayes, Richard J.; Cowan, Frances M.

    2010-01-01

    Poor mental health accounts for considerable disease burden among young people globally. We investigated the prevalence and determinants of affective disorders among rural Zimbabwean youth in 2006. We undertook a cross-sectional survey among 1495 Zimbabwean youth aged 15–23 (median 18) from 12 rural communities in three provinces in south-eastern Zimbabwe. Mental health was assessed using the Shona Symptom Questionnaire (SSQ), a locally validated 14-item indigenous screening tool for affective disorders, notably depression and anxiety disorders. Participants scoring ≥8/14 were considered at risk of being affected and ≥11 as at risk of being severely affected. Most participants (93.1%) completed the SSQ. Of these, 51.7% (95%CI:49.0–54.3%) scored ≥8/14 and 23.8% (95%CI:21.5–26.0%) scored ≥11. Affective disorders were independently associated with household poverty (adjusted odds ratio (AOR) 1.9, 95%CI:1.4–2.7), living in a female-headed household (AOR 1.3, 95%CI:1.0–1.7), having moved home within last 5 years (AOR 1.4, 95%CI:1.0–1.9) and feeling stigmatized (AOR being shunned by others 3.7, 95%CI:2.5–5.7). There was a strong linear association between risk of affective disorders and sexual risk taking (ever sex AOR 1.5, 95%CI:1.0–2.4, and 2.8, 95%CI:1.9–4.2 for affected and severely affected, respectively, test for trend P < 0.001; ≥2 lifetime partners AOR 2.3, 95%CI:1.1–4.8 and 5.4, 95%CI:2.7–10.7, test for trend P < 0.001). This study indicates high levels of psychological morbidity among rural Zimbabwean youth which was associated with sexual risk taking. Interventions to prevent, identify and treat mental health disorders in this vulnerable population are urgently required. In HIV-endemic countries, such interventions may also help reduce HIV transmission. PMID:20571897

  6. Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans

    SciTech Connect

    Ji Qiongmei; Huang, C.-H. . E-mail: chuang@nybloodcenter.org; Peng Jianbin; Hashmi, Sarwar; Ye Tianzhang; Chen Ying

    2007-04-15

    We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans.

  7. Catchment-Scale Conservation Units Identified for the Threatened Yarra Pygmy Perch (Nannoperca obscura) in Highly Modified River Systems

    PubMed Central

    Brauer, Chris J.; Unmack, Peter J.; Hammer, Michael P.; Adams, Mark; Beheregaray, Luciano B.

    2013-01-01

    Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology. PMID:24349405

  8. Zooming in on the human-mouse comparative map: genome conservation re-examined on a high-resolution scale.

    PubMed

    Carver, E A; Stubbs, L

    1997-12-01

    Over the past decade, conservation of genetic linkage groups has been shown in mammals and used to great advantage, fueling significant exchanges of gene mapping and functional information especially between the genomes of humans and mice. As human physical maps increase in resolution from chromosome bands to nucleotide sequence, comparative alignments of mouse and human regions have revealed striking similarities and surprising differences between the genomes of these two best-mapped mammalian species. Whereas, at present, very few mouse and human regions have been compared on the physical level, existing studies provide intriguing insights to genome evolution, including the observation of recent duplications and deletions of genes that may play significant roles in defining some of the biological differences between the two species. Although high-resolution conserved marker-based maps are currently available only for human and mouse, a variety of new methods and resources are speeding the development of comparative maps of additional organisms. These advances mark the first step toward establishment of the human genome as a reference map for vertebrate species, providing evolutionary and functional annotation to human sequence and vast new resources for genetic analysis of a variety of commercially, medically, and ecologically important animal models.

  9. Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems.

    PubMed

    Brauer, Chris J; Unmack, Peter J; Hammer, Michael P; Adams, Mark; Beheregaray, Luciano B

    2013-01-01

    Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.

  10. Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation.

    PubMed

    Kondo, Hidemasa; Hanada, Yuichi; Sugimoto, Hiroshi; Hoshino, Tamotsu; Garnham, Christopher P; Davies, Peter L; Tsuda, Sakae

    2012-06-12

    Antifreeze proteins (AFPs) are found in organisms ranging from fish to bacteria, where they serve different functions to facilitate survival of their host. AFPs that protect freeze-intolerant fish and insects from internal ice growth bind to ice using a regular array of well-conserved residues/motifs. Less is known about the role of AFPs in freeze-tolerant species, which might be to beneficially alter the structure of ice in or around the host. Here we report the 0.95-Å high-resolution crystal structure of a 223-residue secreted AFP from the snow mold fungus Typhula ishikariensis. Its main structural element is an irregular β-helix with six loops of 18 or more residues that lies alongside an α-helix. β-Helices have independently evolved as AFPs on several occasions and seem ideally structured to bind to several planes of ice, including the basal plane. A novelty of the β-helical fold is the nonsequential arrangement of loops that places the N- and C termini inside the solenoid of β-helical coils. The ice-binding site (IBS), which could not be predicted from sequence or structure, was located by site-directed mutagenesis to the flattest surface of the protein. It is remarkable for its lack of regularity and its poor conservation in homologs from psychrophilic diatoms and bacteria and other fungi.

  11. High Elevation Refugia for Bombus terricola (Hymenoptera: Apidae) Conservation and Wild Bees of the White Mountain National Forest.

    PubMed

    Tucker, Erika M; Rehan, Sandra M

    2017-01-01

    Many wild bee species are in global decline, yet much is still unknown about their diversity and contemporary distributions. National parks and forests offer unique areas of refuge important for the conservation of rare and declining species populations. Here we present the results of the first biodiversity survey of the bee fauna in the White Mountain National Forest (WMNF). More than a thousand specimens were collected from pan and sweep samples representing 137 species. Three species were recorded for the first time in New England and an additional seven species were documented for the first time in the state of New Hampshire. Four introduced species were also observed in the specimens collected. A checklist of the species found in the WMNF, as well as those found previously in Strafford County, NH, is included with new state records and introduced species noted as well as a map of collecting locations. Of particular interest was the relatively high abundance of Bombus terricola Kirby 1837 found in many of the higher elevation collection sites and the single specimen documented of Bombus fervidus (Fabricius 1798). Both of these bumble bee species are known to have declining populations in the northeast and are categorized as vulnerable on the International Union for Conservation of Nature's Red List.

  12. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments.

    PubMed

    Karunadharma, Pabalu P; Basisty, Nathan; Chiao, Ying Ann; Dai, Dao-Fu; Drake, Rachel; Levy, Nick; Koh, William J; Emond, Mary J; Kruse, Shane; Marcinek, David; Maccoss, Michael J; Rabinovitch, Peter S

    2015-08-01

    The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.

  13. Circadian expression of the maize catalase Cat3 gene is highly conserved among diverse maize genotypes with structurally different promoters.

    PubMed Central

    Polidoros, A N; Scandalios, J G

    1998-01-01

    The Cat3 gene of maize exhibits a transcriptionally regulated circadian rhythm. In the present study we examined the following: (1) the extent of the circadian Cat3 expression between maize genotypes of diverse origin; (2) the functional significance of a Tourist transposable element located in the Cat3 promoter of the inbred line W64A, which harbors putative regulatory elements (GATA repeat, CCAAT boxes) shown to be involved in the light induction and circadian regulation of the Arabidopsis CAB2, as well as other plant genes; and (3) aspects of the physiological role of CAT-3 in maize metabolism. Results confirm that the circadian Cat3 expression is a general phenomenon in maize. Regulation of Cat3 gene expression is not dependent on the presence of the Tourist element in the promoter of the gene nor on the presence of motifs similar to those found significant in the circadian expression of the Arabidopsis CAB2 gene. Structural diversity was revealed in the Cat3 promoters of maize genotypes of diverse origins. However, highly conserved regions with putative regulatory motifs were identified. Relevance of the conserved regions to the circadian regulation of the gene is discussed. Possible physiological roles of CAT-3 are suggested. PMID:9584112

  14. High Elevation Refugia for Bombus terricola (Hymenoptera: Apidae) Conservation and Wild Bees of the White Mountain National Forest

    PubMed Central

    Tucker, Erika M.; Rehan, Sandra M.

    2017-01-01

    Many wild bee species are in global decline, yet much is still unknown about their diversity and contemporary distributions. National parks and forests offer unique areas of refuge important for the conservation of rare and declining species populations. Here we present the results of the first biodiversity survey of the bee fauna in the White Mountain National Forest (WMNF). More than a thousand specimens were collected from pan and sweep samples representing 137 species. Three species were recorded for the first time in New England and an additional seven species were documented for the first time in the state of New Hampshire. Four introduced species were also observed in the specimens collected. A checklist of the species found in the WMNF, as well as those found previously in Strafford County, NH, is included with new state records and introduced species noted as well as a map of collecting locations. Of particular interest was the relatively high abundance of Bombus terricola Kirby 1837 found in many of the higher elevation collection sites and the single specimen documented of Bombus fervidus (Fabricius 1798). Both of these bumble bee species are known to have declining populations in the northeast and are categorized as vulnerable on the International Union for Conservation of Nature’s Red List. PMID:28130453

  15. A monoclonal antibody targeting a highly conserved epitope in influenza B neuraminidase provides protection against drug resistant strains.

    PubMed

    Doyle, Tracey M; Li, Changgui; Bucher, Doris J; Hashem, Anwar M; Van Domselaar, Gary; Wang, Junzhi; Farnsworth, Aaron; She, Yi-Min; Cyr, Terry; He, Runtao; Brown, Earl G; Hurt, Aeron C; Li, Xuguang

    2013-11-08

    All influenza viral neuraminidases (NA) of both type A and B viruses have only one universally conserved sequence located between amino acids 222-230. A monoclonal antibody against this region has been previously reported to provide broad inhibition against all nine subtypes of influenza A NA; yet its inhibitory effect against influenza B viral NA remained unknown. Here, we report that the monoclonal antibody provides a broad inhibition against various strains of influenza B viruses of both Victoria and Yamagata genetic lineage. Moreover, the growth and NA enzymatic activity of two drug resistant influenza B strains (E117D and D197E) are also inhibited by the antibody even though these two mutations are conformationally proximal to the universal epitope. Collectively, these data suggest that this unique, highly-conserved linear sequence in viral NA is exposed sufficiently to allow access by inhibitory antibody during the course of infection; it could represent a potential target for antiviral agents and vaccine-induced immune responses against diverse strains of type B influenza virus.

  16. Land use and conservation reserve program effects on the persistence of playa wetlands in the High Plains.

    PubMed

    Daniel, Dale W; Smith, Loren M; Haukos, David A; Johnson, Lacrecia A; McMurry, Scott T

    2014-04-15

    Watershed cultivation and subsequent soil erosion remains the greatest threat to the service provisioning of playa wetlands in the High Plains. The U.S. Department of Agriculture's (USDA) Conservation Reserve Program (CRP) plants perennial vegetation cover on cultivated lands including playa watersheds, and therefore, the program influences sediment deposition and accumulation in playas. Our objective was to measure the effects of the CRP on sediment deposition by comparing sediment depth and present/historic size characteristics in 258 playas among three High-Plains subregions (northern, central, and southern) and the three dominant watershed types: cropland, CRP, and native grassland. Sediment depth and resultant volume loss for CRP playas were 40% and 57% lower than cropland playas, but 68% and 76% greater than playas in native grassland. Playas in CRP had remaining volumes exceeding those of cropland playas. Grassland playas had nearly three times more original playa volume and 122% greater wetland area than CRP playas. Overall, playas were larger in the south than other subregions. Sediment depth was also three times greater in the south than the north, which resulted in southern playas losing twice as much total volume as northern playas. However, the larger southern playas provide more remaining volume per playa than those in other subregions. The results of this study demonstrate the importance of proper watershed management in preserving playa wetland ecosystem service provisioning in the High Plains. Furthermore, we identify regional differences in playas that may influence management decisions and provide valuable insight to conservation practitioners trying to maximize wetland services with limited resources.

  17. Comparison of three-dimensional optical coherence tomography and high resolution photography for art conservation studies.

    PubMed

    Adler, Desmond C; Stenger, Jens; Gorczynska, Iwona; Lie, Henry; Hensick, Teri; Spronk, Ron; Wolohojian, Stephan; Khandekar, Narayan; Jiang, James Y; Barry, Scott; Cable, Alex E; Huber, Robert; Fujimoto, James G

    2007-11-26

    Gold punchwork and underdrawing in Renaissance panel paintings are analyzed using both three-dimensional swept source / Fourier domain optical coherence tomography (3D-OCT) and high resolution digital photography. 3D-OCT can generate en face images with micrometer-scale resolutions at arbitrary sectioning depths, rejecting out-of-plane light by coherence gating. Therefore 3D-OCT is well suited for analyzing artwork where a surface layer obscures details of interest. 3D-OCT also enables cross-sectional imaging and quantitative measurement of 3D features such as punch depth, which is beneficial for analyzing the tools and techniques used to create works of art. High volumetric imaging speeds are enabled by the use of a Fourier domain mode locked (FDML) laser as the 3D-OCT light source. High resolution infrared (IR) digital photography is shown to be particularly useful for the analysis of underdrawing, where the materials used for the underdrawing and paint layers have significantly different IR absrption properties. In general, 3D-OCT provides a more flexible and comprehensive analysis of artwork than high resolution photography, but also requires more complex instrumentation and data analysis.

  18. Roles of the highly conserved amino acids in the globular head and stalk region of the Newcastle disease virus HN protein in the membrane fusion process.

    PubMed

    Sun, Chengxi; Wen, Hongling; Chen, Yuzhen; Chu, Fulu; Lin, Bin; Ren, Guijie; Song, Yanyan; Wang, Zhiyu

    2015-02-01

    Newcastle disease virus (NDV), an avain paramyxovirus, has been assigned to the genus Avulavirus within the family Paramyxoviridae. It causes Newcastle disease (ND) that is a highly contagious and fatal viral disease affecting poultry and most species of birds. The hemagglutinin-neuraminidase (HN) protein of NDV has multiple functions including mediating hemadsorption (HAD), neuraminidase (NA), and fusion promotion activities affecting the process of viral attachment, entry, replication and dissemination. Fusion ability of the NDV was highly correlated to its virulence. Mutations in the HN globular head and headless HN of NDV were constructed to determinate the impact of highly conserved amino acids in the globular head of paramyxovirus HN proteins and the roles of the stalk region of HN in the fusion process. It was found that the interaction between F and HN mutants E401A, G402A, G468A, V469A, Y526A, and T527A was equal to that in F and wt HN. The mutations of G402A, G468A, V469A, and T527A had various effects on cell fusion promotion, receptor binding ability, and NA activity, but the membrane merging rate was comparable to wt HN. The elimination of hemadsorption ability and NA activity of E401A and Y526A resulted in the loss of the fusion promotion function of HN. The conclusion was that receptor binding and NA had a common active site and E401 and Y526 amino acids were essential for virus attachment, entry, and dissemination. In addition, G468A mutation made different contributions to HAD and NA, which indicated that G468 was one of the potential key amino acids in switching the two functions between receptor binding and sialic acid destruction of HN. It was also proven that the headless HN of NDV could promote the fusion event mediated by F. Thus, it revealed a novel mechanism in F activation of NDV.

  19. Does Concurrent Radiochemotherapy Affect Cosmetic Results in the Adjuvant Setting After Breast-Conserving Surgery? Results of the ARCOSEIN Multicenter, Phase III Study: Patients' and Doctors' Views

    SciTech Connect

    Toledano, Alain H. . E-mail: alain.toledano@gmail.com; Bollet, Marc A.; Fourquet, Alain; Azria, David; Gligorov, Joseph; Garaud, Pascal; Serin, Daniel; Bosset, Jean-Francois; Miny-Buffet, Joelle; Favre, Anne; Le Foch, Olivier; Calais, Gilles

    2007-05-01

    Purpose: To evaluate the cosmetic results of sequential vs. concurrent adjuvant chemotherapy with radiotherapy after breast-conserving surgery for breast cancer, and to compare ratings by patients and physicians. Methods and Materials: From 1996 to 2000, 716 patients with Stage I-II breast cancers were included in a multicenter, Phase III trial (the ARCOSEIN study) comparing, after breast-conserving surgery with axillary dissection, sequential treatment with chemotherapy first followed by radiotherapy vs. chemotherapy administered concurrently with radiotherapy. Cosmetic results with regard to both the overall aspect of the breast and specific changes (color, scar) were evaluated in a total of 214 patients (107 in each arm) by means of questionnaires to both the patient and a physician whose rating was blinded to treatment allocation. Results: Patients' overall satisfaction with cosmesis was not statistically different between the two arms, with approximately 92% with at least satisfactory results (p = 0.72), although differences between the treated and untreated breasts were greater after the concurrent regimen (29% vs. 14% with more than moderate differences; p 0.0015). Physician assessment of overall cosmesis was less favorable, with lower rates of at least satisfactory results in the concurrent arm (60% vs. 85%; p = 0.001). Consequently, the concordance for overall satisfaction with cosmesis between patients and doctors was only fair ({kappa} = 0.62). Conclusion: After breast-conserving surgery, the concurrent use of chemotherapy with radiotherapy is significantly associated with greater differences between the breasts. These differences do not translate into patients' lessened satisfaction with cosmesis.

  20. Developmental acclimation to low or high humidity conditions affect starvation and heat resistance of Drosophila melanogaster.

    PubMed

    Parkash, Ravi; Ranga, Poonam; Aggarwal, Dau Dayal

    2014-09-01

    Several Drosophila species originating from tropical humid localities are more resistant to starvation and heat stress than populations from high latitudes but mechanistic bases of such physiological changes are largely unknown. In order to test whether humidity levels affect starvation and heat resistance, we investigated developmental acclimation effects of low to high humidity conditions on the storage and utilization of energy resources, body mass, starvation survival, heat knockdown and heat survival of D. melanogaster. Isofemale lines reared under higher humidity (85% RH) stored significantly higher level of lipids and showed greater starvation survival hours but smaller in body size. In contrast, lines reared at low humidity evidenced reduced levels of body lipids and starvation resistance. Starvation resistance and lipid storage level were higher in females than males. However, the rate of utilization of lipids under starvation stress was lower for lines reared under higher humidity. Adult flies of lines reared at 65% RH and acclimated under high or low humidity condition for 200 hours also showed changes in resistance to starvation and heat but such effects were significantly lower as compared with developmental acclimation. Isofemale lines reared under higher humidity showed greater heat knockdown time and heat-shock survival. These laboratory observations on developmental and adult acclimation effects of low versus high humidity conditions have helped in explaining seasonal changes in resistance to starvation and heat of the wild-caught flies of D. melanogaster. Thus, we may suggest that wet versus drier conditions significantly affect starvation and heat resistance of D. melanogaster.

  1. Long-Term Exposure to High Altitude Affects Response Inhibition in the Conflict-monitoring Stage.

    PubMed

    Ma, Hailin; Wang, Yan; Wu, Jianhui; Luo, Ping; Han, Buxin

    2015-09-01

    To investigate the effects of high-altitude exposure on response inhibition, event-related potential (ERP) components N2 and P3 were measured in Go/NoGo task. The participants included an 'immigrant' high-altitude group (who had lived at high altitude for three years but born at low altitude) and a low-altitude group (living in low altitude only). Although the behavioural data showed no significant differences between the two groups, a delayed latency of NoGo-N2 was found in the high-altitude group compared to the low-altitude group. Moreover, larger N2 and smaller P3 amplitudes were found in the high-altitude group compared to the low-altitude group, for both the Go and NoGo conditions. These findings suggest that high-altitude exposure affects response inhibition with regard to processing speed during the conflict monitoring stage. In addition, high altitude generally increases the neural activity in the matching step of information processing and attentional resources. These results may provide some insights into the neurocognitive basis of the effects on high-altitude exposure on response inhibition.

  2. Characterization of an Unusually Conserved Alui Highly Reiterated DNA Sequence Family from the Honeybee, Apis Mellifera

    PubMed Central

    Tares, S.; Cornuet, J. M.; Abad, P.

    1993-01-01

    An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequence is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera. PMID:8104160

  3. Discovery of highly conserved unique peanut and tree nut peptides by LC-MS/MS for multi-allergen detection.

    PubMed

    Sealey-Voyksner, Jennifer; Zweigenbaum, Jerry; Voyksner, Robert

    2016-03-01

    Proteins unique to peanuts and various tree nuts have been extracted, subjected to trypsin digestion and analysis by liquid chromatography/quadrupole time-of-flight mass spectrometry, in order to find highly conserved peptides that can be used as markers to detect peanuts and tree nuts in food. The marker peptide sequences chosen were those found to be present in both native (unroasted) and thermally processed (roasted) forms of peanuts and tree nuts. Each peptide was selected by assuring its presence in food that was processed or unprocessed, its abundance for sensitivity, sequence size, and uniqueness for peanut and each specific variety of tree nut. At least two peptides were selected to represent peanut, almond, pecan, cashew, walnut, hazelnut, pine nut, Brazil nut, macadamia nut, pistachio nut, chestnut and coconut; to determine the presence of trace levels of peanut and tree nuts in food by a novel multiplexed LC-MS method.

  4. Developmental Trajectories of Positive and Negative Affect in Children at High and Low Familial Risk for Depressive Disorder

    ERIC Educational Resources Information Center

    Olino, Thomas M.; Lopez-Duran, Nestor L.; Kovacs, Maria; George, Charles J.; Gentzler, Amy L.; Shaw, Daniel S.

    2011-01-01

    Background: Although low positive affect (PA) and high negative affect (NA) have been posited to predispose to depressive disorders, little is known about the developmental trajectories of these affects in children at familial risk for mood disorders. Methods: We examined 202 offspring of mothers who had a history of juvenile-onset unipolar…

  5. Innovative use of controlled availability fertilizers with high performance for intensive agriculture and environmental conservation.

    PubMed

    Shoji, Sadao

    2005-12-01

    A variety of slow release fertilizers, controlled release (availability) fertilizers (CAFs), and stability fertilizers have been developed in response to the serious drawbacks of the conventional fertilizers since the early 1960's. Of these fertilizers, CAFs which are coated with resin are consumed in the largest quantity in the world. Selecting CAFs with higher performance, the author will discuss about: 1) Innovation of agro-technologies for various field crops including new concepts of fertilizer application, 2) high yielding of field crops, 3) enhancing quality and safety of farm products, and 4) controlling the adverse effect of intensive agriculture on the environment.

  6. Innovative use of controlled availability fertilizers with high performance for intensive agriculture and environmental conservation.

    PubMed

    Shoji, Sadao

    2005-09-01

    A variety of slow release fertilizers, controlled release (availability) fertilizers (CAFs), and stability fertilizers have been developed in response to the serious drawbacks of the conventional fertilizers since the early 1960's. Of these fertilizers, CAFs which are coated with resin are consumed in the largest quantity in the world. Selecting CAFs with higher performance, the author will discuss about: 1) Innovation of agro-technologies for various field crops including new concepts of fertilizer application, 2) high yielding of field crops, 3) enhancing quality and safety of farm products, and 4) controlling the adverse effect of intensive agriculture on the environment.

  7. A new class of high accuracy TVD schemes for hyperbolic conservation laws. [Total Variation Diminishing

    NASA Technical Reports Server (NTRS)

    Chakravarthy, S. R.; Osher, S.

    1985-01-01

    A new family of high accuracy Total Variation Diminishing (TVD) schemes has been developed. Members of the family include the conventional second-order TVD upwind scheme, various other second-order accurate TVD schemes with lower truncation error, and even a third-order accurate TVD approximation. All the schemes are defined with a five-point grid bandwidth. In this paper, the new algorithms are described for scalar equations, systems, and arbitrary coordinates. Selected numerical results are provided to illustrate the new algorithms and their properties.

  8. A remote and highly conserved enhancer supports amygdala specific expression of the gene encoding the anxiogenic neuropeptide substance-P.

    PubMed

    Davidson, S; Miller, K A; Dowell, A; Gildea, A; Mackenzie, A

    2006-04-01

    The neuropeptide substance P (SP), encoded by the preprotachykinin-A (PPTA) gene, is expressed in the central and medial amygdaloid nucleus, where it plays a critical role in modulating fear and anxiety related behaviour. Determining the regulatory systems that support PPTA expression in the amygdala may provide important insights into the causes of depression and anxiety related disorders and will provide avenues for the development of novel therapies. In order to identify the tissue specific regulatory element responsible for supporting expression of the PPTA gene in the amygdala, we used long-range comparative genomics in combination with transgenic analysis and immunohistochemistry. By comparing human and chicken genomes, it was possible to detect and characterise a highly conserved long-range enhancer that supported tissue specific expression in SP expressing cells of the medial and central amygdaloid bodies (ECR1; 158.5 kb 5' of human PPTA ORF). Further bioinformatic analysis using the TRANSFAC database indicated that the ECR1 element contained multiple and highly conserved consensus binding sequences of transcription factors (TFs) such as MEIS1. The results of immunohistochemical analysis of transgenic lines were consistent with the hypothesis that the MEIS1 TF interacts with and maintains ECR1 activity in the central amygdala in vivo. The discovery of ECR1 and the in vivo functional relationship with MEIS1 inferred by our studies suggests a mechanism to the regulatory systems that control PPTA expression in the amygdala. Uncovering these mechanisms may play an important role in the future development of tissue specific therapies for the treatment of anxiety and depression.

  9. The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations.

    PubMed Central

    Berroteran, R W; Ware, D E; Hampsey, M

    1994-01-01

    Mutations in the Saccharomyces cerevisiae sua8 gene were found to be suppressors of an aberrant ATG translation initiation codon in the leader region of the cyc1 gene. Analysis of cyc1 transcripts from sua8 mutants revealed that suppression is a consequence of diminished transcription initiation at the normal start sites in favor of initiation at downstream sites, including a site between the aberrant and normal ATG start codons. This effect is not cyc1 gene specific since initiation at other genes, including ADH1, CYC7, and HIS4, was similarly affected, although initiation at HIS3 and SPT15 was unaffected. The SUA8 gene was cloned and partially sequenced, revealing identity to RPB1, which encodes the largest subunit of RNA polymerase II. The sua8 suppressors are the result of single amino acid replacements of highly conserved residues. Three replacements were found either within or immediately preceding homology block D, and a fourth was found adjacent to homology block H, indicating that these regions play a role in defining start sites in vivo. Nearly identical effects on start site selection were observed for sua7 suppressors, which encode altered forms of TFIIB. Synthetic lethality was associated with double sua7 sua8 suppressor mutations, and recessive sua7 mutants failed to fully complement recessive sua8 mutants in heterozygous diploids (nonallelic noncomplementation). These data indicate that the largest subunit of RNA polymerase II and TFIIB are important determinants of transcription start site selection in S. cerevisiae and suggest that this function might be conferred by interaction between these two proteins. Images PMID:8264591

  10. High Re-Operation Rates Using Conserve Metal-On-Metal Total Hip Articulations

    PubMed Central

    Mogensen, S.L.; Jakobsen, T.; Christoffersen, H.; Krarup, N.

