Science.gov

Sample records for recognizing conserved regions

  1. Vaccine-elicited Human T Cells Recognizing Conserved Protein Regions Inhibit HIV-1

    PubMed Central

    Borthwick, Nicola; Ahmed, Tina; Ondondo, Beatrice; Hayes, Peter; Rose, Annie; Ebrahimsa, Umar; Hayton, Emma-Jo; Black, Antony; Bridgeman, Anne; Rosario, Maximillian; Hill, Adrian VS; Berrie, Eleanor; Moyle, Sarah; Frahm, Nicole; Cox, Josephine; Colloca, Stefano; Nicosia, Alfredo; Gilmour, Jill; McMichael, Andrew J; Dorrell, Lucy; Hanke, Tomáš

    2014-01-01

    Virus diversity and escape from immune responses are the biggest challenges to the development of an effective vaccine against HIV-1. We hypothesized that T-cell vaccines targeting the most conserved regions of the HIV-1 proteome, which are common to most variants and bear fitness costs when mutated, will generate effectors that efficiently recognize and kill virus-infected cells early enough after transmission to potentially impact on HIV-1 replication and will do so more efficiently than whole protein-based T-cell vaccines. Here, we describe the first-ever administration of conserved immunogen vaccines vectored using prime-boost regimens of DNA, simian adenovirus and modified vaccinia virus Ankara to uninfected UK volunteers. The vaccine induced high levels of effector T cells that recognized virus-infected autologous CD4+ cells and inhibited HIV-1 replication by up to 5.79 log10. The virus inhibition was mediated by both Gag- and Pol- specific effector CD8+ T cells targeting epitopes that are typically subdominant in natural infection. These results provide proof of concept for using a vaccine to target T cells at conserved epitopes, showing that these T cells can control HIV-1 replication in vitro. PMID:24166483

  2. Inability to induce consistent T-cell responses recognizing conserved regions within HIIV-1 antigens: a potential mechanism for lack of vaccine efficacy in the step study

    SciTech Connect

    Korber, Bette; Szinger, James

    2009-01-01

    T cell based vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a high probability of matching the epitope induced by vaccination with the infecting viral strain. We compared the frequency and specificity of the CTL epitopes elicited by the replication defective AdS gag/pol/nef vaccine used in the STEP trial with the likelihood of encountering those epitopes among recently sequenced Clade B isolates of HIV-1. On average vaccination elicited only one epitope per gene. Importantly, the highly conserved epitopes in gag, pol, and nef (> 80% of strains in the current collection of the Los Alamos database [www.hiv.lanl.gov]) were rarely elicited by vaccination. Moreover there was a statistically significant skewing of the T cell response to relative variable epitopes of each gene; only 20% of persons possessed > 3 T cell responses to epitopes likely to be found in circulating strains in the CladeB populations in which the Step trial was conducted. This inability to elicit T cell responses likely to be found in circulating viral strains is a likely factor in the lack of efficacy of the vaccine utilized in the STEP trial. Modeling of the epitope specific responses elicited by vaccination, we project that a median of 8-10 CD8+ T cell epitopes are required to provide >80% likelihood of eliciting at least 3 CD8+ T cell epitopes that would be found on a circulating population of viruses. Development of vaccine regimens which elicit either a greater breadth of responses or elicit responses to conserved regions of the HIV-1 genome are needed to fully evaluate the concept of whether induction of T cell immunity can alter HIV-1 in vivo.

  3. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.

    PubMed

    Buffalo, Cosmo Z; Bahn-Suh, Adrian J; Hirakis, Sophia P; Biswas, Tapan; Amaro, Rommie E; Nizet, Victor; Ghosh, Partho

    2016-01-01

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ∼90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant 'reading head' in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M-C4BP interaction, and also inform a path towards vaccine design. PMID:27595425

  4. [Priority conservation regions of threatened plants in Northeast China].

    PubMed

    Cao, Wei; Wu, Yu-Yang; Li, Yan; Cong, Xin-Xin

    2013-02-01

    Based on the identification of the threatened plants in Northeast China and the priority conservation value of plants, the priority conservation regions of the threatened plants in Northeast China were determined. In the 219 counties (or cities) of Northeast China, 119 counties (or cities) had the distribution of threatened plants. The Antu County in Jilin Province had the most species (42) of threatened plants. A total of 16 counties (cities) such as the Antu County of Jilin Province and the Huanren Manchu Autonomous County of Liaoning Provice, etc. were identified as the priority conservation regions of the threatened plants in Northeast China. According to the priority conservation value, five priority conservation regions of threatened plants in Northoast China were divided, including Changbai Mountain conservation region, East Liaoning conservation region, South Liaoning conservation region, Zhangguangcai Mountain conservation region, and Xiaoxing' an Mountain conservation region. The main threatened plants in each priority conservation region were also analyzed.

  5. Recognizing and coping with our own prejudices: Fighting liberal bias without conservative input.

    PubMed

    Baumeister, Roy F

    2015-01-01

    This commentary summarizes my struggle to overcome liberal bias without conservative input. I generally assume I am biased and constantly try to build a good-quality argument for the opposite view. Trying to dispense with one's liberal values can help, if one is willing. Frequent self-tests help. Liberal biases include race, gender, and poverty, but also dislike of business corporations and even Western civilization. Feminism is the single strongest and most powerful bias. PMID:26786852

  6. 76 FR 28060 - Regional Habitat Conservation Plan, Hays County, TX

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

    ... of the RHCP and to evaluate alternatives, along with the draft RHCP (74 FR 56655). We included public... Fish and Wildlife Service Regional Habitat Conservation Plan, Hays County, TX AGENCY: Fish and Wildlife... statement, final Hays County regional habitat conservation plan, and draft record of decision. SUMMARY:...

  7. Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions

    PubMed Central

    Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

    2014-01-01

    Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador's biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation. PMID:25360277

  8. Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions.

    PubMed

    Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

    2014-06-01

    Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador's biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation.

  9. Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions.

    PubMed

    Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

    2014-06-01

    Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador's biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation. PMID:25360277

  10. Setting Priorities for Regional Conservation Planning in the Mediterranean Sea

    PubMed Central

    Micheli, Fiorenza; Levin, Noam; Giakoumi, Sylvaine; Katsanevakis, Stelios; Abdulla, Ameer; Coll, Marta; Fraschetti, Simonetta; Kark, Salit; Koutsoubas, Drosos; Mackelworth, Peter; Maiorano, Luigi; Possingham, Hugh P.

    2013-01-01

    Spatial prioritization in conservation is required to direct limited resources to where actions are most urgently needed and most likely to produce effective conservation outcomes. In an effort to advance the protection of a highly threatened hotspot of marine biodiversity, the Mediterranean Sea, multiple spatial conservation plans have been developed in recent years. Here, we review and integrate these different plans with the goal of identifying priority conservation areas that represent the current consensus among the different initiatives. A review of six existing and twelve proposed conservation initiatives highlights gaps in conservation and management planning, particularly within the southern and eastern regions of the Mediterranean and for offshore and deep sea habitats. The eighteen initiatives vary substantially in their extent (covering 0.1–58.5% of the Mediterranean Sea) and in the location of additional proposed conservation and management areas. Differences in the criteria, approaches and data used explain such variation. Despite the diversity among proposals, our analyses identified ten areas, encompassing 10% of the Mediterranean Sea, that are consistently identified among the existing proposals, with an additional 10% selected by at least five proposals. These areas represent top priorities for immediate conservation action. Despite the plethora of initiatives, major challenges face Mediterranean biodiversity and conservation. These include the need for spatial prioritization within a comprehensive framework for regional conservation planning, the acquisition of additional information from data-poor areas, species or habitats, and addressing the challenges of establishing transboundary governance and collaboration in socially, culturally and politically complex conditions. Collective prioritised action, not new conservation plans, is needed for the north, western, and high seas of the Mediterranean, while developing initial information

  11. Conservation voltage reduction: Estimating methodology for a large regional application

    SciTech Connect

    De Steese, J.G. ); Kennedy, B.W. ); Merrick, S.B. )

    1992-04-01

    Conservation Voltage Reduction (CVR) is an established and cost-effective practice that has motivated many utilities to investigate its application on individual systems. This paper describes a supply-curve methodology that can determine the conservation value of CVR applied to many distribution systems in a region. In the area served by Bonneville Power Administration involving approximately 150 utilities, the systematic implementations of CVR could conserve between 170 and 268 Average Megawatts at a cost of 5 cents/kWh. This was shown to be a larger resource than might be achievable by applying more conventional efficiency improvements to transmission and distribution (T D) systems in the region.

  12. Conservation voltage reduction: Estimating methodology for a large regional application

    SciTech Connect

    De Steese, J.G.; Kennedy, B.W.; Merrick, S.B.

    1992-04-01

    Conservation Voltage Reduction (CVR) is an established and cost-effective practice that has motivated many utilities to investigate its application on individual systems. This paper describes a supply-curve methodology that can determine the conservation value of CVR applied to many distribution systems in a region. In the area served by Bonneville Power Administration involving approximately 150 utilities, the systematic implementations of CVR could conserve between 170 and 268 Average Megawatts at a cost of 5 cents/kWh. This was shown to be a larger resource than might be achievable by applying more conventional efficiency improvements to transmission and distribution (T&D) systems in the region.

  13. The Structure of the Staphylococcus aureus Sortase-Substrate Complex Reveals How the Universally Conserved LPXTG Sorting Signal Is Recognized*

    PubMed Central

    Suree, Nuttee; Liew, Chu Kong; Villareal, Valerie A.; Thieu, William; Fadeev, Evgeny A.; Clemens, Jeremy J.; Jung, Michael E.; Clubb, Robert T.

    2009-01-01

    In Gram-positive bacteria, sortase enzymes assemble surface proteins and pili in the cell wall envelope. Sortases catalyze a transpeptidation reaction that joins a highly conserved LPXTG sorting signal within their polypeptide substrate to the cell wall or to other pilin subunits. The molecular basis of transpeptidation and sorting signal recognition are not well understood, because the intermediates of catalysis are short lived. We have overcome this problem by synthesizing an analog of the LPXTG signal whose stable covalent complex with the enzyme mimics a key thioacyl catalytic intermediate. Here we report the solution structure and dynamics of its covalent complex with the Staphylococcus aureus SrtA sortase. In marked contrast to a previously reported crystal structure, we show that SrtA adaptively recognizes the LPXTG sorting signal by closing and immobilizing an active site loop. We have also used chemical shift mapping experiments to localize the binding site for the triglycine portion of lipid II, the second substrate to which surface proteins are attached. We propose a unified model of the transpeptidation reaction that explains the functions of key active site residues. Since the sortase-catalyzed anchoring reaction is required for the virulence of a number of bacterial pathogens, the results presented here may facilitate the development of new anti-infective agents. PMID:19592495

  14. Serratia ATP-binding cassette protein exporter, Lip, recognizes a protein region upstream of the C terminus for specific secretion.

    PubMed

    Omori, K; Idei, A; Akatsuka, H

    2001-07-20

    Serratia marcescens ATP-binding cassette (ABC) exporter, the Lip system, secretes lipase (LipA(SM)), metalloproteases, and a cell surface layer protein homologue but not a heme acquisition protein, HasA (HasA(SM)). Secretion of HasA(SM) is limited to the Has(SM) system. However, HasA proteins from Pseudomonas fluorescens (HasA(PF)) and Pseudomonas aeruginosa were exported through the Lip and Has(SM) systems. To investigate the specificity in Lip exporter-mediated secretion, secretion analysis was performed using chimeras containing the HasA(PF) and HasA(SM) sequences. The segment Val-Ala-Leu (designated R1 to R3 sites), which is present close to the C terminus of HasA(PF) but not HasA(SM), was revealed to be involved in the substrate specificity of the Lip exporter. Introduction of amino acid substitutions into the R1-R5 region demonstrated that R1, R3, R4, and R5 sites require some specific amino acid residues for Lip-mediated secretion. The amino acid sequence of the region was conserved considerably among the proteins secreted by the Lip exporter. On the contrary, the region was not related to HasA secretion through the Has(SM) system. Interestingly, a typical C-terminal motif, so far regarded as a secretion signal, was not necessary for secretion through either the Lip or the Has(SM) exporter. In LipA(SM) secretion via the Lip system, the typical C-terminal motif was not essential either, but the presence of a sequence similar to Val-Ala-Leu and its location from the C terminus greatly affect the secretion level. Secretion analyses using hybrid exporters and competitors exhibited that the R1-R5 region was recognized by an ABC protein of the Lip exporter, LipB, and that the mutations aborting Lip-mediated secretion in the region resulted in a loss of the affinity to LipB. Thus, a determinant within the secretory protein for Lip-mediated secretion was fully defined.

  15. Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages.

    PubMed

    Zhang, Xianglilan; Kang, Huaixing; Li, Yuyuan; Liu, Xiaodong; Yang, Yu; Li, Shasha; Pei, Guangqian; Sun, Qiang; Shu, Peng; Mi, Zhiqiang; Huang, Yong; Zhang, Zhiyi; Liu, Yannan; An, Xiaoping; Xu, Xiaolu; Tong, Yigang

    2015-12-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing cause of serious infection, both in the community and hospital settings. Despite sophisticated strategies and efforts, the antibiotic options for treating MRSA infection are narrowing because of the limited number of newly developed antimicrobials. Here, four newly-isolated MRSA-virulent phages, IME-SA1, IMESA2, IME-SA118 and IME-SA119, were sequenced and analyzed. Their genome termini were identified using our previously proposed "termini analysis theory". We provide evidence that remarkable conserved terminus sequences are found in IME-SA1/2/118/119, and, moreover, are widespread throughout Twortlikevirus Staphylococcus phage G1 and K species. Results also suggested that each phage of the two species has conserved 5' terminus while the 3' terminus is variable. More importantly, a variable region with a specific pattern was found to be present near the conserved terminus of Twortlikevirus S. phage G1 species. The clone with the longest variable region had variable terminus lengths in successive generations, while the clones with the shortest variable region and with the average length variable region maintained the same terminal length as themselves during successive generations. IME-SA1 bacterial infection experiments showed that the variation is not derived from adaptation of the phage to different host strains. This is the first study of the conserved terminus and variable region of Twortlikevirus S. phages.

  16. Identification of multirestricted immunodominant regions recognized by cytolytic T lymphocytes in the human immunodeficiency virus type 1 Nef protein.

    PubMed

    Culmann-Penciolelli, B; Lamhamedi-Cherradi, S; Couillin, I; Guegan, N; Levy, J P; Guillet, J G; Gomard, E

    1994-11-01

    Peripheral blood mononuclear cells from a large number of human immunodeficiency virus (HIV)-seropositive donors were used to analyze the CD8+ T-cell response to each part of the Nef protein of HIV-1/LAI. This report identifies an immunodominant region (amino acids 73 to 144) in the Nef protein that was recognized by 97% of the NEF responder donors. This peptide sequence was dissected into four epitopic regions (amino acids 73 to 82, 83 to 97, 113 to 128, and 126 to 144), each of which was recognized under different HLA class I restrictions. Short overlapping peptides were used to sensitive the target cells for cytolysis and so to determine if these epitopic regions were multirestricted. Each region was found to contain several epitopes recognized with different HLA molecules. Thus, the central region of the Nef protein, a regulatory protein expressed early in HIV-infected cells, is rich in epitopic sequences which are found to be similar in many infected individuals and which can be recognized in association with at least ten HLA class I molecules. Their implications for the vaccination of humans with peptide sequences are discussed.

  17. The relevance of the Mediterranean Region to colonial waterbird conservation

    USGS Publications Warehouse

    Erwin, R.M.; Crivelli, Alain J.; Hafner, Heinz; Fasola, Mauro; Erwin, R. Michael; McCrimmon, Donald A.=

    1996-01-01

    The Mediterranean Sea is the largest partially enclosed sea in the world and provides habitat to more than 100 species of waterbirds from the Palearctic-North African-Middle Eastern regions. Even though the Mediterranean suffers from pollution, has little tidal influence, and is oligotrophic, more than half of the western Palearctic populations of numerous waterfowl species winter in the region. Thirty-three species of colonial waterbirds breed along the 46,000 km Mediterranean coastline with nine species considered threatened or endangered, mostly because of wetland loss and degradation. The long history of human activity and scientific investigations in the region has taught some valuable lessons. In the area of colonial waterbird biology and conservation, we have learned important lessons about the value of long-term monitoring and research on selected populations. From marking studies of Greater Flamingos (Phoenicopterus ruber roseus) and Little Egrets (Egretta garzetta) results have been used to derive useful information about metapopulation dynamics. Involvement of both African and European biologists allowed year-round Studies of these species that yielded valuable spin-offs for training in avian and wetland conservation. We have also learned the value of man-made wetlands as feeding and nesting sites for some colonial waterbirds. Careful evaluations of the habitat quality of different types of wetlands are required, as in contaminant levels such as lead shot and pesticides. Wetland conservationists have also learned from some instructive mistakes. Dam construction and agricultural incentive programs sponsored by the European Community, the World Bank, and others from the past have largely ignored impacts on wetlands and wildlife. In some areas, economic ventures such as aquaculture operations and salt mining have not involved waterbird habitat needs in their planning. Research and conservation needs include: (1) establishing regional monitoring programs and

  18. Human variation in short regions predisposed to deep evolutionary conservation.

    PubMed

    Loots, Gabriela G; Ovcharenko, Ivan

    2010-06-01

    The landscape of the human genome consists of millions of short islands of conservation that are 100% conserved across multiple vertebrate genomes (termed "bricks"), the majority of which are located in noncoding regions. Several hundred thousand bricks are deeply conserved reaching the genomes of amphibians and fish. Deep phylogenetic conservation of noncoding DNA has been reported to be strongly associated with the presence of gene regulatory elements, introducing bricks as a proxy to the functional noncoding landscape of the human genome. Here, we report a significant overrepresentation of bricks in the promoters of transcription factors and developmental genes, where the high level of phylogenetic conservation correlates with an increase in brick overrepresentation. We also found that the presence of a brick dictates a predisposition to evolutionary constraint, with only 0.7% of the amniota brick central nucleotides being diverged within the primate lineage--an 11-fold reduction in the divergence rate compared with random expectation. Human single-nucleotide polymorphism (SNP) data explains only 3% of primate-specific variation in amniota bricks, thus arguing for a widespread fixation of brick mutations within the primate lineage and prior to human radiation. This variation, in turn, might have been utilized as a driving force for primate- and hominoid-specific adaptation. We also discovered a pronounced deviation from the evolutionary predisposition in the human lineage, with over 20-fold increase in the substitution rate at brick SNP sites over expected values. In addition, contrary to typical brick mutations, brick variation commonly encountered in the human population displays limited, if any, signatures of negative selection as measured by the minor allele frequency and population differentiation (F-statistical measure) measures. These observations argue for the plasticity of gene regulatory mechanisms in vertebrates--with evidence of strong purifying

  19. Integrating regional conservation priorities for multiple objectives into national policy.

    PubMed

    Beger, Maria; McGowan, Jennifer; Treml, Eric A; Green, Alison L; White, Alan T; Wolff, Nicholas H; Klein, Carissa J; Mumby, Peter J; Possingham, Hugh P

    2015-01-01

    Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making. PMID:26364769

  20. Integrating regional conservation priorities for multiple objectives into national policy

    PubMed Central

    Beger, Maria; McGowan, Jennifer; Treml, Eric A.; Green, Alison L.; White, Alan T.; Wolff, Nicholas H.; Klein, Carissa J.; Mumby, Peter J.; Possingham, Hugh P.

    2015-01-01

    Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making. PMID:26364769

  1. Definition of epitopes and antigens recognized by vaccinia specific immune responses: their conservation in variola virus sequences, and use as a model system to study complex pathogens.

    PubMed

    Sette, Alessandro; Grey, Howard; Oseroff, Carla; Peters, Bjoern; Moutaftsi, Magdalini; Crotty, Shane; Assarsson, Erika; Greenbaum, Jay; Kim, Yohan; Kolla, Ravi; Tscharke, David; Koelle, David; Johnson, R Paul; Blum, Janice; Head, Steven; Sidney, John

    2009-12-30

    In the last few years, a wealth of information has become available relating to the targets of vaccinia virus (VACV)-specific CD4(+) T cell, CD8(+) T cell and antibody responses. Due to the large size of its genome, encoding more than 200 different proteins, VACV represents a useful model system to study immunity to complex pathogens. Our data demonstrate that both cellular and humoral responses target a large number of antigens and epitopes. This broad spectrum of targets is detected in both mice and humans. CD4(+) T cell responses target late and structural antigens, while CD8(+) T cells preferentially recognize early antigens. While both CD4(+) and CD8(+) T cell responses target different types of antigens, the antigens recognized by T(H) cells are highly correlated with those recognized by antibody responses. We further show that protein abundance and antibody recognition can be used to predict antigens recognized by CD4(+) T cell responses, while early expression at the mRNA level predicts antigens targeted by CD8(+) T cells. Finally, we find that the vast majority of VACV epitopes are conserved in variola virus (VARV), thus suggesting that the epitopes defined herein also have relevance for the efficacy of VACV as a smallpox vaccine.

  2. Defining and predicting structurally conserved regions in protein superfamilies

    PubMed Central

    Huang, Ivan K.; Grishin, Nick V.

    2013-01-01

    Motivation: The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. Accurate SCR predictions can benefit homology modelling and sequence alignment. Results: Using pairwise DaliLite alignments among a set of homologous structures, we devised a simple measure of structural conservation, termed structural conservation index (SCI). SCI was used to distinguish SCRs from non-SCRs. A database of SCRs was compiled from 386 SCOP superfamilies containing 6489 protein domains. Artificial neural networks were then trained to predict SCRs with various features deduced from a single structure and homologous sequences. Assessment of the predictions via a 5-fold cross-validation method revealed that predictions based on features derived from a single structure perform similarly to ones based on homologous sequences, while combining sequence and structural features was optimal in terms of accuracy (0.755) and Matthews correlation coefficient (0.476). These results suggest that even without information from multiple structures, it is still possible to effectively predict SCRs for a protein. Finally, inspection of the structures with the worst predictions pinpoints difficulties in SCR definitions. Availability: The SCR database and the prediction server can be found at http://prodata.swmed.edu/SCR. Contact: 91huangi@gmail.com or grishin@chop.swmed.edu Supplementary information: Supplementary data are available at Bioinformatics

  3. A Syntenic Region Conserved from Fish to Mammalian X Chromosome

    PubMed Central

    Guan, Guijun; Yi, Meisheng; Kobayashi, Tohru; Hong, Yunhan; Nagahama, Yoshitaka

    2014-01-01

    Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system), the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus), is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH) and the random amplified polymorphic DNA (RAPD) approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes. PMID:25506037

  4. Identification of a conserved linear neutralizing epitope recognized by monoclonal antibody 9A9 against serotype A foot-and-mouth disease virus.

    PubMed

    Liang, Weifeng; Zhou, Guohui; Liu, Wenming; Yang, Baolin; Li, Chaosi; Wang, Haiwei; Yang, Decheng; Ma, Wenge; Yu, Li

    2016-10-01

    Foot-and-mouth disease (FMD), caused by foot-and-mouth disease virus (FMDV), is a highly contagious infectious disease that affects domestic and wild cloven-hoofed animals worldwide. In recent years, a series of outbreaks of serotype A FMD have occurred in many countries. High-affinity neutralizing antibodies against a conserved epitope have the potential to provide protective immunity against diverse subtypes of FMDV serotype A and to protect against future pandemics. In this study, we produced an A serotype FMDV-specific monoclonal antibody (MAb) against the viral capsid protein VP1, designated 9A9, that potently neutralized FMDV A/JLYS/CHA/2014 with a 50 % neutralization titer (NT50) of 4,096. GST-fusion proteins expressing truncated peptides of VP1 were subjected to Western blot analysis using MAb 9A9, and it was found that the peptide (143)RGDLGPLAARL(153) of VP1 was the minimal epitope for MAb 9A9 binding. Western blot analysis also revealed that the epitope peptide could be recognized by positive sera from serotype A FMDV-infected pigs and cattle. Subsequent alanine-scanning mutagenesis analysis revealed that residues Gly(147) and Leu(149) of the 9A9-recognized epitope are crucial for MAb 9A9 binding. Furthermore, under immunological pressure selected by MAb 9A9, a single amino acid residue replacement (L149P) occurred in a viral neutralization-escape mutant, which verified the location of a critical residue of this epitope at Leu(149). Importantly, the epitope (143)RGDLGPLAARL(153) was highly conserved among different topotypes of serotype A FMDV strains in sequence alignment analysis. Thus, the results of this study could have application potential in the development of epitope-based vaccines and a suitable MAb-based diagnostic method for detection of type A FMDV as well as quantitation of antibodies against FMDV serotype A. PMID:27422396

  5. KorB protein of promiscuous plasmid RP4 recognizes inverted sequence repetitions in regions essential for conjugative plasmid transfer.

    PubMed Central

    Balzer, D; Ziegelin, G; Pansegrau, W; Kruft, V; Lanka, E

    1992-01-01

    We have constructed a RP4 KorB overproducing strain and purified the protein to near homogeneity. KorB is a DNA binding protein recognizing defined palindromic 13-bp sequences (TTTAGCSGCTAAA). Inverted sequence repetitions of this type, designated OB, are present on RP4 12 times. OB-sequences are localized in replication and maintenance regions as well as in the regions Tra1 and Tra2 essential for conjugative transfer. All sites found in Tra regions by computer search act as targets for specific binding of KorB protein. KorB-DNA complexes were detected by DNA fragment retardation assay using polyacrylamide gels. The 13-bp symmetric arrangement of the consensus OB-sequence constitutes the core for binding KorB protein since any truncation of this sequence prevents complex assembly or leads to a considerable destabilization of the KorB-DNA complexes. A hydroxyl radical footprint analysis demonstrated complex formation of KorB with the OB-sequence directly and suggests the presence of an unusual DNA structure within the nucleoprotein complex. Images PMID:1579485

  6. A human antibody recognizing a conserved epitope of H5 hemagglutinin broadly neutralizes highly pathogenic avian influenza H5N1 viruses.

    PubMed

    Hu, Hongxing; Voss, Jarrod; Zhang, Guoliang; Buchy, Philippi; Zuo, Teng; Wang, Lulan; Wang, Feng; Zhou, Fan; Wang, Guiqing; Tsai, Cheguo; Calder, Lesley; Gamblin, Steve J; Zhang, Linqi; Deubel, Vincent; Zhou, Boping; Skehel, John J; Zhou, Paul

    2012-03-01

    Influenza A virus infection is a persistent threat to public health worldwide due to its ability to evade immune surveillance through rapid genetic drift and shift. Current vaccines against influenza A virus provide immunity to viral isolates that are similar to vaccine strains. High-affinity neutralizing antibodies against conserved epitopes could provide immunity to diverse influenza virus strains and protection against future pandemic viruses. In this study, by using a highly sensitive H5N1 pseudotype-based neutralization assay to screen human monoclonal antibodies produced by memory B cells from an H5N1-infected individual and molecular cloning techniques, we developed three fully human monoclonal antibodies. Among them, antibody 65C6 exhibited potent neutralization activity against all H5 clades and subclades except for subclade 7.2 and prophylactic and therapeutic efficacy against highly pathogenic avian influenza H5N1 viruses in mice. Studies on hemagglutinin (HA)-antibody complexes by electron microscopy and epitope mapping indicate that antibody 65C6 binds to a conformational epitope comprising amino acid residues at positions 118, 121, 161, 164, and 167 (according to mature H5 numbering) on the tip of the membrane-distal globular domain of HA. Thus, we conclude that antibody 65C6 recognizes a neutralization epitope in the globular head of HA that is conserved among almost all divergent H5N1 influenza stains. PMID:22238297

  7. Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.

    PubMed Central

    Balganesh, T S; Reiners, L; Lauster, R; Noyer-Weidner, M; Wilke, K; Trautner, T A

    1987-01-01

    Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis phages SPR and phi 3T methylate the internal cytosine of the sequence GGCC. They differ in their capacity to methylate additional sequences. These are CCGG and CC(A/T)GG in SPR and GCNGC in phi 3T. Introducing unique restriction sites at equivalent locations within the two genes facilitated the construction of chimeric genes. These expressed Mtase activity at a level comparable to that of the parental genes. The methylation specificity of chimeric enzymes was correlated with the location of chimeric fusions. This analysis, which also included the use of mutant genes, showed that domains involved in the recognition of target sequences unique to each enzyme [CCGG, CC(A/T)GG or GCNGC] are represented by the central non-conserved parts of the proteins, whilst recognition of the sequence (GGCC), which is a target for both enzymes, is determined by an adjacent conserved region. Images Fig. 4. Fig. 5. PMID:2828032

  8. SPECIES DISTRIBUTIONS, SURROGACY, AND IMPORTANT CONSERVATION REGIONS IN CANADA

    EPA Science Inventory

    Conservation actions could be more efficient if there is congruence among taxa in the distribution of species. Patterns in the geographic distribution of species of six taxa were used to identify nationally important sites for conservation in Canada. Species richness and a meas...

  9. Definition of the region on NS3 which contains multiple epitopes recognized by dengue virus serotype-cross-reactive and flavivirus-cross-reactive, HLA-DPw2-restricted CD4+ T cell clones.

    PubMed

    Okamoto, Y; Kurane, I; Leporati, A M; Ennis, F A

    1998-04-01

    The epitopes recognized by six CD4+ CD8- cytotoxic T lymphocyte (CTL) clones established from a dengue-3 virus-immune donor were defined. (i) Three CTL clones, JK10, JK34 and JK39, were cross-reactive for dengue virus types 1-4. (ii) One clone, JK28, was cross-reactive for dengue virus types 1-4 and West Nile virus. (iii) Two clones, JK26 and JK49, were cross-reactive for dengue virus types 1-4, West Nile virus and yellow fever virus. The clones, except for JK49, recognized the same epitope on NS3 in an HLA-DPw2-restricted fashion. The smallest synthetic peptide recognized by the five CTL clones was a 10 aa peptide which comprises aa 255-264 on dengue virus NS3. JK49 recognized the overlapping epitope which comprises aa 257-266 in an HLA-DPw2-restricted fashion. Analysis of T cell receptor (TCR) usage by these T cell clones revealed that (i) JK10 and JK34 use V alpha11, and JK34 and JK28 use V beta23, and (ii) the amino acid sequences of the V(D)J junctional region of the TCR were different among these five CTL clones. There were, however, single amino acid conservations among TCRs of some of these T cell clones. These results indicate that the region on NS3 which comprises aa 255-266 contains multiple epitopes recognized by dengue serotype-cross-reactive and flavivirus-cross-reactive CD4+ CTL in an HLA-DPw2-restricted fashion and that a single epitope can be recognized by T cells which have heterogeneous virus specificities.

  10. Identification of the Single Immunodominant Region of the Native Human CC Chemokine Receptor 6 Recognized by Mouse Monoclonal Antibodies

    PubMed Central

    Dorgham, Karim; Dejou, Cécile; Piesse, Christophe; Gorochov, Guy; Pène, Jérôme

    2016-01-01

    Chemokines and their receptors play an important role in cell trafficking and recruitment. The CCR6 chemokine receptor, selectively expressed on leukocyte populations, has been shown to play a deleterious role in the pathogenesis of various chronic inflammatory diseases and, as such, may constitute a prime target in the development of immunotherapeutic treatment. However, to date no neutralizing mouse monoclonal antibodies (mAbs) specific for this chemokine receptor have been reported, whereas information on small molecules capable of interfering with the interaction of CCR6 and its ligands is scant. Here, we report the failure to generate neutralizing mouse mAbs specific for human (hu)CCR6. Immunization of mice with peptides mimicking extracellular domains, potentially involved in CCR6 function, failed to induce Abs reactive with the native receptor. Although the use of NIH-3T3 cells expressing huCCR6 resulted in the isolation of mAbs specific for this receptor, they were not able to block the interaction between huCCR6 and huCCL20. Investigation of the anti-huCCR6 mAbs generated in the present study, as well as those commercially available, show that all mAbs invariably recognize a unique, non-neutralizing, immunodominant region in the first part of its N-terminal domain. Together, these results indicate that the generation of potential neutralizing anti-huCCR6 mAbs in the mouse is unlikely to succeed and that alternative techniques, such as the use of other animal species for immunization, might constitute a better approach to generate such a potentially therapeutic tool for the treatment of inflammatory disease. PMID:27336468

  11. An HLA-C-restricted CD8+ cytotoxic T-lymphocyte clone recognizes a highly conserved epitope on human immunodeficiency virus type 1 gag.

    PubMed Central

    Littaua, R A; Oldstone, M B; Takeda, A; Debouck, C; Wong, J T; Tuazon, C U; Moss, B; Kievits, F; Ennis, F A

    1991-01-01

    A unique epitope on the gag protein of human immunodeficiency virus type 1 (HIV-1), located at amino acid 145 to 150, has been mapped by using a CD8+ cytotoxic T-lymphocyte (CTL) clone. This epitope is highly conserved among 18 HIV-1 strains. The HIV-1 gag-specific human leukocyte antigen (HLA) class I-restricted CD8+ CTL clone was generated from fresh peripheral blood mononuclear cells of an HIV-seropositive donor by stimulation with gamma-irradiated allogeneic peripheral blood mononuclear cells in the presence of an anti-CD3 monoclonal antibody and recombinant interleukin-2. This gag-specific CTL clone killed autologous target cells infected with a recombinant vaccinia virus containing the gag gene of HIV-1 and target cells pulsed with an authentic p24gag construct expressed in Escherichia coli. Fine specificity was determined by using a panel of overlapping 30-amino-acid-long synthetic peptides and subsequently using smaller peptides to precisely map the CTL domain on p24. The epitope is on a highly conserved region, and it overlaps with a major B-cell epitope of gag. This CD8+ T-cell epitope is restricted by HLA-Cw3, which has not been previously identified as a restricting element for human CTL responses. PMID:1712857

  12. Functional conservation of the promoter regions of vertebrate tyrosinase genes.

    PubMed

    Sato, S; Tanaka, M; Miura, H; Ikeo, K; Gojobori, T; Takeuchi, T; Yamamoto, H

    2001-11-01

    Tyrosinase is the key enzyme for synthesizing melanin pigments, which primarily determine mammalian skin coloration. Considering the important roles of pigments in the evolution and the adaptation of vertebrates, phylogenetic changes in the coding and flanking regulatory sequences of the tyrosinase gene are particularly intriguing. We have now cloned cDNA encoding tyrosinase from Japanese quail and snapping turtle. These nonmammalian cDNA are highly homologous to those of the mouse and human tyrosinases, whereas the 5' flanking sequences are far less conserved except for a few short sequence motifs. Nevertheless, we demonstrate that the 5' flanking sequences from the quail or turtle tyrosinase genes are capable of directing the expression of a fused mouse tyrosinase cDNA when introduced into cultured mouse albino melanocytes. This experimental method, which reveals the functional conservation of regulatory sequences in one cell type (the melanocyte), may be utilized to evaluate phylogenetic differences in mechanisms controlling specific gene expression in many other types of cells. We also provide evidence that the 5' flanking sequences from these nonmammalian genes are functional in vivo by producing transgenic mice. Phylogenetic changes of vertebrate tyrosinase promoters and the possible involvement of conserved sequence motifs in melanocyte-specific expression of tyrosinase are discussed. PMID:11764277

  13. 75 FR 31463 - Comal County Regional Habitat Conservation Plan, Comal County, TX

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-03

    ... Federal Register on October 16, 2008 (73 FR 61433). A public scoping meeting was held on December 4, 2008... Fish and Wildlife Service Comal County Regional Habitat Conservation Plan, Comal County, TX AGENCY... statement, draft habitat conservation plan, and permit application; announcement of a public...

  14. Recognizing faces.

    PubMed

    Ellis, H D

    1975-11-01

    Following a review of the stimulus and subject factors which have been found to affect recognition faces, the question of whether this process can be considered a special one is dealt with. Evidence from studies involving the development of face recognition, the recognition of inverted faces, and the clinical condition prosopagnosia is considered, and in each case found to be inadequate for the unequivocal conclusion that the processes underlying face recognition are qualitatively different from those employed in recognizing other pictorial material.

  15. Regional Geograhpic Network Partnerships Supporting Sustainable Landscapes - An Example: The North Atlantic Landscape Conservation Cooperative

    EPA Science Inventory

    Natural resource management agencies, conservation organizations and other stakeholders are facing increasingly complex environmental challenges that require coordinated management actions at regional and landscape levels. To address these challenges, integrated multi-disciplina...

  16. Multiple Src Homology 3 Binding to the Ubiquitin Ligase Itch Conserved Proline-Rich Region.

    PubMed

    Desrochers, Guillaume; Lussier-Price, Mathieu; Omichinski, James G; Angers, Annie

    2015-12-22

    Itch is a member of the C2-WW-HECT (CWH) family of ubiquitin ligases involved in the control of inflammatory signaling pathways, several transcription factors, and sorting of surface receptors to the degradative pathway. In addition to these common domains, Itch also contains a conserved proline-rich region (PRR) allowing its interaction with Src homology 3 (SH3) domain-containing proteins. This region is composed of 20 amino acids and contains one consensus class I and three class II SH3-binding motifs. Several SH3 domain-containing partners have been shown to recognize the Itch PRR, but their binding properties have been poorly defined. Here we compare a subset of endocytic SH3 domain-containing proteins using bioluminescence resonance energy transfer, isothermal titration calorimetry, and pull-down assays. Results indicate that Endophilin is a high-affinity binding partner of Itch both in vivo and in vitro, with a calculated KD placing this complex among the highest-affinity SH3 domain-mediated interactions reported to date. All of the SH3 domains tested here bind to Itch with a 1:1 stoichiometry, except for β-PIX that binds with a 2:1 stoichiometry. Together, these results indicate that Itch PRR is a versatile binding module that can accommodate several different SH3 domain-containing proteins but has a preference for Endophilin. Interestingly, the catalytic activity of Itch toward different SH3 domain-containing proteins was similar, except for β-PIX that was not readily ubiquitylated even though it could interact with an affinity comparable to those of other substrates tested. PMID:26613292

  17. Regional Effects of Agricultural Conservation Practices on Nutrient Transport in the Upper Mississippi River Basin.

    PubMed

    García, Ana María; Alexander, Richard B; Arnold, Jeffrey G; Norfleet, Lee; White, Michael J; Robertson, Dale M; Schwarz, Gregory

    2016-07-01

    Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to investigate whether spatial differences in conservation intensity were statistically correlated with variations in nutrient loads. In contrast to other forms of water quality data analysis, the application of SPARROW controls for confounding factors such as hydrologic variability, multiple sources and environmental processes. A measure of conservation intensity was derived from the USDA-CEAP regional assessment of the Upper Mississippi River and used as an explanatory variable in a model of the Upper Midwest. The spatial pattern of conservation intensity was negatively correlated (p = 0.003) with the total nitrogen loads in streams in the basin. Total phosphorus loads were weakly negatively correlated with conservation (p = 0.25). Regional nitrogen reductions were estimated to range from 5 to 34% and phosphorus reductions from 1 to 10% in major river basins of the Upper Mississippi region. The statistical associations between conservation and nutrient loads are consistent with hydrological and biogeochemical processes such as denitrification. The results provide empirical evidence at the regional scale that conservation practices have had a larger statistically detectable effect on nitrogen than on phosphorus loadings in streams and rivers of the Upper Mississippi Basin. PMID:27243625

  18. Regional Effects of Agricultural Conservation Practices on Nutrient Transport in the Upper Mississippi River Basin.

    PubMed

    García, Ana María; Alexander, Richard B; Arnold, Jeffrey G; Norfleet, Lee; White, Michael J; Robertson, Dale M; Schwarz, Gregory

    2016-07-01

    Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to investigate whether spatial differences in conservation intensity were statistically correlated with variations in nutrient loads. In contrast to other forms of water quality data analysis, the application of SPARROW controls for confounding factors such as hydrologic variability, multiple sources and environmental processes. A measure of conservation intensity was derived from the USDA-CEAP regional assessment of the Upper Mississippi River and used as an explanatory variable in a model of the Upper Midwest. The spatial pattern of conservation intensity was negatively correlated (p = 0.003) with the total nitrogen loads in streams in the basin. Total phosphorus loads were weakly negatively correlated with conservation (p = 0.25). Regional nitrogen reductions were estimated to range from 5 to 34% and phosphorus reductions from 1 to 10% in major river basins of the Upper Mississippi region. The statistical associations between conservation and nutrient loads are consistent with hydrological and biogeochemical processes such as denitrification. The results provide empirical evidence at the regional scale that conservation practices have had a larger statistically detectable effect on nitrogen than on phosphorus loadings in streams and rivers of the Upper Mississippi Basin.

  19. Regional effects of agricultural conservation practices on nutrient transport in the Upper Mississippi River Basin

    USGS Publications Warehouse

    Garcia, Ana Maria.; Alexander, Richard B.; Arnold, Jeffrey G.; Norfleet, Lee; White, Michael J.; Robertson, Dale; Schwarz, Gregory

    2016-01-01

    Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to investigate whether spatial differences in conservation intensity were statistically correlated with variations in nutrient loads. In contrast to other forms of water quality data analysis, the application of SPARROW controls for confounding factors such as hydrologic variability, multiple sources and environmental processes. A measure of conservation intensity was derived from the USDA-CEAP regional assessment of the Upper Mississippi River and used as an explanatory variable in a model of the Upper Midwest. The spatial pattern of conservation intensity was negatively correlated (p = 0.003) with the total nitrogen loads in streams in the basin. Total phosphorus loads were weakly negatively correlated with conservation (p = 0.25). Regional nitrogen reductions were estimated to range from 5 to 34% and phosphorus reductions from 1 to 10% in major river basins of the Upper Mississippi region. The statistical associations between conservation and nutrient loads are consistent with hydrological and biogeochemical processes such as denitrification. The results provide empirical evidence at the regional scale that conservation practices have had a larger statistically detectable effect on nitrogen than on phosphorus loadings in streams and rivers of the Upper Mississippi Basin.

  20. 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,…

  1. The status of chondrichthyan conservation in the Indo-Australasian region.

    PubMed

    White, W T; Kyne, P M

    2010-06-01

    The status of chondrichthyan (sharks, batoids and chimaeras) conservation in the Indo-Australasian region is examined, and issues relevant to the conservation of this fauna at the subregional level [Australia, Indonesia (excluding West Papua), New Guinea (West Papua and Papua New Guinea), New Caledonia and New Zealand] are discussed. According to the 2009 IUCN Red List of Threatened Species, c. 21% of Indo-Australasian chondrichthyans are classified as threatened (critically endangered, endangered and vulnerable) and c. 40% are of conservation concern (threatened and near threatened). The proportion of threatened species is highest in New Guinea (c. 39%) and Indonesia (c. 35%) and least in New Zealand (c. 11%). In New Guinea, three quarters of the species are of conservation concern; in Indonesia, nearly two thirds are of conservation concern. Within the region, the proportion of threatened batoids (c. 29%) is higher than threatened sharks (c. 17%), while there are no threatened chimaeras. Conservation status is discussed at the order (for sharks), suborder (for batoids) and family level. Issues relating to the conservation status of chondrichthyans vary greatly between each subregion, but they mostly relate to targeted or incidental capture in fisheries. A handful of sharks and batoids are protected within Australian waters, while one species is protected in New Zealand. Both Australia and New Zealand have developed National Plans of Action for the Conservation and Management of Sharks (NPOA-Sharks), but these are lacking elsewhere. Development and implementation of NPOA-Sharks are a priority in order to drive the conservation of the regional fauna. Sustainable fisheries management (including by-catch), confronting the challenge of illegal, unreported and unregulated fishing, species protection where appropriate and marine protected areas (MPA) are all likely to prove vital in ensuring the long-term conservation of Indo-Australasian sharks, batoids and chimaeras.

  2. A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions

    PubMed Central

    Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth

    2016-01-01

    Background Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s

  3. Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation

    PubMed Central

    Wright, Alison E.; Zimmer, Fabian; Harrison, Peter W.; Mank, Judith E.

    2015-01-01

    Regional variation in sex-specific gene regulation has been observed across sex chromosomes in a range of animals and is often a function of sex chromosome age. The avian Z chromosome exhibits substantial regional variation in sex-specific regulation, where older regions show elevated levels of male-biased expression. Distinct sex-specific regulation also has been observed across the male hypermethylated (MHM) region, which has been suggested to be a region of nascent dosage compensation. Intriguingly, MHM region regulatory features have not been observed in distantly related avian species despite the hypothesis that it is situated within the oldest region of the avian Z chromosome and is therefore orthologous across most birds. This situation contrasts with the conservation of other aspects of regional variation in gene expression observed on the avian sex chromosomes but could be the result of sampling bias. We sampled taxa across the Galloanserae, an avian clade spanning 90 million years, to test whether regional variation in sex-specific gene regulation across the Z chromosome is conserved. We show that the MHM region is conserved across a large portion of the avian phylogeny, together with other sex-specific regulatory features of the avian Z chromosome. Our results from multiple lines of evidence suggest that the sex-specific expression pattern of the MHM region is not consistent with nascent dosage compensation. PMID:26245831

  4. Relationship of the human immunodeficiency virus type 1 gp120 third variable loop to a component of the CD4 binding site in the fourth conserved region.

    PubMed Central

    Wyatt, R; Thali, M; Tilley, S; Pinter, A; Posner, M; Ho, D; Robinson, J; Sodroski, J

    1992-01-01

    Neutralizing antibodies that recognize the human immunodeficiency virus gp120 exterior envelope glycoprotein and are directed against either the third variable (V3) loop or conserved, discontinuous epitopes overlapping the CD4 binding region have been described. Here we report several observations that suggest a structural relationship between the V3 loop and amino acids in the fourth conserved (C4) gp120 region that constitute part of the CD4 binding site and the conserved neutralization epitopes. Treatment of the gp120 glycoprotein with ionic detergents resulted in a V3 loop-dependent masking of both linear C4 epitopes and discontinuous neutralization epitopes overlapping the CD4 binding site. Increased recognition of the native gp120 glycoprotein by an anti-V3 loop monoclonal antibody, 9284, resulted from from single amino acid changes either in the base of the V3 loop or in the gp120 C4 region. These amino acid changes also resulted in increased exposure of conserved epitopes overlapping the CD4 binding region. The replication-competent subset of these mutants exhibited increased sensitivity to neutralization by antibody 9284 and anti-CD4 binding site antibodies. The implied relationship of the V3 loop, which mediates post-receptor binding steps in virus entry, and components of the CD4 binding region may be important for the interaction of these functional gp120 domains and for the observed cooperativity of neutralizing antibodies directed against these regions. Images PMID:1279195

  5. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    DOE Data Explorer

    Loots, Gabriela G. [LLNL; Ovcharenko, I. [LLNL

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

  6. Influence of conservation programs on amphibians using seasonal wetlands in the Prairie Pothole Region

    USGS Publications Warehouse

    Balas, Caleb J.; Euliss, Ned H.; Mushnet, David M.

    2012-01-01

    Extensive modification of upland habitats surrounding wetlands to facilitate agricultural production has negatively impacted amphibian communities in the Prairie Pothole Region of North America. In attempts to mitigate ecosystem damage associated with extensive landscape alteration, vast tracks of upland croplands have been returned to perennial vegetative cover (i.e., conservation grasslands) under a variety of U.S. Department of Agriculture programs. We evaluated the influence of these conservation grasslands on amphibian occupancy of seasonal wetlands in the Prairie Pothole Region. Using automated call surveys, aquatic funnel traps, and visual encounter surveys, we detected eight amphibian species using wetlands within three land-use categories (farmed, conservation grasslands, and native prairie grasslands) during the summers of 2005 and 2006. Seasonal wetlands within farmlands were used less frequently by amphibians than those within conservation and native prairie grasslands, and wetlands within conservation grasslands were used less frequently than those within native prairie grasslands by all species and life-stages we successfully modeled. Our results suggest that, while not occupied as frequently as wetlands within native prairie, wetlands within conservation grasslands provide important habitat for maintaining amphibian biodiversity in the Prairie Pothole Region

  7. Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region.

    PubMed

    Ando, Amy W; Mallory, Mindy L

    2012-04-24

    Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit-cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change-induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area. PMID:22451914

  8. Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region.

    PubMed

    Ando, Amy W; Mallory, Mindy L

    2012-04-24

    Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit-cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change-induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area.

  9. A natural IgA-anti-F(ab')2gamma autoantibody occurring in healthy individuals and kidney graft recipients recognizes an IgG1 hinge region epitope.

    PubMed

    Terness, P; Navolan, D; Moroder, L; Siedler, F; Weyher, E; Kohl, I; Dufter, C; Welschof, M; Drugarin, D; Schneider, F; Opelz, G

    1996-11-01

    Natural anti-IgG autoantibodies are found both in healthy individuals and in patients with certain diseases. One group of these Abs recognizes epitopes located in the F(ab')2 region of the IgG molecule. The immunoregulatory role of these Abs in healthy individuals, graft rejection, and disease was previously studied, usually with a focus on the characterization of anti-idiotypic Abs. In the present study, we characterize the epitope recognized by an anti-F(ab')2gamma autoantibody of the IgA isotype, which occurs in the serum of healthy individuals and kidney transplant recipients. The autoantibody described herein reacts strongly with F(ab')2gamma but only poorly with Fab(gamma) fragments, a binding pattern pointing to an epitope located in the hinge region. Using synthetic peptides, we identified a conformational epitope that overlaps the middle and part of the lower hinge region. Structural analyses of peptide constructs showed that a defined conformation of the first three residues of the lower hinge is required for a full expression of the epitope. Binding of IgA to the hinge region of IgG1 covers part of the physiologically active Fc domain, immobilizes the Fab arms, and thereby can be expected to exert immunoregulatory functions.

  10. Cryptosporidium hominis Is a Newly Recognized Pathogen in the Arctic Region of Nunavik, Canada: Molecular Characterization of an Outbreak

    PubMed Central

    Dixon, Brent; Dion, Réjean; Levesque, Benoît; Cantin, Philippe; Cédilotte, Lyne; Ndao, Momar; Proulx, Jean-François; Yansouni, Cedric P.

    2016-01-01

    Background Cryptosporidium is a leading cause of childhood diarrhea in low-resource settings, and has been repeatedly associated with impaired physical and cognitive development. In May 2013, an outbreak of diarrhea caused by Cryptosporidium hominis was identified in the Arctic region of Nunavik, Quebec. Human cryptosporidiosis transmission was previously unknown in this region, and very few previous studies have reported it elsewhere in the Arctic. We report clinical, molecular, and epidemiologic details of a multi-village Cryptosporidium outbreak in the Canadian Arctic. Methodology/Principal Findings We investigated the occurrence of cryptosporidiosis using a descriptive study of cases with onset between April 2013 and April 2014. Cases were defined as Nunavik inhabitants of any age presenting with diarrhea of any duration, in whom Cryptosporidium oocysts were detected by stool microscopy in a specialised reference laboratory. Cryptosporidium was identified in stool from 51 of 283 individuals. The overall annual incidence rate (IR) was 420 / 100,000 inhabitants. The IR was highest among children aged less than 5 years (1290 /100,000 persons). Genetic subtyping for stool specimens from 14/51 cases was determined by DNA sequence analysis of the 60 kDa glycoprotein (gp60) gene. Sequences aligned with C. hominis subtype Id in all cases. No common food or water source of infection was identified. Conclusions/Significance In this first observed outbreak of human cryptosporidiosis in this Arctic region, the high IR seen is cause for concern about the possible long-term effects on growth and development of children in Inuit communities, who face myriad other challenges such as overcrowding and food-insecurity. The temporal and geographic distribution of cases, as well as the identification of C. hominis subtype Id, suggest anthroponotic rather than zoonotic transmission. Barriers to timely diagnosis delayed the recognition of human cryptosporidiosis in this remote

  11. Evaluation of Apis mellifera syriaca Levant region honeybee conservation using comparative genome hybridization.

    PubMed

    Haddad, Nizar Jamal; Batainh, Ahmed; Saini, Deepti; Migdadi, Osama; Aiyaz, Mohamed; Manchiganti, Rushiraj; Krishnamurthy, Venkatesh; Al-Shagour, Banan; Brake, Mohammad; Bourgeois, Lelania; De Guzman, Lilia; Rinderer, Thomas; Hamouri, Zayed Mahoud

    2016-06-01

    Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Levant region. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp and is resistant to Varroa mites. The A. m. syriaca control reference sample (CRS) in this study was originally collected and stored since 2001 from "Wadi Ben Hammad", a remote valley in the southern region of Jordan. Morphometric and mitochondrial DNA markers of these honeybees had shown highest similarity to reference A. m. syriaca samples collected in 1952 by Brother Adam of samples collected from the Middle East. Samples 1-5 were collected from the National Center for Agricultural Research and Extension breeding apiary which was established for the conservation of A. m. syriaca. Our objective was to determine the success of an A. m. syriaca honey bee conservation program using genomic information from an array-based comparative genomic hybridization platform to evaluate genetic similarities to a historic reference collection (CRS). Our results had shown insignificant genomic differences between the current population in the conservation program and the CRS indicated that program is successfully conserving A. m. syriaca. Functional genomic variations were identified which are useful for conservation monitoring and may be useful for breeding programs designed to improve locally adapted strains of A. m. syriaca.

  12. Evaluation of Apis mellifera syriaca Levant region honeybee conservation using comparative genome hybridization.

    PubMed

    Haddad, Nizar Jamal; Batainh, Ahmed; Saini, Deepti; Migdadi, Osama; Aiyaz, Mohamed; Manchiganti, Rushiraj; Krishnamurthy, Venkatesh; Al-Shagour, Banan; Brake, Mohammad; Bourgeois, Lelania; De Guzman, Lilia; Rinderer, Thomas; Hamouri, Zayed Mahoud

    2016-06-01

    Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Levant region. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp and is resistant to Varroa mites. The A. m. syriaca control reference sample (CRS) in this study was originally collected and stored since 2001 from "Wadi Ben Hammad", a remote valley in the southern region of Jordan. Morphometric and mitochondrial DNA markers of these honeybees had shown highest similarity to reference A. m. syriaca samples collected in 1952 by Brother Adam of samples collected from the Middle East. Samples 1-5 were collected from the National Center for Agricultural Research and Extension breeding apiary which was established for the conservation of A. m. syriaca. Our objective was to determine the success of an A. m. syriaca honey bee conservation program using genomic information from an array-based comparative genomic hybridization platform to evaluate genetic similarities to a historic reference collection (CRS). Our results had shown insignificant genomic differences between the current population in the conservation program and the CRS indicated that program is successfully conserving A. m. syriaca. Functional genomic variations were identified which are useful for conservation monitoring and may be useful for breeding programs designed to improve locally adapted strains of A. m. syriaca. PMID:27010806

  13. Use of North American Breeding Bird Survey data to estimate population change for bird conservation regions

    USGS Publications Warehouse

    Sauer, J.R.; Fallon, J.E.; Johnson, R.

    2003-01-01

    Conservation planning requires information at a variety of geographic scales, and it is often unclear whether surveys designed for other purposes will provide appropriate information for management at various scales. We evaluated the use of the North American Breeding Bird Survey (BBS) to meet information needs for conservation planning in Bird Conservation Regions (BCRs). The BBS originally was developed to provide regional estimates for states, provinces, physiographic regions, and larger areas. Many analyses have used physiographic regions within states/provinces as strata. We evaluated potential consequences of using BCRs instead of the BBS physiographic regions, testing for spatial differences in sample intensity within states and provinces. We reclassified the BBS survey routes to BCRs and conducted route regression trend (interval-specific population change) analyses for a variety of regions and time intervals. Our results were similar to those based on traditional BBS regions and suggest minimal consequences of the reclassification for the BBS sample. We summarized population change within BCRs and assessed the efficiency of the BBS in estimating population change for 421 species surveyed. As would be expected from an omnibus survey, many species appeared to be poorly monitored by the BBS, with 42% of species encountered at <1 bird per route from the survey, and 28% of trend estimates too imprecise to detect a 3% per year change over 35 years. Our results indicated that the quality of the survey for estimation of population change varied among BCRs. Population trends of species were heterogeneous over space and time, varying among BCRs for 76% of species and over time for 39% of species. Regional heterogeneity also existed in trends of species groups from the BBS. While 49% of all species in the survey had increasing populations, grassland breeding birds showed consistent declines, with only 18% of species having positive trend estimates. Bird Conservation

  14. Conserved sequence elements in the 5' region of the Ultrabithorax transcription unit

    PubMed Central

    Wilde, C. Deborah; Akam, Michael

    1987-01-01

    Clones homologous to the 5' region of the Ultrabithorax gene of Drosophila melanogaster have been isolated from D. pseudoobscura, D. funebris and Musca domestica. Regions that encode most of the Ubx protein have been sequenced in all three of these species, and the 5' upstream region has been sequenced in D. funebris to a point ˜1000 bases upstream of the probable mRNA start site. Here we compare these sequences with those described elsewhere for D. melanogaster. Deduced amino acid sequences of the Ubx protein show 8% (D. pseudoobscura), 15% (D. funebris) and 22% (M. domestica) divergence from D. melanogaster. However, these figures mask very different rates of evolution in different regions of the protein. A glycine-rich (`hinge') region is conserved in each of these species, although its length is variable. Comparison of D. funebris and D. melanogaster sequences in the long 5' untranslated leader region of the mRNA, and in the region immediately upstream of the start point of transcription, reveals tightly conserved elements embedded in an otherwise non-homologous sequence. These conserved elements include a 118-bp region that spans the mRNA start site, an internally repetitive (TAA)n region in the untranslated leader and a short repeated motif immediately upstream of the ATG codon that initiates the major open reading frame of the Ubx protein. Two other conserved elements were identified upstream of the transcription start site; both elements have structural features consistent with a role as recognition sites for regulatory proteins. ImagesFig. 2. PMID:16453766

  15. Beta-globin locus activation regions: conservation of organization, structure, and function.

    PubMed

    Li, Q L; Zhou, B; Powers, P; Enver, T; Stamatoyannopoulos, G

    1990-11-01

    The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function.

  16. Designing monitoring programs in an adaptive management context for regional multiple species conservation plans

    USGS Publications Warehouse

    Atkinson, A.J.; Trenham, P.C.; Fisher, R.N.; Hathaway, S.A.; Johnson, B.S.; Torres, S.G.; Moore, Y.C.

    2004-01-01

    critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.

  17. Mapping spatial pattern in biodiversity for regional conservation planning: where to from here?

    PubMed

    Ferrier, Simon

    2002-04-01

    Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be used as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping, derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. Although this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if congruence is poor between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by (1) more closely integrating biological and environmental data through predictive modeling, with increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and of varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that can be readily applied across data-poor regions.

  18. Characterization of Two Monoclonal Antibodies That Recognize Linker Region and Carboxyl Terminal Domain of Coronavirus Nucleocapsid Protein

    PubMed Central

    Zhu, Yunnuan; Shi, Hongyan; Chen, Jianfei; Shi, Da; Feng, Li

    2016-01-01

    The transmissible gastroenteritis virus (TGEV) nucleocapsid (N) protein plays important roles in the replication and translation of viral RNA. The present study provides the first description of two monoclonal antibodies (mAbs) (5E8 and 3D7) directed against the TGEV N protein linker region (LKR) and carboxyl terminal domain (CTD). The mAbs 5E8 and 3D7 reacted with native N protein in western blotting and immunofluorescence assay (IFA). Two linear epitopes, 189SVEQAVLAALKKLG202 and 246VTRFYGARSSSA257, located in the LKR and CTD of TGEV N protein, respectively, were identified after truncating the protein and applying a peptide scanning technique. Using mAb 5E8, we observed that the N protein was expressed in the cytoplasm during TGEV replication and that the protein could be immunoprecipitated from TGEV-infected PK-15 cells. The mAb 5E8 can be applied for different approaches to diagnosis of TGEV infection. In addition, the antibodies represent useful tools for investigating the antigenic properties of the N protein. PMID:27689694

  19. Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus).