    2016-01-01

    Introduction: Metal-on-metal hip articulations have been intensely debated after reports of adverse reactions and high failure rates. The aim of this study was to retrospectively evaluate the implant of a metal-on.metal total hip articulation (MOM THA) from a single manufacture in a two-center study. Materials and Methods: 108 CONSERVE® MOM THA were implanted in 92 patients between November 2005 and December 2010. Patients had at time of retrospective evaluation their journals reviewed for re-operations and adverse reactions. Results: 20 hips were re-operated (18.4%) at a mean follow up of 53 months. 4 pseudotumors were diagnosed at time of follow up but no substantiated link was made between adverse reactions and re-operations. Conclusion: The high re-operation rates found in this study raised concern about the usage of the MOM THA and subsequently lead to the termination of implantation of this MOM THA at the two orthopaedic departments. PMID:27099640

  11. Collections Conservation.

    ERIC Educational Resources Information Center

    DeCandido, Robert

    Collections conservation is an approach to the preservation treatment of books and book-like materials that is conceptualized and organized in terms of large groups of materials. This guide is intended to enable a library to evaluate its current collections conservation activities. The introduction describes collections conservation and gives…

  12. Cross-Breeding Is Inevitable to Conserve the Highly Inbred Population of Puffin Hunter: The Norwegian Lundehund

    PubMed Central

    Daverdin, Marc; Helfjord, Turid; Berg, Peer

    2017-01-01

    The Norwegian Lundehund is a highly endangered native dog breed. Low fertility and high frequency predisposition to intestinal disorder imply inbreeding depression. We assessed the genetic diversity of the Lundehund population from pedigree data and evaluated the potential of optimal contribution selection and cross-breeding in the long-term management of the Lundehund population. The current Norwegian Lundehund population is highly inbred and has lost 38.8% of the genetic diversity in the base population. Effective population size estimates varied between 13 and 82 depending on the method used. Optimal contribution selection alone facilitates no improvement in the current situation in the Lundehund due to the extremely high relatedness of the whole population. Addition of (replacement with) 10 breeding candidates of foreign breed to 30 Lundehund breeders reduced the parental additive genetic relationship by 40–42% (48–53%). Immediate actions are needed to increase the genetic diversity in the current Lundehund population. The only option to secure the conservation of this rare breed is to introduce individuals from foreign breeds as breeding candidates. PMID:28107382

  13. Genome-wide analyses reveal a highly conserved Dengue virus envelope peptide which is critical for virus viability and antigenic in humans

    PubMed Central

    Fleith, Renata C.; Lobo, Francisco P.; dos Santos, Paula F.; Rocha, Mariana M.; Bordignon, Juliano; Strottmann, Daisy M.; Patricio, Daniel O.; Pavanelli, Wander R.; Lo Sarzi, Maria; Santos, Claudia N. D.; Ferguson, Brian J.; Mansur, Daniel S.

    2016-01-01

    Targeting regions of proteins that show a high degree of structural conservation has been proposed as a method of developing immunotherapies and vaccines that may bypass the wide genetic variability of RNA viruses. Despite several attempts, a vaccine that protects evenly against the four circulating Dengue virus (DV) serotypes remains elusive. To find critical conserved amino acids in dengue viruses, 120 complete genomes of each serotype were selected at random and used to calculate conservation scores for nucleotide and amino acid sequences. The identified peptide sequences were analysed for their structural conservation and localisation using crystallographic data. The longest, surface exposed, highly conserved peptide of Envelope protein was found to correspond to amino acid residues 250 to 270. Mutation of this peptide in DV1 was lethal, since no replication of the mutant virus was detected in human cells. Antibodies against this peptide were detected in DV naturally infected patients indicating its potential antigenicity. Hence, this study has identified a highly conserved, critical peptide in DV that is a target of antibodies in infected humans. PMID:27805018

  14. Application of X-ray microscopy in food science investigation of high pressure affected bacterial spores

    NASA Astrophysics Data System (ADS)

    Mönch, Susanne; Heinz, Volker; Guttmann, Peter; Knorr, Dietrich

    2000-05-01

    Using the Göttingen transmission X-ray microscope at BESSY the effect of different pressure and temperature levels during the high hydrostatic pressure (HP) treatment was investigated. At 150 MPa and temperatures up to 50 °C the triggering of germination was observed by standard microbiological methods with Bacillus subtilis spores. Increasing the temperature to 70 °C at the same pressure level killed the spores without any indication of germination. By X-ray microscopy images it could be shown that the typical disintegration of the protoplast is inhibited. This suggests that the enzymic reaction pathway is possibly affected under specific pressure temperature conditions.

  15. Energy Conservation

    SciTech Connect

    Simpson, P.

    1995-06-01

    There are two fundamental reasons or motivations for energy conservation: (1) economics; and (2) consideration of energy - its sources and availability. Economics speaks for itself and needs little explanation: a project is undertaken, the cost is recovered in a given period of time (we hope) and our company realizes cost savings thereafter. We study and propose a project; we estimate the payback. If approved, we implement the project. Then, we eagerly watch for its effectiveness - for the proposed payback. The second consideration in regard to energy conservation might - in the foreseeable future - become by far the most important - that of availability. Very knowledgeable persons have stated that this - in reality - is the most serious problem facing our nation today. Readily available, reasonably priced energy has given to the US the high form of living experienced today. An interruption in this flow could catapult our nation in an awesome catastrophe. The energy shortage of the late 70`s might be a forerunner of such an experience.

  16. Development of high-level streptomycin resistance affected by a plasmid in lactic streptococci.

    PubMed

    Sinha, R P

    1986-08-01

    Some lactose-negative (Lac-) mutants of Streptococcus lactis C2 and ML3 exhibited development of very high level streptomycin resistance after incubation with subinhibitory concentrations of the drug for 18 to 22 h. These drug-resistant mutants showed no loss of resistance even after 6 months of subculturing in broth without any drug. The parental Lac+ strains did not show mutation to high-level streptomycin resistance. The Lac+ characteristic of the parental strain was conjugally transferred to Lac- derivatives of C2 and ML3, showing the ability to mutate to high-level resistance. When transconjugants were analyzed for this characteristic, they showed both mutable and nonmutable Lac+ types. The results suggested that genetic information for mutation to high-level streptomycin resistance in lactic streptococci resides on the chromosome, and its expression is affected by a plasmid. The plasmid profiles of strains C2, ML3, C2 Lac-, ML3 Lac-, and two kinds of transconjugants confirmed the presence of a plasmid of approximately 5.5 megadaltons in strains showing no mutation to high-level streptomycin resistance, while strains missing such a plasmid exhibited high-level streptomycin resistance after incubation with subinhibitory concentrations of the drug.

  17. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

    PubMed Central

    Brumm, Phillip J.; De Maayer, Pieter; Mead, David A.; Cowan, Don A.

    2015-01-01

    In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan. PMID:26029180

  18. Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.

    PubMed

    Beeby, Morgan; Ribardo, Deborah A; Brennan, Caitlin A; Ruby, Edward G; Jensen, Grant J; Hendrixson, David R

    2016-03-29

    Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.

  19. High-order conservative finite difference GLM-MHD schemes for cell-centered MHD

    NASA Astrophysics Data System (ADS)

    Mignone, Andrea; Tzeferacos, Petros; Bodo, Gianluigi

    2010-08-01

    We present and compare third- as well as fifth-order accurate finite difference schemes for the numerical solution of the compressible ideal MHD equations in multiple spatial dimensions. The selected methods lean on four different reconstruction techniques based on recently improved versions of the weighted essentially non-oscillatory (WENO) schemes, monotonicity preserving (MP) schemes as well as slope-limited polynomial reconstruction. The proposed numerical methods are highly accurate in smooth regions of the flow, avoid loss of accuracy in proximity of smooth extrema and provide sharp non-oscillatory transitions at discontinuities. We suggest a numerical formulation based on a cell-centered approach where all of the primary flow variables are discretized at the zone center. The divergence-free condition is enforced by augmenting the MHD equations with a generalized Lagrange multiplier yielding a mixed hyperbolic/parabolic correction, as in Dedner et al. [J. Comput. Phys. 175 (2002) 645-673]. The resulting family of schemes is robust, cost-effective and straightforward to implement. Compared to previous existing approaches, it completely avoids the CPU intensive workload associated with an elliptic divergence cleaning step and the additional complexities required by staggered mesh algorithms. Extensive numerical testing demonstrate the robustness and reliability of the proposed framework for computations involving both smooth and discontinuous features.

  20. Velocity measurements in a high-Reynolds-number, momentum-conserving, axisymmetric, turbulent jet

    SciTech Connect

    Hussein, H.J.; Capp, S.P.; George, W.K.

    1994-01-01

    The turbulent flow resulting from a top-hat jet exhausting into a large room was investigated. The Reynolds number based on exit conditions was approximately 10(exp 5). Velocity moments to third order were obtained using flying and stationary hot-wire and burst-mode laser-Doppler anemometry (LDA) techniques. The entire room was fully seeded for the LDA measurements. The measurements are shown to satisfy the differential and integral momentum equations for a round jet in an infinite environment. The results differ substantially from those reported by some earlier investigators, both in the level and shape of the profiles. These differences are attributed to the smaller enclosures used in the earlier works and the recirculation within them. Also, the flying hot-wire and burst-mode LDA measurements made here differ from the stationary wire measurements, especially the higher moments and away from the flow centreline. These differences are attributed to the cross-flow and rectification errors on the latter at the high turbulence intensities present in this flow (30% minimum at centreline). The measurements are used, together with recent dissipation measurements, to compute the energy balance for the jet, and an attempt is made to estimate the pressure-velocity and pressure-strain rate correlations.

  1. The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation

    PubMed Central

    Palevsky, Noa; Shemer, Benjamin; Connolly, James P. R.; Belkin, Shimshon

    2016-01-01

    The aromatic compound 2,4-dinitrotoluene (DNT), a common impurity in 2,4,6-trinitrotoluene (TNT) production, has been suggested as a tracer for the presence of TNT-based landmines due to its stability and high volatility. We have previously described an Escherichia coli bioreporter capable of detecting the presence of DNT vapors, harboring a fusion of the yqjF gene promoter to a reporter element. However, the DNT metabolite which is the direct inducer of yqjF, has not yet been identified, nor has the regulatory mechanism of the induction been clarified. We demonstrate here that the YhaJ protein, a member of the LysR type family, acts as a transcriptional regulator of yqjF activation, as well as of a panel of additional E. coli genes. This group of genes share a common sequence motif in their promoters, which is suggested here as a putative YhaJ-box. In addition, we have linked YhaJ to the regulation of quinol-like compound degradation in the cell, and identified yhaK as playing a role in the degradation of DNT. PMID:27713734

  2. Conservation and behavioral neuroendocrinology.

    PubMed

    Cockrem, J F

    2005-11-01

    The total number of threatened species of vertebrates is likely to be more than 10,000, with approximately one quarter of the world's mammal species, one eighth of the birds and one third of the amphibians threatened with extinction. The rate of loss of animal species and hence of biodiversity is increasing and may become even greater as ecosystems become affected by climate change due to global warming. Behavioral neuroendocrinology, which considers interactions between behavior and neuroendocrine function in animals from all vertebrate taxa, can contribute to animal conservation. Research with laboratory animals can address questions in basic biology relevant to conservation and develop methods for use with threatened animals. Field work with free-living animals considers the basic biology of new species and the use of endocrine tools to assess the susceptibility of species to threats. Non-invasive measurements of hormone concentrations, especially fecal steroids, are extensively used to assess reproductive function and the stress status of animals in captive breeding programs and in the wild. Biodiversity and natural selection both depend on individual variation, and conservation programs often work with animals on an individual basis. The consideration of data from individuals is essential in conservation endocrinology. Direct contributions to conservation programs are challenging as study situations are determined by practical conservation concerns. Indirect contributions such as the provision of scientific input to conservation plans and participation in public education programs offer significant benefits for conservation programs. Directly and indirectly, there are many opportunities for behavioral neuroendocrinologists to contribute to conservation.

  3. Living on the edge: Conservation genetics of seven thermophilous plant species in a High Arctic archipelago.

    PubMed

    Birkeland, Siri; Elisabeth Borgen Skjetne, Idunn; Krag Brysting, Anne; Elven, Reidar; Greve Alsos, Inger

    2017-01-20

    Small, isolated, and/or peripheral populations are expected to harbour low levels of genetic variation and may therefore have reduced adaptability to environmental change, including climate warming. In the Arctic, global warming has already caused vegetation change across the region and is acting as a significant stressor on Arctic biodiversity. Many of the rare plants in the Arctic are relicts from early Holocene warm periods, but their ability to benefit from the current warming is dependent on the viability of their populations. We therefore examined Amplified Fragment Length Polymorphism (AFLP) data from regional red listed vascular plant species in the High Arctic archipelago of Svalbard and reference populations from the main distribution area of: 1) Botrychium lunaria, 2) Carex capillaris ssp. fuscidula, 3) Comastoma tenellum, 4) Kobresia simpliciuscula ssp. subholarctica, 5) Ranunculus wilanderi, 6) Sibbaldia procumbens and 7) Tofieldia pusilla In addition, we gathered population size data in Svalbard. The Svalbard populations had low genetic diversity and distinctiveness and few or no private markers compared to populations outside the archipelago. This is similar to observations in other rare species in Svalbard and the genetic depletion may be due to an initial founder effect and/or a genetic bottleneck caused by late Holocene cooling. There seems to be limited gene flow from other areas and the Svalbard populations should therefore be considered as demographically independent management units. Overall, these management units have small and/or few populations and are therefore prone to stochastic events which may further increase vulnerability to inbreeding depression, loss of genetic variation, and reduced evolutionary potential. Our results support theory predicting lower levels of genetic diversity in small, isolated and/or peripheral populations and may be of importance for management of other rare plant species in the Arctic.

  4. COLOR SUPERCONDUCTIVITY, INSTANTONS AND PARITY (NON?)-CONSERVATION AT HIGH BARYON DENSITY-VOLUME 5.

    SciTech Connect

    GYULASSY,M.

    1997-11-11

    This one day Riken BNL Research Center workshop was organized to follow-up on the rapidly developing theoretical work on color super-conductivity, instanton dynamics, and possible signatures of parity violation in strong interactions that was stimulated by the talk of Frank Wilczek during the Riken BNL September Symposium. The workshop was held on November 11, 1997 at the center with over 30 participants. The program consisted of four talks on theory in the morning followed by two talks in the afternoon by experimentalists and open discussion. Krishna Rajagopal (MIT) first reviewed the status of the chiral condensate calculations at high baryon density within the instanton model and the percolation transition at moderate densities restoring chiral symmetry. Mark Alford (Princeton) then discussed the nature of the novel color super-conducting diquark condensates. The main result was that the largest gap on the order of 100 MeV was found for the 0{sup +} condensate, with only a tiny gap << MeV for the other possible 1{sup +}. Thomas Schaefer (INT) gave a complete overview of the instanton effects on correlators and showed independent calculations in collaboration with Shuryak (SUNY) and Velkovsky (BNL) confirming the updated results of the Wilczek group (Princeton, MIT). Yang Pang (Columbia) addressed the general question of how breaking of discrete symmetries by any condensate with suitable quantum numbers could be searched for experimentally especially at the AGS through longitudinal A polarization measurements. Nicholas Samios (BNL) reviewed the history of measurements on {Lambda} polarization and suggested specific kinematical variables for such analysis. Brian Cole (Columbia) showed recent E910 measurements of {Lambda} production at the AGS in nuclear collisions and focused on the systematic biases that must be considered when looking for small symmetry breaking effects. Lively discussions led by Robert Jaffe (MIT) focused especially on speculations on the still

  5. Patterns in the bony skull development of marsupials: high variation in onset of ossification and conserved regions of bone contact

    PubMed Central

    Spiekman, Stephan N. F.; Werneburg, Ingmar

    2017-01-01

    Development in marsupials is specialized towards an extremely short gestation and highly altricial newborns. As a result, marsupial neonates display morphological adaptations at birth related to functional constraints. However, little is known about the variability of marsupial skull development and its relation to morphological diversity. We studied bony skull development in five marsupial species. The relative timing of the onset of ossification was compared to literature data and the ossification sequence of the marsupial ancestor was reconstructed using squared-change parsimony. The high range of variation in the onset of ossification meant that no patterns could be observed that differentiate species. This finding challenges traditional studies concentrating on the onset of ossification as a marker for phylogeny or as a functional proxy. Our study presents observations on the developmental timing of cranial bone-to-bone contacts and their evolutionary implications. Although certain bone contacts display high levels of variation, connections of early and late development are quite conserved and informative. Bones that surround the oral cavity are generally the first to connect and the bones of the occipital region are among the last. We conclude that bone contact is preferable over onset of ossification for studying cranial bone development. PMID:28233826

  6. Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays.

    PubMed

    Guttman, Mitchell; Mies, Carolyn; Dudycz-Sulicz, Katarzyna; Diskin, Sharon J; Baldwin, Don A; Stoeckert, Christian J; Grant, Gregory R

    2007-08-01

    Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication machinery that results in an accumulation of genomic aberrations in the form of duplications, deletions, translocations, and other genomic alterations. Microarray methods allow for finer mapping of these aberrations than has previously been possible; however, data processing and analysis methods have not taken full advantage of this higher resolution. Attention has primarily been given to analysis on the single sample level, where multiple adjacent probes are necessarily used as replicates for the local region containing their target sequences. However, regions of concordant aberration can be short enough to be detected by only one, or very few, array elements. We describe a method called Multiple Sample Analysis for assessing the significance of concordant genomic aberrations across multiple experiments that does not require a-priori definition of aberration calls for each sample. If there are multiple samples, representing a class, then by exploiting the replication across samples our method can detect concordant aberrations at much higher resolution than can be derived from current single sample approaches. Additionally, this method provides a meaningful approach to addressing population-based questions such as determining important regions for a cancer subtype of interest or determining regions of copy number variation in a population. Multiple Sample Analysis also provides single sample aberration calls in the locations of significant concordance, producing high resolution calls per sample, in concordant regions. The approach is demonstrated on a dataset representing a challenging but important resource: breast tumors that have been formalin-fixed, paraffin-embedded, archived, and subsequently UV-laser capture microdissected and hybridized to two-channel BAC arrays

  7. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family.

    PubMed Central

    Braun, E L; Fuge, E K; Padilla, P A; Werner-Washburne, M

    1996-01-01

    The regulation of cellular growth and proliferation in response to environmental cues is critical for development and the maintenance of viability in all organisms. In unicellular organisms, such as the budding yeast Saccharomyces cerevisiae, growth and proliferation are regulated by nutrient availability. We have described changes in the pattern of protein synthesis during the growth of S. cerevisiae cells to stationary phase (E. K. Fuge, E. L. Braun, and M. Werner-Washburne, J. Bacteriol. 176:5802-5813, 1994) and noted a protein, which we designated Snz1p (p35), that shows increased synthesis after entry into stationary phase. We report here the identification of the SNZ1 gene, which encodes this protein. We detected increased SNZ1 mRNA accumulation almost 2 days after glucose exhaustion, significantly later than that of mRNAs encoded by other postexponential genes. SNZ1-related sequences were detected in phylogenetically diverse organisms by sequence comparisons and low-stringency hybridization. Multiple SNZ1-related sequences were detected in some organisms, including S. cerevisiae. Snz1p was found to be among the most evolutionarily conserved proteins currently identified, indicating that we have identified a novel, highly conserved protein involved in growth arrest in S. cerevisiae. The broad phylogenetic distribution, the regulation of the SNZ1 mRNA and protein in S. cerevisiae, and identification of a Snz protein modified during sporulation in the gram-positive bacterium Bacillus subtilis support the hypothesis that Snz proteins are part of an ancient response that occurs during nutrient limitation and growth arrest. PMID:8955308

  8. Highly Conserved Cysteines Are Involved in the Oligomerization of Occludin—Redox Dependency of the Second Extracellular Loop

    PubMed Central

    Bellmann, Christian; Schreivogel, Sophie; Günther, Ramona; Dabrowski, Sebastian; Schümann, Michael; Wolburg, Hartwig

    2014-01-01

    Abstract The tight junction (TJ) marker occludin is a 4-transmembrane domain (TMD) protein with unclear physiological and pathological functions, interacting with other TJ proteins. It oligomerizes and is redox sensitive. However, oligomerization sites and mechanisms are unknown. Aims: To identify hypoxia-sensitive binding sites, we investigated the consequences of amino-acid substitutions of highly conserved cysteines in human occludin, under normal and hypoxic incubations. Results: (i) The extracellular loop 2 (ECL2) showed homophilic trans- and cis-association between opposing cells and along the cell membrane, respectively, caused by a loop properly folded via an intraloop disulfide bridge between the shielded C216 and C237. Hypoxia and reductants prevented the associations. (ii) C82 in TMD1 directly cis-associated without disulfide formation. (iii) C76 in TMD1 and C148 in TMD2 limited the trans-interaction; C76 also limited occludin-related paracellular tightness and changed the strand morphology of claudin-1. (iv) The diminished binding strength found after substituting C82, C216, or C237 was accompanied by increased occludin mobility in the cell membrane. Innovation: The data enable the first experimentally proven structural model of occludin and its homophilic interaction sites, in which the ECL2, via intraloop disulfide formation, has a central role in occludin's hypoxia-sensitive oligomerization and to regulate the structure of TJs. Conclusion: Our findings support the new concept that occludin acts as a hypoxiasensor and contributes toward regulating the TJ assembly redox dependently. This is of pathogenic relevance for tissue barrier injury with reducing conditions. The ECL2 disulfide might be a model for four TMD proteins in TJs with two conserved cysteines in an ECL. Antioxid. Redox Signal. 20, 855–867. PMID:23923978

  9. EBS7 is a plant-specific component of a highly conserved endoplasmic reticulum-associated degradation system in Arabidopsis

    PubMed Central

    Liu, Yidan; Zhang, Congcong; Wang, Dinghe; Su, Wei; Liu, Linchuan; Wang, Muyang; Li, Jianming

    2015-01-01

    Endoplasmic reticulum (ER)-associated degradation (ERAD) is an essential part of an ER-localized protein quality-control system for eliminating terminally misfolded proteins. Recent studies have demonstrated that the ERAD machinery is conserved among yeast, animals, and plants; however, it remains unknown if the plant ERAD system involves plant-specific components. Here we report that the Arabidopsis ethyl methanesulfonate-mutagenized brassinosteroid-insensitive 1 suppressor 7 (EBS7) gene encodes an ER membrane-localized ERAD component that is highly conserved in land plants. Loss-of-function ebs7 mutations prevent ERAD of brassinosteroid insensitive 1-9 (bri1-9) and bri1-5, two ER-retained mutant variants of the cell-surface receptor for brassinosteroids (BRs). As a result, the two mutant receptors accumulate in the ER and consequently leak to the plasma membrane, resulting in the restoration of BR sensitivity and phenotypic suppression of the bri1-9 and bri1-5 mutants. EBS7 accumulates under ER stress, and its mutations lead to hypersensitivity to ER and salt stresses. EBS7 interacts with the ER membrane-anchored ubiquitin ligase Arabidopsis thaliana HMG-CoA reductase degradation 1a (AtHrd1a), one of the central components of the Arabidopsis ERAD machinery, and an ebs7 mutation destabilizes AtHrd1a to reduce polyubiquitination of bri1-9. Taken together, our results uncover a plant-specific component of a plant ERAD pathway and also suggest its likely biochemical function. PMID:26371323

  10. Does Augmented Reality Affect High School Students' Learning Outcomes in Chemistry?

    NASA Astrophysics Data System (ADS)

    Renner, Jonathan Christopher

    Some teens may prefer using a self-directed, constructivist, and technologic approach to learning rather than traditional classroom instruction. If it can be demonstrated, educators may adjust their teaching methodology. The guiding research question for this study focused on how augmented reality affects high school students' learning outcomes in chemistry, as measured by a pretest and posttest methodology when ensuring that the individual outcomes were not the result of group collaboration. This study employed a quantitative, quasi-experimental study design that used a comparison and experimental group. Inferential statistical analysis was employed. The study was conducted at a high school in southwest Colorado. Eighty-nine respondents returned completed and signed consent forms, and 78 participants completed the study. Results demonstrated that augmented reality instruction caused posttest scores to significantly increase, as compared to pretest scores, but it was not as effective as traditional classroom instruction. Scores did improve under both types of instruction; therefore, more research is needed in this area. The present study was the first quantitative experiment controlling for individual learning to validate augmented reality using mobile handheld digital devices that affected individual students' learning outcomes without group collaboration. This topic was important to the field of education as it may help educators understand how students learn and it may also change the way students are taught.

  11. Folic acid supplementation affects apoptosis and differentiation of embryonic neural stem cells exposed to high glucose.

    PubMed

    Jia, De-yong; Liu, Hui-juan; Wang, Fu-wu; Liu, Shang-ming; Ling, Eng-Ang; Liu, Kai; Hao, Ai-jun

    2008-07-25

    Folic acid (FA) supplementation has been shown to be extremely effective in reducing the occurrence of neural tube defects (NTDs), one of the most common birth defects associated with diabetic pregnancy. However, the antiteratogenic mechanism of FA in diabetes-induced NTDs is unclear. This study investigated the neuroprotective mechanism of FA in neural stem cells (NSCs) exposed to high glucose in vitro. The undifferentiated or differentiated NSCs were cultured in normal D-glucose concentration (NG) or high D-glucose concentration (HG) with or without FA. FA supplementation significantly decreased apoptosis induced by HG and lowered the expression of p53 in the nucleus of undifferentiated NSCs exposed to HG. Administration of FA in differentiated NSCs did not alter their precocious differentiation induced by HG. The increased mRNA expression levels of the basic helix-loop-helix factors including Neurog1, Neurog2, NeuroD2, Mash1, Id1, Id2, and Hes5 in the presence of HG were not significantly affected by FA. The present results provided a cellular mechanism by which FA supplementation may have a potential role in prevention of NTDs in diabetic pregnancies. On the other hand, FA increased the mRNA expression levels of the above transcription factors and accelerated the differentiation of NSCs in the NG medium, suggesting that it may adversely affect the normal differentiation of NSCs. Therefore, the timing and dose of FA would be critical factors in considering FA supplementation in normal maternal pregnancy.

  12. The "Affective Place-Making" Practices of Girls at a High School in Cape Town, South Africa

    ERIC Educational Resources Information Center

    Rinquest, Elzahn; Fataar, Aslam

    2016-01-01

    This article focuses on the "affective place-making" practices of girls at a private high school on the outskirts of Cape Town. The article responds to the question: How do high school girls' affects and social bodies contribute to their place-making practices and to the type of place they make of their school? Our focus is on…

  13. Cotton nitrogen management in a high-residue conservation system: nitrogen source, rate, application method and application timing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Conservation tillage systems are promoted in many parts of the world to help achieve environmental sustainability in agriculture. In-service training programs are used to educate extension agents as means to diffuse conservation tillage practices. However, changing extension agents’ attitudes is a c...

  14. Immunosuppressive drugs affect high-mannose/hybrid N-glycans on human allostimulated leukocytes.

    PubMed

    Pocheć, Ewa; Bocian, Katarzyna; Ząbczyńska, Marta; Korczak-Kowalska, Grażyna; Lityńska, Anna

    2015-01-01

    N-glycosylation plays an important role in the majority of physiological and pathological processes occurring in the immune system. Alteration of the type and abundance of glycans is an element of lymphocyte differentiation; it is also common in the development of immune-mediated inflammatory diseases. The N-glycosylation process is very sensitive to different environmental agents, among them the pharmacological environment of immunosuppressive drugs. Some results show that high-mannose oligosaccharides have the ability to suppress different stages of the immune response. We evaluated the effects of cyclosporin A (CsA) and rapamycin (Rapa) on high-mannose/hybrid-type glycosylation in human leukocytes activated in a two-way mixed leukocyte reaction (MLR). CsA significantly reduced the number of leukocytes covered by high-mannose/hybrid N-glycans, and the synergistic action of CsA and Rapa led to an increase of these structures on the remaining leukocytes. This is the first study indicating that β1 and β3 integrins bearing high-mannose/hybrid structures are affected by Rapa and CsA. Rapa taken separately and together with CsA changed the expression of β1 and β3 integrins and, by regulating the protein amount, increased the oligomannose/hybrid-type N-glycosylation on the leukocyte surface. We suggest that the changes in the glycosylation profile of leukocytes may promote the development of tolerance in transplantation.

  15. Fasting and sampling time affect liver gene expression of high-fat diet-fed mice.

    PubMed

    Lee, C Y

    2010-05-01

    Several physiological and biological variables are known to affect peroxisome proliferator-activated receptor (PPAR)-α-dependent signaling pathway and plasma biochemical profiles. However, less is known about the effect of these variables on high-fat diet-fed mice. In a 5-week study, C57BL/6 mice were divided into control (C) and high-fat diet-fed (H) groups, whereby before dissection, each group was subdivided into non-fasted (nC and nH) and a 15-h fasted mice (fC and fH) killed in the early light cycle, and a 15-h fasted mice (eC and eH) killed in the late phase of the light cycle. Liver and blood from the vena cava were collected. Non-fasted nC and nH mice have a marginal difference in their body weight gain, whereas significant differences were found for fasted mice. In nH mice, PPAR-α, acyl-CoA oxidase and insulin-like growth factor-binding protein expressions were significantly elevated, in contrast to fatty acid synthase (Fasn), stearoyl CoA-desaturase (SCD)-1, and elongase (ELOVL)-6 expressions. Fasn was profoundly induced in fH mice, while decreased sterol regulatory-binding protein-1 and SCD-1 were found only in eH mice. Different from the gene expression profiles, plasma total cholesterol level of the eH mice was higher than controls, whereas nH mice have increased plasma non-esterified fatty acids. Only glucose level of the fH mice was higher than that observed for controls. Results showed that fasting and sampling time have significantly affected liver gene expression and plasma biochemical indices of the high-fat diet-treated mice. An overlook in these aspects can cause serious discrepancies in the experimental data and their interpretations.

  16. Localization of a highly conserved human potassium channel gene (NGK2-KV4-KCNC1) to chromosome 11p15

    SciTech Connect

    Ried, T.; Ward, D.C. ); Rudy, B.; Miera, V.S. de; Lau, D.; Sen, K. )

    1993-02-01

    Several genes (the Shaker or Sh gene family) encoding components of voltage-gated K[sub +] channels have been identified in various species. Based on sequence similarities Sh genes are classified into four groups or subfamilies. Mammalian genes of each one of these subfamilies also show high levels of sequence similarity to one of four related Drosophila genes: Shaker, Shab, Shaw, and Shal. Here we report the isolation of human cDNAs for a Shaw-related product (NGK2,KV2.1a) previously identified in rat and mice. A comparison of the nucleotide and deduced amino acid sequence of NGK2 in rodents and humans shows that this product is highly conserved in mammals; the human NGK2 protein shows over 99% amino acid sequence identity to its rodent homologue. The gene (NGK2-KV4; KCNC1) encoding NGK2 was mapped to human chromosome 11p15 by fluorescence in situ hybridization with the human NGK2 cDNAs. 65 refs., 2 figs., 1 tab.

  17. Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection

    PubMed Central

    Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry AF; Rothman, Alan L; Mathew, Anuja

    2014-01-01

    Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS126–34-specific CD8+ T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS126–34-specific and other DENV epitope-specific CD8+ T cells, as well as total CD8+ T cells, expressed an activated phenotype (CD69+ and/or CD38+) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8+ T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. PMID:23941420

  18. Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection.

    PubMed

    Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry A F; Rothman, Alan L; Mathew, Anuja

    2014-01-01

    Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS1(26-34) -specific CD8(+) T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS1(26-34) -specific and other DENV epitope-specific CD8(+) T cells, as well as total CD8(+) T cells, expressed an activated phenotype (CD69(+) and/or CD38(+)) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8(+) T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation.

  19. Mutations in proteins of the Conserved Oligomeric Golgi Complex affect polarity, cell wall structure, and glycosylation in the filamentous fungus Aspergillus nidulans.

    PubMed

    Gremillion, S K; Harris, S D; Jackson-Hayes, L; Kaminskyj, S G W; Loprete, D M; Gauthier, A C; Mercer, S; Ravita, A J; Hill, T W

    2014-12-01

    We have described two Aspergillus nidulans gene mutations, designated podB1 (polarity defective) and swoP1 (swollen cell), which cause temperature-sensitive defects during polarization. Mutant strains also displayed unevenness and abnormal thickness of cell walls. Un-polarized or poorly-polarized mutant cells were capable of establishing normal polarity after a shift to a permissive temperature, and mutant hyphae shifted from permissive to restrictive temperature show wall and polarity abnormalities in subsequent growth. The mutated genes (podB=AN8226.3; swoP=AN7462.3) were identified as homologues of COG2 and COG4, respectively, each predicted to encode a subunit of the multi-protein COG (Conserved Oligomeric Golgi) Complex involved in retrograde vesicle trafficking in the Golgi apparatus. Down-regulation of COG2 or COG4 resulted in abnormal polarization and cell wall staining. The GFP-tagged COG2 and COG4 homologues displayed punctate, Golgi-like localization. Lectin-blotting indicated that protein glycosylation was altered in the mutant strains compared to the wild type. A multicopy expression experiment showed evidence for functional interactions between the homologues COG2 and COG4 as well as between COG2 and COG3. To date, this work is the first regarding a functional role of the COG proteins in the development of a filamentous fungus.

  20. A Web-Based GIS for Reporting Water Usage in the High Plains Underground Water Conservation District

    NASA Astrophysics Data System (ADS)

    Jia, M.; Deeds, N.; Winckler, M.

    2012-12-01

    The High Plains Underground Water Conservation District (HPWD) is the largest and oldest of the Texas water conservation districts, and oversees approximately 1.7 million irrigated acres. Recent rule changes have motivated HPWD to develop a more automated system to allow owners and operators to report well locations, meter locations, meter readings, the association between meters and wells, and contiguous acres. INTERA, Inc. has developed a web-based interactive system for HPWD water users to report water usage and for the district to better manage its water resources. The HPWD web management system utilizes state-of-the-art GIS techniques, including cloud-based Amazon EC2 virtual machine, ArcGIS Server, ArcSDE and ArcGIS Viewer for Flex, to support web-based water use management. The system enables users to navigate to their area of interest using a well-established base-map and perform a variety of operations and inquiries against their spatial features. The application currently has six components: user privilege management, property management, water meter registration, area registration, meter-well association and water use report. The system is composed of two main databases: spatial database and non-spatial database. With the help of Adobe Flex application at the front end and ArcGIS Server as the middle-ware, the spatial feature geometry and attributes update will be reflected immediately in the back end. As a result, property owners, along with the HPWD staff, collaborate together to weave the fabric of the spatial database. Interactions between the spatial and non-spatial databases are established by Windows Communication Foundation (WCF) services to record water-use report, user-property associations, owner-area associations, as well as meter-well associations. Mobile capabilities will be enabled in the near future for field workers to collect data and synchronize them to the spatial database. The entire solution is built on a highly scalable cloud

  1. Bi-Temporal Analysis of High-Resolution Satellite Imagery in Support of a Forest Conservation Program in Western Uganda

    NASA Astrophysics Data System (ADS)

    Thomas, N.; Lambin, E.; Audy, R.; Biryahwaho, B.; de Laat, J.; Jayachandran, S.

    2014-12-01

    Recent studies in land use sustainability have shown the conservation value of even small forest fragments in tropical smallholder agricultural regions. Forest patches provide important ecosystem services, wildlife habitat, and support human livelihoods. Our study incorporates multiple dates of high-resolution Quickbird imagery to map forest disturbance and regrowth in a smallholder agricultural landscape in western Uganda. This work is in support of a payments for ecosystem services (PES) project which uses a randomized controlled trial to assess the efficacy of PES for enhancing forest conservation. The research presented here details the remote sensing phase of this project. We developed an object-based methodology for detecting forest change from high-resolution imagery that calculates per class image reflectance and change statistics to determine persistent forest, non-forest, forest gain, and forest loss classes. The large study area (~ 2,400 km2) necessitated using a combination of 10 different image pairs of varying seasonality, sun angle, and viewing angle. We discuss the impact of these factors on mapping results. Reflectance data was used in conjunction with texture measures and knowledge-driven modeling to derive forest change maps. First, baseline Quickbird images were mapped into tree cover and non-tree categories based on segmented image objects and field inventory data, applied through a classification and regression tree (CART) classifier. Then a bi-temporal segmentation layer was generated and a series of object metrics from both image dates were extracted. A sample set of persistent forest objects that remained undisturbed was derived from the tree cover map and the red band (B3) change values. We calculated a variety of statistical indices for these persistent tree cover objects from the post- survey imagery to create maps of both forest cover loss and forest cover gain. These results are compared to visually assessed image objects in addition

  2. The Fire-Walker’s High: Affect and Physiological Responses in an Extreme Collective Ritual

    PubMed Central

    Fischer, Ronald; Xygalatas, Dimitris; Mitkidis, Panagiotis; Reddish, Paul; Tok, Penny; Konvalinka, Ivana; Bulbulia, Joseph

    2014-01-01

    How do people feel during extreme collective rituals? Despite longstanding speculation, few studies have attempted to quantify ritual experiences. Using a novel pre/post design, we quantified physiological fluctuations (heart rates) and self-reported affective states from a collective fire-walking ritual in a Mauritian Hindu community. Specifically, we compared changes in levels of happiness, fatigue, and heart rate reactivity among high-ordeal participants (fire-walkers), low-ordeal participants (non-fire-walking participants with familial bonds to fire-walkers) and spectators (unrelated/unknown to the fire-walkers). We observed that fire-walkers experienced the highest increase in heart rate and reported greater happiness post-ritual compared to low-ordeal participants and spectators. Low-ordeal participants reported increased fatigue after the ritual compared to both fire-walkers and spectators, suggesting empathetic identification effects. Thus, witnessing the ritualistic suffering of loved ones may be more exhausting than experiencing suffering oneself. The findings demonstrate that the level of ritual involvement is important for shaping affective responses to collective rituals. Enduring a ritual ordeal is associated with greater happiness, whereas observing a loved-one endure a ritual ordeal is associated with greater fatigue post-ritual. PMID:24586315

  3. Factors Affecting the Inclusion Potency for Acicular Ferrite Nucleation in High-Strength Steel Welds

    NASA Astrophysics Data System (ADS)

    Kang, Yongjoon; Jeong, Seonghoon; Kang, Joo-Hee; Lee, Changhee

    2016-06-01

    Factors affecting the inclusion potency for acicular ferrite nucleation in high-strength weld metals were investigated and the contribution of each factor was qualitatively evaluated. Two kinds of weld metals with different hardenabilities were prepared, in both, MnTi2O4-rich spinel formed as the predominant inclusion phase. To evaluate the factors determining the inclusion potency, the inclusion characteristics of size, phase distribution in the multiphase inclusion, orientation relationship with ferrite, and Mn distribution near the inclusion were analyzed. Three factors affecting the ferrite nucleation potency of inclusions were evaluated: the Baker-Nutting (B-N) orientation relationship between ferrite and the inclusion; the formation of an Mn-depleted zone (MDZ) near the inclusion; and the strain energy around the inclusion. Among these, the first two factors were found to be the most important. In addition, it was concluded that the increased chemical driving force brought about by the formation of an MDZ contributed more to the formation of acicular ferrite in higher-strength weld metals, because the B-N orientation relationship between ferrite and the inclusion was less likely to form as the transformation temperature decreased.

  4. The fire-walker's high: affect and physiological responses in an extreme collective ritual.

    PubMed

    Fischer, Ronald; Xygalatas, Dimitris; Mitkidis, Panagiotis; Reddish, Paul; Tok, Penny; Konvalinka, Ivana; Bulbulia, Joseph

    2014-01-01

    How do people feel during extreme collective rituals? Despite longstanding speculation, few studies have attempted to quantify ritual experiences. Using a novel pre/post design, we quantified physiological fluctuations (heart rates) and self-reported affective states from a collective fire-walking ritual in a Mauritian Hindu community. Specifically, we compared changes in levels of happiness, fatigue, and heart rate reactivity among high-ordeal participants (fire-walkers), low-ordeal participants (non-fire-walking participants with familial bonds to fire-walkers) and spectators (unrelated/unknown to the fire-walkers). We observed that fire-walkers experienced the highest increase in heart rate and reported greater happiness post-ritual compared to low-ordeal participants and spectators. Low-ordeal participants reported increased fatigue after the ritual compared to both fire-walkers and spectators, suggesting empathetic identification effects. Thus, witnessing the ritualistic suffering of loved ones may be more exhausting than experiencing suffering oneself. The findings demonstrate that the level of ritual involvement is important for shaping affective responses to collective rituals. Enduring a ritual ordeal is associated with greater happiness, whereas observing a loved-one endure a ritual ordeal is associated with greater fatigue post-ritual.

  5. Beyond sensation seeking: affect regulation as a framework for predicting risk-taking behaviors in high-risk sport.

    PubMed

    Castanier, Carole; Le Scanff, Christine; Woodman, Tim

    2010-10-01

    Sensation seeking has been widely studied when investigating individual differences in the propensity for taking risks. However, risk taking can serve many different goals beyond the simple management of physiological arousal. The present study is an investigation of affect self-regulation as a predictor of risk-taking behaviors in high-risk sport. Risk-taking behaviors, negative affectivity, escape self-awareness strategy, and sensation seeking data were obtained from 265 high-risk sportsmen. Moderated hierarchical regression analysis revealed significant main and interaction effects of negative affectivity and escape self-awareness strategy in predicting risk-taking behaviors: high-risk sportsmen's negative affectivity leads them to adopt risk-taking behaviors only if they also use escape self-awareness strategy. Furthermore, the affective model remained significant when controlling for sensation seeking. The present study contributes to an in-depth understanding of risk taking in high-risk sport.

  6. Conservation Laws

    NASA Astrophysics Data System (ADS)

    Dewitt, Bryce; Christensen, Steven M.

    In the case of the free particle, we interpreted various components of the energy-momentum-stress density as fluxes of energy and momentum. This interpretation can obviously be extended also to particle ensembles and gases. When we speak of fluxes we usually think of quantities that are conserved. In special relativity, energy and momentum are conserved. In general relativity, they are no longer generally conserved, at least if we do not include the energy and momentum of the gravitational field itself. Nevertheless, their densities and fluxes satisfy a covariant generalization of a true conservation law, which is quite easy to obtain.

  7. How instant messaging affects the satisfaction of virtual interpersonal behavior of Taiwan junior high school students.

    PubMed

    Lin, Chien-Huang; Sun, Ya-Chung; Lee, Yueh-Chiang; Wu, Shih-Chia

    2007-01-01

    Although Instant Messaging (IM) has established itself as one of the most popular modes of communication, little empirical research has explored how adolescents are affected by its use to satisfy their virtual interpersonal relationships. This research investigates cause and effect in the satisfaction of these relationships among adolescents in both their real and virtual life by using IM. Data were collected from 401 junior high school students via a questionnaire. Descriptive statistics, factor analysis, and SEM analysis methods were used to analyze the data. Primary findings indicate that (1) there is significant cause and effect on the adolescents' satisfaction with their interpersonal relationships between their real life and the virtual world (via IM); and (2) adolescents may enhance their interpersonal behavior by using IM, leading to an increase in satisfaction with their interpersonal relationships in the virtual world.

  8. Carbohydrate ingestion during prolonged high-intensity intermittent exercise: impact on affect and perceived exertion.

    PubMed

    Backhouse, S H; Ali, A; Biddle, S J H; Williams, C

    2007-10-01

    This study was designed to determine the effects of ingesting a carbohydrate (CHO) solution on affective states and rating of perceived exertion (RPE) during prolonged intermittent high-intensity exercise. Seventeen male soccer players completed a prolonged intermittent high-intensity exercise protocol for 90 min on two occasions, separated by at least 7 days. Participants consumed either a 6.4% CHO (0.6 g/kg body mass (BM)/h) or an artificially sweetened placebo (PLA) solution immediately before (8 mL/kg BM) and every 15 min (3 mL/kg BM) during exercise in a double-blind, counterbalanced design. Pleasure-displeasure, perceived activation, RPE and plasma glucose concentration was assessed. The results showed that compared with the CHO trial, perceived activation were lower in the placebo trial during the last 30 min of exercise and this was accompanied by lowered plasma glucose concentrations. In the CHO trial, RPE was maintained in the last 30 min of exercise but carried on increasing in the PLA trial. Therefore, CHO ingestion during prolonged high-intensity exercise appears to elicit an enhanced perceived activation profile that may impact upon task persistence and performance. This finding is in addition to the physiological and metabolic benefits of the exogenous energy supply.

  9. Pea DNA helicase 45 overexpression in tobacco confers high salinity tolerance without affecting yield.

    PubMed

    Sanan-Mishra, Neeti; Pham, Xuan Hoi; Sopory, Sudhir K; Tuteja, Narendra

    2005-01-11

    Salt tolerance is an important trait that is required to overcome salinity-induced reduction in plant productivity. We have reported previously the isolation of a pea DNA helicase 45 (PDH45) that exhibits striking homology with the eukaryotic translation initiation factor eIF-4A. Here, we report that PDH45 mRNA is induced in pea seedlings in response to high salt, and its overexpression driven by a constitutive cauliflower mosaic virus-(35)S promoter in tobacco plants confers salinity tolerance, thus suggesting a previously undescribed pathway for manipulating stress tolerance in crop plants. The T(0) transgenic plants showed high levels of PDH45 protein in normal and stress conditions, as compared with WT plants. The T(0) transgenics also showed tolerance to high salinity as tested by a leaf disk senescence assay. The T(1) transgenics were able to grow to maturity and set normal viable seeds under continuous salinity stress without any reduction in plant yield in terms of seed weight. Measurement of Na(+) ions in different parts of the plant showed higher accumulation in the old leaves and negligible accumulation in seeds of T(1) transgenic lines as compared with the WT plants. The possible mechanism of salinity tolerance is discussed. Overexpression of PDH45 provides a possible example of the exploitation of DNA/RNA unwinding pathways for engineering salinity tolerance without affecting yield in crop plants.

  10. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

    PubMed

    Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

    2015-12-01

    It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.

  11. A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks.

    PubMed

    Lin, Chen-Ching; Mitra, Ramkrishna; Zhao, Zhongming

    2014-01-01

    MicroRNAs are small non-coding RNAs that can regulate expressions of their target genes at the post-transcriptional level. In this study, we propose a tri-component strategy that combines the conservation of microRNAs, homology of mRNA coding regions, and conserved microRNA binding sites in the 3' untranslated regions to discover conserved microRNA-mRNA interactions. To validate the performance of our conservation strategy, we collected the experimentally validated microRNA-mRNA interactions from three databases as the golden standard. We found that the proposed strategy can improve the performance of existing target prediction algorithms by approximately 2-4 fold. In addition, we demonstrated that the proposed strategy could efficiently retain highly confident interactions from the intersection results of the existing algorithms and filter out the possible false positive predictions in the union one. Furthermore, this strategy can facilitate our ability to trace the homologues in different species that are targeted by the same miRNA family because it combines these three features to identify the conserved miRNA-mRNA interactions during evolution. Through an extensive application of the proposed conservation strategy to a study of the miR-1/206 regulatory network, we demonstrate that the target mRNA recruiting process could be associated with expansion of miRNA family during its evolution. We also uncovered the functional evolution of the miR-1/206 regulatory network. In this network, the early targeted genes tend to participate in more general and development-related functions. In summary, the conservation strategy is capable of helping to highlight the highly confident miRNA-mRNA interactions and can be further applied to reveal the evolutionary features of miRNA regulatory network and functions.

  12. RegB/RegA, a Highly Conserved Redox-Responding Global Two-Component Regulatory System

    PubMed Central

    Elsen, Sylvie; Swem, Lee R.; Swem, Danielle L.; Bauer, Carl E.

    2004-01-01

    The Reg regulon from Rhodobacter capsulatus and Rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. The redox signal that is detected by the membrane-bound sensor kinase, RegB, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c oxidase result in constitutive RegB autophosphorylation. Regulation of RegB autophosphorylation also involves a redox-active cysteine that is present in the cytosolic region of RegB. Both phosphorylated and unphosphorylated forms of the cognate response regulator RegA are capable of activating or repressing a variety of genes in the regulon. Highly conserved homologues of RegB and RegA have been found in a wide number of photosynthetic and nonphotosynthetic bacteria, with evidence suggesting that RegB/RegA plays a fundamental role in the transcription of redox-regulated genes in many bacterial species. PMID:15187184

  13. The conserved lymphokine element-0 in the IL5 promoter binds to a high mobility group-1 protein.

    PubMed

    Marrugo, J; Marsh, D G; Ghosh, B

    1996-10-01

    The conserved lymphokine elements-0 (CLE0) in the IL5 promoter is essential for the expression of IL-5. Here, we report the cloning and expression of a cDNA encoding a novel CLE0-binding protein, CLEBP-1 from a mouse Th2 clone, D10.G4.1. Interestingly, it was found that the CLEBP1 cDNA sequence was almost identical to the sequences of known high mobility group-1 (HMG1) cDNAs. When expressed as a recombinant fusion protein in Escherichia coli, CLEBP-1 was shown to bind to the IL5-CLE0 element in electrophoretic mobility-shift assays (EMSA) and southwestern blot analysis. The CLEBP-1 fusion protein cross-reacts with and-HMG-1/2 in Western blot analysis. It also binds to the CLE0 elements of IL4, GMCSF and GCSF genes. CLEBP-1 and closely related HMG-1 and HMG-2 proteins may play key roles in facilitating the expression of the lymphokine genes that contain CLE0 elements.

  14. The master switchers in the aging of cardiovascular system, reverse senescence by microRNA signatures; as highly conserved molecules.

    PubMed

    Pourrajab, Fatemeh; Vakili Zarch, Abbas; Hekmatimoghaddam, Seyedhossein; Zare-Khormizi, Mohamad Reza

    2015-11-01

    The incidence of CVD increases with aging, because of long-term exposure to risk factors/stressors. Aging is a complex biological process resulting in progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death. The main hallmarks of aging are cellular senescence, stem cell exhaustion, and altered intracellular communication. The major hallmarks of senescence are mitochondrial dysfunction, genomic instability, telomere attrition and epigenetic alterations, all of which contributing to cellular aging. Such events are controls by a family of small, non-coding RNAs (miRNAs) that interact with component of cellular senescence pathway; mitochondrial biogenesis/removal, DNA damage response machinery and IGF-1 signaling pathway. Here, we review recent in vivo/in vitro reports that miRNAs are key modulators of heart senescence, and act as master switchers to influence reprogramming pathway. We discuss evidence that abrupt deregulation of some mit-miRNAs governing senescence programs underlies age-associated CVD. In particular, due to the highly conserved nature and well-recognized target sites, miRNAs have been defined as master switchers in controlling heart progenitor cell biology. Modulation of mit-miRNA expression holds the great promise in switching off/on cellular senescence/reprogramming to rejuvenate stem cells to aid regenerative process.

  15. Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations

    PubMed Central

    Ma, Zhihong; Yang, Xuefen; Bercsenyi, Miklos; Wu, Junjie; Yu, Yongyao; Wei, Kaijian; Fan, Qixue; Yang, Ruibin

    2015-01-01

    To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species. PMID:26492246

  16. Genetic Determinants of Sindbis Virus Mosquito Infection Are Associated with a Highly Conserved Alphavirus and Flavivirus Envelope Sequence▿

    PubMed Central

    Pierro, Dennis J.; Powers, Erik L.; Olson, Ken E.

    2008-01-01

    Wild-type Sindbis virus (SINV) strain MRE16 efficiently infects Aedes aegypti midgut epithelial cells (MEC), but laboratory-derived neurovirulent SINV strain TE/5′2J infects MEC poorly. SINV determinants for MEC infection have been localized to the E2 glycoprotein. The E2 amino acid sequences of MRE16 and TE/5′2J differ at 60 residue sites. To identify the genetic determinants of MEC infection of MRE16, the TE/5′2J virus genome was altered to contain either domain chimeras or more focused nucleotide substitutions of MRE16. The growth patterns of derived viruses in cell culture were determined, as were the midgut infection rates (MIR) in A. aegypti mosquitoes. The results showed that substitutions of MRE16 E2 aa 95 to 96 and 116 to 119 into the TE/5′2J virus increased MIR both independently and in combination with each other. In addition, a unique PPF/.GDS amino acid motif was located between these two sites that was found to be a highly conserved sequence among alphaviruses and flaviviruses but not other arboviruses. PMID:18160430

  17. The highly conserved human cytomegalovirus UL136 ORF generates multiple Golgi-localizing protein isoforms through differential translation initiation.

    PubMed

    Liao, Huanan; Lee, Jung-Hyun; Kondo, Rikita; Katata, Marei; Imadome, Ken-Ichi; Miyado, Kenji; Inoue, Naoki; Fujiwara, Shigeyoshi; Nakamura, Hiroyuki

    2014-01-22

    The UL133-UL138 locus in the unique long b' (ULb') region of the human cytomegalovirus (HCMV) genome is considered to play certain roles in viral replication, dissemination and latency in a host cell type-dependent manner. Here we characterized the proteins encoded by UL136, one of the open reading frames (ORFs) in the locus. Comparative sequence analysis of UL136 among clinical isolates and laboratory strains indicates that its predicted amino-acid sequence is highly conserved. A polyclonal antibody against UL136 proteins (pUL136s) was raised against its carboxy-terminal region and this antibody specifically recognized at least five UL136-encoded protein isoforms of 29-17 kDa both in HCMV-infected cells and in cells transfected with a construct expressing pUL136. Immunofluorescence analysis with this antibody revealed localization of pUL136 in the Golgi apparatus. Analysis of several pUL136 mutants indicated that the putative transmembrane domain of pUL136 is required for its Golgi localization. Mutational analysis of multiple AUG codons in UL136 demonstrated that translation initiation from these AUG codons contributes in the generation of pUL136 isoforms.

  18. Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping.

    PubMed

    Raudsepp, Terje; Lee, Eun-Joon; Kata, Srinivas R; Brinkmeyer, Candice; Mickelson, James R; Skow, Loren C; Womack, James E; Chowdhary, Bhanu P

    2004-02-24

    Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse x hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescence in situ hybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previous data, the new map comprises a total of 175 markers (139 genes and 36 short tandem repeats, of which 53 are fluorescence in situ hybridization mapped) distributed on average at approximately 880-kb intervals along the chromosome. This is the densest and most uniformly distributed chromosomal map presently available in any mammalian species other than humans and rodents. Comparison of the horse and human X chromosome maps shows remarkable conservation of gene order along the entire span of the chromosomes, including the location of the centromere. An overview of the status of the horse map in relation to mouse, livestock, and companion animal species is also provided. The map will be instrumental for analysis of X linked health and fertility traits in horses by facilitating identification of targeted chromosomal regions for isolation of polymorphic markers, building bacterial artificial chromosome contigs, or sequencing.

  19. The sequence organization of Yp/proximal Xq homologous regions of the human sex chromosomes is highly conserved

    SciTech Connect

    Sargent, C.A.; Briggs, H.; Chalmers, I.J.