    PubMed

    Ahrens, Collin W; James, Elizabeth A

    2016-05-01

    Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity. PMID:26865733

  20. Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus).

    PubMed

    Ahrens, Collin W; James, Elizabeth A

    2016-05-01

    Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity.

  1. Brandon RHA recognized for energy efficiency.

    PubMed

    Waddington, Kent; Neal, Gordon

    2002-01-01

    In a recent national competition recognizing leadership in energy efficiency and greenhouse gas education, Brandon Regional Health Authority was recognized for conscientious use of resources. PMID:12357581

  2. A regional perspective on the diversity and conservation of tropical Andean fishes.

    PubMed

    Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

    2011-02-01

    The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives.

  3. Auditory sequence processing reveals evolutionarily conserved regions of frontal cortex in macaques and humans

    PubMed Central

    Wilson, Benjamin; Kikuchi, Yukiko; Sun, Li; Hunter, David; Dick, Frederic; Smith, Kenny; Thiele, Alexander; Griffiths, Timothy D.; Marslen-Wilson, William D.; Petkov, Christopher I.

    2015-01-01

    An evolutionary account of human language as a neurobiological system must distinguish between human-unique neurocognitive processes supporting language and evolutionarily conserved, domain-general processes that can be traced back to our primate ancestors. Neuroimaging studies across species may determine whether candidate neural processes are supported by homologous, functionally conserved brain areas or by different neurobiological substrates. Here we use functional magnetic resonance imaging in Rhesus macaques and humans to examine the brain regions involved in processing the ordering relationships between auditory nonsense words in rule-based sequences. We find that key regions in the human ventral frontal and opercular cortex have functional counterparts in the monkey brain. These regions are also known to be associated with initial stages of human syntactic processing. This study raises the possibility that certain ventral frontal neural systems, which play a significant role in language function in modern humans, originally evolved to support domain-general abilities involved in sequence processing. PMID:26573340

  4. Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions.

    PubMed

    Tayal, Nitish; Choudhary, Preeti; Pandit, Shashi B; Sandhu, Kuljeet Singh

    2014-06-01

    Despite recent advances, it is yet not clear how intrinsically disordered regions in proteins recognize their targets without any defined structures. Short linear motifs had been proposed to mediate molecular recognition by disordered regions; however, the underlying structural prerequisite remains elusive. Moreover, the role of short linear motifs in DNA recognition has not been studied. We report a repertoire of short evolutionarily Conserved Recognition Elements (CoREs) in long intrinsically disordered regions, which have very distinct amino-acid propensities from those of known motifs, and exhibit a strong tendency to retain their three-dimensional conformations compared to adjacent regions. The majority of CoREs directly interact with the DNA in the available 3D structures, which is further supported by literature evidence, analyses of ΔΔG values of DNA-binding energies and threading-based prediction of DNA binding potential. CoREs were enriched in cancer-associated missense mutations, further strengthening their functional nature. Significant enrichment of glycines in CoREs and the preference of glycyl ϕ-Ψ values within the left-handed bridge range in the l-disallowed region of the Ramachandran plot suggest that Gly-to-nonGly mutations within CoREs might alter the backbone conformation and consequently the function, a hypothesis that we reconciled using available mutation data. We conclude that CoREs might serve as bait for DNA recognition by long disordered regions and that certain mutations in these peptides can disrupt their DNA binding potential and consequently the protein function. We further hypothesize that the preferred conformations of CoREs and of glycyl residues therein might play an important role in DNA binding. The highly ordered nature of CoREs hints at a therapeutic strategy to inhibit malicious molecular interactions using small molecules mimicking CoRE conformations.

  5. Human monoclonal antibody that recognizes the V3 region of human immunodeficiency virus gp120 and neutralizes the human T-lymphotropic virus type IIIMN strain.

    PubMed Central

    Scott, C F; Silver, S; Profy, A T; Putney, S D; Langlois, A; Weinhold, K; Robinson, J E

    1990-01-01

    We describe a human IgG1 monoclonal antibody (N701.9b) derived by Epstein-Barr virus transformation of B cells from a human immunodeficiency virus-seropositive asymptomatic donor. This antibody was shown to recognize the principal neutralizing domain contained within the V3 region of gp120 of the MN strain of human immunodeficiency virus and MN-like strains, as determined by binding to the PB-1 fragment of MN gp120 and to synthetic peptides corresponding to the V3 region of MN and related virus strains. The epitope identified by monoclonal antibody N701.9b was mapped to a segment of V3 containing at least 7 amino acids (amino acids 316-322), which is located in the "tip" and "right" side of the V3 loop of the MN strain. Furthermore, this antibody manifested potent type-specific fusion-inhibitory activity against the MN strain but not against the IIIB or RF virus strains. This antibody also neutralized four virus isolates that had MN-like V3 region sequences and failed to neutralize three other strains containing unrelated V3 region sequences. Our findings confirm that the V3 region stimulates type-specific neutralizing antibody during natural human immunodeficiency virus infection in humans. The potential clinical use of this antibody is discussed. PMID:1700435

  6. A Forty-Year Retrospective 1950-1990: The Metropolitan Toronto and Region Conservation Authority's Conservation Education Programmes.

    ERIC Educational Resources Information Center

    Carr, Allen Terry

    1996-01-01

    Recounts the growth of Conservation Authorities in Ontario from the first partnerships between schools and conservation in the 1950s, to the opening of a pioneer village, flood control dam, nature trails, and residential conservation education centers through the 1960s and 1970s. Increased public environmental concern sparked more growth in the…

  7. Effects of Conservation Policies on Forest Cover Change in Giant Panda Habitat Regions, China

    PubMed Central

    Li, Yu; Viña, Andrés; Yang, Wu; Chen, Xiaodong; Zhang, Jindong; Ouyang, Zhiyun; Liang, Zai; Liu, Jianguo

    2014-01-01

    After long periods of deforestation, forest transition has occurred globally, but the causes of forest transition in different countries are highly variable. Conservation policies may play important roles in facilitating forest transition around the world, including China. To restore forests and protect the remaining natural forests, the Chinese government initiated two nationwide conservation policies in the late 1990s -- the Natural Forest Conservation Program (NFCP) and the Grain-To-Green Program (GTGP). While some studies have discussed the environmental and socioeconomic effects of each of these policies independently and others have attributed forest recovery to both policies without rigorous and quantitative analysis, it is necessary to rigorously quantify the outcomes of these two conservation policies simultaneously because the two policies have been implemented at the same time. To fill the knowledge gap, this study quantitatively evaluated the effects of the two conservation policies on forest cover change between 2001 and 2008 in 108 townships located in two important giant panda habitat regions -- the Qinling Mountains region in Shaanxi Province and the Sichuan Giant Panda Sanctuary in Sichuan Province. Forest cover change was evaluated using a land-cover product (MCD12Q1) derived from the Moderate Resolution Imaging Spectroradiometer (MODIS). This product proved to be highly accurate in the study region (overall accuracy was ca. 87%, using 425 ground truth points collected in the field), thus suitable for the forest change analysis performed. Results showed that within the timeframe evaluated, most townships in both regions exhibited either increases or no changes in forest cover. After accounting for a variety of socioeconomic and biophysical attributes, an Ordinary Least Square (OLS) regression model suggests that the two policies had statistically significant positive effects on forest cover change after seven years of implementation, while

  8. 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

  9. Ecosystem service benefits of contrasting conservation strategies in a human-dominated region

    PubMed Central

    Eigenbrod, Felix; Anderson, Barbara J.; Armsworth, Paul R.; Heinemeyer, Andreas; Jackson, Sarah F.; Parnell, Mark; Thomas, Chris D.; Gaston, Kevin J.

    2009-01-01

    The hope among policy-makers and scientists alike is that conservation strategies designed to protect biodiversity also provide direct benefits to people by protecting other vital ecosystem services. The few studies that have examined the delivery of ecosystem services by existing conservation efforts have concentrated on large, ‘wilderness’-style biodiversity reserves. However, such reserves are not realistic options for densely populated regions. Here, we provide the first analyses that compare representation of biodiversity and three other ecosystem services across several contrasting conservation strategies in a human-dominated landscape (England). We show that small protected areas and protected landscapes (restrictive zoning) deliver high carbon storage and biodiversity, while existing incentive payment (agri-environment) schemes target areas that offer little advantage over other parts of England in terms of biodiversity, carbon storage and agricultural production. A fourth ecosystem service—recreation—is under-represented by all three strategies. Our findings are encouraging as they illustrate that restrictive zoning can play a major role in protecting natural capital assets in densely populated regions. However, trade-offs exist even among the four ecosystem services we considered, suggesting that a portfolio of conservation and sustainability investments will be needed to deliver both biodiversity and the other ecosystem services demanded by society. PMID:19474040

  10. CO{sub 2} emissions reduction using energy conservation measures: EPA Region IV`s experience

    SciTech Connect

    Berish, C.; Day, R.; Sibold, K.; Tiller, J.

    1994-12-31

    EPA Region 4 concluded in a recent comparative environmental risk evaluation that global climate change could substantially impact the Southeast. To address this risk, Region 4 developed an action plan to promote cost-effective pollution prevention and reduce greenhouse gas emissions, The regional plan contains programs that aye specific to Region 4 as well as geographic components of the national Climate Change Action Plan. Sources of carbon dioxide emissions were targeted for pollution prevention based on an energy model that allows the user to create energy efficiency scenarios in four sectors: residential, commercial, industrial, and transportation. Activities were selected using the modeled information on sector reduction potentials and resource and cost-effectiveness criteria. Given the high level of uncertainty associated with climate change projections, the programs developed are all cost effective, prevent pollution and/or result in sound adaptation policies. Currently, policy makers at national, regional, and local levels are deciding on what types of energy efficiency programs to implement. The region`s action plan is composed of several programs and approaches. The authors have developed implemented, and/or participated in the following: energy scenario model. EARTHWALK (residential energy conservation); energy conservation in affordable homes (new residences); Cool Communities Program (strategic tree planting and light colored surfaces); EPA`s Green Lights Program; WAVE (water conservation), the Plant Protection Center; QUEST TO SAVE THE EARTH (outreach tools); energy and water use planning for the 1996 Olympic Games, and planning for sea-level rise. Reviewing the practices of the above programs will be the focus of this paper.

  11. Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

    PubMed Central

    Platts, Adrian E.; Hazzouri, Khaled M.; Haudry, Annabelle; Blanchette, Mathieu; Wright, Stephen I.

    2014-01-01

    The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5′ and 3′ untranslated regions (UTRs). However, estimates of selection on noncoding regions conserved across the Brassicaceae family show strong signals of selection. Additionally, we see reductions in neutral diversity around functional substitutions in both coding and conserved noncoding regions, indicating recent selective sweeps at these sites. Finally, using expression data from leaf tissue we show that genes that are more highly expressed experience stronger negative selection but comparable levels of positive selection to lowly expressed genes. Overall, we observe widespread positive and negative selection in coding and regulatory regions, but our results also suggest that both positive and negative selection on plant noncoding sequence are considerably rarer than in animal genomes. PMID:25255320

  12. RapA2 Is a Calcium-binding Lectin Composed of Two Highly Conserved Cadherin-like Domains That Specifically Recognize Rhizobium leguminosarum Acidic Exopolysaccharides*

    PubMed Central

    Abdian, Patricia L.; Caramelo, Julio J.; Ausmees, Nora; Zorreguieta, Angeles

    2013-01-01

    In silico analyses have revealed a conserved protein domain (CHDL) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. A CHDL domain was shown to be present in RapA, a protein that is involved in autoaggregation of Rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. Structural similarity to cadherins suggested calcium-dependent oligomerization of CHDL domains as a mechanistic basis for RapA action. Here we show by circular dichroism spectroscopy, light scattering, isothermal titration calorimetry, and other methods that RapA2 from Rhizobium leguminosarum indeed exhibits a cadherin-like β-sheet conformation and that its proper folding and stability are dependent on the binding of one calcium ion per protein molecule. By further in silico analysis we also reveal that RapA2 consists of two CHDL domains and expand the range of CHDL-containing proteins in bacteria and archaea. However, light scattering assays at various concentrations of added calcium revealed that RapA2 formed neither homo-oligomers nor hetero-oligomers with RapB (a distinct CHDL protein), indicating that RapA2 does not mediate cellular interactions through a cadherin-like mechanism. Instead, we demonstrate that RapA2 interacts specifically with the acidic exopolysaccharides (EPSs) produced by R. leguminosarum in a calcium-dependent manner, sustaining a role of these proteins in the development of the biofilm matrix made of EPS. Because EPS binding by RapA2 can only be attributed to its two CHDL domains, we propose that RapA2 is a calcium-dependent lectin and that CHDL domains in various bacterial and archaeal proteins confer carbohydrate binding activity to these proteins. PMID:23235153

  13. Induction of a major histocompatibility complex class I-restricted cytotoxic T-lymphocyte response to a highly conserved region of human immunodeficiency virus type 1 (HIV-1) gp120 in seronegative humans immunized with a candidate HIV-1 vaccine.

    PubMed Central

    Johnson, R P; Hammond, S A; Trocha, A; Siliciano, R F; Walker, B D

    1994-01-01

    Efforts to induce broadly reactive immunity against human immunodeficiency virus type 1 (HIV-1) have been impaired by the extent of sequence variation exhibited by this lentivirus. Cytotoxic T lymphocytes (CTL) specific for other viruses such as influenza virus have been shown to mediate immunity against divergent viral strains, a property that is related to the ability of CTL to recognize processed antigen derived from conserved viral proteins. A recent candidate HIV-1 vaccine regimen has been described in which subjects receive a primary immunization with a recombinant vaccinia virus expressing gp160 and then a booster immunization with recombinant gp160. Volunteers immunized with this regimen have exhibited augmented humoral responses and have also developed CD4+ and CD8+ CTL specific for gp160. In this report, we have identified the epitopes recognized by CD4+ and CD8+ CTL obtained from two vaccines. An immunodominant CD8+ CTL response was HLA-A3.1 restricted and recognized a 10-amino-acid epitope (gp120/38-47) in a highly conserved region of gp120. CTL specific for the epitope gp120/38-47 were able to lyse targets sensitized with peptides corresponding to all known natural sequence variants in this region. In addition, other HLA class I-restricted CTL epitopes were identified in relatively conserved regions of gp120 and gp41, and CD4+ CTL were shown to recognize two different regions of gp120. Thus, in these two volunteers, immunization with a single strain of HIV-1 induced CD4+ and CD8+ CTL that are specific for multiple conserved regions of HIV-1 and would be expected to recognize a broad range of viral isolates. PMID:7908700

  14. Identification of a conserved sequence in the non-coding regions of many human genes.

    PubMed Central

    Donehower, L A; Slagle, B L; Wilde, M; Darlington, G; Butel, J S

    1989-01-01

    We have analyzed a sequence of approximately 70 base pairs (bp) that shows a high degree of similarity to sequences present in the non-coding regions of a number of human and other mammalian genes. The sequence was discovered in a fragment of human genomic DNA adjacent to an integrated hepatitis B virus genome in cells derived from human hepatocellular carcinoma tissue. When one of the viral flanking sequences was compared to nucleotide sequences in GenBank, more than thirty human genes were identified that contained a similar sequence in their non-coding regions. The sequence element was usually found once or twice in a gene, either in an intron or in the 5' or 3' flanking regions. It did not share any similarities with known short interspersed nucleotide elements (SINEs) or presently known gene regulatory elements. This element was highly conserved at the same position within the corresponding human and mouse genes for myoglobin and N-myc, indicating evolutionary conservation and possible functional importance. Preliminary DNase I footprinting data suggested that the element or its adjacent sequences may bind nuclear factors to generate specific DNase I hypersensitive sites. The size, structure, and evolutionary conservation of this sequence indicates that it is distinct from other types of short interspersed repetitive elements. It is possible that the element may have a cis-acting functional role in the genome. Images PMID:2536922

  15. Rewilding the tropics, and other conservation translocations strategies in the tropical Asia-Pacific region.

    PubMed

    Louys, Julien; Corlett, Richard T; Price, Gilbert J; Hawkins, Stuart; Piper, Philip J

    2014-11-01

    Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of 'at-risk' species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large-scale ecological restoration and species introductions. The term 'rewilding' has come to apply to this large-scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges-but outside historical ranges-are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large-bodied taxa in tropical Asia-Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as 'endangered' or 'critically endangered' by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian-Pacific tropics remains

  16. Rewilding the tropics, and other conservation translocations strategies in the tropical Asia-Pacific region

    PubMed Central

    Louys, Julien; Corlett, Richard T; Price, Gilbert J; Hawkins, Stuart; Piper, Philip J

    2014-01-01

    Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at-risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large-scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large-scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large-bodied taxa in tropical Asia-Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian

  17. Conservation in metropolitan regions: assessing trends and threats of urban development and climate change

    NASA Astrophysics Data System (ADS)

    Thorne, J. H.; Santos, M. J.; Bjorkman, J.

    2011-12-01

    Two global challenges to successful conservation are urban expansion and climate change. Rapid urban growth threatens biodiversity and associated ecosystem services, while climate change may make currently protected areas unsuitable for species that exist within them. We examined three measures of landscape change for 8800 km2 of the San Francisco Bay metropolitan region over 80 years past and future: urban growth, protected area establishment, and natural vegetation type extents. The Bay Area is a good test bed for conservation assessment of the impacts of temporal and spatial of urban growth and land cover change. The region is geographically rather small, with over 40% of its lands already dedicated to protected park and open space lands, they are well-documented, and, the area has had extensive population growth in the past and is projected to continue to grow. The ten-county region within which our study area is a subset has grown from 1.78 million people in 1930, to 6.97 million in 2000 and is estimated to grow to 10.94 million by 2050. With such an influx of people into a small geographic area, it is imperative to both examine the past urban expansion and estimate how the future population will be accommodated into the landscape. We quantify these trends to assess conservation 'success' through time. We used historical and current landcover maps to assess trend, and a GIS-based urban modeling (UPlan) to assess future urban growth impacts in the region, under three policy scenarios- business as usual, smart growth, and urban redevelopment. Impacts are measured by the amount of open space targeted by conservation planners in the region that will be urbanized under each urban growth policy. Impacts are also measured by estimates of the energy consumption projected for each of the scenarios on household and business unit level. The 'business as usual' and 'smart growth' scenarios differed little in their impacts to targeted conservation lands, because so little

  18. Building on IUCN regional red lists to produce lists of species of conservation priority: a model with Irish bees.

    PubMed

    Fitzpatrick, Una; Murray, Tomás E; Paxton, Robert J; Brown, Mark J F

    2007-10-01

    A World Conservation Union (IUCN) regional red list is an objective assessment of regional extinction risk and is not the same as a list of conservation priority species. Recent research reveals the widespread, but incorrect, assumption that IUCN Red List categories represent a hierarchical list of priorities for conservation action. We developed a simple eight-step priority-setting process and applied it to the conservation of bees in Ireland. Our model is based on the national red list but also considers the global significance of the national population; the conservation status at global, continental, and regional levels; key biological, economic, and societal factors; and is compatible with existing conservation agreements and legislation. Throughout Ireland, almost one-third of the bee fauna is threatened (30 of 100 species), but our methodology resulted in a reduced list of only 17 priority species. We did not use the priority species list to broadly categorize species to the conservation action required; instead, we indicated the individual action required for all threatened, near-threatened, and data-deficient species on the national red list based on the IUCN's conservation-actions template file. Priority species lists will strongly influence prioritization of conservation actions at national levels, but action should not be exclusive to listed species. In addition, all species on this list will not necessarily require immediate action. Our method is transparent, reproducible, and readily applicable to other taxa and regions.

  19. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    SciTech Connect

    Loots, G; Ovcharenko, I

    2006-08-08

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

  20. Hot Spots and Hot Times: Wildlife Road Mortality in a Regional Conservation Corridor.

    PubMed

    Garrah, Evelyn; Danby, Ryan K; Eberhardt, Ewen; Cunnington, Glenn M; Mitchell, Scott

    2015-10-01

    Strategies to reduce wildlife road mortality have become a significant component of many conservation efforts. However, their success depends on knowledge of the temporal and spatial patterns of mortality. We studied these patterns along the 1000 Islands Parkway in Ontario, Canada, a 37 km road that runs adjacent to the St. Lawrence River and bisects the Algonquin-to-Adirondacks international conservation corridor. Characteristics of all vertebrate road kill were recorded during 209 bicycle surveys conducted from 2008 to 2011. We estimate that over 16,700 vertebrates are killed on the road from April to October each year; most are amphibians, but high numbers of birds, mammals, and reptiles were also found, including six reptiles considered at-risk in Canada. Regression tree analysis was used to assess the importance of seasonality, weather, and traffic on road kill magnitude. All taxa except mammals exhibited distinct temporal peaks corresponding to phases in annual life cycles. Variations in weather and traffic were only important outside these peak times. Getis-Ord analysis was used to identify spatial clusters of mortality. Hot spots were found in all years for all taxa, but locations varied annually. A significant spatial association was found between multiyear hot spots and wetlands. The results underscore the notion that multi-species conservation efforts must account for differences in the seasonality of road mortality among species and that multiple years of data are necessary to identify locations where the greatest conservation good can be achieved. This information can be used to inform mitigation strategies with implications for conservation at regional scales. PMID:26108412

  1. Hot Spots and Hot Times: Wildlife Road Mortality in a Regional Conservation Corridor

    NASA Astrophysics Data System (ADS)

    Garrah, Evelyn; Danby, Ryan K.; Eberhardt, Ewen; Cunnington, Glenn M.; Mitchell, Scott

    2015-10-01

    Strategies to reduce wildlife road mortality have become a significant component of many conservation efforts. However, their success depends on knowledge of the temporal and spatial patterns of mortality. We studied these patterns along the 1000 Islands Parkway in Ontario, Canada, a 37 km road that runs adjacent to the St. Lawrence River and bisects the Algonquin-to-Adirondacks international conservation corridor. Characteristics of all vertebrate road kill were recorded during 209 bicycle surveys conducted from 2008 to 2011. We estimate that over 16,700 vertebrates are killed on the road from April to October each year; most are amphibians, but high numbers of birds, mammals, and reptiles were also found, including six reptiles considered at-risk in Canada. Regression tree analysis was used to assess the importance of seasonality, weather, and traffic on road kill magnitude. All taxa except mammals exhibited distinct temporal peaks corresponding to phases in annual life cycles. Variations in weather and traffic were only important outside these peak times. Getis-Ord analysis was used to identify spatial clusters of mortality. Hot spots were found in all years for all taxa, but locations varied annually. A significant spatial association was found between multiyear hot spots and wetlands. The results underscore the notion that multi-species conservation efforts must account for differences in the seasonality of road mortality among species and that multiple years of data are necessary to identify locations where the greatest conservation good can be achieved. This information can be used to inform mitigation strategies with implications for conservation at regional scales.

  2. Hot Spots and Hot Times: Wildlife Road Mortality in a Regional Conservation Corridor.

    PubMed

    Garrah, Evelyn; Danby, Ryan K; Eberhardt, Ewen; Cunnington, Glenn M; Mitchell, Scott

    2015-10-01

    Strategies to reduce wildlife road mortality have become a significant component of many conservation efforts. However, their success depends on knowledge of the temporal and spatial patterns of mortality. We studied these patterns along the 1000 Islands Parkway in Ontario, Canada, a 37 km road that runs adjacent to the St. Lawrence River and bisects the Algonquin-to-Adirondacks international conservation corridor. Characteristics of all vertebrate road kill were recorded during 209 bicycle surveys conducted from 2008 to 2011. We estimate that over 16,700 vertebrates are killed on the road from April to October each year; most are amphibians, but high numbers of birds, mammals, and reptiles were also found, including six reptiles considered at-risk in Canada. Regression tree analysis was used to assess the importance of seasonality, weather, and traffic on road kill magnitude. All taxa except mammals exhibited distinct temporal peaks corresponding to phases in annual life cycles. Variations in weather and traffic were only important outside these peak times. Getis-Ord analysis was used to identify spatial clusters of mortality. Hot spots were found in all years for all taxa, but locations varied annually. A significant spatial association was found between multiyear hot spots and wetlands. The results underscore the notion that multi-species conservation efforts must account for differences in the seasonality of road mortality among species and that multiple years of data are necessary to identify locations where the greatest conservation good can be achieved. This information can be used to inform mitigation strategies with implications for conservation at regional scales.

  3. Understanding Drought and Regional Conservation Efforts on Urban Ecohydrology in Southern California

    NASA Astrophysics Data System (ADS)

    Hogue, T. S.

    2015-12-01

    Cities in the western U.S. are under increasing pressure to reduce the demand of imported water through increasing conservation efforts, altering non-native landscapes, and enhancing local water supplies. The State of California adopted emergency regulations implementing a mandatory 25% statewide reduction in potable urban water use and agricultural restrictions have also been enacted. The complexities in urban water flows and lack of granular data make understanding the impact of conservation and demand change on regional ecohydrology difficult. This presentation highlights ongoing work to better understand the coupling between humans, water and ecosystems in semi-arid urban cities, using metropolitan southern California as a case study. We evaluate historical and contemporary ecohydrologic behavior and human impacts through intensive data collection, remote sensing and high resolution modeling. The change in outdoor irrigation rates due to recent conservation measures (2008-2010) has resulted in overall decreased greenness and reduced dry season streamflow; however significant variability in conservation response is observed. Groundwater recharge, artificially supported by landscape irrigation, is also being impacted. In general, anthropogenic water fluxes (irrigation, pipe leakage, spreading grounds) are not parameterized in hydrologic and land surface models applied over urban areas. Inclusion of landscape irrigation significantly improves neighborhood scale simulations of evaporative fluxes and land surface temperatures and results in shifts in the energy partitioning. The cooling effects of irrigation on daily air temperatures has the largest influence over low intensity residential areas, with an average 2°C decrease observed in coupled model simulations (WRF-Noah-UCM). Ultimately, we strive to improve predictions of human-water interactions in semi-arid cities to better understand the effectiveness and impacts of ongoing drought and conservation efforts

  4. Babesia gibsoni internal transcribed spacer 1 region is highly conserved amongst isolates from dogs across Japan

    PubMed Central

    LIU, Mingming; CAO, Shinuo; VUDRIKO, Patrick; SUZUKI, Hiroshi; SOMA, Takehisa; XUAN, Xuenan

    2016-01-01

    Babesia gibsoni is a tick-borne apicomplexan parasite of dogs that often causes fever and hemolytic anemia with highly variable clinical outcome. In this study, we sequenced the 254bp Internal Transcribed Spacer 1 region (ITS1) of 54 B. gibsoni isolates from 14 different geographical regions of Japan. The 54 isolates shared high sequence identity with each other and with B. gibsoni isolates reported in GenBank database (97.2–100%). Consistent with previous reports, phylogenetic analysis showed that B. gibsoni isolates from Japan formed the same clade with those from U.S.A., Australia, India and Taiwan. Our finding indicates that B. gibsoni ITS1 region is highly conserved among isolates from dogs in Japan, making it a useful genetic marker for molecular epidemiology of the parasite. PMID:26806537

  5. Discovery of functional non-coding conserved regions in the α-synuclein gene locus

    PubMed Central

    Sterling, Lori; Walter, Michael; Ting, Dennis; Schüle, Birgitt

    2014-01-01

    Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein ( SNCA) gene have consistently been shown to be associated with Parkinson’s disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in the SNCA genomic region regulate expression of SNCA, and that SNPs in these regions could be functionally modulating the expression of SNCA, thus contributing to neuronal demise and predisposing to Parkinson’s disease. In a pair-wise comparison of a 206kb genomic region encompassing the SNCA gene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of the SNCA gene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of the SNCA gene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream of SNCA had a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity. Our results demonstrate that the SNCA gene contains cis-regulatory regions that might regulate the transcription and expression of SNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson’s disease-associated SNPs and its function in the disease process. PMID:25566351

  6. Discovery of functional non-coding conserved regions in the α-synuclein gene locus.

    PubMed

    Sterling, Lori; Walter, Michael; Ting, Dennis; Schüle, Birgitt

    2014-01-01

    Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein ( SNCA) gene have consistently been shown to be associated with Parkinson's disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in the SNCA genomic region regulate expression of SNCA, and that SNPs in these regions could be functionally modulating the expression of SNCA, thus contributing to neuronal demise and predisposing to Parkinson's disease. In a pair-wise comparison of a 206kb genomic region encompassing the SNCA gene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of the SNCA gene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of the SNCA gene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream of SNCA had a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity. Our results demonstrate that the SNCA gene contains cis-regulatory regions that might regulate the transcription and expression of SNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson's disease-associated SNPs and its function in the disease process.

  7. Water Use Conservation Scenarios for the Mississippi Delta Using an Existing Regional Groundwater Flow Model

    NASA Astrophysics Data System (ADS)

    Barlow, J. R.; Clark, B. R.

    2010-12-01

    The alluvial plain in northwestern Mississippi, locally referred to as the Delta, is a major agricultural area, which contributes significantly to the economy of Mississippi. Land use in this area can be greater than 90 percent agriculture, primarily for growing catfish, corn, cotton, rice, and soybean. Irrigation is needed to smooth out the vagaries of climate and is necessary for the cultivation of rice and for the optimization of corn and soybean. The Mississippi River Valley alluvial (MRVA) aquifer, which underlies the Delta, is the sole source of water for irrigation, and over use of the aquifer has led to water-level declines, particularly in the central region. The Yazoo-Mississippi-Delta Joint Water Management District (YMD), which is responsible for water issues in the 17-county area that makes up the Delta, is directing resources to reduce the use of water through conservation efforts. The U.S. Geological Survey (USGS) recently completed a regional groundwater flow model of the entire Mississippi embayment, including the Mississippi Delta region, to further our understanding of water availability within the embayment system. This model is being used by the USGS to assist YMD in optimizing their conservation efforts by applying various water-use reduction scenarios, either uniformly throughout the Delta, or in focused areas where there have been large groundwater declines in the MRVA aquifer.

  8. Criteria for protected areas and other conservation measures in the Antarctic region

    SciTech Connect

    Angel, M.V.

    1987-01-01

    The Antarctic region is threatened by three major anthropogenic influences: climatic change brought about by increases in atmospheric carbon dioxide, the effects of persistent pollutants carried into the region via atmosphere and ocean, and the increase in Man's activities. These include radioactive wastes, organochlorides, freons, PCBs and heavy metals. Vulnerable ecosystems can be considered as those which are under direct pressure from Man's activities, whereas fragile ecosystems are the more likely to suffer irreversible change when perturbed, but are not necessarily threatened at present. Three of the main habitat types, terrestrial, inland waters, and islands, are likely to be fragile. However, all these can be conserved reasonably adequately with a system of protected and managed areas, so long as the area covered is adequate and representative. The fourth habitat type, the oceanic ecosystem, contains few fragile elements because it is dominated by the highly dynamic physical oceanic processes. Elements of the ecosystem are vulnerable to further exploitation, and although only the whales and some of the fish stocks can be regarded as fragile, there is considerably uncertainty as what synergistic effect exploitation of apparently key elements of the ecosystem, such as the krill, will have on other important components of the communities. The highly dynamic structure of oceanic environments renders the concept of conservation based on limited protected areas developed for terrestrial environments ineffective in the majority of marine environments. Instead the whole marine environment of the Antarctic region must be considered to be a single entity and managed as such.

  9. An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

    PubMed Central

    Sweeney, R; Chen, L; Yao, M C

    1994-01-01

    Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably. Images PMID:8196658

  10. In the QTL region surrounding porcine MHC, gene order is conserved with human genome.

    PubMed

    Genêt, C; Renard, C; Cabau, C; Rogel-Gaillard, C; Gellin, J; Milan, D

    2001-03-01

    On the porcine genome, the region surrounding the Major Histocompatibility Complex, also called Swine Leukocyte Antigens (SLA), is of particular interest not only owing to itq role in the control of immune response, but also because of its influence on many traits such as growth, fatness, and meat quality. To help in the identification of responsible genes, detailed comparative maps of the MHC region in mammalian species and powerful mapping tools allowing accurate ordering of genes and markers in this region are needed. In this report, we describe the use of the recently developed IMpRH radiation hybrid panel, to construct a higher density radiation hybrid map of swine Sscr 7p-q12, containing 23 additional loci. Our results show that the gene order is conserved between the two MHC-containing regions, even if an inversion is observed above the QTL region in the region containing DEK, SCA1, and EDN1 genes. The framework map produced shows that the IMpRH panel permits the ordering of genes and markers in the three MHC classes and would thus allow accurate localization of ESTs and candidate genes. PMID:11252175

  11. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

    PubMed

    Dufresnes, Christophe; Wassef, Jérôme; Ghali, Karim; Brelsford, Alan; Stöck, Matthias; Lymberakis, Petros; Crnobrnja-Isailovic, Jelka; Perrin, Nicolas

    2013-11-01

    Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies. PMID:24102652

  12. The Association Between Biological Subtype and Isolated Regional Nodal Failure After Breast-Conserving Therapy

    SciTech Connect

    Wo, Jennifer Y.; Taghian, Alphonse G.; Nguyen, Paul L.; Raad, Rita Abi; Sreedhara, Meera B.A.; Bellon, Jennifer R.; Wong, Julia S.; Gadd, Michele A.; Smith, Barbara L.; Harris, Jay R.

    2010-05-01

    Purpose: To evaluate the risk of isolated regional nodal failure (RNF) among women with invasive breast cancer treated with breast-conserving surgery (BCS) and radiation therapy (RT) and to determine factors, including biological subtype, associated with RNF. Methods and Materials: We retrospectively studied 1,000 consecutive women with invasive breast cancer who received breast-conserving surgery and RT from 1997 through 2002. Ninety percent of patients received adjuvant systemic therapy; none received trastuzumab. Sentinel lymph node biopsy was done in 617 patients (62%). Of patients with one to three positive nodes, 34% received regional nodal irradiation (RNI). Biological subtype classification into luminal A, luminal B, HER-2, and basal subtypes was based on estrogen receptor status-, progesterone receptor status-, and HER-2-status of the primary tumor. Results: Median follow-up was 77 months. Isolated RNF occurred in 6 patients (0.6%). On univariate analysis, biological subtype (p = 0.0002), lymph node involvement (p = 0.008), lymphovascular invasion (p = 0.02), and Grade 3 histology (p = 0.01) were associated with significantly higher RNF rates. Compared with luminal A, the HER-2 (p = 0.01) and basal (p = 0.08) subtypes were associated with higher RNF rates. The 5-year RNF rate among patients with one to three positive nodes treated with tangents alone was 2.4%; we could not identify a subset of these patients with a substantial risk of RNF. Conclusions: Isolated RNF is a rare occurrence after breast-conserving therapy. Patients with the HER-2 (not treated with trastuzumab) and basal subtypes appear to be at higher risk of developing RNF although this risk is not high enough to justify the addition of RNI. Low rates of RNF in patients with one to three positive nodes suggest that tangential RT without RNI is reasonable in most patients.

  13. Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.

    PubMed

    Yau, Anthony C Y; Tuncel, Jonatan; Haag, Sabrina; Norin, Ulrika; Houtman, Miranda; Padyukov, Leonid; Holmdahl, Rikard

    2016-06-28

    Genome-wide association studies have revealed many genetic loci associated with complex autoimmune diseases. In rheumatoid arthritis (RA), the MHC gene HLA-DRB1 is the strongest candidate predicting disease development. It has been suggested that other immune-regulating genes in the MHC contribute to the disease risk, but this contribution has been difficult to show because of the strong linkage disequilibrium within the MHC. We isolated genomic regions in the form of congenic fragments in rats to test whether there are additional susceptibility loci in the MHC. By both congenic mapping in inbred strains and SNP typing in wild rats, we identified a conserved, 33-kb large haplotype Ltab-Ncr3 in the MHC-III region, which regulates the onset, severity, and chronicity of arthritis. The Ltab-Ncr3 haplotype consists of five polymorphic immunoregulatory genes: Lta (lymphotoxin-α), Tnf, Ltb (lymphotoxin-β), Lst1 (leukocyte-specific transcript 1), and Ncr3 (natural cytotoxicity-triggering receptor 3). Significant correlation in the expression of the Ltab-Ncr3 genes suggests that interaction of these genes may be important in keeping these genes clustered together as a conserved haplotype. We studied the arthritis association and the spliceo-transcriptome of four different Ltab-Ncr3 haplotypes and showed that higher Ltb and Ncr3 expression, lower Lst1 expression, and the expression of a shorter splice variant of Lst1 correlate with reduced arthritis severity in rats. Interestingly, patients with mild RA also showed higher NCR3 expression and lower LST1 expression than patients with severe RA. These data demonstrate the importance of a conserved haplotype in the regulation of complex diseases such as arthritis. PMID:27303036

  14. Rational sub-division of plant trypanosomes (Phytomonas spp.) based on minicircle conserved region analysis.

    PubMed

    Sturm, Nancy R; Dollet, Michel; Lukes, Julius; Campbell, David A

    2007-09-01

    The sequences of minicircle conserved regions from various plant trypanosomatids have been determined and analyzed. The goal of this study was to add another tool to the arsenal of molecular probes for distinguishing between the different trypanosomatids occurring in plants: systemic trypanosomatids multiplying in the sap, those from the laticiferous tubes, and those developing in fruits, seeds or flowers but not in the plant itself and that are frequently considered as opportunistic insect trypanosomatids. As some plant intraphloemic trypanosomatids are the causative agents of important diseases, a clear definition of the different types of trypanosomatids is critical. The conserved region of the mitochondrial minicircle provides several specific features in a small sequence region containing three functionally elements required for minicircle replication. Trees generated from the analysis recapitulated trees drawn from analyses of isoenzymes, RAPD, and particular gene sequences, supporting the validity of the small region used in this work. Three groups of isolates were significant and in accordance with previous work. The peculiarity of phloem-restricted trypanosomatids associated with wilts of coconut and oil palm in Latin America - group H - is confirmed. In agreement with previous studies on their biological and serological properties the results highlighted this group called 'phloemicola'. It always differentiated from all other latex and fruit isolates or opportunistic trypanosomatids, like insect trypanosomatids. We can assert that phloemicola is the only well-defined taxon among all plant trypanosomatids. A group of non-pathogenic latex isolates from South American euphorbs (G), and a heterogenous group (A) including one fruit, one possible latex and one insect isolate are clearly distinct groups. The group of Mediterranean isolates from latex (D), even with a low boostrap, stood out well from other groups. The remainder of the isolates fell into a

  15. Ranking European regions as providers of structural riparian corridors for conservation and management purposes

    NASA Astrophysics Data System (ADS)

    Clerici, Nicola; Vogt, Peter

    2013-04-01

    Riparian zones are of utmost importance in providing a wide range of ecological and societal services. Among these, their role in maintaining landscape connectivity through ecological corridors for animals and plants is of major interest from a conservation and management perspective. This paper describes a methodology to identify European regions as providers of structural riparian corridors, and to rank them with reference to conservation priority. Physical riparian connectors among core habitat patches are identified through a recent segmentation technique, the Morphological Spatial Pattern Analysis. A multi-scale approach is followed by considering different edge distances to identify core and peripheral habitats for a range of hypothetical species. The ranking is performed using a simple set of indices that take into account the degree of environmental pressure and the presence of land protection schemes. An example for environmental reporting is carried out using European administrative regions and major rivers to summarize indices value. The approach is based on freely available software and simple metrics which can be easily reproduced in a GIS environment.

  16. Interactions between the Conserved Hydrophobic Region of the Prion Protein and Dodecylphosphocholine Micelles*

    PubMed Central

    Sauvé, Simon; Buijs, Daniel; Gingras, Geneviève; Aubin, Yves

    2012-01-01

    The three-dimensional structure of PrP110–136, a peptide encompassing the conserved hydrophobic region of the human prion protein, has been determined at high resolution in dodecylphosphocholine micelles by NMR. The results support the conclusion that the CtmPrP, a transmembrane form of the prion protein, adopts a different conformation than the reported structures of the normal prion protein determined in solution. Paramagnetic relaxation enhancement studies with gadolinium-diethylenetriaminepentaacetic acid indicated that the conserved hydrophobic region peptide is not inserted symmetrically in the micelle, thus suggesting the presence of a guanidium-phosphate ion pair involving the side chain of the terminal arginine and the detergent headgroup. Titration of dodecylphosphocholine into a solution of PrP110–136 revealed the presence of a surface-bound species. In addition, paramagnetic probes located the surface-bound peptide somewhere below the micelle-water interface when using the inserted helix as a positional reference. This localization of the unknown population would allow a similar ion pair interaction. PMID:22128151

  17. Spatial genetic structure and regional demography in the southern torrent salamander: Implications for conservation and management

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Wagner, R.S.

    2006-01-01

    The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

  18. Northwest Climate Science Center: Integrating Regional Research, Conservation and Natural Resource Management

    NASA Astrophysics Data System (ADS)

    Mote, P.; Bisbal, G.

    2012-12-01

    The Northwest Climate Science Center (NW CSC) was established in 2010, among the first three of eight regional Climate Science Centers created by the Department of the Interior (DOI). The NW CSC is supported by an academic consortium (Oregon State University, University of Idaho, and the University of Washington), which has the capacity to generate and coordinate decision-relevant science related to climate, thus serving stakeholders across the Pacific Northwest region. The NW CSC has overlapping boundaries with three Landscape Conservation Cooperatives (LCCs): the Great Northern, the Great Basin, and the North Pacific. Collaboration between the NW CSC and these three LCCs addresses the highest priority regional climate science needs of Northwest natural and cultural resource managers. Early in 2012, the NW CSC released its first Strategic Plan for the period 2012-2015. The plan offers a practical blueprint for operation and describes five core services that the NW CSC provides to the Northwest community. These core services emphasize (a) bringing together the regional resource management and science communities to calibrate priorities and ensure efficient integration of climate science resources and tools when addressing practical issues of regional significance; (b) developing and implementing a stakeholder-driven science agenda which highlights the NW CSC's regional leadership in generating scenarios of the future environment of the NW; (c) supporting and training graduate students at the three consortium universities, including through an annual 'Climate science boot camp'; (d) providing a platform for effective climate-change-related communication among scientists, resource managers, and the general public; and (e) national leadership in data management and climate scenario development.

  19. Conserving Prairie Pothole Region wetlands and surrounding grasslands: evaluating effects on amphibians

    USGS Publications Warehouse

    Mushet, David M.; Neau, Jordan L.

    2014-01-01

    The maintenance of viable and genetically diverse populations of amphibians in the Prairie Pothole Region of the United States depends on upland as well as wetland over-wintering and landscape level habitat features. Prairie pothole wetlands provide important amphibian breeding habitat while grasslands surrounding these wetlands provide foraging habitat for adults, overwintering habitat for some species, and important connectivity among breeding wetlands. Grasslands surrounding wetlands were found to be especially important for wood frogs and northern leopard frogs, while croplands dominated habitat utilized by Great Plains toads and Woodhouse’s toads. Habitat suitability mapping highlighted (1) the influence of deep-water overwintering wetlands on suitable habitat for four of five anuran species encountered; (2) the lack of overlap between areas of core habitat for both the northern leopard frog and wood frog compared to the core habitat for both toad species; and (3) the importance of conservation programs in providing grassland components of northern leopard frog and wood frog habitat. Currently, there are approximately 7.2 million acres (2.9 million hectares, ha) of habitat in the PPR identified as suitable for amphibians. WRP and CRP wetland and grassland habitats accounted for approximately 1.9 million acres (0.75 million ha) or 26 percent of this total area. Continued loss of amphibian habitat resulting from an ongoing trend of returning PPR conservation lands to crop production, will likely have significant negative effects on the region’s ability to maintain amphibian biodiversity. Conversely, increases in conservation wetlands and surrounding grasslands on the PPR landscape have great potential to positively influence the region’s amphibian populations.

  20. Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences.

    PubMed

    Hahn, C S; Hahn, Y S; Rice, C M; Lee, E; Dalgarno, L; Strauss, E G; Strauss, J H

    1987-11-01

    We have isolated a cDNA clone after reverse transcription of the genomic RNA of Asibi yellow fever virus whose structure suggests it was formed by self-priming from a 3'-terminal hairpin of 87 nucleotides in the genomic RNA. We have also isolated a clone from cDNA made to Murray Valley encephalitis virus RNA that also appears to have arisen by self-priming from a 3'-terminal structure very similar or identical to that of yellow fever. In addition, 3'-terminal sequencing of the S1 strain of dengue 2 RNA shows that this RNA is also capable of forming a 3'-terminal hairpin of 79 nucleotides. Furthermore, we have identified two 20-nucleotide sequence elements which are present in the 3' untranslated region of all three viruses; one of these sequence elements is repeated in Murray Valley encephalitis and dengue 2 RNA but not in yellow fever RNA. In all three viruses, which represent the three major serological subgroups of the mosquito-borne flaviviruses, the 3'-proximal conserved sequence element, which is found immediately adjacent to the potential 3'-terminal hairpin, is complementary to another conserved domain near the 5' end of the viral RNAs, suggesting that flavivirus RNAs can cyclize (calculated delta G less than -11 kcal; 1 kcal = 4.184 kJ).

  1. The lncRNA SLNCR1 mediates melanoma invasion through a conserved SRA1-like region

    PubMed Central

    Schmidt, Karyn; Joyce, Cailin E.; Buquicchio, Frank; Brown, Adam; Ritz, Justin; Distel, Robert J.; Yoon, Charles H.; Novina, Carl D.

    2016-01-01

    SUMMARY Long non-coding RNAs (lncRNAs) have been implicated in numerous physiological processes and diseases, most notably cancers. However, little is known about the mechanism of many functional lncRNAs. We identified an abundantly-expressed lncRNA associated with decreased melanoma patient survival. Increased expression of this lncRNA, SLNCR1, mediates melanoma invasion through a highly-conserved sequence similar to the lncRNA SRA1. Using a sensitive technique we term RATA (RNA-associated transcription factor array), we show that the brain-specific homeobox protein 3a (Brn3a) and the androgen receptor (AR) bind within and adjacent to SLNCR1’s conserved region, respectively. SLNCR1, AR, and Brn3a are specifically required for transcriptional activation of matrix metalloproteinase 9 (MMP9) and increased melanoma invasion. Our observations directly link AR to melanoma invasion, possibly explaining why males experience more melanoma metastases and have an overall lower survival as compared to females. PMID:27210747

  2. Identification and characterization of conserved and variable regions of lime witches' broom phytoplasma genome.

    PubMed

    Siampour, Majid; Izadpanah, Keramatollah; Marzachi, Cristina; Salehi Abarkoohi, Mohammad

    2015-09-01

    Several segments (∼20  kbp) of the lime witches' broom (LWB) phytoplasma genome (16SrII group) were sequenced and analysed. A 5.7  kbp segment (LWB-C) included conserved genes whose phylogenetic tree was consistent with that generated using 16S rRNA genes. Another 6.4  kbp LWB phytoplasma genome segment (LWB-NC) was structurally similar to the putative mobile unit or sequence variable mosaic genomic region of phytoplasmas, although it represented a new arrangement of genes or pseudogenes such as phage-related protein genes and tra5 insertion sequences. Sequence- and phylogenetic-based evidence suggested that LWB-NC is a genomic region which includes horizontally transferred genes and could be regarded as a hot region to incorporate more foreign genes into the genome of LWB phytoplasma. The presence of phylogenetically related fragments of retroelements was also verified in the LWB phytoplasma genome. Putative intragenomic retrotransposition or retrohoming of these elements might have been determinant in shaping and manipulating the LWB phytoplasma genome. Altogether, the results of this study suggested that the genome of LWB phytoplasma is colonized by a variety of genes that have been acquired through horizontal gene transfer events, which may have further affected the genome through intragenomic mobility and insertion at cognate or incognate sites. Some of these genes are expected to have been involved in the development of features specific to LWB phytoplasma.

  3. How to Maximally Support Local and Regional Biodiversity in Applied Conservation? Insights from Pond Management

    PubMed Central

    Lemmens, Pieter; Mergeay, Joachim; De Bie, Tom; Van Wichelen, Jeroen; De Meester, Luc; Declerck, Steven A. J.

    2013-01-01

    Biodiversity and nature values in anthropogenic landscapes often depend on land use practices and management. Evaluations of the association between management and biodiversity remain, however, comparatively scarce, especially in aquatic systems. Furthermore, studies also tend to focus on a limited set of organism groups at the local scale, whereas a multi-group approach at the landscape scale is to be preferred. This study aims to investigate the effect of pond management on the diversity of multiple aquatic organism groups (e.g. phytoplankton, zooplankton, several groups of macro-invertebrates, submerged and emergent macrophytes) at local and regional spatial scales. For this purpose, we performed a field study of 39 shallow man-made ponds representing five different management types. Our results indicate that fish stock management and periodic pond drainage are crucial drivers of pond biodiversity. Furthermore, this study provides insight in how the management of eutrophied ponds can contribute to aquatic biodiversity. A combination of regular draining of ponds with efforts to keep ponds free of fish seems to be highly beneficial for the biodiversity of many groups of aquatic organisms at local and regional scales. Regular draining combined with a stocking of fish at low biomass is also preferable to infrequent draining and lack of fish stock control. These insights are essential for the development of conservation programs that aim long-term maintenance of regional biodiversity in pond areas across Europe. PMID:23951328

  4. Ancient conserved regions in new gene sequences and the protein databases

    SciTech Connect

    Green, P.; Hillier, L.; Waterston, R. ); Lipman, D.; States, D.; Claverie, J.M. )

    1993-03-19

    Sets of new gene sequences from human, nematode, and yeast were compared with each other and with a set of Escherichia coli genes in order to detect ancient evolutionarily conserved regions (ACRs) in the encoded proteins. Nearly all of the ACRs so identified were found to be homologous to sequences in the protein databases. This suggests that currently known proteins may already include representatives of most ACRs and that new sequences not similar to any database sequence are unlikely to contain ACRs. Preliminary analyses indicate that moderately expressed genes may be more likely to contain ACRs than rarely expressed genes. It is estimated that there are fewer than 900 ACRs in all. 20 refs., 2 figs., 4 tabs.

  5. Illicit crops and armed conflict as constraints on biodiversity conservation in the Andes region.

    PubMed

    Fjeldså, Jon; Alvarez, María D; Lazcano, Juan Mario; León, Blanca

    2005-05-01

    Coca, once grown for local consumption in the Andes, is now produced for external markets, often in areas with armed conflict. Internationally financed eradication campaigns force traffickers and growers to constantly relocate, making drug-related activities a principal cause of forest loss. The impact on biodiversity is known only in general terms, and this article presents the first regional analysis to identify areas of special concern, using bird data as proxy. The aim of conserving all species may be significantly constrained in the Santa Marta and Perijá mountains, Darién, some parts of the Central Andes in Colombia, and between the middle Marañón and middle Huallaga valleys in Peru. Solutions to the problem must address the root causes: international drug markets, long-lasting armed conflict, and lack of alternative income for the rural poor.

  6. Illicit crops and armed conflict as constraints on biodiversity conservation in the Andes region.

    PubMed

    Fjeldså, Jon; Alvarez, María D; Lazcano, Juan Mario; León, Blanca

    2005-05-01

    Coca, once grown for local consumption in the Andes, is now produced for external markets, often in areas with armed conflict. Internationally financed eradication campaigns force traffickers and growers to constantly relocate, making drug-related activities a principal cause of forest loss. The impact on biodiversity is known only in general terms, and this article presents the first regional analysis to identify areas of special concern, using bird data as proxy. The aim of conserving all species may be significantly constrained in the Santa Marta and Perijá mountains, Darién, some parts of the Central Andes in Colombia, and between the middle Marañón and middle Huallaga valleys in Peru. Solutions to the problem must address the root causes: international drug markets, long-lasting armed conflict, and lack of alternative income for the rural poor. PMID:16042278

  7. A new region of conservation is defined between human and mouse X chromosomes

    SciTech Connect

    Dinulos, M.B.; Disteche, C.M.; Bassi, M.T.

    1996-07-01

    Comparative mapping of the X chromosome in eutherian mammals have revealed distinct regions of conservation as well as evolutionary rearrangements between human and mouse. Recently, we and others mapped the murine homologue of CLCN4 (Chloride channel 4) to band F4 of the X chromosome in Mus spretus but to chromosome 7 in laboratory strains. We now report the mapping of the murine homologues of APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), two genes that are located on the human X chromosome at band p22.3 and in close proximity to CLCN4. Interestingly, Oa1 and Apxl map to bands F2-F3 in both M. spretus and the laboratory strain C57BL/6J, defining a new rearrangement between human and mouse X chromosomes. 17 refs., 2 figs., 1 tab.

  8. Importance of regional variation in conservation planning: A rangewide example of the Greater Sage-Grouse

    USGS Publications Warehouse

    Doherty, Kevin E; Evans, Jeffrey S.; Coates, Peter S.; Juliusson, Lara; Fedy, Bradley C.

    2016-01-01

    We developed rangewide population and habitat models for Greater Sage-Grouse (Centrocercus urophasianus) that account for regional variation in habitat selection and relative densities of birds for use in conservation planning and risk assessments. We developed a probabilistic model of occupied breeding habitat by statistically linking habitat characteristics within 4 miles of an occupied lek using a nonlinear machine learning technique (Random Forests). Habitat characteristics used were quantified in GIS and represent standard abiotic and biotic variables related to sage-grouse biology. Statistical model fit was high (mean correctly classified = 82.0%, range = 75.4–88.0%) as were cross-validation statistics (mean = 80.9%, range = 75.1–85.8%). We also developed a spatially explicit model to quantify the relative density of breeding birds across each Greater Sage-Grouse management zone. The models demonstrate distinct clustering of relative abundance of sage-grouse populations across all management zones. On average, approximately half of the breeding population is predicted to be within 10% of the occupied range. We also found that 80% of sage-grouse populations were contained in 25–34% of the occupied range within each management zone. Our rangewide population and habitat models account for regional variation in habitat selection and the relative densities of birds, and thus, they can serve as a consistent and common currency to assess how sage-grouse habitat and populations overlap with conservation actions or threats over the entire sage-grouse range. We also quantified differences in functional habitat responses and disturbance thresholds across the Western Association of Fish and Wildlife Agencies (WAFWA) management zones using statistical relationships identified during habitat modeling. Even for a species as specialized as Greater Sage-Grouse, our results show that ecological context matters in both the strength of habitat selection (i

  9. Economic efficiency and cost implications of habitat conservation: An example in the context of the Edwards Aquifer region

    NASA Astrophysics Data System (ADS)

    Gillig, Dhazn; McCarl, Bruce A.; Jones, Lonnie L.; Boadu, Frederick

    2004-04-01

    Groundwater management in the Edwards Aquifer in Texas is in the process of moving away from a traditional right of capture economic regime toward a more environmentally sensitive scheme designed to preserve endangered species habitats. This study explores economic and environmental implications of proposed groundwater management and water development strategies under a proposed regional Habitat Conservation Plan. Results show that enhancing the habitat by augmenting water flow costs $109-1427 per acre-foot and that regional water development would be accelerated by the more extreme possibilities under the Habitat Conservation Plan. The findings also indicate that a water market would improve regional welfare and lower water development but worsen environmental attributes.

  10. Specific lysis of human immunodeficiency virus type 1-infected cells by a HLA-A3.1-restricted CD8+ cytotoxic T-lymphocyte clone that recognizes a conserved peptide sequence within the gp41 subunit of the envelope protein.

    PubMed Central

    Takahashi, K; Dai, L C; Fuerst, T R; Biddison, W E; Earl, P L; Moss, B; Ennis, F A

    1991-01-01

    A HLA-A3.1-restricted CD8+ cytotoxic T-cell clone, E7.20, that lyses cells infected with human immunodeficiency virus type 1 was isolated from an infected individual. The epitope was localized to amino acids 768-778 (RLRDLLLIVTR, NL43 env sequence) of the cytoplasmic domain of gp41 by successive use of a panel of recombinant vaccinia viruses that express truncated env genes and synthetic peptides. The epitope is conserved on 7 (NL43, BRU, HXB2, BRVA, SC, JH3, and JFL) of 13 human immunodeficiency virus type 1 isolates from North America. Synthetic peptides of this region of strains RF and CDC4 are also recognized by E7.20 despite a nonconservative Thr----Val or Thr----Ala change at amino acid 777; however, an MN peptide, which has four amino acid substitutions, was not reactive. The epitope recognized by E7.20 has a predicted hydrophobic alpha-helical structure, with three contiguous Leu residues followed by Ile and Val at amino acids 772-776. Cytotoxicity was restricted by HLA-A3.1 using allogeneic target cells that shared HLA class I antigens with the donor and an HLA-A and -B negative human plasma cell line transfected with the HLA-A3.1 gene. The transfected cells were infectable by human immunodeficiency virus type 1 strains IIIB and MN but only the former virus sensitized them to killing by E7.20. The ability of E7.20 to specifically lyse a human lymphocyte line infected with a human immunodeficiency virus type 1 strain carrying the conserved epitope is consistent with an important role for cytotoxic T cells in controlling infection. PMID:1719555

  11. Adenovirus transcriptional regulatory regions are conserved in mammalian cells and Saccharomyces cerevisiae.

    PubMed Central

    Kornuc, M; Altman, R; Harrich, D; Garcia, J; Chao, J; Kayne, P; Gaynor, R

    1988-01-01

    The adenovirus early region 3 (E3) promoter is an early viral promoter which is strongly induced by the adenovirus transactivator protein E1A. DNase I footprinting with HeLa cell extracts has identified four factor-binding domains which appear to be involved in basal and E1A-induced transcriptional regulation. These binding domains may bind TATA region-binding factors (site I), the CREB/ATF protein (site II), the AP-1 protein (site III), and nuclear factor I/CTF (site IV). Recently, it has been shown that the DNA-binding domain of transcription factor AP-1 has homology with the yeast transcription factor GCN4 and that the yeast transactivator protein GAL4 is able to stimulate transcription in HeLa cells from promoters containing GAL4-binding sites. These results suggest an evolutionary conservation of both transcription factors and the mechanisms responsible for transcriptional activation in Saccharomyces cerevisiae and higher eucaryotic organisms. To determine whether similar patterns of transcriptional regulation were seen with the E3 promoter in HeLa and yeast cells, the E3 promoter fused to the chloramphenicol acetyltransferase (cat) gene was cloned into a high-copy-number plasmid and stably introduced into yeast cells. S1 analysis revealed that similar E3 promoter mRNA start sites were found in yeast and HeLa cells. DNase I footprinting with partially purified yeast extracts revealed that four regions of the E3 promoter were protected. Several of these regions were similar to binding sites determined by using HeLa cell extracts. Oligonucleotide mutagenesis of these binding domains indicated their importance in the transcriptional regulation of the E3 promoter in yeast cells. These results suggest that similar cellular transcription factor-binding sites may be involved in the regulation of promoters in both yeast and mammalian cells. Images PMID:2975753

  12. Adenovirus transcriptional regulatory regions are conserved in mammalian cells and Saccharomyces cerevisiae.

    PubMed

    Kornuc, M; Altman, R; Harrich, D; Garcia, J; Chao, J; Kayne, P; Gaynor, R

    1988-09-01

    The adenovirus early region 3 (E3) promoter is an early viral promoter which is strongly induced by the adenovirus transactivator protein E1A. DNase I footprinting with HeLa cell extracts has identified four factor-binding domains which appear to be involved in basal and E1A-induced transcriptional regulation. These binding domains may bind TATA region-binding factors (site I), the CREB/ATF protein (site II), the AP-1 protein (site III), and nuclear factor I/CTF (site IV). Recently, it has been shown that the DNA-binding domain of transcription factor AP-1 has homology with the yeast transcription factor GCN4 and that the yeast transactivator protein GAL4 is able to stimulate transcription in HeLa cells from promoters containing GAL4-binding sites. These results suggest an evolutionary conservation of both transcription factors and the mechanisms responsible for transcriptional activation in Saccharomyces cerevisiae and higher eucaryotic organisms. To determine whether similar patterns of transcriptional regulation were seen with the E3 promoter in HeLa and yeast cells, the E3 promoter fused to the chloramphenicol acetyltransferase (cat) gene was cloned into a high-copy-number plasmid and stably introduced into yeast cells. S1 analysis revealed that similar E3 promoter mRNA start sites were found in yeast and HeLa cells. DNase I footprinting with partially purified yeast extracts revealed that four regions of the E3 promoter were protected. Several of these regions were similar to binding sites determined by using HeLa cell extracts. Oligonucleotide mutagenesis of these binding domains indicated their importance in the transcriptional regulation of the E3 promoter in yeast cells. These results suggest that similar cellular transcription factor-binding sites may be involved in the regulation of promoters in both yeast and mammalian cells.

  13. Conserving the Greater Sage-grouse: A social-ecological systems case study from the California-Nevada region

    USGS Publications Warehouse

    Duvall, Alison L; Metcalf, Alexander L.; Coates, Peter S.

    2016-01-01

    The Endangered Species Act (ESA) continues to serve as one of the most powerful and contested federal legislative mandates for conservation. In the midst of heated debates, researchers, policy makers, and conservation practitioners champion the importance of cooperative conservation and social-ecological systems approaches, which forge partnerships at multiple levels and scales to address complex ecosystem challenges. However, few real-world examples exist to demonstrate how multifaceted collaborations among stakeholders who share a common goal of conserving at-risk species may be nested within a systems framework to achieve social and ecological goals. Here, we present a case study of Greater Sage-grouse (Centrocercus urophasianus) conservation efforts in the “Bi-State” region of California and Nevada, United States. Using key-informant interviews, we explored dimensions and drivers of this landscape-scale conservation effort. Three themes emerged from the interviews, including 1) ESA action was transformed into opportunity for system-wide conservation; 2) a diverse, locally based partnership anchored collaboration and engagement across multiple levels and scales; and 3) best-available science combined with local knowledge led to “certainty of effectiveness and implementation”—the criteria used by the US Fish and Wildlife Service to evaluate conservation efforts when making listing decisions. Ultimately, collaborative conservation through multistakeholder engagement at various levels and scales led to proactive planning and implementation of conservation measures and precluded the need for an ESA listing of the Bi-State population of Greater Sage-grouse. This article presents a potent example of how a systems approach integrating policy, management, and learning can be used to successfully overcome the conflict-laden and “wicked” challenges that surround at-risk species conservation.

  14. The Neurospora crassa carotenoid biosynthetic gene (albino 3) reveals highly conserved regions among prenyltransferases.

    PubMed

    Carattoli, A; Romano, N; Ballario, P; Morelli, G; Macino, G

    1991-03-25

    In the filamentous fungus Neurospora crassa the biosynthesis of carotenoids is regulated by blue light. Here we report the characterization of the albino-3 (al-3) gene of N. crassa, which encodes the carotenoid biosynthetic enzyme geranylgeranyl-pyrophosphate synthetase. This is the first geranylgeranyl-pyrophosphate synthetase gene isolated. Nucleotide sequence comparison of al-3 genomic and cDNA clones revealed that the al-3 gene is not interrupted by introns. Transcription of the al-3 gene has been examined in dark-grown and light-induced mycelia. The analysis revealed that the al-3 gene is not expressed in the dark and that its transcription is induced by blue light (Nelson, M. A., Morelli, G., Carattoli, A., Romano, N., and Macino, G. (1989) Mol. Cell. Biol. 9, 1271-1276). The al-3 gene encodes a polypeptide of 428 amino acids. Comparison of the deduced amino acid sequence of al-3 with the sequences of prenyltransferases of other species, from bacteria to humans, showed three highly conserved homologous regions. These homologous regions may be involved in the formation of the catalytic site of the prenyltransferases.

  15. Duck nest success on Conservation Reserve Program land in the prairie pothole region

    USGS Publications Warehouse

    Kantrud, H.A.

    1993-01-01

    Habitat fragmentation from intensified farming has concentrated nesting waterfowl and their predators in the remaining, relatively small untitled habitats of the prairie pothole region in the United States. The areas of land that have been enrolled in the Conservation Reserve Program (CRP) in this area could help disperse these concentrations and reduce losses to predators. The presence of CRP land may influence decisions about intensive management of public lands devoted to waterfowl production. During 1989–1991, waterfowl nest success on CRP fields in areas of high wetland density in the prairie pothole region was 23.1 percent compared to 8.2 percent on similar covers on federal waterfowl production areas. CRP fields thus provided more secure nesting cover for upland-nesting ducks than waterfowl production areas. However, nest success and use of the fields by ducks varied greatly. CRP fields are abundant and of a wide variety of age classes and sizes. These characteristics make CRP fields well suited as study sites for determining the effects of cover area, distance to water, and cover age on nest success of ducks.

  16. Conservation value of a native forest fragment in a region of extensive agriculture.

    PubMed

    Chiarello

    2000-05-01

    A survey of mammals and birds was carried out in a semi-deciduous forest fragment of 150 ha located in a zone of intensive agriculture in Ribeirão Preto, State of São Paulo, south-eastern Brazil. Line transect sampling was used to census mammals and birds during six days, totalling 27.8 km of trails and 27.8 hours of observation. Twenty mammal species were confirmed in the area (except bats and small mammals), including rare or endangered species, such as the mountain lion (Puma concolor), the maned wolf (Chrysocyon brachyurus), and the ocelot (Leopardus pardalis). The brown capuchin monkey (Cebus apella) and the black-tufted-ear marmoset (Callithrix penicillata) were found frequently, suggesting high population density in the fragment. Regarding the avifauna, 49 bird species were recorded, most of them typical of open areas or forest edges. Some confirmed species, however, are becoming increasingly rare in the region, as for example the muscovy duck (Cairina moschata) and the toco toucan (Ramphastos toco). The results demonstrate that forest fragment of this size are refuges for native fauna in a region dominated almost exclusively by sugar-cane plantations. Besides faunal aspects, the conservation of these fragments is of great importance for the establishment of studies related to species preservation in the long term, including reintroduction and translocation projects, as well as studies related to genetic health of isolated populations.

  17. Duck nest success on Conservation Reserve Program land in the prairie pothole region

    USGS Publications Warehouse

    Kantrud, H.A.

    1993-01-01

    Habitat fragmentation from intensified farming has concentrated nesting waterfowl and their predators in the remaining, relatively small untitled habitats of the prairie pothole region in the United States. The areas of land that have been enrolled in the Conservation Reserve Program (CRP) in this area could help disperse these concentrations and reduce losses to predators. The presence of CRP land may influence decisions about intensive management of public lands devoted to waterfowl production. During 1989-1991, waterfowl nest success on CRP fields in areas of high wetland density in the prairie pothole region was 23.1 percent compared to 8.2 percent on similar covers on federal waterfowl production areas. CRP fields thus provided more secure nesting cover for upland-nesting ducks than waterfowl production areas. However, nest success and use of the fields by ducks varied greatly. CRP fields are abundant and of a wide variety of age classes and sizes. These characteristics make CRP fields well suited as study sites for determining the effects of cover area, distance to water, and cover age on nest success of ducks.

  18. Association between adjuvant regional radiotherapy and cognitive function in breast cancer patients treated with conservation therapy

    PubMed Central

    Shibayama, Osamu; Yoshiuchi, Kazuhiro; Inagaki, Masatoshi; Matsuoka, Yutaka; Yoshikawa, Eisho; Sugawara, Yuriko; Akechi, Tatsuo; Wada, Noriaki; Imoto, Shigeru; Murakami, Koji; Ogawa, Asao; Akabayashi, Akira; Uchitomi, Yosuke

    2014-01-01

    Although protracted cognitive impairment has been reported to occur after radiotherapy even when such therapy is not directed to brain areas, the mechanism remains unclear. This study investigated whether breast cancer patients exposed to local radiotherapy showed lower cognitive function mediated by higher plasma interleukin (IL)-6 levels than those unexposed. We performed the Wechsler Memory Scale-Revised (WMS-R) and measured plasma IL-6 levels for 105 breast cancer surgical patients within 1 year after the initial therapy. The group differences in each of the indices of WMS-R were investigated between cancer patients exposed to adjuvant regional radiotherapy (n = 51) and those unexposed (n = 54) using analysis of covariance. We further investigated a mediation effect by plasma IL-6 levels on the relationship between radiotherapy and the indices of WMS-R using the bootstrapping method. The radiotherapy group showed significantly lower Immediate Verbal Memory Index and Delayed Recall Index (P = 0.001, P = 0.008, respectively). Radiotherapy exerted an indirect effect on the lower Delayed Recall Index of WMS-R through elevation of plasma IL-6 levels (bootstrap 95% confidence interval = −2.6626 to −0.0402). This study showed that breast cancer patients exposed to adjuvant regional radiotherapy in conservation therapy might have cognitive impairment even several months after their treatment. The relationship between the therapy and the cognitive impairment could be partially mediated by elevation of plasma IL-6 levels. PMID:24756915

  19. Recognition of a highly conserved region of human immunodeficiency virus type 1 gp120 by an HLA-Cw4-restricted cytotoxic T-lymphocyte clone.

    PubMed Central

    Johnson, R P; Trocha, A; Buchanan, T M; Walker, B D

    1993-01-01

    Human immunodeficiency virus type 1 (HIV-1) isolates exhibit extensive sequence variation, particularly in the gp120 subunit of the envelope glycoprotein, and the degree of this variation has raised questions as to whether conserved regions of the HIV-1 envelope can be recognized by the host immune response. A CD8+ cytotoxic T-lymphocyte (CTL) clone specific for the HIV-1 envelope was derived by culturing peripheral blood mononuclear cells from an HIV-1 seropositive subject in the presence of a CD3-specific monoclonal antibody, interleukin-2, and irradiated allogeneic peripheral blood mononuclear cells. Lysis of target cells was restricted by an HLA-C molecule, Cw4, which has not been previously shown to present viral antigen to CTL. Mapping of the specificity of this CTL clone by using synthetic HIV-1 peptides localized the epitope to an 8-amino-acid region of gp120 (amino acids 376 to 383) which is conserved among approximately 90% of sequenced viral isolates. Examination of the recognition of variant peptides by this CTL clone demonstrated that a single, nonconservative amino acid substitution within the 8-amino-acid minimal epitope could abrogate lysis of targets incubated with the variant peptide. The identification of a CTL epitope in a highly conserved region of gp120 documents the ability of cellular immune responses of infected persons to respond to relatively invariant portions of this highly variable envelope glycoprotein. However, the ability of even a single-amino-acid change in gp120 to abolish lysis by CTL supports the hypothesis that sequence variation in HIV-1 may serve as a mechanism of immune escape. In addition, the identification of an HLA-C molecule presenting viral antigen to CTL supports a functional role for these molecules. PMID:7677956

  20. Biodiversity conservation in local planning.

    PubMed

    Miller, James R; Groom, Martha; Hess, George R; Steelman, Toddi; Stokes, David L; Thompson, Jan; Bowman, Troy; Fricke, Laura; King, Brandon; Marquardt, Ryan

    2009-02-01

    Local land-use policy is increasingly being recognized as fundamental to biodiversity conservation in the United States. Many planners and conservation scientists have called for broader use of planning and regulatory tools to support the conservation of biodiversity at local scales. Yet little is known about the pervasiveness of these practices. We conducted an on-line survey of county, municipal, and tribal planning directors (n =116) in 3 geographic regions of the United States: metropolitan Seattle, Washington; metropolitan Des Moines, Iowa; and the Research Triangle, North Carolina. Our objectives were to gauge the extent to which local planning departments address biodiversity conservation and to identify factors that facilitate or hinder conservation actions in local planning. We found that biodiversity conservation was seldom a major consideration in these departments. Staff time was mainly devoted to development mandates and little time was spent on biodiversity conservation. Regulations requiring conservation actions that might benefit biodiversity were uncommon, with the exception of rules governing water quality in all 3 regions and the protection of threatened and endangered species in the Seattle region. Planning tools that could enhance habitat conservation were used infrequently. Collaboration across jurisdictions was widespread, but rarely focused on conservation. Departments with a conservation specialist on staff tended to be associated with higher levels of conservation actions. Jurisdictions in the Seattle region also reported higher levels of conservation action, largely driven by state and federal mandates. Increased funding was most frequently cited as a factor that would facilitate greater consideration of biodiversity in local planning. There are numerous opportunities for conservation biologists to play a role in improving conservation planning at local scales.

  1. Waterfowl Conservation in the US Prairie Pothole Region: Confronting the Complexities of Climate Change

    PubMed Central

    Niemuth, Neal D.; Fleming, Kathleen K.; Reynolds, Ronald E.

    2014-01-01

    The Prairie Pothole Region (PPR) is the most important waterfowl production area in North America. However, waterfowl populations there are predicted to decline because of climate-related drying of wetlands. Consequently, changes in the geographic focus of PPR waterfowl conservation have been recommended, which could have long-lasting and costly impacts. We used a 40-year dataset of pond counts collected in the PPR to test hypotheses about climate-related drying. We assessed May (1974–2013) and July (1974–2003) pond numbers in 20 waterfowl survey strata to determine if trends in pond numbers were consistent with predictions of drying. We also assessed trends in precipitation and temperature for the 20 strata and developed models describing May pond numbers from 1974 through 2010 as a function of precipitation, temperature, the previous year’s pond numbers, and location. None of the 20 strata showed significant declines in May pond numbers, although seven strata showed increases over time. July pond numbers declined significantly in one stratum, and increased in seven strata. An index to hydroperiod showed significant increasing trends in three strata, and no strata had decreasing trends. Precipitation increased significantly in two strata and decreased in two from 1974 to 2010; no strata showed significant changes in temperature. The best linear model described pond numbers within all strata as a function of precipitation, temperature, the previous year’s pond numbers, and the latitude and longitude of the stratum, and explained 62% of annual variation in pond numbers. We hypothesize that direct effects of climate change on prairie pothole wetlands and waterfowl may be overshadowed by indirect effects such as intensified land use and increased pressure to drain wetlands. We recommend that an adaptive, data-driven approach be used to resolve uncertainties regarding direct and indirect effects of climate change on prairie wetlands and waterfowl, and guide

  2. Neutralizing activities of caprine antibodies towards conserved regions of the HCV envelope glycoprotein E2

    PubMed Central

    2011-01-01

    Anti HCV vaccine is not currently available and the present antiviral therapies fail to cure approximately half of the treated HCV patients. This study was designed to assess the immunogenic properties of genetically conserved peptides derived from the C-terminal region of HVR-1 and test their neutralizing activities in a step towards developing therapeutic and/or prophylactic immunogens against HCV infection. Antibodies were generated by vaccination of goats with synthetic peptides derived from HCV E2. Viral neutralizing capacity of the generated anti E2 antibodies was tested using in vitro assays. Goats immunized with E2 synthetic peptides termed p412 [a.a 412-419], p430 [a.a 430-447] and p517 [a.a 517-531] generated high titers of antibody responses 2 to 4.5 fold higher than comparable titers of antibodies to the same epitopes in chronic HCV patients. In post infection experiments of native HCV into cultured Huh7.5 cells anti p412 and anti p 517 were proven to be neutralizing to HCV genotype 4a from patients' sera (87.5% and 75% respectively). On the contrary anti p430 exhibited weak viral neutralization capacity on the same samples (31.25%). Furthermore Ab mixes containing anti p430 exhibited reduced viral neutralization properties. From these experiments one could predict that neutralization by Abs towards different E2-epitopes varies considerably and success in the enrichment of neutralization epitope-specific antibodies may be accompanied by favorable results in combating HCV infection. Also, E2 conserved peptides p517 and p412 represent potential components of a candidate peptide vaccine against HCV infection. PMID:21819575

  3. Waterfowl conservation in the US Prairie Pothole Region: confronting the complexities of climate change.

    PubMed

    Niemuth, Neal D; Fleming, Kathleen K; Reynolds, Ronald E

    2014-01-01

    The Prairie Pothole Region (PPR) is the most important waterfowl production area in North America. However, waterfowl populations there are predicted to decline because of climate-related drying of wetlands. Consequently, changes in the geographic focus of PPR waterfowl conservation have been recommended, which could have long-lasting and costly impacts. We used a 40-year dataset of pond counts collected in the PPR to test hypotheses about climate-related drying. We assessed May (1974-2013) and July (1974-2003) pond numbers in 20 waterfowl survey strata to determine if trends in pond numbers were consistent with predictions of drying. We also assessed trends in precipitation and temperature for the 20 strata and developed models describing May pond numbers from 1974 through 2010 as a function of precipitation, temperature, the previous year's pond numbers, and location. None of the 20 strata showed significant declines in May pond numbers, although seven strata showed increases over time. July pond numbers declined significantly in one stratum, and increased in seven strata. An index to hydroperiod showed significant increasing trends in three strata, and no strata had decreasing trends. Precipitation increased significantly in two strata and decreased in two from 1974 to 2010; no strata showed significant changes in temperature. The best linear model described pond numbers within all strata as a function of precipitation, temperature, the previous year's pond numbers, and the latitude and longitude of the stratum, and explained 62% of annual variation in pond numbers. We hypothesize that direct effects of climate change on prairie pothole wetlands and waterfowl may be overshadowed by indirect effects such as intensified land use and increased pressure to drain wetlands. We recommend that an adaptive, data-driven approach be used to resolve uncertainties regarding direct and indirect effects of climate change on prairie wetlands and waterfowl, and guide future

  4. Primary structure of the variable region of monoclonal antibody 2B10, capable of inducing anti-idiotypic antibodies that recognize the C-terminal region of MSA-1 of Plasmodium falciparum.

    PubMed Central

    Su, S; Yang, S; Ding, R; Davidson, E A

    1996-01-01

    Previously, we reported on the properties of a monoclonal antibody, 2B10, which has the same determinant on the human erythrocyte as MSA-1 of Plasmodium falciparum (FCR3 strain); the binding of both ligands to erythrocyte receptors was totally sialic acid dependent. In this work, rabbit anti-2B10 idiopathic antibodies were generated. The anti-idiotypic antibodies recognized both the erythrocyte binding site of 2B10 and the C-terminal region of MSA-1 (amino acids 1047 to 1640); they were able to inhibit 2B10 and MSA-1 binding to erythrocytes and partially prevent P. falciparum merozoites from invading erythrocytes. The utility of 2B10 in the study of the interaction between MSA-1 and human erythrocytes prompted us to determine the nucleotide and deduced amino acid sequences of its VH and VL regions. The data show that the 2B10 VH region is part of the J558 family and is especially homologous to BALB/c anti-nitrophenyl monoclonal antibody 21.1.43; the VL region belongs to the VK1 subgroup and comes from the same genomic locus as (NZB x W)F1 anti-DNA and C57BL anti-dextran monoclonal antibodies BXW-14 and 42.48.12.2, respectively. Most of the differences among the VH and VL segments are located in CDR1 and -3. The binding site of 2B10 contains both negatively and positively charged amino acid residues. The amino acid sequences of the 2B10 VH region and a region of MSA-1 from the Wellcome strain of P. falciparum (amino acids 1002 to 1115) share 43% similarity, and the amino acid sequences between the 2B10 VL region and another segment of the same MSA-1 (amino acids 1247 to 1394) share 48% similarity. We conclude that the interactions between erythrocyte receptors and their ligands, 2B10 and MSA-1, are related and that the C-terminal region of MSA-1 is the erythrocyte binding domain. PMID:8557359

  5. [Geographic distribution of birds in the Sierra Madre Oriental of San Luis Potosi, Mexico: a regional analysis of conservation status].

    PubMed

    Sahagún Sánchez, Francisco Javier; Navarro, Jaime Castro; Reyes Hernández, Humberto

    2013-06-01

    The Sierra Madre Oriental region in the mexican state of San Luis Potosi is a relevant place for bird conservation at a country level. Therefore the main goal of this study was to analyze the geographic patterns of distribution and the conservation current state of the birds, to support the needs to expand the conservation areas in the future. Data was collected from various databases of zoological museums and collections, and field sampling methods conducted from January 2009 to May 2011. Potential distributions were modeled for 284 species using GARP software and then a map was developed to determine areas with favorable environmental characteristics for the distribution of species richness. Finally, the importance of conservation areas for the potential distribution of birds in the region was evaluated. A total of 359 species were recorded of which 71.4% are permanent residents, 19% are winter migrants and 4% are summer residents. From this total, 41 species were endemic, 47 were species at risk and 149 were neotropical migrants. The largest species richness correspond to oak forests, cloud forests, and tropical moist forests located at altitudes from 100m to 1 500m. Their potential distribution was concentrated towards the center and Southeast of the study area. Only 10% of areas with a high potential conservation was included in areas of priority for bird conservation (AICA) and just 3% of all potential areas were under some governmental category of protection. However, no conservation area has a management plan currently applied and monitored. The information generated is important for the development of management proposals for birds conservation in the region. PMID:23885599

  6. [Geographic distribution of birds in the Sierra Madre Oriental of San Luis Potosi, Mexico: a regional analysis of conservation status].

    PubMed

    Sahagún Sánchez, Francisco Javier; Navarro, Jaime Castro; Reyes Hernández, Humberto

    2013-06-01

    The Sierra Madre Oriental region in the mexican state of San Luis Potosi is a relevant place for bird conservation at a country level. Therefore the main goal of this study was to analyze the geographic patterns of distribution and the conservation current state of the birds, to support the needs to expand the conservation areas in the future. Data was collected from various databases of zoological museums and collections, and field sampling methods conducted from January 2009 to May 2011. Potential distributions were modeled for 284 species using GARP software and then a map was developed to determine areas with favorable environmental characteristics for the distribution of species richness. Finally, the importance of conservation areas for the potential distribution of birds in the region was evaluated. A total of 359 species were recorded of which 71.4% are permanent residents, 19% are winter migrants and 4% are summer residents. From this total, 41 species were endemic, 47 were species at risk and 149 were neotropical migrants. The largest species richness correspond to oak forests, cloud forests, and tropical moist forests located at altitudes from 100m to 1 500m. Their potential distribution was concentrated towards the center and Southeast of the study area. Only 10% of areas with a high potential conservation was included in areas of priority for bird conservation (AICA) and just 3% of all potential areas were under some governmental category of protection. However, no conservation area has a management plan currently applied and monitored. The information generated is important for the development of management proposals for birds conservation in the region.

  7. Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

    PubMed Central

    Tsai, Chen-Hsun; Liao, Rick; Chou, Brendan; Palumbo, Michael

    2014-01-01

    Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5′ and 3′ untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms. PMID:25313390

  8. Fire mosaics and reptile conservation in a fire-prone region.

    PubMed

    Nimmo, D G; Kelly, L T; Spence-Bailey, L M; Watson, S J; Taylor, R S; Clarke, M F; Bennett, A F

    2013-04-01

    Fire influences the distribution of fauna in terrestrial biomes throughout the world. Use of fire to achieve a mosaic of vegetation in different stages of succession after burning (i.e., patch-mosaic burning) is a dominant conservation practice in many regions. Despite this, knowledge of how the spatial attributes of vegetation mosaics created by fire affect fauna is extremely scarce, and it is unclear what kind of mosaic land managers should aim to achieve. We selected 28 landscapes (each 12.6 km(2) ) that varied in the spatial extent and diversity of vegetation succession after fire in a 104,000 km(2) area in the semiarid region of southeastern Australia. We surveyed for reptiles at 280 sites nested within the 28 landscapes. The landscape-level occurrence of 9 of the 22 species modeled was associated with the spatial extent of vegetation age classes created by fire. Biogeographic context and the extent of a vegetation type influenced 7 and 4 species, respectively. No species were associated with the diversity of vegetation ages within a landscape. Negative relations between reptile occurrence and both extent of recently burned vegetation (≤10 years postfire, n = 6) and long unburned vegetation (>35 years postfire, n = 4) suggested that a coarse-grained mosaic of areas (e.g. >1000 ha) of midsuccessional vegetation (11-35 years postfire) may support the fire-sensitive reptile species we modeled. This age class coincides with a peak in spinifex cover, a keystone structure for reptiles in semiarid and arid Australia. Maintaining over the long term a coarse-grained mosaic of large areas of midsuccessional vegetation in mallee ecosystems will need to be balanced against the short-term negative effects of large fires on many reptile species and a documented preference by species from other taxonomic groups, particularly birds, for older vegetation.

  9. Prey Preferences of the Snow Leopard (Panthera uncia): Regional Diet Specificity Holds Global Significance for Conservation

    PubMed Central

    Lyngdoh, Salvador; Shrotriya, Shivam; Goyal, Surendra P.; Clements, Hayley; Hayward, Matthew W.; Habib, Bilal

    2014-01-01

    The endangered snow leopard is a large felid that is distributed over 1.83 million km2 globally. Throughout its range it relies on a limited number of prey species in some of the most inhospitable landscapes on the planet where high rates of human persecution exist for both predator and prey. We reviewed 14 published and 11 unpublished studies pertaining to snow leopard diet throughout its range. We calculated prey consumption in terms of frequency of occurrence and biomass consumed based on 1696 analysed scats from throughout the snow leopard's range. Prey biomass consumed was calculated based on the Ackerman's linear correction factor. We identified four distinct physiographic and snow leopard prey type zones, using cluster analysis that had unique prey assemblages and had key prey characteristics which supported snow leopard occurrence there. Levin's index showed the snow leopard had a specialized dietary niche breadth. The main prey of the snow leopard were Siberian ibex (Capra sibrica), blue sheep (Pseudois nayaur), Himalayan tahr (Hemitragus jemlahicus), argali (Ovis ammon) and marmots (Marmota spp). The significantly preferred prey species of snow leopard weighed 55±5 kg, while the preferred prey weight range of snow leopard was 36–76 kg with a significant preference for Siberian ibex and blue sheep. Our meta-analysis identified critical dietary resources for snow leopards throughout their distribution and illustrates the importance of understanding regional variation in species ecology; particularly prey species that have global implications for conservation. PMID:24533080

  10. Prey preferences of the snow leopard (Panthera uncia): regional diet specificity holds global significance for conservation.

    PubMed

    Lyngdoh, Salvador; Shrotriya, Shivam; Goyal, Surendra P; Clements, Hayley; Hayward, Matthew W; Habib, Bilal

    2014-01-01

    The endangered snow leopard is a large felid that is distributed over 1.83 million km(2) globally. Throughout its range it relies on a limited number of prey species in some of the most inhospitable landscapes on the planet where high rates of human persecution exist for both predator and prey. We reviewed 14 published and 11 unpublished studies pertaining to snow leopard diet throughout its range. We calculated prey consumption in terms of frequency of occurrence and biomass consumed based on 1696 analysed scats from throughout the snow leopard's range. Prey biomass consumed was calculated based on the Ackerman's linear correction factor. We identified four distinct physiographic and snow leopard prey type zones, using cluster analysis that had unique prey assemblages and had key prey characteristics which supported snow leopard occurrence there. Levin's index showed the snow leopard had a specialized dietary niche breadth. The main prey of the snow leopard were Siberian ibex (Capra sibrica), blue sheep (Pseudois nayaur), Himalayan tahr (Hemitragus jemlahicus), argali (Ovis ammon) and marmots (Marmota spp). The significantly preferred prey species of snow leopard weighed 55±5 kg, while the preferred prey weight range of snow leopard was 36-76 kg with a significant preference for Siberian ibex and blue sheep. Our meta-analysis identified critical dietary resources for snow leopards throughout their distribution and illustrates the importance of understanding regional variation in species ecology; particularly prey species that have global implications for conservation.

  11. Prey preferences of the snow leopard (Panthera uncia): regional diet specificity holds global significance for conservation.

    PubMed

    Lyngdoh, Salvador; Shrotriya, Shivam; Goyal, Surendra P; Clements, Hayley; Hayward, Matthew W; Habib, Bilal

    2014-01-01

    The endangered snow leopard is a large felid that is distributed over 1.83 million km(2) globally. Throughout its range it relies on a limited number of prey species in some of the most inhospitable landscapes on the planet where high rates of human persecution exist for both predator and prey. We reviewed 14 published and 11 unpublished studies pertaining to snow leopard diet throughout its range. We calculated prey consumption in terms of frequency of occurrence and biomass consumed based on 1696 analysed scats from throughout the snow leopard's range. Prey biomass consumed was calculated based on the Ackerman's linear correction factor. We identified four distinct physiographic and snow leopard prey type zones, using cluster analysis that had unique prey assemblages and had key prey characteristics which supported snow leopard occurrence there. Levin's index showed the snow leopard had a specialized dietary niche breadth. The main prey of the snow leopard were Siberian ibex (Capra sibrica), blue sheep (Pseudois nayaur), Himalayan tahr (Hemitragus jemlahicus), argali (Ovis ammon) and marmots (Marmota spp). The significantly preferred prey species of snow leopard weighed 55±5 kg, while the preferred prey weight range of snow leopard was 36-76 kg with a significant preference for Siberian ibex and blue sheep. Our meta-analysis identified critical dietary resources for snow leopards throughout their distribution and illustrates the importance of understanding regional variation in species ecology; particularly prey species that have global implications for conservation. PMID:24533080

  12. Deletion mapping of the rotavirus metalloprotein NS53 (NSP1): the conserved cysteine-rich region is essential for virus-specific RNA binding.

    PubMed Central

    Hua, J; Chen, X; Patton, J T

    1994-01-01

    NS53 (NSP1), the gene 5 product of the group A rotaviruses, is a minor nonstructural protein of 486 to 495 amino acids which binds zinc and contains an amino-terminal highly conserved cysteine-rich region that may form one or two zinc fingers. To study the structure-function of the gene 5 product, wild-type and mutant forms of NS53 were produced by using a recombinant baculovirus expression system and a recombinant vaccinia virus/T7 (vTF7-3) expression system. Analysis of the RNA-binding activity of the wild-type NS53 immobilized onto protein A-Sepharose beads with NS53-specific antiserum showed that the protein exhibited specific affinity for all 11 rotavirus mRNAs. The use of short virus-specific RNA probes indicated that NS53 specifically recognizes an element located near the 5' ends of viral mRNAs. Analysis of the RNA-binding activity of deletion mutants of NS53 showed that the RNA-binding domain resides within the first 81 amino acids of the protein and that the highly conserved cysteine-rich region within this region of the protein is essential for the activity. Gel electrophoresis and Western immunoblot analyses of intracellular fractions derived from infected cells revealed that large amounts of NS53 were present in the cytosol and in association with the cytoskeletal matrix. Indirect immunofluorescence analysis of cells programmed to transiently express mutant forms of NS53 using vTF7-3 indicated that the intracellular localization domain resides between amino acids 84 and 176 of NS53. Together, these data show that the RNA-binding domain and the intracellular localization domain lie upstream from the region of NS53 previously determined not to be essential for replication of rotaviruses in cell culture (J. Hua and J. T. Patton, Virology 198:567-576, 1994). Images PMID:8189533

  13. Simulation of water-use conservation scenarios for the Mississippi Delta using an existing regional groundwater flow model

    USGS Publications Warehouse

    Barlow, Jeannie R.B.; Clark, Brian R.

    2011-01-01

    The Mississippi River alluvial plain in northwestern Mississippi (referred to as the Delta), once a floodplain to the Mississippi River covered with hardwoods and marshland, is now a highly productive agricultural region of large economic importance to Mississippi. Water for irrigation is supplied primarily by the Mississippi River Valley alluvial aquifer, and although the alluvial aquifer has a large reserve, there is evidence that the current rate of water use from the alluvial aquifer is not sustainable. Using an existing regional groundwater flow model, conservation scenarios were developed for the alluvial aquifer underlying the Delta region in northwestern Mississippi to assess where the implementation of water-use conservation efforts would have the greatest effect on future water availability-either uniformly throughout the Delta, or focused on a cone of depression in the alluvial aquifer underlying the central part of the Delta. Five scenarios were simulated with the Mississippi Embayment Regional Aquifer Study groundwater flow model: (1) a base scenario in which water use remained constant at 2007 rates throughout the entire simulation; (2) a 5-percent 'Delta-wide' conservation scenario in which water use across the Delta was decreased by 5 percent; (3) a 5-percent 'cone-equivalent' conservation scenario in which water use within the area of the cone of depression was decreased by 11 percent (a volume equivalent to the 5-percent Delta-wide conservation scenario); (4) a 25-percent Delta-wide conservation scenario in which water use across the Delta was decreased by 25 percent; and (5) a 25-percent cone-equivalent conservation scenario in which water use within the area of the cone of depression was decreased by 55 percent (a volume equivalent to the 25-percent Delta-wide conservation scenario). The Delta-wide scenarios result in greater average water-level improvements (relative to the base scenario) for the entire Delta area than the cone

  14. Performance of 12 DIR algorithms in low-contrast regions for mass and density conserving deformation

    SciTech Connect

    Yeo, U. J.; Supple, J. R.; Franich, R. D.; Taylor, M. L.; Smith, R.; Kron, T.

    2013-10-15

    Purpose: Deformable image registration (DIR) has become a key tool for adaptive radiotherapy to account for inter- and intrafraction organ deformation. Of contemporary interest, the application to deformable dose accumulation requires accurate deformation even in low contrast regions where dose gradients may exist within near-uniform tissues. One expects high-contrast features to generally be deformed more accurately by DIR algorithms. The authors systematically assess the accuracy of 12 DIR algorithms and quantitatively examine, in particular, low-contrast regions, where accuracy has not previously been established.Methods: This work investigates DIR algorithms in three dimensions using deformable gel (DEFGEL) [U. J. Yeo, M. L. Taylor, L. Dunn, R. L. Smith, T. Kron, and R. D. Franich, “A novel methodology for 3D deformable dosimetry,” Med. Phys. 39, 2203–2213 (2012)], for application to mass- and density-conserving deformations. CT images of DEFGEL phantoms with 16 fiducial markers (FMs) implanted were acquired in deformed and undeformed states for three different representative deformation geometries. Nonrigid image registration was performed using 12 common algorithms in the public domain. The optimum parameter setup was identified for each algorithm and each was tested for deformation accuracy in three scenarios: (I) original images of the DEFGEL with 16 FMs; (II) images with eight of the FMs mathematically erased; and (III) images with all FMs mathematically erased. The deformation vector fields obtained for scenarios II and III were then applied to the original images containing all 16 FMs. The locations of the FMs estimated by the algorithms were compared to actual locations determined by CT imaging. The accuracy of the algorithms was assessed by evaluation of three-dimensional vectors between true marker locations and predicted marker locations.Results: The mean magnitude of 16 error vectors per sample ranged from 0.3 to 3.7, 1.0 to 6.3, and 1.3 to 7

  15. 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...

  16. Conservation program and practice effects on ecosystem services in the mid atlantic region of the U.S

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. Department of Agriculture (USDA) Mid-Atlantic Regional (MIAR) Wetland Conservation Effects Assessment Project (CEAP-Wetland) study area covers approximately ~58,000 km2 in the eastern United States, including areas of within five states (North Carolina, Virginia, Maryland, Delaware, and New...

  17. A Novel Universal Neutralizing Monoclonal Antibody against Enterovirus 71 That Targets the Highly Conserved “Knob” Region of VP3 Protein

    PubMed Central

    Meng, Tao; Chow, Vincent Tak Kwong; Kwang, Jimmy

    2014-01-01

    Hand, foot and mouth disease caused by enterovirus 71(EV71) leads to the majority of neurological complications and death in young children. While putative inactivated vaccines are only now undergoing clinical trials, no specific treatment options exist yet. Ideally, EV71 specific intravenous immunoglobulins could be developed for targeted treatment of severe cases. To date, only a single universally neutralizing monoclonal antibody against a conserved linear epitope of VP1 has been identified. Other enteroviruses have been shown to possess major conformational neutralizing epitopes on both the VP2 and VP3 capsid proteins. Hence, we attempted to isolate such neutralizing antibodies against conformational epitopes for their potential in the treatment of infection as well as differential diagnosis and vaccine optimization. Here we describe a universal neutralizing monoclonal antibody that recognizes a conserved conformational epitope of EV71 which was mapped using escape mutants. Eight escape mutants from different subgenogroups (A, B2, B4, C2, C4) were rescued; they harbored three essential mutations either at amino acid positions 59, 62 or 67 of the VP3 protein which are all situated in the “knob” region. The escape mutant phenotype could be mimicked by incorporating these mutations into reverse genetically engineered viruses showing that P59L, A62D, A62P and E67D abolish both monoclonal antibody binding and neutralization activity. This is the first conformational neutralization epitope mapped on VP3 for EV71. PMID:24875055

  18. Regional Nodal Recurrence After Breast Conservation Treatment With Radiotherapy for Women With Early-Stage Breast Carcinoma

    SciTech Connect

    Lukens, J. Nicholas Vapiwala, Neha; Hwang, W.-T.; Solin, Lawrence J.

    2009-04-01

    Purpose: To report the long-term outcomes for women presenting with regional lymph node recurrence after breast conservation treatment with radiotherapy for Stage I and II invasive breast carcinoma. Methods and Materials: Of the women with pathologic Stage I and II invasive breast carcinoma treated with breast conservation treatment at University of Pennsylvania, 29 developed regional nodal recurrence as their first site of failure. An analysis of the patterns of regional nodal recurrence and their prognosis after recurrence was undertaken. The median follow-up from regional nodal recurrence was 5.4 years. Results: The pattern of regional nodal recurrence was as follows: 14 (48%) with simultaneous local and axillary recurrence, 7 (24%) with recurrence in the axilla only, 5 (17%) with recurrence in the supraclavicular region only, and 3 (10%) with multiple nodal sites of recurrence. For the entire study group, the 5-, 10-, and 15-year overall survival rate was 70%, 37%, and 28%, respectively. The 10-year overall survival rate for patients with locoregional recurrence was 32% compared with 45% for patients with regional-only recurrence (p = 0.50). The 10-year overall survival rate for patients with axillary recurrence discovered on pathologic examination of the mastectomy specimen was 31% compared with 42% for patients with palpable regional lymphadenopathy (p = 0.83). Conclusion: Patients with regional nodal recurrence after breast conservation treatment with radiotherapy for early-stage breast carcinoma are potentially salvageable. The prognosis after regional nodal recurrence was not significantly different when stratified by the presence or absence of simultaneous in-breast recurrence or the method of detection.

  19. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region.

    PubMed

    Peñas, Julio; Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species. PMID:26844014

  20. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region

    PubMed Central

    Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M. Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species. PMID:26844014

  1. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region.

    PubMed

    Peñas, Julio; Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.

  2. [Effects of artificial seabuckthorn forest on soil and water conservation in loess hilly region].

    PubMed

    Chen, Yunming; Liu, Guobin; Xu, Bingcheng

    2005-04-01

    Seabuckthorn is regarded as a main eco-economical tree species, and plays an increasing important role in eco-environmental construction in Northwest, Northeast and North China. Our study on artificial seabuckthorn forest in loess hilly region showed that the average rainfall interception rate of 7-10 ages seabuckthorn canopy was 8.5%, and the litter layer of 5-10 ages seabuckthorn forest could intercept 0.89 mm rainfall. Seabuckthorn forest could improve soil infiltration and anti-strike ability through improving soil physical and chemical properties, and the numbers of its hair roots and the depth of its litter layer were the main indices of soil anti-strike ability. The effects of seabuckthorn forest on soil and water conservation increased with its increasing age. In 2-3 ages stage, the effects were weak, and the runoff and sediment were mainly affected by the characters of rainfall. In 4-5 ages stage when the forest became maturing, the annual runoff depth and annual erosion modulus were 1.8-3.2 mm and 24.64 t x km(-2), respectively. In 6-12 ages stage when the forest matured, the runoff and sediment on seabuckthorn woodland changed slowly, the annual runoff depth and annual erosion modulus being 0.3 -3.4 mm and 0-6.75 t x km(-2), respectively, and the characters of rainfall had much less effect on them. In the stage from young (2-5 ages) to mature forest, the sediment charge in runoff changed sharply, ranged from 77. 31 kg x m(-3) to 9.12 kg x m(-3), but in 6-12 ages stage, the sediment content in runoff changed very slowly, and the range was 0-5.09 kg x m(-3).

  3. The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice.

    PubMed

    Qi, Lili; Friebe, Bernd; Wu, Jiajie; Gu, Yongqiang; Qian, Chen; Gill, Bikram S

    2010-11-01

    The evolution of five chromosomes of Brachypodium distachyon from a 12-chromosome ancestor of all grasses by dysploidy raises an interesting question about the fate of redundant centromeres. Three independent but complementary approaches were pursued to study centromeric region homologies among the chromosomes of Brachypodium, wheat, and rice. The genes present in pericentromeres of the basic set of seven chromosomes of wheat and the Triticeae, and the 80 rice centromeric genes spanning the CENH3 binding domain of centromeres 3, 4, 5, 7, and 8 were used as "anchor" markers to identify centromere locations in the B. distachyon chromosomes. A total of 53 B. distachyon bacterial artificial chromosome (BAC) clones anchored by wheat pericentromeric expressed sequence tags (ESTs) were used as probes for BAC-fluorescence in situ hybridization (FISH) analysis of B. distachyon mitotic chromosomes. Integrated sequence alignment and BAC-FISH data were used to determine the approximate positions of active and inactive centromeres in the five B. distachyon chromosomes. The following syntenic relationships of the centromeres for Brachypodium (Bd), rice (R), and wheat (W) were evident: Bd1-R6, Bd2-R5-W1, Bd3-R10, Bd4-R11-W4, and Bd5-R4. Six rice centromeres syntenic to five wheat centromeres were inactive in Brachypodium chromosomes. The conservation of centromere gene synteny among several sets of homologous centromeres of three species indicates that active genes can persist in ancient centromeres with more than 40 million years of shared evolutionary history. Annotation of a BAC contig spanning an inactive centromere in chromosome Bd3 which is syntenic to rice Cen8 and W7 pericentromeres, along with BAC FISH data from inactive centromeres revealed that the centromere inactivation was accompanied by the loss of centromeric retrotransposons and turnover of centromere-specific satellites during Bd chromosome evolution.

  4. Conserved sequences in both coding and 5' flanking regions of mammalian opal suppressor tRNA genes.

    PubMed Central

    Pratt, K; Eden, F C; You, K H; O'Neill, V A; Hatfield, D

    1985-01-01

    The rabbit genome encodes an opal suppressor tRNA gene. The coding region is strictly conserved between the rabbit gene and the corresponding gene in the human genome. The rabbit opal suppressor gene contains the consensus sequence in the 3' internal control region but like the human and chicken genes, the rabbit 5' internal control region contains two additional nucleotides. The 5' flanking sequences of the rabbit and the human opal suppressor genes contain extensive regions of homology. A subset of these homologies is also present 5' to the chicken opal suppressor gene. Both the rabbit and the human genomes also encode a pseudogene. That of the rabbit lacks the 3' half of the coding region. Neither pseudogene has homologous regions to the 5' flanking regions of the genes. The presence of 5' homologies flanking only the transcribed genes and not the pseudogenes suggests that these regions may be regulatory control elements specifically involved in the expression of the eukaryotic opal suppressor gene. Moreover the strict conservation of coding sequences indicates functional importance for the opal suppressor tRNA genes. Images PMID:4022772

  5. Management of the Regional Lymph Nodes Following Breast-Conservation Therapy for Early-Stage Breast Cancer: An Evolving Paradigm

    SciTech Connect

    Warren, Laura E.G.; Punglia, Rinaa S.; Wong, Julia S.; Bellon, Jennifer R.

    2014-11-15

    Radiation therapy to the breast following breast conservation surgery has been the standard of care since randomized trials demonstrated equivalent survival compared to mastectomy and improved local control and survival compared to breast conservation surgery alone. Recent controversies regarding adjuvant radiation therapy have included the potential role of additional radiation to the regional lymph nodes. This review summarizes the evolution of regional nodal management focusing on 2 topics: first, the changing paradigm with regard to surgical evaluation of the axilla; second, the role for regional lymph node irradiation and optimal design of treatment fields. Contemporary data reaffirm prior studies showing that complete axillary dissection may not provide additional benefit relative to sentinel lymph node biopsy in select patient populations. Preliminary data also suggest that directed nodal radiation therapy to the supraclavicular and internal mammary lymph nodes may prove beneficial; publication of several studies are awaited to confirm these results and to help define subgroups with the greatest likelihood of benefit.

  6. USE OF POPULATION VIABILITY ANALYSIS AND RESERVE SELECTION ALGORITHMS IN REGIONAL CONSERVATION PLANS

    EPA Science Inventory

    Current reserve selection algorithms have difficulty evaluating connectivity and other factors
    necessary to conserve wide-ranging species in developing landscapes. Conversely, population viability analyses may incorporate detailed demographic data but often lack sufficient spa...

  7. Income level and regional policies, underlying factors associated with unwarranted variations in conservative breast cancer surgery in Spain

    PubMed Central

    2011-01-01

    Background Geographical variations in medical practice are expected to be small when the evidence about the effectiveness and safety of a particular technology is abundant. This would be the case of the prescription of conservative surgery in breast cancer patients. In these cases, when variation is larger than expected by need, socioeconomic factors have been argued as an explanation. Objectives: Using an ecologic design, our study aims at describing the variability in the use of surgical conservative versus non-conservative treatment. Additionally, it seeks to establish whether the socioeconomic status of the healthcare area influences the use of one or the other technique. Methods 81,868 mastectomies performed between 2002 and 2006 in 180 healthcare areas were studied. Standardized utilization rates of breast cancer conservative (CS) and non-conservative (NCS) procedures were estimated as well as the variation among areas, using small area statistics. Concentration curves and dominance tests were estimated to determine the impact of income and instruction levels in the healthcare area on surgery rates. Multilevel analyses were performed to determine the influence of regional policies. Results Variation in the use of CS was massive (4-fold factor between the highest and the lowest rate) and larger than in the case of NCS (2-fold), whichever the age group. Healthcare areas with higher economic and instruction levels showed highest rates of CS, regardless of the age group, while areas with lower economic and educational levels yielded higher rates of NCS interventions. Living in a particular Autonomous Community (AC), explained a substantial part of the CS residual variance (up to a 60.5% in women 50 to 70). Conclusion The place where a woman lives -income level and regional policies- explain the unexpectedly high variation found in utilization rates of conservative breast cancer surgery. PMID:21504577

  8. Recognizing medical emergencies

    MedlinePlus

    Medical emergencies - how to recognize them ... According to the American College of Emergency Physicians, the following are warning signs of a medical emergency: Bleeding that will not stop Breathing problems ( difficulty breathing , shortness of breath ) ...

  9. Tight junction protein Par6 interacts with an evolutionarily conserved region in the amino terminus of PALS1/stardust.

    PubMed

    Wang, Qian; Hurd, Toby W; Margolis, Ben

    2004-07-16

    Tight junctions are the structures in mammalian epithelial cells that separate the apical and basolateral membranes and may also be important in the establishment of cell polarity. Two evolutionarily conserved multiprotein complexes, Crumbs-PALS1 (Stardust)-PATJ and Cdc42-Par6-Par3-atypical protein kinase C, have been implicated in the assembly of tight junctions and in polarization of Drosophila melanogaster epithelia. These two complexes have been linked physically and functionally by an interaction between PALS1 and Par6. Here we identify an evolutionarily conserved region in the amino terminus of PALS1 as the Par6 binding site and identify valine and aspartic acid residues in this region as essential for interacting with the PDZ domain of Par6. We have also characterized, in more detail, the amino terminus of Drosophila Stardust and demonstrate that the interaction mechanism between Stardust and Drosophila Par6 is evolutionarily conserved. Par6 interferes with PATJ in binding PALS1, and these two interactions do not appear to function synergistically. Taken together, these results define the molecular mechanisms linking two conserved polarity complexes.

  10. C-terminal-binding protein interacting protein binds directly to adenovirus early region 1A through its N-terminal region and conserved region 3.

    PubMed

    Bruton, R K; Rasti, M; Mapp, K L; Young, N; Carter, R Z; Abramowicz, I A; Sedgwick, G G; Onion, D F; Shuen, M; Mymryk, J S; Turnell, A S; Grand, R J A

    2007-11-22

    C-terminal-binding protein interacting protein (CtIP) was first isolated as a binding partner of C-terminal-binding protein (CtBP). It is considered to contribute to the transcriptional repression and cell cycle regulatory properties of the retinoblastoma (Rb) family of proteins and to have a role in the cellular response to DNA damage. Here, we have shown that CtIP is a novel target for the adenovirus oncoprotein early region 1A (AdE1A). AdE1A associates with CtIP in both Ad5E1-transformed cells and Ad5-infected cells and binds directly in glutathione-S-transferase pull-down assays. Two binding sites have been mapped on Ad5E1A - the N-terminal alpha-helical region (residues 1-30) and conserved region 3 (CR3) - the transcriptional activation domain. CtIP can bind AdE1A and CtBP independently, raising the possibility that ternary complexes exist in Ad-transformed and -infected cells. Significantly, reduction of CtIP expression with small interfering RNAs results in reduction of the ability of a Gal4 DNA-binding domain-CR3 construct to transactivate a Gal 4-responsive luciferase reporter and this effect is reversed by reduction of CtBP expression. Therefore, in this model, CtIP acts as a transcriptional co-activator of AdE1A when dissociated from CtBP, through the action of AdE1A. These data are consistent with observations that CtIP expression is induced by AdE1A during viral infection and that reduction of CtIP expression with RNA interference can retard virus replication. In addition, AdE1A causes disruption of the CtIP/Rb complex during viral infection by its interaction with CtIP, possibly contributing to transcriptional derepression. PMID:17546052

  11. A Regional Assessment of the Effects of Conservation Practices on In-stream Water Quality

    NASA Astrophysics Data System (ADS)

    Garcia, A. M.; Alexander, R. B.; Arnold, J.; Norfleet, L.; Robertson, D. M.; White, M.

    2011-12-01

    The Conservation Effects Assessment Program (CEAP), initiated by USDA Natural Resources Conservation Service (NRCS), has the goal of quantifying the environmental benefits of agricultural conservation practices. As part of this effort, detailed farmer surveys were compiled to document the adoption of conservation practices. Survey data showed that up to 38 percent of cropland in the Upper Mississippi River basin is managed to reduce sediment, nutrient and pesticide loads from agricultural activities. The broader effects of these practices on downstream water quality are challenging to quantify. The USDA-NRCS recently reported results of a study that combined farmer surveys with process-based models to deduce the effect of conservation practices on sediment and chemical loads in farm runoff and downstream waters. As a follow-up collaboration, USGS and USDA scientists conducted a semi-empirical assessment of the same suite of practices using the USGS SPARROW (SPAtially Referenced Regression On Watershed attributes) modeling framework. SPARROW is a hybrid statistical and mechanistic stream water quality model of annual conditions that has been used extensively in studies of nutrient sources and delivery. In this assessment, the USDA simulations of the effects of conservation practices on loads in farm runoff were used as an explanatory variable (i.e., change in farm loads per unit area) in a component of an existing a SPARROW model of the Upper Midwest. The model was then re-calibrated and tested to determine whether the USDA estimate of conservation adoption intensity explained a statistically significant proportion of the spatial variability in stream nutrient loads in the Upper Mississippi River basin. The results showed that the suite of conservation practices that NRCS has catalogued as complete nutrient and sediment management are a statistically significant feature in the Midwestern landscape associated with phosphorous runoff and delivery to downstream waters

  12. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs

    PubMed Central

    Moore, Cordelia H.; Radford, Ben T.; Possingham, Hugh P.; Heyward, Andrew J.; Stewart, Romola R.; Watts, Matthew E.; Prescott, Jim; Newman, Stephen J.; Harvey, Euan S.; Fisher, Rebecca; Bryce, Clay W.; Lowe, Ryan J.; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

    2016-01-01

    Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia–a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation. PMID:27556689

  13. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs

    NASA Astrophysics Data System (ADS)

    Moore, Cordelia H.; Radford, Ben T.; Possingham, Hugh P.; Heyward, Andrew J.; Stewart, Romola R.; Watts, Matthew E.; Prescott, Jim; Newman, Stephen J.; Harvey, Euan S.; Fisher, Rebecca; Bryce, Clay W.; Lowe, Ryan J.; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

    2016-08-01

    Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia–a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

  14. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs.

    PubMed

    Moore, Cordelia H; Radford, Ben T; Possingham, Hugh P; Heyward, Andrew J; Stewart, Romola R; Watts, Matthew E; Prescott, Jim; Newman, Stephen J; Harvey, Euan S; Fisher, Rebecca; Bryce, Clay W; Lowe, Ryan J; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

    2016-01-01

    Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia-a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation. PMID:27556689

  15. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs.

    PubMed

    Moore, Cordelia H; Radford, Ben T; Possingham, Hugh P; Heyward, Andrew J; Stewart, Romola R; Watts, Matthew E; Prescott, Jim; Newman, Stephen J; Harvey, Euan S; Fisher, Rebecca; Bryce, Clay W; Lowe, Ryan J; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

    2016-08-24

    Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia-a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

  16. Conserved localization of Pax6 and Pax7 transcripts in the brain of representatives of sarcopterygian vertebrates during development supports homologous brain regionalization

    PubMed Central

    Moreno, Nerea; Joven, Alberto; Morona, Ruth; Bandín, Sandra; López, Jesús M.; González, Agustín

    2014-01-01

    Many of the genes involved in brain patterning during development are highly conserved in vertebrates and similarities in their expression patterns help to recognize homologous cell types or brain regions. Among these genes, Pax6 and Pax7 are expressed in regionally restricted patterns in the brain and are essential for its development. In the present immunohistochemical study we analyzed the distribution of Pax6 and Pax7 cells in the brain of six representative species of tetrapods and lungfishes, the closest living relatives of tetrapods, at several developmental stages. The distribution patterns of these transcription factors were largely comparable across species. In all species only Pax6 was expressed in the telencephalon, including the olfactory bulbs, septum, striatum, and amygdaloid complex. In the diencephalon, Pax6 and Pax7 were distinct in the alar and basal parts, mainly in prosomeres 1 and 3. Pax7 specifically labeled cells in the optic tectum (superior colliculus) and Pax6, but not Pax7, cells were found in the tegmentum. Pax6 was found in most granule cells of the cerebellum and Pax7 labeling was detected in cells of the ventricular zone of the rostral alar plate and in migrated cells in the basal plate, including the griseum centrale and the interpeduncular nucleus. Caudally, Pax6 cells formed a column, whereas the ventricular zone of the alar plate expressed Pax7. Since the observed Pax6 and Pax7 expression patterns are largely conserved they can be used to identify subdivisions in the brain across vertebrates that are not clearly discernible with classical techniques. PMID:25147506

  17. Conclusions and recommendations of the Latin America and Caribbean Regional Energy Conservation Seminar, Alajuela, Costa Rica, January 14-17, 1985

    SciTech Connect

    Not Available

    1985-03-29

    Reports were given on active energy-conservation projects in the region (Barbados, Jamaica, Central American region and Panama, Peru, Ecuador, the Dominican Republic, and Costa Rica). In addition, there were presentations on energy auditing, fuel substitution, and financing energy conservation. Although the seminar concentrated on the industrial sector, it also explored opportunities for energy-efficiency improvements in the building and transportation sectors.

  18. A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

    PubMed Central

    Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimarães

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

  19. Secondary structures for 5′ regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints

    PubMed Central

    Kierzek, Elzbieta; Christensen, Shawn M.; Eickbush, Thomas H.; Moss, Walter N.

    2009-01-01

    Summary Sequences from the 5′ region of R2 retrotransposons of four species of silk moth are reported. In Bombyx mori, this region of the R2 messenger RNA contains a binding site for R2 protein and mediates interactions critical to R2 element insertion into the host genome. A model of secondary structure for this RNA fragment is proposed on the basis of binding to oligonucleotide microarrays, chemical mapping, and comparative sequence analysis. Five regions of conserved secondary structure are identified, including a novel pseudoknot. There is an apparent transition from an entirely RNA structure coding function in most of the 5′ segment of the fragment to a protein coding function in the 3′ segment. This suggests that regions evolved under separate functional constraints (structural, coding, or both). PMID:19397915

  20. Nature Conservancy of Canada (NCC)--Manitoba Region's Environmental Education Program

    ERIC Educational Resources Information Center

    Shaluk, Cathy

    2007-01-01

    The Nature Conservancy of Canada (NCC) is excited and proud to offer its first ever in-class education programs on the Tall Grass Prairie Ecosystem. These curriculum-based programs are offered to students from Kindergarten through to Grade 12. This experience gives many students who may never have the opportunity to visit a real live prairie to…

  1. Regional effects of agricultural conservation practices on nutrient transport in the Upper Mississippi River Basin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite progress in the implementation of conservation practices, related improvements in water quality have been challenging to measure in larger river systems. In this paper we quantify these downstream effects by applying the empirical U.S. Geological Survey water-quality model SPARROW to inves...

  2. Structure-sequence based analysis for identification of conserved regions in proteins

    DOEpatents

    Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

    2013-05-28

    Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

  3. Conservation Tillage as a Solution to Drought in Both the Southeastern and Western Peanut Growing Regions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Conservation tillage cropping systems were introduced in the 1970s and much research has documented positive benefits such as decreased erosion, general soil improvement (carbon sequestration), and decreased labor, time, and fuel devoted to land preparation. Strip tillage, in-row subsoiling followe...

  4. Picking up the pieces: conserving remnant natural areas in the post-industrial landscape of the Calumet Region

    USGS Publications Warehouse

    Labus, Paul; Whitman, Richard L.; Nevers, Meredith Becker

    1999-01-01

    The Calumet Region was shaped by geologic forces, succession, and interacting biomes converging on a unique natural landscape. Over the past 4500 years, a strand plain has formed to the north of a geologic area called Toleston Beach. Sequential and differential primary succession of dune and swale communities in this region allowed species from different biomes to interact freely. In the mid-nineteenth century, commerce and settlement drastically changed the area, and natural areas were fragmented, manipulated, and degraded by cultural intrusions and industrialization. Despite the near obliteration of dune and swale habitat, small fragments of natural land escaped destruction. These native fragments maintained some semblance of the landscape that once covered the region. Currently, these native fragments are threatened by the lingering intrusion of historic contamination and the continuing presence of industry and commerce. Restoration and conservation of these remnants will need to be a process of integrating biological diversity goals into the landscape of the industrialized region through planning and design. We outline here the natural history of the region, the philosophical rationale for conservation, and possible approaches for integrating and maintaining these valuable remnant resources and processes.

  5. The upstream conserved regions (UCRs) mediate homo- and hetero-oligomerization of type 4 cyclic nucleotide phosphodiesterases (PDE4s).

    PubMed

    Xie, Moses; Blackman, Brigitte; Scheitrum, Colleen; Mika, Delphine; Blanchard, Elise; Lei, Tao; Conti, Marco; Richter, Wito

    2014-05-01

    PDE4s (type 4 cyclic nucleotide phosphodiesterases) are divided into long and short forms by the presence or absence of conserved N-terminal domains termed UCRs (upstream conserved regions). We have shown previously that PDE4D2, a short variant, is a monomer, whereas PDE4D3, a long variant, is a dimer. In the present study, we have determined the apparent molecular masses of various long and short PDE4 variants by size-exclusion chromatography and sucrose density-gradient centrifugation. Our results indicate that dimerization is a conserved property of all long PDE4 forms, whereas short forms are monomers. Dimerization is mediated by the UCR domains. Given their high sequence conservation, the UCR domains mediate not only homo-oligomerization, but also hetero-oligomerization of distinct PDE4 long forms as detected by co-immunoprecipitation assays and FRET microscopy. Endogenous PDE4 hetero-oligomers are, however, low in abundance compared with homo-dimers, revealing the presence of mechanisms that predispose PDE4s towards homo-oligomerization. Oligomerization is a prerequisite for the regulatory properties of the PDE4 long forms, such as their PKA (protein kinase A)-dependent activation, but is not necessary for PDE4 protein-protein interactions. As a result, individual PDE4 protomers may independently mediate protein-protein interactions, providing a mechanism whereby PDE4s contribute to the assembly of macromolecular signalling complexes.