    1996-03-01

    Detailed deletion analysis of patients with breakpoints in Yp has allowed the definition of two distinct intervals on the Y chromosome short arm outside the pseudoautosomal region that are homologous to Xq21.3. Detailed YAC contigs have been developed over these regions on both the X and Y chromosomes, and the relative order of markers has been compared to assess whether rearrangements on either sex chromosome have occurred since the transposition events creating these patterns of homology. On the X chromosome, the region forms almost one contiguous block of homology, whereas on the Y chromosome, there has been one major rearrangement leading to the two separate Yp-Xq21 blocks of homology. The rearrangement breakpoint has been mapped. Within these separate X-Y homologous blocks on Yp, the order of loci homologous to X has been conserved to a high degree between the sex chromosomes. With the exception of the amelogenin gene (proximal Yp block), all the X-Y homologous sequences in the two Yp blocks have homologues in Xq21.3, with the former having its X counterpart in Xp22.2. This suggests an independent evolutionary event leading to the formation of the amelogenin X-Y homology. 45 refs., 4 figs., 1 tab.

  20. Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations.

    PubMed

    Ma, Zhihong; Yang, Xuefen; Bercsenyi, Miklos; Wu, Junjie; Yu, Yongyao; Wei, Kaijian; Fan, Qixue; Yang, Ruibin

    2015-10-20

    To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.

  1. An entropy-residual shock detector for solving conservation laws using high-order discontinuous Galerkin methods

    NASA Astrophysics Data System (ADS)

    Lv, Yu; See, Yee Chee; Ihme, Matthias

    2016-10-01

    This manuscript is concerned with the detection of shock discontinuities in the solution of conservation laws for high-order discontinuous Galerkin methods. A shock detector based on the entropy residual is proposed to distinguish smooth and non-smooth parts of the solution. The numerical analysis shows that the proposed entropy residual converges if the true solution is smooth and sufficiently regularized in space and time. To precisely localize discontinuities of different natures, an approach is developed that dynamically sets the threshold on the detection function, such that the detection criterion retains its sensitivity to the characteristics of the local solution. The implementation is conducted in an entropy-bounded discontinuous Galerkin framework, and numerical tests confirm the convergence property of the entropy-residual formulation and the effectiveness of the thresholding procedure. This shock detector is combined with an artificial viscosity scheme for shock stabilization. Comparison with other detectors is performed to demonstrate the excellent performance of the entropy-residual based shock detector for a wide range of problems on regular and triangular grids.

  2. The implications of RCRA (Resource Conservation and Recovery Act) regulation for the disposal of transuranic and high-level waste

    SciTech Connect

    Sigmon, C.F.; Sharples, F.E.; Smith, E.D.

    1988-01-01

    In May of 1987 the Department of Energy (DOE) published a rule interpreting the definition of ''byproduct'' under the Atomic Energy Act. This byproduct rule clarified the role of the Resource Conservation and Recovery Act (RCRA) in the regulation of DOE's radioactive waste management activities. According to the rule, only the radioactive portion of DOE's mixed radioactive and hazardous waste (mixed waste), including mixed transuranic (TRU) and high-level waste (HLW), is exempt from RCRA under the byproduct exemption. The portion of a waste that is hazardous as defined by RCRA is subject to full regulation under RCRA. Because the radioactive and hazardous portions of m any, if not most, DOE wastes are likely to be inseparable, the rule in effect makes most mixed wastes subject to dual regulation. The potential application of RCRA to facilities such as the Waste Isolation Pilot Plant (WIPP) and the HLW repository creates unique challenges for both the DOE and regulatory authorities. Strategies must be developed to assure compliance with RCRA without either causing excessive administrative burdens or abandoning the goal of minimizing radiation exposure. This paper will explore some of the potential regulatory options for and recent trends in the regulation of TRU and HLW under RCRA.

  3. The Principal Forces of Oocyte Polarity Are Evolutionary Conserved but May Not Affect the Contribution of the First Two Blastomeres to the Blastocyst Development in Mammals

    PubMed Central

    Hosseini, Sayyed-Morteza; Moulavi, Fariba; Tanhaie-Vash, Nima; Asgari, Vajihe; Ghanaei, Hamid-Reza; Abedi-Dorche, Maryam; Jafarzadeh, Naser; Gourabi, Hossein; Shahverdi, Abdol-Hossein; Dizaj, Ahmad Vosough; Shirazi, Abolfazl; Nasr-Esfahani, Mohammad-Hossein

    2016-01-01

    Oocyte polarity and embryonic patterning are well-established features of development in lower species. Whether a similar form of pre-patterning exists in mammals is currently under hot debate in mice. This study investigated this issue for the first time in ovine as a large mammal model. Microsurgical trisection of unfertilized MII-oocytes revealed that cortical cytoplasm around spindle (S) contained significant amounts of total maternal mRNAs and proteins compared to matched cytoplast hemispheres that were located either near (NS) or far (FS) -to-spindle. RT-qPCR provided striking examples of maternal mRNA localized to subcellular substructures S (NPM2, GMNN, H19, PCAF, DNMT3A, DNMT1, and STELLA), NS (SOX2, NANOG, POU5F1, and TET1), and FS (GCN) of MII oocyte. Immunoblotting revealed that specific maternal proteins DNMT3A and NANOG were asymmetrically enriched in MII-spindle-half of the oocytes. Topological analysis of sperm entry point (SEP) revealed that sperm preferentially entered via the MII-spindle-half of the oocytes. Even though, the topological position of first cleavage plane with regard to SEP was quite stochastic. Spatial comparison of lipid content revealed symmetrical distribution of lipids between 2-cell blastomeres. Lineage tracing using Dil, a fluorescent dye, revealed that while the progeny of leading blastomere of 2-cell embryos contributed to more cells in the developed blastocysts compared to lagging counterpart, the contributions of leading and lagging blastomeres to the embryonic-abembryonic parts of the developed blastocysts were almost unbiased. And finally, separated sister blastomeres of 2-cell embryos had an overall similar probability to arrest at any stage before the blastocyst (2-cell, 4-cell, 8-cell, and morula) or to achieve the blastocyst stage. It was concluded that the localization of maternal mRNAs and proteins at the spindle are evolutionarily conserved between mammals unfertilized ovine oocyte could be considered polar with

  4. Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.

    PubMed

    Melia, Tisha; Hao, Pengying; Yilmaz, Feyza; Waxman, David J

    2016-01-01

    Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. To investigate the potential for functionality, we focused on the responses of the liver lincRNAs to growth hormone stimulation, which imparts clinically relevant sex differences to hepatic metabolism and liver disease susceptibility. Sex-biased expression characterized 247 liver lincRNAs, with many being nuclear RNA enriched and regulated by growth hormone. The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). Repression of female-specific lincRNAs in male liver, but not that of male-specific lincRNAs in female liver, was associated with enrichment of H3K27me3-associated inactive states and poised (bivalent) enhancer states. Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. Orthologs for many liver lincRNAs were identified in one or more supraprimates, including two rat lincRNAs showing the same growth hormone-regulated, sex-biased expression as their mouse counterparts. This integrative analysis of liver lincRNA chromatin states, transcription factor occupancy, and growth hormone regulation provides novel insights into the

  5. High and Low Contrast Visual Acuity Are Not Affected in Amyotrophic Lateral Sclerosis.

    PubMed

    Moss, Heather E; Samelson, Monica; Mohan, Girish; Jiang, Qin Li

    2016-01-01

    The afferent visual system may be affected by neuro-degeneration in amyotrophic lateral sclerosis (ALS) based on observations of visual function impairment and retinal inclusions on histopathology in ALS patients. To test the hypothesis that visual acuity is impaired in ALS, we compared three measures of visual acuity in ALS patients (n = 25) attending a multidisciplinary ALS clinic and age matched control subjects (n = 25). Bilateral monocular and binocular visual acuities were assessed using high contrast (black letters on white background) and low contrast (2.5%, 1.25% grey letters on white background) visual acuity charts under controlled lighting conditions following refraction. Binocular summation was calculated as the difference between binocular and best monocular acuity scores. There were no associations between binocular or monocular high contrast visual acuity or low contrast visual acuity and amyotrophic lateral sclerosis diagnosis (generalized estimating equation models accounting for age). Binocular summation was similar in both amyotrophic lateral sclerosis and control subjects. There was a small magnitude association between increased duration of ALS symptoms and reduced 1.25% low contrast visual acuity. This study does not confirm prior observations of impaired visual acuity in patients with amyotrophic lateral sclerosis and does not support this particular measure of visual function for use in broad scale assessment of visual pathway involvement in ALS patients.

  6. High and Low Contrast Visual Acuity Are Not Affected in Amyotrophic Lateral Sclerosis

    PubMed Central

    Samelson, Monica; Mohan, Girish; Jiang, Qin Li

    2016-01-01

    The afferent visual system may be affected by neuro-degeneration in amyotrophic lateral sclerosis (ALS) based on observations of visual function impairment and retinal inclusions on histopathology in ALS patients. To test the hypothesis that visual acuity is impaired in ALS, we compared three measures of visual acuity in ALS patients (n = 25) attending a multidisciplinary ALS clinic and age matched control subjects (n = 25). Bilateral monocular and binocular visual acuities were assessed using high contrast (black letters on white background) and low contrast (2.5%, 1.25% grey letters on white background) visual acuity charts under controlled lighting conditions following refraction. Binocular summation was calculated as the difference between binocular and best monocular acuity scores. There were no associations between binocular or monocular high contrast visual acuity or low contrast visual acuity and amyotrophic lateral sclerosis diagnosis (generalized estimating equation models accounting for age). Binocular summation was similar in both amyotrophic lateral sclerosis and control subjects. There was a small magnitude association between increased duration of ALS symptoms and reduced 1.25% low contrast visual acuity. This study does not confirm prior observations of impaired visual acuity in patients with amyotrophic lateral sclerosis and does not support this particular measure of visual function for use in broad scale assessment of visual pathway involvement in ALS patients. PMID:28033389

  7. Material deprivation affects high sexual risk behavior among young people in urban slums, South Africa.

    PubMed

    Kamndaya, Mphatso; Thomas, Liz; Vearey, Jo; Sartorius, Benn; Kazembe, Lawrence

    2014-06-01

    Young people in urban slums adopt HIV risk behaviors influenced by their neighborhood factors. Three critical factors in urban slums of Southern and Eastern Africa--the region most affected by the HIV epidemic in the world--are unmet needs of housing, food, and health care, which are associated with HIV sexual risks. Yet, there has been limited attention on how the combination of unmet needs of housing, food, and health care--i.e., material deprivation-relates to sexual risk behavior among young people in urban slums. Cross-sectional data were extracted from the LoveLife survey in South African four provinces--KwaZulu Natal, Mpumalanga, Eastern Cape, and Gauteng, to examine the association between material deprivation and sexual risk behavior among young people aged 18-23 years (263 males, 267 females) in urban slums. Adjusted logistic regression models showed that material deprivation was significantly associated with increased odds of high sexual risk taking for young men (adjusted OR = 1.20; 95 % CI = 1.10, 5.58) and young women (adjusted OR = 1.43; 95 % CI = 1.35, 3.28). Financial difficulty--a proxy for other deprivations--was the most salient influence on young women's high sexual risk taking (adjusted OR = 2.11; 95 % CI = 1.66, 2.70). Localized behavioral HIV prevention interventions should target young people in deprived households.

  8. High conservation level of CD8(+) T cell immunogenic regions within an unusual H1N2 human influenza variant.

    PubMed

    Komadina, Naomi; Quiñones-Parra, Sergio M; Kedzierska, Katherine; McCaw, James M; Kelso, Anne; Leder, Karin; McVernon, Jodie

    2016-10-01

    Current seasonal influenza vaccines require regular updates due to antigenic drift causing loss of effectiveness and therefore providing little or no protection against novel influenza A subtypes. Next generation vaccines capable of eliciting CD8(+) T cell (CTL) mediated cross-protective immunity may offer a long-term alternative strategy. However, measuring pre- and existing levels of CTL cross-protection in humans is confounded by differences in infection histories across individuals. During 2000-2003, H1N2 viruses circulated persistently in the human population for the first time and we hypothesized that the viral nucleoprotein (NP) contained novel CTL epitopes that may have contributed to the survival of the viruses. This study describes the immunogenic NP peptides of H1N1, H2N2, and H3N2 influenza viruses isolated from humans over the past century, 1918-2003, by comparing this historical dataset to reference NP peptides from H1N2 that circulated in humans during 2000-2003. Observed peptides sequences ranged from highly conserved (15%) to highly variable (12%), with variation unrelated to reported immunodominance. No unique NP peptides which were exclusive to the H1N2 viruses were noted. However, the virus had inherited the NP from a recently emerged H3N2 variant containing novel peptides, which may have assisted its persistence. Any advantage due to this novelty was subsequently lost with emergence of a newer H3N2 variant in 2003. Our approach has potential to provide insight into the population context in which influenza viruses emerge, and may help to inform immunogenic peptide selection for CTL-inducing influenza vaccines. J. Med. Virol. 88:1725-1732, 2016. © 2016 Wiley Periodicals, Inc.

  9. Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout

    PubMed Central

    Uren Webster, Tamsyn M.; Shears, Janice A.; Moore, Karen

    2015-01-01

    Estrogenic chemicals are major contaminants of surface waters and can threaten the sustainability of natural fish populations. Characterization of the global molecular mechanisms of toxicity of environmental contaminants has been conducted primarily in model species rather than species with limited existing transcriptomic or genomic sequence information. We aimed to investigate the global mechanisms of toxicity of an endocrine disrupting chemical of environmental concern [17β-estradiol (E2)] using high-throughput RNA sequencing (RNA-Seq) in an environmentally relevant species, brown trout (Salmo trutta). We exposed mature males to measured concentrations of 1.94, 18.06, and 34.38 ng E2/l for 4 days and sequenced three individual liver samples per treatment using an Illumina HiSeq 2500 platform. Exposure to 34.4 ng E2/L resulted in 2,113 differentially regulated transcripts (FDR < 0.05). Functional analysis revealed upregulation of processes associated with vitellogenesis, including lipid metabolism, cellular proliferation, and ribosome biogenesis, together with a downregulation of carbohydrate metabolism. Using real-time quantitative PCR, we validated the expression of eight target genes and identified significant differences in the regulation of several known estrogen-responsive transcripts in fish exposed to the lower treatment concentrations (including esr1 and zp2.5). We successfully used RNA-Seq to identify highly conserved responses to estrogen and also identified some estrogen-responsive transcripts that have been less well characterized, including nots and tgm2l. These results demonstrate the potential application of RNA-Seq as a valuable tool for assessing mechanistic effects of pollutants in ecologically relevant species for which little genomic information is available. PMID:26082144

  10. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits

    PubMed Central

    Ravel, Catherine; Fiquet, Samuel; Boudet, Julie; Dardevet, Mireille; Vincent, Jonathan; Merlino, Marielle; Michard, Robin; Martre, Pierre

    2014-01-01

    The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression. PMID:25429295

  11. High summer temperatures affect the survival and reproduction of olive fruit fly (Diptera: Tephritidae).

    PubMed

    Wang, Xin-Geng; Johnson, Marshall W; Daane, Kent M; Nadel, Hannah

    2009-10-01

    The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is an invasive pest in California. Identifying environmental constraints that affect the geographic distribution and abundance of any invasive insect pest is fundamental to its effective management. California's Central Valley, where most commercial olives are grown, is extremely hot during the summer, with maximum daily temperatures consistently >35.0 degrees C. This study examined the effects of two diurnal temperature regimens (low 18.3 degrees C, high 35.0 or 37.8 degrees C) reflecting summer conditions in the valley, and one control temperature regimen (low 18.3 degrees C, high 23.9 degrees C) on the fly's survival and reproductive success in the laboratory. The temperature regimen of 18.3-35.0 degrees C resulted in delayed egg maturation and reduced production of mature eggs compared with the control temperature regimen. Egg maturation was possible at the higher temperature regimen when females were provided with water and food, and egg-laying occurred during the cold phase of the temperature cycle. Access to olive fruit and oviposition itself further promoted egg maturation. Under exposure to the 18.3-35.0 degrees C temperature regimen, approximately 50% of eggs died, and the remainder that hatched died as first instars. No egg hatch occurred at the temperature treatment of 18.3-37.8 degrees C. We confirmed these laboratory results through field cage studies with adult B. oleae, conducted in the summer of 2007 and 2008. Under ambient summer temperatures, adult B. oleae survived for 1-2 wk, and females readily laid eggs when provided water and food. No offspring developed in midsummer of 2007, and <2% of the offspring developed to adults in summer 2008 trials. These results suggest that high summer temperatures limit the fly's abundance in California's Central Valley.

  12. Comparing the cost-effectiveness of water conservation policies in a depleting aquifer:A dynamic analysis of the Kansas High Plains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This research analyzes two groundwater conservation policies in the Kansas High Plains located within the Ogallala aquifer: 1) cost-share assistance to increase irrigation efficiency; and 2) incentive payments to convert irrigated crop production to dryland crop production. To compare the cost-effec...

  13. Methyl ketones in high altitude Ecuadorian Andosols confirm excellent conservation of plant-specific n-alkane patterns

    NASA Astrophysics Data System (ADS)

    Jansen, B.; Nierop, K. G. J.

    2009-04-01

    Montane forest composition and specifically the position of the upper forest line (UFL) is very sensitive to climate change and human interference. As a consequence, reconstructions of past altitudinal UFL dynamics and forest species composition are crucial instruments to infer relationships between climate change and vegetation dynamics, and assess the impact of (pre)historic human settlement. One of the most detailed methods available to date to reconstruct past vegetation dynamics is the analysis of fossil pollen. Unfortunately, fossil pollen analysis does not distinguish beyond family or generic level in most cases, while its spatial resolution is limited amongst others by windblown dispersal of pollen, affecting the accuracy of pollen based reconstructions of UFL positions. To overcome these limitations, we developed a new method based on the analysis of plant-specific groups of biomarkers preserved in suitable archives, such as peat deposits, that are unravelled into the plant species of origin by the newly developed VERHIB model. In a study of UFL positions in the Northern Ecuadorian Andes we found longer chain-length n-alkanes, (C19-C35) to occur in plant-specific patterns in the dominant vegetation in the area as well as preliminary soil and peat samples. A crucial factor in determining the applicability of these n-alkanes as biomarkers for past vegetation is their preservation in soils and peat deposits. Therefore, we investigated the preservation of C19-C35 n-alkanes in a peat core and in five excavations along an altitudinal transect (3500-3860 m.a.s.l) in the study area. We were able to establish that n-methyl ketones are the main degradation product of the n-alkanes in question, while the degradation of the n-alkanes was the main source of the n-methyl ketones. This allowed us to use the relationship between the concentrations and carbon chain length patterns of n-alkanes and n-methyl ketones to assess possible (selective) degradation of the n

  14. Snowmelt Processes At High Altitude. How Does A Partly Frozen Ground Affect Alpine Aquifer During Snowmelt?

    NASA Astrophysics Data System (ADS)

    Bayard, D.; Stähli, M.; Turberg, P.; Parriaux, A.

    In alpine areas, the snow cover plays an important role as water reservoir, especially at high altitudes (over 2000 meters). Water is stored as snow over the winter and re- leased in spring, recharging mountain aquifers through infiltration. These aquifers are essential, especially for the supply of human activities with water during dry seasons. But these snow reservoirs may produce severe flooding, in particular when snowmelt is combined with heavy rainfall and a frozen underground. Surface frost can drastically reduce water infiltration by several orders of magnitude and therefore affect groundwater recharge. Evaluating the impact of frost on snowmelt runoff at selected sites in the Alps enables us to quantify water exportation processes (i.e. surface runoff, subsurface runoff and deep percolation) from the snow pack. The main objectives of this research project consisted (a) in studying the different pro- cesses influencing groundwater recharge during snowmelt periods, i.e. snow cover evolution, ground frost depth, snowmelt water runoff types on specific sites, (b) in as- sessing the variability of frost formation while taking into account spatial, altitudinal and climatic differences, (c) in identifying meteorological situations that are critical with respect to flooding. Two experimental sites were selected in the southern Swiss Alps, one at Hannigalp (2100 m) and the other at the Gd St-Bernard pass (2500 m). The Hannigalp site is characterized by a rather dry (600 mm/year) and wind free climate, whereas high amounts of precipitation (2100 mm/year) and strong winds are encountered at the Grand St Bernard. To investigate the delay in snowmelt due to the orientation and altitude, two secondary sites were additionally chosen near the Gd St-Bernard pass. In spite of a very thick snow pack, water balance measurements of winter 2000/01 showed for Grächen null to very low surface and subsurface flow due to the fact that soil frost was local. At the Gd St Bernard

  15. High resolution three-dimensional (256 to the 3rd) spatio-temporal measurements of the conserved scalar field in turbulent shear flows

    NASA Astrophysics Data System (ADS)

    Dahm, Werner J. A.; Buch, Kenneth A.

    Results from highly resolved three-dimensional spatio-temporal measurements of the conserved scalar field zeta(x,t) in a turbulent shear flow. Each of these experiments consists of 256 to the 3rd individual point measurements of the local instantaneous conserved scalar value in the flow. The spatial and temporal resolution of these measurements reach beyond the local Kolmogorov scale and resolve the local strain-limited molecular diffusion scale in the flow. The results clearly show molecular mixing occurring in thin strained laminar diffusion layers in a turbulent flow.

  16. Evaluation of Heat-affected Zone Hydrogen-induced Cracking in High-strength Steels

    NASA Astrophysics Data System (ADS)

    Yue, Xin

    Shipbuilding is heavily reliant on welding as a primary fabrication technique. Any high performance naval steel must also possess good weldability. It is therefore of great practical importance to conduct weldability testing of naval steels. Among various weldability issues of high-strength steels, hydrogen-induced cracking (HIC) in the heat-affected zone (HAZ) following welding is one of the biggest concerns. As a result, in the present work, research was conducted to study the HAZ HIC susceptibility of several naval steels. Since the coarse-grained heat-affected zone (CGHAZ) is generally known to be the most susceptible to HIC in the HAZ region, the continuous cooling transformation (CCT) behavior of the CGHAZ of naval steels HSLA-65, HSLA-100, and HY-100 was investigated. The CGHAZ microstructure over a range of cooling rates was characterized, and corresponding CCT diagrams were constructed. It was found that depending on the cooling rate, martensite, bainite, ferrite and pearlite can form in the CGHAZ of HSLA-65. For HSLA-100 and HY-100, only martensite and bainite formed over the range of cooling rates that were simulated. The constructed CCT diagrams can be used as a reference to select welding parameters to avoid the formation of high-hardness martensite in the CGHAZ, in order to ensure resistance to hydrogen-induced cracking. Implant testing was conducted on the naval steels to evaluate their susceptibility to HAZ HIC. Stress vs. time to failure curves were plotted, and the lower critical stress (LCS), normalized critical stress ratio (NCSR) and embrittlement index (EI) for each steel were determined, which were used to quantitatively compare HIC susceptibility. The CGHAZ microstructure of the naval steels was characterized, and the HIC fracture behavior was studied. Intergranular (IG), quasi-cleavage (QC) and microvoid coalescence (MVC) fracture modes were found to occur in sequence during the crack initiation and propagation process. This was

  17. [Conservative treatment of idiopathic facial palsy--effects of the administration of high-dose steroids in Bell's palsy].

    PubMed

    Inamura, H; Tojima, H; Saito, O; Maeyama, H; Takeda, K; Aoyagi, M; Koike, Y

    1992-02-01

    The etiology of Bell's palsy is still obscure and its treatment remains controversial. As a conservative treatment for Bell's palsy, Stennert developed a new treatment method for the purpose of improving microcirculation, and reported an extremely high cure rate of 96%, drawing a great deal of attention. However, since the electrophysiological findings and side effects in these patients were not described satisfactorily in his report, this method has not yet come into wide clinical use. In the present study the efficacy of Stennert's method was assessed by electrophysiological examination in patients, and was compared with patients treated by conventional methods. The subjects of this study were 157 patients with Bell's palsy who were treated with a modification of Stennert's method between September 1987 and August 1990. The treatment protocol for the modified Stennert's method was as follows: hydroxyethyl starch 40 with 20% mannitol is given instead of Dextran 40 and prednisolone is stopped depending on the findings of electrical examinations. Fifty-three patients with Bell's palsy treated by the conventional method used in our clinic between November 1983 and August 1987 were used for the control group. The most remarkable difference between these two methods was the initial dose of prednisolone. In the group treated by the modified Stennert's method, 111 patients (70.7%) showed complete recovery within 1 month, and 154 patients presented (98.1%) showed complete recovery within 6 months, 3 cases presented slight sequelae. In the conventional treatment group, on the other hand, only 2 patients (3.8%) recovered within 1 month, and 43 patients (81.0%) recovered within 6 months.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Grassland bird associations with introduced and native grass Conservation Reserve Program fields in the Southern High Plains

    USGS Publications Warehouse

    Thompson, Thomas R.; Boal, Clint W.; Lucia, Duane

    2009-01-01

    We examined relative abundances of grassland birds among Conservation Reserve Program (CRP) fields seeded with 2 monocultures of introduced grass species and 2 mixes of native grasses in the Southern High Plains of Texas. We assessed bird compositions among these 4 cover types and between the cover types pooled into categories of introduced and native fields. Breeding season bird diversity and total abundance did not differ among cover types or between introduced and native fields. Grasshopper Sparrows (Ammodramus savannarum), Cassin's Sparrows (Aimophila cassinii), and Western Meadowlarks (Sturnella neglecta) accounted for more than 90% of breeding season detections. Grasshopper Sparrows were the most abundant and found in all cover types. Cassin's Sparrows were 38% to 170% more abundant among the native seed mix without buffalograss (Buchloë dactyloides) compared to 3 other cover types. Although this association was statistically lost when cover types were pooled into introduced or native fields (U = 93.5, P = 0.91), the species was still 50% more abundant among native CRP than introduced CRP fields. Meadowlarks occurred ubiquitously but at very low numbers during the breeding season. During winter, avian abundance was 44% greater among native CRP than introduced CRP fields. Meadowlarks, Homed Larks (Eremophila alpestris), and Savannah Sparrows (Passerculus sandwichensis) accounted for 94% of all winter detections. Meadowlarks occurred ubiquitously, but Horned Larks and Savannah Sparrows were 157% and 96% more abundant, respectively, among native CRP than introduced CRP fields. Our data suggest that monocultures of introduced grasses may benefit some bird species but also that native seed mixes may have a more positive influence through increased diversity and abundance of grassland birds. However, pooling cover types into the broader categories of introduced or native grasses may dampen or occlude biologically meaningful results. It may be prudent to avoid

  19. High-intensity pulsed electric field variables affecting Staphylococcus aureus inoculated in milk.

    PubMed

    Sobrino-López, A; Raybaudi-Massilia, R; Martín-Belloso, O

    2006-10-01

    Staphylococcus aureus is an important milk-related pathogen that is inactivated by high-intensity pulsed electric fields (HIPEF). In this study, inactivation of Staph. aureus suspended in milk by HIPEF was studied using a response surface methodology, in which electric field intensity, pulse number, pulse width, pulse polarity, and the fat content of milk were the controlled variables. It was found that the fat content of milk did not significantly affect the microbial inactivation of Staph. aureus. A maximum value of 4.5 log reductions was obtained by applying 150 bipolar pulses of 8 mus each at 35 kV/cm. Bipolar pulses were more effective than those applied in the monopolar mode. An increase in electric field intensity, pulse number, or pulse width resulted in a drop in the survival fraction of Staph. aureus. Pulse widths close to 6.7 micros lead to greater microbial death with a minimum number of applied pulses. At a constant treatment time, a greater number of shorter pulses achieved better inactivation than those treatments performed at a lower number of longer pulses. The combined action of pulse number and electric field intensity followed a similar pattern, indicating that the same fraction of microbial death can be reached with different combinations of the variables. The behavior and relationship among the electrical variables suggest that the energy input of HIPEF processing might be optimized without decreasing the microbial death.