  6. Decreased Adherence of Enterohemorrhagic Escherichia coli to HEp-2 Cells in the Presence of Antibodies That Recognize the C-Terminal Region of Intimin

    PubMed Central

    Gansheroff, Lisa J.; Wachtel, Marian R.; O'Brien, Alison D.

    1999-01-01

    Antiserum raised against intimin from enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain 86-24 has been shown previously by our laboratory to inhibit adherence of this strain to HEp-2 cells. In the present study, we sought to identify the region(s) of intimin important for the effect of anti-intimin antisera on EHEC adherence and to determine whether antisera raised against intimin from an O157:H7 strain could reduce adherence of other strains. Compared to preimmune serum controls, polyclonal sera raised against the histidine-tagged intimin protein RIHisEae (intiminO157) or against His-tagged C-terminal fragments of intimin from strain 86-24 reduced adherence of this strain. Furthermore, an antibody fraction purified from the anti-RIHisEae serum that contained antibodies to the C-terminal third of intimin, the putative receptor-binding domain, also reduced adherence of strain 86-24, but a purified fraction containing antibodies to the N-terminal two-thirds of intimin did not inhibit adherence. The polyclonal anti-intiminO157 serum raised against RIHisEae inhibited, to different degrees, the adherence of another O157:H7 strain, an EHEC O55:H7 strain, one of two independent EHEC O111:NM isolates tested, and one of two EHEC O26:H11 strains tested. Adherence of the other O26:H11 and O111:NM strains and an EPEC O127:H6 strain was not reduced. Finally, immunoblot analysis indicated a correlation between the antigenic divergence in the C-terminal third of intimins from different strains and the capacity of anti-intiminO157 antiserum to reduce adherence of heterologous strains. Taken together, these data suggest that intiminO157 could be used as an immunogen to elicit adherence-blocking antibodies against O157:H7 strains and closely-related EHEC. PMID:10569757

  7. Potential conservation opportunities from the use of improved irrigation scheduling in the Pacific Northwest region

    SciTech Connect

    Harrer, B J; Lezberg, A J

    1985-03-01

    This report documents research to identify the potential energy savings and the costs per kWh saved from using systematic rather than traditional irrigation scheduling to reduce water usage in the irrigated agricultural sector of the Pacific Northwest. This research is part of an overall project aimed at developing a computer model and data base that will allow for estimation of the potential energy savings and cost effectiveness of a number of conservation technologies that are available for use in irrigated agriculture.

  8. Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

    PubMed Central

    Brown, Jenna R.; Livesay, Dennis R.

    2015-01-01

    β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme. PMID:26018804

  9. Identification and Potential Regulatory Properties of Evolutionary Conserved Regions (ECRs) at the Schizophrenia-Associated MIR137 Locus.

    PubMed

    Gianfrancesco, Olympia; Griffiths, Daniel; Myers, Paul; Collier, David A; Bubb, Vivien J; Quinn, John P

    2016-10-01

    Genome-wide association studies (GWAS) have identified a region at chromosome 1p21.3, containing the microRNA MIR137, to be among the most significant associations for schizophrenia. However, the mechanism by which genetic variation at this locus increases risk of schizophrenia is unknown. Identifying key regulatory regions around MIR137 is crucial to understanding the potential role of this gene in the aetiology of psychiatric disorders. Through alignment of vertebrate genomes, we identified seven non-coding regions at the MIR137 locus with conservation comparable to exons (>70 %). Bioinformatic analysis using the Psychiatric Genomics Consortium GWAS dataset for schizophrenia showed five of the ECRs to have genome-wide significant SNPs in or adjacent to their sequence. Analysis of available datasets on chromatin marks and histone modification data showed that three of the ECRs were predicted to be functional in the human brain, and three in development. In vitro analysis of ECR activity using reporter gene assays showed that all seven of the selected ECRs displayed transcriptional regulatory activity in the SH-SY5Y neuroblastoma cell line. This data suggests a regulatory role in the developing and adult brain for these highly conserved regions at the MIR137 schizophrenia-associated locus and further that these domains could act individually or synergistically to regulate levels of MIR137 expression. PMID:27525637

  10. Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.

    PubMed

    Kierzek, Elzbieta; Christensen, Shawn M; Eickbush, Thomas H; Kierzek, Ryszard; Turner, Douglas H; Moss, Walter N

    2009-07-17

    Sequences from the 5' region of R2 retrotransposons of four species of silk moth are reported. In Bombyx mori, this region of the R2 messenger RNA contains a binding site for R2 protein and mediates interactions critical to R2 element insertion into the host genome. A model of secondary structure for a segment of this RNA is proposed on the basis of binding to oligonucleotide microarrays, chemical mapping, and comparative sequence analysis. Five conserved secondary structures are identified, including a novel pseudoknot. There is an apparent transition from an entirely RNA structure coding function in most of the 5' segment to a protein coding function near the 3' end. This suggests that local regions evolved under separate functional constraints (structural, coding, or both).

  11. Integrated assessment of conservation opportunities in the irrigated agriculture sector of the Pacific Northwest Region

    SciTech Connect

    Harrer, B.J.; Lezberg, A.J.; Wilfert, G.L.

    1985-02-01

    This report documents research to identify the potential energy savings and cost per kWh saved for implementing currently available energy conservation measures in the irrigated agriculture sector of the Pacific Northwest. A computer model that simulates the energy consumption process of irrigation systems and estimates the levelized costs of undertaking conservation investments is the primary analytical tool used in this research. Using engineering and economic input parameters for the various conservation measures that could potentially be implemented in irrigated agriculture, the Irrigation Sector Energy Planning (ISEP) model generates estimates of energy savings and cost per kWh saved for the measures. All parameters input to the ISEP model are based upon empirical field data. Results provided by the ISEP model indicate tht by the year 2003 a total of approximately 158.6 average MW of energy could potentially be saved in the Pacific Northwest irrigation sector on all sprinkler-irrigated acres. Approximately 130.4 average MW can be saved on acres currently by sprinkler, while an additional 28.2 average MW could be saved on new acres that are forecast to come under irrigation in the next 20 years. The largest share of the total savings (47%) is estimated to come from the use of low-pressure irrigation. Over 60% of the total potential savings 158.6 average MW is estimated to be available for a cost per kWh saved of 20 mills or less and over 75% could be achieved for a cost of 30 mills or less. Savings from low-pressure irrigation and the redesign of fittings and mainlines will normally cost less than 20 mills per kWh saved. Almost all of the savings that are estimated to cost more than 30 mills per kWh saved to obtain are savings from improved irrigation scheduling on irrigated acres that use surface water and have low average pumping lifts.

  12. Evaluation of Apis mellifera syriaca Levant Region honeybee conservation using Comparative Genome Hybridization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Levant Region. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp and is resistant to Varroa mites. The A. m. syriaca control r...

  13. Conserved tertiary structural elements in the 5' nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs.

    PubMed Central

    Le, S Y; Chen, J H; Sonenberg, N; Maizel, J V

    1993-01-01

    Statistical analyses of RNA folding in 5' nontranslated regions (5'NTR) of encephalomyocarditis virus, Theiler's murine encephalomyelitis virus, foot-and-mouth disease virus, and hepatitis A virus indicate that two highly significant folding regions occur in the 5' and 3' portions of the 5'NTR. The conserved tertiary structural elements are predicted in the unusual folding regions (UFR) for these viral RNAs. The theoretical, common structural elements predicted in the 3' parts of the 5'NTR occur in a cis-acting element that is critical for internal ribosome binding. These structural motifs are expected to be highly significant from extensive Monte Carlo simulations. Nucleotides (nt) in the conserved single-stranded polypyrimidine tract for these RNAs are involved in a distinctively tertiary interaction that is located at about 15 nt prior to the initiator AUG. Intriguingly, the proposed common tertiary structure in this study shares a similar structural feature to that proposed in human enteroviruses and rhinoviruses. Based on these common structural features, plausible base pairing models between these viral RNAs and 18 S rRNA are suggested, which are consistent with a general mechanism for regulation of internal initiation of cap-independent translation. PMID:8389442

  14. Conservation of socioculturally important local crop biodiversity in the Oromia region of Ethiopia: a case study.

    PubMed

    Balemie, Kebu; Singh, Ranjay K

    2012-09-01

    In this study, we surveyed diversity in a range of local crops in the Lume and Gimbichu districts of Ethiopia, together with the knowledge of local people regarding crop uses, socio-economic importance, conservation, management and existing threats. Data were collected using semistructured interviews and participant observation. The study identified 28 farmers' varieties of 12 crop species. Among these, wheat (Triticum turgidum) and tef (Eragrostis tef) have high intra-specific diversity, with 9 and 6 varieties respectively. Self-seed supply or seed saving was the main (80 %) source of seeds for replanting. Agronomic performance (yield and pest resistance), market demand, nutritional and use diversity attributes of the crop varieties were highlighted as important criteria for making decisions regarding planting and maintenance. Over 74 % of the informants grow a combination of "improved" and farmers' varieties. Of the farmers' varieties, the most obvious decline and/or loss was reported for wheat varieties. Introduction of improved wheat varieties, pest infestation, shortage of land, low yield performance and climate variability were identified as the principal factors contributing to this loss or decline. Appropriate interventions for future conservation and sustainable use of farmers' varieties were suggested. PMID:22729809

  15. Conservation of Socioculturally Important Local Crop Biodiversity in the Oromia Region of Ethiopia: A Case Study

    NASA Astrophysics Data System (ADS)

    Balemie, Kebu; Singh, Ranjay K.

    2012-09-01

    In this study, we surveyed diversity in a range of local crops in the Lume and Gimbichu districts of Ethiopia, together with the knowledge of local people regarding crop uses, socio-economic importance, conservation, management and existing threats. Data were collected using semistructured interviews and participant observation. The study identified 28 farmers' varieties of 12 crop species. Among these, wheat ( Triticum turgidum) and tef ( Eragrostis tef) have high intra-specific diversity, with 9 and 6 varieties respectively. Self-seed supply or seed saving was the main (80 %) source of seeds for replanting. Agronomic performance (yield and pest resistance), market demand, nutritional and use diversity attributes of the crop varieties were highlighted as important criteria for making decisions regarding planting and maintenance. Over 74 % of the informants grow a combination of "improved" and farmers' varieties. Of the farmers' varieties, the most obvious decline and/or loss was reported for wheat varieties. Introduction of improved wheat varieties, pest infestation, shortage of land, low yield performance and climate variability were identified as the principal factors contributing to this loss or decline. Appropriate interventions for future conservation and sustainable use of farmers' varieties were suggested.

  16. Conservation of cultural heritage in minority ethnic regions in northwestern china—an exploration at Kuqa, Xinjiang

    NASA Astrophysics Data System (ADS)

    Wu, N.; Zhang, X.

    2015-08-01

    Kuqa, Xinjiang, is located at northwestern inland china. Traditionally a bridge between eastern and western civilizations, Kuqa had a history of cultural fusion and was left with abundant cultural heritage. As population increase, economic growth and social changes occurred, spontaneous renovation of the old city was affected, in which street fabric and scenes underwent damages. The paper demonstrates attempts made in various projects to achieve conservation of cultural heritage in agreement with economic development and improvement of living condition. The lessons learnt in these projects will be of value to development of other historic cities, especially in minority ethnic regions in China.

  17. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

    SciTech Connect

    Fleishman, Sarel J.; Whitehead, Timothy A.; Ekiert, Damian C.; Dreyfus, Cyrille; Corn, Jacob E.; Strauch, Eva-Maria; Wilson, Ian A.; Baker, David

    2011-09-28

    We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.

  18. Intelligent irrigation performance: evaluation and quantifying its ability for conserving water in arid region

    NASA Astrophysics Data System (ADS)

    Al-Ghobari, Hussein M.; Mohammad, Fawzi S.

    2011-12-01

    Intelligent irrigation technologies have been developed in recent years to apply irrigation to turf and landscape plants. These technologies are an evapotranspiration (ET)-based irrigation controller, which calculates ET for local microclimate. Then, the controller creates a program for loading and communicating automatically with drip or sprinkler system controllers. The main objective of this study was to evaluate the effectiveness of the new ET sensors in ability to irrigate agricultural crops and to conserve water use for crop in arid climatic conditions. This paper presents the case for water conservation using intelligent irrigation system (IIS) application technology. The IIS for automating irrigation scheduling was implemented and tested with sprinkle and drip irrigation systems to irrigate wheat and tomato crops. Another irrigation scheduling system was also installed and operated as another treatment, which is based on weather data that retrieved from an automatic weather station. This irrigation control system was running in parallel to the former system (IIS) to be control experiments for comparison purposes. However, this article discusses the implementation of IIS, its installation, testing and calibration of various components. The experiments conducted for one growing season 2009-2010 and the results were represented and discussed herein. Data from all plots were analyzed, which were including soil water status, water consumption, and crop yield. The initial results indicate that up to 25% water saving by intelligent irrigation compared to control method, while maintaining competing yield. Results show that the crop evapotranspiration values for control experiments were higher than that of ET-System in consistent trend during whole growth season. The analysis points out that the values of the two treatments were somewhat close to each other's only in the initial development stages. Generally, the ET-System, with some modification was precise in

  19. Recognizing Battered Wife Syndrome

    PubMed Central

    Swanson, Richard W.

    1985-01-01

    Battered wife syndrome is difficult to detect because the women usually do not volunteer the diagnosis. They often present with vague somatic complaints such as headache, lower back pain, abdominal pain, pelvic pain and dyspareunia. Four case histories demonstrate the difficulty in recognizing the cause of these complaints. The diagnosis was often missed because straight-forward, non-threatening, open-ended questions were not asked initially. The family physician's primary role is to identify the syndrome and initiate psychotherapy. Psychotherapy is centred on reversing “learned helplessness” and developing a new self-concept. This can be enhanced by an interval or transition house. PMID:21274067

  20. [Vegetation structures and conservation of Mediterranean temporary wetlands: Mogods region (northern Tunisia)].

    PubMed

    Ferchichi-Ben Jamaa, Hafawa; Muller, Serge D; Daoud-Bouattour, Amina; Ghrabi-Gammar, Zeineb; Rhazi, Laïla; Soulié-Märsche, Ingeborg; Ouali, Mounira; Saad-Limam, Semia Ben

    2010-03-01

    Floristic surveys and phytoecological relevés were conducted on 36 temporary wetlands of Mogods region. Multivariate analyses (CA, AHC) performed on these data reveal the high specific and biocoenotic diversity of Mogods wetlands, which appear controlled by substrate nature and hydrology. Among the 128 hydrophytic species inventoried, 38 are presently in precarious status and 6 are presumed extinct. The Mogods region harbours, moreover, very rare habitats (peatlands and semi-permanent lakes), and a vast plain so-called Garâa Sejenane, exceptionally rich in temporary wetlands. These results underline the urgency of an adapted conservatory management, based on the development of scientific studies dealing with structure and functioning of hydrophytic communities of the region.

  1. Phylogenetic footprinting reveals evolutionarily conserved regions of the gonadotropin-releasing hormone gene that enhance cell-specific expression.

    PubMed

    Givens, Marjory L; Kurotani, Reiko; Rave-Harel, Naama; Miller, Nichol L G; Mellon, Pamela L

    2004-12-01

    Reproductive function is controlled by the hypothalamic neuropeptide, GnRH, which serves as the central regulator of the hypothalamic-pituitary-gonadal axis. GnRH expression is limited to a small population of neurons in the hypothalamus. Targeting this minute population of neurons (as few as 800 in the mouse) requires regulatory elements upstream of the GnRH gene that remain to be fully characterized. Previously, we have identified an evolutionarily conserved promoter region (-173 to +1) and an enhancer (-1863 to -1571) in the rat gene that targets a subset of the GnRH neurons in vivo. In the present study, we used phylogenetic sequence comparison between human and rodents and analysis of the transcription factor clusters within conserved regions in an attempt to identify additional upstream regulatory elements. This approach led to the characterization of a new upstream enhancer that regulates expression of GnRH in a cell-specific manner. Within this upstream enhancer are nine binding sites for Octamer-binding transcription factor 1 (OCT1), known to be an important transcriptional regulator of GnRH gene expression. In addition, we have identified nuclear factor I (NF1) binding to multiple elements in the GnRH-regulatory regions, each in close proximity to OCT1. We show that OCT1 and NF1 physically and functionally interact. Moreover, the OCT1 and NF1 binding sites in the regulatory regions appear to be essential for appropriate GnRH gene expression. These findings indicate a role for this upstream enhancer and novel OCT1/NF1 complexes in neuron-restricted expression of the GnRH gene.

  2. Insular Ecosystems of the Southeastern United States- A Regional Synthesis to Support Biodiversity Conservation in a Changing Climate

    USGS Publications Warehouse

    Cartwright, Jennifer M.; Wolfe, William J.

    2016-01-01

    In the southeastern United States, insular ecosystems—such as rock outcrops, depression wetlands, high-elevation balds, flood-scoured riparian corridors, and insular prairies and barrens—occupy a small fraction of land area but constitute an important source of regional and global biodiversity, including concentrations of rare and endemic plant taxa. Maintenance of this biodiversity depends upon regimes of abiotic stress and disturbance, incorporating factors such as soil surface temperature, widely fluctuating hydrologic conditions, fires, flood scouring, and episodic droughts that may be subject to alteration by climate change. Over several decades, numerous localized, site-level investigations have yielded important information about the floristics, physical environments, and ecological dynamics of these insular ecosystems; however, the literature from these investigations has generally remained fragmented. This report consists of literature syntheses for eight categories of insular ecosystems of the southeastern United States, concerning (1) physical geography, (2) ecological determinants of community structures including vegetation dynamics and regimes of abiotic stress and disturbance, (3) contributions to regional and global biodiversity, (4) historical and current anthropogenic threats and conservation approaches, and (5) key knowledge gaps relevant to conservation, particularly in terms of climate-change effects on biodiversity. This regional synthesis was undertaken to discern patterns across ecosystems, identify knowledge gaps, and lay the groundwork for future analyses of climate-change vulnerability. Findings from this synthesis indicate that, despite their importance to regional and global biodiversity, insular ecosystems of the southeastern United States have been subjected to a variety of direct and indirect human alterations. In many cases, important questions remain concerning key determinants of ecosystem function. In particular, few

  3. Insular ecosystems of the southeastern United States—A regional synthesis to support biodiversity conservation in a changing climate

    USGS Publications Warehouse

    Cartwright, Jennifer M.; Wolfe, William J.

    2016-08-11

    In the southeastern United States, insular ecosystems—such as rock outcrops, depression wetlands, high-elevation balds, flood-scoured riparian corridors, and insular prairies and barrens—occupy a small fraction of land area but constitute an important source of regional and global biodiversity, including concentrations of rare and endemic plant taxa. Maintenance of this biodiversity depends upon regimes of abiotic stress and disturbance, incorporating factors such as soil surface temperature, widely fluctuating hydrologic conditions, fires, flood scouring, and episodic droughts that may be subject to alteration by climate change. Over several decades, numerous localized, site-level investigations have yielded important information about the floristics, physical environments, and ecological dynamics of these insular ecosystems; however, the literature from these investigations has generally remained fragmented. This report consists of literature syntheses for eight categories of insular ecosystems of the southeastern United States, concerning (1) physical geography, (2) ecological determinants of community structures including vegetation dynamics and regimes of abiotic stress and disturbance, (3) contributions to regional and global biodiversity, (4) historical and current anthropogenic threats and conservation approaches, and (5) key knowledge gaps relevant to conservation, particularly in terms of climate-change effects on biodiversity. This regional synthesis was undertaken to discern patterns across ecosystems, identify knowledge gaps, and lay the groundwork for future analyses of climate-change vulnerability. Findings from this synthesis indicate that, despite their importance to regional and global biodiversity, insular ecosystems of the southeastern United States have been subjected to a variety of direct and indirect human alterations. In many cases, important questions remain concerning key determinants of ecosystem function. In particular, few

  4. Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation.

    PubMed

    Roode, Sarah C; Rotroff, Daniel; Avery, Anne C; Suter, Steven E; Bienzle, Dorothee; Schiffman, Joshua D; Motsinger-Reif, Alison; Breen, Matthew

    2015-12-01

    Leukemia in dogs is a heterogeneous disease with survival ranging from days to years, depending on the subtype. Strides have been made in both human and canine leukemia to improve classification and understanding of pathogenesis through immunophenotyping, yet classification and choosing appropriate therapy remains challenging. In this study, we assessed 123 cases of canine leukemia (28 ALLs, 24 AMLs, 25 B-CLLs, and 46 T-CLLs) using high-resolution oligonucleotide array comparative genomic hybridization (oaCGH) to detect DNA copy number alterations (CNAs). For the first time, such data were used to identify recurrent CNAs and inclusive genes that may be potential drivers of subtype-specific pathogenesis. We performed predictive modeling to identify CNAs that could reliably differentiate acute subtypes (ALL vs. AML) and chronic subtypes (B-CLL vs. T-CLL) and used this model to differentiate cases with up to 83.3 and 95.8 % precision, respectively, based on CNAs at only one to three genomic regions. In addition, CGH datasets for canine and human leukemia were compared to reveal evolutionarily conserved copy number changes between species, including the shared gain of HSA 21q in ALL and ∼25 Mb of shared gain of HSA 12 and loss of HSA 13q14 in CLL. These findings support the use of canine leukemia as a relevant in vivo model for human leukemia and justify the need to further explore the conserved genomic regions of interest for their clinical impact.

  5. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.

    PubMed

    Patra, Ajit Kumar; Kwon, Yong Min; Kang, Sung Gyun; Fujiwara, Yoshihiro; Kim, Sang-Jin

    2016-04-01

    The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions. PMID:26776396

  6. Mapping of the gene for a major penicillin-binding protein to a genetically conserved region of the Bacillus subtilis chromosome and conservation of the protein among related species of Bacillus.

    PubMed Central

    Buchanan, C E; Gustafson, A

    1991-01-01

    Penicillin-binding protein 5 is the most abundant penicillin-binding protein in the vegetative membranes of Bacillus subtilis and accounts for 95% of the D,D-carboxypeptidase activity of the cell. The structural gene for penicillin-binding protein 5 was mapped to a genetically conserved region near guaB at 0 degrees on the B. subtilis chromosome, and immunoassays revealed that there is conservation of this major penicillin-binding protein among related species. Images PMID:1900282

  7. 76 FR 76328 - Energy Conservation Program: Enforcement of Regional Standards for Residential Furnaces and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-07

    ... these products that established regional standards. 76 FR 37549. In addition to the current base... effective date and compliance dates for the direct final rule on October 31, 2011 (76 FR 67037), requiring... Residential Furnaces and Central Air Conditioners and Heat Pumps AGENCY: Office of Energy Efficiency...

  8. Analysing biodiversity and conservation knowledge products to support regional environmental assessments.

    PubMed

    Brooks, Thomas M; Akçakaya, H Resit; Burgess, Neil D; Butchart, Stuart H M; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C; Rodrigues, Ana S L; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E

    2016-02-16

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird &Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.

  9. Analysing biodiversity and conservation knowledge products to support regional environmental assessments.

    PubMed

    Brooks, Thomas M; Akçakaya, H Resit; Burgess, Neil D; Butchart, Stuart H M; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C; Rodrigues, Ana S L; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E

    2016-01-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird &Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments. PMID:26881749

  10. Analysing biodiversity and conservation knowledge products to support regional environmental assessments

    PubMed Central

    Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H.M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S.L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

    2016-01-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments. PMID:26881749

  11. The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The evolution of five chromosomes of Brachypodium distachyon from a 12-chromosome ancestor of all grasses by dysploidy raises an interesting question about the fate of redundant centromeres. Three independent but complementary approaches were pursued to study centromeric region homologies among the ...

  12. A conserved karyotype of Sternopygus macrurus (Sternopygidae, Gymnotiformes) in the Amazon region: differences from other hydrographic basins suggest cryptic speciation.

    PubMed

    dos Santos Silva, Danillo; Milhomem, Susana Suely Rodrigues; de Souza, Augusto Cezar Paes; Pieczarka, Julio Cesar; Nagamachi, Cleusa Yoshiko

    2008-12-01

    We studied the karyotypes of 35 Sternopygus macrurus fishes of four localities from rivers of the Eastern Amazon basin. In these four places the karyotypes have 2n=46 chromosomes, NF=92, where 30 are metacentric (M) and 16 submetacentric (SM). The constitutive heterochromatin (CH) is found in the centromeric region of most chromosomes and in the pericentromeric region of pairs 5, 17 and 19. Pair 1 has a large and not common heterochromatic block in the short arm, useful as a marker for this species if not found in other Sternopygus taxa. The NOR is located in the distal region of the short arm of pair 1, showing a size heteromorphism in some specimens. The CMA(3) and DAPI fluorochrome bandings and the fluorescent in situ hybridization (FISH), using pantelomeric human probes techniques are described for the first time for this species. DAPI has banding coincident with the C-banded regions, which suggests that the CH is AT base-pair-rich. CMA(3) banding is coincident with the NOR, meaning that this region is GC base-pair-rich. The FISH showed that the probes hybridized only with the telomeric regions, without any sign of interstitial telomeric regions. The karyotype of the samples from different places in the Amazon basin is quite conserved, probably because of the gene flow among the populations. The karyotype differences among the Sternopygus macrurus from the Amazon basin and the São Francisco and Paraná rivers suggest that these taxa may be different species. PMID:18486480

  13. Conserved nucleotide sequences in the open reading frame and 3' untranslated region of selenoprotein P mRNA.

    PubMed Central

    Hill, K E; Lloyd, R S; Burk, R F

    1993-01-01

    Rat liver selenoprotein P contains 10 selenocysteine residues in its primary structure (deduced). It is the only selenoprotein characterized to date that has more than one selenocysteine residue. Selenoprotein P cDNA has been cloned from human liver and heart cDNA libraries and sequenced. The open reading frames are identical and contain a signal peptide, indicating that the protein is secreted by both organs and is therefore not exclusively produced in the liver. Ten selenocysteine residues (deduced) are present. Comparison of the open reading frame of the human cDNA with the rat cDNA reveals a 69% identity of the nucleotide sequence and 72% identity of the deduced amino acid sequence. Two regions in the 3' untranslated portion have high conservation between human and rat. Each of these regions contains a predicted stable stem-loop structure similar to the single stem-loop structures reported in 3' untranslated regions of type I iodothyronine 5'-deiodinase and glutathione peroxidase. The stem-loop structure of type I iodothyronine 5'-deiodinase has been shown to be necessary for incorporation of the selenocysteine residue at the UGA codon. Because only two stem-loop structures are present in the 3' untranslated region of selenoprotein P mRNA, it can be concluded that a separate stem-loop structure is not required for each selenocysteine residue. Images PMID:8421687

  14. Recognizing the Trends

    NASA Technical Reports Server (NTRS)

    Marley, Mark Scott

    2016-01-01

    Solar system planetary science has traditionally focused on understanding in depth individual planets. While there have been some efforts at synergy, most studies have focused on understanding the details of individual planets. Now that we are in the era of exoplanet science, with thousands of known planets and hundreds that have been characterized to varying degrees, the systematics of planetary science are becoming apparent. This also means that, for the first time, what had previously been seen as individual quirks of solar system planets are instead being recognized as part of the normal range of planetary behavior. In my talk I will consider a number of such characteristics and explain how we are now starting to understand their true context. In particular I will discuss the atmospheric composition, clouds, hazes, and winds of giant planets, trace gasses in the atmosphere of Venus, and the presence and absence of atmospheres on various terrestrial worlds.

  15. Conserved Regional Patterns of GABA-Related Transcript Expression in the Neocortex of Subjects With Schizophrenia

    PubMed Central

    Hashimoto, Takanori; Bazmi, H. Holly; Mirnics, Karoly; Wu, Qiang; Sampson, Allan R.; Lewis, David A.

    2010-01-01

    Objective Individuals with schizophrenia exhibit disturbances in a number of cognitive, affective, sensory, and motor functions that depend on the circuitry of different cortical areas. The cognitive deficits associated with dysfunction of the dorsolateral prefrontal cortex result, at least in part, from abnormalities in GABA neurotransmission, as reflected in a specific pattern of altered expression of GABA-related genes. Consequently, the authors sought to determine whether this pattern of altered gene expression is restricted to the dorsolateral prefrontal cortex or could also contribute to the dysfunction of other cortical areas in subjects with schizophrenia. Method Real-time quantitative polymerase chain reaction was used to assess the levels of eight GABA-related transcripts in four cortical areas (dorsolateral prefrontal cortex, anterior cingulate cortex, and primary motor and primary visual cortices) of subjects (N=12) with schizophrenia and matched normal comparison subjects. Results Expression levels of seven transcripts were lower in subjects with schizophrenia, with the magnitude of reduction for each transcript comparable across the four areas. The largest reductions were detected for mRNA encoding somatostatin and parvalbumin, followed by moderate decreases in mRNA expression for the 67-kilodalton isoform of glutamic acid decarboxylase, the GABA membrane transporter GAT-1, and the α1 and δ subunits of GABAA receptors. In contrast, the expression of calretinin mRNA did not differ between the subject groups in any of the four areas. Conclusions Because the areas examined represent the major functional domains (e.g., association, limbic, motor, and sensory) of the cerebral cortex, our findings suggest that a conserved set of molecular alterations affecting GABA neurotransmission contribute to the pathophysiology of different clinical features of schizophrenia. PMID:18281411

  16. Use of empirically derived source-destination models to map regional conservation corridors.

    PubMed

    Cushman, Samuel A; McKelvey, Kevin S; Schwartz, Michael K

    2009-04-01

    The ability of populations to be connected across large landscapes via dispersal is critical to long-term viability for many species. One means to mitigate population isolation is the protection of movement corridors among habitat patches. Nevertheless, the utility of small, narrow, linear features as habitat corridors has been hotly debated. Here, we argue that analysis of movement across continuously resistant landscapes allows a shift to a broader consideration of how landscape patterns influence connectivity at scales relevant to conservation. We further argue that this change in scale and definition of the connectivity problem improves one's ability to find solutions and may help resolve long-standing disputes regarding scale and definition of movement corridors and their importance to population connectivity. We used a new method that combines empirically derived landscape-resistance maps and least-cost path analysis between multiple source and destination locations to assess habitat isolation and identify corridors and barriers to organism movement. Specifically, we used a genetically based landscape resistance model for American black bears (Ursus americanus) to identify major movement corridors and barriers to population connectivity between Yellowstone National Park and the Canadian border. Even though western Montana and northern Idaho contain abundant public lands and the largest wilderness areas in the contiguous United States, moving from the Canadian border to Yellowstone Park along those paths indicated by modeled gene flow required bears to cross at least 6 potential barriers. Our methods are generic and can be applied to virtually any species for which reliable maps of landscape resistance can be developed. PMID:19016821

  17. Interfacial partitioning of a loop hinge residue contributes to diacylglycerol affinity of conserved region 1 domains.

    PubMed

    Stewart, Mikaela D; Cole, Taylor R; Igumenova, Tatyana I

    2014-10-01

    Conventional and novel isoenzymes of PKC are activated by the membrane-embedded second messenger diacylglycerol (DAG) through its interactions with the C1 regulatory domain. The affinity of C1 domains to DAG varies considerably among PKCs. To gain insight into the origin of differential DAG affinities, we conducted high-resolution NMR studies of C1B domain from PKCδ (C1Bδ) and its W252Y variant. The W252Y mutation was previously shown to render C1Bδ less responsive to DAG (Dries, D. R., Gallegos, L. L., and Newton, A. C. (2007) A single residue in the C1 domain sensitizes novel protein kinase C isoforms to cellular diacylglycerol production. J. Biol. Chem. 282, 826-830) and thereby emulate the behavior of C1B domains from conventional PKCs that have a conserved Tyr at the equivalent position. Our data revealed that W252Y mutation did not perturb the conformation of C1Bδ in solution but significantly reduced its propensity to partition into a membrane-mimicking environment in the absence of DAG. Using detergent micelles doped with a paramagnetic lipid, we determined that both the residue identity at position 252 and complexation with diacylglycerol influence the geometry of C1Bδ-micelle interactions. In addition, we identified the C-terminal helix α1 of C1Bδ as an interaction site with the head groups of phosphatidylserine, a known activator of PKCδ. Taken together, our studies (i) reveal the identities of C1Bδ residues involved in interactions with membrane-mimicking environment, DAG, and phosphatidylserine, as well as the affinities associated with each event and (ii) suggest that the initial ligand-independent membrane recruitment of C1B domains, which is greatly facilitated by the interfacial partitioning of Trp-252, is responsible, at least in part, for the differential DAG affinities.

  18. The contribution of the conserved hinge region residues of alpha1-antitrypsin to its reaction with elastase.

    PubMed

    Hopkins, P C; Stone, S R

    1995-12-01

    The hinge region of serpins is a conserved sequence of 8 amino acids located 7 residues away from the scissile bond at P8 to P15, on the edge of the protease-binding domain. In the inhibitory serpins the P8 to P12 residues of this motif are usually small side-chain amino acids, most commonly alanine. Each of these residues in alpha1-antitrypsin was mutated to a glutamate, and the effect of a hinge-region glutamic acid substitution was found. While substitutions at positions P10 and P12 affected the inhibitory characteristics of alpha1-antitrypsin, substitutions at positions P7, P8, P9, and P11 had no effect on inhibition. Thus, the conservation of residues with small side chains at the latter positions does not appear to be related to an essential function in the inhibitory mechanism. Following the glutamate substitution at P10, alpha1-antitrypsin remained a rapid inhibitor of elastase, but the elastase--serpin complex slowly broke down to yield active elastase and cleaved alpha1-antitrypsin. The glutamate substitution at P12 caused the resultant molecule (P12 Ala-->Glu) to become a partial substrate of elastase such that four moles of inhibitor were required to inhibit one mole of enzyme, and led to a 12-fold decrease in the association rate constant. The data could be interpreted in terms of the suicide substrate inhibition model for serpin-protease interactions and allowed a further refinement of the role of the hinge region in this process.

  19. Barcoding Chrysomelidae: a resource for taxonomy and biodiversity conservation in the Mediterranean Region

    PubMed Central

    Magoga, Giulia; Sassi, Davide; Daccordi, Mauro; Leonardi, Carlo; Mirzaei, Mostafa; Regalin, Renato; Lozzia, Giuseppe; Montagna, Matteo

    2016-01-01

    Abstract The Mediterranean Region is one of the world’s biodiversity hot-spots, which is also characterized by high level of endemism. Approximately 2100 species of leaf beetle (Coleoptera; Chrysomelidae) are known from this area, a number that increases year after year and represents 5/6% of the known species. These features, associated with the urgent need to develop a DNA-based species identification approach for a broad spectrum of leaf beetle species, prompted us to develop a database of nucleotide sequences, with a solid taxonomic background, for all the Chrysomelidae Latreille, 1802 sensu latu inhabiting the Mediterranean region. The Mediterranean Chrysomelidae Barcoding project, which has started in 2009, involves more than fifty entomologists and molecular biologists from different European countries. Numerous collecting campaigns have been organized during the first seven years of the project, which led to the collection of more than 5000 leaf beetle specimens. In addition, during these collecting campaigns two new allochthonous species for Europe, namely Ophraella communa LeSage, 1986 and Colasposoma dauricum Mannerheim, 1849, were intercepted and some species new to science were discovered (e.g., Pachybrachis sassii Montagna, 2011 and Pachybrachis holerorum Montagna et al., 2013). DNA was extracted from 1006 specimens (~13% of the species inhabiting the Mediterranean region) and a total of 910 cox1 gene sequences were obtained (PCR amplification efficiency of 93.8%). Here we report the list of the barcoded subfamilies, genera and the number of species for which cox1 gene sequences were obtained; the metadata associated with each specimen and a list of problematic species for which marker amplification failed. In addition, the nucleotide divergence within and between species and genera was estimated and values of intraspecific nucleotide divergence greater than the average have been discussed. Cryptocephalus quadripunctatus G. A. Olivier, 1808

  20. Barcoding Chrysomelidae: a resource for taxonomy and biodiversity conservation in the Mediterranean Region.

    PubMed

    Magoga, Giulia; Sassi, Davide; Daccordi, Mauro; Leonardi, Carlo; Mirzaei, Mostafa; Regalin, Renato; Lozzia, Giuseppe; Montagna, Matteo

    2016-01-01

    The Mediterranean Region is one of the world's biodiversity hot-spots, which is also characterized by high level of endemism. Approximately 2100 species of leaf beetle (Coleoptera; Chrysomelidae) are known from this area, a number that increases year after year and represents 5/6% of the known species. These features, associated with the urgent need to develop a DNA-based species identification approach for a broad spectrum of leaf beetle species, prompted us to develop a database of nucleotide sequences, with a solid taxonomic background, for all the Chrysomelidae Latreille, 1802 sensu latu inhabiting the Mediterranean region. The Mediterranean Chrysomelidae Barcoding project, which has started in 2009, involves more than fifty entomologists and molecular biologists from different European countries. Numerous collecting campaigns have been organized during the first seven years of the project, which led to the collection of more than 5000 leaf beetle specimens. In addition, during these collecting campaigns two new allochthonous species for Europe, namely Ophraella communa LeSage, 1986 and Colasposoma dauricum Mannerheim, 1849, were intercepted and some species new to science were discovered (e.g., Pachybrachis sassii Montagna, 2011 and Pachybrachis holerorum Montagna et al., 2013). DNA was extracted from 1006 specimens (~13% of the species inhabiting the Mediterranean region) and a total of 910 cox1 gene sequences were obtained (PCR amplification efficiency of 93.8%). Here we report the list of the barcoded subfamilies, genera and the number of species for which cox1 gene sequences were obtained; the metadata associated with each specimen and a list of problematic species for which marker amplification failed. In addition, the nucleotide divergence within and between species and genera was estimated and values of intraspecific nucleotide divergence greater than the average have been discussed. Cryptocephalus quadripunctatus G. A. Olivier, 1808, Cryptocephalus

  1. Expanded conserved linkage group between human 16p13 and the Scid region of the mouse chromosome 16

    SciTech Connect

    Deng, Z.M.; Siciliano, M.J.; Davisson, M.T.

    1994-09-01

    Knowledge of homologies between human and mouse chromosomes is essential for understanding chromosomal evolution and the development of experimental models for human disease. We have reported the identification of a conserved linkage group between human 16p13 and the centromeric portion of the mouse 16. Defining the extent of this linkage conservation has significant biomedical implications since that region of mouse genome contains the Scid mutation and the human 16p13 contains genes that are involved in DNA repair and certain types of human leukemia as well as other diseases such as Rubinstein-Taybi Syndrome. Here, this conserved linkage group has been defined and expanded. It now contains 5 genetic loci and spans more than 3 Mb in human and 23 cM in mouse. The 5 loci are PRM1,2 (protamine 1 and 2), NOP3 (a subclone of D16S237), GSPT1 (a gene involved in the regulation of G1 to S phase transition), MYH11 (a human smooth muscle myosin heavy chain gene) and MRP (multi-drug resistant-associated protein gene). Using a panel of human-rodent hybrids that are informative for different portions of human 16, we have established the following order on human 16p: telomere-NOP3-PRM1,2-GSPT1-(MYH11,MRP)-centromere. The genes were assigned to the mouse chromosome 16 by a mouse-Chinese hamster somatic cell hybrid panel informative for mouse chromosomes. Linkage analysis using backcross mice informative for the Scid mutation indicated the following order and genetic distance (in cM) in mouse: centromere-Nop3-11.7-Prm1-1.4-Gspt1-8.2-(Myh11,Mrp)-1.4-Scid-telomere.

  2. Role of forest conservation in lessening land degradation in a temperate region: the Monarch Butterfly Biosphere Reserve, Mexico.

    PubMed

    Manzo-Delgado, Lilia; López-García, José; Alcántara-Ayala, Irasema

    2014-06-01

    With international concern about the rates of deforestation worldwide, particular attention has been paid to Latin America. Forest conservation programmes in Mexico include Payment for Environmental Services (PES), a scheme that has been successfully introduced in the Monarch Butterfly Biosphere Reserve. To seek further evidence of the role of PES in lessening land degradation processes in a temperate region, the conservation state of the Cerro Prieto ejido within the Reserve was assessed by an analysis of changes in vegetation cover and land-use between 1971 and 2013. There were no changes in the total forest surface area, but the relative proportions of the different classes of cover density had changed. In 1971, closed and semi-closed forest occupied 247.81 ha and 5.38 ha, 82.33% and 1.79% of the total area of the ejido, respectively. By 2013, closed forest had decreased to 230.38 ha (76.54% of the ejido), and semi-closed cover was 17.23 ha (5.72% of the ejido), suggesting that some semi-closed forest had achieved closed status. The final balance between forest losses and recovery was: 29.63 ha were lost, whereas 13.72 ha were recovered. Losses were mainly linked to a sanitation harvest programme to control the bark beetle Scolytus mundus. Ecotourism associated with forest conservation in the Cerro Prieto ejido has been considered by inhabitants as a focal alternative for economic development. Consequently, it is essential to develop a well-planned and solidly structured approach based on social cohesion to foster a community-led sustainable development at local level.

  3. Role of forest conservation in lessening land degradation in a temperate region: the Monarch Butterfly Biosphere Reserve, Mexico.

    PubMed

    Manzo-Delgado, Lilia; López-García, José; Alcántara-Ayala, Irasema

    2014-06-01

    With international concern about the rates of deforestation worldwide, particular attention has been paid to Latin America. Forest conservation programmes in Mexico include Payment for Environmental Services (PES), a scheme that has been successfully introduced in the Monarch Butterfly Biosphere Reserve. To seek further evidence of the role of PES in lessening land degradation processes in a temperate region, the conservation state of the Cerro Prieto ejido within the Reserve was assessed by an analysis of changes in vegetation cover and land-use between 1971 and 2013. There were no changes in the total forest surface area, but the relative proportions of the different classes of cover density had changed. In 1971, closed and semi-closed forest occupied 247.81 ha and 5.38 ha, 82.33% and 1.79% of the total area of the ejido, respectively. By 2013, closed forest had decreased to 230.38 ha (76.54% of the ejido), and semi-closed cover was 17.23 ha (5.72% of the ejido), suggesting that some semi-closed forest had achieved closed status. The final balance between forest losses and recovery was: 29.63 ha were lost, whereas 13.72 ha were recovered. Losses were mainly linked to a sanitation harvest programme to control the bark beetle Scolytus mundus. Ecotourism associated with forest conservation in the Cerro Prieto ejido has been considered by inhabitants as a focal alternative for economic development. Consequently, it is essential to develop a well-planned and solidly structured approach based on social cohesion to foster a community-led sustainable development at local level. PMID:24332200

  4. Covalent protein modification with ISG15 via a conserved cysteine in the hinge region.

    PubMed

    Bade, Veronika N; Nickels, Jochen; Keusekotten, Kirstin; Praefcke, Gerrit J K

    2012-01-01

    The ubiquitin-like protein ISG15 (interferon-stimulated gene of 15 kDa) is strongly induced by type I interferons and displays antiviral activity. As other ubiquitin-like proteins (Ubls), ISG15 is post-translationally conjugated to substrate proteins by an isopeptide bond between the C-terminal glycine of ISG15 and the side chains of lysine residues in the substrates (ISGylation). ISG15 consists of two ubiquitin-like domains that are separated by a hinge region. In many orthologs, this region contains a single highly reactive cysteine residue. Several hundred potential substrates for ISGylation have been identified but only a few of them have been rigorously verified. In order to investigate the modification of several ISG15 substrates, we have purified ISG15 conjugates from cell extracts by metal-chelate affinity purification and immunoprecipitations. We found that the levels of proteins modified by human ISG15 can be decreased by the addition of reducing agents. With the help of thiol blocking reagents, a mutational analysis and miRNA mediated knock-down of ISG15 expression, we revealed that this modification occurs in living cells via a disulphide bridge between the substrates and Cys78 in the hinge region of ISG15. While the ISG15 activating enzyme UBE1L is conjugated by ISG15 in the classical way, we show that the ubiquitin conjugating enzyme Ubc13 can either be classically conjugated by ISG15 or can form a disulphide bridge with ISG15 at the active site cysteine 87. The latter modification would interfere with its function as ubiquitin conjugating enzyme. However, we found no evidence for an ISG15 modification of the dynamin-like GTPases MxA and hGBP1. These findings indicate that the analysis of potential substrates for ISG15 conjugation must be performed with great care to distinguish between the two types of modification since many assays such as immunoprecipitation or metal-chelate affinity purification are performed with little or no reducing agent

  5. Genetic and functional interaction of evolutionarily conserved regions of the Prp18 protein and the U5 snRNA.

    PubMed

    Bacíková, Dagmar; Horowitz, David S

    2005-03-01

    Both the Prp18 protein and the U5 snRNA function in the second step of pre-mRNA splicing. We identified suppressors of mutant prp18 alleles in the gene for the U5 snRNA (SNR7). The suppressors' U5 snRNAs have either a U4-to-A or an A8-to-C mutation in the evolutionarily invariant loop 1 of U5. Suppression is specific for prp18 alleles that encode proteins with mutations in a highly conserved region of Prp18 which forms an unstructured loop in crystals of Prp18. The snr7 suppressors partly restored the pre-mRNA splicing activity that was lost in the prp18 mutants. The close functional relationship of Prp18 and U5 is emphasized by the finding that two snr7 alleles, U5A and U6A, are dominant synthetic lethal with prp18 alleles. Our results support the idea that Prp18 and the U5 snRNA act in concert during the second step of pre-mRNA splicing and suggest a model in which the conserved loop of Prp18 acts to stabilize the interaction of loop 1 of the U5 snRNA with the splicing intermediates.

  6. Projecting regional potentials for cost-effective energy conservation and renewable resource applications: a feasibility study

    SciTech Connect

    Not Available

    1980-01-01

    The feasibility is discussed of preparing an instruction manual that would enable a modeler in a particular region to set up a calculation method for predicting energy use. Such a manual would concern itself primarily with the three energy-consuming sectors most relevant to utilities' demand projections. Data requriements for each of the three sectors (residential, commercial, and industrial) are described and some initial guidance is provided as to how these needs can be filled. The methods for separate calculations of energy consumed by each end use in each sector are described. Each end use is discussed separately for the residential sector, but only in aggregate for the commercial and industrial sectors. (MCW)

  7. Evolutionary conservation of mechanisms for neural regionalization, proliferation and interconnection in brain development

    PubMed Central

    Reichert, Heinrich

    2008-01-01

    Comparative studies of brain development in vertebrate and invertebrate model systems demonstrate remarkable similarities in expression and action of developmental control genes during embryonic patterning, neural proliferation and circuit formation in the brain. Thus, comparable sets of developmental control genes are involved in specifying the early brain primordium as well as in regionalized patterning along its anteroposterior and dorsoventral axes. Furthermore, similar cellular and molecular mechanisms underlie the formation and proliferation of neural stem cell-like progenitors that generate the neurons in the central nervous systems. Finally, neural identity and some complex circuit interconnections in specific brain domains appear to be comparable in vertebrates and invertebrates and may depend on similar developmental control genes. PMID:18755655

  8. Desalination as Groundwater Conservation: The Cost of Protecting Cultural and Environmental Resources in Chile's Region II

    NASA Astrophysics Data System (ADS)

    Edwards, E. C.; Cristi, O.; Libecap, G. D.

    2012-12-01

    of the empirical work, the theoretical development provides an important perspective into groundwater management and the important role of understanding the physical system in water marketing. Worldwide, subsidized and scarce water is allocated to farmers for social and political reasons. The losses from this type of allocation are often ignored or marginalized. The Chilean case demonstrates that the losses due to economically inefficient allocation are real, because the alternative is greater consumption of other resources (fossil fuels in this case), not conservation. The Chilean case also demonstrates the difficulty of adequately defining water rights for efficient markets due to the physical properties of hydrologic systems. Because groundwater and surface water systems are linked and water is partially recycled, water markets may over allocate water to consumptive users or those with preferable extraction locations. This paper provides a theoretical exposition of how water rights that fail incorporate important properties of the physical system may lead to inefficient water markets.

  9. A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

    PubMed Central

    2015-01-01

    Background Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte antigen molecules. However, experimental studies have shown that T cells often target diverse regions in highly variable viral pathogens and this diversity may need to be addressed through redefinition of suitable peptide targets. Methods We have developed a method for antigen assessment and target selection for polyvalent vaccines, with which we identified immune epitopes from variable regions, where all variants bind HLA. These regions, although variable, can thus be considered stable in terms of HLA binding and represent valuable vaccine targets. Results We applied this method to predict CD8+ T-cell targets in influenza A H7N9 hemagglutinin and significantly increased the number of potential vaccine targets compared to the number of targets discovered using the traditional approach where low-frequency peptides are excluded. Conclusions We developed a webserver with an intuitive visualization scheme for summarizing the T cell-based antigenic potential of any given protein or proteome using human leukocyte antigen binding predictions and made a web-accessible software implementation freely available at http://met-hilab.cbs.dtu.dk/blockcons/. PMID:26679766

  10. cDNA sequence, genomic organization, and evolutionary conservation of a novel gene from the WAGR region

    SciTech Connect

    Schwartz, F.; Eisenman, R.; Knoll, J.; Bruns, G.

    1995-09-20

    A new gene (239FB) with predominant and differential expression in fetal brain has recently been isolated from a chromosome 11p13-p14 boundary area near FSHB. The corresponding mRNA has an open reading frame of 294 amino acids, a 3` untranslated region of 1247 nucleotides, and a highly GC-rich 5` untranslated region. The coding and 3` UT sequence is specified by 6 exons within nearly 87 kb of isolated genomic locus. The 5` end region of the transcript maps adjacent to the only genomically defined CpG island in a chromosomal subregion that may be associated with part of the mental retardation of some WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome patients. In addition to nucleotide and amino acid similarity to an EST from a normalized infant brain cDNA library, the predicted protein has extensive similarity to Caenorhbditis elegans polypeptides of, as yet, unknown function. The 239FB locus is, therefore, likely part of a family of genes with two members expressed in human brain. The extensive conservation of the predicted protein suggests a fundamental function of the gene product and will enable evaluation of the role of the 239FB gene in neurogenesis in model organisms. 48 refs., 4 figs., 1 tab.

  11. Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6.

    PubMed

    Kumar, Nitin; Radhakrishnan, Abhijith; Su, Chih-Chia; Osteryoung, Katherine W; Yu, Edward W

    2016-02-01

    The chloroplast division machinery is composed of numerous proteins that assemble as a large complex to divide double-membraned chloroplasts through binary fission. A key mediator of division-complex formation is ARC6, a chloroplast inner envelope protein and evolutionary descendant of the cyanobacterial cell division protein Ftn2. ARC6 connects stromal and cytosolic contractile rings across the two membranes through interaction with an outer envelope protein within the intermembrane space (IMS). The ARC6 IMS region bears a structurally uncharacterized domain of unknown function, DUF4101, that is highly conserved among ARC6 and Ftn2 proteins. Here we report the crystal structure of this domain from Arabidopsis thaliana ARC6. The domain forms an α/β barrel open towards the outer envelope membrane but closed towards the inner envelope membrane. These findings provide new clues into how ARC6 and its homologs contribute to chloroplast and cyanobacterial cell division.

  12. Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6.

    PubMed

    Kumar, Nitin; Radhakrishnan, Abhijith; Su, Chih-Chia; Osteryoung, Katherine W; Yu, Edward W

    2016-02-01

    The chloroplast division machinery is composed of numerous proteins that assemble as a large complex to divide double-membraned chloroplasts through binary fission. A key mediator of division-complex formation is ARC6, a chloroplast inner envelope protein and evolutionary descendant of the cyanobacterial cell division protein Ftn2. ARC6 connects stromal and cytosolic contractile rings across the two membranes through interaction with an outer envelope protein within the intermembrane space (IMS). The ARC6 IMS region bears a structurally uncharacterized domain of unknown function, DUF4101, that is highly conserved among ARC6 and Ftn2 proteins. Here we report the crystal structure of this domain from Arabidopsis thaliana ARC6. The domain forms an α/β barrel open towards the outer envelope membrane but closed towards the inner envelope membrane. These findings provide new clues into how ARC6 and its homologs contribute to chloroplast and cyanobacterial cell division. PMID:26452626

  13. How legumes recognize rhizobia.

    PubMed

    Via, Virginia Dalla; Zanetti, María Eugenia; Blanco, Flavio

    2016-01-01

    Legume plants have developed the capacity to establish symbiotic interactions with soil bacteria (known as rhizobia) that can convert N2 to molecular forms that are incorporated into the plant metabolism. The first step of this relationship is the recognition of bacteria by the plant, which allows to distinguish potentially harmful species from symbiotic partners. The main molecular determinant of this symbiotic interaction is the Nod Factor, a diffusible lipochitooligosaccharide molecule produced by rhizobia and perceived by LysM receptor kinases; however, other important molecules involved in the specific recognition have emerged over the years. Secreted exopolysaccharides and the lipopolysaccharides present in the bacterial cell wall have been proposed to act as signaling molecules, triggering the expression of specific genes related to the symbiotic process. In this review we will briefly discuss how transcriptomic analysis are helping to understand how multiple signaling pathways, triggered by the perception of different molecules produced by rhizobia, control the genetic programs of root nodule organogenesis and bacterial infection. This knowledge can help to understand how legumes have evolved to recognize and establish complex ecological relationships with particular species and strains of rhizobia, adjusting gene expression in response to identity determinants of bacteria. PMID:26636731

  14. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes.

    PubMed

    ElHefnawi, Mahmoud; Kim, TaeKyu; Kamar, Mona A; Min, Saehong; Hassan, Nafisa M; El-Ahwany, Eman; Kim, Heeyoung; Zada, Suher; Amer, Marwa; Windisch, Marc P

    2016-01-01

    RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide

  15. Quantifying landscape linkages among giant panda subpopulations in regional scale conservation.

    PubMed

    Qi, Dunwu; Hu, Yibo; Gu, Xiaodong; Yang, Xuyi; Yang, Guang; Wei, Fuwen

    2012-06-01

    Understanding habitat requirements and identifying landscape linkages are essential for the survival of isolated populations of endangered species. Currently, some of the giant panda populations are isolated, which threatens their long-term survival, particularly in the Xiaoxiangling mountains. In the present study, we quantified niche requirements and then identified potential linkages of giant panda subpopulations in the most isolated region, using ecological niche factor analysis and a least-cost path model. Giant pandas preferred habitat with conifer forest and gentle slopes (>20 to ≤30°). Based on spatial distribution of suitable habitat, linkages were identified for the Yele subpopulation to 4 other subpopulations (Liziping, Matou, Xinmin and Wanba). Their lengths ranged from 15 to 54 km. The accumulated cost ranged from 693 to 3166 and conifer forest covered over 31%. However, a variety of features (e.g. major roads, human settlements and large unforested areas) might act as barriers along the linkages for giant panda dispersal. Our analysis quantified giant panda subpopulation connectivity to ensure long-term survival.

  16. Use of a storm water retention system for conservation of regionally endangered fishes

    USGS Publications Warehouse

    Schaeffer, Jeffrey S.; Bland, James K.; Janssen, John

    2012-01-01

    Maintaining aquatic biodiversity in urban or suburban areas can be problematic because urban landscapes can be nearly devoid of aquatic habitats other than engineered basins for storm water management. These areas are usually of questionable value for fish, but we examined a case study in which five regionally imperiled fish species were reintroduced into an artificial storm water detention pond and subsequently thrived. Although not a formal experiment, postintroduction survey data suggested that three of the five species maintained high population densities for 10 years after initial stocking, and two persisted in lower numbers. Success was likely due to a combination of unique design features and prior habitat preparation that resulted in clear water conditions that supported dense vegetation. Stocked fish persisted despite occasional bouts of low dissolved oxygen and increased chloride levels resulting from road salt application within the watershed. Transplanted fish served as a source population for both research and further reintroduction experiments. We suggest that, for some fish species, habitat preservation has a middle ground between natural habitats and completely artificial environments that require constant husbandry and that storm water systems could be used to create engineered sanctuaries within the human landscape that have many potential benefits for both humans and fish.

  17. Quantifying landscape linkages among giant panda subpopulations in regional scale conservation.

    PubMed

    Qi, Dunwu; Hu, Yibo; Gu, Xiaodong; Yang, Xuyi; Yang, Guang; Wei, Fuwen

    2012-06-01

    Understanding habitat requirements and identifying landscape linkages are essential for the survival of isolated populations of endangered species. Currently, some of the giant panda populations are isolated, which threatens their long-term survival, particularly in the Xiaoxiangling mountains. In the present study, we quantified niche requirements and then identified potential linkages of giant panda subpopulations in the most isolated region, using ecological niche factor analysis and a least-cost path model. Giant pandas preferred habitat with conifer forest and gentle slopes (>20 to ≤30°). Based on spatial distribution of suitable habitat, linkages were identified for the Yele subpopulation to 4 other subpopulations (Liziping, Matou, Xinmin and Wanba). Their lengths ranged from 15 to 54 km. The accumulated cost ranged from 693 to 3166 and conifer forest covered over 31%. However, a variety of features (e.g. major roads, human settlements and large unforested areas) might act as barriers along the linkages for giant panda dispersal. Our analysis quantified giant panda subpopulation connectivity to ensure long-term survival. PMID:22691200

  18. Characterization of conservative somatic instability of the CAG repeat region in Huntington`s disease

    SciTech Connect

    Schaefer, F.V.; Calikoglu, A.S.; Whetsell, L.H.

    1994-09-01

    Instability and enlargement of a CAG repeat region at the beginning of the huntingtin gene (IT-15) has been linked with Huntington`s disease. The CAG repeat size shows a highly significant correlation with age-of-onset of clinicial features in individuals with 40 or more repeats who have Huntington disease. The clinical status of nonsymptomatic individuals with 30 to 39 CAG repeats is considered ambiguous. In order to define more carefully the nature of the HD expansion instability, we examined patients in our HD population using a discriminating fluorescence-based PCR approach. The degree of somatic mutation increases with both earlier age of onset and the size of the inherited allele. A single prominent band one repeat larger than the index peak was typical in individuals with 40-41 CAG repeats. Three to four larger bands are typically discerned in individuals with 50 or more repeats. In an extreme example, an individual with approximately 95 repeats had at least 8 prominent bands. Plotting the degree of somatic mutation relative to the size of the HD allele shows somatic mutation activity increases with size. By this approach 40-60% of the alleles in a 40-41 CAG repeat HD loci is represented in the primary allele. In contrast, the primary allele represents a relatively minor proportion of the total alleles for expansions greater than 50 CAG repeats (10-20%). The limited range of somatic mutation suggest that the instability is restricted to very early stages of embryogenesis before tissue development diverges or that persistent somatic instability occurs at a slow rate. Therefore, the properties of somatic instability in Huntington`s disease have aspects that are both in common but also different from that found in other trinucleotide repeat expanding diseases such as myotonic muscular dystrophy and fragile X syndrome.

  19. Does Lymphovascular Invasion Predict Regional Nodal Failure in Breast Cancer Patients With Zero to Three Positive Lymph Nodes Treated With Conserving Surgery and Radiotherapy? Implications for Regional Radiation

    SciTech Connect

    Boutrus, Rimoun; Abi-Raad, Rita; Niemierko, Andrzej; Brachtel, Elena F.; Rizk, Levi; Kelada, Alexandra; Taghian, Alphonse G.

    2010-11-01

    Purpose: To examine the relationship between lymphovascular invasion (LVI) and regional nodal failure (RNF) in breast cancer patients with zero to three positive nodes treated with breast-conservation therapy (BCT). Methods and Materials: The records of 1,257 breast cancer patients with zero to three positive lymph nodes were reviewed. All patients were treated with BCT at Massachusetts General Hospital from 1980 to December 2003. Lymphovascular invasion was diagnosed by hematoxylin and eosin-stained sections and in some cases supported by immunohistochemical stains. Regional nodal failure was defined as recurrence in the ipsilateral supraclavicular, axillary, or internal mammary lymph nodes. Regional nodal failure was diagnosed by clinical and/or radiologic examination. Results: The median follow-up was 8 years (range, 0.1-21 years). Lymphovascular invasion was present in 211 patients (17%). In univariate analysis, patients with LVI had a higher rate of RNF (3.32% vs. 1.15%; p = 0.02). In multivariate analysis, only tumor size, grade, and local failure were significant predictors of RNF (p = 0.049, 0.013, and 0.0001, respectively), whereas LVI did not show a significant relationship with RNF (hazard ratio = 2.07; 95% CI, 0.8-5.5; p = 0.143). The presence of LVI in the T2/3 population did not increase the risk of RNF over that for those with no LVI (p = 0.15). In addition, patients with Grade 3 tumors and positive LVI did not have a higher risk of RNF than those without LVI (p = 0.96). Conclusion: These results suggest that LVI can not be used as a sole indicator for regional nodal irradiation in breast cancer patients with zero to three positive lymph nodes treated with BCT.

  20. Mutations of Conserved Residues in the Major Homology Region Arrest Assembling HIV-1 Gag as a Membrane-Targeted Intermediate Containing Genomic RNA and Cellular Proteins

    PubMed Central

    Tanaka, Motoko; Robinson, Bridget A.; Chutiraka, Kasana; Geary, Clair D.; Reed, Jonathan C.

    2015-01-01

    ABSTRACT The major homology region (MHR) is a highly conserved motif that is found within the Gag protein of all orthoretroviruses and some retrotransposons. While it is widely accepted that the MHR is critical for assembly of HIV-1 and other retroviruses, how the MHR functions and why it is so highly conserved are not understood. Moreover, consensus is lacking on when HIV-1 MHR residues function during assembly. Here, we first addressed previous conflicting reports by confirming that MHR deletion, like conserved MHR residue substitution, leads to a dramatic reduction in particle production in human and nonhuman primate cells expressing HIV-1 proviruses. Next, we used biochemical analyses and immunoelectron microscopy to demonstrate that conserved residues in the MHR are required after assembling Gag has associated with genomic RNA, recruited critical host factors involved in assembly, and targeted to the plasma membrane. The exact point of inhibition at the plasma membrane differed depending on the specific mutation, with one MHR mutant arrested as a membrane-associated intermediate that is stable upon high-salt treatment and other MHR mutants arrested as labile, membrane-associated intermediates. Finally, we observed the same assembly-defective phenotypes when the MHR deletion or conserved MHR residue substitutions were engineered into Gag from a subtype B, lab-adapted provirus or Gag from a subtype C primary isolate that was codon optimized. Together, our data support a model in which MHR residues act just after membrane targeting, with some MHR residues promoting stability and another promoting multimerization of the membrane-targeted assembling Gag oligomer. IMPORTANCE The retroviral Gag protein exhibits extensive amino acid sequence variation overall; however, one region of Gag, termed the major homology region, is conserved among all retroviruses and even some yeast retrotransposons, although the reason for this conservation remains poorly understood. Highly

  1. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes.

    PubMed

    ElHefnawi, Mahmoud; Kim, TaeKyu; Kamar, Mona A; Min, Saehong; Hassan, Nafisa M; El-Ahwany, Eman; Kim, Heeyoung; Zada, Suher; Amer, Marwa; Windisch, Marc P

    2016-01-01

    RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide

  2. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes

    PubMed Central

    ElHefnawi, Mahmoud; Kim, TaeKyu; Kamar, Mona A.; Min, Saehong; Hassan, Nafisa M.; El-Ahwany, Eman; Kim, Heeyoung; Zada, Suher; Amer, Marwa; Windisch, Marc P.

    2016-01-01

    RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide

  3. Quantifying the effects of conservation practices on soil, water, and nutrients in the Loess Mesa Ravine Region of the Loess Plateau, China.

    PubMed

    Xu, Xiang-Zhou; Li, Mei-Juan; Liu, Bin; Kuang, Shang-Fu; Xu, Shi-Guo

    2012-05-01

    A large number of soil and water conservation programs have been implemented on the Loess Plateau of China since the 1950s. To comprehensively assess the merits and demerits of the conservation practices is of great importance in further supervising the conservation strategy for the Loess Plateau. This study calculates the impact factors of conservation practices on soil, water, and nutrients during the period 1954-2004 in the Nanxiaohegou Catchment, a representative catchment in the Loess Mesa Ravine Region of the Loess Plateau, China. Brief conclusions could be drawn as follows: (1) Soil erosion and nutrient loss had been greatly mitigated through various conservation practices. About half of the total transported water and 94.8 % of the total transported soil and nutrients, had been locally retained in the selected catchment. The soil retained from small watersheds do not only form large-scale fertile farmland but also safeguard the Yellow River against overflow. (2) Check dam was the most appropriate conservation practice on the Loess Plateau. In the selected catchment, more than 90 % of the retained soil and water were accomplished by the dam farmland, although the dam farmland occupied only 2.3 % of the total area of all conservation measures. Retention abilities of the characteristic conservation practices were in the following order: dam farmland > terrace farmland > forest land and grassland. (3) The conservation practices were more powerful in retaining sediment than in reducing runoff from the Loess Plateau, and the negative effects of the conservation practices on reducing water to the Yellow River were relatively slight.

  4. Characterizing stopover sites of migrating passerine birds in the lower Chesapeake Bay region for conservation: an integrated radar-habitat study

    USGS Publications Warehouse

    Mabey, S.; Watts, B.; Paxton, B.; Smith, F.; Truitt, B.; Dawson, D.

    2005-01-01

    Many conservation organizations and initiatives including Partners-in-Flight and the U.S. Fish and Wildlife Service's regional Joint Ventures have identified migratory songbird stopover habitat as a priority conservation target. However, the spatial and temporal variability inherent in migration presents a number of challenges to both identifying and characterizing stopover habitat. Scarce conservation resources further demand that stopover sites be classified on a scale of priority so that conservation action can proceed according to ecological value. We are applying weather surveillance radar data collected from the National Weather Service WSR-88D at Wakefield, VA, and NASA's Doppler radar, NPOL, in Oyster, VA, to identify passerine stopover sites in the lower Chesapeake Bay region and develop spatial models to characterize these sites based on relative migrant abundance and consistency of use between and within seasons. We are using the stopover patterns to generate hypotheses regarding the habitat, geographic, and stochastic factors contributing to the distribution of migrants at a regional scale. We are testing these hypotheses with detailed habitat data and ground surveys of migrating birds with the goal of creating a generalized prioritization system for stopover site conservation.

  5. Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation and Research across Multiple Scales

    PubMed Central

    Wallace, Bryan P.; DiMatteo, Andrew D.; Hurley, Brendan J.; Finkbeiner, Elena M.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jerome; Bowen, Brian W.; Dueñas, Raquel Briseño; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Girard, Alexandre; Girondot, Marc; Godfrey, Matthew H.; Hamann, Mark; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Mortimer, Jeanne A.; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Seminoff, Jeffrey A.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

    2010-01-01

    Background Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques — including site-based monitoring, genetic analyses, mark-recapture studies and telemetry — can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition

  6. Mutations in a conserved region of RNA polymerase II influence the accuracy of mRNA start site selection.

    PubMed Central

    Hekmatpanah, D S; Young, R A

    1991-01-01

    A sensitive phenotypic assay has been used to identify mutations affecting transcription initiation in the genes encoding the two large subunits of Saccharomyces cerevisiae RNA polymerase II (RPB1 and RPB2). The rpb1 and rpb2 mutations alter the ratio of transcripts initiated at two adjacent start sites of a delta-insertion promoter. Of a large number of rpb1 and rpb2 mutations screened, only a few affect transcription initiation patterns at delta-insertion promoters, and these mutations are in close proximity to each other within both RPB1 and RPB2. The two rpb1 mutations alter amino acid residues within homology block G, a region conserved in the large subunits of all RNA polymerases. The three strong rpb2 mutations alter adjacent amino acids. At a wild-type promoter, the rpb1 mutations affect the accuracy of mRNA start site selection by producing a small but detectable increase in the 5'-end heterogeneity of transcripts. These RNA polymerase II mutations implicate specific portions of the enzyme in aspects of transcription initiation. Images PMID:1922077

  7. [Topsoil phosphorus forms and availability of different soil and water conservation plantations in typical black soil region, northeast China].

    PubMed

    Yang, Xiao-Yan; Fan, Rui-Ying; Wang, En-Heng; Xia, Xiang-You; Chen, Xiang-Wei

    2014-06-01

    Aiming to understand soil phosphorus status of plantations in typical black soil region of Northeast China, the topsoil (0-10 cm) phosphorus fractionations and its availability were examined in four soil and water conservation plantations dominantly composed of Larix gmelini, Fraxinus mandshurica, Pinus sylvestris var. mongolica and Populus nigra var. italica x P. cathayan, respectively. The results showed that total P, Olsen-P and the concentration of different P fractionations in F. mandshurica and P. nigra var. italica x P. cathayan plantations were significantly higher than that of the other two coniferous plantations. Organic P was the major fractionation in the four plantations' topsoil, and sodium hydroxide extractable organic P (NaOH-Po ) representing moderately labile organic phosphorus was predominant, which accounted for 58.9% of total P. The contents of H2O-Pi and NaHCO3-P which were more labile to plant were lower, only accounting for 1.2% and 6.6% of total P, respectively. Except for NaHCO3-Po, all the other P fractions of four plantations correlated with each other, and they also had significant correlations with soil organic matter, total P, Olsen-P. Compared with the coniferous plantations, the broadleaf plantations presented higher availability of phosphorus.

  8. Trichodiene synthase. Probing the role of the highly conserved aspartate-rich region by site-directed mutagenesis.

    PubMed

    Cane, D E; Xue, Q; Fitzsimons, B C

    1996-09-24

    Trichodiene synthase catalyzes the cyclization of farnesyl diphosphate to the sesquiterpene hydrocarbon trichodiene. The enzyme normally requires a divalent cation, Mg2+, which can be substituted by Mn2+. Trichodiene synthase from Fusarium sporotrichioides has a highly conserved aspartate rich region, aa 100-104 (DDSKD). Three mutants were constructed by site-directed mutagenesis in which each aspartate residue was individually replaced by glutamate. The mutants were each overexpressed and purified to homogeneity. The importance of Asp100 and Asp101 for catalysis was established by the observation of an increase in Km as well as a reduction in kcat in the corresponding Glu mutants. Replacement of the Asp104 residue with Glu had little effect on either Km or kcat. All three mutants produced anomalous sesquiterpene products in addition to trichodiene when incubated with farnesyl diphosphate. Interestingly, when Mg2+ was replaced by Mn2+ in the incubation buffer, the kcat/Km of both wild type trichodiene synthase and the D104E dropped significantly, while those of the other two mutants were not much affected. The proportion of anomalous products increased significantly when the D100E and D101E mutants were incubated in the presence of Mn2+. These observations all lend weight to the proposal that the aspartate residues mediate substrate binding by chelation of the divalent metal ion. Asp100 and Asp101 appear to play a relatively more important role than Asp104. PMID:8823172

  9. Conserving biological diversity: A strategy for protected areas in the Asia-Pacific region. World Bank technical paper

    SciTech Connect

    Braatz, S.; Davis, G.; Shen, S.; Rees, C.

    1992-01-01

    The paper acknowledges the importance of biodiversity conservation and suggests that policy change coupled with the establishment of protected area systems will be critical to success. A wide range of interventions will be needed to support these efforts toward conserving biodiversity-interventions involving national and local governments, national and international nongovernmental organizations and, most importantly, local people. The strategy defined in the paper is intended to complement existing national and international initiatives and to build partnerships in conservation for the 1990s.

  10. A national geographic framework for guiding conservation on a landscape scale

    USGS Publications Warehouse

    Millard, Michael J.; Czarnecki, Craig A.; Morton, John M.; Brandt, Laura A.; Briggs, Jennifer S.; Shipley, Frank S.; Sayre, Roger G.; Sponholtz, Pamela J.; Perkins, David; Simpkins, Darin G.; Taylor, Janith

    2012-01-01

    The U.S. Fish and Wildlife Service, along with the global conservation community, has recognized that the conservation challenges of the 21st century far exceed the responsibilities and footprint of any individual agency or program. The ecological effects of climate change and other anthropogenic stressors do not recognize geopolitical boundaries and, as such, demand a national geographic framework to provide structure for cross-jurisdictional and landscape-scale conservation strategies. In 2009, a new map of ecologically based conservation regions in which to organize capacity and implement strategic habitat conservation was developed using rapid prototyping and expert elicitation by an interagency team of U.S. Fish and Wildlife Service and U.S. Geological Survey scientists and conservation professionals. Incorporating Bird Conservation Regions, Freshwater Ecoregions, and U.S. Geological Survey hydrologic unit codes, the new geographic framework provides a spatial template for building conservation capacity and focusing biological planning and conservation design efforts. The Department of Interior's Landscape Conservation Cooperatives are being organized in these new conservation regions as multi-stakeholder collaborations for improved conservation science and management.

  11. The Cysteine-Rich Interdomain Region from the Highly Variable Plasmodium falciparum Erythrocyte Membrane Protein-1 Exhibits a Conserved Structure

    PubMed Central

    Su, Hua-Poo; Makobongo, Morris O.; Moore, Jaime M.; Singh, Sanjay; Miller, Louis H.; Garboczi, David N.

    2008-01-01

    Plasmodium falciparum malaria parasites, living in red blood cells, express proteins of the erythrocyte membrane protein-1 (PfEMP1) family on the red blood cell surface. The binding of PfEMP1 molecules to human cell surface receptors mediates the adherence of infected red blood cells to human tissues. The sequences of the 60 PfEMP1 genes in each parasite genome vary greatly from parasite to parasite, yet the variant PfEMP1 proteins maintain receptor binding. Almost all parasites isolated directly from patients bind the human CD36 receptor. Of the several kinds of highly polymorphic cysteine-rich interdomain region (CIDR) domains classified by sequence, only the CIDR1α domains bind CD36. Here we describe the CD36-binding portion of a CIDR1α domain, MC179, as a bundle of three α-helices that are connected by a loop and three additional helices. The MC179 structure, containing seven conserved cysteines and 10 conserved hydrophobic residues, predicts similar structures for the hundreds of CIDR sequences from the many genome sequences now known. Comparison of MC179 with the CIDR domains in the genome of the P. falciparum 3D7 strain provides insights into CIDR domain structure. The CIDR1α three-helix bundle exhibits less than 20% sequence identity with the three-helix bundles of Duffy-binding like (DBL) domains, but the two kinds of bundles are almost identical. Despite the enormous diversity of PfEMP1 sequences, the CIDR1α and DBL protein structures, taken together, predict that a PfEMP1 molecule is a polymer of three-helix bundles elaborated by a variety of connecting helices and loops. From the structures also comes the insight that DBL1α domains are approximately 100 residues larger and that CIDR1α domains are approximately 100 residues smaller than sequence alignments predict. This new understanding of PfEMP1 structure will allow the use of better-defined PfEMP1 domains for functional studies, for the design of candidate vaccines, and for understanding the

  12. Conserved POU/OCT- and GATA-binding sites in 5'-flanking promoter region of mammalian WNT8B orthologs.

    PubMed

    Katoh, Masuko; Katoh, Masaru

    2007-05-01

    WNT family members are secreted-type glycoproteins regulating cell fate, planar cell polarity, cell adhesion, and cell movement. WNT signals are context-dependently transduced to the canonical pathway for the transcriptional up-regulation of MYC, CCND1, FGF20, JAG1, WISP1 and DKK1 genes, and also to the non-canonical pathway for the activation of RHOA, JNK, PKC, NFAT and NLK signaling cascades. We cloned and characterized the wild-type human WNT8B, while another group the aberrant human WNT8B with Gly230Ala and Arg284Leu amino-acid substitutions. Although WNT8B is undetectable in normal adult tissues by using Northern blot analyses, WNT8B is expressed in gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, and embryonal tumors. Here, comparative integromics on WNT8B orthologs were investigated by using bioinformatics (Techint) and human intelligence (Humint). Cow Wnt8b gene was identified within NW_001494361.1 genome sequence. Predicted sequence XM_582222.3 was an artificial cow Wnt8b with aberrant prediction for the first exon. Cow Wnt8b complete coding sequence was found to encode a 350-amino-acid protein, which showed 96.9% total-amino-acid identity with human WNT8B. Comparative proteomics revealed that N-terminal signal peptide, 22 Cys residues, two Asn-linked glycosylation sites, Gly230, and Arg284 of human WNT8B were conserved among mammalian WNT8B orthologs. Comparative genomics revealed that POU/OCT- and GATA-binding sites in the 5'-flanking promoter region were conserved among human, chimpanzee, cow, mouse, and rat WNT8B orthologs. In silico expression analyses revealed that human WNT8B was expressed in embryoid body derived from embryonic stem (ES) cells, hepatocyte progenitors derived from ES cells, fetal brain, diffuse-type gastric cancer, colorectal cancer, prostate cancer, and ovarian fibrotheoma. Based on the expression profiles of POU and GATA family transcription factors, it was revealed that WNT8B expression in hepatocyte

  13. Autoantibody germ-line gene segment encodes V{sub H} and V{sub L} regions of a human anti-streptococcal monoclonal antibody recognizing streptococcal M protein and human cardiac myosin epitopes

    SciTech Connect

    Quinn, A.; Cunningham, M.W.; Adderson, E.E.

    1995-04-15

    Cross-reactivity of anti-streptococcal Abs with human cardiac myosin may result in sequelae following group A streptococcal infections. Molecular mimicry between group A streptococcal M protein and cardiac myosin may be the basis for the immunologic cross-reactivity. In this study, a cross-reactive human anti-streptococcal/antimyosin mAb (10.2.3) was characterized, and the myosin epitopes were recognized by the Ab identified. mAb 10.2.3 reacted with four peptides from the light meromyosin (LMM) tail fragment of human cardiac myosin, including LMM-10 (1411-1428), LMM-23 (1580-1597), LMM-27 (1632-1649), and LMM-30 (1671-1687). Only LMM-30 inhibited binding of mAb 10.2.3 to streptococcal M protein and human cardiac myosin. Human mAb 10.2.3 labeled cytoskeletal structures within rat heart cells in indirect immunofluorescence, and reacted with group A streptococci expressing various M protein serotypes, PepM5, and recombinant M protein. The nucleotide sequence of gene segments encoding the Ig heavy and light chain V region of mAb 10.2.3 was determined. The light chain V segment was encoded by a VK1 gene segment that was 98.5% identical with germ-line gene humig{sub K}Vi5. The V segment of the heavy chain was encoded by a V{sub H}3a gene segment that differed from the V{sub H}26 germ-line gene by a single base change. V{sub H}26 is expressed preferentially in early development and encodes autoantibodies with anti-DNA and rheumatoid factor specificities. Anti-streptococcal mAb 10.2.3 is an autoantibody encoded by V{sub H} and V{sub L} genes, with little or no somatic mutation. 63 refs., 11 figs.

  14. Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region

    USGS Publications Warehouse

    Bowker, M.A.; Miller, M.E.; Belnap, J.; Sisk, T.D.; Johnson, N.C.

    2008-01-01

    Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.

  15. A GIS-based approach for assessing the regional conservation status of genetic diversity: an example from the southern Appalachians.

    PubMed

    Ji, Wei Wayne; Leberg, Paul

    2002-04-01

    Conserving genetic diversity requires an assessment of the distribution of genetic variants in relation to patterns of land use and environmental variation at a regional scale. This assessment requires a novel approach to integrating and analyzing the genetic and environmental data across spatial scales. To explore the integration of genetic data with other geospatial data sets, we developed a GIS-based approach for examining patterns of genetic diversity for several species of salamanders in southern Appalachians. The genetic data, from allozyme surveys in the genetics literature, were integrated into a GIS database along with related attributes including population identifications and spatial locations. Using existing geospatial data, we classified sample locations as being either protected from anthropogenic disturbance (e.g., National Parks, Wilderness Areas) or as unprotected (e.g., private lands, multiple-use lands in National Forests). We used multidimensional scaling of allelic frequencies and contributions of populations to interpopulation differences in allelic richness to determine which populations had genetic characteristics most different from other populations in the sample. Measures of genetic differentiation were integrated into the GIS database to facilitate spatial analysis and visualization of the indices in relation to land use. This approach was useful for both identification of populations with components of genetic variation that were not well represented at protected sites and for identifying areas of species distributions where more genetic sampling would be necessary to make informed management decisions. Our approach could be readily adapted for use by managers and geneticists working with other species and types of genetic markers.

  16. Regional Extinctions and Quaternary Shifts in the Geographic Range of Lestodelphys halli, the Southernmost Living Marsupial: Clues for Its Conservation.

    PubMed

    Formoso, Anahí E; Martin, Gabriel M; Teta, Pablo; Carbajo, Aníbal E; Sauthier, Daniel E Udrizar; Pardiñas, Ulyses F J

    2015-01-01

    The Patagonian opossum (Lestodelphys halli), the southernmost living marsupial, inhabits dry and open environments, mainly in the Patagonian steppe (between ~32 °S and ~49 °S). Its rich fossil record shows its occurrence further north in Central Argentina during the Quaternary. The paleoenvironmental meaning of the past distribution of L. halli has been mostly addressed in a subjective framework without an explicit connection with the climatic "space" currently occupied by this animal. Here, we assessed the potential distribution of this species and the changes occurred in its geographic range during late Pleistocene-Holocene times and linked the results obtained with conservation issues. To this end, we generated three potential distribution models with fossil records and three with current ones, using MaxEnt software. These models showed a decrease in the suitable habitat conditions for the species, highlighting a range shift from Central-Eastern to South-Western Argentina. Our results support that the presence of L. halli in the Pampean region during the Pleistocene-Holocene can be related to precipitation and temperature variables and that its current presence in Patagonia is more related to temperature and dominant soils. The models obtained suggest that the species has been experiencing a reduction in its geographic range since the middle Holocene, a process that is in accordance with a general increase in moisture and temperature in Central Argentina. Considering the findings of our work and the future scenario of global warming projected for Patagonia, we might expect a harsh impact on the distribution range of this opossum in the near future.

  17. Regional Extinctions and Quaternary Shifts in the Geographic Range of Lestodelphys halli, the Southernmost Living Marsupial: Clues for Its Conservation.

    PubMed

    Formoso, Anahí E; Martin, Gabriel M; Teta, Pablo; Carbajo, Aníbal E; Sauthier, Daniel E Udrizar; Pardiñas, Ulyses F J

    2015-01-01

    The Patagonian opossum (Lestodelphys halli), the southernmost living marsupial, inhabits dry and open environments, mainly in the Patagonian steppe (between ~32 °S and ~49 °S). Its rich fossil record shows its occurrence further north in Central Argentina during the Quaternary. The paleoenvironmental meaning of the past distribution of L. halli has been mostly addressed in a subjective framework without an explicit connection with the climatic "space" currently occupied by this animal. Here, we assessed the potential distribution of this species and the changes occurred in its geographic range during late Pleistocene-Holocene times and linked the results obtained with conservation issues. To this end, we generated three potential distribution models with fossil records and three with current ones, using MaxEnt software. These models showed a decrease in the suitable habitat conditions for the species, highlighting a range shift from Central-Eastern to South-Western Argentina. Our results support that the presence of L. halli in the Pampean region during the Pleistocene-Holocene can be related to precipitation and temperature variables and that its current presence in Patagonia is more related to temperature and dominant soils. The models obtained suggest that the species has been experiencing a reduction in its geographic range since the middle Holocene, a process that is in accordance with a general increase in moisture and temperature in Central Argentina. Considering the findings of our work and the future scenario of global warming projected for Patagonia, we might expect a harsh impact on the distribution range of this opossum in the near future. PMID:26203650

  18. Conserved region 3 of human papillomavirus 16 E7 contributes to deregulation of the retinoblastoma tumor suppressor.

    PubMed

    Todorovic, Biljana; Hung, Katherine; Massimi, Paola; Avvakumov, Nikita; Dick, Frederick A; Shaw, Gary S; Banks, Lawrence; Mymryk, Joe S

    2012-12-01

    The human papillomavirus (HPV) E7 oncoprotein binds cellular factors, preventing or retargeting their function and thereby making the infected cell conducive for viral replication. A key target of E7 is the product of the retinoblastoma susceptibility locus (pRb). This interaction results in the release of E2F transcription factors and drives the host cell into the S phase of the cell cycle. E7 binds pRb via a high-affinity binding site in conserved region 2 (CR2) and also targets a portion of cellular pRb for degradation via the proteasome. Evidence suggests that a secondary binding site exists in CR3, and that this interaction influences pRb deregulation. Additionally, evidence suggests that CR3 also participates in the degradation of pRb. We have systematically analyzed the molecular mechanisms by which CR3 contributes to deregulation of the pRb pathway by utilizing a comprehensive series of mutations in residues predicted to be exposed on the surface of HPV16 E7 CR3. Despite differences in the ability to interact with cullin 2, all CR3 mutants degrade pRb comparably to wild-type E7. We identified two specific patches of residues on the surface of CR3 that contribute to pRb binding independently of the high-affinity CR2 binding site. Mutants within CR3 that affect pRb binding are less effective than the wild-type E7 in overcoming pRb-induced cell cycle arrest. This demonstrates that the interaction between HPV16 E7 CR3 and pRb is functionally important for alteration of the cell cycle. PMID:23015707

  19. Regional Extinctions and Quaternary Shifts in the Geographic Range of Lestodelphys halli, the Southernmost Living Marsupial: Clues for Its Conservation

    PubMed Central

    Formoso, Anahí E.; Martin, Gabriel M.; Teta, Pablo; Carbajo, Aníbal E.; Sauthier, Daniel E. Udrizar; Pardiñas, Ulyses F. J.

    2015-01-01

    The Patagonian opossum (Lestodelphys halli), the southernmost living marsupial, inhabits dry and open environments, mainly in the Patagonian steppe (between ~32°S and ~49°S). Its rich fossil record shows its occurrence further north in Central Argentina during the Quaternary. The paleoenvironmental meaning of the past distribution of L. halli has been mostly addressed in a subjective framework without an explicit connection with the climatic “space” currently occupied by this animal. Here, we assessed the potential distribution of this species and the changes occurred in its geographic range during late Pleistocene-Holocene times and linked the results obtained with conservation issues. To this end, we generated three potential distribution models with fossil records and three with current ones, using MaxEnt software. These models showed a decrease in the suitable habitat conditions for the species, highlighting a range shift from Central-Eastern to South-Western Argentina. Our results support that the presence of L. halli in the Pampean region during the Pleistocene-Holocene can be related to precipitation and temperature variables and that its current presence in Patagonia is more related to temperature and dominant soils. The models obtained suggest that the species has been experiencing a reduction in its geographic range since the middle Holocene, a process that is in accordance with a general increase in moisture and temperature in Central Argentina. Considering the findings of our work and the future scenario of global warming projected for Patagonia, we might expect a harsh impact on the distribution range of this opossum in the near future. PMID:26203650

  20. [Analysis of soil respiration and influence factors in wheat farmland under conservation tillage in southwest hilly region].

    PubMed

    Zhang, Sai; Zhang, Xiao-Yu; Wang, Long-Chang; Luo, Hai-Xiu; Zhou, Hang-Fei; Ma, Zhong-Lian; Zhang, Cui-Wei

    2013-07-01

    In order to investigate the effect of conservation tillage on soil respiration in dry cropping farmland in southwest purple hilly region, the LI6400-09 respiratory chamber was adopted in the experiment conducted in the experimental field in Southwest University in Beibei, Chongqing. The respiration and the hydrothermal and biotic factors of soil were measured and analyzed during the growth period of wheat in the triple intercropping system of wheat/maize/soybean. There were four treatments including T (traditional tillage), R (ridge tillage), TS (traditional tillage + straw mulching) and RS (ridge tillage + straw mulching), which were all in triplicates. The results indicated that the soil respiration rate changed in the range of 1.100-2.508 micromol x (m2 x s)(-1) during the reproductive growth stage of wheat. There were significant differences in soil respiration rate among different treatments, which could be ranked as RS > R > TS > T. The soil temperature in the 10cm layer was ranked as T > R > TS > RS. The relationship between soil respiration and soil temperature fitted well with an exponential function, in which the Q10 values were 1.25, 1.20, 1.31 and 1.26, respectively. The soil moisture in the 5cm layer was ranked as TS > RS > T > R. The best fitting model between soil moisture and soil respiration was a parabolic curve, indicating the presence of soil moisture with the strongest soil respiration. The response threshold of wheat to soil moisture was 14.80%-17.47% during the reproductive stage. The dominant groups of soil animals were Collembola and Acarina, which were correlated with soil respiration to some extent. The correlation was high in the treatments T and R, ranged from 0.669-0.921, whereas there was no remarkable correlation in the other treatments. PMID:24028018

  1. [Analysis of soil respiration and influence factors in wheat farmland under conservation tillage in southwest hilly region].

    PubMed

    Zhang, Sai; Zhang, Xiao-Yu; Wang, Long-Chang; Luo, Hai-Xiu; Zhou, Hang-Fei; Ma, Zhong-Lian; Zhang, Cui-Wei

    2013-07-01

    In order to investigate the effect of conservation tillage on soil respiration in dry cropping farmland in southwest purple hilly region, the LI6400-09 respiratory chamber was adopted in the experiment conducted in the experimental field in Southwest University in Beibei, Chongqing. The respiration and the hydrothermal and biotic factors of soil were measured and analyzed during the growth period of wheat in the triple intercropping system of wheat/maize/soybean. There were four treatments including T (traditional tillage), R (ridge tillage), TS (traditional tillage + straw mulching) and RS (ridge tillage + straw mulching), which were all in triplicates. The results indicated that the soil respiration rate changed in the range of 1.100-2.508 micromol x (m2 x s)(-1) during the reproductive growth stage of wheat. There were significant differences in soil respiration rate among different treatments, which could be ranked as RS > R > TS > T. The soil temperature in the 10cm layer was ranked as T > R > TS > RS. The relationship between soil respiration and soil temperature fitted well with an exponential function, in which the Q10 values were 1.25, 1.20, 1.31 and 1.26, respectively. The soil moisture in the 5cm layer was ranked as TS > RS > T > R. The best fitting model between soil moisture and soil respiration was a parabolic curve, indicating the presence of soil moisture with the strongest soil respiration. The response threshold of wheat to soil moisture was 14.80%-17.47% during the reproductive stage. The dominant groups of soil animals were Collembola and Acarina, which were correlated with soil respiration to some extent. The correlation was high in the treatments T and R, ranged from 0.669-0.921, whereas there was no remarkable correlation in the other treatments.

  2. Impact of the Conservation Reserve Program on duck recruitment in the U.S. Prairie Pothole Region

    USGS Publications Warehouse

    Reynolds, Ronald E.; Shaffer, Terry L.; Renner, Randy W.; Newton, Wesley E.; Batt, Bruce D. J.

    2001-01-01

    The U.S. Department of Agriculture (USDA)'s Conservation Reserve Program (CRP) resulted in the conversion of about 1.9 million ha of cropland to perennial grass cover in the Prairie Pothole Region of North Dakota, South Dakota, and northeastern Montana by 1992. Many wildlife managers believed this cover would provide benefits to wildlife, including upland nesting ducks. During 1992-1995, we evaluated success of 5 duck species nesting in CRP fields and nearby Waterfowl Production Areas (WPA) throughout the region. We examined relationships between daily survival rates (DSR) of duck nests in CRP cover and landscape-level habitat and population parameters. We computed DSR of duck nests in other major cover types in our study area from data collected during 1980-1984 (pre-CRP) and 1990-1994 (CRP) periods. We then applied recruitment models to estimate duck production in our study area during peak CRP years (1992-1997) and compared these results with those that simulated the scenario in which cropland was in place of CRP cover (i.e., the CRP had not occurred). DSR were higher in all habitats combined during the CRP period compared to the pre-CRP period. Regressions of DSR in CRP cover on the percent of each study plot in perennial cover and geographic location were significant (P < 0.01) for 4 of 5 duck (Anas spp.) species. Estimated nest success and recruitment rates for the 5 species combined during 1992-1997 were 46% and 30% higher, respectively, with CRP cover on the landscape compared to a scenario where we simulated cropland in place of CRP. Our model estimated an additional 12.4 million recruits from our study area to the fall flight as a consequence of the CRP during 1992-1997. Our results document benefits to 5 duck species in the northern plains associated with a farm program that provided financial incentives to landowners for planting undisturbed grass cover as an alternative to annual crops.

  3. Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region.

    PubMed

    Bowker, Matthew A; Miller, Mark E; Belnap, Jayne; Sisk, Thomas D; Johnson, Nancy C

    2008-12-01

    Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r= 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands.

  4. Regional estimates of ecological services derived from U.S. Department of Agriculture conservation programs in the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Faulkner, Stephen P.; Baldwin, Michael J.; Barrow, Wylie C.; Waddle, Hardin; Keeland, Bobby D.; Walls, Susan C.; James, Dale; Moorman, Tom

    2010-01-01

    The degree to which these conservation practices can restore ecosystem functions and services is not well known. This project was initiated to quantify existing ecological services derived from USDA conservation practices in the MAV as part of the USDA Conservation Effects Assessment Project, Wetlands Component (CEAP-Wetlands). The U.S. Geological Survey (USGS), in collaboration with the USDA Natural Resources Conservation Service, the USDA Farm Service Agency, the U.S. Fish and Wildlife Service, and Ducks Unlimited, collected data on soils, vegetation, nitrogen cycling, migratory birds, and amphibians from 88 different sites between 2006 and 2008. Results from restored WRP sites were compared to baseline data from active agricultural cropland (AG) to evaluate changes in ecosystem services.

  5. Red states, blue states, and divorce: understanding the impact of conservative Protestantism on regional variation in divorce rates.

    PubMed

    Glass, Jennifer; Levchak, Philip

    2014-01-01

    Why do states with larger proportions of religious conservatives have higher divorce rates than states with lower proportions of religious conservatives? This project examines whether earlier transitions to marriage and parenthood among conservative Protestants (known risk factors for divorce) contribute to this paradox while attending to other plausible explanations. County-level demographic information from all 50 states is combined from a variety of public data sources and merged with individual records from the National Surveys of Family Growth to estimate both aggregated county and multilevel individual models of divorce. Results show that individual religious conservatism is positively related to individual divorce risk, solely through the earlier transitions to adulthood and lower incomes of conservative Protestants. However, the proportion of conservative Protestants in a county is also independently and positively associated with both the divorce rate in that county and an individual's likelihood of divorcing. The earlier family formation and lower levels of educational attainment and income in counties with a higher proportion of conservative Protestants can explain a substantial portion of this association. Little support is found for alternative explanations of the association between religious conservatism and divorce rates, including the relative popularity of marriage versus cohabitation across counties.

  6. Construction of attenuated Salmonella typhimurium Strain expressing Helicobacter pylori conservative region of adhesin antigen and its immunogenicity

    PubMed Central

    Bai, Yang; Zhang, Ya-Li; Wang, Ji-De; Zhang, Zhao-Shan; Zhou, Dian-Yuan

    2004-01-01

    AIM: To construct a non-resistant and attenuated Salmonella typhimurium (S. typhimurium) strain which expresses conservative region of adhesion AB of Helicobacter pylori (H pylori) and evaluate its immunogenicity. METHODS: The AB gene amplified by PCR was inserted into the expression vector pYA248 containing asd gene and through two transformations introduced into the delta Cya, delta Crp, delta Asd attenuated Salmonella typhimurium strain, constructing balanced lethal attenuated Salmonella typhimurium strains X4072 (pYA248-AB). Bridged ELISA method was used to measure the expression of AB antigen in sonicate and culture supernatant. According to the method described by Meacock, stability of the recombinant was evaluated. Semi-lethal capacity test was used to evaluate the safety of recombinant. The immunogenicity of recombinant was evaluated with animal experiments. RESULTS: The attenuated S. typhimurium X4072 (pYA248-AB) which expresses AB was successfully constructed. Furthermore, bridged ELISA assay showed that the content of AB in recombinant X4072 (pYA248- AB) culture supernatant was higher than that was in thallus lytic liquor. And after recombinant X4072 (pYA248- AB) was cultured for 100 generations without selection pressure, the entire recombinant bacteria selected randomly could grow, and the AB antigen was defected positive by ELISA. The growth curve of the recombinant bacteria showed that the growth states of X4072 (pYA248) and X4072 (pYA248-AB) were basically consistent. The survival rate of C57BL/6 was still 100%, at 30 d after mice taking X4072 (pYA248-AB) 1.0 × 1010 cfu orally. Oral immunization of mice with X4072 (pYA248-AB) induced a specific immune response. CONCLUSION: In vitro recombinant plasmid appears to be stable and experiments on animals showed that the recombinant strains were safe and immunogenic in vitro, which providing a new live oral vaccine candidate for protection and care of H pylori infection. PMID:15300892

  7. 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.

  8. The X chromosome of monotremes shares a highly conserved region with the eutherian and marsupial X chromosomes despite the absence of X chromosome inactivation.

    PubMed

    Watson, J M; Spencer, J A; Riggs, A D; Graves, J A

    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. We 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.

  9. Note: Utilization of polymer gel as a bolus compensator and a dosimeter in the near-surface buildup region for breast-conserving therapy

    NASA Astrophysics Data System (ADS)

    Fuse, Hiraku; Shinoda, Kazuya; Inohira, Masaya; Kawamura, Hiraku; Miyamoto, Katsumi; Sakae, Takeji; Fujisaki, Tatsuya

    2015-09-01

    Tangential beam radiotherapy is routinely used for radiation therapy after breast conserving surgery. A tissue-equivalent bolus placed on the irradiated area shifts the depth of the dose distribution; this bolus provides uniform dose distribution to the breast. The gel bolus made by the BANG-Pro® polymer gel and in an oxygen non-transmission pack was applicable as a dosimeter to measure dose distribution in near-surface buildup region. We validated the use of the gel bolus to improve in the whole-breast/chest wall, including the near-surface buildup region.

  10. Note: Utilization of polymer gel as a bolus compensator and a dosimeter in the near-surface buildup region for breast-conserving therapy.

    PubMed

    Fuse, Hiraku; Shinoda, Kazuya; Inohira, Masaya; Kawamura, Hiraku; Miyamoto, Katsumi; Sakae, Takeji; Fujisaki, Tatsuya

    2015-09-01

    Tangential beam radiotherapy is routinely used for radiation therapy after breast conserving surgery. A tissue-equivalent bolus placed on the irradiated area shifts the depth of the dose distribution; this bolus provides uniform dose distribution to the breast. The gel bolus made by the BANG-Pro(®) polymer gel and in an oxygen non-transmission pack was applicable as a dosimeter to measure dose distribution in near-surface buildup region. We validated the use of the gel bolus to improve in the whole-breast/chest wall, including the near-surface buildup region.

  11. Note: Utilization of polymer gel as a bolus compensator and a dosimeter in the near-surface buildup region for breast-conserving therapy

    SciTech Connect

    Fuse, Hiraku Inohira, Masaya; Kawamura, Hiraku; Fujisaki, Tatsuya; Shinoda, Kazuya; Miyamoto, Katsumi; Sakae, Takeji

    2015-09-15

    Tangential beam radiotherapy is routinely used for radiation therapy after breast conserving surgery. A tissue-equivalent bolus placed on the irradiated area shifts the depth of the dose distribution; this bolus provides uniform dose distribution to the breast. The gel bolus made by the BANG-Pro{sup ®} polymer gel and in an oxygen non-transmission pack was applicable as a dosimeter to measure dose distribution in near-surface buildup region. We validated the use of the gel bolus to improve in the whole-breast/chest wall, including the near-surface buildup region.

  12. [Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

    PubMed

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

    The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.

  13. Ecosystem Services Derived from Wetland Conservation Practices in the United States Prairie Pothole Region with an Emphasis on the U.S. Department of Agriculture Conservation Reserve and Wetlands Reserve Programs

    USGS Publications Warehouse

    Gleason, Robert A.; Laubhan, Murray K.; Euliss, Ned H.

    2008-01-01

    Implementation of the U.S. Department of Agriculture (USDA) Conservation Reserve Program (CRP) and Wetlands Reserve Program (WRP) has resulted in the restoration of approximately 2,200,000 ha (5,436,200 acres) of wetland and grassland habitats in the Prairie Pothole Region. These restored habitats are known to provide various ecosystem services; however, little work has been conducted to quantify and verify benefits on program lands (lands enrolled in the CRP and WRP) in agriculturally dominated landscapes of the Prairie Pothole Region. To address this need, the U.S. Geological Survey (USGS), in collaboration with the USDA Farm Service Agency and Natural Resources Conservation Service, initiated a study to develop and apply approaches to quantify changes in ecosystem services resulting from wetland restoration activities funded by the USDA. To accomplish this goal, the USGS conducted a comprehensive, stratified survey of 204 catchments (wetland and surrounding uplands contributing runoff to the wetland) in 1997 and 270 catchments in 2004 to gather data necessary for estimating various ecosystem services. In 1997 and 2004, the surveys included catchments with seasonal and semipermanent wetlands that were restored as part of USDA conservation programs, as well as nonprogram catchments in native prairie. Additionally, in 2004 data collection was expanded to include temporary wetlands for all treatments and nonprogram cropped catchments for all wetland classes: temporary, seasonal, and semipermanent. A key element in the sample design is that catchments span an alteration gradient ranging from highly altered, such as cropland, to minimally altered, such as native prairie. Therefore, we evaluated restoration programs by comparing changes in program (restored) catchments to nonprogram (cropland and native prairie) catchments. Information collected during both surveys included easily measured soil, vegetation, and morphological variables that were used to estimate the

  14. Utility of Clinical Breast Exams in Detecting Local-Regional Breast Events after Breast-Conservation in Women with a Personal History of High-risk Breast Cancer

    PubMed Central

    Neuman, Heather B.; Schumacher, Jessica R.; Francescatti, Amanda B.; Adesoye, Taiwo; SB, Edge; ES, Burnside; DJ, Vanness; M, Yu; Y, Si; D, McKellar; DP, Winchester; Greenberg, Caprice C.

    2016-01-01

    Introduction Although breast cancer follow-up guidelines emphasize the importance of clinical exams, prior studies suggest a small fraction of local-regional events occurring after breast conservation are detected by exam alone. Our objective was to examine how local-regional events are detected in a contemporary, national cohort of high-risk breast cancer survivors. Methods A stage-stratified sample of stage II/III breast cancer patients diagnosed in 2006-2007 (n=11,099) were identified from 1,217 facilities within the National Cancer Data Base. Additional data on local-regional and distant breast events, method of event detection, imaging received, and mortality was collected. We further limited the cohort to patients with breast conservation (n=4,854). Summary statistics describe local-regional event rates and detection method. Results Local-regional events were detected in 5.5% (n=265). 83% were ipsilateral or contralateral in-breast events, and 17% within ipsilateral lymph nodes. 48% of local-regional events were detected on asymptomatic breast imaging, 29% by patients, and 10% on clinical exam. Overall, 0.5% of the 4,854 patients had a local-regional event detected on exam. Exams detected a higher proportion of lymph node (8/45) compared to in-breast events (18/220). No factors were associated with method of event detection. Discussion Clinical exams, as an adjunct to screening mammography, have a modest effect on local-regional event detection. This contradicts current belief that exams are a critical adjunct to mammographic screening. These findings can help to streamline follow-up care, potentially improving follow-up efficiency and quality. PMID:27491784

  15. A highly conserved sequence in the 3'-untranslated region of the drosophila Adh gene plays a functional role in Adh expression.

    PubMed Central

    Parsch, J; Stephan, W; Tanda, S

    1999-01-01

    Phylogenetic analysis identified a highly conserved eight-base sequence (AAGGCTGA) within the 3'-untranslated region (UTR) of the Drosophila alcohol dehydrogenase gene, Adh. To examine the functional significance of this conserved motif, we performed in vitro deletion mutagenesis on the D. melanogaster Adh gene followed by P-element-mediated germline transformation. Deletion of all or part of the eight-base sequence leads to a twofold increase in in vivo ADH enzymatic activity. The increase in activity is temporally and spatially general and is the result of an underlying increase in Adh transcript. These results indicate that the conserved 3'-UTR motif plays a functional role in the negative regulation of Adh gene expression. The evolutionary significance of our results may be understood in the context of the amino acid change that produces the ADH-F allele and also leads to a twofold increase in ADH activity. While there is compelling evidence that the amino acid replacement has been a target of positive selection, the conservation of the 3'-UTR sequence suggests that it is under strong purifying selection. The selective difference between these two sequence changes, which have similar effects on ADH activity, may be explained by different metabolic costs associated with the increase in activity. PMID:9927459

  16. Recognizing Prefixes in Scientific Quantities

    ERIC Educational Resources Information Center

    Sokolowski, Andrzej

    2015-01-01

    Although recognizing prefixes in physical quantities is inherent for practitioners, it might not be inherent for students, who do not use prefixes in their everyday life experiences. This deficiency surfaces in AP Physics exams. For example, readers of an AP Physics exam reported "a common mistake of incorrectly converting nanometers to…

  17. Do You Recognize This Parent?

    ERIC Educational Resources Information Center

    Wallace, Edna

    1997-01-01

    Suggests effective ways to work with parents who may be permissive, busy, detached, overprotective, or negative. Recommends that child care professionals be sensitive and understanding, recognize other demands on parents' time and communicate competitively with them, use terms parents understand, accept various levels of parental involvement, be…

  18. CBF mediates adenovirus Ela trans-activation by interaction at the C-terminal promoter targeting domain of conserved region 3.

    PubMed

    Agoff, S N; Wu, B

    1994-12-01

    Genetic and biochemical evidence suggest that conserved region 3 (CR3) of the adenovirus Ela polypeptide can provide two distinct and separable functions: an N-terminal transcriptional activation region and a C-terminal promoter targeting region. It is thought that the promoter targeting region of Ela CR3 interacts with promoter-specific transcription factors, thereby bringing the activation region of Ela CR3 in proximity of the promoter. Here we report that CBF, a CCAAT-box-binding factor that regulates hsp70 gene expression and mediates Ela trans-activation in vivo, interacts with the promoter targeting region of Ela CR3 in vitro. Point mutations in Ela CR3 that are defective in stimulating transcription from the hsp70 promoter are also defective in stimulating transcription directed by a synthetic activator, GAL-CBF, composed of the DNA-binding domain of yeast GAL4 fused to CBF. These mutations fall into two classes with respect to their abilities to interact with CBF in vitro. Mutations in the transcriptional activation region of Ela CR3 do not affect binding to CBF, but mutation of the promoter targeting region of Ela CR3 prevents association with CBF in vitro.

  19. Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion

    PubMed Central

    Tan, Chunjian; Cao, Xue; Yuan, Shuai; Wang, Weiyu; Feng, Yongzhong; Qiao, Bo

    2015-01-01

    Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrients in soils subjected to non-traditional tillage treatments decreased during the first several years and then remained stable over the last several years of the experiment. The soil organic matter and total nitrogen content increased gradually over 6 years in all treatments except CK. The nutrient content of soils subjected to conservative tillage methods, such as NT and SM, were significantly higher than those in soils under the CK treatment. Straw mulching and film mulching effectively reduced an observed decrease in soybean yield. Over the final 6 years of the experiment, soybean yields followed the trend RPM > PM > SM > NT > CK > In. This trend has implications for controlling soil erosion and preventing non-point source pollution in sloping fields by sacrificing some food production. PMID:26621049

  20. Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion.

    PubMed

    Tan, Chunjian; Cao, Xue; Yuan, Shuai; Wang, Weiyu; Feng, Yongzhong; Qiao, Bo

    2015-12-01

    Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrients in soils subjected to non-traditional tillage treatments decreased during the first several years and then remained stable over the last several years of the experiment. The soil organic matter and total nitrogen content increased gradually over 6 years in all treatments except CK. The nutrient content of soils subjected to conservative tillage methods, such as NT and SM, were significantly higher than those in soils under the CK treatment. Straw mulching and film mulching effectively reduced an observed decrease in soybean yield. Over the final 6 years of the experiment, soybean yields followed the trend RPM > PM > SM > NT > CK > In. This trend has implications for controlling soil erosion and preventing non-point source pollution in sloping fields by sacrificing some food production.

  1. Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion

    NASA Astrophysics Data System (ADS)

    Tan, Chunjian; Cao, Xue; Yuan, Shuai; Wang, Weiyu; Feng, Yongzhong; Qiao, Bo

    2015-12-01

    Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrients in soils subjected to non-traditional tillage treatments decreased during the first several years and then remained stable over the last several years of the experiment. The soil organic matter and total nitrogen content increased gradually over 6 years in all treatments except CK. The nutrient content of soils subjected to conservative tillage methods, such as NT and SM, were significantly higher than those in soils under the CK treatment. Straw mulching and film mulching effectively reduced an observed decrease in soybean yield. Over the final 6 years of the experiment, soybean yields followed the trend RPM > PM > SM > NT > CK > In. This trend has implications for controlling soil erosion and preventing non-point source pollution in sloping fields by sacrificing some food production.

  2. Conserved Regions as Markers of Different Patterns of Expression and Distribution of the Mucin-Associated Surface Proteins of Trypanosoma cruzi

    PubMed Central

    De Pablos, Luis M.

    2012-01-01

    The MASP gene family is the second most widely represented gene family in the genome of Trypanosoma cruzi. One of its main characteristics is that its 5′ and 3′ regions are highly conserved. We assessed the expression of these conserved regions as a marker for T. cruzi and also analyzed the expression of the masp genes and MASP proteins. In parasite strains CL-Brener (DTUVI lineage) and PAN4 (DTUI lineage), masp genes were expressed at different levels both with regard to the two strains and between stages in the parasite's life cycle. We also studied the expression of the family during the intracellular cycle of T. cruzi, using antibodies against the conserved MASP signal peptide (SP). Fluorescence intensity showed an increase in expression from 24 h onwards, with a peak in intensity at 72 h postinfection. After 24 and 48 h, the MASP proteins were expressed in 33.33% and 57.14% of the amastigotes, respectively. Our data show that not only the extracellular forms of T. cruzi but also the intracellular phases express this type of protein, though to different extents in the various forms of the parasite. PMID:22025509

  3. Upstream regions of the human cardiac actin gene that modulate its transcription in muscle cells: presence of an evolutionarily conserved repeated motif.

    PubMed Central

    Minty, A; Kedes, L

    1986-01-01

    Transfection into cultured cell lines was used to investigate the transcriptional regulation of the human cardiac actin gene. We first demonstrated that in both human heart and human skeletal muscle, cardiac actin mRNAs initiate at the identical site and contain the same first exon, which is separated from the first coding exon by an intron of 700 base pairs. A region of 485 base pairs upstream from the transcription initiation site of the human cardiac actin gene directs high-level transient expression of the bacterial chloramphenicol acetyltransferase gene in differentiated myotubes of the mouse C2C12 muscle cell line, but not in mouse L fibroblast or rat PC-G2 pheochromocytoma cells. Deletion analysis of this region showed that at least two physically separated sequence elements are involved, a distal one starting between -443 and -395 and a proximal one starting between -177 and -118, and suggested that these sequences interact with positively acting transcriptional factors in muscle cells. When these two sequence elements are inserted separately upstream of a heterologous (simian virus 40) promoter, they do not affect transcription but do give a small (four- to fivefold) stimulation when tested together. Overall, these regulatory regions upstream of the cap site of the human cardiac actin gene show remarkably high sequence conservation with the equivalent regions of the mouse and chick genes. Furthermore, there is an evolutionarily conserved repeated motif that may be important in the transcriptional regulation of actin and other contractile protein genes. Images PMID:3785189

  4. Threats, conservation strategies, and prognosis for suckers (Catostomidae) in North America: insights from regional case studies of a diverse family of non-game fishes

    USGS Publications Warehouse

    Cooke, Steven J.; Bunt, Christopher M.; Hamilton, Steven J.; Jennings, Cecil A.; Pearson, Micheal P.; Cooperman, Micheal S.; Markle, Douglas F.

    2005-01-01

    Catostomid fishes are a diverse family of 76+ freshwater species that are distributed across North America in many different habitats. This group of fish is facing a variety of impacts and conservation issues that are somewhat unique relative to more economically valuable and heavily managed fish species. Here, we present a brief series of case studies to highlight the threats such as migration barriers, flow regulation, environmental contamination, habitat degradation, exploitation and impacts from introduced (non-native) species that are facing catostomids in different regions. Collectively, the case studies reveal that individual species usually are not threatened by a single, isolated factor. Instead, species in general face numerous stressors that threaten multiple stages of their life history. Several factors have retarded sucker conservation including widespread inabilities of field workers to distinguish some species, lack of basic natural history and ecological knowledge of life history, and the misconception that suckers are tolerant of degraded conditions and are of little social or ecological value. Without a specific constituent group lobbying for conservation of non-game fishes, all such species, including members of the catostomid family, will continue to face serious risks because of neglect, ignorance, and misunderstanding. We suggest that conservation strategies should incorporate research and education/outreach components. Other conservation strategies that would be effective for protecting suckers include freshwater protected areas for critical habitat, restoration of degraded habitat, and design of catostomid-friendly fish bypass facilities. We believe that the plight of the catostomids is representative of the threats facing many other non-game freshwater fishes with diverse life-history strategies globally.

  5. Recognizing Body Dysmorphic Disorder (Dysmorphophobia)

    PubMed Central

    Varma, Anukriti; Rastogi, Rajesh

    2015-01-01

    Dysmorphophobia is a psychiatric condition which frequently presents in the clinics of dermatologists and plastic surgeons. This disorder (also called body dysmorphic disorder) is troublesome to the patient whilst being confusing for the doctor. This commonly undiagnosed condition can be detected by a few simple steps. Timely referral to a psychiatrist benefits most patients suffering from it. This article describes with a case vignette, how to recognize body dysmorphic disorder presenting in the dermatological or aesthetic surgery set up. Diagnostic criteria, eitiology, approach to patient, management strategy and when to refer are important learning points. The importance of recognizing this disorder timely and referring the patient to the psychiatrist for appropriate treatment is crucial. This article covers all aspects of body dysmorphic disorder relevant to dermatologists and plastic surgeons and hopes to be useful in a better understanding of this disorder. PMID:26644741

  6. Automatic Target Recognizer Database Requirements

    NASA Astrophysics Data System (ADS)

    Power, David R.

    1987-09-01

    Data representative of imaging sensors and scenarios which form the inputs for automatic target recognizers (ATRs) is critical to their development, testing and performance evaluation. The Data Base Committee of the Automatic Target Recognizer Working Group provides a forum and produces products to assist collection, distribution and use of data for development of military ATR systems. Examples discussed in the paper include digital image data exchange format specifications. Requirements for ground and image truth data have been the subject of surveys. Such inputs are intended as recommendations for consideration by imagery data collection activities whose products are potentially useful for ATR development. Other topics concerning collection, reduction, use and exchange of imaging sensor data are outlined but not discussed in detail.

  7. Recognizing Prefixes in Scientific Quantities

    NASA Astrophysics Data System (ADS)

    Sokolowski, Andrzej

    2015-09-01

    Although recognizing prefixes in physical quantities is inherent for practitioners, it might not be inherent for students, who do not use prefixes in their everyday life experiences. This deficiency surfaces in AP Physics exams. For example, readers of an AP Physics exam reported "a common mistake of incorrectly converting nanometers to meters." Similar students' mistakes were reported also by AP Chemistry readers "as in previous years, students still had difficulty converting kJ to J." While traditional teaching focuses on memorizing the symbols of prefixes, little attention is given to helping learners recognize a prefix in a given quantity. I noticed in my teaching practice that by making the processes of identifying prefixes more explicit, students make fewer mistakes on unit conversion. Thus, this paper presents an outline of a lesson that focuses on prefix recognition. It is designed for a first-year college physics class; however, its key points can be addressed to any group of physics students.

  8. Recognizing species, present and past.

    PubMed

    Tattersall, Ian

    2014-01-01

    Nobody disputes that nature is meaningfully "packaged" in some way. But debate persists over exactly how (and even whether) the boundaries dividing taxa should (can) be drawn. At one end of the scale, some zealots abstrusely deny real existence to higher taxa.(1) At the other, laborers at the taxonomic rock-face confront genuine challenges in recognizing and delineating the species that systematists agree constitute the most fundamental unit of taxonomic analysis.

  9. Regions.

    ERIC Educational Resources Information Center

    Moulin-Acevedo, Madeleine; And Others

    1993-01-01

    Includes "From School to Jobs: Africa's Dilemma" (Moulin-Acevedo); "Helping Change in Eastern Europe"; "Recognizing the Dignity of Indigenous Peoples"; "An Employment Plan for Pakistan"; and "Around the Continents." (JOW)

  10. Molecular dissection of a contiguous gene syndrome: Frequent submicroscopic deletions, evolutionarily conserved sequences, and a hypomethylated island in the Miller-Dieker chromosome region

    SciTech Connect

    Ledbetter, D.H.; Ledbetter, S.A.; vanTuinen, P.; Summers, K.M.; Robinson, T.J.; Nakamura, Yusuke; Wolff, R.; White, R.; Barker, D.F.; Wallace, M.R.; Collins, F.S.; Dobyns, W.B. )

    1989-07-01

    The Miller-Dieker syndrome (MDS), composed of characteristic facial abnormalities and a severe neuronal migration disorder affecting the cerebral cortex, is caused by visible or submicroscopic deletions of chromosome band 17p13. Twelve anonymous DNA markers were tested against a panel of somatic cell hybrids containing 17p deletions from seven MDS patients. All patients, including three with normal karyotypes, are deleted for a variable set of 5-12 markers. Two highly polymorphic VNTR (variable number of tandem repeats) probes, YNZ22 and YNH37, are codeleted in all patients tested and make molecular diagnosis for this disorder feasible. By pulsed-field gel electrophoresis, YNZ22 and YNH37 were shown to be within 30 kilobases (kb) of each other. Cosmid clones containing both VNTR sequences were identified, and restriction mapping showed them to be <15 kb apart. Three overlapping cosmids spanning >100 kb were completely deleted in all patients, providing a minimum estimate of the size of the MDS critical region. A hypomethylated island and evolutionarily conserved sequences were identified within this 100-kb region, indications of the presence of one or more expressed sequences potentially involved in the pathophysiology of this disorder. The conserved sequences were mapped to mouse chromosome 11 by using mouse-rat somatic cell hybrids, extending the remarkable homology between human chromosome 17 and mouse chromosome 11 by 30 centimorgans, into the 17p telomere region.

  11. A conserved amphipathic helix in the N-terminal regulatory region of the papillomavirus E1 helicase is required for efficient viral DNA replication.