  20. High-Density Lipoprotein Binds to Mycobacterium avium and Affects the Infection of THP-1 Macrophages

    PubMed Central

    Ichimura, Naoya; Sato, Megumi; Yoshimoto, Akira; Yano, Kouji; Ohkawa, Ryunosuke; Kasama, Takeshi

    2016-01-01

    High-density lipoprotein (HDL) is involved in innate immunity toward various infectious diseases. Concerning bacteria, HDL is known to bind to lipopolysaccharide (LPS) and to neutralize its physiological activity. On the other hand, cholesterol is known to play an important role in mycobacterial entry into host cells and in survival in the intracellular environment. However, the pathogenicity of Mycobacterium avium (M. avium) infection, which tends to increase worldwide, remains poorly studied. Here we report that HDL indicated a stronger interaction with M. avium than that with other Gram-negative bacteria containing abundant LPS. A binding of apolipoprotein (apo) A-I, the main protein component of HDL, with a specific lipid of M. avium might participate in this interaction. HDL did not have a direct bactericidal activity toward M. avium but attenuated the engulfment of M. avium by THP-1 macrophages. HDL also did not affect bacterial killing after ingestion of live M. avium by THP-1 macrophage. Furthermore, HDL strongly promoted the formation of lipid droplets in M. avium-infected THP-1 macrophages. These observations provide new insights into the relationship between M. avium infection and host lipoproteins, especially HDL. Thus, HDL may help M. avium to escape from host innate immunity. PMID:27516907

  1. Effects of autonomous motivational priming on motivation and affective responses towards high-intensity interval training.

    PubMed

    Brown, Denver M Y; Teseo, Amanda J; Bray, Steven R

    2016-08-01

    This study examined the effect of autonomous motivational priming on motivation, attitudes and intentions towards high-intensity interval training (HIT). Participants (N = 42) performed a graded exercise test to determine their peak aerobic power (WPEAK). At a subsequent testing session, participants were randomised to complete either an autonomous or neutral motivational priming task followed by a 10 × 1 HIT exercise protocol, alternating 1-min bouts of hard (70% WPEAK) and light (12.5% WPEAK) exercises for 20 min. Participants primed with autonomous motivation reported greater enjoyment, P = .009, ηp(2) = .16, and perceived competence, P = .005, ηp(2) = .18, post-exercise compared to those in the neutral priming condition. Participants in the autonomous motivational priming condition also reported more positive attitudes, P = .014, ηp(2) = .14, towards HIT; however, there was no difference between the conditions for task motivation during HIT or intentions, P = .53, ηp(2) = .01, to engage in HIT. These findings highlight autonomous motivational priming as a method of enhancing affective and motivational experiences regarding HIT.

  2. Nitrogen Addition Significantly Affects Forest Litter Decomposition under High Levels of Ambient Nitrogen Deposition

    PubMed Central

    Chen, Gang; Peng, Yong; Xiao, Yin-long; Hu, Ting-xing; Zhang, Jian; Li, Xian-wei; Liu, Li; Tang, Yi

    2014-01-01

    Background Forest litter decomposition is a major component of the global carbon (C) budget, and is greatly affected by the atmospheric nitrogen (N) deposition observed globally. However, the effects of N addition on forest litter decomposition, in ecosystems receiving increasingly higher levels of ambient N deposition, are poorly understood. Methodology/Principal Findings We conducted a two-year field experiment in five forests along the western edge of the Sichuan Basin in China, where atmospheric N deposition was up to 82–114 kg N ha–1 in the study sites. Four levels of N treatments were applied: (1) control (no N added), (2) low-N (50 kg N ha–1 year–1), (3) medium-N (150 kg N ha–1 year–1), and (4) high-N (300 kg N ha–1 year–1), N additions ranging from 40% to 370% of ambient N deposition. The decomposition processes of ten types of forest litters were then studied. Nitrogen additions significantly decreased the decomposition rates of six types of forest litters. N additions decreased forest litter decomposition, and the mass of residual litter was closely correlated to residual lignin during the decomposition process over the study period. The inhibitory effect of N addition on litter decomposition can be primarily explained by the inhibition of lignin decomposition by exogenous inorganic N. The overall decomposition rate of ten investigated substrates exhibited a significant negative linear relationship with initial tissue C/N and lignin/N, and significant positive relationships with initial tissue K and N concentrations; these relationships exhibited linear and logarithmic curves, respectively. Conclusions/Significance This study suggests that the expected progressive increases in N deposition may have a potential important impact on forest litter decomposition in the study area in the presence of high levels of ambient N deposition. PMID:24551152

  3. High Heating Rates Affect Greatly the Inactivation Rate of Escherichia coli

    PubMed Central

    Huertas, Juan-Pablo; Aznar, Arantxa; Esnoz, Arturo; Fernández, Pablo S.; Iguaz, Asunción; Periago, Paula M.; Palop, Alfredo

    2016-01-01

    Heat resistance of microorganisms can be affected by different influencing factors. Although, the effect of heating rates has been scarcely explored by the scientific community, recent researches have unraveled its important effect on the thermal resistance of different species of vegetative bacteria. Typically heating rates described in the literature ranged from 1 to 20°C/min but the impact of much higher heating rates is unclear. The aim of this research was to explore the effect of different heating rates, such as those currently achieved in the heat exchangers used in the food industry, on the heat resistance of Escherichia coli. A pilot plant tubular heat exchanger and a thermoresistometer Mastia were used for this purpose. Results showed that fast heating rates had a deep impact on the thermal resistance of E. coli. Heating rates between 20 and 50°C/min were achieved in the heat exchanger, which were much slower than those around 20°C/s achieved in the thermoresistometer. In all cases, these high heating rates led to higher inactivation than expected: in the heat exchanger, for all the experiments performed, when the observed inactivation had reached about seven log cycles, the predictions estimated about 1 log cycle of inactivation; in the thermoresistometer these differences between observed and predicted values were even more than 10 times higher, from 4.07 log cycles observed to 0.34 predicted at a flow rate of 70 mL/min and a maximum heating rate of 14.7°C/s. A quantification of the impact of the heating rates on the level of inactivation achieved was established. These results point out the important effect that the heating rate has on the thermal resistance of E. coli, with high heating rates resulting in an additional sensitization to heat and therefore an effective food safety strategy in terms of food processing. PMID:27563300

  4. Large herbivore grazing affects the vegetation structure and greenhouse gas balance in a high arctic mire

    NASA Astrophysics Data System (ADS)

    Falk, Julie Maria; Schmidt, Niels Martin; Christensen, Torben R.; Ström, Lena

    2015-04-01

    Herbivory is an important part of most ecosystems and affects the ecosystems’ carbon balance both directly and indirectly. Little is known about herbivory and its impact on the carbon balance in high arctic mire ecosystems. We hypothesized that trampling and grazing by large herbivores influences the vegetation density and composition and thereby also the carbon balance. In 2010, we established fenced exclosures in high arctic Greenland to prevent muskoxen (Ovibos moschatus) from grazing. During the growing seasons of 2011 to 2013 we measured CO2 and CH4 fluxes in these ungrazed blocks and compared them to blocks subjected to natural grazing. Additionally, we measured depth of the water table and active layer, soil temperature, and in 2011 and 2013 an inventory of the vegetation density and composition were made. In 2013 a significant decrease in total number of vascular plant (33-44%) and Eriophorum scheuchzeri (51-53%) tillers were found in ungrazed plots, the moss-layer and amount of litter had also increased substantially in these plots. This resulted in a significant decrease in net ecosystem uptake of CO2 (47%) and likewise a decrease in CH4 emission (44%) in ungrazed plots in 2013. While the future of the muskoxen in a changing arctic is unknown, this experiment points to a potentially large effect of large herbivores on the carbon balance in natural Arctic ecosystems. It thus sheds light on the importance of grazing mammals, and hence adds to our understanding of natural ecosystem greenhouse gas balance in the past and in the future.

  5. High Heating Rates Affect Greatly the Inactivation Rate of Escherichia coli.

    PubMed

    Huertas, Juan-Pablo; Aznar, Arantxa; Esnoz, Arturo; Fernández, Pablo S; Iguaz, Asunción; Periago, Paula M; Palop, Alfredo

    2016-01-01

    Heat resistance of microorganisms can be affected by different influencing factors. Although, the effect of heating rates has been scarcely explored by the scientific community, recent researches have unraveled its important effect on the thermal resistance of different species of vegetative bacteria. Typically heating rates described in the literature ranged from 1 to 20°C/min but the impact of much higher heating rates is unclear. The aim of this research was to explore the effect of different heating rates, such as those currently achieved in the heat exchangers used in the food industry, on the heat resistance of Escherichia coli. A pilot plant tubular heat exchanger and a thermoresistometer Mastia were used for this purpose. Results showed that fast heating rates had a deep impact on the thermal resistance of E. coli. Heating rates between 20 and 50°C/min were achieved in the heat exchanger, which were much slower than those around 20°C/s achieved in the thermoresistometer. In all cases, these high heating rates led to higher inactivation than expected: in the heat exchanger, for all the experiments performed, when the observed inactivation had reached about seven log cycles, the predictions estimated about 1 log cycle of inactivation; in the thermoresistometer these differences between observed and predicted values were even more than 10 times higher, from 4.07 log cycles observed to 0.34 predicted at a flow rate of 70 mL/min and a maximum heating rate of 14.7°C/s. A quantification of the impact of the heating rates on the level of inactivation achieved was established. These results point out the important effect that the heating rate has on the thermal resistance of E. coli, with high heating rates resulting in an additional sensitization to heat and therefore an effective food safety strategy in terms of food processing.

  6. Acute stress differentially affects spatial configuration learning in high and low cortisol-responding healthy adults

    PubMed Central

    Meyer, Thomas; Smeets, Tom; Giesbrecht, Timo; Quaedflieg, Conny W. E. M.; Merckelbach, Harald

    2013-01-01

    Background Stress and stress hormones modulate memory formation in various ways that are relevant to our understanding of stress-related psychopathology, such as posttraumatic stress disorder (PTSD). Particular relevance is attributed to efficient memory formation sustained by the hippocampus and parahippocampus. This process is thought to reduce the occurrence of intrusions and flashbacks following trauma, but may be negatively affected by acute stress. Moreover, recent evidence suggests that the efficiency of visuo-spatial processing and learning based on the hippocampal area is related to PTSD symptoms. Objective The current study investigated the effect of acute stress on spatial configuration learning using a spatial contextual cueing task (SCCT) known to heavily rely on structures in the parahippocampus. Method Acute stress was induced by subjecting participants (N = 34) to the Maastricht Acute Stress Test (MAST). Following a counterbalanced within-subject approach, the effects of stress and the ensuing hormonal (i.e., cortisol) activity on subsequent SCCT performance were compared to SCCT performance following a no-stress control condition. Results Acute stress did not impact SCCT learning overall, but opposing effects emerged for high versus low cortisol responders to the MAST. Learning scores following stress were reduced in low cortisol responders, while high cortisol-responding participants showed improved learning. Conclusions The effects of stress on spatial configuration learning were moderated by the magnitude of endogenous cortisol secretion. These findings suggest a possible mechanism by which cortisol responses serve an adaptive function during stress and trauma, and this may prove to be a promising route for future research in this area. PMID:23671762

  7. Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences.

    PubMed

    Doğan, Tunca; Karaçalı, Bilge

    2013-01-01

    Identifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.

  8. A review of the allozyme data set for the Canarian endemic flora: causes of the high genetic diversity levels and implications for conservation.

    PubMed

    Pérez de Paz, Julia; Caujapé-Castells, Juli

    2013-06-01

    Background and Aims Allozyme and reproductive data sets for the Canarian flora are updated in order to assess how the present levels and structuring of genetic variation have been influenced by the abiotic island traits and by phylogenetically determined biotic traits of the corresponding taxa; and in order to suggest conservation guidelines. Methods Kruskal-Wallis tests are conducted to assess the relationships of 27 variables with genetic diversity (estimated by A, P, Ho and He) and structuring (GST) of 123 taxa representing 309 populations and 16 families. Multiple linear regression analyses (MLRAs) are carried out to determine the relative influence of the less correlated significant abiotic and biotic factors on the genetic diversity levels. Key Results and Conclusions The interactions between biotic features of the colonizing taxa and the abiotic island features drive plant diversification in the Canarian flora. However, the lower weight of closeness to the mainland than of (respectively) high basic chromosome number, partial or total self-incompatibility and polyploidy in the MLRAs indicates substantial phylogenetic constraint; the importance of a high chromosome number is feasibly due to the generation of a larger number of linkage groups, which increase gametic and genotypic diversity. Genetic structure is also more influenced by biotic factors (long-range seed dispersal, basic chromosome number and partial or total self-incompatibility) than by distance to the mainland. Conservation-wise, genetic structure estimates (FST/GST) only reflect endangerment under intensive population sampling designs, and neutral genetic variation levels do not directly relate to threat status or to small population sizes. Habitat protection is emphasized, but the results suggest the need for urgent implementation of elementary reproductive studies in all cases, and for ex situ conservation measures for the most endangered taxa, even without prior studies. In non

  9. A review of the allozyme data set for the Canarian endemic flora: causes of the high genetic diversity levels and implications for conservation

    PubMed Central

    de Paz, Julia Pérez; Caujapé-Castells, Juli

    2013-01-01

    Background and Aims Allozyme and reproductive data sets for the Canarian flora are updated in order to assess how the present levels and structuring of genetic variation have been influenced by the abiotic island traits and by phylogenetically determined biotic traits of the corresponding taxa; and in order to suggest conservation guidelines. Methods Kruskal–Wallis tests are conducted to assess the relationships of 27 variables with genetic diversity (estimated by A, P, Ho and He) and structuring (GST) of 123 taxa representing 309 populations and 16 families. Multiple linear regression analyses (MLRAs) are carried out to determine the relative influence of the less correlated significant abiotic and biotic factors on the genetic diversity levels. Key Results and Conclusions The interactions between biotic features of the colonizing taxa and the abiotic island features drive plant diversification in the Canarian flora. However, the lower weight of closeness to the mainland than of (respectively) high basic chromosome number, partial or total self-incompatibility and polyploidy in the MLRAs indicates substantial phylogenetic constraint; the importance of a high chromosome number is feasibly due to the generation of a larger number of linkage groups, which increase gametic and genotypic diversity. Genetic structure is also more influenced by biotic factors (long-range seed dispersal, basic chromosome number and partial or total self-incompatibility) than by distance to the mainland. Conservation-wise, genetic structure estimates (FST/GST) only reflect endangerment under intensive population sampling designs, and neutral genetic variation levels do not directly relate to threat status or to small population sizes. Habitat protection is emphasized, but the results suggest the need for urgent implementation of elementary reproductive studies in all cases, and for ex situ conservation measures for the most endangered taxa, even without prior studies. In non

  10. Conservation of the S10-spc-α Locus within Otherwise Highly Plastic Genomes Provides Phylogenetic Insight into the Genus Leptospira

    PubMed Central

    Zuerner, Richard L.; Ahmed, Niyaz; Bulach, Dieter M.; Quinteiro, Javier; Hartskeerl, Rudy A.

    2008-01-01

    S10-spc-α is a 17.5 kb cluster of 32 genes encoding ribosomal proteins. This locus has an unusual composition and organization in Leptospira interrogans. We demonstrate the highly conserved nature of this region among diverse Leptospira and show its utility as a phylogenetically informative region. Comparative analyses were performed by PCR using primer sets covering the whole locus. Correctly sized fragments were obtained by PCR from all L. interrogans strains tested for each primer set indicating that this locus is well conserved in this species. Few differences were detected in amplification profiles between different pathogenic species, indicating that the S10-spc-α locus is conserved among pathogenic Leptospira. In contrast, PCR analysis of this locus using DNA from saprophytic Leptospira species and species with an intermediate pathogenic capacity generated varied results. Sequence alignment of the S10-spc-α locus from two pathogenic species, L. interrogans and L. borgpetersenii, with the corresponding locus from the saprophyte L. biflexa serovar Patoc showed that genetic organization of this locus is well conserved within Leptospira. Multilocus sequence typing (MLST) of four conserved regions resulted in the construction of well-defined phylogenetic trees that help resolve questions about the interrelationships of pathogenic Leptospira. Based on the results of secY sequence analysis, we found that reliable species identification of pathogenic Leptospira is possible by comparative analysis of a 245 bp region commonly used as a target for diagnostic PCR for leptospirosis. Comparative analysis of Leptospira strains revealed that strain H6 previously classified as L. inadai actually belongs to the pathogenic species L. interrogans and that L. meyeri strain ICF phylogenetically co-localized with the pathogenic clusters. These findings demonstrate that the S10-spc-α locus is highly conserved throughout the genus and may be more useful in comparing evolution of

  11. Well-balanced high-order centred schemes for non-conservative hyperbolic systems. Applications to shallow water equations with fixed and mobile bed

    NASA Astrophysics Data System (ADS)

    Canestrelli, Alberto; Siviglia, Annunziato; Dumbser, Michael; Toro, Eleuterio F.

    2009-06-01

    This paper concerns the development of high-order accurate centred schemes for the numerical solution of one-dimensional hyperbolic systems containing non-conservative products and source terms. Combining the PRICE-T method developed in [Toro E, Siviglia A. PRICE: primitive centred schemes for hyperbolic system of equations. Int J Numer Methods Fluids 2003;42:1263-91] with the theoretical insights gained by the recently developed path-conservative schemes [Castro M, Gallardo J, Parés C. High-order finite volume schemes based on reconstruction of states for solving hyperbolic systems with nonconservative products applications to shallow-water systems. Math Comput 2006;75:1103-34; Parés C. Numerical methods for nonconservative hyperbolic systems: a theoretical framework. SIAM J Numer Anal 2006;44:300-21], we propose the new PRICE-C scheme that automatically reduces to a modified conservative FORCE scheme if the underlying PDE system is a conservation law. The resulting first-order accurate centred method is then extended to high order of accuracy in space and time via the ADER approach together with a WENO reconstruction technique. The well-balanced properties of the PRICE-C method are investigated for the shallow water equations. Finally, we apply the new scheme to the shallow water equations with fix bottom topography and with variable bottom solving an additional sediment transport equation.

  12. The highly conserved aspartic acid residue between hypervariable regions 1 and 2 of human immunodeficiency virus type 1 gp120 is important for early stages of virus replication.

    PubMed Central

    Wang, W K; Essex, M; Lee, T H

    1995-01-01

    Between hypervariable regions V1 and V2 of human immunodeficiency virus type 1 (HIV-1) gp120 lies a cluster of relatively conserved residues. The contribution of nine charged residues in this region to virus infectivity was evaluated by single-amino-acid substitutions in an infectious provirus clone. Three of the HIV-1 mutants studied had slower growth kinetics than the wild-type virus. The delay was most pronounced in a mutant with an alanine substituted for an aspartic acid residue at position 180. This aspartic acid is conserved by all HIV-1 isolates with known nucleotide sequences. Substitutions with three other residues at this position, including a negatively charged glutamic acid, all affected virus infectivity. The defect identified in these mutants suggests that this aspartic acid residue is involved in the early stages of HIV-1 replication. PMID:7983752

  13. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation

    PubMed Central

    Turchetto, Caroline; Segatto, Ana Lúcia A.; Mäder, Geraldo; Rodrigues, Daniele M.; Bonatto, Sandro L.; Freitas, Loreta B.

    2016-01-01

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently. PMID:26768602

  14. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation.

    PubMed

    Turchetto, Caroline; Segatto, Ana Lúcia A; Mäder, Geraldo; Rodrigues, Daniele M; Bonatto, Sandro L; Freitas, Loreta B

    2016-01-13

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently.

  15. Energy Conservation

    ERIC Educational Resources Information Center

    Abelson, Philip H.

    1972-01-01

    Comments on The Potential for Energy Conservation,'' a study by the Office of Emergency Preparedness, emphasizing the coming dependence on foreign oil, and presses for government influence to encourage development of more efficient cars. (AL)

  16. Conservation Presentation.

    ERIC Educational Resources Information Center

    Friday, Gerald

    2001-01-01

    Introduces a project in which students teach about the importance of recycling and conservation by presenting demonstrations. Includes demonstrations on water, plastic, and other recycling products such as steel. (YDS)

  17. Differences in Factors Affecting Various Crash Types with High Numbers of Fatalities and Injuries in China

    PubMed Central

    Wang, Kai; He, Jie; Ding, Jianxun; Shi, Qin; Wang, Changjun; Li, Pingfan

    2016-01-01

    Objectives Road traffic crashes that involve very high numbers of fatalities and injuries arouse public concern wherever they occur. In China, there are two categories of such crashes: a crash that results in 10–30 fatalities, 50–100 serious injuries or a total cost of 50–100 million RMB ($US8-16m) is a “serious road traffic crash” (SRTC), while a crash that is even more severe or costly is a “particularly serious road traffic crash” (PSRTC). The aim of this study is to identify the main factors affecting different types of these crashes (single-vehicle, head-on, rear-end and side impact) with the ultimate goal of informing prevention activities and policies. Methods Detailed descriptions of the SRTCs and PSRTCs that occurred from 2007 to 2014 were collected from the database “In-depth Investigation and Analysis System for Major Road Traffic Crashes” (IIASMRTC), which is maintained by the Traffic Management Research Institute of the Ministry of Public Security of China (TMRI). 18 main risk factors, which were categorized into four areas (participant, vehicle, road and environment-related) were chosen as potential independent variables for the multinomial logistic regression analysis. Comparisons were made among the single-vehicle, head-on, rear-end and side impact crashes in terms of factors affecting crash occurrence. Findings Five risk factors were significant for the six multinomial logistic regression models, which were location, vertical alignment, roadside safety rating, driver distraction and overloading of cargo. It was indicated that intersections were more likely to have side impact SRTCs and PSRTCs, especially with poor visibility at night. Overloaded freight vehicles were more likely to be involved in a rear-end crash than other freight vehicles. Driver distraction is an important risk factor for head-on crashes, while vertical alignment and roadside safety rating are positively associated with single-vehicle crashes. Conclusion Based

  18. Emotional Processing in High-Functioning Autism--Physiological Reactivity and Affective Report

    ERIC Educational Resources Information Center

    Bolte, Sven; Feineis-Matthews, Sabine; Poustka, Fritz

    2008-01-01

    This study examined physiological response and affective report in 10 adult individuals with autism and 10 typically developing controls. An emotion induction paradigm using stimuli from the International Affective Picture System was applied. Blood pressure, heart and self-ratings of experienced valence (pleasure), arousal and dominance (control)…

  19. Validity of a Brief Measure of Parental Affective Attitudes in High-Risk Preschoolers

    ERIC Educational Resources Information Center

    Waller, Rebecca; Gardner, Frances; Dishion, Thomas J.; Shaw, Daniel S.; Wilson, Melvin N.

    2012-01-01

    The current study investigated psychometric properties of the Family Affective Attitude Rating Scale (FAARS) for assessing parents' thoughts and feelings about their child, coded from a 5-min speech sample. Parental affective attitudes derive from previous experiences of parenting and child behavior, representations of the parent-child…

  20. Identification of Structural and Catalytic Classes of Highly Conserved Amino Acid Residues in Lysine 2,3-Aminomutase †

    PubMed Central

    Chen, Dawei; Frey, Perry A.; Lepore, Bryan W.; Ringe, Dagmar; Ruzicka, Frank J.

    2008-01-01

    Lysine 2,3-aminomutase (LAM) from Clostridium subterminale SB4 catalyzes the interconversion of (S)-lysine and (S)-β-lysine by a radical mechanism involving coenzymatic actions of S-adenosylmethionine (SAM), a [4Fe-4S] cluster, and pyridoxal-5′-phosphate (PLP). The enzyme contains a number of conserved acidic residues and a cysteine and arginine-rich motif, that binds iron and sulfide in the [4Fe–4S] cluster. The results of activity and iron, sulfide, and PLP analysis of variants resulting from site-specific mutations of the conserved acidic residues and the arginine residues in the iron-sulfide binding motif indicate two classes of conserved residues of each type. Mutation of the conserved residues Arg134, Asp293, and Asp330 abolish all enzymatic activity. Based on the x-ray crystal structure, these residues bind the ε-aminium and α-carboxylate groups of (S)-lysine. However, among these residues only Asp293 appears to be important for stabilizing the [4Fe–4S] cluster. Members of a second group of conserved residues appear to stabilize the structure of LAM. Mutations of arginine residues 130, 135, and 136 and acidic residues Glu86, Asp165, Glu236, and Asp172 dramatically decrease iron and sulfide contents in the purified variants. Mutation of Asp96 significantly decreases iron and sulfide content. Variants in Arg130 or Asp172 display no detectable activity, whereas variants in the other positions display low to very low activities. Structural roles are assigned to this latter class of conserved amino acids. In particular, a network of hydrogen bonded interactions of Arg130, Glu86, Arg135 and the main chain carbonyl groups of Cys132 and Leu55 appears to stabilize the [4Fe–4S] cluster. PMID:17042481

  1. Defining population structure and genetic signatures of decline in the giant garter snake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes

    USGS Publications Warehouse

    Wood, Dustin A.; Halstead, Brian J.; Casazza, Michael L.; Hansen, Eric C.; Wylie, Glenn D.; Vandergast, Amy

    2015-01-01

    Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake (Thamnophis gigas) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population

  2. Identification of novel and conserved miRNAs involved in pollen development in Brassica campestris ssp. chinensis by high-throughput sequencing and degradome analysis

    PubMed Central

    2014-01-01

    Background microRNAs (miRNAs) are endogenous, noncoding, small RNAs that have essential regulatory functions in plant growth, development, and stress response processes. However, limited information is available about their functions in sexual reproduction of flowering plants. Pollen development is an important process in the life cycle of a flowering plant and is a major factor that affects the yield and quality of crop seeds. Results This study aims to identify miRNAs involved in pollen development. Two independent small RNA libraries were constructed from the flower buds of the male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) of Brassica campestris ssp. chinensis. The libraries were subjected to high-throughput sequencing by using the Illumina Solexa system. Eight novel miRNAs on the other arm of known pre-miRNAs, 54 new conserved miRNAs, and 8 novel miRNA members were identified. Twenty-five pairs of novel miRNA/miRNA* were found. Among all the identified miRNAs, 18 differentially expressed miRNAs with over two-fold change between flower buds of male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) were identified. qRT-PCR analysis revealed that most of the differentially expressed miRNAs were preferentially expressed in flower buds of the male fertile line (Bcajh97-01B). Degradome analysis showed that a total of 15 genes were predicted to be the targets of seven miRNAs. Conclusions Our findings provide an overview of potential miRNAs involved in pollen development and interactions between miRNAs and their corresponding targets, which may provide important clues on the function of miRNAs in pollen development. PMID:24559317

  3. Cognitive and affective perspective-taking in conduct-disordered children high and low on callous-unemotional traits

    PubMed Central

    Anastassiou-Hadjicharalambous, Xenia; Warden, David

    2008-01-01

    Background Deficits in cognitive and/or affective perspective-taking have been implicated in Conduct-Disorder (CD), but empirical investigations produced equivocal results. Two factors may be implicated: (a) distinct deficits underlying the antisocial conduct of CD subgroups, (b) plausible disjunction between cognitive and affective perspective-taking with subgroups presenting either cognitive or affective-specific deficits. Method This study employed a second-order false-belief paradigm in which the cognitive perspective-taking questions tapped the character's thoughts and the affective perspective-taking questions tapped the emotions generated by these thoughts. Affective and cognitive perspective-taking was compared across three groups of children: (a) CD elevated on Callous-Unemotional traits (CD-high-CU, n = 30), (b) CD low on CU traits (CD-low-CU, n = 42), and (c) a 'typically-developing' comparison group (n = 50), matched in age (7.5 – 10.8), gender and socioeconomic background. Results The results revealed deficits in CD-low-CU children for both affective and cognitive perspective-taking. In contrast CD-high-CU children showed relative competency in cognitive, but deficits in affective-perspective taking, a finding that suggests an affective-specific defect and a plausible dissociation of affective and cognitive perspective-taking in CD-high-CU children. Conclusion Present findings indicate that deficits in cognitive perspective-taking that have long been implicated in CD appear to be characteristic of a subset of CD children. In contrast affective perspective-taking deficits characterise both CD subgroups, but these defects seem to be following diverse developmental paths that warrant further investigation. PMID:18601753

  4. "Toward High School Biology": Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    ERIC Educational Resources Information Center

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better…

  5. The regulatory benefits of high levels of affect perception accuracy: a process analysis of reactions to stressors in daily life.