    PubMed

    Morin, Geneviève; Fradet-Turcotte, Amélie; Di Lello, Paola; Bergeron-Labrecque, Fanny; Omichinski, James G; Archambault, Jacques

    2011-06-01

    The papillomavirus E1 helicase, with the help of E2, assembles at the viral origin into a double hexamer that orchestrates replication of the viral genome. The N-terminal region (NTR) of E1 is essential for DNA replication in vivo but dispensable in vitro, suggesting that it has a regulatory function. By deletion analysis, we identified a conserved region of the E1 NTR needed for efficient replication of viral DNA. This region is predicted to form an amphipathic α-helix (AH) and shows sequence similarity to portions of the p53 and herpes simplex virus (HSV) VP16 transactivation domains known as transactivation domain 2 (TAD2) and VP16C, which fold into α-helices upon binding their target proteins, including the Tfb1/p62 (Saccharomyces cerevisiae/human) subunit of general transcription factor TFIIH. By nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), we found that a peptide spanning the E1 AH binds Tfb1 on the same surface as TAD2/VP16C and with a comparable affinity, suggesting that it does bind as an α-helix. Furthermore, the E1 NTRs from several human papillomavirus (HPV) types could activate transcription in yeast, and to a lesser extent in mammalian cells, when fused to a heterologous DNA-binding domain. Mutation of the three conserved hydrophobic residues in the E1 AH, analogous to those in TAD2/VP16C that directly contact their target proteins, decreased transactivation activity and, importantly, also reduced by 50% the ability of E1 to support transient replication of DNA in C33A cells, at a step following assembly of the E1-E2-ori preinitiation complex. These results demonstrate the existence of a conserved TAD2/VP16C-like AH in E1 that is required for efficient replication of viral DNA.

  12. A conserved amphipathic helix in the N-terminal regulatory region of the papillomavirus E1 helicase is required for efficient viral DNA replication.

    PubMed

    Morin, Geneviève; Fradet-Turcotte, Amélie; Di Lello, Paola; Bergeron-Labrecque, Fanny; Omichinski, James G; Archambault, Jacques

    2011-06-01

    The papillomavirus E1 helicase, with the help of E2, assembles at the viral origin into a double hexamer that orchestrates replication of the viral genome. The N-terminal region (NTR) of E1 is essential for DNA replication in vivo but dispensable in vitro, suggesting that it has a regulatory function. By deletion analysis, we identified a conserved region of the E1 NTR needed for efficient replication of viral DNA. This region is predicted to form an amphipathic α-helix (AH) and shows sequence similarity to portions of the p53 and herpes simplex virus (HSV) VP16 transactivation domains known as transactivation domain 2 (TAD2) and VP16C, which fold into α-helices upon binding their target proteins, including the Tfb1/p62 (Saccharomyces cerevisiae/human) subunit of general transcription factor TFIIH. By nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), we found that a peptide spanning the E1 AH binds Tfb1 on the same surface as TAD2/VP16C and with a comparable affinity, suggesting that it does bind as an α-helix. Furthermore, the E1 NTRs from several human papillomavirus (HPV) types could activate transcription in yeast, and to a lesser extent in mammalian cells, when fused to a heterologous DNA-binding domain. Mutation of the three conserved hydrophobic residues in the E1 AH, analogous to those in TAD2/VP16C that directly contact their target proteins, decreased transactivation activity and, importantly, also reduced by 50% the ability of E1 to support transient replication of DNA in C33A cells, at a step following assembly of the E1-E2-ori preinitiation complex. These results demonstrate the existence of a conserved TAD2/VP16C-like AH in E1 that is required for efficient replication of viral DNA. PMID:21450828

  13. A Conserved Amphipathic Helix in the N-Terminal Regulatory Region of the Papillomavirus E1 Helicase Is Required for Efficient Viral DNA Replication▿†

    PubMed Central

    Morin, Geneviève; Fradet-Turcotte, Amélie; Di Lello, Paola; Bergeron-Labrecque, Fanny; Omichinski, James G.; Archambault, Jacques

    2011-01-01

    The papillomavirus E1 helicase, with the help of E2, assembles at the viral origin into a double hexamer that orchestrates replication of the viral genome. The N-terminal region (NTR) of E1 is essential for DNA replication in vivo but dispensable in vitro, suggesting that it has a regulatory function. By deletion analysis, we identified a conserved region of the E1 NTR needed for efficient replication of viral DNA. This region is predicted to form an amphipathic α-helix (AH) and shows sequence similarity to portions of the p53 and herpes simplex virus (HSV) VP16 transactivation domains known as transactivation domain 2 (TAD2) and VP16C, which fold into α-helices upon binding their target proteins, including the Tfb1/p62 (Saccharomyces cerevisiae/human) subunit of general transcription factor TFIIH. By nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), we found that a peptide spanning the E1 AH binds Tfb1 on the same surface as TAD2/VP16C and with a comparable affinity, suggesting that it does bind as an α-helix. Furthermore, the E1 NTRs from several human papillomavirus (HPV) types could activate transcription in yeast, and to a lesser extent in mammalian cells, when fused to a heterologous DNA-binding domain. Mutation of the three conserved hydrophobic residues in the E1 AH, analogous to those in TAD2/VP16C that directly contact their target proteins, decreased transactivation activity and, importantly, also reduced by 50% the ability of E1 to support transient replication of DNA in C33A cells, at a step following assembly of the E1-E2-ori preinitiation complex. These results demonstrate the existence of a conserved TAD2/VP16C-like AH in E1 that is required for efficient replication of viral DNA. PMID:21450828

  14. Movement patterns of Antillean manatees in Chetumal Bay (Mexico) and coastal Belize: A challenge for regional conservation

    USGS Publications Warehouse

    Castelblanco-Martínez, Delma Nataly; Padilla-Saldivar, J.; Hernández-Arana, Héctor Abuid; Slone, D.H.; Reid, J.P.; Morales-Vela, B.

    2013-01-01

    Information from 15 satellite-tracked Antillean manatees (Trichechus manatus manatus) was analyzed in order to assess individual movements, home ranges, and high-use areas for conservation decisions. Manatees were captured in Chetumal Bay, Mexico, and tagged with Argos-monitored satellite transmitters. Location of the manatees and physical characteristics were assessed to describe habitat properties. Most manatees traveled to freshwater sources. The Maximum Area Size (MAS) for each manatee was determined using the observation-area method. Additional kernel densities of 95% home range and 50% Center of Activity (COA) were also calculated, with manatees having 1–3 COAs. Manatees exhibited two different movement patterns: remaining in Chetumal Bay, and long-distance (up to 240 km in 89 d). The residence time in Chetumal Bay was higher for females (89.6% of time) than for males (72.0%), but the daily travel rate (0.4–0.5 km/d) was similar for both sexes. Most of the COAs fell within Natural Protected Areas (NPA). However, manatees also travel for long distances into unprotected areas, where they face uncontrolled boat traffic, fishing activities, and habitat loss. Conservation of movement corridors may promote long-distance movements and facilitate genetic exchange.

  15. 36 CFR 242.11 - Regional advisory councils.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... by substantial evidence, be consistent with recognized principles of fish and wildlife conservation... subsistence taking and uses of fish and wildlife resources on public lands. The Regional Councils shall... public meetings related to subsistence uses of fish and wildlife within their respective regions,...

  16. 36 CFR 242.11 - Regional advisory councils.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... by substantial evidence, be consistent with recognized principles of fish and wildlife conservation... subsistence taking and uses of fish and wildlife resources on public lands. The Regional Councils shall... public meetings related to subsistence uses of fish and wildlife within their respective regions,...

  17. 36 CFR 242.11 - Regional advisory councils.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... by substantial evidence, be consistent with recognized principles of fish and wildlife conservation... subsistence taking and uses of fish and wildlife resources on public lands. The Regional Councils shall... public meetings related to subsistence uses of fish and wildlife within their respective regions,...

  18. 36 CFR 242.11 - Regional advisory councils.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... by substantial evidence, be consistent with recognized principles of fish and wildlife conservation... subsistence taking and uses of fish and wildlife resources on public lands. The Regional Councils shall... public meetings related to subsistence uses of fish and wildlife within their respective regions,...

  19. Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions.

    PubMed

    Anderson, O D; Larka, L; Christoffers, M J; McCue, K F; Gustafson, J P

    2002-04-01

    Extended flanking DNA sequences were characterized for five members of the wheat high molecular weight (HMW) glutenin gene family to understand more of the structure, control, and evolution of these genes. Analysis revealed more sequence conservation among orthologous regions than between paralogous regions, with differences mainly owing to transposition events involving putative retrotransposons and several miniature inverted transposable elements (MITEs). Both gyspy-like long terminal repeat (LTR) and non-LTR retrotransposon sequences are represented in the flanking DNAs. One of the MITEs is a novel class, but another MITE is related to the maize Stowaway family and is widely represented in Triticeae express sequence tags (ESTs). Flanking DNA of the longest sequence, a 20 425-bp fragment including and surrounding the HMW-glutenin Bx7 gene, showed additional cereal gene-like sequences both immediately 5' and 3' to the HMW-glutenin coding region. The transcriptional activities of sequences related to these flanking putative genes and the retrotransposon-related regions were indicated by matches to wheat and other Triticeae ESTs. Predictive analysis of matrix-attachment regions (MARs) of the HMW glutenin and several alpha-, gamma-, and omega-gliadin flanking DNAs indicate potential MARs immediately flanking each of the genes. Matrix binding activity in the predicted regions was confirmed for two of the HMW-glutenin genes.

  20. [Isolation and amplification cDNA of 8H07 gene conservative region of nematode Heterodera schachtii with high relationship to its rape homolog].

    PubMed

    Tsyhankova, V A; Andrusevych, Ia V; Ponomarenko, S P; Halkin, A P; Blium, Ia B

    2012-01-01

    Original method of small regulatory si/miRNA isolation from plant cells was elaborated. PCR amplification of fragment cDNA 8H07 nematode Heterodera schachtii gene was carried out. Using Northern-blot method hybridization of plant si/miRNA with cDNA fragment of conservative region 8H07 gene the presence of their high homology is found out. The amplified cDNA fragment of nematode 8H07 gene in future will be used for creation recombinant gene with complementary antisense dsRNA sequence for increasing resistance of rape plants to parasitic nematodes.

  1. Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

    PubMed Central

    Mayer, Klaus; Murphy, George; Tarchini, Renato; Wambutt, Rolf; Volckaert, Guido; Pohl, Thomas; Düsterhöft, Andreas; Stiekema, Willem; Entian, Karl-Dieter; Terryn, Nancy; Lemcke, Kai; Haase, Dirk; Hall, Caroline R.; van Dodeweerd, Anne-Marie; Tingey, Scott V.; Mewes, Hans-Werner; Bevan, Michael W.; Bancroft, Ian

    2001-01-01

    The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that the Arabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes. PMID:11435398

  2. Preventing and Recognizing Prescription Drug Abuse

    MedlinePlus

    ... Abuse » Preventing and recognizing prescription drug abuse Prescription Drug Abuse Email Facebook Twitter Preventing and recognizing prescription drug abuse To ensure proper medical care, patients should discuss ...

  3. Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea

    PubMed Central

    2013-01-01

    Background The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. Results Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. Conclusions Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage. PMID:23586706

  4. Use of conserved genomic regions and degenerate primers in a PCR-based assay for the detection of members of the genus Caulimovirus.

    PubMed

    Pappu, H R; Druffel, K L

    2009-04-01

    The genus Caulimovirus consists of several distinct virus species with a double-stranded DNA genome that infect diverse plant species. A comparative analysis of the sequences of known Caulimovirus species revealed two regions that are conserved in all Caulimovirus species with the exception of Strawberry vein banding virus. Degenerate primers based on these two regions were designed and tested in a polymerase chain reaction-based assay for broad spectrum detection of members of this genus. Cauliflower mosaic virus, Figwort mosaic virus and three distinct caulimoviruses associated with dahlia (Dahlia variabilis) were used to show the utility of this test in detecting diverse caulimoviruses. The primer pair gave an amplicon of expected size (840bp). Amplicons from each virus were cloned and sequenced to verify their identity. The primer pair and the PCR assay provide approach for the broad spectrum detection of several members of the genus Caulimovirus.

  5. Use of conserved genomic regions and degenerate primers in a PCR-based assay for the detection of members of the genus Caulimovirus.

    PubMed

    Pappu, H R; Druffel, K L

    2009-04-01

    The genus Caulimovirus consists of several distinct virus species with a double-stranded DNA genome that infect diverse plant species. A comparative analysis of the sequences of known Caulimovirus species revealed two regions that are conserved in all Caulimovirus species with the exception of Strawberry vein banding virus. Degenerate primers based on these two regions were designed and tested in a polymerase chain reaction-based assay for broad spectrum detection of members of this genus. Cauliflower mosaic virus, Figwort mosaic virus and three distinct caulimoviruses associated with dahlia (Dahlia variabilis) were used to show the utility of this test in detecting diverse caulimoviruses. The primer pair gave an amplicon of expected size (840bp). Amplicons from each virus were cloned and sequenced to verify their identity. The primer pair and the PCR assay provide approach for the broad spectrum detection of several members of the genus Caulimovirus. PMID:19100290

  6. Bacillus thuringiensis insecticidal Cry1Aa toxin binds to a highly conserved region of aminopeptidase N in the host insect leading to its evolutionary success.

    PubMed

    Nakanishi, K; Yaoi, K; Shimada, N; Kadotani, T; Sato, R

    1999-06-15

    Bacillus thuringiensis insecticidal protein, Cry1Aa toxin, binds to a specific receptor in insect midguts and has insecticidal activity. Therefore, the structure of the receptor molecule is probably a key factor in determining the binding affinity of the toxin and insect susceptibility. The cDNA fragment (PX frg1) encoding the Cry1Aa toxin-binding region of an aminopeptidase N (APN) or an APN family protein from diamondback moth, Plutella xylostella midgut was cloned and sequenced. A comparison between the deduced amino acid sequence of PX frg1 and other insect APN sequences shows that Cry1Aa toxin binds to a highly conserved region of APN family protein. In this paper, we propose a model to explain the mechanism that causes B. thuringiensis evolutionary success and differing insect susceptibility to Cry1Aa toxin. PMID:10366728

  7. Energy Conservation Simplified

    ERIC Educational Resources Information Center

    Hecht, Eugene

    2008-01-01

    The standard formulation of energy conservation involves the subsidiary ideas of kinetic energy ("KE"), work ("W"), thermal energy, internal energy, and a half-dozen different kinds of potential energy ("PE"): elastic, chemical, nuclear, gravitational, and so forth. These quantities came to be recognized during the centuries over which the…

  8. A highly conserved region between amino acids 221 and 266 of dengue virus non-structural protein 1 is a major epitope region in infected patients.

    PubMed

    Omokoko, Magot Diata; Pambudi, Sabar; Phanthanawiboon, Supranee; Masrinoul, Promsin; Setthapramote, Chayanee; Sasaki, Tadahiro; Kuhara, Motoki; Ramasoota, Pongrama; Yamashita, Akifumi; Hirai, Itaru; Ikuta, Kazuyoshi; Kurosu, Takeshi

    2014-07-01

    The immune response to dengue virus (DENV) infection generates high levels of antibodies (Abs) against the DENV non-structural protein 1 (NS1), particularly in cases of secondary infection. Therefore, anti-NS1 Abs may play a role in severe dengue infections, possibly by interacting (directly or indirectly) with host factors or regulating virus production. If it does play a role, NS1 may contain epitopes that mimic those epitopes of host molecules. Previous attempts to map immunogenic regions within DENV-NS1 were undertaken using mouse monoclonal Abs (MAbs). The aim of this study was to characterize the epitope regions of nine anti-NS1 human monoclonal Abs (HuMAbs) derived from six patients secondarily infected with DENV-2. These anti-NS1 HuMAbs were cross-reactive with DENV-1, -2, and -3 but not DENV-4. All HuMAbs bound a common epitope region located between amino acids 221 and 266 of NS1. This study is the first report to map a DENV-NS1 epitope region using anti-DENV MAbs derived from patients. PMID:24778195

  9. Antarctic skuas recognize individual humans.

    PubMed

    Lee, Won Young; Han, Yeong-Deok; Lee, Sang-Im; Jablonski, Piotr G; Jung, Jin-Woo; Kim, Jeong-Hoon

    2016-07-01

    Recent findings report that wild animals can recognize individual humans. To explain how the animals distinguish humans, two hypotheses are proposed. The high cognitive abilities hypothesis implies that pre-existing high intelligence enabled animals to acquire such abilities. The pre-exposure to stimuli hypothesis suggests that frequent encounters with humans promote the acquisition of discriminatory abilities in these species. Here, we examine individual human recognition abilities in a wild Antarctic species, the brown skua (Stercorarius antarcticus), which lives away from typical human settlements and was only recently exposed to humans due to activities at Antarctic stations. We found that, as nest visits were repeated, the skua parents responded at further distances and were more likely to attack the nest intruder. Also, we demonstrated that seven out of seven breeding pairs of skuas selectively responded to a human nest intruder with aggression and ignored a neutral human who had not previously approached the nest. The results indicate that Antarctic skuas, a species that typically inhabited in human-free areas, are able to recognize individual humans who disturbed their nests. Our findings generally support the high cognitive abilities hypothesis, but this ability can be acquired during a relatively short period in the life of an individual as a result of interactions between individual birds and humans.

  10. Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis

    PubMed Central

    Justice, Cristina M.; Bishop, Kevin; Carrington, Blake; Mullikin, Jim C.; Swindle, Kandice; Marosy, Beth; Sood, Raman; Miller, Nancy H.; Wilson, Alexander F.

    2016-01-01

    Because of genetic heterogeneity present in idiopathic scoliosis, we previously defined clinical subsets (a priori) from a sample of families with idiopathic scoliosis to find genes involved with spinal curvature. Previous genome-wide linkage analysis of seven families with at least two individuals with kyphoscoliosis found linkage (P-value = 0.002) in a 3.5-Mb region on 5p13.3 containing only three known genes, IRX1, IRX2, and IRX4. In this study, the exons of IRX1, IRX2, and IRX4, the conserved noncoding elements in the region, and the exons of a nonprotein coding RNA, LOC285577, were sequenced. No functional sequence variants were identified. An intrafamilial test of association found several associated noncoding single nucleotide variants. The strongest association was with rs12517904 (P = 0.00004), located 6.5 kb downstream from IRX1. In one family, the genotypes of nine variants differed from the reference allele in all individuals with kyphoscoliosis, and two of three individuals with scoliosis, but did not differ from the reference allele in all other genotyped individuals. One of these variants, rs117273909, was located in a conserved noncoding region that functions as an enhancer in mice. To test whether the variant allele at rs117273909 had an effect on enhancer activity, zebrafish transgenesis was performed with overlapping fragments of 198 and 687 bp containing either the wild type or the variant allele. Our data suggests that this region acts as a regulatory element; however, its size and target gene(s) need to be identified to determine its role in idiopathic scoliosis. PMID:27172222

  11. DNA sequence analysis of conserved and unique regions of swinepox virus: identification of genetic elements supporting phenotypic observations including a novel G protein-coupled receptor homologue.

    PubMed

    Massung, R F; Jayarama, V; Moyer, R W

    1993-12-01

    Swinepox virus (SPV) contains a double-stranded cross-linked linear DNA genome of approximately 175 kilobase pairs with terminal inverted repetitions (TIRs) of 4.3 kb. The nucleotide sequence was determined for fragments from several regions of the genome including a 2.85-kb fragment from the central potentially conserved portion and two fragments within the presumed variable near-terminal regions which tend to be unique to a given poxvirus. The core sequence contains one partial and two complete open reading frames that are highly conserved and colinear with three contiguous ORFs within the HindIII D fragment of vaccinia virus (VV). The two near-terminal fragments, encompassing 14.2 and 3.6 kb, are respectively located 2.1 kb internal to the left and right cross-linked termini of the DNA and span the TIR junctions. The sequences encode 25 open reading frames including numerous proteins predicted to be membrane-bound or secreted in infected cells. Several ORFs unique to SPV were identified that may be involved in cell attachment, immune modulation, and pathogenesis including a novel poxvirus G protein-coupled receptor. In addition, several polypeptides encoded within the near-terminal regions of vaccinia virus DNA that function as host range or virulence factors are lacking within this region of swinepox virus including the VV growth factor, complement-binding protein, and ORFs C7L and K1L, associated with host range. The lack of these functional homologues could explain the characteristic attenuated phenotype and limited host range of SPV.

  12. Results of the global conservation assessment of the freshwater crabs (Brachyura, Pseudothelphusidae and Trichodactylidae): The Neotropical region, with an update on diversity.

    PubMed

    Cumberlidge, Neil; Alvarez, Fernando; Villalobos, Jose-Luis

    2014-01-01

    The freshwater crabs of the Neotropics comprise 311 species in two families (Pseudothelphusidae and Trichodactylidae) and one or both of these families are found in all of the countries in the Neotropical region (except for Chile and some of the Caribbean islands). Colombia (102 species, 81% endemic) and Mexico (67 species, 95% endemic) are the biodiversity hotspots of freshwater crab species richness and country-level endemism for this region. The results of the IUCN Red List conservation assessments show that 34% of pseudothelphusids and 10% of trichodactylids have an elevated risk of extinction, 29% of pseudothelphusids and 75% of trichodactylids are not at-risk (Least Concern), and although none are actually extinct, 56% of pseudothelphusids and 17% of trichodactylids are too poorly known to assess (Data Deficient). Colombia (14 species), Venezuela (7 species), Mexico (6 species), and Ecuador (5 species) are the countries with the highest number of threatened species of Neotropical freshwater crabs. The majority of threatened species are restricted-range semiterrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. These results represent a baseline that can be used to design strategies to save threatened Neotropical species of freshwater crabs. PMID:25561834

  13. Characterization of an Egyptian Spodoptera littoralis nucleopolyhedrovirus and a possible use of a highly conserved region from polyhedrin gene for nucleopolyhedrovirus detection

    PubMed Central

    Seufi, AlaaEddeen M

    2008-01-01

    An Egyptian isolate of Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) was tested for its potential as biocontrol agent in comparison to Autographa californica multiple nucleopolyhedrovirus (AcMNPV). Comparative assays of SpliNPV and AcMNPV against 2nd instar larvae of Spodoptera littoralis revealed 4-fold greater susceptibility of S. littoralis to AcMNPV than to SpliNPV based on LC50 values for the two viruses. The LT50s determined for SpliNPV and AcMNPV using LC50 of the virus against 2nd instar larvae were 4.2 and 5.8 days, respectively. A DNA segment of 405 bp containing highly conserved region from polyhedrin gene of SpliNPV (Polh-cr) was successfully amplified by PCR. Subsequently, this DNA segment was cloned and sequenced. Nucleotide sequence and its deduced amino acid sequence were compared to all available sequences in GenBank. Sequence alignment results revealed that Polh-cr showed significant similarities with 91 different baculovirus isolates. The percentage of homology ranged from 78% for Plusia orichalcea NPV to 99% for SpliNPV. This highly conserved region provides a candidate that could be used in easy, fast and economic prospective systems for virus detection as well as in biological control strategies. PMID:18215282

  14. Results of the global conservation assessment of the freshwater crabs (Brachyura, Pseudothelphusidae and Trichodactylidae): The Neotropical region, with an update on diversity

    PubMed Central

    Cumberlidge, Neil; Alvarez, Fernando; Villalobos, Jose-Luis

    2014-01-01

    Abstract The freshwater crabs of the Neotropics comprise 311 species in two families (Pseudothelphusidae and Trichodactylidae) and one or both of these families are found in all of the countries in the Neotropical region (except for Chile and some of the Caribbean islands). Colombia (102 species, 81% endemic) and Mexico (67 species, 95% endemic) are the biodiversity hotspots of freshwater crab species richness and country-level endemism for this region. The results of the IUCN Red List conservation assessments show that 34% of pseudothelphusids and 10% of trichodactylids have an elevated risk of extinction, 29% of pseudothelphusids and 75% of trichodactylids are not at-risk (Least Concern), and although none are actually extinct, 56% of pseudothelphusids and 17% of trichodactylids are too poorly known to assess (Data Deficient). Colombia (14 species), Venezuela (7 species), Mexico (6 species), and Ecuador (5 species) are the countries with the highest number of threatened species of Neotropical freshwater crabs. The majority of threatened species are restricted-range semiterrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. These results represent a baseline that can be used to design strategies to save threatened Neotropical species of freshwater crabs. PMID:25561834

  15. Results of the global conservation assessment of the freshwater crabs (Brachyura, Pseudothelphusidae and Trichodactylidae): The Neotropical region, with an update on diversity.

    PubMed

    Cumberlidge, Neil; Alvarez, Fernando; Villalobos, Jose-Luis

    2014-01-01

    The freshwater crabs of the Neotropics comprise 311 species in two families (Pseudothelphusidae and Trichodactylidae) and one or both of these families are found in all of the countries in the Neotropical region (except for Chile and some of the Caribbean islands). Colombia (102 species, 81% endemic) and Mexico (67 species, 95% endemic) are the biodiversity hotspots of freshwater crab species richness and country-level endemism for this region. The results of the IUCN Red List conservation assessments show that 34% of pseudothelphusids and 10% of trichodactylids have an elevated risk of extinction, 29% of pseudothelphusids and 75% of trichodactylids are not at-risk (Least Concern), and although none are actually extinct, 56% of pseudothelphusids and 17% of trichodactylids are too poorly known to assess (Data Deficient). Colombia (14 species), Venezuela (7 species), Mexico (6 species), and Ecuador (5 species) are the countries with the highest number of threatened species of Neotropical freshwater crabs. The majority of threatened species are restricted-range semiterrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. These results represent a baseline that can be used to design strategies to save threatened Neotropical species of freshwater crabs.

  16. Global Conservation Priorities for Marine Turtles

    PubMed Central

    Wallace, Bryan P.; DiMatteo, Andrew D.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Mortimer, Jeanne A.; Seminoff, Jeffrey A.; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jérôme; Bowen, Brian W.; Briseño Dueñas, Raquel; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Finkbeiner, Elena M.; Girard, Alexandre; Girondot, Marc; Hamann, Mark; Hurley, Brendan J.; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

    2011-01-01

    Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a “conservation priorities portfolio” system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for

  17. Health assessment for Environmental Conservation and Chemical Ccorporation, Zionsville, Indiana, Region 5. CERCLIS No. IND084259951. Final report

    SciTech Connect

    Not Available

    1987-03-23

    The Environmental Conservation and Chemical Corporation (ECC) Site is located off U.S. Highway 421, Zionsville, Boone County, Indiana, 10 miles northwest of Indianapolis. The ECC Corporation began operations in August 1977 as a solvent processing and reclaiming facility. Wastes such as resins, paint sludges, waste oils, and flammable solvents were received from approximately 350 industrial generators. On-site accumulation and unauthorized discharge of contaminated storm water, poor management of drum inventory, unapproved burning of chlorinated hydrocarbons and other solvents, and several spill incidents brought about State and EPA investigations. Remedial investigations characterized current on-site contamination as consisting primarily of volatile organic compounds, phthalates, phenols, and polychlorinated biphenyls. The current principal source of contamination is the subsurface soil. As a result of previous remedial actions at the site, the major sources of contamination have been removed; however, there appear to be individual areas of the site which would warrant further investigation to determine their potential for further contamination. The trend in the available monitoring data show low levels of contamination off-site. There are few potential exposure routes and, therefore, only limited public health concerns at this time.

  18. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.

    PubMed

    Salas-Leiva, Dayana E; Meerow, Alan W; Francisco-Ortega, Javier; Calonje, Michael; Griffith, M Patrick; Stevenson, Dennis W; Nakamura, Kyoko

    2014-07-01

    Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera. PMID:24444413

  19. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.

    PubMed

    Salas-Leiva, Dayana E; Meerow, Alan W; Francisco-Ortega, Javier; Calonje, Michael; Griffith, M Patrick; Stevenson, Dennis W; Nakamura, Kyoko

    2014-07-01

    Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.

  20. Genetic analysis of tumorigenesis: a conserved region in the human and Chinese hamster genomes contains genetically identified tumor-suppressor genes

    SciTech Connect

    Stenman, G.; Sager, R.

    1987-12-01

    Regional chromosome homologies were found in a comparison of human 11p with Chinese hamster 3p. By use of probes that recognize six genes of human 11p (INS, CAT, HBBC, CALC, PTH, and HRAS), the corresponding genes were localized by in situ hybridization on Chinese hamster chromosome 3. INS and CAT were located close to the centromere on 3p, whereas HBBC, CALC, and PTH were at 3q3-4 and HRAS at 3q4. Extensive prior data from chromosome studies of tumorigenic and tumor-derived Chinese hamster cells have suggested the presence of a tumor-suppressor gene on 3p. Two tumor-suppressor genes have been described on human 11p, one linked to CAT and one to INS. The present study raises the possibility that the Chinese hamster suppressor may be closely linked to INS or CAT.

  1. 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.

  2. 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.

  3. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region

    USGS Publications Warehouse

    Pinkney, Alfred E.; Driscoll, Charles T.; Evers, David C.; Hooper, Michael J.; Horan, Jeffrey; Jones, Jess W.; Lazarus, Rebecca; Marshall, Harold G.; Milliken, Andrew; Rattner, Barnett A.; Schmerfeld, John J.; Sparling, Donald W.

    2015-01-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public–private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena—freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures

  4. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

    PubMed

    Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

    2015-07-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and

  5. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

    PubMed

    Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

    2015-07-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and

  6. Right-hand border regions of octopine T-DNA are recognized by RNA polymerase of Agrobacterium as well as by VirD1 and VirD2 proteins.

    PubMed Central

    Niwa, Y; Yamamoto, A; Machida, C; Takebe, I; Machida, Y

    1988-01-01

    The T-DNA of octopine Ti plasmid of Agrobacterium tumefaciens contains TL- and TR-DNA regions each bounded by 25 base-pair-repeats (designated A, B, C and D from left to right). Short DNA segments containing the borders B, C and D were found to function as promoter when placed in the rightward orientation upstream of promoter-less lacZ. Promoter consensus sequence of Agrobacterium were found within these border repeats and in their adjacent regions. The expression of lacZ was low when the segments contained the overdrive, a sequence known to enhance T-DNA transfer. Simultaneous overproduction of VirD1 and D2 proteins, endonuclease acting on the border repeats, interfered with the promoter functions of the border segments. In spite of their activity under these conditions, the border regions do not seem to be involved in the gene expression, because they are not followed by appropriate open reading frames. We propose that RNA polymerase of Agrobacterium competes with VirD products for T-DNA borders and thereby affects the transfer of T-DNA. PMID:3412897

  7. Use of the V delta 1 variable region in the functional T-cell receptor alpha chain of a WT31+ cytotoxic T lymphocyte clone which specifically recognizes HLA-A2 molecule.

    PubMed

    Castelli, C; Mazzocchi, A; Salvi, S; Anichini, A; Sensi, M

    1992-04-01

    We report here the molecular characterization of the T-cell receptor (TCR) expressed by a human HLA-A2 specific cytotoxic T-cell clone named CTL 49. Flow cytometry analysis with a panel of anti-TCR antibodies revealed an OKT3+, WT31+, A13+, BB3-, TCR delta-, delta TCS1-, TCR gamma/delta 1-, OKT4-, and OKT8+ phenotype, suggesting that, in CTL 49, the V delta 1-encoded A13 epitope could be included in its alpha beta TCR. Northern blot analysis confirmed the presence of C alpha, C beta and V delta 1 specific transcripts while no hybridization signal was detected by a C delta specific probe. Polymerase chain reaction (PCR) amplification of the first strand cDNA from CTL 49 with TCR-specific primers and sequence analysis revealed that V delta 1 region is productively rearranged to J alpha and to C alpha regions. This alpha chain pairs with a beta chain composed of V beta 13.2/D beta/J beta 2.3/C beta 2 leading to the expression of a functional TCR complex. These results, in addition to providing further evidence for the sharing of V delta 1 by alpha/beta and gamma/delta TCR, indicate that an alpha/beta T-cell receptor which includes the V delta 1 variable region can be involved in alloreactive recognition. PMID:1313600

  8. Recognizing, Determining, and Addressing Entrepreneurial Innovations by Superintendents of Emerging or Established Educational Service Agencies

    ERIC Educational Resources Information Center

    Arfstrom, Kari M.

    2009-01-01

    This dissertation describes how entrepreneurial superintendents of educational service agencies (ESAs) recognize, determine and address common and distinct innovative characteristics within emerging or established regional educational environments. Because internal and external factors assist in recognizing innovative practices, this study…

  9. Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes

    PubMed Central

    Guyot, Romain; de la Mare, Marion; Viader, Véronique; Hamon, Perla; Coriton, Olivier; Bustamante-Porras, José; Poncet, Valérie; Campa, Claudine; Hamon, Serge; de Kochko, Alexandre

    2009-01-01

    Background Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of ≈ 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. Results This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. Conclusion This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V

  10. Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth.

    PubMed

    Xiao, Shijun; Wang, Panpan; Zhang, Yan; Fang, Lujing; Liu, Yang; Li, Jiong-Tang; Wang, Zhi-Yong

    2015-12-22

    The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker.

  11. Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth

    PubMed Central

    Xiao, Shijun; Wang, Panpan; Zhang, Yan; Fang, Lujing; Liu, Yang; Li, Jiong-Tang; Wang, Zhi-Yong

    2015-01-01

    The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker. PMID:26689832

  12. Assessment of Micro-Basin Tillage as a Soil and Water Conservation Practice in the Black Soil Region of Northeast China

    PubMed Central

    Sui, Yuanyuan; Ou, Yang; Yan, Baixing; Xu, Xiaohong; Rousseau, Alain N.; Zhang, Yu

    2016-01-01

    Micro-basin tillage is a soil and water conservation practice that requires building individual earth blocks along furrows. In this study, plot experiments were conducted to assess the efficiency of micro-basin tillage on sloping croplands between 2012 and 2013 (5°and 7°). The conceptual, optimal, block interval model was used to design micro-basins which are meant to capture the maximum amount of water per unit area. Results indicated that when compared to the up-down slope tillage, micro-basin tillage could increase soil water content and maize yield by about 45% and 17%, and reduce runoff, sediment and nutrients loads by about 63%, 96% and 86%, respectively. Meanwhile, micro-basin tillage could reduce the peak runoff rates and delay the initial runoff-yielding time. In addition, micro-basin tillage with the optimal block interval proved to be the best one among all treatments with different intervals. Compared with treatments of other block intervals, the optimal block interval treatments increased soil moisture by around 10% and reduced runoff rate by around 15%. In general, micro-basin tillage with optimal block interval represents an effective soil and water conservation practice for sloping farmland of the black soil region. PMID:27031339

  13. (1)H, (15)N and (13)C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein.

    PubMed

    Kataoka, Saori; Furuita, Kyoko; Hattori, Yoshikazu; Kobayashi, Naohiro; Ikegami, Takahisa; Shiozaki, Kazuhiro; Fujiwara, Toshimichi; Kojima, Chojiro

    2015-04-01

    SAPK-interacting protein 1 (Sin1) is an important component of the target of rapamycin (TOR) complex 2 (TORC2). TOR is a serine/threonine-specific protein kinase and forms functionally distinct protein complexes referred to as TORC1 and TORC2. TORC2, conserved from yeast to humans, phosphorylates AGC-family protein kinases and has many cellular functions including the regulation of actin cytoskeleton. The Sin1 subunit of TORC2 is required for the binding of TORC2 to substrates, and the conserved region in the middle (CRIM) domain of Sin1 is important in the substrate recognition of TORC2. Here, we report on the (1)H, (13)C and (15)N resonance assignments of fission yeast Schizosaccharomyces pombe Sin1 (amino acids 247-400) (Sin1CRIM), which possesses the CRIM domain. These data contribute toward the structure determination of Sin1CRIM and an understanding of the interactions of Sin1CRIM with substrates of TORC2.

  14. Conserved expression of mouse Six1 in the pre-placodal region (PPR) and identification of an enhancer for the rostral PPR.

    PubMed

    Sato, Shigeru; Ikeda, Keiko; Shioi, Go; Ochi, Haruki; Ogino, Hajime; Yajima, Hiroshi; Kawakami, Kiyoshi

    2010-08-01

    All cranial sensory organs and sensory neurons of vertebrates develop from cranial placodes. In chick, amphibians and zebrafish, all placodes originate from a common precursor domain, the pre-placodal region (PPR), marked by the expression of Six1/4 and Eya1/2. However, the PPR has never been described in mammals and the mechanism involved in the formation of PPR is poorly defined. Here, we report the expression of Six1 in the horseshoe-shaped mouse ectoderm surrounding the anterior neural plate in a pattern broadly similar to that of non-mammalian vertebrates. To elucidate the identity of Six1-positive mouse ectoderm, we searched for enhancers responsible for Six1 expression by in vivo enhancer assays. One conserved non-coding sequence, Six1-14, showed specific enhancer activity in the rostral PPR of chick and Xenopus and in the mouse ectoderm. These results strongly suggest the presence of PPR in mouse and that it is conserved in vertebrates. Moreover, we show the importance of the homeodomain protein-binding sites of Six1-14, the Six1 rostral PPR enhancer, for enhancer activity, and that Dlx5, Msx1 and Pax7 are candidate binding factors that regulate the level and area of Six1 expression, and thereby the location of the PPR. Our findings provide critical information and tools to elucidate the molecular mechanism of early sensory development and have implications for the development of sensory precursor/stem cells.

  15. Assessment of Micro-Basin Tillage as a Soil and Water Conservation Practice in the Black Soil Region of Northeast China.

    PubMed

    Sui, Yuanyuan; Ou, Yang; Yan, Baixing; Xu, Xiaohong; Rousseau, Alain N; Zhang, Yu

    2016-01-01

    Micro-basin tillage is a soil and water conservation practice that requires building individual earth blocks along furrows. In this study, plot experiments were conducted to assess the efficiency of micro-basin tillage on sloping croplands between 2012 and 2013 (5°and 7°). The conceptual, optimal, block interval model was used to design micro-basins which are meant to capture the maximum amount of water per unit area. Results indicated that when compared to the up-down slope tillage, micro-basin tillage could increase soil water content and maize yield by about 45% and 17%, and reduce runoff, sediment and nutrients loads by about 63%, 96% and 86%, respectively. Meanwhile, micro-basin tillage could reduce the peak runoff rates and delay the initial runoff-yielding time. In addition, micro-basin tillage with the optimal block interval proved to be the best one among all treatments with different intervals. Compared with treatments of other block intervals, the optimal block interval treatments increased soil moisture by around 10% and reduced runoff rate by around 15%. In general, micro-basin tillage with optimal block interval represents an effective soil and water conservation practice for sloping farmland of the black soil region.

  16. spalt encodes an evolutionarily conserved zinc finger protein of novel structure which provides homeotic gene function in the head and tail region of the Drosophila embryo.

    PubMed Central

    Kühnlein, R P; Frommer, G; Friedrich, M; Gonzalez-Gaitan, M; Weber, A; Wagner-Bernholz, J F; Gehring, W J; Jäckle, H; Schuh, R

    1994-01-01

    The region specific homeotic gene spalt (sal) of Drosophila melanogaster promotes the specification of terminal pattern elements as opposed to segments in the trunk. Our results show that the previously reported sal transcription unit was misidentified. Based on P-element mediated germ line transformation and DNA sequence analysis of sal mutant alleles, we identified the transcription unit that carries sal function. sal is located close to the misidentified transcription unit, and it is expressed in similar temporal and spatial patterns during embryogenesis. The sal gene encodes a zinc finger protein of novel structure composed of three widely spaced 'double zinc finger' motifs of internally conserved sequences and a single zinc finger motif of different sequence. Antibodies produced against the sal protein show that sal is first expressed at the blastoderm stage and later in restricted areas of the embryonic nervous system as well as in the developing trachea. The antibodies detect sal homologous proteins in corresponding spatial and temporal patterns in the embryos of related insect species. Sequence analysis of the sal gene of Drosophila virilis, a species which is phylogenetically separated by approximately 60 million years, suggests that the sal function is conserved during evolution, consistent with its proposed role in head formation during arthropod evolution. Images PMID:7905822

  17. The TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy to promote transcriptional activation.

    PubMed

    Saint, Malika; Sawhney, Sonal; Sinha, Ishani; Singh, Rana Pratap; Dahiya, Rashmi; Thakur, Anushikha; Siddharthan, Rahul; Natarajan, Krishnamurthy

    2014-05-01

    A common function of the TFIID and SAGA complexes, which are recruited by transcriptional activators, is to deliver TBP to promoters to stimulate transcription. Neither the relative contributions of the five shared TBP-associated factor (TAF) subunits in TFIID and SAGA nor the requirement for different domains in shared TAFs for transcriptional activation is well understood. In this study, we uncovered the essential requirement for the highly conserved C-terminal region (CRD) of Taf9, a shared TAF, for transcriptional activation in yeast. Transcriptome profiling performed under Gcn4-activating conditions showed that the Taf9 CRD is required for induced expression of ∼9% of the yeast genome. The CRD was not essential for the Taf9-Taf6 interaction, TFIID or SAGA integrity, or Gcn4 interaction with SAGA in cell extracts. Microarray profiling of a SAGA mutant (spt20Δ) yielded a common set of genes induced by Spt20 and the Taf9 CRD. Chromatin immunoprecipitation (ChIP) assays showed that, although the Taf9 CRD mutation did not impair Gcn4 occupancy, the occupancies of TFIID, SAGA, and the preinitiation complex were severely impaired at several promoters. These results suggest a crucial role for the Taf9 CRD in genome-wide transcription and highlight the importance of conserved domains, other than histone fold domains, as a common determinant for TFIID and SAGA functions.

  18. A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer

    SciTech Connect

    Shen Huaishun; Cao Kaiming; Wang Xiping

    2007-10-19

    Two putative Arabidopsis E group bZIP transcript factors, AtbZIP34 and AtbZIP61, are nuclear-localized and their transcriptional activation domain is in their N-terminal region. By searching GenBank, we found other eight plant homologues of AtbZIP34 and AtbZIP61. All of them have a proline residue in the third heptad of zipper region. Yeast two-hybrid assay and EMSA showed that AtbZIP34 and AtbZIP61 could not form homodimer while their mutant forms, AtbZIP34m and AtbZIP61m, which the proline residue was replaced by an alanine residue in the zipper region, could form homodimer and bind G-box element. These results suggest that the conserved proline residue interferes with the homodimer formation. However, both AtbZIP34 and AtbZIP61 could form heterodimers with members of I group and S group transcription factors in which some members involved in vascular development. So we speculate that AtbZIP34 and AtbZIP61 may participate in plant development via interacting with other group bZIP transcription factors.

  19. Regions outside of conserved PxxPxR motifs drive the high affinity interaction of GRB2 with SH3 domain ligands.

    PubMed

    Bartelt, Rebekah R; Light, Jonathan; Vacaflores, Aldo; Butcher, Alayna; Pandian, Madhana; Nash, Piers; Houtman, Jon C D

    2015-10-01

    SH3 domains are evolutionarily conserved protein interaction domains that control nearly all cellular processes in eukaryotes. The current model is that most SH3 domains bind discreet PxxPxR motifs with weak affinity and relatively low selectivity. However, the interactions of full-length SH3 domain-containing proteins with ligands are highly specific and have much stronger affinity. This suggests that regions outside of PxxPxR motifs drive these interactions. In this study, we observed that PxxPxR motifs were required for the binding of the adaptor protein GRB2 to short peptides from its ligand SOS1. Surprisingly, PxxPxR motifs from the proline rich region of SOS1 or CBL were neither necessary nor sufficient for the in vitro or in vivo interaction with full-length GRB2. Together, our findings show that regions outside of the consensus PxxPxR sites drive the high affinity association of GRB2 with SH3 domain ligands, suggesting that the binding mechanism for this and other SH3 domain interactions may be more complex than originally thought.

  20. Evidence for a quadruplex structure in the polymorphic hs1.2 enhancer of the immunoglobulin heavy chain 3' regulatory regions and its conservation in mammals.

    PubMed

    Sette, Marco; D'Addabbo, Pietro; Kelly, Geoffrey; Cicconi, Alessandro; Micheli, Emanuela; Cacchione, Stefano; Poma, Anna; Gargioli, Cesare; Giambra, Vincenzo; Frezza, Domenico

    2016-11-01

    Regulatory regions in the genome can act through a variety of mechanisms that range from the occurrence of histone modifications to the presence of protein-binding loci for self-annealing sequences. The final result is often the induction of a conformational change of the DNA double helix, which alters the accessibility of a region to transcription factors and consequently gene expression. A ∼300 kb regulatory region on chromosome 14 at the 3' end (3'RR) of immunoglobulin (Ig) heavy-chain genes shows very peculiar features, conserved in mammals, including enhancers and transcription factor binding sites. In primates, the 3'RR is present in two copies, both having a central enhancer named hs1.2. We previously demonstrated the association between different hs1.2 alleles and Ig plasma levels in immunopathology. Here, we present the analysis of a putative G-quadruplex structure (tetraplex) consensus site embedded in a variable number tandem repeat (one to four copies) of hs1.2 that is a distinctive element among the enhancer alleles, and an investigation of its three-dimensional structure using bioinformatics and spectroscopic approaches. We suggest that both the role of the enhancer and the alternative effect of the hs1.2 alleles may be achieved through their peculiar three-dimensional-conformational rearrangement. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 768-778, 2016. PMID:27287611

  1. Understanding the Distribution of Marine Megafauna in the English Channel Region: Identifying Key Habitats for Conservation within the Busiest Seaway on Earth

    PubMed Central

    McClellan, Catherine M.; Brereton, Tom; Dell'Amico, Florence; Johns, David G.; Cucknell, Anna-C.; Patrick, Samantha C.; Penrose, Rod; Ridoux, Vincent; Solandt, Jean-Luc; Stephan, Eric; Votier, Stephen C.; Williams, Ruth; Godley, Brendan J.

    2014-01-01

    The temperate waters of the North-Eastern Atlantic have a long history of maritime resource richness and, as a result, the European Union is endeavouring to maintain regional productivity and biodiversity. At the intersection of these aims lies potential conflict, signalling the need for integrated, cross-border management approaches. This paper focuses on the marine megafauna of the region. This guild of consumers was formerly abundant, but is now depleted and protected under various national and international legislative structures. We present a meta-analysis of available megafauna datasets using presence-only distribution models to characterise suitable habitat and identify spatially-important regions within the English Channel and southern bight of the North Sea. The integration of studies from dedicated and opportunistic observer programmes in the United Kingdom and France provide a valuable perspective on the spatial and seasonal distribution of various taxonomic groups, including large pelagic fishes and sharks, marine mammals, seabirds and marine turtles. The Western English Channel emerged as a hotspot of biodiversity for megafauna, while species richness was low in the Eastern English Channel. Spatial conservation planning is complicated by the highly mobile nature of marine megafauna, however they are important components of the marine environment and understanding their distribution is a first crucial step toward their inclusion into marine ecosystem management. PMID:24586985

  2. A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer.

    PubMed

    Shen, Huaishun; Cao, Kaiming; Wang, Xiping

    2007-10-19

    Two putative Arabidopsis E group bZIP transcript factors, AtbZIP34 and AtbZIP61, are nuclear-localized and their transcriptional activation domain is in their N-terminal region. By searching GenBank, we found other eight plant homologues of AtbZIP34 and AtbZIP61. All of them have a proline residue in the third heptad of zipper region. Yeast two-hybrid assay and EMSA showed that AtbZIP34 and AtbZIP61 could not form homodimer while their mutant forms, AtbZIP34m and AtbZIP61m, which the proline residue was replaced by an alanine residue in the zipper region, could form homodimer and bind G-box element. These results suggest that the conserved proline residue interferes with the homodimer formation. However, both AtbZIP34 and AtbZIP61 could form heterodimers with members of I group and S group transcription factors in which some members involved in vascular development. So we speculate that AtbZIP34 and AtbZIP61 may participate in plant development via interacting with other group bZIP transcription factors. PMID:17719007

  3. Hormone-induced modifications of the chromatin structure surrounding upstream regulatory regions conserved between the mouse and rabbit whey acidic protein genes.

    PubMed Central

    Millot, Benjamin; Montoliu, Lluís; Fontaine, Marie-Louise; Mata, Teresa; Devinoy, Eve

    2003-01-01

    The upstream regulatory regions of the mouse and rabbit whey acidic protein (WAP) genes have been used extensively to target the efficient expression of foreign genes into the mammary gland of transgenic animals. Therefore both regions have been studied to elucidate fully the mechanisms controlling WAP gene expression. Three DNase I-hypersensitive sites (HSS0, HSS1 and HSS2) have been described upstream of the rabbit WAP gene in the lactating mammary gland and correspond to important regulatory regions. These sites are surrounded by variable chromatin structures during mammary-gland development. In the present study, we describe the upstream sequence of the mouse WAP gene. Analysis of genomic sequences shows that the mouse WAP gene is situated between two widely expressed genes (Cpr2 and Ramp3). We show that the hypersensitive sites found upstream of the rabbit WAP gene are also detected in the mouse WAP gene. Further, they encompass functional signal transducer and activator of transcription 5-binding sites, as has been observed in the rabbit. A new hypersensitive site (HSS3), not specific to the mammary gland, was mapped 8 kb upstream of the rabbit WAP gene. Unlike the three HSSs described above, HSS3 is also detected in the liver, but similar to HSS1, it does not depend on lactogenic hormone treatments during cell culture. The region surrounding HSS3 encompasses a potential matrix attachment region, which is also conserved upstream of the mouse WAP gene and contains a functional transcription factor Ets-1 (E26 transformation-specific-1)-binding site. Finally, we demonstrate for the first time that variations in the chromatin structure are dependent on prolactin alone. PMID:12580766

  4. Fetal hemoglobin in sickle cell anemia: examination of phylogenetically conserved sequences within the locus control region but outside the cores of hypersensitive sites 2 and 3.

    PubMed

    Figueiredo, M S; Steinberg, M H

    1997-08-01

    Regulatory elements linked to the beta-globin gene cluster modulates gamma-globin gene expression. The location of all of these elements and their mechanisms of action are still incompletely defined. Phylogenetically conserved DNA within the beta-globin gene cluster locus control region (LCR), but outside the core sequences of its hypersensitive sites (HS), were identified and we searched for any differences between HS 3 and HS 2, and HS 2 and HS 1, among patients with sickle cell anemia with different levels of Hb F who were homozygous for the common haplotypes. DNA was amplified with and without GC clamps, digested with restriction endonucleases, and examined by denaturing gradient gel electrophoresis (DGGE). We found limited fragment size diversity. However, the type of differences found and their distribution among haplotypes did not suggest that they represented distinctive changes that might explain the differential expression of the gamma-globin genes in sickle cell anemia.

  5. Strategic development of the conserved region of the M protein and other candidates as vaccines to prevent infection with group A streptococci.

    PubMed

    Good, Michael F; Pandey, Manisha; Batzloff, Michael R; Tyrrell, Gregory J

    2015-01-01

    Group A streptococcal (Streptococcus pyogenes) diseases remain a major public health problem in developing countries as well as in the indigenous populations of developed countries. In view of the large number of Group A streptococcal infections and the potential for sequelae such as rheumatic heart disease, control strategies including the development of an anti-streptococcal vaccine that is able to prevent infection and colonization is important. In this article, we discuss the epidemiology and strain variability of Group A streptococcus and how this is rendering vaccine development more challenging. We discuss vaccine strategies with a focus on the conserved region of the M protein and present a viewpoint for the impediments and the way forward.

  6. D2 Region of the 28S RNA Gene: A Too-Conserved Fragment for Inferences on Phylogeny of South American Triatomines.

    PubMed

    Guerra, Ana Letícia; Alevi, Kaio Cesar Chaboli; Banho, Cecília Artico; de Oliveira, Jader; da Rosa, João Aristeu; Vilela de Azeredo-Oliveira, Maria Tercília

    2016-09-01

    The brasiliensis complex is composed of five triatomine species, and different approaches suggest that Triatoma lenti and Triatoma petrochiae may be the new members. Therefore, this study sought to analyze the phylogenetic relationships within this complex by means of the D2 region of the 28S RNA gene, and to analyze the degree of polymorphism and phylogenetic significance of this gene for South American triatomines. Phylogenetic analysis by using sequence fragments of the D2 domain did not allow to perform phylogenetic inferences on species within the brasiliensis complex, because the gene alignment composed of a matrix with 37 specimens exhibited only two variable sites along the 567 base pairs used. Furthermore, if all South American species are included, only four variable sites were detected, reflecting the high degree of gene conservation. Therefore, we do not recommend the use of this gene for phylogenetic reconstruction for this group of Chagas disease vectors. PMID:27382073

  7. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production

    PubMed Central

    Ng, Ivan H. W.; Chan, Kitti W. K.; Zhao, Yongqian; Ooi, Eng Eong; Lescar, Julien; Jans, David A.; Forwood, Jade K.

    2016-01-01

    Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18) alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα), allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization. PMID:27622521

  8. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production.

    PubMed

    Tay, Moon Y F; Smith, Kate; Ng, Ivan H W; Chan, Kitti W K; Zhao, Yongqian; Ooi, Eng Eong; Lescar, Julien; Luo, Dahai; Jans, David A; Forwood, Jade K; Vasudevan, Subhash G

    2016-09-01

    Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18) alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα), allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization. PMID:27622521

  9. The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120.

    PubMed

    Karasavvas, Nicos; Billings, Erik; Rao, Mangala; Williams, Constance; Zolla-Pazner, Susan; Bailer, Robert T; Koup, Richard A; Madnote, Sirinan; Arworn, Duangnapa; Shen, Xiaoying; Tomaras, Georgia D; Currier, Jeffrey R; Jiang, Mike; Magaret, Craig; Andrews, Charla; Gottardo, Raphael; Gilbert, Peter; Cardozo, Timothy J; Rerks-Ngarm, Supachai; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Paris, Robert; Greene, Kelli; Gao, Hongmei; Gurunathan, Sanjay; Tartaglia, Jim; Sinangil, Faruk; Korber, Bette T; Montefiori, David C; Mascola, John R; Robb, Merlin L; Haynes, Barton F; Ngauy, Viseth; Michael, Nelson L; Kim, Jerome H; de Souza, Mark S

    2012-11-01

    The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200-3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100-200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169-184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100-800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100-3200) and 3570 (range: 200-12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition.

  10. A comparison among root soil-conservation effects for nine herbs at the cold region highway in north-eastern China

    NASA Astrophysics Data System (ADS)

    Xu, W.; Wang, X.; Zhang, Y.; Liu, Y.

    2014-12-01

    High soil-conservation herbs are very important for slope vegetation restoration of a highway in serious sandstorm regions. In this study, nine common herbs in northeast China were selected and compared to study soil-conservation effects by using an undisturbed-soil trough scouring method for soil anti-scourability enhancement and hydrostatic collapse method for soil anti-erodibility. Further, principal components analysis was used to identify significant root features that affected soil erosion resistance. Results indicated that different herbs had distinct enhancement effects on soil erosion resistance. Soil anti-scourability enhancement index decreased with increases of soil depth, slope gradient and rainfall amount. Relationship between soil anti-erodibility enhancement index ( S) and immersion time ( t) is a cubic spline in each different herb type ( R 2 ≥ 0.88). Herb root features such as micro-aggregates, organic matter, net leaf weight, thick root length, fine root length and biomass contributed a leading role in soil erosion resistance enhancement effect, and all their common factor variances were more than 0.81. Descending order of soil erosion resistance enhancement effect in soil anti-scourability for nine herbs is Poa pratensis, Medicago sativa, Viola philippica, Rudbeckia hirta, Clematis heracleifolia, Kalimeris indica, Cosmos bipinnata, Hemerocallis fulva and Sedum elatinoides, while the sequence of soil anti-erodibility is M. sativa, S. elatinoides, P. pratensis, R. hirta, H. fulva, V. philippica, C. heracleifolia, C. bipinnata and K. indica. Therefore, we concluded that P. pratensis and M. sativa were the most suitable herbs for resisting soil erosion and recommended to be widely planted for road vegetation recovery in this region.

  11. Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation.

    PubMed

    Weber, Kristina; Zuschin, Martin

    2013-01-15

    Life-death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats and in practice this has to be distinguished using taphonomic preservation pattern and estimates of time-averaging. It remains to be rigorously evaluated, however, how to distinguish between sources of LD disagreement. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). The northern Adriatic Sea is an ecosystem under anthropogenic pressure, and we studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) associated with the delta of the Isonzo River (Gulf of Trieste). Specifically we evaluated the fidelity of richness, evenness, abundance, habitat discrimination and beta diversity. A total of 10,740 molluscs from fifteen tidal flat and fourteen sublittoral sites were analyzed for species composition and distribution of living and dead molluscs. Of 78 recorded species, only eleven were numerically abundant. There were many more dead than living individuals and rarefied species richness in the DA was higher at all spatial scales, but the differences are lower in habitats and in the region than at individual stations. Evenness was always higher in death assemblages, and probably due to temporally more variable LAs the differences are stronger in the sublittoral habitats. Distinct assemblages characterized intertidal and sublittoral habitats, and the distribution and abundance of empty shells generally corresponded to that of the living species. Death assemblages have lower beta diversity than life assemblages, but empty shells capture compositional differences between habitats to a higher degree than living shells

  12. Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation

    PubMed Central

    Weber, Kristina; Zuschin, Martin

    2013-01-01

    Life–death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats and in practice this has to be distinguished using taphonomic preservation pattern and estimates of time-averaging. It remains to be rigorously evaluated, however, how to distinguish between sources of LD disagreement. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). The northern Adriatic Sea is an ecosystem under anthropogenic pressure, and we studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) associated with the delta of the Isonzo River (Gulf of Trieste). Specifically we evaluated the fidelity of richness, evenness, abundance, habitat discrimination and beta diversity. A total of 10,740 molluscs from fifteen tidal flat and fourteen sublittoral sites were analyzed for species composition and distribution of living and dead molluscs. Of 78 recorded species, only eleven were numerically abundant. There were many more dead than living individuals and rarefied species richness in the DA was higher at all spatial scales, but the differences are lower in habitats and in the region than at individual stations. Evenness was always higher in death assemblages, and probably due to temporally more variable LAs the differences are stronger in the sublittoral habitats. Distinct assemblages characterized intertidal and sublittoral habitats, and the distribution and abundance of empty shells generally corresponded to that of the living species. Death assemblages have lower beta diversity than life assemblages, but empty shells capture compositional differences between habitats to a higher degree than living shells

  13. The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences.

    PubMed

    Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

    2014-01-01

    The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two "star" clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent. PMID:25184236

  14. The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences

    PubMed Central

    Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

    2014-01-01

    The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent. PMID:25184236

  15. Recognizing child maltreatment in Bangladesh.

    PubMed

    Khan, N Z; Lynch, M A

    1997-08-01

    Concern is increasing in Bangladesh over child abuse, neglect, and exploitation. Children from all walks of life are being treated at the Child Development Center (CDC) Dhaka Shishu Hospital for neurodevelopmental problems resulting from abuse and neglect. Efforts to protect children from sexual harassment result in girls being isolated at home or married at an early age. Some young brides are eventually abandoned and forced into prostitution. Early marriage reflects the lack of acknowledgement of a period of adolescence and the belief that puberty is a marker of adulthood. Many girls aged 8-16 are employed as live-in domestic servants, and many suffer sexual as well as emotional abuse. Garment factories, on the other hand, offer girls an escape from extreme poverty, domestic service, and early marriage but are threatened by forces that condemn child labor. Rather than ending such opportunities, employers should be encouraged to provide employees with educational and welfare facilities. The CDC seeks to explore the extent and depth of the problem of child abuse while recognizing the special circumstances at work in Bangladesh. It is also necessary to raise awareness of these issues and of the discrepancies between the law and cultural practices. For example, the legal marriage age of 18 years for a woman and 21 years for a man is often ignored. Additional forms of abuse receiving the attention of women's organizations and human rights groups include the trafficking of children. A network of concerned organizations should be created to work against the child abuse, neglect, and exploitation that Bangladesh has pledged to overcome by signing the UN Convention on the Rights of the Child.