    PubMed

    Robinson, Michael D; Moeller, Sara K; Buchholz, Maria M; Boyd, Ryan L; Troop-Gordon, Wendy

    2012-08-01

    Individuals attuned to affective signals from the environment may possess an advantage in the emotion-regulation realm. In two studies (total n = 151), individual differences in affective perception accuracy were assessed in an objective, performance-based manner. Subsequently, the same individuals completed daily diary protocols in which daily stressor levels were reported as well as problematic states shown to be stress-reactive in previous studies. In both studies, individual differences in affect perception accuracy interacted with daily stressor levels to predict the problematic outcomes. Daily stressors precipitated problematic reactions--whether depressive feelings (study 1) or somatic symptoms (study 2)--at low levels of affect perception accuracy, but did not do so at high levels of affect perception accuracy. The findings support a regulatory view of such perceptual abilities. Implications for understanding emotion regulation processes, emotional intelligence, and individual differences in reactivity are discussed.

  6. Lysosomal localization of Japanese medaka (Oryzias latipes) Neu1 sialidase and its highly conserved enzymatic profiles with human.

    PubMed

    Ryuzono, Sena; Takase, Ryo; Oishi, Kazuki; Ikeda, Asami; Chigwechokha, Petros Kingstone; Funahashi, Aki; Komatsu, Masaharu; Miyagi, Taeko; Shiozaki, Kazuhiro

    2016-01-10

    Desialylation in the lysosome is a crucial step for glycoprotein degradation. The abnormality of lysosomal desialylation by NEU1 sialidase is involved in diseases of mammals such as sialidosis and galactosialidosis. Mammalian Neu1 sialidase is also localized at plasma membrane where it regulates several signaling pathways through glycoprotein desialylation. In fish, on the other hand, the mechanism of desialylation in the lysosome and functions of Neu1 sialidase are still unclear. Here, to understand the significance of fish Neu1 sialidase, neu1 gene was cloned from medaka brain and the profiles of its polypeptides were analyzed. Open reading frame of medaka neu1 consisted 1,182 bp and the similarity of its deduced amino acids with human NEU1 was 57%. As this recombinant polypeptide did not show significant sialidase activity, medaka cathepsin A, known in mammals as protective protein activating Neu1, was cloned and then co-expressed with medaka Neu1 to examine whether medaka cathepsin A activates Neu1 activity. As a result, Neu1/cathepsin A showed a drastic increase of sialidase activity toward MU-NANA. Major substrate of medaka Neu1 was 3-sialyllactose and its optimal pH was 4.0. With immunofluorescence analysis, signal of overexpressed medaka Neu1 was found to coincide with Lysotracker signals (organelle marker of lysosome) and co-localized with medaka cathepsin A in fish hepatic Hepa-T1 cells. Furthermore, part of medaka Neu1 was also detected at plasma membrane. Medaka Neu1 possessed signal peptide sequence at N-terminal and incomplete lysosomal targeting sequence at C-terminus. Medaka neu1 gene was ubiquitously expressed in various medaka tissues, and its expression level was significantly higher than other sialidase genes such as neu3a, neu3b and neu4. The present study revealed the profiles of fish Neu1 sialidase and indicated its high conservation with human NEU1 for the first time, suggesting the presence of similar desialylation system in the medaka

  7. Conservation law for self-paced movements

    PubMed Central

    Huh, Dongsung; Sejnowski, Terrence J.

    2016-01-01

    Optimal control models of biological movements introduce external task factors to specify the pace of movements. Here, we present the dual to the principle of optimality based on a conserved quantity, called “drive,” that represents the influence of internal motivation level on movement pace. Optimal control and drive conservation provide equivalent descriptions for the regularities observed within individual movements. For regularities across movements, drive conservation predicts a previously unidentified scaling law between the overall size and speed of various self-paced hand movements in the absence of any external tasks, which we confirmed with psychophysical experiments. Drive can be interpreted as a high-level control variable that sets the overall pace of movements and may be represented in the brain as the tonic levels of neuromodulators that control the level of internal motivation, thus providing insights into how internal states affect biological motor control. PMID:27418602

  8. The Space-Time Conservation Element and Solution Element Method: A New High-Resolution and Genuinely Multidimensional Paradigm for Solving Conservation Laws. 1; The Two Dimensional Time Marching Schemes

    NASA Technical Reports Server (NTRS)

    Chang, Sin-Chung; Wang, Xiao-Yen; Chow, Chuen-Yen

    1998-01-01

    A new high resolution and genuinely multidimensional numerical method for solving conservation laws is being, developed. It was designed to avoid the limitations of the traditional methods. and was built from round zero with extensive physics considerations. Nevertheless, its foundation is mathmatically simple enough that one can build from it a coherent, robust. efficient and accurate numerical framework. Two basic beliefs that set the new method apart from the established methods are at the core of its development. The first belief is that, in order to capture physics more efficiently and realistically, the modeling, focus should be placed on the original integral form of the physical conservation laws, rather than the differential form. The latter form follows from the integral form under the additional assumption that the physical solution is smooth, an assumption that is difficult to realize numerically in a region of rapid chance. such as a boundary layer or a shock. The second belief is that, with proper modeling of the integral and differential forms themselves, the resulting, numerical solution should automatically be consistent with the properties derived front the integral and differential forms, e.g., the jump conditions across a shock and the properties of characteristics. Therefore a much simpler and more robust method can be developed by not using the above derived properties explicitly.

  9. Hyperfunctional affections of the stato-kinetic apparatus specific to sportsmen of high performance

    PubMed Central

    Nicolae, S.

    1970-01-01

    The statistical analysis of the traumatic affections treated by the author during 1967 in the traumatic service of the Centre of Sports Medicine, Bucharest shows the fact that traumatic affections amount to 34.1% whereas hyperfunctional lesions to 22.9%. The author does not agree with the denomination of “sportive microtraumatisms” given to these affections because of the aetio-pathogeny and the sportive specificity of this kind of lesions. Relying on clinical history and examination; on physiopathological and especially on biochemical and histological and histochemical date, he proposes the name of hyper-functional localized affections. Among the arguments put forward by the author the following are to be retained: parallelism between biochemical data (increase of syalic acid and generally of blood mucoproteins) and histochemical aspects of tissue mucopolysaccharides of lesions (proved by microscopic sections which underwent enzymatic extractions). The author considers these affections to be expressions of some forms of overtraining, localized in the stato-kinetic apparatus, admitting as an aetio-pathogenic mechanism, the imbalance between biochemical stresses of the training effort “technopathy” and physiochemical dismetabolic and functional properties of the respective tissue, expressed by imbalance of tissue enzymes within the complex limits of the changes of overtraining.

  10. A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes.

    PubMed

    Uhl, Juli D; Zandvakili, Arya; Gebelein, Brian

    2016-04-01

    cis-regulatory modules (CRMs) generate precise expression patterns by integrating numerous transcription factors (TFs). Surprisingly, CRMs that control essential gene patterns can differ greatly in conservation, suggesting distinct constraints on TF binding sites. Here, we show that a highly conserved Distal-less regulatory element (DCRE) that controls gene expression in leg precursor cells recruits multiple Hox, Extradenticle (Exd) and Homothorax (Hth) complexes to mediate dual outputs: thoracic activation and abdominal repression. Using reporter assays, we found that abdominal repression is particularly robust, as neither individual binding site mutations nor a DNA binding deficient Hth protein abolished cooperative DNA binding and in vivo repression. Moreover, a re-engineered DCRE containing a distinct configuration of Hox, Exd, and Hth sites also mediated abdominal Hox repression. However, the re-engineered DCRE failed to perform additional segment-specific functions such as thoracic activation. These findings are consistent with two emerging concepts in gene regulation: First, the abdominal Hox/Exd/Hth factors utilize protein-protein and protein-DNA interactions to form repression complexes on flexible combinations of sites, consistent with the TF collective model of CRM organization. Second, the conserved DCRE mediates multiple cell-type specific outputs, consistent with recent findings that pleiotropic CRMs are associated with conserved TF binding and added evolutionary constraints.

  11. A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes

    PubMed Central

    Uhl, Juli D.; Zandvakili, Arya; Gebelein, Brian

    2016-01-01

    cis-regulatory modules (CRMs) generate precise expression patterns by integrating numerous transcription factors (TFs). Surprisingly, CRMs that control essential gene patterns can differ greatly in conservation, suggesting distinct constraints on TF binding sites. Here, we show that a highly conserved Distal-less regulatory element (DCRE) that controls gene expression in leg precursor cells recruits multiple Hox, Extradenticle (Exd) and Homothorax (Hth) complexes to mediate dual outputs: thoracic activation and abdominal repression. Using reporter assays, we found that abdominal repression is particularly robust, as neither individual binding site mutations nor a DNA binding deficient Hth protein abolished cooperative DNA binding and in vivo repression. Moreover, a re-engineered DCRE containing a distinct configuration of Hox, Exd, and Hth sites also mediated abdominal Hox repression. However, the re-engineered DCRE failed to perform additional segment-specific functions such as thoracic activation. These findings are consistent with two emerging concepts in gene regulation: First, the abdominal Hox/Exd/Hth factors utilize protein-protein and protein-DNA interactions to form repression complexes on flexible combinations of sites, consistent with the TF collective model of CRM organization. Second, the conserved DCRE mediates multiple cell-type specific outputs, consistent with recent findings that pleiotropic CRMs are associated with conserved TF binding and added evolutionary constraints. PMID:27058369

  12. Effective primate conservation education: gaps and opportunities.

    PubMed

    Jacobson, Susan K

    2010-05-01

    Conservation education goals generally include influencing people's conservation awareness, attitudes, and behaviors. Effective programs can help foster sustainable behavior, improve public support for conservation, reduce vandalism and poaching in protected areas, improve compliance with conservation regulations, increase recreation carrying capacities, and influence policies and decisions that affect the environment. Primate conservation problems cut across many disciplines, and primate conservation education must likewise address cross-disciplinary issues. Conservation educators must incorporate both theoretical and practical knowledge and skills to develop effective programs, and the skill set must stretch beyond pedagogy. Expertise needed comes from the areas of planning, collaboration, psychology, entertainment, and evaluation. Integration of these elements can lead to greater program success.

  13. Structure-Function Analysis of Escherichia coli MnmG (GidA), a Highly Conserved tRNA-Modifying Enzyme

    SciTech Connect

    Shi, Rong; Villarroya, Magda; Ruiz-Partida, Rafael; Li, Yunge; Proteau, Ariane; Prado, Silvia; Moukadiri, Ismaïl; Benítez-Páez, Alfonso; Lomas, Rodrigo; Wagner, John; Matte, Allan; Velázquez-Campoy, Adrián; Armengod, M.-Eugenia; Cygler, Miroslaw

    2010-01-12

    The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-{angstrom} resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

  14. Conservation Research and Development/ New Ultra-Low Carbon High Strength Steels with Improved Bake Hardenability for Enhanced Stretch Formability and Dent Resistance

    SciTech Connect

    Anthony J. DeArdo; C. Isaac Garcia

    2003-12-15

    Conservation Research and Development/New Ultra-Low Carbon High Strength Steels with Improved Bake Hardenability for Enhanced Stretch Formability and Dent Resistance. The experimental work can be divided into four phases. In each phase, the materials were received or designed, processed and tested, to evaluate the BH increment or response, as a function of compositions and processing conditions. Microstructural characterization by various techniques was performed in order to gain insights into the mechanisms of flow stress increment by bake hardening.

  15. A Highly Conserved Residue of the HIV-1 gp120 Inner Domain Is Important for Antibody-Dependent Cellular Cytotoxicity Responses Mediated by Anti-cluster A Antibodies

    PubMed Central

    Ding, Shilei; Veillette, Maxime; Coutu, Mathieu; Prévost, Jérémie; Scharf, Louise; Bjorkman, Pamela J.; Ferrari, Guido; Robinson, James E.; Stürzel, Christina; Hahn, Beatrice H.; Sauter, Daniel; Kirchhoff, Frank; Lewis, George K.; Pazgier, Marzena

    2015-01-01

    Previous studies have shown that sera from HIV-1-infected individuals contain antibodies able to mediate antibody-dependent cellular cytotoxicity (ADCC). These antibodies preferentially recognize envelope glycoprotein (Env) epitopes induced upon CD4 binding. Here, we show that a highly conserved tryptophan at position 69 of the gp120 inner domain is important for ADCC mediated by anti-cluster A antibodies and sera from HIV-1-infected individuals. PMID:26637462

  16. Structure-function Analysis of Escherichia coli MnmG (GidA) a Highly Conserved tRNA-modifying Enzyme

    SciTech Connect

    R Shi; M Villarroya; R Ruiz-Partida; Y Li; A Proteau; S prado; I Moukafiri; A Benatez-Paez; R Lomas; et al.

    2011-12-31

    The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-{angstrom} resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

  17. The gp63 Gene Cluster Is Highly Polymorphic in Natural Leishmania (Viannia) braziliensis Populations, but Functional Sites Are Conserved

    PubMed Central

    Medina, Lilian S.; Souza, Bruno Araújo; Queiroz, Adriano; Guimarães, Luiz Henrique; Lima Machado, Paulo Roberto; M Carvalho, Edgar; Wilson, Mary Edythe; Schriefer, Albert

    2016-01-01

    GP63 or leishmanolysin is the major surface protease of Leishmania spp. involved in parasite virulence and host cell interaction. As such, GP63 is a potential target of eventual vaccines against these protozoa. In the current study we evaluate the polymorphism of gp63 in Leishmania (Viannia) braziliensis isolated from two sets of American tegumentary leishmaniasis (ATL) cases from Corte de Pedra, Brazil, including 35 cases diagnosed between 1994 and 2001 and 6 cases diagnosed between 2008 and 2011. Parasites were obtained from lesions by needle aspiration and cultivation. Genomic DNA was extracted, and 405 bp fragments, including sequences encoding the putative macrophage interacting sites, were amplified from gp63 genes of all isolates. DNA amplicons were cloned into plasmid vectors and ten clones per L. (V.) braziliensis isolate were sequenced. Alignment of cloned sequences showed extensive polymorphism among gp63 genes within, and between parasite isolates. Overall, 45 different polymorphic alleles were detected in all samples, which could be segregated into two clusters. Cluster one included 25, and cluster two included 20 such genotypes. The predicted peptides showed overall conservation below 50%. In marked contrast, the conservation at segments with putative functional domains approached 90% (Fisher’s exact test p<0.0001). These findings show that gp63 is very polymorphic even among parasites from a same endemic focus, but the functional domains interacting with the mammalian host environment are conserved. PMID:27648939

  18. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

    PubMed Central

    Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

    2014-01-01

    Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

  19. Genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pRet42a from Rhizobium etli CFN42 participate in modulating transfer and affect conjugation from different donors

    PubMed Central

    López-Fuentes, Eunice; Torres-Tejerizo, Gonzalo; Cervantes, Laura; Brom, Susana

    2015-01-01

    Among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. In bacterial genomes, genes related to a similar function are often located in contiguous regions. The presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. Plasmid pRet42a from Rhizobium etli CFN42 is a conjugative plasmid containing a segment of approximately 30 Kb encoding genes involved in conjugative transfer. In addition to genes responsible for Dtr (DNA transfer and replication), Mpf (Mating pair formation) and regulation, it has two chp-encoding genes (RHE_PA00163 and RHE_PA00164) and a transcriptional regulator (RHE_PA00165). RHE_PA00163 encodes an uncharacterized protein conserved in bacteria that presents a COG4634 conserved domain, and RHE_PA00164 encodes an uncharacterized conserved protein with a DUF433 domain of unknown function. RHE_PA00165 presents a HTH_XRE domain, characteristic of DNA-binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Interestingly, genes similar to these are also present in transfer regions of plasmids from other bacteria. To determine if these genes participate in conjugative transfer, we mutagenized them and analyzed their conjugative phenotype. A mutant in RHE_PA00163 showed a slight (10 times) but reproducible increase in transfer frequency from Rhizobium donors, while mutants in RHE_PA00164 and RHE_PA00165 lost their ability to transfer the plasmid from some Agrobacterium donors. Our results indicate that the chp-encoding genes located among conjugation genes are indeed related to this function. However, the participation of RHE_PA00164 and RHE_PA00165 is only revealed under very specific circumstances, and is not perceived when the plasmid is transferred from the original host. RHE_PA00163 seems to be a fine-tuning modulator for conjugative transfer

  20. Reconciling nature conservation and traditional farming practices: a spatially explicit framework to assess the extent of High Nature Value farmlands in the European countryside

    PubMed Central

    Lomba, Angela; Alves, Paulo; Jongman, Rob H G; McCracken, David I

    2015-01-01

    Agriculture constitutes a dominant land cover worldwide, and rural landscapes under extensive farming practices acknowledged due to high biodiversity levels. The High Nature Value farmland (HNVf) concept has been highlighted in the EU environmental and rural policies due to their inherent potential to help characterize and direct financial support to European landscapes where high nature and/or conservation value is dependent on the continuation of specific low-intensity farming systems. Assessing the extent of HNV farmland by necessity relies on the availability of both ecological and farming systems' data, and difficulties associated with making such assessments have been widely described across Europe. A spatially explicit framework of data collection, building out from local administrative units, has recently been suggested as a means of addressing such difficulties. This manuscript tests the relevance of the proposed approach, describes the spatially explicit framework in a case study area in northern Portugal, and discusses the potential of the approach to help better inform the implementation of conservation and rural development policies. Synthesis and applications: The potential of a novel approach (combining land use/cover, farming and environmental data) to provide more accurate and efficient mapping and monitoring of HNV farmlands is tested at the local level in northern Portugal. The approach is considered to constitute a step forward toward a more precise targeting of landscapes for agri-environment schemes, as it allowed a more accurate discrimination of areas within the case study landscape that have a higher value for nature conservation. PMID:25798221

  1. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  2. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Instructional units deal with each aspect of conservation: forests, wildlife, rangelands, water, minerals, and soil. The area of the secondary school curriculum with which each is correlated is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the topic, questions to…

  3. Marketing Conservation.

    ERIC Educational Resources Information Center

    Ellis, William B.

    1987-01-01

    In 1986, Northeast Utilities began helping shool administrators combat school building energy wastage through a program called Energy Alliance. The typical school can reduce its energy bill by 30 percent by adopting a wide range of conservation measures, including cogeneration, relamping, and energy audits. (MLH)

  4. Lighting Conservation

    ERIC Educational Resources Information Center

    Arnold, Frank D.

    1975-01-01

    With the energy crisis has come an awareness of wasteful consumption practices. One area where research is being done is in lighting conservation. Information in this article is concerned with finding more effective and efficient lighting designs which include daylight utilization, task-oriented lighting, and lighting controls. (MA)

  5. Colorful Conservation

    ERIC Educational Resources Information Center

    Skophammer, Karen

    2011-01-01

    Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

  6. Do Changes in Tympanic Temperature Predict Changes in Affective Valence during High-Intensity Exercise?

    ERIC Educational Resources Information Center

    Legrand, Fabien D.; Joly, Philippe M.; Bertucci, William M.

    2015-01-01

    Purpose: Increased core (brain or body) temperature that accompanies exercise has been posited to play an influential role in affective responses to exercise. However, findings in support of this hypothesis have been equivocal, and most of the performed studies have been done in relation to anxiety. The aim of the present study was to investigate…

  7. Exploring relationships between the use of affect in science instruction and the pressures of a high-stakes testing environment

    NASA Astrophysics Data System (ADS)

    Jerome, Diane C.

    This study explored how science teachers and school administrators perceive the use of the affective domain during science instruction situated within a high-stakes testing environment. Through a multimethodological inquiry using phenomenology and critical ethnography, the researcher conducted semi-structured interviews with six fifth-grade science teachers and two administrators from two Texas school districts. Data reconstructions from interviews formed a bricolage of diagrams that trace the researcher's steps through a reflective exploration of these phenomena. This study addressed the following research questions: (a) What are the attitudes, interests, and values (affective domain) that fifth-grade science teachers integrate into science instruction? (b) How do fifth-grade science teachers attempt to integrate attitudes, interests and values (affective domain) in science instruction? and (c) How do fifth-grade science teachers manage to balance the tension from the seeming pressures caused by a high-stakes testing environment and the integration of attitudes, interests and values (affective domain) in science instruction? The findings from this study indicate that as teachers tried to integrate the affective domain during science instruction, (a) their work was set within a framework of institutional values, (b) teaching science for understanding looked different before and after the onset of the science Texas Assessment of Knowledge and Skills (TAKS), and (c) upon administration of the science TAKS---teachers broadened their aim, raised their expectations, and furthered their professional development. The integration of the affective domain fell into two distinct categories: 1) teachers targeted student affect and 2) teachers modeled affective behavior.

  8. Quantifying solute transport processes: are chemically "conservative" tracers electrically conservative?

    USGS Publications Warehouse

    Singha, Kamini; Li, Li; Day-Lewis, Frederick D.; Regberg, Aaron B.

    2012-01-01

    The concept of a nonreactive or conservative tracer, commonly invoked in investigations of solute transport, requires additional study in the context of electrical geophysical monitoring. Tracers that are commonly considered conservative may undergo reactive processes, such as ion exchange, thus changing the aqueous composition of the system. As a result, the measured electrical conductivity may reflect not only solute transport but also reactive processes. We have evaluated the impacts of ion exchange reactions, rate-limited mass transfer, and surface conduction on quantifying tracer mass, mean arrival time, and temporal variance in laboratory-scale column experiments. Numerical examples showed that (1) ion exchange can lead to resistivity-estimated tracer mass, velocity, and dispersivity that may be inaccurate; (2) mass transfer leads to an overestimate in the mobile tracer mass and an underestimate in velocity when using electrical methods; and (3) surface conductance does not notably affect estimated moments when high-concentration tracers are used, although this phenomenon may be important at low concentrations or in sediments with high and/or spatially variable cation-exchange capacity. In all cases, colocated groundwater concentration measurements are of high importance for interpreting geophysical data with respect to the controlling transport processes of interest.

  9. Affective and Enjoyment Responses to High-Intensity Interval Training in Overweight-to-Obese and Insufficiently Active Adults.

    PubMed

    Martinez, Nic; Kilpatrick, Marcus W; Salomon, Kristen; Jung, Mary E; Little, Jonathan P

    2015-04-01

    High-intensity interval training (HIIT) has many known physiological benefits, but research investigating the psychological aspects of this training is limited. The purpose of the current study is to investigate the affective and enjoyment responses to continuous and high-intensity interval exercise sessions. Twenty overweight-to-obese, insufficiently active adults completed four counterbalanced trials: a 20-min trial of heavy continuous exercise and three 24-min HIIT trials that used 30-s, 60-s, and 120-s intervals. Affect declined during all trials (p < .05), but affect at the completion of trials was more positive in the shorter interval trials (p < .05). Enjoyment declined in the 120-s interval and heavy continuous conditions only (p < .05). Postexercise enjoyment was higher in the 60-s trial than in the 120-s trial and heavy continuous condition (p < .05). Findings suggest that pleasure and enjoyment are higher during shorter interval trials than during a longer interval or heavy continuous exercise.

  10. The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism

    PubMed Central

    2012-01-01

    Background Hepatitis B virus (HBV) encodes an oncogenic factor, HBx, which is a multifunctional protein that can induce dysfunctional regulation of signaling pathways, transcription, and cell cycle progression, among other processes, through interactions with target host factors. The subcellular localization of HBx is both cytoplasmic and nuclear. This dynamic distribution of HBx could be essential to the multiple roles of the protein at different stages during HBV infection. Transactivational functions of HBx may be exerted both in the nucleus, via interaction with host DNA-binding proteins, and in the cytoplasm, via signaling pathways. Although there have been many studies describing different pathways altered by HBx, and its innumerable binding partners, the molecular mechanism that regulates its different roles has been difficult to elucidate. Methods In the current study, we took a bioinformatics approach to investigate whether the viral protein HBx might be regulated via phosphorylation by an evolutionarily conserved mechanism. Results We found that the phylogenetically conserved residues Ser25 and Ser41 (both within the negative regulatory domain), and Thr81 (in the transactivation domain) are predicted to be phosphorylated. By molecular 3D modeling of HBx, we further show these residues are all predicted to be exposed on the surface of the protein, making them easily accesible to these types of modifications. Furthermore, we have also identified Yin Yang sites that might have the potential to be phosphorylated and O-β-GlcNAc interplay at the same residues. Conclusions Thus, we propose that the different roles of HBx displayed in different subcellular locations might be regulated by an evolutionarily conserved mechanism of posttranslational modification, via phosphorylation. PMID:23079056

  11. Alignment of U3 region sequences of mammalian type C viruses: identification of highly conserved motifs and implications for enhancer design.

    PubMed Central

    Golemis, E A; Speck, N A; Hopkins, N

    1990-01-01

    We aligned published sequences for the U3 region of 35 type C mammalian retroviruses. The alignment reveals that certain sequence motifs within the U3 region are strikingly conserved. A number of these motifs correspond to previously identified sites. In particular, we found that the enhancer region of most of the viruses examined contains a binding site for leukemia virus factor b, a viral corelike element, the consensus motif for nuclear factor 1, and the glucocorticoid response element. Most viruses containing more than one copy of enhancer sequences include these binding sites in both copies of the repeat. We consider this set of binding sites to constitute a framework for the enhancers of this set of viruses. Other highly conserved motifs in the U3 region include the retrovirus inverted repeat sequence, a negative regulatory element, and the CCAAT and TATA boxes. In addition, we identified two novel motifs in the promoter region that were exceptionally highly conserved but have not been previously described. PMID:2153223

  12. The chicken FMR1 gene is highly conserved with a CCT 5{prime} - untranslated repeat and encodes an RNA-binding protein

    SciTech Connect

    Price, D.K.; Zhang, F.; Ashley, C.T. Jr.; Warren, S.T.

    1996-01-01

    The transcriptional silencing of the human gene, fragile X metal retardation 1 (FMR1), is due to abnormal methylation in response to an expanded 5{prime}-untranslated CGG trinucleotide repeat and accounts for most cases of fragile X syndrome, a frequent inherited form of metal retardation. Although the encoded fragile X mental retardation protein (FMRP) is known to have properties of a RNA-binding protein, the precise function of FMRP remains to be elucidated. We report the cloning of the chicken homolog of FMR1 and show strong evolutionary conservation, with nucleotide and amino acid identities of 85 and 92%, respectively, between chicken and human. In place of the mammalian CGG trinucleotide repeat, a 99-nt tripartite repetitive element containing a CCT trinucleotide repeat flanked on both sides by dinucleotide repeats was identified. Blocks of highly conserved 3{prime}-untranslated sequence were also found. Within the coding region, two copies each of the highly conserved K homology motif and the Arg-Gly-Gly (RGG) box motif, both ribonucleotide particle family domains implicated in RNA binding, were identified. Chicken FMRP was found to bind RNA in vitro, and this activity correlated with the presence of the carboxy-terminal portion of the protein that includes the RGG motifs. 49 refs., 7 figs.

  13. Exploring Relationships between the Use of Affect in Science Instruction and the Pressures of a High-Stakes Testing Environment

    ERIC Educational Resources Information Center

    Jerome, Diane C.

    2010-01-01

    This study explored how science teachers and school administrators perceive the use of the affective domain during science instruction situated within a high-stakes testing environment. Through a multimethodological inquiry using phenomenology and critical ethnography, the researcher conducted semi-structured interviews with six fifth-grade…

  14. The X chromosome of monotremes shares a highly conserved region with the eutherian and marsupial X chromosomes despite the absence of X chromosome inactivation

    SciTech Connect

    Watson, J.M.; Spencer, J.A.; Graves, J.A.M. ); Riggs, A.D. )

    1990-09-01

    Eight genes, located on the long arm of the human X chromosome and present on the marsupial X chromosome, were mapped by in situ hybridization to the chromosomes of the platypus Ornithorhynchus anatinus, one of the three species of monotreme mammals. All were located on the X chromosome. The authors conclude that the long arm of the human X chromosome represents a highly conserved region that formed part of the X chromosome in a mammalian ancestor at least 150 million years ago. Since three of these genes are located on the long arm of the platypus X chromosome, which is G-band homologous to the Y chromosome and apparently exempt from X chromosome inactivation, the conservation of this region has evidently not depended on isolation by X-Y chromosome differentiation and X chromosome inactivation.

  15. Importance of Highly Conserved Peptide Sites of Human Cytomegalovirus gO for Formation of the gH/gL/gO Complex.

    PubMed

    Stegmann, Cora; Abdellatif, Mohamed E A; Laib Sampaio, Kerstin; Walther, Paul; Sinzger, Christian

    2017-01-01

    The glycoprotein O (gO) is betaherpesvirus specific. Together with the viral glycoproteins H and L, gO forms a covalent trimeric complex that is part of the viral envelope. This trimer is crucial for cell-free infectivity of human cytomegalovirus (HCMV) but dispensable for cell-associated spread. We hypothesized that the amino acids that are conserved among gOs of different cytomegaloviruses are important for the formation of the trimeric complex and hence for efficient virus spread. In a mutational approach, nine peptide sites, containing all 13 highly conserved amino acids, were analyzed in the context of HCMV strain TB40-BAC4 with regard to infection efficiency and formation of the gH/gL/gO complex. Mutation of amino acids (aa) 181 to 186 or aa 193 to 198 resulted in the loss of the trimer and a complete small-plaque phenotype, whereas mutation of aa 108 or aa 249 to 254 caused an intermediate phenotype. While individual mutations of the five conserved cysteines had little impact, their relevance was revealed in a combined mutation, which abrogated both complex formation and cell-free infectivity. C343 was unique, as it was sufficient and necessary for covalent binding of gO to gH/gL. Remarkably, however, C218 together with C167 rescued infectivity in the absence of detectable covalent complex formation. We conclude that all highly conserved amino acids contribute to the function of gO to some extent but that aa 181 to 198 and cysteines 343, 218, and 167 are particularly relevant. Surprisingly, covalent binding of gO to gH/gL is required neither for its incorporation into virions nor for proper function in cell-free infection.

  16. Heron conservation

    USGS Publications Warehouse

    Kushlan, J.A.; Hafner, H.

    2000-01-01

    Herons are large, popular and, in many cases, spectacular birds found in wetlands world-wide, both tropical and temperate, natural and man-made. Some populations are very small and localized, some have decreased, some have expanded their ranges, and a few are pests of human activities. In the fifteen years since the publication of the latest monographic treatment of the family, The Herons Handbook, there has been a tremendous increase in our knowledge of heron status and conservation requirements, set against a backdrop of increasing concern about the future of the world?s wetland habitats. This book provides a comprehensive update following two distinct threads. The status and conservation needs of herons are first presented on a regional basis, in a series of chapters set at a continental or subcontinental scale. Over 200 biologists and heron conservationists have contributed to the data summarized here, and the very latest census and survey results provide the most up-to-date and detailed picture of heron populations currently available. Chapters discussing several critical issues in heron conservation follow, tending to focus on the international nature of the problems.

  17. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute.

    PubMed

    Islam, Md Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

    2015-01-01

    MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

  18. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

    PubMed Central

    Islam, Md. Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

    2015-01-01

    MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. PMID:25861616

  19. The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.

    PubMed

    Zuccolo, Andrea; Scofield, Douglas G; De Paoli, Emanuele; Morgante, Michele

    2015-08-15

    Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms.

  20. Conservative whole-organ scaling contrasts with highly labile suborgan scaling differences among compound eyes of closely related Formica ants.

    PubMed

    Perl, Craig D; Rossoni, Sergio; Niven, Jeremy E

    2017-03-01

    Static allometries determine how organ size scales in relation to body mass. The extent to which these allometric relationships are free to evolve, and how they differ among closely related species, has been debated extensively and remains unclear; changes in intercept appear common, but changes in slope are far rarer. Here, we compare the scaling relationships that govern the structure of compound eyes of four closely related ant species from the genus Formica. Comparison among these species revealed changes in intercept but not slope in the allometric scaling relationships governing eye area, facet number, and mean facet diameter. Moreover, the scaling between facet diameter and number was conserved across all four species. In contrast, facet diameters from distinct regions of the compound eye differed in both intercept and slope within a single species and when comparing homologous regions among species. Thus, even when species are conservative in the scaling of whole organs, they can differ substantially in regional scaling within organs. This, at least partly, explains how species can produce organs that adhere to genus wide scaling relationships while still being able to invest differentially in particular regions of organs to produce specific features that match their ecology.

  1. Comprehensive Sequence Analysis of the Human IL23A Gene Defines New Variation Content and High Rate of Evolutionary Conservation

    PubMed Central

    Tindall, Elizabeth A.; Hayes, Vanessa M.

    2010-01-01

    A newly described heterodimeric cytokine, interleukin-23 (IL-23) is emerging as a key player in both the innate and the adaptive T helper (Th)17 driven immune response as well as an initiator of several autoimmune diseases. The rate-limiting element of IL-23 production is believed to be driven by expression of the unique p19 subunit encoded by IL23A. We set out to perform comprehensive DNA sequencing of this previously under-studied gene in 96 individuals from two evolutionary distinct human population groups, Southern African Bantu and European. We observed a total of 33 different DNA variants within these two groups, 22 (67%) of which are currently not reported in any available database. We further demonstrate both inter-population and intra-species sequence conservation within the coding and known regulatory regions of IL23A, supporting a critical physiological role for IL-23. We conclude that IL23A may have undergone positive selection pressure directed towards conservation, suggesting that functional genetic variants within IL23A will have a significant impact on the host immune response. PMID:20154336

  2. Strategy of mutual compensation of green and red mutants of firefly luciferase identifies a mutation of the highly conservative residue E457 with a strong red shift of bioluminescence.

    PubMed

    Koksharov, Mikhail I; Ugarova, Natalia N

    2013-11-01

    Bioluminescence spectra of firefly luciferases demonstrate highly pH-sensitive spectra changing the color from green to red light when pH is lowered from alkaline to acidic. This reflects a change of ratio of the green and red emitters in the bimodal spectra of bioluminescence. We show that the mutations strongly stabilizing green (Y35N) or red (H433Y) emission compensate each other leading to the WT color of firefly luciferase. We further used this compensating ability of Y35N to search for strong red-shifting mutations in the C-domain of firefly luciferase by random mutagenesis. The discovered mutation E457K substantially increased the contribution of the red emitter and caused a 12 nm red shift of the green emitter as well. E457 is highly conservative not only in beetle luciferases but also in a whole ANL superfamily of adenylating enzymes and forms a conservative structural hydrogen bond with V471. Our results suggest that the removal of this hydrogen bond only mildly affects luciferase properties and that most of the effect of E457K is caused by the introduction of positive charge. E457 forms a salt bridge with R534 in most ANL enzymes including pH-insensitive luciferases which is absent in pH-sensitive firefly luciferases. The mutant A534R shows that this salt bridge is not important for pH-sensitivity but considerably improves in vivo thermostability. Although E457 is located far from the oxyluciferin-binding site, the properties of the mutant E457K suggest that it affects color by influencing the AMP binding.

  3. Energy Conservation and Mentally Retarded Citizens.

    ERIC Educational Resources Information Center

    Fogelman, Charles J.; And Others

    Suggested are some principles of developing energy conservation programs where retarded persons might be particularly affected, ways to conserve energy, and pertinent references. It is thought that the retarded, particularly the retarded in institutions, are more likely to suffer from energy conservation measures than members of the larger…

  4. Socioeconomic Factors Affecting Minority Physics Taking in U.S. High Schools

    ERIC Educational Resources Information Center

    Physics Teacher, 2011

    2011-01-01

    In the September issue, we saw that a lower proportion of Hispanics and blacks take physics in U.S. high schools than do whites and Asians. Last month, we examined physics offerings and students by socioeconomic profile of the high school as reported by the principal. We saw that there were more physics classes and more physics students at…

  5. Factors That Affect Retention of Novice Teachers in Hard-to-Staff High Schools in Virginia

    ERIC Educational Resources Information Center

    Blunt, Mechelle Savedge

    2013-01-01

    The mobility rates within the Kindergarten-Grade 12 teacher workforce are distressing, and the teaching profession has a relatively high turnover rate compared to other occupations. The Commonwealth of Virginia encounters many challenges when attempting to retain highly qualified teachers in schools. Despite the state's efforts to staff all…

  6. Identifying Aspects of Parental Involvement that Affect the Academic Achievement of High School Students

    ERIC Educational Resources Information Center

    Roulette-McIntyre, Ovella; Bagaka's, Joshua G.; Drake, Daniel D.

    2005-01-01

    This study identified parental practices that relate positively to high school students' academic performance. Parents of 643 high school students participated in the study. Data analysis, using a multiple linear regression model, shows parent-school connection, student gender, and race are significant predictors of student academic performance.…

  7. Factors Affecting High School Baseball Coaches' Enforcement of School Tobacco Policy

    ERIC Educational Resources Information Center

    Eaves, Ted; Strack, Robert W.

    2015-01-01

    In spite of policy bans and recommendations against spit tobacco (ST) use, baseball athletes have demonstrated ST prevalence rates ranging from 34% to 50% in high school, 42% in the National Collegiate Athletic Association (NCAA), and 50% in the professional ranks. To evaluate enforcement of ST bans, high school baseball coaches in North Carolina…

  8. Nutrition Information at the Point of Selection in High Schools Does Not Affect Purchases

    ERIC Educational Resources Information Center

    Rainville, Alice Jo; Choi, Kyunghee; Ragg, Mark; King, Amber; Carr, Deborah H.

    2010-01-01

    Purpose/Objectives: Nutrition information can be an important component of local wellness policies. There are very few studies regarding nutrition information at the point of selection (POS) in high schools. The purpose of this study was to investigate the effects of posting entree nutrition information at the POS in high schools nationwide.…

  9. Factors Affecting Students' Information Literacy as They Transition from High School to College

    ERIC Educational Resources Information Center

    Varlejs, Jana; Stec, Eileen

    2014-01-01

    Despite the considerable attention paid to the need to increase the information literacy of high school students in preparation for the transition to college, poor research skills still seem to be the norm. To gain insight into the problem, library instruction environments of nineteen high schools were explored. The schools were selected based on…

  10. Identification of a Highly Conserved H1 Subtype-Specific Epitope with Diagnostic Potential in the Hemagglutinin Protein of Influenza A Virus

    PubMed Central

    Guo, Li; Wu, Chao; Gonzalez, Richard; Paranhos-Baccalà, Gláucia; Vernet, Guy; Wang, Jianwei; Hung, Tao

    2011-01-01

    Subtype specificity of influenza A virus (IAV) is determined by its two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). For HA, 16 distinct subtypes (H1–H16) exist, while nine exist for NA. The epidemic strains of H1N1 IAV change frequently and cause annual seasonal epidemics as well as occasional pandemics, such as the notorious 1918 influenza pandemic. The recent introduction of pandemic A/H1N1 IAV (H1N1pdm virus) into humans re-emphasizes the public health concern about H1N1 IAV. Several studies have identified conserved epitopes within specific HA subtypes that can be used for diagnostics. However, immune specific epitopes in H1N1 IAV have not been completely assessed. In this study, linear epitopes on the H1N1pdm viral HA protein were identified by peptide scanning using libraries of overlapping peptides against convalescent sera from H1N1pdm patients. One epitope, P5 (aa 58–72) was found to be immunodominant in patients and to evoke high titer antibodies in mice. Multiple sequence alignments and in silico coverage analysis showed that this epitope is highly conserved in influenza H1 HA [with a coverage of 91.6% (9,860/10,767)] and almost completely absent in other subtypes [with a coverage of 3.3% (792/23,895)]. This previously unidentified linear epitope is located outside the five well-recognized antigenic sites in HA. A peptide ELISA method based on this epitope was developed and showed high correlation (χ2 = 51.81, P<0.01, Pearson correlation coefficient R = 0.741) with a hemagglutination inhibition test. The highly conserved H1 subtype-specific immunodominant epitope may form the basis for developing novel assays for sero-diagnosis and active surveillance against H1N1 IAVs. PMID:21886787

  11. Delivering High-Quality Family Planning Services in Crisis-Affected Settings I: Program Implementation

    PubMed Central

    Curry, Dora Ward; Rattan, Jesse; Nzau, Jean Jose; Giri, Kamlesh

    2015-01-01

    ABSTRACT In 2012, about 43 million women of reproductive age experienced the effects of conflict. Provision of basic sexual and reproductive health services, including family planning, is a recognized right and need of refugees and internally displaced people, but funding and services for family planning have been inadequate. This article describes lessons learned during the first 2.5 years of implementing the ongoing Supporting Access to Family Planning and Post-Abortion Care in Emergencies (SAFPAC) initiative, led by CARE, which supports government health systems to deliver family planning services in 5 crisis-affected settings (Chad, Democratic Republic of the Congo, Djibouti, Mali, and Pakistan). SAFPAC's strategy focuses on 4 broad interventions drawn from public health best practices in more stable settings: competency-based training for providers, improved supply chain management, regular supervision, and community mobilization to influence attitudes and norms related to family planning. Between July 2011 and December 2013, the initiative reached 52,616 new users of modern contraceptive methods across the 5 countries (catchment population of 698,053 women of reproductive age), 61% of whom chose long-acting methods of implants or intrauterine devices. Prudent use of data to inform decision making has been an underpinning to the project's approach. A key approach to ensuring sustained ability to train and supervise new providers has been to build capacity in clinical skills training and supervision by establishing in-country training centers. In addition, monthly supervision using simple checklists has improved program and service quality, particularly with infection prevention procedures and stock management. We have generally instituted a “pull” system to manage commodities and other supplies, whereby health facilities place resupply orders as needed based on actual consumption patterns and stock-alert thresholds. Finally, reaching the community with

  12. Delivering high-quality family planning services in crisis-affected settings I: program implementation.

    PubMed

    Curry, Dora Ward; Rattan, Jesse; Nzau, Jean Jose; Giri, Kamlesh

    2015-02-04

    In 2012, about 43 million women of reproductive age experienced the effects of conflict. Provision of basic sexual and reproductive health services, including family planning, is a recognized right and need of refugees and internally displaced people, but funding and services for family planning have been inadequate. This article describes lessons learned during the first 2.5 years of implementing the ongoing Supporting Access to Family Planning and Post-Abortion Care in Emergencies (SAFPAC) initiative, led by CARE, which supports government health systems to deliver family planning services in 5 crisis-affected settings (Chad, Democratic Republic of the Congo, Djibouti, Mali, and Pakistan). SAFPAC's strategy focuses on 4 broad interventions drawn from public health best practices in more stable settings: competency-based training for providers, improved supply chain management, regular supervision, and community mobilization to influence attitudes and norms related to family planning. Between July 2011 and December 2013, the initiative reached 52,616 new users of modern contraceptive methods across the 5 countries (catchment population of 698,053 women of reproductive age), 61% of whom chose long-acting methods of implants or intrauterine devices. Prudent use of data to inform decision making has been an underpinning to the project's approach. A key approach to ensuring sustained ability to train and supervise new providers has been to build capacity in clinical skills training and supervision by establishing in-country training centers. In addition, monthly supervision using simple checklists has improved program and service quality, particularly with infection prevention procedures and stock management. We have generally instituted a "pull" system to manage commodities and other supplies, whereby health facilities place resupply orders as needed based on actual consumption patterns and stock-alert thresholds. Finally, reaching the community with mobilization

  13. The main factors that affect coupling efficiency of high-power semiconductor laser array and selfoc lens array

    NASA Astrophysics Data System (ADS)

    Jiang, Xiaoping; Liu, Desen

    2008-03-01

    The coupling technique of high-power semiconductor laser array is an advancing key project. A high power density collimated beam, which facula is much smaller, can be get by coupling high-power laser array with selfoc lens array. At the same time, the coupling efficiency is higher. The factors which affect the coupling efficiency mainly include NA, diameter, length and end surface fabricating of selfoc lens and coupling technique. In this paper, an 1×19 linear laser array which maximum continuous output power is 22W is coupled with a corresponding selfoc lens array. The maximum coupling efficiency is 58.2%.

  14. Plant traits affecting herbivory on tree recruits in highly diverse subtropical forests.

    PubMed

    Schuldt, Andreas; Bruelheide, Helge; Durka, Walter; Eichenberg, David; Fischer, Markus; Kröber, Wenzel; Härdtle, Werner; Ma, Keping; Michalski, Stefan G; Palm, Wolf-Ulrich; Schmid, Bernhard; Welk, Erik; Zhou, Hongzhang; Assmann, Thorsten

    2012-07-01

    Differences in herbivory among woody species can greatly affect the functioning of forest ecosystems, particularly in species-rich (sub)tropical regions. However, the relative importance of the different plant traits which determine herbivore damage remains unclear. Defence traits can have strong effects on herbivory, but rarely studied geographical range characteristics could complement these effects through evolutionary associations with herbivores. Herein, we use a large number of morphological, chemical, phylogenetic and biogeographical characteristics to analyse interspecific differences in herbivory on tree saplings in subtropical China. Unexpectedly, we found no significant effects of chemical defence traits. Rather, herbivory was related to the plants' leaf morphology, local abundance and climatic niche characteristics, which together explained 70% of the interspecific variation in herbivory in phylogenetic regression. Our study indicates that besides defence traits and apparency to herbivores, previously neglected measures of large-scale geographical host distribution are important factors influencing local herbivory patterns among plant species.

  15. Groundwater Storage Dynamics in High Elevation Meadows Affected By Complex Aquifer Geometry

    NASA Astrophysics Data System (ADS)

    Ciruzzi, D.; Lowry, C.

    2014-12-01

    The Sierra Nevada represents a cascading hydrologic cycle where snowpack, meadow aquifers, and streams are all hydrologically connected. Monitoring the water balance within high elevation meadows is vital in order to effectively quantify watershed scale storage dynamics, which support meadow ecological communities as well as downstream users. In this case, much of the San Francisco, CA water supply originates from the seasonally released snowmelt from high elevation meadows to downstream reservoirs. In previous studies of high elevation meadows, the water mass balance was closed under the assumption that the meadow sediment was spatially uniform in thickness. Here, complex aquifer geometry was identified in Tuolumne Meadows, CA from a high-resolution ground-penetrating radar survey. This new geometry was compared to the previous geologic model of high elevation meadow aquifers using numerical models simulating both current and future snowmelt scenarios. In addition, the impact of variability in meadow sediment and slope were evaluated to quantify storage properties of representative Sierra Nevada meadow types. Results demonstrate that the previous aquifer geometry model significantly overestimates both the spatial and temporal volumetric storage and release of groundwater to streams. These implications are noteworthy for ecosystem restoration and water supply strategies that aim to rectify water supply to and from these meadows especially when considering drought scenarios. In order to move forward and effectively and efficiently monitor the seasonal volume of water stored within the Sierra Nevada, complex aquifer geometry within high elevation meadows must be considered.

  16. Power affects performance when the pressure is on: evidence for low-power threat and high-power lift.

    PubMed

    Kang, Sonia K; Galinsky, Adam D; Kray, Laura J; Shirako, Aiwa

    2015-05-01

    The current research examines how power affects performance in pressure-filled contexts. We present low-power-threat and high-power-lift effects, whereby performance in high-stakes situations suffers or is enhanced depending on one's power; that is, the power inherent to a situational role can produce effects similar to stereotype threat and lift. Three negotiations experiments demonstrate that role-based power affects outcomes but only when the negotiation is diagnostic of ability and, therefore, pressure-filled. We link these outcomes conceptually to threat and lift effects by showing that (a) role power affects performance more strongly when the negotiation is diagnostic of ability and (b) underperformance disappears when the low-power negotiator has an opportunity to self-affirm. These results suggest that stereotype threat and lift effects may represent a more general phenomenon: When the stakes are raised high, relative power can act as either a toxic brew (stereotype/low-power threat) or a beneficial elixir (stereotype/high-power lift) for performance.

  17. High progesterone levels in women with high ovarian response do not affect clinical outcomes: a retrospective cohort study

    PubMed Central

    2014-01-01

    Background The potentially detrimental role of progesterone during the follicular phase has been a matter of controversy for several years; however, few studies have analyzed the effects of combined raised estradiol and progesterone levels on pregnancy outcomes. The aim of the present study was to determine the influence of high progesterone levels on clinical outcomes in the context of high ovarian response. Methods We performed a retrospective cohort study that included 2850 women classified as high responders. The women were subdivided into six groups depending on their progesterone concentration on the day of human chorionic gonadotropin (hCG) administration: <0.5 ng/ml (1.81 ng/ml (>p90). Ovarian response was classified as high when > =20 oocytes were retrieved or when estradiol was > =3000 pg/ml. Clinical outcomes of each subgroup were analyzed. We also examined data from frozen-thawed embryo transfers. Results were analyzed with Student’s t- test to compare continuous variables and chi-squared test to compare proportions. A p-value of < =0.05 was considered statistically significant. Results The progesterone concentration increased with ovarian response, and elevated progesterone did not show a significant clinical impact on implantation rate and pregnancy rates. These data provide evidence that progesterone levels higher than 1.8 ng/ml do not have detrimental effect on oocyte quality or endometrial receptivity. Conclusions These data allow us to conclude that high progesterone levels correlate significantly with high estradiol levels and that in high responder women; progesterone levels do not show a significant clinical impact on results. PMID:25064138

  18. Delivering High-Quality Family Planning Services in Crisis-Affected Settings II: Results

    PubMed Central

    Curry, Dora Ward; Rattan, Jesse; Huang, Shuyuan; Noznesky, Elizabeth

    2015-01-01

    ABSTRACT An estimated 43 million women of reproductive age experienced the effects of conflict in 2012. Already vulnerable from the insecurity of the emergency, women must also face the continuing risk of unwanted pregnancy but often are unable to obtain family planning services. The ongoing Supporting Access to Family Planning and Post-Abortion Care (SAFPAC) initiative, led by CARE, has provided contraceptives, including long-acting reversible contraceptives (LARCs), to refugees, internally displaced persons, and conflict-affected resident populations in Chad, the Democratic Republic of the Congo (DRC), Djibouti, Mali, and Pakistan. The project works through the Ministry of Health in 4 key areas: (1) competency-based training, (2) supply chain management, (3) systematic supervision, and (4) community mobilization to raise awareness and shift norms related to family planning. This article presents data on program results from July 2011 to December 2013 from the 5 countries. Project staff summarized monthly data from client registers using hard-copy forms and recorded the data electronically in Microsoft Excel for compilation and analysis. The initiative reached 52,616 new users of modern contraceptive methods across the 5 countries, ranging from 575 in Djibouti to 21,191 in Chad. LARCs have predominated overall, representing 61% of new modern method users. The percentage of new users choosing LARCs varied by country: 78% in the DRC, 72% in Chad, and 51% in Mali, but only 29% in Pakistan. In Djibouti, those methods were not offered in the country through SAFPAC during the period discussed here. In Chad, the DRC, and Mali, implants have been the most popular LARC method, while in Pakistan the IUD has been more popular. Use of IUDs, however, has comprised a larger share of the method mix over time in all 4 of these countries. These results to date suggest that it is feasible to work with the public sector in fragile, crisis-affected states to deliver a wide range of

  19. High-fat, cholesterol-rich diet affects leptin expression in the aortic layers.

    PubMed

    Krawczynska, Agata; Olczak, Elzbieta; Rembiszewska, Alina; Gromadzka-Ostrowska, Joanna

    2013-01-01

    Leptin is stated to be an important mediator between obesity and cardiovascular disease. However, whether leptin location in the aorta is dependent on diet and its atherogenic character is still unknown. This study examined the relationship between a high-fat diet with or without cholesterol and the expression of leptin in aortic layers. Forty male rats were fed a high-fat diet with fish or grape seed oil as a dietary fat source, with or without cholesterol, to enhance the atherogenic character of their diet. The experiments lasted for three and six weeks, respectively. Plasma lipid profile, plasma leptin concentration and leptin expression in the endothelium (E), myometrium (M) and adventitia (A) were examined. The length of feeding was a key factor which influenced both the lipid profile and leptin expression in the aorta. Leptin concentration positively correlated with body weight and plasma triglycerides only in the three-week experiment, which suggests that the physiological actions of leptin can be disturbed by prolonged consumption of a high-fat diet. Short-term intake of a high-fat diet with fish oil, increasing high density lipoprotein cholesterol (HDL) level and decreasing total cholesterol (TC)/HDL ratio, enhanced leptin expression in E in comparison to the group fed grape seed oil. However, in the group with the highest diet intake, leptin expression in each layer was lowest. Generally, leptin expression was most common in E; however, an extension of the period of feeding in groups fed a diet with grape seed oil with or without additional cholesterol increased leptin presence in M and A in comparison to the group fed fish oil. Significantly higher values of TC and HDL in the same groups may suggest that leptin changes in the aorta and the atherogenic impact of grape seed oil can be connected when the consumption of a high-fat diet is excessive.

  20. UK114, a YjgF/Yer057p/UK114 family protein highly conserved from bacteria to mammals, is localized in rat liver peroxisomes

    SciTech Connect

    Antonenkov, Vasily D. . E-mail: vasily.antonenkov@oulu.fi; Ohlmeier, Steffen; Sormunen, Raija T.; Hiltunen, J. Kalervo

    2007-05-25

    Mammalian UK114 belongs to a highly conserved family of proteins with unknown functions. Although it is believed that UK114 is a cytosolic or mitochondrial protein there is no detailed study of its intracellular localization. Using analytical subcellular fractionation, electron microscopic colloidal gold technique, and two-dimensional gel electrophoresis of peroxisomal matrix proteins combined with mass spectrometric analysis we show here that a large portion of UK114 is present in rat liver peroxisomes. The peroxisomal UK114 is a soluble matrix protein and it is not inducible by the peroxisomal proliferator clofibrate. The data predict involvement of UK114 in peroxisomal metabolism.