  16. Reasons to Conserve Nature.

    PubMed

    Pearson, Richard G

    2016-05-01

    Is it sufficient to base arguments for conservation on the intrinsic value of nature, regardless of the services and economic benefits that biodiversity provides for humans? This question underlies much recent debate that has been at times acrimonious and has led to calls for a more inclusive approach to conservation. Yet melding different ideologies within a unified conceptual framework has proven difficult. Here I describe an approach that recognizes the importance of the level of biological organization and spatial extent in determining the strength of alternative arguments for why we should conserve nature. I argue that the framework helps reconcile contrasting viewpoints and brings clarity to when different conservation management approaches (for instance, regulation versus monetary valuation) are most appropriate. PMID:26936225

  17. THE THREATENED AND THE IRREPLACEABLE: IDENTIFYING AREAS FOR THE CONSERVATION OF FAUNAL SPECIES DIVERSITY IN THE MIDDLE-ATLANTIC REGION OF THE UNITED STATES

    EPA Science Inventory

    One fundamental step in conservation planning involves determining where to concentrate efforts to protect conservation targets. Here we demonstrate an approach to prioritizing areas based on both species composition and potential threats facing the species. First, we determine...

  18. Conservative Remapper

    2006-03-31

    Conservative Remapper (CORE) is a C++ language software library for remapping cell masses and cell-averaged densities on unstructured two dimensional grids, maintaining conservation of total mass in the process. CORE contains implementation of two remapping algorithms: a new, efficient "swept region" algorithm, and a more traditional algorithm basedon the computation of cell intersections. Grids may be Cartesian or cylindrical, and cells may have three or more vertices, with no upper limit. CORE can run inmore » serial and in parallel, but in order to achieve wide applicability, CORE used no particular parallel communication library. Instead it achieves parallel communication through strategically placed, user defined callbacks. Users can also provide callbacks to redefine different parts or subcomponents of the remapping process. CORE allows the use of different data types, e.g. single-, double-, and quadruple- precision floating-point numbers, through the use of C++ templates. Using CORE is simple, and requires no configuration scripts or makefiles.« less

  19. A Conserved Virulence Plasmidic Region Contributes to the Virulence of the Multiresistant Escherichia coli Meningitis Strain S286 Belonging to Phylogenetic Group C

    PubMed Central

    Caro, Valérie; Diancourt, Laure; Bingen, Edouard; Bidet, Philippe; Bonacorsi, Stéphane

    2013-01-01

    Recent isolation of the non-K1 Escherichia coli neonatal meningitis strain S286, belonging to phylogroup C, which is closely related to major group B1, and producing an extended-spectrum beta-lactamase, encouraged us to seek the genetic determinants responsible for its virulence. We show that S286 belongs to the sequence O type ST23O78 and harbors 4 large plasmids. The largest one, pS286colV (∼120 kb), not related to resistance, contains genes characteristic of a Conserved Virulence Plasmidic (CVP) region initially identified in B2 extra-intestinal avian pathogenic E. coli (APEC) strains and in the B2 neonatal meningitis E. coli strain S88. The sequence of this CVP region has a strong homology (98%) with that of the recently sequenced plasmid pChi7122-1 of the O78 APEC strain Chi7122. A CVP plasmid-cured variant of S286 was less virulent than the wild type strain in a neonatal rat sepsis model with a significant lower level of bacteremia at 24 h (4.1±1.41 versus 2.60±0.16 log CFU/ml, p = 0.001) and mortality. However, the mortality in the model of adult mice was comparable between wild type and variant indicating that pS286colV is not sufficient by itself to fully explain the virulence of S286. Gene expression analysis of pS286colV in iron depleted environment was very close to that of pS88, suggesting that genes of CVP region may be expressed similarly in two very different genetic backgrounds (group C versus group B2). Screening a collection of 178 human A/B1 extraintestinal pathogenic E. coli (ExPEC) strains revealed that the CVP region is highly prevalent (23%) and MLST analysis indicated that these CVP positive strains belong to several clusters and mostly to phylogroup C. The virulence of S286 is explained in part by the presence of CVP region and this region has spread in different clusters of human A/B1 ExPEC, especially in group C. PMID:24086343

  20. Conserved residues within the putative S4-S5 region serve distinct functions among thermosensitive vanilloid transient receptor potential (TRPV) channels.

    PubMed

    Boukalova, Stepana; Marsakova, Lenka; Teisinger, Jan; Vlachova, Viktorie

    2010-12-31

    The vanilloid transient receptor potential channel TRPV1 is a tetrameric six-transmembrane segment (S1-S6) channel that can be synergistically activated by various proalgesic agents such as capsaicin, protons, heat, or highly depolarizing voltages, and also by 2-aminoethoxydiphenyl borate (2-APB), a common activator of the related thermally gated vanilloid TRP channels TRPV1, TRPV2, and TRPV3. In these channels, the conserved charged residues in the intracellular S4-S5 region have been proposed to constitute part of a voltage sensor that acts in concert with other stimuli to regulate channel activation. The molecular basis of this gating event is poorly understood. We mutated charged residues all along the S4 and the S4-S5 linker of TRPV1 and identified four potential voltage-sensing residues (Arg(557), Glu(570), Asp(576), and Arg(579)) that, when specifically mutated, altered the functionality of the channel with respect to voltage, capsaicin, heat, 2-APB, and/or their interactions in different ways. The nonfunctional charge-reversing mutations R557E and R579E were partially rescued by the charge-swapping mutations R557E/E570R and D576R/R579E, indicating that electrostatic interactions contribute to allosteric coupling between the voltage-, temperature- and capsaicin-dependent activation mechanisms. The mutant K571E was normal in all aspects of TRPV1 activation except for 2-APB, revealing the specific role of Lys(571) in chemical sensitivity. Surprisingly, substitutions at homologous residues in TRPV2 or TRPV3 had no effect on temperature- and 2-APB-induced activity. Thus, the charged residues in S4 and the S4-S5 linker contribute to voltage sensing in TRPV1 and, despite their highly conserved nature, regulate the temperature and chemical gating in the various TRPV channels in different ways.

  1. Hepatocyte Nuclear Factor 1 Regulates the Expression of the Organic Cation Transporter 1 via Binding to an Evolutionary Conserved Region in Intron 1 of the OCT1 Gene

    PubMed Central

    O’Brien, Valerie P.; Bokelmann, Kristin; Ramírez, Jacqueline; Jobst, Karoline; Ratain, Mark J.; Brockmöller, Jürgen

    2013-01-01

    The organic cation transporter 1 (OCT1), also known as solute carrier family 22 member 1, is strongly and specifically expressed in the human liver. Here we show that the hepatocyte nuclear factor 1 (HNF1) regulates OCT1 transcription and contributes to the strong, liver-specific expression of OCT1. Bioinformatic analyses revealed strong conservation of HNF1 binding motifs in an evolutionary conserved region (ECR) in intron 1 of the OCT1 gene. Electrophoretic mobility shift and chromatin immunoprecipitation assays confirmed the specific binding of HNF1 to the intron 1 ECR. In reporter gene assays performed in HepG2 cells, the intron 1 ECR increased SV40 promoter activity by 22-fold and OCT1 promoter activity by 13-fold. The increase was reversed when the HNF1 binding sites in the intron 1 ECR were mutated or the endogenous HNF1α expression was downregulated with small interfering RNA. Following HNF1α overexpression in Huh7 cells, the intron 1 ECR increased SV40 promoter activity by 11-fold and OCT1 promoter activity by 6-fold. Without HNF1α overexpression, the increases were only 3- and 2-fold, respectively. Finally, in human liver samples, high HNF1 expression was significantly correlated with high OCT1 expression (r = 0.48, P = 0.002, n = 40). In conclusion, HNF1 is a strong regulator of OCT1 expression. It remains to be determined whether genetic variants, disease conditions, or drugs that affect HNF1 activity may affect the pharmacokinetics and efficacy of OCT1-transported drugs such as morphine, tropisetron, ondansetron, tramadol, and metformin. Beyond OCT1, this study demonstrates the validity and usefulness of interspecies comparisons in the discovery of functionally relevant genomic sequences. PMID:23922447

  2. Arabic word recognizer for mobile applications

    NASA Astrophysics Data System (ADS)

    Khanna, Nitin; Abdollahian, Golnaz; Brame, Ben; Boutin, Mireille; Delp, Edward J.

    2011-03-01

    When traveling in a region where the local language is not written using a "Roman alphabet," translating written text (e.g., documents, road signs, or placards) is a particularly difficult problem since the text cannot be easily entered into a translation device or searched using a dictionary. To address this problem, we are developing the "Rosetta Phone," a handheld device (e.g., PDA or mobile telephone) capable of acquiring an image of the text, locating the region (word) of interest within the image, and producing both an audio and a visual English interpretation of the text. This paper presents a system targeted for interpreting words written in Arabic script. The goal of this work is to develop an autonomous, segmentation-free Arabic phrase recognizer, with computational complexity low enough to deploy on a mobile device. A prototype of the proposed system has been deployed on an iPhone with a suitable user interface. The system was tested on a number of noisy images, in addition to the images acquired from the iPhone's camera. It identifies Arabic words or phrases by extracting appropriate features and assigning "codewords" to each word or phrase. On a dictionary of 5,000 words, the system uniquely mapped (word-image to codeword) 99.9% of the words. The system has a 82% recognition accuracy on images of words captured using the iPhone's built-in camera.

  3. Paradigms for parasite conservation.

    PubMed

    Dougherty, Eric R; Carlson, Colin J; Bueno, Veronica M; Burgio, Kevin R; Cizauskas, Carrie A; Clements, Christopher F; Seidel, Dana P; Harris, Nyeema C

    2016-08-01

    Parasitic species, which depend directly on host species for their survival, represent a major regulatory force in ecosystems and a significant component of Earth's biodiversity. Yet the negative impacts of parasites observed at the host level have motivated a conservation paradigm of eradication, moving us farther from attainment of taxonomically unbiased conservation goals. Despite a growing body of literature highlighting the importance of parasite-inclusive conservation, most parasite species remain understudied, underfunded, and underappreciated. We argue the protection of parasitic biodiversity requires a paradigm shift in the perception and valuation of their role as consumer species, similar to that of apex predators in the mid-20th century. Beyond recognizing parasites as vital trophic regulators, existing tools available to conservation practitioners should explicitly account for the unique threats facing dependent species. We built upon concepts from epidemiology and economics (e.g., host-density threshold and cost-benefit analysis) to devise novel metrics of margin of error and minimum investment for parasite conservation. We define margin of error as the risk of accidental host extinction from misestimating equilibrium population sizes and predicted oscillations, while minimum investment represents the cost associated with conserving the additional hosts required to maintain viable parasite populations. This framework will aid in the identification of readily conserved parasites that present minimal health risks. To establish parasite conservation, we propose an extension of population viability analysis for host-parasite assemblages to assess extinction risk. In the direst cases, ex situ breeding programs for parasites should be evaluated to maximize success without undermining host protection. Though parasitic species pose a considerable conservation challenge, adaptations to conservation tools will help protect parasite biodiversity in the face of

  4. Paradigms for parasite conservation.

    PubMed

    Dougherty, Eric R; Carlson, Colin J; Bueno, Veronica M; Burgio, Kevin R; Cizauskas, Carrie A; Clements, Christopher F; Seidel, Dana P; Harris, Nyeema C

    2016-08-01

    Parasitic species, which depend directly on host species for their survival, represent a major regulatory force in ecosystems and a significant component of Earth's biodiversity. Yet the negative impacts of parasites observed at the host level have motivated a conservation paradigm of eradication, moving us farther from attainment of taxonomically unbiased conservation goals. Despite a growing body of literature highlighting the importance of parasite-inclusive conservation, most parasite species remain understudied, underfunded, and underappreciated. We argue the protection of parasitic biodiversity requires a paradigm shift in the perception and valuation of their role as consumer species, similar to that of apex predators in the mid-20th century. Beyond recognizing parasites as vital trophic regulators, existing tools available to conservation practitioners should explicitly account for the unique threats facing dependent species. We built upon concepts from epidemiology and economics (e.g., host-density threshold and cost-benefit analysis) to devise novel metrics of margin of error and minimum investment for parasite conservation. We define margin of error as the risk of accidental host extinction from misestimating equilibrium population sizes and predicted oscillations, while minimum investment represents the cost associated with conserving the additional hosts required to maintain viable parasite populations. This framework will aid in the identification of readily conserved parasites that present minimal health risks. To establish parasite conservation, we propose an extension of population viability analysis for host-parasite assemblages to assess extinction risk. In the direst cases, ex situ breeding programs for parasites should be evaluated to maximize success without undermining host protection. Though parasitic species pose a considerable conservation challenge, adaptations to conservation tools will help protect parasite biodiversity in the face of

  5. Evidence on How a Conserved Glycine in the Hinge Region of HapR Regulates Its DNA Binding Ability: LESSONS FROM A NATURAL VARIANT.

    SciTech Connect

    M Dongre; N Singh; C Dureja; N Peddada; A Solanki; F Ashish; S Raychaudhuri

    2011-12-31

    HapR has been recognized as a quorum-sensing master regulator in Vibrio cholerae. Because it controls a plethora of disparate cellular events, the absence of a functional HapR affects the physiology of V. cholerae to a great extent. In the current study, we pursued an understanding of an observation of a natural protease-deficient non-O1, non-O139 variant V. cholerae strain V2. Intriguingly, a nonfunctional HapR (henceforth designated as HapRV2) harboring a substitution of glycine to aspartate at position 39 of the N-terminal hinge region has been identified. An in vitro gel shift assay clearly suggested the inability of HapRV2 to interact with various cognate promoters. Reinstatement of glycine at position 39 restores DNA binding ability of HapRV2 (HapRV2G), thereby rescuing the protease-negative phenotype of this strain. The elution profile of HapRV2 and HapRV2G proteins in size-exclusion chromatography and their circular dichroism spectra did not reflect any significant differences to explain the functional discrepancies between the two proteins. To gain insight into the structure-function relationship of these two proteins, we acquired small/wide angle x-ray scattering data from samples of the native and G39D mutant. Although Guinier analysis and indirect Fourier transformation of scattering indicated only a slight difference in the shape parameters, structure reconstruction using dummy amino acids concluded that although HapR adopts a 'Y' shape similar to its crystal structure, the G39D mutation in hinge drastically altered the DNA binding domains by bringing them in close proximity. This altered spatial orientation of the helix-turn-helix domains in this natural variant provides the first structural evidence on the functional role of the hinge region in quorum sensing-related DNA-binding regulatory proteins of Vibrio spp.

  6. 50 CFR 100.11 - Regional advisory councils.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... consistent with recognized principles of fish and wildlife conservation, and not be detrimental to the... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false Regional advisory councils. 100.11 Section 100.11 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE...

  7. 50 CFR 100.11 - Regional advisory councils.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... consistent with recognized principles of fish and wildlife conservation, and not be detrimental to the... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false Regional advisory councils. 100.11 Section 100.11 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE...

  8. 50 CFR 100.11 - Regional advisory councils.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... consistent with recognized principles of fish and wildlife conservation, and not be detrimental to the... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false Regional advisory councils. 100.11 Section 100.11 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE...

  9. 50 CFR 100.11 - Regional advisory councils.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... consistent with recognized principles of fish and wildlife conservation, and not be detrimental to the... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false Regional advisory councils. 100.11 Section 100.11 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE...

  10. Naturally processed HLA class II peptides reveal highly conserved immunogenic flanking region sequence preferences that reflect antigen processing rather than peptide-MHC interactions.

    PubMed

    Godkin, A J; Smith, K J; Willis, A; Tejada-Simon, M V; Zhang, J; Elliott, T; Hill, A V

    2001-06-01

    MHC class II heterodimers bind peptides 12-20 aa in length. The peptide flanking residues (PFRs) of these ligands extend from a central binding core consisting of nine amino acids. Increasing evidence suggests that the PFRs can alter the immunogenicity of T cell epitopes. We have previously noted that eluted peptide pool sequence data derived from an MHC class II Ag reflect patterns of enrichment not only in the core binding region but also in the PFRS: We sought to distinguish whether these enrichments reflect cellular processes or direct MHC-peptide interactions. Using the multiple sclerosis-associated allele HLA-DR2, pool sequence data from naturally processed ligands were compared with the patterns of enrichment obtained by binding semicombinatorial peptide libraries to empty HLA-DR2 molecules. Naturally processed ligands revealed patterns of enrichment reflecting both the binding motif of HLA-DR2 (position (P)1, aliphatic; P4, bulky hydrophobic; and P6, polar) as well as the nonbound flanking regions, including acidic residues at the N terminus and basic residues at the C terminus. These PFR enrichments were independent of MHC-peptide interactions. Further studies revealed similar patterns in nine other HLA alleles, with the C-terminal basic residues being as highly conserved as the previously described N-terminal prolines of MHC class II ligands. There is evidence that addition of C-terminal basic PFRs to known peptide epitopes is able to enhance both processing as well as T cell activation. Recognition of these allele-transcending patterns in the PFRs may prove useful in epitope identification and vaccine design.

  11. A conserved African swine fever virus right variable region gene, l11L, is non-essential for growth in vitro and virulence in domestic swine.

    PubMed

    Kleiboeker, S B; Kutish, G F; Neilan, J G; Lu, Z; Zsak, L; Rock, D L

    1998-05-01

    The right variable region of the African swine fever virus (ASFV) genome is known to contain genes with functions involving virus virulence and host range in swine. A novel open reading frame, ORF l11L, which was absent in the non-pathogenic, cell culture-adapted European isolate BA71V, was identified in the pathogenic African isolate Malawi Lil-20/1. The location of l11L in the right variable region, together with its absence in BA71V, suggested that l11L may have a function in virus virulence and/or host range. Here, we show that the l11L gene is highly conserved among pathogenic African, European and Caribbean ASFV field isolates and that it exists either in a short form, encoding a protein of 77-78 amino acids (9.1 kDa) or in a longer form of 93-94 amino acids (11.1 kDa). The presence of two predicted membrane-spanning segments suggests that l11L is an integral membrane protein. RT-PCR analysis demonstrated that l11L mRNA is expressed late in the virus replication cycle. A recombinant l11L gene deletion mutant, deltal11L, was constructed from the ASFV isolate Malawi Lil-20/1 to examine gene function. Deletion of l11L did not affect virus replication in swine macrophage cell cultures nor virulence in domestic pigs, indicating that l11L is non-essential for growth in vitro and for virus virulence in domestic swine.

  12. Residues in three conserved regions of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase are required for quaternary structure

    SciTech Connect

    Fitchen, J.H.; McIntosh, L. ); Knight, S.; Andersson, I.; Branden, C.I. )

    1990-08-01

    To explore the role of individual residues in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, small subunits with single amino acid substitutions in three regions of relative sequence conservation were produced by directed mutagenesis of the rbcS gene from Anabaena 7120. These altered small subunits were cosythesized with large subunits (from an expressed Anabaena rbcL gene) in Escherichia coli. Mutants were analyzed for effects on quaternary structure and catalytic activity. Changing Glu-13S (numbering used is that of the spinach enzyme) to Val, Trp-67S to Arg, Pro-73S to His, or Tyr-98S to Asn prevented accumulation of stable holoenzyme. Interpretation of these results using a model for the three-dimensional structure of the spinach enzyme based on x-ray crystallographic data suggests that our small subunit mutants containing substitutions at positions 13S and 67S probably do not assemble because of mispairing or nonpairing of charged residues on the interfacing surfaces of the large and small subunits. The failure of small subunits substituted at positions 73S or 98S to assemble correctly may result from disruption of intersubunit or intrasubunit hydrophobic pockets, respectively.

  13. Aspects of rabies infection and control in the conservation of the African wild dog (Lycaon pictus) in the Serengeti region, Tanzania.

    PubMed

    Gascoyne, S C; King, A A; Laurenson, M K; Borner, M; Schildger, B; Barrat, J

    1993-12-01

    Lycaon pictus is amongst the most endangered wildlife species in Africa. In 1990 rabies virus was isolated from the brain of an adult Lycaon found dead in the Serengeti region of Tanzania. One adult and six pups of the same pack feeding on the carcass showed clinical signs and rabies was suspected; within two days they had disappeared and are presumed to have died. Subsequently, two Lycaon packs in the Serengeti National Park were given inactivated rabies vaccine either by dart or by parenteral inoculation following anaesthesia. Lycaon sera which had been collected over the previous two years and sera collected pre- and post-vaccination were examined for the presence of rabies virus neutralizing antibody. Three of 12 unvaccinated Lycaon had antibody levels > 0.5 IU/ml; post-vaccination samples from two Lycaon showed increased antibody levels. Between four and ten months post-vaccination, at least four of the vaccinated animals had died from unknown causes. Issues relating to wildlife vaccination and veterinary intervention in conservation are discussed.

  14. Systematic Analysis of the Amino Acid Residues of Human Papillomavirus Type 16 E7 Conserved Region 3 Involved in Dimerization and Transformation ▿

    PubMed Central

    Todorovic, Biljana; Massimi, Paola; Hung, Katherine; Shaw, Gary S.; Banks, Lawrence; Mymryk, Joe S.

    2011-01-01

    The human papillomavirus (HPV) E7 oncoprotein exists as a dimer and acts by binding to many cellular factors, preventing or retargeting their function and thereby making the infected cell conducive for viral replication. Dimerization of E7 is attributed primarily to the C-terminal domain, referred to as conserved region 3 (CR3). CR3 is highly structured and is necessary for E7's transformation ability. It is also required for binding of numerous E7 cellular targets. To systematically analyze the molecular mechanisms by which HPV16 E7 CR3 contributes to carcinogenesis, we created a comprehensive panel of mutations in residues predicted to be exposed on the surface of CR3. We analyzed our novel collection of mutants, as well as mutants targeting predicted hydrophobic core residues of the dimer, for the ability to dimerize. The same set of mutants was also assessed functionally for transformation capability in a baby rat kidney cell assay in conjugation with activated ras. We show that some mutants of HPV16 E7 CR3 failed to dimerize yet were still able to transform baby rat kidney cells. Our results identify several novel E7 mutants that abrogate transformation and also indicate that E7 does not need to exist as a stable dimer in order to transform cells. PMID:21775462

  15. A Missense Mutation in a Highly Conserved Region of CASQ2 Is Associated with Autosomal Recessive Catecholamine-Induced Polymorphic Ventricular Tachycardia in Bedouin Families from Israel

    PubMed Central

    Lahat, Hadas; Pras, Elon; Olender, Tsviya; Avidan, Nili; Ben-Asher, Edna; Man, Orna; Levy-Nissenbaum, Etgar; Khoury, Asad; Lorber, Avraham; Goldman, Boleslaw; Lancet, Doron; Eldar, Michael

    2001-01-01

    Catecholamine-induced polymorphic ventricular tachycardia (PVT) is characterized by episodes of syncope, seizures, or sudden death, in response to physical activity or emotional stress. Two modes of inheritance have been described: autosomal dominant and autosomal recessive. Mutations in the ryanodine receptor 2 gene (RYR2), which encodes a cardiac sarcoplasmic reticulum (SR) Ca2+-release channel, were recently shown to cause the autosomal dominant form of the disease. In the present report, we describe a missense mutation in a highly conserved region of the calsequestrin 2 gene (CASQ2) as the potential cause of the autosomal recessive form. The CASQ2 protein serves as the major Ca2+ reservoir within the SR of cardiac myocytes and is part of a protein complex that contains the ryanodine receptor. The mutation, which is in full segregation in seven Bedouin families affected by the disorder, converts a negatively charged aspartic acid into a positively charged histidine, in a highly negatively charged domain, and is likely to exert its deleterious effect by disrupting Ca2+ binding. PMID:11704930

  16. Inhibition of hepatitis B virus by the CRISPR/Cas9 system via targeting the conserved regions of the viral genome.

    PubMed

    Liu, Xing; Hao, Ruidong; Chen, Shuliang; Guo, Deyin; Chen, Yu

    2015-08-01

    Hepatitis B virus (HBV) remains a global health threat as chronic HBV infection may lead to liver cirrhosis or cancer. Current antiviral therapies with nucleoside analogues can inhibit the replication of HBV, but do not disrupt the already existing HBV covalently closed circular DNA. The newly developed CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated 9) system is a powerful tool to target cellular genome DNA for gene editing. In order to investigate the possibility of using the CRISPR/Cas9 system to disrupt the HBV DNA templates, we designed eight guide RNAs (gRNAs) that targeted the conserved regions of different HBV genotypes, which could significantly inhibit HBV replication both in vitro and in vivo. Moreover, the HBV-specific gRNA/Cas9 system could inhibit the replication of HBV of different genotypes in cells, and the viral DNA was significantly reduced by a single gRNA/Cas9 system and cleared by a combination of different gRNA/Cas9 systems.

  17. Integration of land-sharing and land-sparing conservation strategies through regional networking: the Mesoamerican Biological Corridor as a lifeline for carnivores in El Salvador.

    PubMed

    Crespin, Silvio J; García-Villalta, Jorge E

    2014-10-01

    Nations with little remaining natural habitat and small extent are challenged when trying to achieve biodiversity targets. We show that the Central American nation of El Salvador cannot viably sustain populations of 87 % of its extant carnivores, especially in the case of large-bodied species with low population densities. Current land-sparing strategies will not suffice; therefore we propose that land-sharing strategies be implemented in tandem with protected areas to expand current conservation efforts via new regional networks. In Central America such a network can be established by linking international protected area systems in a way that implements the existing vision for the Mesoamerican Biological Corridor. Specifically, we propose a re-envisioning of the Mesoamerican Biological Corridor in which land-sharing practices are adopted throughout the agricultural matrix while ensuring formal protection of the remaining natural habitat. Such an integration of land-sparing and land-sharing could result in the creation of an effective network of protected areas, thereby increasing the probability of safeguarding species with populations that overlap national borders.

  18. Sternocostoclavicular Hyperostosis: An Ill-Recognized Disease

    PubMed Central

    Roed, Bolette; Kristensen, Tatiana; Thorsen, Søren; Poulsen Bloch, Klaus; Afzelius, Pia

    2016-01-01

    Sternocostoclavicular hyperostosis (SCCH) is an ill-recognized, rarely diagnosed disease. Today, SCCH is widely considered part of the synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome. SCCH develops over years with intermittent attacks of pain, swelling, and reddening of the sternocostoclavicular region. The disease causes progressive hyperostosis, fusion of the sternocostoclavicular joints, and soft tissue ossification. SCCH is chronic, non-malignant, and occurs predominantly bilaterally in middle-aged women. The incidence of the disease is unknown. We present a case of isolated SCCH, where chest radiographs showed a clear development of bilateral disease over the course of more than a decade. Whole-body bone scintigraphy was performed and was suggestive of SCCH. The diagnosis was established as late as 14 years from the onset of symptoms. During this period, the patient underwent several inconclusive examinations, resulting in a delay of diagnosis and in prolonged and aggravated symptoms. With this case report, we want to draw attention to SCCH and the importance of early diagnosis of the disease. PMID:27527220

  19. Sternocostoclavicular Hyperostosis: An Ill-Recognized Disease.

    PubMed

    Roed, Bolette; Kristensen, Tatiana; Thorsen, Søren; Poulsen Bloch, Klaus; Afzelius, Pia

    2016-01-01

    Sternocostoclavicular hyperostosis (SCCH) is an ill-recognized, rarely diagnosed disease. Today, SCCH is widely considered part of the synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome. SCCH develops over years with intermittent attacks of pain, swelling, and reddening of the sternocostoclavicular region. The disease causes progressive hyperostosis, fusion of the sternocostoclavicular joints, and soft tissue ossification. SCCH is chronic, non-malignant, and occurs predominantly bilaterally in middle-aged women. The incidence of the disease is unknown. We present a case of isolated SCCH, where chest radiographs showed a clear development of bilateral disease over the course of more than a decade. Whole-body bone scintigraphy was performed and was suggestive of SCCH. The diagnosis was established as late as 14 years from the onset of symptoms. During this period, the patient underwent several inconclusive examinations, resulting in a delay of diagnosis and in prolonged and aggravated symptoms. With this case report, we want to draw attention to SCCH and the importance of early diagnosis of the disease. PMID:27527220

  20. Mechanism by which a LINE protein recognizes its 3' tail RNA.

    PubMed

    Hayashi, Yoshinori; Kajikawa, Masaki; Matsumoto, Takuma; Okada, Norihiro

    2014-01-01

    LINEs mobilize their own copies via retrotransposition. LINEs can be divided into two types. One is a stringent type, which constitutes a majority of LINEs. The other is a relaxed type. To elucidate the molecular mechanism of retrotransposition, we used here two different zebrafish LINEs belonging to the stringent type. By using retrotransposition assays, we demonstrated that proteins (ORF2) encoded by an individual LINE recognize the cognate 3' tail sequence of the LINE RNA strictly. By conducting in vitro binding assays with a variety of ORF2 proteins, we demonstrated that the region between the endonuclease and reverse transcriptase domains in ORF2 is the site at which the proteins bind the stem-loop structure of the 3' tail RNA, showing that the strict recognition of the stem-loop structure by the cognate ORF2 protein is an important step in retrotransposition. This recognition can be bipartite, involving the general recognition of the stem by cTBR (conserved tail-binding region) of ORF2 and the specific recognition of the loop by vTBR (variable tail-binding region). This is the first report that clearly characterized the RNA-binding region in ORF2, providing the generality for the recognition mechanism of the RNA tail by the ORF2 protein encoded by LINEs. PMID:25143533

  1. Biodiversity funds and conservation needs in the EU under climate change

    PubMed Central

    Lung, Tobias; Meller, Laura; van Teeffelen, Astrid J.A.; Thuiller, Wilfried; Cabeza, Mar

    2014-01-01

    Despite ambitious biodiversity policy goals, less than a fifth of the European Union’s (EU) legally protected species and habitats show a favorable conservation status. The recent EU biodiversity strategy recognizes that climate change adds to the challenge of halting biodiversity loss, and that an optimal distribution of financial resources is needed. Here, we analyze recent EU biodiversity funding from a climate change perspective. We compare the allocation of funds to the distribution of both current conservation priorities (within and beyond Natura 2000) and future conservation needs at the level of NUTS-2 regions, using modelled bird distributions as indicators of conservation value. We find that funding is reasonably well aligned with current conservation efforts but poorly fit with future needs under climate change, indicating obstacles for implementing adaptation measures. We suggest revising EU biodiversity funding instruments for the 2014-2020 budget period to better account for potential climate change impacts on biodiversity. PMID:25264456

  2. Higher-Order Neural Networks Recognize Patterns

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Spirkovska, Lilly; Ochoa, Ellen

    1996-01-01

    Networks of higher order have enhanced capabilities to distinguish between different two-dimensional patterns and to recognize those patterns. Also enhanced capabilities to "learn" patterns to be recognized: "trained" with far fewer examples and, therefore, in less time than necessary to train comparable first-order neural networks.

  3. Vitrification: Machines learn to recognize glasses

    NASA Astrophysics Data System (ADS)

    Ceriotti, Michele; Vitelli, Vincenzo

    2016-05-01

    The dynamics of a viscous liquid undergo a dramatic slowdown when it is cooled to form a solid glass. Recognizing the structural changes across such a transition remains a major challenge. Machine-learning methods, similar to those Facebook uses to recognize groups of friends, have now been applied to this problem.

  4. Teaching Students to Recognize Irony

    ERIC Educational Resources Information Center

    Milner, Joseph O.; Hawkins, Robin H.; Milner, Lucy M.

    2014-01-01

    This article exposes the problem of using declarative rather than procedural knowledge to help K--12 students recognize irony in stories. It offers commonplace procedures drawn from students' everyday language experience together with more abstract irony clues to help students recognize irony in stories and increase their story comprehension.…

  5. Conservation of wading birds

    USGS Publications Warehouse

    Kushlan, J.A.

    1996-01-01

    The conservation and management of wading birds has received considerable attention over the past twenty years, through research, population monitoring, habitat protection, and through activities of specialist groups devoted to all three groups, the herons, ibises and allies, and flamingos. While populations are best known in North America, greatest advances in knowledge may have come in Australasia. The status of most species and many populations is now sufficiently known to allow assessment of risk. Conservation and management techniques allow creation of global and regional action plans for conservation of many species. Global action plans are being developed, but few regional plans have been undertaken. Management of nesting sites is now particularly well appreciated. Although known in broad stroke, much remains to be learned about managing feeding habitat. Problems related to disturbance, conflict with humans, habitat loss, contaminants and other environmental stresses remain for some species and many populations. New challenges lie in creating conservation action that account for genetic stocks.

  6. Transgenically mediated shRNAs targeting conserved regions of foot-and-mouth disease virus provide heritable resistance in porcine cell lines and suckling mice

    PubMed Central

    2013-01-01

    Foot-and-mouth disease virus (FMDV) is responsible for substantial economic losses in livestock breeding each year, and the development of new strategies is needed to overcome the limitations of existing vaccines and antiviral drugs. In this study, we evaluated the antiviral potential of transgenic porcine cells and suckling mice that simultaneously expressed two short-hairpin RNAs (shRNAs) targeting the conserved regions of the viral polymerase protein 3D and the non-structural protein 2B. First, two recombinant shRNA-expressing plasmids, PB-EN3D2B and PB-N3D2B, were constructed and the efficiency of the constructs for suppressing an artificial target was demonstrated in BHK-21 cells. We then integrated PB-EN3D2B into the genome of the porcine cell line IBRS-2 using the piggyBac transposon system, and stable monoclonal transgenic cell lines (MTCL) were selected. Of the 6 MTCL that were used in the antiviral assay, 3 exhibited significant resistance with suppressing ratios of more than 94% at 48 hours post-challenge (hpc) to both serotype O and serotype Asia 1 FMDV. MTCL IB-3D2B-6 displayed the strongest antiviral activity, which resulted in 100% inhibition of FMDV replication until 72 hpc. Moreover, the shRNA-expressing fragment of PB-N3D2B was integrated into the mouse genome by DNA microinjection to produce transgenic mice. When challenged with serotype O FMDV, the offspring of the transgenic mouse lines N3D2B-18 and N3D2B-81 exhibited higher survival rates of 19% to 27% relative to their non-transgenic littermates. The results suggest that these heritable shRNAs were able to suppress FMDV replication in the transgenic cell lines and suckling mice. PMID:23822604

  7. Sensitive and specific serodiagnosis of Lyme disease by enzyme-linked immunosorbent assay with a peptide based on an immunodominant conserved region of Borrelia burgdorferi vlsE.

    PubMed

    Liang, F T; Steere, A C; Marques, A R; Johnson, B J; Miller, J N; Philipp, M T

    1999-12-01

    VlsE, the variable surface antigen of Borrelia burgdorferi, contains an immunodominant conserved region named IR(6). In the present study, the diagnostic performance of a peptide enzyme-linked immunosorbent assay (ELISA) based on a 26-mer synthetic peptide (C(6)) with the IR(6) sequence was explored. Sensitivity was assessed with serum samples (n = 210) collected from patients with clinically defined Lyme disease at the acute (early localized or early disseminated disease), convalescent, or late disease phase. The sensitivities for acute-, convalescent-, and late-phase specimens were 74% (29 of 39), 85 to 90% (34 of 40 to 35 of 39), and 100% (59 of 59), respectively. Serum specimens from early neuroborreliosis patients were 95% positive (19 of 20), and those from an additional group of patients with posttreatment Lyme disease syndrome yielded a sensitivity of 62% (8 of 13). To assess the specificity of the peptide ELISA, 77 serum samples from patients with other spirochetal or chronic infections, autoimmune diseases, or neurologic diseases and 99 serum specimens from hospitalized patients in an area where Lyme disease is not endemic were examined. Only two potential false positives from the hospitalized patients were found, and the overall specificity was 99% (174 of 176). Precision, which was assessed with a panel of positive and negative serum specimens arranged in blinded duplicates, was 100%. Four serum samples with very high anti-OspA antibody titers obtained from four monkeys given the OspA vaccine did not react with the C(6) peptide. This simple, sensitive, specific, and precise ELISA may contribute to alleviate some of the remaining problems in Lyme disease serodiagnosis. Because of its synthetic peptide base, it will be inexpensive to manufacture. It also will be applicable to serum specimens from OspA-vaccinated subjects.

  8. Sensitive and Specific Serodiagnosis of Lyme Disease by Enzyme-Linked Immunosorbent Assay with a Peptide Based on an Immunodominant Conserved Region of Borrelia burgdorferi VlsE

    PubMed Central

    Liang, Fang Ting; Steere, Allen C.; Marques, Adriana R.; Johnson, Barbara J. B.; Miller, James N.; Philipp, Mario T.

    1999-01-01

    VlsE, the variable surface antigen of Borrelia burgdorferi, contains an immunodominant conserved region named IR6. In the present study, the diagnostic performance of a peptide enzyme-linked immunosorbent assay (ELISA) based on a 26-mer synthetic peptide (C6) with the IR6 sequence was explored. Sensitivity was assessed with serum samples (n = 210) collected from patients with clinically defined Lyme disease at the acute (early localized or early disseminated disease), convalescent, or late disease phase. The sensitivities for acute-, convalescent-, and late-phase specimens were 74% (29 of 39), 85 to 90% (34 of 40 to 35 of 39), and 100% (59 of 59), respectively. Serum specimens from early neuroborreliosis patients were 95% positive (19 of 20), and those from an additional group of patients with posttreatment Lyme disease syndrome yielded a sensitivity of 62% (8 of 13). To assess the specificity of the peptide ELISA, 77 serum samples from patients with other spirochetal or chronic infections, autoimmune diseases, or neurologic diseases and 99 serum specimens from hospitalized patients in an area where Lyme disease is not endemic were examined. Only two potential false positives from the hospitalized patients were found, and the overall specificity was 99% (174 of 176). Precision, which was assessed with a panel of positive and negative serum specimens arranged in blinded duplicates, was 100%. Four serum samples with very high anti-OspA antibody titers obtained from four monkeys given the OspA vaccine did not react with the C6 peptide. This simple, sensitive, specific, and precise ELISA may contribute to alleviate some of the remaining problems in Lyme disease serodiagnosis. Because of its synthetic peptide base, it will be inexpensive to manufacture. It also will be applicable to serum specimens from OspA-vaccinated subjects. PMID:10565920

  9. Analysis of the murine Hox-2.7 gene: conserved alternative transcripts with differential distributions in the nervous system and the potential for shared regulatory regions.

    PubMed Central

    Sham, M H; Hunt, P; Nonchev, S; Papalopulu, N; Graham, A; Boncinelli, E; Krumlauf, R

    1992-01-01

    In this study we have investigated the organization and regulation of the mouse Hox-2.7 gene. There are several alternative transcripts some of which are conserved between mouse and humans. By Northern and in situ analysis we are able to identify at least three types of transcripts which are different in size and splicing pattern and have distinctly different boundaries of expression in the nervous system. One subset of the endogenous transcripts has a boundary of expression that corresponds to the adjacent Hox-2.8 gene instead of Hox-2.7. In another type of transcript there is an alternative reading frame which predicts a protein that has homology to an enzyme ATPase and suggests that a non-homeobox containing gene may be located in the Hox-2 cluster. A Hox-2.7-lacZ transgene is expressed in a similar pattern to the endogenous gene in that spatially-restricted domains of expression are seen in the branchial arches, neural tube, paraxial mesoderm (somites), cranial ganglia, neural crest and gut. However, the anterior boundaries of transgene expression only correspond to the subset of Hox-2.7 transcripts which map to the Hox-2.8 boundary. The proximity of a Hox-2.7 promoter to regions which regulate the adjacent Hox-2.6 gene and the expression of transgenic and endogenous transcripts in a Hox-2.8 pattern, suggest that regulatory elements may be shared by neighbouring genes to establish the complete expression pattern. Images PMID:1582411

  10. Multiple, conserved iron-responsive elements in the 3'-untranslated region of transferrin receptor mRNA enhance binding of iron regulatory protein 2.

    PubMed

    Erlitzki, Ronit; Long, Joanne C; Theil, Elizabeth C

    2002-11-01

    Synthesis of proteins for iron homeostasis is regulated by specific, combinatorial mRNA/protein interactions between RNA stem-loop structures (iron-responsive elements, IREs) and iron-regulatory proteins (IRP1 and IRP2), controlling either mRNA translation or stability. The transferrin receptor 3'-untranslated region (TfR-3'-UTR) mRNA is unique in having five IREs, linked by AU-rich elements. A C-bulge in the stem of each TfR-IRE folds into an IRE that has low IRP2 binding, whereas a loop/bulge in the stem of the ferritin-IRE allows equivalent IRP1 and IRP2 binding. Effects of multiple IRE interactions with IRP1 and IRP2 were compared between the native TfR-3'-UTR sequence (5xIRE) and RNA with only 3 or 2 IREs. We show 1) equivalent IRP1 and IRP2 binding to multiple TfR-IRE RNAs; 2) increased IRP-dependent nuclease resistance of 5xIRE compared with lower IRE copy-number RNAs; 3) distorted TfR-IRE helix structure within the context of 5xIRE, detected by Cu-(phen)(2) binding/cleavage, that coincides with ferritin-IRE conformation and enhanced IRP2 binding; and 4) variable IRP1 and IRP2 expression in human cells and during development (IRP2-mRNA predominated). Changes in TfR-IRE structure conferred by the full length TfR-3'-UTR mRNA explain in part evolutionary conservation of multiple IRE-RNA, which allows TfR mRNA stabilization and receptor synthesis when IRP activity varies, and ensures iron uptake for cell growth.

  11. Conservative management.

    PubMed

    Kruis, W; Leifeld, L; Pfützer, R

    2012-01-01

    Treatment of diverticulitis comprises at least two options: conservative or surgical management. There is a recent trend to limit surgical treatment of acute diverticulitis and to favor conservative management. This review addresses general aspects of conservative patient care with special focus on the treatment of patients with a first attack of diverticulitis. The presentation does not include a discussion of specific drugs which is given in other sections of this issue.

  12. Immune Cells in Blood Recognize Tumors

    Cancer.gov

    NCI scientists have developed a novel strategy for identifying immune cells circulating in the blood that recognize specific proteins on tumor cells, a finding they believe may have potential implications for immune-based therapies.

  13. 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)

  14. Conservation assessment of the terrestrial ecoregions of latin America and the Caribbean

    SciTech Connect

    Dinerstein, E.; Olson, D.M.; Graham, D.J.; Webster, A.L.; Primm, S.A.

    1995-09-01

    This priority-setting study elevates, as a first principle, maintaining the representation of all ecosystem and habitat types in regional investment portfolios. Second, it recognizes landscape-level features as an essential guide for effective conservation planning. The study`s biogeographic approach to setting conservation priorities begins by dividing LaC into 5 major ecosystem types (METs), 11 major habitat types (MHTs), and 191 ecoregions. This last number includes 13 mangrove complexes but otherwise includes marine areas and freshwater habitats (except large, geographically continguous freshwater ecosystems).

  15. Conservation businesses and conservation planning in a biological diversity hotspot.

    PubMed

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. PMID:23565917

  16. Conservation businesses and conservation planning in a biological diversity hotspot.

    PubMed

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action.

  17. Species of conservation concern and environmental stressors: local regional and global effects: Chapter 6 in The Southern Nevada Agency Partnership science and research synthesis: science to support land management in southern Nevada

    USGS Publications Warehouse

    Ostoja, Steven M.; Brooks, Matthew L.; Chambers, Jeanne C.; Pendleton, Burton

    2013-01-01

    Species conservation has traditionally been based on individual species within the context of their requisite habitat, which is generally defined as the communities and ecosystems deemed necessary for their presence. Conservation decisions are hampered by the fact that environmental stressors that poetically threaten the persistence of species can operate at organizational levels larger than the habitat or home range of a focal species. Resource managers must therefore simultaneously consider local, regional, and/or global scale stressors for effective conservation and management of species of concern. The wide ranging effects associated with global stressors such as climate change may exceed or exacerbate the effects of local or regional stressors, they still need to understand the direct and interactive effects of global stressors and ultimately how they affect the lands they manage. Conservation of species in southern Nevada is further complication by the fact that the region includes one of the largest and fastest growing urban centers in North America. To accomplish the goal of species conservation, resource managers must identify actionable management options that mitigate the effects of local and regional stressor in the context of the effects of global stressors that are beyond their control. Species conservation is typically focused on a subset often referred to as species of conservation concern that have either demonstrated considerable decline or are naturally rare or have limited distributions. Stressors can directly and indirectly impact species in a variety of ways and through a diversity of mechanisms. Some stressors have been more intense in the past (e.g., livestock grazing) whereas other are now only emerging as new stressors (e.g., solar energy development, climate change). The primary stressors affecting southern Nevada ecosystems are listed in table 2.1 and reviewed in detail in Chapter 2. This chapter addresses Dub-goal 1.4 in the SNAP

  18. Equipping African American Clergy to Recognize Depression.

    PubMed

    Anthony, Jean Spann; Morris, Edith; Collins, Charles W; Watson, Albert; Williams, Jennifer E; Ferguson, Bʼnai; Ruhlman, Deborah L

    2016-01-01

    Many African Americans (AAs) use clergy as their primary source of help for depression, with few being referred to mental health providers. This study used face-to-face workshops to train AA clergy to recognize the symptoms and levels of severity of depression. A pretest/posttest format was used to test knowledge (N = 42) about depression symptoms. Results showed that the participation improved the clergy's ability to recognize depression symptoms. Faith community nurses can develop workshops for clergy to improve recognition and treatment of depression.

  19. Equipping African American Clergy to Recognize Depression.

    PubMed

    Anthony, Jean Spann; Morris, Edith; Collins, Charles W; Watson, Albert; Williams, Jennifer E; Ferguson, Bʼnai; Ruhlman, Deborah L

    2016-01-01

    Many African Americans (AAs) use clergy as their primary source of help for depression, with few being referred to mental health providers. This study used face-to-face workshops to train AA clergy to recognize the symptoms and levels of severity of depression. A pretest/posttest format was used to test knowledge (N = 42) about depression symptoms. Results showed that the participation improved the clergy's ability to recognize depression symptoms. Faith community nurses can develop workshops for clergy to improve recognition and treatment of depression. PMID:27610907

  20. Recognizing, Confronting, and Eliminating Workplace Bullying.

    PubMed

    Berry, Peggy Ann; Gillespie, Gordon L; Fisher, Bonnie S; Gormley, Denise K

    2016-07-01

    Workplace bullying (WPB) behaviors negatively affect nurse productivity, satisfaction, and retention, and hinder safe patient care. The purpose of this article is to define WPB, differentiate between incivility and WPB, and recommend actions to prevent WPB behaviors. Informed occupational and environmental health nurses and nurse leaders must recognize, confront, and eliminate WPB in their facilities and organizations. Recognizing, confronting, and eliminating WPB behaviors in health care is a crucial first step toward sustained improvements in patient care quality and the health and safety of health care employees. PMID:27053288

  1. Recognizing and Responding to Adolescent Depression.

    ERIC Educational Resources Information Center

    King, Stephen R.

    1991-01-01

    Depression is increasingly recognized as a problem affecting adolescents as well as adults. Adolescents are underserved with regard to treatment facilities. One solution is the comprehensive health care clinic providing a holistic approach to assessment and intervention. Policy recommendations, which include a role for the school system, are made.…

  2. Great Apes' Capacities to Recognize Relational Similarity

    ERIC Educational Resources Information Center

    Haun, Daniel B. M.; Call, Josep

    2009-01-01

    Recognizing relational similarity relies on the ability to understand that defining object properties might not lie in the objects individually, but in the relations of the properties of various object to each other. This aptitude is highly relevant for many important human skills such as language, reasoning, categorization and understanding…

  3. How Should a Speech Recognizer Work?

    ERIC Educational Resources Information Center

    Scharenborg, Odette; Norris, Dennis; ten Bosch, Louis; McQueen, James M.

    2005-01-01

    Although researchers studying human speech recognition (HSR) and automatic speech recognition (ASR) share a common interest in how information processing systems (human or machine) recognize spoken language, there is little communication between the two disciplines. We suggest that this lack of communication follows largely from the fact that…

  4. 26 CFR 601.502 - Recognized representative.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 20 2010-04-01 2010-04-01 false Recognized representative. 601.502 Section 601.502 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INTERNAL REVENUE... before the Internal Revenue Service and is in active status pursuant to the requirements of Circular...

  5. 10 CFR 431.20 - Department of Energy recognition of nationally recognized certification programs.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... conflict of interest for the certification program in operating a certification system for compliance by... certification programs. 431.20 Section 431.20 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY... recognized certification programs. (a) Petition. For a certification program to be classified by...

  6. 10 CFR 431.447 - Department of Energy recognition of nationally recognized certification programs.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... independence in operating a certification program. (3) Qualifications to operate a certification system... certification programs. 431.447 Section 431.447 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY... Standards § 431.447 Department of Energy recognition of nationally recognized certification programs....

  7. 10 CFR 431.20 - Department of Energy recognition of nationally recognized certification programs.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... conflict of interest for the certification program in operating a certification system for compliance by... certification programs. 431.20 Section 431.20 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY... recognized certification programs. (a) Petition. For a certification program to be classified by...

  8. 10 CFR 431.447 - Department of Energy recognition of nationally recognized certification programs.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... independence in operating a certification program. (3) Qualifications to operate a certification system... certification programs. 431.447 Section 431.447 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY... Standards § 431.447 Department of Energy recognition of nationally recognized certification programs....

  9. Federally-Recognized Tribes of the Columbia-Snake Basin.

    SciTech Connect

    United States. Bonneville Power Administration

    1997-11-01

    This is an omnibus publication about the federally-recognized Indian tribes of the Columbia-Snake river basin, as presented by themselves. It showcases several figurative and literal snapshots of each tribe, bits and pieces of each tribe`s story. Each individual tribe or tribal confederation either submitted its own section to this publication, or developed its own section with the assistance of the writer-editor. A federally-recognized tribe is an individual Indian group, or confederation of Indian groups, officially acknowledged by the US government for purposes of legislation, consultation and benefits. This publication is designed to be used both as a resource and as an introduction to the tribes. Taken together, the sections present a rich picture of regional indian culture and history, as told by the tribes.

  10. Leadership: a new frontier in conservation science.

    PubMed

    Manolis, Jim C; Chan, Kai M; Finkelstein, Myra E; Stephens, Scott; Nelson, Cara R; Grant, Jacqualine B; Dombeck, Michael P

    2009-08-01

    Leadership is a critical tool for expanding the influence of conservation science, but recent advances in leadership concepts and practice remain underutilized by conservation scientists. Furthermore, an explicit conceptual foundation and definition of leadership in conservation science are not available in the literature. Here we drew on our diverse leadership experiences, our reading of leadership literature, and discussions with selected conservation science leaders to define conservation-science leadership, summarize an exploratory set of leadership principles that are applicable to conservation science, and recommend actions to expand leadership capacity among conservation scientists and practitioners. We define 2 types of conservation-science leadership: shaping conservation science through path-breaking research, and advancing the integration of conservation science into policy, management, and society at large. We focused on the second, integrative type of leadership because we believe it presents the greatest opportunity for improving conservation effectiveness. We identified 8 leadership principles derived mainly from the "adaptive leadership" literature: recognize the social dimension of the problem; cycle frequently through action and reflection; get and maintain attention; combine strengths of multiple leaders; extend your reach through networks of relationships; strategically time your effort; nurture productive conflict; and cultivate diversity. Conservation scientists and practitioners should strive to develop themselves as leaders, and the Society for Conservation Biology, conservation organizations, and academia should support this effort through professional development, mentoring, teaching, and research. PMID:19183215

  11. Biodiversity conservation: challenges beyond 2010.

    PubMed

    Rands, Michael R W; Adams, William M; Bennun, Leon; Butchart, Stuart H M; Clements, Andrew; Coomes, David; Entwistle, Abigail; Hodge, Ian; Kapos, Valerie; Scharlemann, Jörn P W; Sutherland, William J; Vira, Bhaskar

    2010-09-10

    The continued growth of human populations and of per capita consumption have resulted in unsustainable exploitation of Earth's biological diversity, exacerbated by climate change, ocean acidification, and other anthropogenic environmental impacts. We argue that effective conservation of biodiversity is essential for human survival and the maintenance of ecosystem processes. Despite some conservation successes (especially at local scales) and increasing public and government interest in living sustainably, biodiversity continues to decline. Moving beyond 2010, successful conservation approaches need to be reinforced and adequately financed. In addition, however, more radical changes are required that recognize biodiversity as a global public good, that integrate biodiversity conservation into policies and decision frameworks for resource production and consumption, and that focus on wider institutional and societal changes to enable more effective implementation of policy.

  12. Evaluating Local Benefits from Conservation in Nepal's Annapurna Conservation Area

    NASA Astrophysics Data System (ADS)

    Spiteri, Arian; Nepal, Sanjay K.

    2008-09-01

    Protected areas are integral to the global effort to conserve biodiversity, and, over the past two decades, protected area managers have begun to recognize that conservation objectives are next to impossible to achieve without considering the needs and concerns of local communities. Incentive-based programs (IBPs) have become a favored approach to protected area management, geared at fostering local stewardship by delivering benefits tied to conservation to local people. Effective IBPs require benefits to accrue to and be recognized by those experiencing the greatest consequences as a result of the protected area, and those likely to continue extractive activities if their livelihood needs are compromised. This research examines dispersal of IBP benefits, as perceived by local residents in Nepal’s Annapurna Conservation Area. Results reported here are based on questionnaire interviews with 188 households conducted between September and December 2004. Results indicate that local residents primarily identify benefits from social development activities, provisions for resource extraction, and economic opportunities. Overall, benefits have been dispersed equally to households in villages on and off the main tourist route, and regardless of a household’s participation in tourism. However, benefits are not effectively targeted to poorer residents, those highly dependent on natural resources, and those experiencing the most crop damage and livestock loss from protected wildlife. This article provides several suggestions for improving the delivery of conservation incentives.

  13. Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes.

    PubMed

    Schaubert, Keri L; Price, David A; Salkowitz, Janelle R; Sewell, Andrew K; Sidney, John; Asher, Tedi E; Blondelle, Sylvie E; Adams, Sharon; Marincola, Francesco M; Joseph, Aviva; Sette, Alessandro; Douek, Daniel C; Ayyavoo, Velpandi; Storkus, Walter; Leung, Ming-Ying; Ng, Hwee L; Yang, Otto O; Goldstein, Harris; Wilson, Darcy B; Kan-Mitchell, June

    2010-07-01

    HLA-A 0201-restricted virus-specific CD8(+) CTL do not appear to control HIV effectively in vivo. To enhance the immunogenicity of a highly conserved subdominant epitope, TV9 (TLNAWVKVV, p24 Gag(19-27)), mimotopes were designed by screening a large combinatorial nonapeptide library with TV9-specific CTL primed in vitro from healthy donors. A mimic peptide with a low binding affinity to HLA-A 0201, TV9p6 (KINAWIKVV), was studied further. Parallel cultures of in vitro-primed CTL showed that TV9p6 consistently activated cross-reactive and equally functional CTL as measured by cytotoxicity, cytokine production and suppression of HIV replication in vitro. Comparison of TCRB gene usage between CTL primed from the same donors with TV9 or TV9p6 revealed a degree of clonal overlap in some cases and an example of a conserved TCRB sequence encoded distinctly at the nucleotide level between individuals (a "public" TCR); however, in the main, distinct clonotypes were recruited by each peptide antigen. These findings indicate that mimotopes can mobilize functional cross-reactive clonotypes that are less readily recruited from the naïve T-cell pool by the corresponding WT epitope. Mimotope-induced repertoire diversification could potentially override subdominance under certain circumstances and enhance vaccine-induced responses to conserved but poorly immunogenic determinants within the HIV proteome. PMID:20432235

  14. Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes.

    PubMed

    Schaubert, Keri L; Price, David A; Salkowitz, Janelle R; Sewell, Andrew K; Sidney, John; Asher, Tedi E; Blondelle, Sylvie E; Adams, Sharon; Marincola, Francesco M; Joseph, Aviva; Sette, Alessandro; Douek, Daniel C; Ayyavoo, Velpandi; Storkus, Walter; Leung, Ming-Ying; Ng, Hwee L; Yang, Otto O; Goldstein, Harris; Wilson, Darcy B; Kan-Mitchell, June

    2010-07-01

    HLA-A 0201-restricted virus-specific CD8(+) CTL do not appear to control HIV effectively in vivo. To enhance the immunogenicity of a highly conserved subdominant epitope, TV9 (TLNAWVKVV, p24 Gag(19-27)), mimotopes were designed by screening a large combinatorial nonapeptide library with TV9-specific CTL primed in vitro from healthy donors. A mimic peptide with a low binding affinity to HLA-A 0201, TV9p6 (KINAWIKVV), was studied further. Parallel cultures of in vitro-primed CTL showed that TV9p6 consistently activated cross-reactive and equally functional CTL as measured by cytotoxicity, cytokine production and suppression of HIV replication in vitro. Comparison of TCRB gene usage between CTL primed from the same donors with TV9 or TV9p6 revealed a degree of clonal overlap in some cases and an example of a conserved TCRB sequence encoded distinctly at the nucleotide level between individuals (a "public" TCR); however, in the main, distinct clonotypes were recruited by each peptide antigen. These findings indicate that mimotopes can mobilize functional cross-reactive clonotypes that are less readily recruited from the naïve T-cell pool by the corresponding WT epitope. Mimotope-induced repertoire diversification could potentially override subdominance under certain circumstances and enhance vaccine-induced responses to conserved but poorly immunogenic determinants within the HIV proteome.

  15. How are necrotic cells recognized by their predators?

    PubMed

    Li, Zao; Zhou, Zheng

    2016-01-01

    Necrosis is a type of cell death often caused by cell injury and is linked to human diseases including neuron degeneration, stroke, and cancer. Cells undergoing necrosis are engulfed and degraded by engulfing cells, their predators. The mechanisms by which necrotic cells are recognized and removed remain elusive. Here we comment on our recent findings that reveal new molecular mechanisms of necrotic-cell recognition. Through studying the C. elegans touch neurons undergoing excitotoxic necrosis, we identified a receptor/ligand pair that enables engulfing cells to recognize necrotic neurons. The phagocytic receptor CED-1 is activated through interaction with its ligand phosphatidylserine (PS), exposed on the surface of necrotic cells. Furthermore, against the common belief that necrotic cells have ruptured plasma membrane, we found that necrotic C. elegans touch neurons actively present PS on their outer surfaces while maintaining plasma membrane integrity. We further identified 2 mechanisms governing the presentation of PS, one of which is shared with cells undergoing apoptosis, a "cell suicide" event, whereas the other is unique to necrotic neurons. The influx of Ca(2+), a key necrosis-triggering factor, is implicated in activating a neuronal PS-scramblase for PS exposure. We propose that the mechanisms controlling PS-exposure and necrotic-cell recognition by engulfing cells are likely conserved from worms to humans. PMID:27073733

  16. Energy Conservation.

    ERIC Educational Resources Information Center

    Land, Amy A.