  1. Measuring the Influences That Affect Technological Literacy in Rhode Island High Schools

    ERIC Educational Resources Information Center

    Walach, Michael

    2015-01-01

    This study sampled the current state of technological literacy in Rhode Island high schools using a new instrument, the Technological Literacy Assessment, which was developed for this study. Gender inequalities in technological literacy were discovered, and possible causes and solutions are presented. This study suggests possible next steps for…

  2. How Stimulus and Task Complexity Affect Monitoring in High-Functioning Adults with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Koolen, Sophieke; Vissers, Constance Th. W. M.; Egger, Jos I. M.; Verhoeven, Ludo

    2014-01-01

    The present study examined whether individuals with autism spectrum disorder (ASD) are able to update and monitor working memory representations of visual input, and whether performance is influenced by stimulus and task complexity. 15 high-functioning adults with ASD and 15 controls were asked to allocate either elements of abstract figures or…

  3. High pressure treatment of human norovirus-like particles: factors affecting destruction efficacy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Human norovirus (HuNoV) is the leading cause of foodborne diseases worldwide. High pressure processing (HPP) is considered a promising non-thermal technology to inactivate viral pathogens in foods. However, the effectiveness of HPP on inactivating HuNoV remains poorly understood because it cannot be...

  4. Does High School Facility Quality Affect Student Achievement? A Two-Level Hierarchical Linear Model

    ERIC Educational Resources Information Center

    Bowers, Alex J.; Urick, Angela

    2011-01-01

    The purpose of this study is to isolate the independent effects of high school facility quality on student achievement using a large, nationally representative U.S. database of student achievement and school facility quality. Prior research on linking school facility quality to student achievement has been mixed. Studies that relate overall…

  5. Can Contrived Success Affect Self-Efficacy among Junior High School Students?

    ERIC Educational Resources Information Center

    Mori, Kazuo; Uchida, Akitoshi

    2009-01-01

    Twenty-four junior high school students with academic achievement in the 26-50 percentiles were given easier anagram tasks while their 183 classmates were given more difficult ones by means of a presentation trick using polarizing filters. The two series of anagram tasks were projected simultaneously on the same screen, but each of two groups of…

  6. Do high-commitment work systems affect creativity? A multilevel combinational approach to employee creativity.

    PubMed

    Chang, Song; Jia, Liangding; Takeuchi, Riki; Cai, Yahua

    2014-07-01

    In this article, some information about the data used in the article and a citation were not included. The details of the corrections are provided.] This study uses 3-level, 2-wave time-lagged data from a random sample of 55 high-technology firms, 238 teams, and 1,059 individuals in China to investigate a multilevel combinational model of employee creativity. First, we hypothesize that firm (macrolevel) high-commitment work systems are conducive to individual (microlevel) creativity. Furthermore, we hypothesize that this positive crosslevel main impact may be combined with middle-level (mesolevel) factors, including team cohesion and team task complexity, such that the positive impact of firm high-commitment work systems on individual creativity is stronger when team cohesion is high and the team task more complex. The findings from random coefficient modeling analyses provide support for our hypotheses. These sets of results offer novel insight into how firms can use macrolevel and mesolevel contextual variables in a systematic manner to promote employee creativity in the workplace, despite its complex nature.

  7. Histone modifying proteins Gcn5 and Hda1 affect flocculation in Saccharomyces cerevisiae during high-gravity fermentation.

    PubMed

    Dietvorst, Judith; Brandt, Anders

    2010-02-01

    The performance of yeast is often limited by the constantly changing environmental conditions present during high-gravity fermentation. Poor yeast performance contributes to incomplete and slow utilization of the main fermentable sugars which can lead to flavour problems in beer production. The expression of the FLO and MAL genes, which are important for the performance of yeast during industrial fermentations, is affected by complex proteins associated with Set1 (COMPASS) resulting in the induction of flocculation and improved maltose fermentation capacity during the early stages of high-gravity fermentation. In this study, we investigated a possible role for other histone modifying proteins. To this end, we tested a number of histone deacetylases (HDACs) and histone acetyltransferases and we report that flocculation is induced in absence of the histone deacetylase Hda1 or the histone acetyltransferase Gcn5 during high-gravity fermentation. The absence of Gcn5 protein also improved utilization of high concentrations of maltose. Deletion of SIR2 encoding the HDA of the silent informator regulator complex, did not affect flocculation under high-gravity fermentation conditions. Despite the obvious roles for Hda1 and Gcn5 in flocculation, this work indicates that COMPASS mediated silencing is the most important amongst the histone modifying components to control the expression of the FLO genes during high-gravity fermentation.

  8. High temperature specifically affects the photoprotective responses of chlorophyll b-deficient wheat mutant lines.

    PubMed

    Brestic, Marian; Zivcak, Marek; Kunderlikova, Kristyna; Allakhverdiev, Suleyman I

    2016-12-01

    The effects of high temperature on CO2 assimilation rate, processes associated with photosynthetic electron and proton transport, as well as photoprotective responses, were studied in chlorophyll b-deficient mutant lines (ANK-32A and ANK-32B) and wild type (WT) of wheat (Triticum aestivum L.). Despite the low chlorophyll content and chlorophyll a-to-b ratio, the non-stressed mutant plants had the similar level of CO2 assimilation and photosynthetic responses as WT. However, in ANK mutant plants exposed to prolonged high temperature episode (42 °C for ~10 h), we observed lower CO2 assimilation compared to WT, especially when a high CO2 supply was provided. In all heat-exposed plants, we found approximately the same level of PSII photoinhibition, but the decrease in content of photooxidizable PSI was higher in ANK mutant plants compared to WT. The PSI damage can be well explained by the level of overreduction of PSI acceptor side observed in plants exposed to high temperature, which was, in turn, the result of the insufficient transthylakoid proton gradient associated with low non-photochemical quenching and lack of ability to downregulate the linear electron transport to keep the reduction state of PSI acceptor side low enough. Compared to WT, the ANK mutant lines had lower capacity to drive the cyclic electron transport around PSI in moderate and high light; it confirms the protective role of cyclic electron transport for the protection of PSI against photoinhibition. Our results, however, also suggest that the inactivation of PSI in heat stress conditions can be the protective mechanism against photooxidative damage of chloroplast and cell structures.

  9. Water Deficit and Heat Affect the Tolerance to High Illumination in Hibiscus Plants

    PubMed Central

    Muñoz, Romualdo; Quiles, María José

    2013-01-01

    This work studies the effects of water deficit and heat, as well as the involvement of chlororespiration and the ferredoxin-mediated cyclic pathway, on the tolerance of photosynthesis to high light intensity in Hibiscus rosa-sinensis plants. Drought and heat resulted in the down–regulation of photosynthetic linear electron transport in the leaves, although only a slight decrease in variable fluorescence (Fv)/maximal fluorescence (Fm) was observed, indicating that the chloroplast was protected by mechanisms that dissipate excess excitation energy to prevent damage to the photosynthetic apparatus. The incubation of leaves from unstressed plants under high light intensity resulted in an increase of the activity of electron donation by nicotinamide adenine dinucleotide phosphate (NADPH) and ferredoxin to plastoquinone, but no increase was observed in plants exposed to water deficit, suggesting that cyclic electron transport was stimulated by high light only in control plants. In contrast, the activities of the chlororespiration enzymes (NADH dehydrogenase (NDH) complex and plastid terminal oxidase (PTOX)) increased after incubation under high light intensity in leaves of the water deficit plants, but not in control plants, suggesting that chlororespiration was stimulated in stressed plants. The results indicate that the relative importance of chlororespiration and the cyclic electron pathway in the tolerance of photosynthesis to high illumination differs under stress conditions. When plants were not subjected to stress, the contribution of chlororespiration to photosynthetic electron flow regulation was not relevant, and another pathway, such as the ferredoxin-mediated cyclic pathway, was more important. However, when plants were subjected to water deficit and heat, chlororespiration was probably essential. PMID:23470922

  10. The Immunosuppressive Properties of the HIV Vpr Protein Are Linked to a Single Highly Conserved Residue, R90

    PubMed Central

    Tcherepanova, Irina; Starr, Aijing; Lackford, Brad; Adams, Melissa D.; Routy, Jean-Pierre; Boulassel, Mohamed Rachid; Calderhead, David; Healey, Don; Nicolette, Charles

    2009-01-01

    Background A hallmark of AIDS progression is a switch of cytokines from Th1 to Th2 in the plasma of patients. IL-12, a critical Th1 cytokine secreted by antigen presenting cells (APCs) is suppressed by Vpr, implicating it as an important virulence factor. We hypothesize that Vpr protein packaged in the virion may be required for disabling APCs of the first infected mucosal tissues. Consistent with this idea are reports that defects in the C-terminus of Vpr are associated with long-term non-progression. Principal Findings Vpr RNA amplified from various sources was electroporated into monocyte-derived DC and IL-12 levels in supernatants were analyzed. The analysis of previously reported C-terminal Vpr mutations demonstrate that they do not alleviate the block of IL-12 secretion. However, a novel single conservative amino acid substitution, R90K, reverses the IL-12 suppression. Analysis of 1226 Vpr protein sequences demonstrated arginine (R) present at position 90 in 98.8%, with other substitutions at low frequency. Furthermore, none of sequences report lysine (K) in position 90. Vpr clones harboring the reported substitutions in position 90 were studied for their ability to suppress IL-12. Our data demonstrates that none of tested substitutions other than K relieve IL-12 suppression. This suggests a natural selection for sequences which suppress IL-12 secretion by DC and against mutations which relieve such suppression. Further analyses demonstrated that the R90K, as well as deletion of the C-terminus, directs the Vpr protein for rapid degradation. Conclusion This study supports Vpr as an HIV virulence factor during HIV infection and for the first time provides a link between evolutionary conservation of Vpr and its ability to suppress IL-12 secretion by DC. DC activated in the presence of Vpr would be defective in the production of IL-12, thus contributing to the prevailing Th2 cytokine profile associated with progressive HIV disease. These findings should be

  11. Conserved arginine residues in the carboxyl terminus of the equine arteritis virus E protein may play a role in heparin binding but may not affect viral infectivity in equine endothelial cells.

    PubMed

    Lu, Zhengchun; Sarkar, Sanjay; Zhang, Jianqiang; Balasuriya, Udeni B R

    2016-04-01

    Equine arteritis virus (EAV), the causative agent of equine viral arteritis, has relatively broad cell tropism in vitro. In horses, EAV primarily replicates in macrophages and endothelial cells of small blood vessels. Until now, neither the cellular receptor(s) nor the mechanism(s) of virus attachment and entry have been determined for this virus. In this study, we investigated the effect of heparin on EAV infection in equine endothelial cells (EECs). Heparin, but not other glycosaminoglycans, could reduce EAV infection up to 93 %. Sequence analysis of the EAV E minor envelope protein revealed a conserved amino acid sequence (52 RSLVARCSRGARYR 65) at the carboxy terminus of the E protein, which was predicted to be the heparin-binding domain. The basic arginine (R) amino acid residues were subsequently mutated to glycine by site-directed mutagenesis of ORF2a in an E protein expression vector and an infectious cDNA clone of EAV. Two single mutations in E (R52G and R57G) did not affect the heparin-binding capability, whereas the E double mutation (R52,60G) completely eliminated the interaction between the E protein and heparin. Although the mutant R52,60G EAV did not bind heparin, the mutations did not completely abolish infectivity, indicating that heparin is not the only critical factor for EAV infection. This also suggested that other viral envelope protein(s) might be involved in attachment through heparin or other cell-surface molecules, and this warrants further investigation.

  12. High intensity exercise affects diurnal variation of some biological markers in trained subjects.

    PubMed

    Hammouda, O; Chtourou, H; Chahed, H; Ferchichi, S; Chaouachi, A; Kallel, C; Miled, A; Chamari, K; Souissi, N

    2012-11-01

    The study investigated if markers of muscle injury and antioxidant status were affected by a Wingate test performed at 2 different times of day. 15 young male footballers performed 2 tests (randomized) at 07:00-h and 17:00-h. Fasting blood samples were collected before and 3 min after each test for assessment of markers of muscle injury and antioxidant status. Resting oral temperature was recorded during each session. Peak power (10.76 ± 1.05 vs. 11.15 ± 0.83 W.kg( - 1)) and fatigue index (0.41 ± 0.04 vs. 0.49 ± 0.13%) during the Wingate test, and core temperature, were significantly higher (all p<0.05) in the evening. Markers of muscle injury were significantly higher in the evening before and after exercise (e. g., 148.7 ± 67.05 vs. 195 ± 74.6 and 191.6 ± 79.52 vs. 263.6 ± 96.06 IU.L (- 1), respectively, for creatine kinase; both p<0.001). Antioxidant parameters increased after the Wingate test but only resting values were significantly higher in the morning (e. g., 1.33 ± 0.19 vs. 1.19 ± 0.14 µmol.L (- 1) for total antioxidant status; p<0.05). The results indicate that muscle injury and antioxidant activity after the Wingate test were higher in the evening, suggesting a possible link between the biochemical measures and the diurnal fluctuation of anaerobic performance. However, repetition of this study after prescribed rather than self-selected exercise intensity is recommended.

  13. Does high scatter affect the predictive validity of WAIS-III IQs?

    PubMed

    Ryan, Joseph J; Kreiner, David S; Burton, D Bradley

    2002-01-01

    We tested the assumption that high amounts of intersubtest scatter on the Wechsler Adult Intelligence Scale-Third Edition (WAIS-III) subtest profiles compromise predictive validity of the IQs for predicting Wechsler Memory Scale-Third Edition (WMS-III) indexes. Data from a sample of 80 male Veteran's Administration medical center patients were analyzed, half with high intersubtest scatter and half with low scatter. The 2 groups were matched on Full Scale IQ. Correlations of WAIS-III Full Scale IQ with WMS-III indexes were not significantly different between the 2 groups. Further, the regression equations for predicting WMS-III indexes did not depend on the amount of scatter. The results suggest that, when differences in IQ are controlled, the validity of WAIS-III scores in predicting memory performance does not depend on the amount of intersubtest scatter. Further research is needed with samples from different populations using a variety of criterion variables.

  14. Motivations and attitudes affecting high school students' choice of foreign language.

    PubMed

    Stewart-Strobelt, Jody; Chen, Huabin

    2003-01-01

    There are some foreign languages that enjoy great status in the United States, while other foreign languages are rarely represented at the high school level. The present study explored the following questions: Why do students choose to take a particular foreign language? Do students gravitate toward it because it is widely thought to be the easiest language to learn or because they perceive greater career opportunities with proficiency in this particular language, or is it simply because there are more classes offered? As long as foreign language study is elective in high schools and as long as a variety of languages are offered, the answers to these questions will remain important for foreign language educators, especially in schools where the various language programs compete with one another for student enrollments and the programs' ultimate survival.

  15. Physiology in conservation translocations

    PubMed Central

    Tarszisz, Esther; Dickman, Christopher R.; Munn, Adam J.

    2014-01-01

    Conservation translocations aim to restore species to their indigenous ranges, protect populations from threats and/or reinstate ecosystem functions. They are particularly important for the conservation and management of rare and threatened species. Despite tremendous efforts and advancement in recent years, animal conservation translocations generally have variable success, and the reasons for this are often uncertain. We suggest that when little is known about the physiology and wellbeing of individuals either before or after release, it will be difficult to determine their likelihood of survival, and this could limit advancements in the science of translocations for conservation. In this regard, we argue that physiology offers novel approaches that could substantially improve translocations and associated practices. As a discipline, it is apparent that physiology may be undervalued, perhaps because of the invasive nature of some physiological measurement techniques (e.g. sampling body fluids, surgical implantation). We examined 232 publications that dealt with translocations of terrestrial vertebrates and aquatic mammals and, defining ‘success’ as high or low, determined how many of these studies explicitly incorporated physiological aspects into their protocols and monitoring. From this review, it is apparent that physiological evaluation before and after animal releases could progress and improve translocation/reintroduction successes. We propose a suite of physiological measures, in addition to animal health indices, for assisting conservation translocations over the short term and also for longer term post-release monitoring. Perhaps most importantly, we argue that the incorporation of physiological assessments of animals at all stages of translocation can have important welfare implications by helping to reduce the total number of animals used. Physiological indicators can also help to refine conservation translocation methods. These approaches fall

  16. High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

    PubMed Central

    Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

    2017-01-01

    Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure. PMID:28382948

  17. High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles.

    PubMed

    Golub, M; Lehofer, B; Martinez, N; Ollivier, J; Kohlbrecher, J; Prassl, R; Peters, J

    2017-04-06

    Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.

  18. High-resolution Monte Carlo simulation of flow and conservative transport in heterogeneous porous media 2. Transport results

    USGS Publications Warehouse

    Naff, R.L.; Haley, D.F.; Sudicky, E.A.

    1998-01-01

    In this, the second of two papers concerned with the use of numerical simulation to examine flow and transport parameters in heterogeneous porous media via Monte Carlo methods, results from the transport aspect of these simulations are reported on. Transport simulations contained herein assume a finite pulse input of conservative tracer, and the numerical technique endeavors to realistically simulate tracer spreading as the cloud moves through a heterogeneous medium. Medium heterogeneity is limited to the hydraulic conductivity field, and generation of this field assumes that the hydraulic- conductivity process is second-order stationary. Methods of estimating cloud moments, and the interpretation of these moments, are discussed. Techniques for estimation of large-time macrodispersivities from cloud second-moment data, and for the approximation of the standard errors associated with these macrodispersivities, are also presented. These moment and macrodispersivity estimation techniques were applied to tracer clouds resulting from transport scenarios generated by specific Monte Carlo simulations. Where feasible, moments and macrodispersivities resulting from the Monte Carlo simulations are compared with first- and second-order perturbation analyses. Some limited results concerning the possible ergodic nature of these simulations, and the presence of non- Gaussian behavior of the mean cloud, are reported on as well.

  19. Legume nodules from nutrient-poor soils exhibit high plasticity of cellular phosphorus recycling and conservation during variable phosphorus supply.

    PubMed

    Vardien, Waafeka; Steenkamp, Emma T; Valentine, Alexander J

    2016-02-01

    Nitrogen fixing legumes rely on phosphorus for nodule formation, nodule function and the energy costs of fixation. Phosphorus is however very limited in soils, especially in ancient sandstone-derived soils such as those in the Cape Floristic Region of South Africa. Plants growing in such areas have evolved the ability to tolerate phosphorus stress by eliciting an array of physiological and biochemical responses. In this study we investigated the effects of phosphorus limitation on N2 fixation and phosphorus recycling in the nodules of Virgilia divaricata (Adamson), a legume native to the Cape Floristic Region. In particular, we focused on nutrient acquisition efficiencies, phosphorus fractions and the exudation and accumulation of phosphatases. Our finding indicate that during low phosphorus supply, V. divaricata internally recycles phosphorus and has a lower uptake rate of phosphorus, as well as lower levels adenylates but greater levels of phosphohydrolase exudation suggesting it engages in recycling internal nodule phosphorus pools and making use of alternate bypass routes in order to conserve phosphorus.

  20. Highly conserved functions of the Brachyury gene on morphogenetic movements: insight from the early-diverging phylum Ctenophora.

    PubMed

    Yamada, Atsuko; Martindale, Mark Q; Fukui, Akimasa; Tochinai, Shin

    2010-03-01

    Brachyury, a member of the T-box transcription family identified in a diverse array of metazoans, was initially recognized for its function in mesoderm formation and notochord differentiation in vertebrates; however, its ancestral role has been suggested to be in control of morphogenetic movements. Here, we show that morpholino oligonucleotide knockdown of Brachyury (MlBra) in embryos of a ctenophore, one of the most ancient groups of animals, prevents the invagination of MlBra expressing stomodeal cells and is rescued with corresponding RNA injections. Injection of RNA encoding a dominant-interfering construct of MlBra causes identical phenotypes to that of RNA encoding a dominant-interfering form of Xenopus Brachyury (Xbra) in Xenopus embryos. Both injected embryos down-regulate Xbra downstream genes, Xbra itself and Xwnt11 but not axial mesodermal markers, resulting in failure to complete gastrulation due to loss of convergent extension movements. Moreover, animal cap assay reveals that MlBra induces Xwnt11 like Xbra. Overall results using Xenopus embryos show that these two genes are functionally interchangeable. These functional experiments demonstrate for the first time in a basal metazoan that the primitive role of Brachyury is to regulate morphogenetic movements, rather than to specify endomesodermal fates, and the role is conserved between non-bilaterian metazoans and vertebrates.

  1. A high-order finite-volume method for hyperbolic conservation laws on locally-refined grids

    SciTech Connect

    McCorquodale, Peter; Colella, Phillip

    2011-01-28

    We present a fourth-order accurate finite-volume method for solving time-dependent hyperbolic systems of conservation laws on Cartesian grids with multiple levels of refinement. The underlying method is a generalization of that in [5] to nonlinear systems, and is based on using fourth-order accurate quadratures for computing fluxes on faces, combined with fourth-order accurate Runge?Kutta discretization in time. To interpolate boundary conditions at refinement boundaries, we interpolate in time in a manner consistent with the individual stages of the Runge-Kutta method, and interpolate in space by solving a least-squares problem over a neighborhood of each target cell for the coefficients of a cubic polynomial. The method also uses a variation on the extremum-preserving limiter in [8], as well as slope flattening and a fourth-order accurate artificial viscosity for strong shocks. We show that the resulting method is fourth-order accurate for smooth solutions, and is robust in the presence of complex combinations of shocks and smooth flows.

  2. Toward High School Biology: Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    PubMed Central

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts. Six eighth grade teachers and their students participated in a test of the unit during the Spring of 2013. Two of the teachers had used an earlier version of the unit the previous spring. The other four teachers were randomly assigned either to implement the unit or to continue teaching the same content using existing materials. Pre- and posttests were administered, and the data were analyzed using Rasch modeling and hierarchical linear modeling. The results showed that, when controlling for pretest score, gender, language, and ethnicity, students who used the curricular intervention performed better on the posttest than the students using existing materials. Additionally, students who participated in the intervention held fewer misconceptions. These results demonstrate the unit’s promise in improving students’ understanding of the targeted ideas. PMID:27909024

  3. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.

    PubMed

    Havird, Justin C; Whitehill, Nicholas S; Snow, Christopher D; Sloan, Daniel B

    2015-12-01

    Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories.

  4. Toward High School Biology: Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems.

    PubMed

    Herrmann-Abell, Cari F; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts. Six eighth grade teachers and their students participated in a test of the unit during the Spring of 2013. Two of the teachers had used an earlier version of the unit the previous spring. The other four teachers were randomly assigned either to implement the unit or to continue teaching the same content using existing materials. Pre- and posttests were administered, and the data were analyzed using Rasch modeling and hierarchical linear modeling. The results showed that, when controlling for pretest score, gender, language, and ethnicity, students who used the curricular intervention performed better on the posttest than the students using existing materials. Additionally, students who participated in the intervention held fewer misconceptions. These results demonstrate the unit's promise in improving students' understanding of the targeted ideas.

  5. Long-range forces affecting equilibrium inertial focusing behavior in straight high aspect ratio microfluidic channels

    NASA Astrophysics Data System (ADS)

    Reece, Amy E.; Oakey, John

    2016-04-01

    The controlled and directed focusing of particles within flowing fluids is a problem of fundamental and technological significance. Microfluidic inertial focusing provides passive and precise lateral and longitudinal alignment of small particles without the need for external actuation or sheath fluid. The benefits of inertial focusing have quickly enabled the development of miniaturized flow cytometers, size-selective sorting devices, and other high-throughput particle screening tools. Straight channel inertial focusing device design requires knowledge of fluid properties and particle-channel size ratio. Equilibrium behavior of inertially focused particles has been extensively characterized and the constitutive phenomena described by scaling relationships for straight channels of square and rectangular cross section. In concentrated particle suspensions, however, long-range hydrodynamic repulsions give rise to complex particle ordering that, while interesting and potentially useful, can also dramatically diminish the technique's effectiveness for high-throughput particle handling applications. We have empirically investigated particle focusing behavior within channels of increasing aspect ratio and have identified three scaling regimes that produce varying degrees of geometrical ordering between focused particles. To explore the limits of inertial particle focusing and identify the origins of these long-range interparticle forces, we have explored equilibrium focusing behavior as a function of channel geometry and particle concentration. Experimental results for highly concentrated particle solutions identify equilibrium thresholds for focusing that scale weakly with concentration and strongly with channel geometry. Balancing geometry mediated inertial forces with estimates for interparticle repulsive forces now provide a complete picture of pattern formation among concentrated inertially focused particles and enhance our understanding of the fundamental limits of

  6. High resolution mapping of genetic factors affecting abdominal bristle number in Drosophila melanogaster

    SciTech Connect

    Long, A.D. |; Mullaney, S.L.; Langley, C.H.; Reid, L.A.; Fry, J.D.; Mackay, T.F.C.

    1995-03-01

    Factors responsible for selection response for abdominal bristle number and correlated responses in sternopleural bristle number were mapped to the X and third chromosome of Drosophila melanogaster. Lines divergent for high and low abdominal bristle number were created by 25 generations of artificial selection from a large base population, with an intensity of 25 individuals of each sex selected from 100 individuals of each sex scored per generation. Isogenic chromosome substitution lines in which the high (H) X or third chromosome were placed in an isogenic low (L) background were derived from the selection lines and from the 93 recombinant isogenic (RI) HL X and 67 RI chromosome 3 lines constructed from them. Highly polymorphic neutral roo transposable elements were hybridized in situ to the polytene chromosomes of the RI lines to create a set of cytogenetic markers. These techniques yielded a dense map with an average spacing of 4 cM between informative markers. Two factors with large effects on abdominal bristle number were mapped on the X chromosome and five factors on the third chromosome. One factor with a large effect on sternopleural bristle number was mapped to the X and two were mapped to the third chromosome; all factors with sternopleural effects corresponded to those with effects on abdominal bristle number. Two of the chromosome 3 factors with large effects on abdominal bristle number were also associated with reduced viability. Significant sex-specific effects and epistatic interactions between mapped factors of the same order of magnitude as the additive effects were observed. All factors mapped to the approximate positions of likely candidate loci previously characterized by mutations with large effects on bristle number. 55 refs., 4 figs., 7 tabs.

  7. Long-range forces affecting equilibrium inertial focusing behavior in straight high aspect ratio microfluidic channels.

    PubMed

    Reece, Amy E; Oakey, John

    2016-04-01

    The controlled and directed focusing of particles within flowing fluids is a problem of fundamental and technological significance. Microfluidic inertial focusing provides passive and precise lateral and longitudinal alignment of small particles without the need for external actuation or sheath fluid. The benefits of inertial focusing have quickly enabled the development of miniaturized flow cytometers, size-selective sorting devices, and other high-throughput particle screening tools. Straight channel inertial focusing device design requires knowledge of fluid properties and particle-channel size ratio. Equilibrium behavior of inertially focused particles has been extensively characterized and the constitutive phenomena described by scaling relationships for straight channels of square and rectangular cross section. In concentrated particle suspensions, however, long-range hydrodynamic repulsions give rise to complex particle ordering that, while interesting and potentially useful, can also dramatically diminish the technique's effectiveness for high-throughput particle handling applications. We have empirically investigated particle focusing behavior within channels of increasing aspect ratio and have identified three scaling regimes that produce varying degrees of geometrical ordering between focused particles. To explore the limits of inertial particle focusing and identify the origins of these long-range interparticle forces, we have explored equilibrium focusing behavior as a function of channel geometry and particle concentration. Experimental results for highly concentrated particle solutions identify equilibrium thresholds for focusing that scale weakly