    This selection of class activities involves a sequence of 10 class sessions. The goal of the collection is to aid students in learning the concepts of energy conservation and to put this knowledge into practice. Attention is also given to the development of alternate energy sources. Each lesson includes an activity title, motivational hints,…

  17. [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…

  18. [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…

  19. 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…

  20. Design Alternatives for Evaluating the Impact of Conservation Projects

    ERIC Educational Resources Information Center

    Margoluis, Richard; Stem, Caroline; Salafsky, Nick; Brown, Marcia

    2009-01-01

    Historically, examples of project evaluation in conservation were rare. In recent years, however, conservation professionals have begun to recognize the importance of evaluation both for accountability and for improving project interventions. Even with this growing interest in evaluation, the conservation community has paid little attention to…

  1. Recognize sex work as legitimate work.

    PubMed

    Reynaga, Elena

    2008-12-01

    It is not sex work per se that makes sex workers vulnerable to HIV, but rather the policies that repress them. In this article, based on her presentation at a plenary session at the conference, Elena Reynaga, who is a sex worker, describes how these policies deprive sex workers of their rights and subject them to physical and sexual violence. The author concludes that at the heart of the problem lies the fact that sex work is not recognized as legitimate work.

  2. Recognizing Action Units for Facial Expression Analysis.

    PubMed

    Tian, Ying-Li; Kanade, Takeo; Cohn, Jeffrey F

    2001-02-01

    Most automatic expression analysis systems attempt to recognize a small set of prototypic expressions, such as happiness, anger, surprise, and fear. Such prototypic expressions, however, occur rather infrequently. Human emotions and intentions are more often communicated by changes in one or a few discrete facial features. In this paper, we develop an Automatic Face Analysis (AFA) system to analyze facial expressions based on both permanent facial features (brows, eyes, mouth) and transient facial features (deepening of facial furrows) in a nearly frontal-view face image sequence. The AFA system recognizes fine-grained changes in facial expression into action units (AUs) of the Facial Action Coding System (FACS), instead of a few prototypic expressions. Multistate face and facial component models are proposed for tracking and modeling the various facial features, including lips, eyes, brows, cheeks, and furrows. During tracking, detailed parametric descriptions of the facial features are extracted. With these parameters as the inputs, a group of action units (neutral expression, six upper face AUs and 10 lower face AUs) are recognized whether they occur alone or in combinations. The system has achieved average recognition rates of 96.4 percent (95.4 percent if neutral expressions are excluded) for upper face AUs and 96.7 percent (95.6 percent with neutral expressions excluded) for lower face AUs. The generalizability of the system has been tested by using independent image databases collected and FACS-coded for ground-truth by different research teams.

  3. Recognizing Materials using Perceptually Inspired Features

    PubMed Central

    Sharan, Lavanya; Liu, Ce; Rosenholtz, Ruth; Adelson, Edward H.

    2013-01-01

    Our world consists not only of objects and scenes but also of materials of various kinds. Being able to recognize the materials that surround us (e.g., plastic, glass, concrete) is important for humans as well as for computer vision systems. Unfortunately, materials have received little attention in the visual recognition literature, and very few computer vision systems have been designed specifically to recognize materials. In this paper, we present a system for recognizing material categories from single images. We propose a set of low and mid-level image features that are based on studies of human material recognition, and we combine these features using an SVM classifier. Our system outperforms a state-of-the-art system [Varma and Zisserman, 2009] on a challenging database of real-world material categories [Sharan et al., 2009]. When the performance of our system is compared directly to that of human observers, humans outperform our system quite easily. However, when we account for the local nature of our image features and the surface properties they measure (e.g., color, texture, local shape), our system rivals human performance. We suggest that future progress in material recognition will come from: (1) a deeper understanding of the role of non-local surface properties (e.g., extended highlights, object identity); and (2) efforts to model such non-local surface properties in images. PMID:23914070

  4. Global versus local conservation focus of U.S. state agency endangered bird species lists.

    PubMed

    Wells, Jeffrey V; Robertson, Bruce; Rosenberg, Kenneth V; Mehlman, David W

    2010-01-06

    The development of species priorities for conservation at local or regional scales (for example, within a state or province) poses an interesting paradox. One the one hand, locally or regionally-derived species priorities may lead to greater interest in and resources directed to biodiversity conservation by local or regional institutions. On the other hand, locally or regionally-derived species priorities could overlook national or global priorities. We assessed U.S. state government agency endangered-threatened bird lists to determine the comparative representation of species of global versus local conservation significance on them. State lists tended to be represented primarily by species of low global risk-low global responsibility (range: 15-100%; mean 51%) and high global risk-high global responsibility (range: 0-73%; mean 35%). In 25 states, more than half of the species on the state lists were in the low global risk-low global responsibility category. Most U.S. state agency lists represent a combined strategy of highlighting species of both local and global conservation significance. Even with this combined local-global strategy, most state lists were predominated by species that represent local but not global conservation significance. Such a strategy could have profound negative consequences for many species that are not formally recognized under national endangered species protections but that are also left off of state-level endangered species lists.

  5. Structural basis of Zika virus helicase in recognizing its substrates.

    PubMed

    Tian, Hongliang; Ji, Xiaoyun; Yang, Xiaoyun; Zhang, Zhongxin; Lu, Zuokun; Yang, Kailin; Chen, Cheng; Zhao, Qi; Chi, Heng; Mu, Zhongyu; Xie, Wei; Wang, Zefang; Lou, Huiqiang; Yang, Haitao; Rao, Zihe

    2016-08-01

    The recent explosive outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn(2+) and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn(2+). The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication. PMID:27430951

  6. Structural basis of Zika virus helicase in recognizing its substrates.

    PubMed

    Tian, Hongliang; Ji, Xiaoyun; Yang, Xiaoyun; Zhang, Zhongxin; Lu, Zuokun; Yang, Kailin; Chen, Cheng; Zhao, Qi; Chi, Heng; Mu, Zhongyu; Xie, Wei; Wang, Zefang; Lou, Huiqiang; Yang, Haitao; Rao, Zihe

    2016-08-01

    The recent explosive outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn(2+) and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn(2+). The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.

  7. Multi-Season Regional Analysis of Multi-Species Occupancy: Implications for Bird Conservation in Agricultural Lands in East-Central Argentina

    PubMed Central

    Goijman, Andrea Paula; Conroy, Michael. J.; Bernardos, Jaime Nicolás; Zaccagnini, María Elena

    2015-01-01

    Rapid expansion and intensification of agriculture create challenges for the conservation of biodiversity and associated ecosystem services. In Argentina, the total row crop planted area has increased in recent decades with the expansion of soybean cultivation, homogenizing the landscape. In 2003 we started the first long-term, large-scale bird monitoring program in agroecosystems of central Argentina, in portions of the Pampas and Espinal ecoregions. Using data from this program, we evaluated the effect of land use and cover extent on birds between 2003-2012, accounting for imperfect detection probabilities using a Bayesian hierarchical, multi-species and multi-season occupancy model. We tested predictions that species diversity is positively related to habitat heterogeneity, which in intensified agroecosystems is thought to be mediated by food availability; thus the extent of land use and cover is predicted to affect foraging guilds differently. We also infer about ecosystem services provisioning and inform management recommendations for conservation of birds. Overall our results support the predictions. Although many species within each guild responded differently to land use and native forest cover, we identified generalities for most trophic guilds. For example, granivorous gleaners, ground insectivores and omnivores responded negatively to high proportions of soybean, while insectivore gleaners and aerial foragers seemed more tolerant. Habitat heterogeneity would likely benefit most species in an intensified agroecosystem, and can be achieved with a diversity of crops, pastures, and natural areas within the landscape. Although most studied species are insectivores, potentially beneficial for pest control, some guilds such as ground insectivores are poorly represented, suggesting that agricultural intensification reduces ecological functions, which may be recovered through management. Continuation of the bird monitoring program will allow us to continue to

  8. Multi-Season Regional Analysis of Multi-Species Occupancy: Implications for Bird Conservation in Agricultural Lands in East-Central Argentina.

    PubMed

    Goijman, Andrea Paula; Conroy, Michael J; Bernardos, Jaime Nicolás; Zaccagnini, María Elena

    2015-01-01

    Rapid expansion and intensification of agriculture create challenges for the conservation of biodiversity and associated ecosystem services. In Argentina, the total row crop planted area has increased in recent decades with the expansion of soybean cultivation, homogenizing the landscape. In 2003 we started the first long-term, large-scale bird monitoring program in agroecosystems of central Argentina, in portions of the Pampas and Espinal ecoregions. Using data from this program, we evaluated the effect of land use and cover extent on birds between 2003-2012, accounting for imperfect detection probabilities using a Bayesian hierarchical, multi-species and multi-season occupancy model. We tested predictions that species diversity is positively related to habitat heterogeneity, which in intensified agroecosystems is thought to be mediated by food availability; thus the extent of land use and cover is predicted to affect foraging guilds differently. We also infer about ecosystem services provisioning and inform management recommendations for conservation of birds. Overall our results support the predictions. Although many species within each guild responded differently to land use and native forest cover, we identified generalities for most trophic guilds. For example, granivorous gleaners, ground insectivores and omnivores responded negatively to high proportions of soybean, while insectivore gleaners and aerial foragers seemed more tolerant. Habitat heterogeneity would likely benefit most species in an intensified agroecosystem, and can be achieved with a diversity of crops, pastures, and natural areas within the landscape. Although most studied species are insectivores, potentially beneficial for pest control, some guilds such as ground insectivores are poorly represented, suggesting that agricultural intensification reduces ecological functions, which may be recovered through management. Continuation of the bird monitoring program will allow us to continue to

  9. Multi-Season Regional Analysis of Multi-Species Occupancy: Implications for Bird Conservation in Agricultural Lands in East-Central Argentina.

    PubMed

    Goijman, Andrea Paula; Conroy, Michael J; Bernardos, Jaime Nicolás; Zaccagnini, María Elena

    2015-01-01

    Rapid expansion and intensification of agriculture create challenges for the conservation of biodiversity and associated ecosystem services. In Argentina, the total row crop planted area has increased in recent decades with the expansion of soybean cultivation, homogenizing the landscape. In 2003 we started the first long-term, large-scale bird monitoring program in agroecosystems of central Argentina, in portions of the Pampas and Espinal ecoregions. Using data from this program, we evaluated the effect of land use and cover extent on birds between 2003-2012, accounting for imperfect detection probabilities using a Bayesian hierarchical, multi-species and multi-season occupancy model. We tested predictions that species diversity is positively related to habitat heterogeneity, which in intensified agroecosystems is thought to be mediated by food availability; thus the extent of land use and cover is predicted to affect foraging guilds differently. We also infer about ecosystem services provisioning and inform management recommendations for conservation of birds. Overall our results support the predictions. Although many species within each guild responded differently to land use and native forest cover, we identified generalities for most trophic guilds. For example, granivorous gleaners, ground insectivores and omnivores responded negatively to high proportions of soybean, while insectivore gleaners and aerial foragers seemed more tolerant. Habitat heterogeneity would likely benefit most species in an intensified agroecosystem, and can be achieved with a diversity of crops, pastures, and natural areas within the landscape. Although most studied species are insectivores, potentially beneficial for pest control, some guilds such as ground insectivores are poorly represented, suggesting that agricultural intensification reduces ecological functions, which may be recovered through management. Continuation of the bird monitoring program will allow us to continue to

  10. The Cost of Conserved Carbon: Weighing the Monetary, Social, and Climactic Implications of Regional-, National-, and Global-Scale Carbon Abatement Strategies

    NASA Astrophysics Data System (ADS)

    Kantner, J. W.; Hoffman, I.; Johnston, J. L.; Kammen, D. M.; Levin, J. E.; Komiyama, R.; Motschenbacher, A.; Gimon, E.

    2008-05-01

    Previous schema for analyzing carbon mitigation methods often have lacked realistic costs, comprehensive accounting of trade-offs, and methodological transparency. We offer a dynamic model for evaluating diverse carbon mitigation scenarios based on economics, policy traction, and interplay with climate, society and ecosystems. The model will test the impacts of policy changes across more than two dozen strategies for conserving or avoiding carbon emissions. Users will be able to access the model at rael-c3.berkeley.edu and change underlying assumptions as desired.

  11. Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness

    NASA Astrophysics Data System (ADS)

    Keshvari, J.; Kivento, M.; Christ, A.; Bit-Babik, G.

    2016-04-01

    This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

  12. Islamic Headdress Influences How Emotion is Recognized from the Eyes

    PubMed Central

    Kret, Mariska Esther; de Gelder, Beatrice

    2012-01-01

    Previous research has shown a negative bias in the perception of whole facial expressions from out-group members. Whether or not emotion recognition from the eyes is already sensitive to contextual information is presently a matter of debate. In three experiments we tested whether emotions can be recognized when just the eyes are visible and whether this recognition is affected by context cues, such as various Islamic headdresses vs. a cap or a scarf. Our results indicate that fear is still well recognized from a briefly flashed (100 ms) image of a women wearing a burqa with less than 20% transparency of the eye region. Moreover, the type of headdress influences how emotions are recognized. In a group of participants from non-Islamic background, fear was recognized better from women wearing a niqāb than from women wearing a cap and a shawl, whereas the opposite was observed for happy and sad expressions. The response patterns showed that fearful and anger labels were more often attributed to women with a niqāb vs. a cap and a shawl and again, an opposite pattern was observed for the happy response. However, there was no general response bias: both correct and incorrect responses were influenced by the facial expression as well. Anxiety levels and/or explicit negative associations with the Islam as measured via questionnaires did not mediate the effects. Consistent with the face literature, we conclude that the recognition of emotions from the eyes is also influenced by context. PMID:22557983

  13. The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein.

    PubMed

    Naue, Natalie; Beerbaum, Monika; Bogutzki, Andrea; Schmieder, Peter; Curth, Ute

    2013-04-01

    During bacterial DNA replication, DnaG primase and the χ subunit of DNA polymerase III compete for binding to single-stranded DNA-binding protein (SSB), thus facilitating the switch between priming and elongation. SSB proteins play an essential role in DNA metabolism by protecting single-stranded DNA and by mediating several important protein-protein interactions. Although an interaction of SSB with primase has been previously reported, it was unclear which domains of the two proteins are involved. This study identifies the C-terminal helicase-binding domain of DnaG primase (DnaG-C) and the highly conserved C-terminal region of SSB as interaction sites. By ConSurf analysis, it can be shown that an array of conserved amino acids on DnaG-C forms a hydrophobic pocket surrounded by basic residues, reminiscent of known SSB-binding sites on other proteins. Using protein-protein cross-linking, site-directed mutagenesis, analytical ultracentrifugation and nuclear magnetic resonance spectroscopy, we demonstrate that these conserved amino acid residues are involved in the interaction with SSB. Even though the C-terminal domain of DnaG primase also participates in the interaction with DnaB helicase, the respective binding sites on the surface of DnaG-C do not overlap, as SSB binds to the N-terminal subdomain, whereas DnaB interacts with the ultimate C-terminus.

  14. Recognizing Patterns In Log-Polar Coordinates

    NASA Technical Reports Server (NTRS)

    Weiman, Carl F. R.

    1992-01-01

    Log-Hough transform is basis of improved method for recognition of patterns - particularly, straight lines - in noisy images. Takes advantage of rotational and scale invariance of mapping from Cartesian to log-polar coordinates, and offers economy of representation and computation. Unification of iconic and Hough domains simplifies computations in recognition and eliminates erroneous quantization of slopes attributable to finite spacing of Cartesian coordinate grid of classical Hough transform. Equally efficient recognizing curves. Log-Hough transform more amenable to massively parallel computing architectures than traditional Cartesian Hough transform. "In-place" nature makes it possible to apply local pixel-neighborhood processing.

  15. Recognizing and treating patients with envenomations.

    PubMed

    Hurt, John B; Maday, Kristopher R

    2016-07-01

    Venomous spiders and snakes are found throughout the United States, and clinicians often encounter patients with suspected spider or snakebites. Due to the significant morbidity and mortality that can be related to a particular envenomation, clinicians must be able to recognize the species of spiders and snakes that are capable of delivering a venomous bite. Through proper species identification, recognition of the specific signs and symptoms that specific venom produces, and understanding the treatment guidelines for the envenomation, clinicians can properly diagnosis, treat, and manage patients with venomous bites. PMID:27351646

  16. Recognizing women in the archaeological record

    SciTech Connect

    Bumsted, M.P.

    1987-01-01

    Primary sexual characteristics are usually absent in the archaeological record. The recovered secondary sex markers in bone morphology or mortuary context reflect the lifelong integrated biocultural experience of the individual man or woman. Internal patterns of variability within and between sexes can be recognized but are too frequently masked by traditional descriptive and univariate analyses. Fortunately, a more detailed picture of life experience is gained by analyzing chemical composition (isotopic and elemental) of hard tissues using an analytical anthropology approach and by examining the variation in novel ways. 7 figs.

  17. Modeling effects of climatological variability and management practices on conservation of groundwater from the Mississippi River Valley Shallow Alluvial Aquifer in the Mississippi Delta region

    NASA Astrophysics Data System (ADS)

    Thornton, Robert Frank

    Ninety-eight percent of water taken from the Mississippi River Shallow Alluvial Aquifer, hereafter referred to as "the aquifer" or "MRVA," is used by the agricultural industry for irrigation. Mississippi Delta agriculture is increasingly using more water from the MRVA and the aquifer has been losing about 300,000 acre-feet per year. This research expands on previous work in which a model was developed that simulates the effects of climatic variability, crop acreage changes, and specific irrigation methods on consequent variations in the water volume of the MRVA. This study corrects an identified problem by replacing total growing season precipitation with an irrigation demand driver based on evaporation and crop coefficients and changing the time scale from the entire growing season to a daily resolution. The calculated irrigation demand, as a climatological driver for the model, captures effective precipitation more precisely than the initial growing season precipitation driver. Predictive equations resulting from regression analyses of measured versus calculated irrigation water use showed R2 and correlations of 0.33 and 0.57, 0.77 and 0.88, 0.71 and 0.84, and 0.68 and 0.82 for cotton, corn, soybeans and rice, respectively. Ninety-five percent of the predicted values fall within a range of + or - about 23,000 acre-feet, an error of about 10-percent. The study also adds an additional conservation strategy through the use of surface water from on-farm reservoirs in lieu of groundwater. Analyses show that climate could provide the entire water need of the plants in 70-percent of the years for corn, 65-percent of the years for soybeans and cotton, and even 5-percent of the years for rice. Storing precipitation in on-farm structures is an effective way to reduce reliance of Delta producers on groundwater. If producers adopted, at a minimum, the 97.5:2.5 ratio suggested management practice, this minimal management strategy could potentially conserve 48-percent, 35

  18. Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins.

    PubMed Central

    Machesky, L M; Reeves, E; Wientjes, F; Mattheyse, F J; Grogan, A; Totty, N F; Burlingame, A L; Hsuan, J J; Segal, A W

    1997-01-01

    Human neutrophils contain a complex of proteins similar to the actin-related protein 2/3 (Arp2/3) complex of Acanthamoeba. We have obtained peptide sequence information for each member of the putative seven-protein complex previously described for Acanthamoeba and human platelets. From the peptide sequences we have identified cDNA species encoding three novel proteins in this complex. We find that in addition to Arp2 and Arp3, this complex contains a relative of the human (Suppressor of Profilin) SOP2Hs protein and four previously unknown proteins. These proteins localize in the cytoplasm of fibroblasts that lack lamellipodia, but are enriched in lamellipodia on stimulation with serum or platelet-derived growth factor. We propose a conserved and dynamic role for this complex in the organization of the actin cytoskeleton. PMID:9359840

  19. Local Responses to Participatory Conservation in Annapurna Conservation Area, Nepal

    NASA Astrophysics Data System (ADS)

    Khadka, Damodar; Nepal, Sanjay K.

    2010-02-01

    Biodiversity conservation has undergone a profound change in philosophy, policies and management approaches over the last forty years. The traditional top-down approach to nature protection has been widely criticized for failing to include critical social elements in management practices, and is being gradually replaced by a slew of participatory strategies under the rubric of bottom-up conservation. The new approach recognizes local communities as key partners in wildlife management and seeks their participation in social development and biodiversity conservation. However, every social context is different in its structure and functions, and in the way social groups respond to calls for participation. In order to gain a better understanding of the approach and the barriers encountered in its implementation, a questionnaire survey of 188 households was employed in the communities of the Upper Mustang extension of Annapurna Conservation Area (ACA) in Nepal. The study provides a comparative analysis of community participation and its barriers between Non-Tourist (NT) and Tourist (TV) villages. The results revealed important differences between the two groups in terms of their participation in community programs, barriers to participation, and perception of benefits from participation. Owing to their distinct spatial, demographic and attitudinal differences, the two village groups have their own sets of needs, values and motivation factors which cannot be generalized and treated as such. The research clearly identifies the need for the conservation agency to be creative in devising strategies and initiatives appropriate to specific social groups so as to optimize their input in participatory conservation.

  20. Local responses to participatory conservation in Annapurna conservation area, Nepal.

    PubMed

    Khadka, Damodar; Nepal, Sanjay K

    2010-02-01

    Biodiversity conservation has undergone a profound change in philosophy, policies and management approaches over the last forty years. The traditional top-down approach to nature protection has been widely criticized for failing to include critical social elements in management practices, and is being gradually replaced by a slew of participatory strategies under the rubric of bottom-up conservation. The new approach recognizes local communities as key partners in wildlife management and seeks their participation in social development and biodiversity conservation. However, every social context is different in its structure and functions, and in the way social groups respond to calls for participation. In order to gain a better understanding of the approach and the barriers encountered in its implementation, a questionnaire survey of 188 households was employed in the communities of the Upper Mustang extension of Annapurna Conservation Area (ACA) in Nepal. The study provides a comparative analysis of community participation and its barriers between Non-Tourist (NT) and Tourist (TV) villages. The results revealed important differences between the two groups in terms of their participation in community programs, barriers to participation, and perception of benefits from participation. Owing to their distinct spatial, demographic and attitudinal differences, the two village groups have their own sets of needs, values and motivation factors which cannot be generalized and treated as such. The research clearly identifies the need for the conservation agency to be creative in devising strategies and initiatives appropriate to specific social groups so as to optimize their input in participatory conservation. PMID:19967362

  1. How do infants recognize joint attention?

    PubMed

    Gustafsson, Erik; Brisson, Julie; Beaulieu, Christelle; Mainville, Marc; Mailloux, Dominique; Sirois, Sylvain

    2015-08-01

    The emergence of joint attention is still a matter of vigorous debate. It involves diverse hypotheses ranging from innate modules dedicated to intention reading to more neuro-constructivist approaches. The aim of this study was to assess whether 12-month-old infants are able to recognize a "joint attention" situation when observing such a social interaction. Using a violation-of-expectation paradigm, we habituated infants to a "joint attention" video and then compared their looking time durations between "divergent attention" videos and "joint attention" ones using a 2 (familiar or novel perceptual component)×2 (familiar or novel conceptual component) factorial design. These results were enriched with measures of pupil dilation, which are considered to be reliable measures of cognitive load. Infants looked longer at test events that involved novel speaker and divergent attention but no changes in infants' pupil dilation were observed in any conditions. Although looking time data suggest that infants may appreciate discrepancies from expectations related to joint attention behavior, in the absence of clear evidence from pupillometry, the results show no demonstration of understanding of joint attention, even at a tacit level. Our results suggest that infants may be sensitive to relevant perceptual variables in joint attention situations, which would help scaffold social cognitive development. This study supports a gradual, learning interpretation of how infants come to recognize, understand, and participate in joint attention.

  2. Ants recognize foes and not friends.

    PubMed

    Guerrieri, Fernando J; Nehring, Volker; Jørgensen, Charlotte G; Nielsen, John; Galizia, C Giovanni; d'Ettorre, Patrizia

    2009-07-01

    Discriminating among individuals and rejecting non-group members is essential for the evolution and stability of animal societies. Ants are good models for studying recognition mechanisms, because they are typically very efficient in discriminating 'friends' (nest-mates) from 'foes' (non-nest-mates). Recognition in ants involves multicomponent cues encoded in cuticular hydrocarbon profiles. Here, we tested whether workers of the carpenter ant Camponotus herculeanus use the presence and/or absence of cuticular hydrocarbons to discriminate between nest-mates and non-nest-mates. We supplemented the cuticular profile with synthetic hydrocarbons mixed to liquid food and then assessed behavioural responses using two different bioassays. Our results show that (i) the presence, but not the absence, of an additional hydrocarbon elicited aggression and that (ii) among the three classes of hydrocarbons tested (unbranched, mono-methylated and dimethylated alkanes; for mono-methylated alkanes, we present a new synthetic pathway), only the dimethylated alkane was effective in eliciting aggression. Our results suggest that carpenter ants use a fundamentally different mechanism for nest-mate recognition than previously thought. They do not specifically recognize nest-mates, but rather recognize and reject non-nest-mates bearing odour cues that are novel to their own colony cuticular hydrocarbon profile. This begs for a reappraisal of the mechanisms underlying recognition systems in social insects.

  3. Ants recognize foes and not friends.

    PubMed

    Guerrieri, Fernando J; Nehring, Volker; Jørgensen, Charlotte G; Nielsen, John; Galizia, C Giovanni; d'Ettorre, Patrizia

    2009-07-01

    Discriminating among individuals and rejecting non-group members is essential for the evolution and stability of animal societies. Ants are good models for studying recognition mechanisms, because they are typically very efficient in discriminating 'friends' (nest-mates) from 'foes' (non-nest-mates). Recognition in ants involves multicomponent cues encoded in cuticular hydrocarbon profiles. Here, we tested whether workers of the carpenter ant Camponotus herculeanus use the presence and/or absence of cuticular hydrocarbons to discriminate between nest-mates and non-nest-mates. We supplemented the cuticular profile with synthetic hydrocarbons mixed to liquid food and then assessed behavioural responses using two different bioassays. Our results show that (i) the presence, but not the absence, of an additional hydrocarbon elicited aggression and that (ii) among the three classes of hydrocarbons tested (unbranched, mono-methylated and dimethylated alkanes; for mono-methylated alkanes, we present a new synthetic pathway), only the dimethylated alkane was effective in eliciting aggression. Our results suggest that carpenter ants use a fundamentally different mechanism for nest-mate recognition than previously thought. They do not specifically recognize nest-mates, but rather recognize and reject non-nest-mates bearing odour cues that are novel to their own colony cuticular hydrocarbon profile. This begs for a reappraisal of the mechanisms underlying recognition systems in social insects. PMID:19364750

  4. How do infants recognize joint attention?

    PubMed

    Gustafsson, Erik; Brisson, Julie; Beaulieu, Christelle; Mainville, Marc; Mailloux, Dominique; Sirois, Sylvain

    2015-08-01

    The emergence of joint attention is still a matter of vigorous debate. It involves diverse hypotheses ranging from innate modules dedicated to intention reading to more neuro-constructivist approaches. The aim of this study was to assess whether 12-month-old infants are able to recognize a "joint attention" situation when observing such a social interaction. Using a violation-of-expectation paradigm, we habituated infants to a "joint attention" video and then compared their looking time durations between "divergent attention" videos and "joint attention" ones using a 2 (familiar or novel perceptual component)×2 (familiar or novel conceptual component) factorial design. These results were enriched with measures of pupil dilation, which are considered to be reliable measures of cognitive load. Infants looked longer at test events that involved novel speaker and divergent attention but no changes in infants' pupil dilation were observed in any conditions. Although looking time data suggest that infants may appreciate discrepancies from expectations related to joint attention behavior, in the absence of clear evidence from pupillometry, the results show no demonstration of understanding of joint attention, even at a tacit level. Our results suggest that infants may be sensitive to relevant perceptual variables in joint attention situations, which would help scaffold social cognitive development. This study supports a gradual, learning interpretation of how infants come to recognize, understand, and participate in joint attention. PMID:26036712

  5. 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

  6. Predicting the conservation status of data-deficient species.

    PubMed

    Bland, Lucie M; Collen, Ben; Orme, C David L; Bielby, Jon

    2015-02-01

    There is little appreciation of the level of extinction risk faced by one-sixth of the over 65,000 species assessed by the International Union for Conservation of Nature. Determining the status of these data-deficient (DD) species is essential to developing an accurate picture of global biodiversity and identifying potentially threatened DD species. To address this knowledge gap, we used predictive models incorporating species' life history, geography, and threat information to predict the conservation status of DD terrestrial mammals. We constructed the models with 7 machine learning (ML) tools trained on species of known status. The resultant models showed very high species classification accuracy (up to 92%) and ability to correctly identify centers of threatened species richness. Applying the best model to DD species, we predicted 313 of 493 DD species (64%) to be at risk of extinction, which increases the estimated proportion of threatened terrestrial mammals from 22% to 27%. Regions predicted to contain large numbers of threatened DD species are already conservation priorities, but species in these areas show considerably higher levels of risk than previously recognized. We conclude that unless directly targeted for monitoring, species classified as DD are likely to go extinct without notice. Taking into account information on DD species may therefore help alleviate data gaps in biodiversity indicators and conserve poorly known biodiversity.

  7. Optimal Conservation of Migratory Species

    PubMed Central

    Martin, Tara G.; Chadès, Iadine; Arcese, Peter; Marra, Peter P.; Possingham, Hugh P.; Norris, D. Ryan

    2007-01-01

    Background Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea–regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity) bringing into question the utility and efficiency of current conservation efforts. Methodology/Principal Findings Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. Conclusions/Significance We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of migratory

  8. Evaluation of Land Use, Land Management and Soil Conservation Strategies to Reduce Non-Point Source Pollution Loads in the Three Gorges Region, China

    NASA Astrophysics Data System (ADS)

    Strehmel, Alexander; Schmalz, Britta; Fohrer, Nicola

    2016-11-01

    The construction of the Three Gorges Dam in China and the subsequent impoundment of the Yangtze River have induced a major land use change in the Three Gorges Reservoir Region, which fosters increased inputs of sediment and nutrients from diffuse sources into the water bodies. Several government programs have been implemented to mitigate high sediment and nutrient loads to the reservoir. However, institutional weaknesses and a focus on economic development have so far widely counteracted the effectiveness of these programs. In this study, the eco-hydrological model soil and water assessment tool is used to assess the effects of changes in fertilizer amounts and the conditions of bench terraces in the Xiangxi catchment in the Three Gorges Reservoir Region on diffuse matter releases. With this, the study aims at identifying efficient management measures, which should have priority. The results show that a reduction of fertilizer amounts cannot reduce phosphorus loads considerably without inhibiting crop productivity. The condition of terraces in the catchment has a strong impact on soil erosion and phosphorus releases from agricultural areas. Hence, if economically feasible, programmes focusing on the construction and maintenance of terraces in the region should be implemented. Additionally, intercropping on corn fields as well as more efficient fertilization schemes for agricultural land were identified as potential instruments to reduce diffuse matter loads further. While the study was carried out in the Three Gorges Region, its findings may also beneficial for the reduction of water pollution in other mountainous areas with strong agricultural use.

  9. Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning

    PubMed Central

    Gaiotto, Tiziano; Hufton, Simon E.

    2016-01-01

    Cross-neutralising monoclonal antibodies against influenza hemagglutinin (HA) are of considerable interest as both therapeutics and diagnostic tools. We have recently described five different single domain antibodies (nanobodies) which share this cross-neutralising activity and suggest their small size, high stability, and cleft binding properties may present distinct advantages over equivalent conventional antibodies. We have used yeast display in combination with deep mutational scanning to give residue level resolution of positions in the antibody-HA interface which are crucial for binding. In addition, we have mapped positions within HA predicted to have minimal effect on antibody binding when mutated. Our cross-neutralising nanobodies were shown to bind to a highly conserved pocket in the HA2 domain of A(H1N1)pdm09 influenza virus overlapping with the fusion peptide suggesting their mechanism of action is through the inhibition of viral membrane fusion. We also note that the epitope overlaps with that of CR6261 and F10 which are human monoclonal antibodies in clinical development as immunotherapeutics. Although all five nanobodies mapped to the same highly conserved binding pocket we observed differences in the size of the epitope footprint which has implications in comparing the relative genetic barrier each nanobody presents to a rapidly evolving influenza virus. To further refine our epitope map, we have re-created naturally occurring mutations within this HA stem epitope and tested their effect on binding using yeast display. We have shown that a D46N mutation in the HA2 stem domain uniquely interferes with binding of R2b-E8. Further testing of this substitution in the context of full length purified HA from 1918 H1N1 pandemic (Spanish flu), 2009 H1N1 pandemic (swine flu) and highly pathogenic avian influenza H5N1 demonstrated binding which correlated with D46 whereas binding to seasonal H1N1 strains carrying N46 was absent. In addition, our deep sequence

  10. Conservation reaches new heights.

    PubMed

    Pepall, J; Khanal, P

    1992-10-01

    The conservation program with the management assistance of the Woodlands Mountain Institute in 2 contiguous parks, the Mount Everest National Park in Nepal and the Qomolangma Nature Reserve in China, in 2 countries is described. The focus is on conservation of the complex ecosystem with sustainable development by showing local people how to benefit from the park without environmental damage. Cultural diversity is as important as biological diversity. The area has been designated by UNESCO as a World Heritage Site with the "last pure ecological seed" of the Himalayas. The regional geography and culture are presented. Population growth has impacted natural resources through overgrazing, cultivation of marginal land, and deforestation; future plans to build a dam and road bordering the nature reserve pose other threats. Proposed management plans for the Makalu-Barun Nature Park (established in November 1991) and Conservation Area include a division of the park into nature reserve areas free of human activity, protected areas which permit traditional land use, and special sites and trail for tourists and religious pilgrims. The conservation area will act as a buffer for the park and provide economic opportunities; further subdivisions include land use for biodiversity protection, community forest and pasture, agroforestry, and agriculture and settlement. Efforts will be made to increase the welfare of women and local people; proposed projects include the introduction of higher milk-producing animals for stall feeding. Also proposed is a cultural and natural history museum. 70% of the project's resources will be directed to local community participation in consultation and park maintenance. The project is a model of how conservation and protection of natural resources can coexist with local economic development and participation; an integration of preservation of biological diversity, mountain wisdom, and the value of local people as resources for conservation.

  11. Conservation reaches new heights.

    PubMed

    Pepall, J; Khanal, P

    1992-10-01

    The conservation program with the management assistance of the Woodlands Mountain Institute in 2 contiguous parks, the Mount Everest National Park in Nepal and the Qomolangma Nature Reserve in China, in 2 countries is described. The focus is on conservation of the complex ecosystem with sustainable development by showing local people how to benefit from the park without environmental damage. Cultural diversity is as important as biological diversity. The area has been designated by UNESCO as a World Heritage Site with the "last pure ecological seed" of the Himalayas. The regional geography and culture are presented. Population growth has impacted natural resources through overgrazing, cultivation of marginal land, and deforestation; future plans to build a dam and road bordering the nature reserve pose other threats. Proposed management plans for the Makalu-Barun Nature Park (established in November 1991) and Conservation Area include a division of the park into nature reserve areas free of human activity, protected areas which permit traditional land use, and special sites and trail for tourists and religious pilgrims. The conservation area will act as a buffer for the park and provide economic opportunities; further subdivisions include land use for biodiversity protection, community forest and pasture, agroforestry, and agriculture and settlement. Efforts will be made to increase the welfare of women and local people; proposed projects include the introduction of higher milk-producing animals for stall feeding. Also proposed is a cultural and natural history museum. 70% of the project's resources will be directed to local community participation in consultation and park maintenance. The project is a model of how conservation and protection of natural resources can coexist with local economic development and participation; an integration of preservation of biological diversity, mountain wisdom, and the value of local people as resources for conservation. PMID

  12. Sensitivity analysis of conservation targets in systematic conservation planning.

    PubMed

    Levin, Noam; Mazor, Tessa; Brokovich, Eran; Jablon, Pierre-Elie; Kark, Salit

    2015-10-01

    Systematic conservation planning has rapidly advanced in the past decade and has been increasingly incorporated in multiple studies and conservation projects. One of its requirements is a quantitative definition of conservation targets. While the Convention on Biological Diversity aims to expand the world's protected area network to 17% of the land surface, in many cases such uniform policy-driven targets may not be appropriate for achieving persistence of various species. Targets are often set arbitrarily, often because information required for the persistence of each species is unavailable or unknown in the focal region. Conservation planners therefore need to establish complementary novel approaches to address the gaps in setting targets. Here, we develop and present a novel method that aims to help guide the selection of conservation targets, providing support for decision makers, planners, and managers. This is achieved by examining the overall flexibility of the conservation network resulting from conservation prioritization, and aiming for greater flexibility. To test this approach we applied the decision support tool Marxan to determine marine conservation priority areas in the eastern Mediterranean Sea as a case study. We assessed the flexibility of the conservation network by comparing 80 different scenarios in which conservation targets were gradually increased and assessed by a range of calculated metrics (e.g., the percentage of the total area selected, the overall connectivity). We discovered that when conservation targets were set too low (i.e., below 10% of the distribution range of each species), very few areas were identified as irreplaceable and the conservation network was not well defined. Interestingly, when conservation targets were set too high (over 50% of the species' range), too many conservation priority areas were selected as irreplaceable, an outcome which is realistically infeasible to implement. As a general guideline, we found that

  13. 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.

  14. Octopuses (Enteroctopus dofleini) recognize individual humans.

    PubMed

    Anderson, Roland C; Mather, Jennifer A; Monette, Mathieu Q; Zimsen, Stephanie R M

    2010-01-01

    This study exposed 8 Enteroctopus dofleini separately to 2 unfamiliar individual humans over a 2-week period under differing circumstances. One person consistently fed the octopuses and the other touched them with a bristly stick. Each human recorded octopus body patterns, behaviors, and respiration rates directly after each treatment. At the end of 2 weeks, a body pattern (a dark Eyebar) and 2 behaviors (reaching arms toward or away from the tester and funnel direction) were significantly different in response to the 2 humans. The respiration rate of the 4 larger octopuses changed significantly in response to the 2 treatments; however, there was no significant difference in the 4 smaller octopuses' respiration. Octopuses' ability to recognize humans enlarges our knowledge of the perceptual ability of this nonhuman animal, which depends heavily on learning in response to visual information. Any training paradigm should take such individual recognition into consideration as it could significantly alter the octopuses' responses.

  15. Octopuses (Enteroctopus dofleini) recognize individual humans.

    PubMed

    Anderson, Roland C; Mather, Jennifer A; Monette, Mathieu Q; Zimsen, Stephanie R M

    2010-01-01

    This study exposed 8 Enteroctopus dofleini separately to 2 unfamiliar individual humans over a 2-week period under differing circumstances. One person consistently fed the octopuses and the other touched them with a bristly stick. Each human recorded octopus body patterns, behaviors, and respiration rates directly after each treatment. At the end of 2 weeks, a body pattern (a dark Eyebar) and 2 behaviors (reaching arms toward or away from the tester and funnel direction) were significantly different in response to the 2 humans. The respiration rate of the 4 larger octopuses changed significantly in response to the 2 treatments; however, there was no significant difference in the 4 smaller octopuses' respiration. Octopuses' ability to recognize humans enlarges our knowledge of the perceptual ability of this nonhuman animal, which depends heavily on learning in response to visual information. Any training paradigm should take such individual recognition into consideration as it could significantly alter the octopuses' responses. PMID:20563906

  16. Recognizing familial myeloid leukemia in adults

    PubMed Central

    Nickels, Eric M.; Soodalter, Jesse; Churpek, Jane E.

    2013-01-01

    Germline testing for familial cases of myeloid leukemia in adults is becoming more common with the recognition of multiple genetic syndromes predisposing people to bone marrow disease. Currently, Clinical Laboratory Improvement Amendments approved testing exists for several myeloid leukemia predisposition syndromes: familial platelet disorder with propensity to acute myeloid leukemia (FPD/AML), caused by mutations in RUNX1; familial AML with mutated CEBPA; familial myelodysplastic syndrome and acute leukemia with mutated GATA2; and the inherited bone marrow failure syndromes, including dyskeratosis congenita, a disease of abnormal telomere maintenance. With the recognition of additional families with a genetic component to their leukemia, new predisposition alleles will likely be identified. We highlight how to recognize and manage these cases as well as outline the characteristics of the major known syndromes. We look forward to future research increasing our understanding of the scope of inherited myeloid leukemia syndromes. PMID:23926458

  17. Recognizing asthma mimics and asthma complications.

    PubMed

    Amundson, Dennis; Seda, Gilbert; Daheshia, Massoud

    2011-10-01

    Asthma is a chronic inflammatory disorder of the airways characterized by airflow obstruction, bronchial hyperreactivity, and underlying inflammation. Two common reasons asthmatics fail standard therapy are incorrect diagnosis and failure to recognize underlying contributing factors. A correct diagnosis of asthma is of great importance to military practitioners since misdiagnosis or uncontrolled asthma affects an individual's operational readiness or determines whether one can receive a medical waiver to enlist in military service. This article presents four cases of patients with dyspnea that have conditions which mimic asthma or complicate asthma management: vocal cord dysfunction misdiagnosed as asthma, respiratory bronchiolitis interstitial lung disease mistaken as asthma, difficult-to-control asthma because of bronchiectasis and allergic bronchopulmonary aspergillosis, and difficult and fatal asthma. Asthma is contrasted to other respiratory disorders, and an outlined approach to asthma diagnosis and management is presented using the Global Initiative for Asthma guidelines.

  18. Position, rotation, and intensity invariant recognizing method

    DOEpatents

    Ochoa, Ellen; Schils, George F.; Sweeney, Donald W.

    1989-01-01

    A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output The U.S. Government has rights in this invention pursuant to Contract No. DE-AC04-76DP00789 between the U.S. Department of Energy and AT&T Technologies, Inc.

  19. Obstacle detection by recognizing binary expansion patterns

    NASA Technical Reports Server (NTRS)

    Baram, Yoram; Barniv, Yair

    1993-01-01

    This paper describes a technique for obstacle detection, based on the expansion of the image-plane projection of a textured object, as its distance from the sensor decreases. Information is conveyed by vectors whose components represent first-order temporal and spatial derivatives of the image intensity, which are related to the time to collision through the local divergence. Such vectors may be characterized as patterns corresponding to 'safe' or 'dangerous' situations. We show that essential information is conveyed by single-bit vector components, representing the signs of the relevant derivatives. We use two recently developed, high capacity classifiers, employing neural learning techniques, to recognize the imminence of collision from such patterns.

  20. Recognizing Charles Bonnet syndrome in the elderly.

    PubMed

    Walsh, Christina M; Hilas, Olga

    2009-04-01

    Charles Bonnet syndrome (CBS) is an under-recognized and commonly misdiagnosed condition characterized by the presence of visual hallucinations that psychologically normal people acknowledge as being unreal. It is commonly associated with ocular pathology and usually observed in elderly individuals with visual impairment. The exact etiology of CBS is unknown; however, the presentation of hallucinations is believed to be a result of functional deterioration of the central and peripheral nervous systems. Eradication of hallucinations and recurrent episodes has been seen with the use of neuroleptic and anticonvulsant agents. Correction of underlying ocular disorders and low-vision rehabilitation may also help in the resolution of visions. Careful patient assessment is necessary to appropriately diagnose CBS and determine the best approach to management.

  1. [Recognizing difference: the challenge of ethnopsychiatry].

    PubMed

    Pocreau, Jean-Bernard; Martins Borges, Lucienne

    2006-01-01

    Recognizing difference of the Other is the basis of legitimacy of ethnopsychiatry that is necessarily multiple, changing, and itself bearing subtleties and variations. It is from their practice at the Service d'aide psychologique spécialisée aux immigrants et réfugiés (SAPSIR), that the authors propose another perspective of this discipline taking into account of course, the cultural and psychological dimension of the individual; they also consider existential and humanistic universals such as the need of giving meaning, of continuity of the self and coherence as well as the various dimensions of identity. Their clinical approach, respectful of the principles of ethnopsychiatry, is structured around three axis : work on links, work on different dimensions of identity, work on coherence and meaning of situations experienced. This approach allows to accompany and facilitate essential elaborations involved in the psychological work of refugees as well as individuals exposed to extreme situations such as torture.

  2. How can we recognize continuous quality improvement?

    PubMed Central

    Rubenstein, Lisa; Khodyakov, Dmitry; Hempel, Susanne; Danz, Margie; Salem-Schatz, Susanne; Foy, Robbie; O'Neill, Sean; Dalal, Siddhartha; Shekelle, Paul

    2014-01-01

    Objective Continuous quality improvement (CQI) methods are foundational approaches to improving healthcare delivery. Publications using the term CQI, however, are methodologically heterogeneous, and labels other than CQI are used to signify relevant approaches. Standards for identifying the use of CQI based on its key methodological features could enable more effective learning across quality improvement (QI) efforts. The objective was to identify essential methodological features for recognizing CQI. Design Previous work with a 12-member international expert panel identified reliably abstracted CQI methodological features. We tested which features met rigorous a priori standards as essential features of CQI using a three-phase online modified-Delphi process. Setting Primarily United States and Canada. Participants 119 QI experts randomly assigned into four on-line panels. Intervention(s) Participants rated CQI features and discussed their answers using online, anonymous and asynchronous discussion boards. We analyzed ratings quantitatively and discussion threads qualitatively. Main outcome measure(s) Panel consensus on definitional CQI features. Results Seventy-nine (66%) panelists completed the process. Thirty-three completers self-identified as QI researchers, 18 as QI practitioners and 28 as both equally. The features ‘systematic data guided activities,’ ‘designing with local conditions in mind’ and ‘iterative development and testing’ met a priori standards as essential CQI features. Qualitative analyses showed cross-cutting themes focused on differences between QI and CQI. Conclusions We found consensus among a broad group of CQI researchers and practitioners on three features as essential for identifying QI work more specifically as ‘CQI.’ All three features are needed as a minimum standard for recognizing CQI methods. PMID:24311732

  3. Predicted effect of landscape position on wildlife habitat value of Conservation Reserve Enhancement Program wetlands in a tile-drained agricultural region

    USGS Publications Warehouse

    Otis, David L.; Crumpton, William R.; Green, David; Loan-Wilsey, Anna; Cooper, Tom; Johnson, Rex R.

    2013-01-01

    Justification for investment in restored or constructed wetland projects are often based on presumed net increases in ecosystem services. However, quantitative assessment of performance metrics is often difficult and restricted to a single objective. More comprehensive performance assessments could help inform decision-makers about trade-offs in services provided by alternative restoration program design attributes. The primary goal of the Iowa Conservation Reserve Enhancement Program is to establish wetlands that efficiently remove nitrates from tile-drained agricultural landscapes. A secondary objective is provision of wildlife habitat. We used existing wildlife habitat models to compare relative net change in potential wildlife habitat value for four alternative landscape positions of wetlands within the watershed. Predicted species richness and habitat value for birds, mammals, amphibians, and reptiles generally increased as the wetland position moved lower in the watershed. However, predicted average net increase between pre- and post-project value was dependent on taxonomic group. The increased average wetland area and changes in surrounding upland habitat composition among landscape positions were responsible for these differences. Net change in predicted densities of several grassland bird species at the four landscape positions was variable and species-dependent. Predicted waterfowl breeding activity was greater for lower drainage position wetlands. Although our models are simplistic and provide only a predictive index of potential habitat value, we believe such assessment exercises can provide a tool for coarse-level comparisons of alternative proposed project attributes and a basis for constructing informed hypotheses in auxiliary empirical field studies.

  4. 46 CFR 162.039-5 - Recognized laboratory.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 6 2013-10-01 2013-10-01 false Recognized laboratory. 162.039-5 Section 162.039-5... Recognized laboratory. (a) A recognized laboratory is one which is regularly engaged in the examination... motorboats. The following laboratories are recognized, and the semiportable fire extinguishers bearing...

  5. 46 CFR 160.077-9 - Recognized laboratory.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 6 2010-10-01 2010-10-01 false Recognized laboratory. 160.077-9 Section 160.077-9... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  6. 46 CFR 160.077-9 - Recognized laboratory.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Recognized laboratory. 160.077-9 Section 160.077-9... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  7. 46 CFR 160.076-19 - Recognized laboratories.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Recognized laboratories. 160.076-19 Section 160.076-19... Recognized laboratories. The approval and production oversight functions that this subpart requires to be conducted by a recognized laboratory must be conducted by an independent laboratory recognized by the...

  8. 46 CFR 160.077-9 - Recognized laboratory.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 6 2011-10-01 2011-10-01 false Recognized laboratory. 160.077-9 Section 160.077-9... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  9. 46 CFR 160.048-8 - Recognized laboratory.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 6 2013-10-01 2013-10-01 false Recognized laboratory. 160.048-8 Section 160.048-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  10. 46 CFR 160.048-8 - Recognized laboratory.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Recognized laboratory. 160.048-8 Section 160.048-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  11. 46 CFR 160.048-8 - Recognized laboratory.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 6 2011-10-01 2011-10-01 false Recognized laboratory. 160.048-8 Section 160.048-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  12. 46 CFR 162.039-5 - Recognized laboratory.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Recognized laboratory. 162.039-5 Section 162.039-5... Recognized laboratory. (a) A recognized laboratory is one which is regularly engaged in the examination... motorboats. The following laboratories are recognized, and the semiportable fire extinguishers bearing...

  13. 46 CFR 160.049-8 - Recognized laboratory.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Recognized laboratory. 160.049-8 Section 160.049-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  14. 46 CFR 162.039-5 - Recognized laboratory.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Recognized laboratory. 162.039-5 Section 162.039-5... Recognized laboratory. (a) A recognized laboratory is one which is regularly engaged in the examination... motorboats. The following laboratories are recognized, and the semiportable fire extinguishers bearing...

  15. 46 CFR 160.076-19 - Recognized laboratories.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Recognized laboratories. 160.076-19 Section 160.076-19... Recognized laboratories. The approval and production oversight functions that this subpart requires to be conducted by a recognized laboratory must be conducted by an independent laboratory recognized by the...

  16. 46 CFR 160.049-8 - Recognized laboratory.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 6 2011-10-01 2011-10-01 false Recognized laboratory. 160.049-8 Section 160.049-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  17. 46 CFR 160.048-8 - Recognized laboratory.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Recognized laboratory. 160.048-8 Section 160.048-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  18. 46 CFR 160.077-9 - Recognized laboratory.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 6 2013-10-01 2013-10-01 false Recognized laboratory. 160.077-9 Section 160.077-9... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  19. 46 CFR 162.039-5 - Recognized laboratory.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 6 2010-10-01 2010-10-01 false Recognized laboratory. 162.039-5 Section 162.039-5... Recognized laboratory. (a) A recognized laboratory is one which is regularly engaged in the examination... motorboats. The following laboratories are recognized, and the semiportable fire extinguishers bearing...

  20. 46 CFR 160.076-19 - Recognized laboratories.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 6 2013-10-01 2013-10-01 false Recognized laboratories. 160.076-19 Section 160.076-19... Recognized laboratories. The approval and production oversight functions that this subpart requires to be conducted by a recognized laboratory must be conducted by an independent laboratory recognized by the...

  1. 46 CFR 160.077-9 - Recognized laboratory.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Recognized laboratory. 160.077-9 Section 160.077-9... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  2. 46 CFR 160.048-8 - Recognized laboratory.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 6 2010-10-01 2010-10-01 false Recognized laboratory. 160.048-8 Section 160.048-8... Recognized laboratory. (a) A manufacturer seeking Coast Guard approval of a product under this subpart shall... to a recognized independent laboratory. The following laboratories are recognized under §...

  3. 46 CFR 162.039-5 - Recognized laboratory.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 6 2011-10-01 2011-10-01 false Recognized laboratory. 162.039-5 Section 162.039-5... Recognized laboratory. (a) A recognized laboratory is one which is regularly engaged in the examination... motorboats. The following laboratories are recognized, and the semiportable fire extinguishers bearing...

  4. Facial Expressions and Ability to Recognize Emotions From Eyes or Mouth in Children.

    PubMed

    Guarnera, Maria; Hichy, Zira; Cascio, Maura I; Carrubba, Stefano

    2015-05-01

    This research aims to contribute to the literature on the ability to recognize anger, happiness, fear, surprise, sadness, disgust and neutral emotions from facial information. By investigating children's performance in detecting these emotions from a specific face region, we were interested to know whether children would show differences in recognizing these expressions from the upper or lower face, and if any difference between specific facial regions depended on the emotion in question. For this purpose, a group of 6-7 year-old children was selected. Participants were asked to recognize emotions by using a labeling task with three stimulus types (region of the eyes, of the mouth, and full face). The findings seem to indicate that children correctly recognize basic facial expressions when pictures represent the whole face, except for a neutral expression, which was recognized from the mouth, and sadness, which was recognized from the eyes. Children are also able to identify anger from the eyes as well as from the whole face. With respect to gender differences, there is no female advantage in emotional recognition. The results indicate a significant interaction 'gender x face region' only for anger and neutral emotions. PMID:27247651

  5. Facial Expressions and Ability to Recognize Emotions From Eyes or Mouth in Children.

    PubMed

    Guarnera, Maria; Hichy, Zira; Cascio, Maura I; Carrubba, Stefano

    2015-05-01

    This research aims to contribute to the literature on the ability to recognize anger, happiness, fear, surprise, sadness, disgust and neutral emotions from facial information. By investigating children's performance in detecting these emotions from a specific face region, we were interested to know whether children would show differences in recognizing these expressions from the upper or lower face, and if any difference between specific facial regions depended on the emotion in question. For this purpose, a group of 6-7 year-old children was selected. Participants were asked to recognize emotions by using a labeling task with three stimulus types (region of the eyes, of the mouth, and full face). The findings seem to indicate that children correctly recognize basic facial expressions when pictures represent the whole face, except for a neutral expression, which was recognized from the mouth, and sadness, which was recognized from the eyes. Children are also able to identify anger from the eyes as well as from the whole face. With respect to gender differences, there is no female advantage in emotional recognition. The results indicate a significant interaction 'gender x face region' only for anger and neutral emotions.

  6. Socioeconomic contexts of primate conservation: population, poverty, global economic demands, and sustainable land use.

    PubMed

    Estrada, Alejandro

    2013-01-01

    Recent assessments by the International Union for Conservation of Nature (IUCN) indicate the existence of about 612 recognized primate species and subspecies (IUCN RedList, 2012), but close to 50% of these taxa are at risk of extinction as a result of human action. In this article, I call attention to underlying regional and global socioeconomic contexts of primate conservation. Using information from FAO and UN databases and other sources, I examine, for the Neotropics, sub-Saharan Africa, and Southeast Asia, trends in forest loss and human demographics and social condition, discuss the impact of global market pressures upon primate habitats, and examine land-use patterns that may favor primate conservation. Between 1990 and 2010, an estimated 149 million ha of forest were lost in the three regions and additional losses are expected in the future. Global human population will increase from 7 billion in 2012 to 9 billion in 2050. Currently, 2 billion people live in the three primate range regions under high levels of poverty. Large-scale deforestation is related to global market demands, especially from developed and developing nations, for food (e.g., cattle), domestic animal feed (e.g., soybeans), biofuel-based crops (e.g., oil palm), and industrial round wood. The growth of protected areas in the three regions has been steady for several decades, but it is not enough to ensure long-term conservation of many primate taxa. Other conservations tools involving sustainable land use and biodiversity conservation corridors are required at the landscape level. The above assessment can easily be applied at the local level by primatologists, giving more precision to conservation initiatives.

  7. Credibility and advocacy in conservation science

    PubMed Central

    Horton, Cristi C.; Peterson, Tarla Rai; Banerjee, Paulami

    2015-01-01

    Abstract Conservation policy sits at the nexus of natural science and politics. On the one hand, conservation scientists strive to maintain scientific credibility by emphasizing that their research findings are the result of disinterested observations of reality. On the other hand, conservation scientists are committed to conservation even if they do not advocate a particular policy. The professional conservation literature offers guidance on negotiating the relationship between scientific objectivity and political advocacy without damaging conservation science's credibility. The value of this guidance, however, may be restricted by limited recognition of credibility's multidimensionality and emergent nature: it emerges through perceptions of expertise, goodwill, and trustworthiness. We used content analysis of the literature to determine how credibility is framed in conservation science as it relates to apparent contradictions between science and advocacy. Credibility typically was framed as a static entity lacking dimensionality. Authors identified expertise or trustworthiness as important, but rarely mentioned goodwill. They usually did not identify expertise, goodwill, or trustworthiness as dimensions of credibility or recognize interactions among these 3 dimensions of credibility. This oversimplification may limit the ability of conservation scientists to contribute to biodiversity conservation. Accounting for the emergent quality and multidimensionality of credibility should enable conservation scientists to advance biodiversity conservation more effectively. PMID:26041036

  8. Credibility and advocacy in conservation science.

    PubMed

    Horton, Cristi C; Peterson, Tarla Rai; Banerjee, Paulami; Peterson, Markus J

    2016-02-01

    Conservation policy sits at the nexus of natural science and politics. On the one hand, conservation scientists strive to maintain scientific credibility by emphasizing that their research findings are the result of disinterested observations of reality. On the other hand, conservation scientists are committed to conservation even if they do not advocate a particular policy. The professional conservation literature offers guidance on negotiating the relationship between scientific objectivity and political advocacy without damaging conservation science's credibility. The value of this guidance, however, may be restricted by limited recognition of credibility's multidimensionality and emergent nature: it emerges through perceptions of expertise, goodwill, and trustworthiness. We used content analysis of the literature to determine how credibility is framed in conservation science as it relates to apparent contradictions between science and advocacy. Credibility typically was framed as a static entity lacking dimensionality. Authors identified expertise or trustworthiness as important, but rarely mentioned goodwill. They usually did not identify expertise, goodwill, or trustworthiness as dimensions of credibility or recognize interactions among these 3 dimensions of credibility. This oversimplification may limit the ability of conservation scientists to contribute to biodiversity conservation. Accounting for the emergent quality and multidimensionality of credibility should enable conservation scientists to advance biodiversity conservation more effectively. PMID:26041036

  9. Credibility and advocacy in conservation science.

    PubMed

    Horton, Cristi C; Peterson, Tarla Rai; Banerjee, Paulami; Peterson, Markus J

    2016-02-01

    Conservation policy sits at the nexus of natural science and politics. On the one hand, conservation scientists strive to maintain scientific credibility by emphasizing that their research findings are the result of disinterested observations of reality. On the other hand, conservation scientists are committed to conservation even if they do not advocate a particular policy. The professional conservation literature offers guidance on negotiating the relationship between scientific objectivity and political advocacy without damaging conservation science's credibility. The value of this guidance, however, may be restricted by limited recognition of credibility's multidimensionality and emergent nature: it emerges through perceptions of expertise, goodwill, and trustworthiness. We used content analysis of the literature to determine how credibility is framed in conservation science as it relates to apparent contradictions between science and advocacy. Credibility typically was framed as a static entity lacking dimensionality. Authors identified expertise or trustworthiness as important, but rarely mentioned goodwill. They usually did not identify expertise, goodwill, or trustworthiness as dimensions of credibility or recognize interactions among these 3 dimensions of credibility. This oversimplification may limit the ability of conservation scientists to contribute to biodiversity conservation. Accounting for the emergent quality and multidimensionality of credibility should enable conservation scientists to advance biodiversity conservation more effectively.

  10. Selling energy conservation.

    PubMed

    Hinrichsen, D

    1995-01-01

    This article concerns the Organization of the Petroleum Exporting Countries (OPEC) crisis and its impact on energy efficiency measures in the US. In 1985, when the OPEC collapsed, the US government had avoided the need to construct 350 gigawatts of new electric capacity. The most successful efficiency improvements, especially in household appliances and equipment, lighting and tightened energy efficiency standards in new buildings, resulted from the OPEC event. The real innovation of that time was the change in profit rules for utilities. This revolution and the way some US utilities view energy have not caught on elsewhere. Despite the initiative toward improving energy efficiency in homes, offices and industries, the change has been slow. Partly to blame are the big development banks, which pointed out that short-term conservation and efficiency measures could save at least 15% of the total energy demand without the need for major investment. The benefits of energy conservation was shown during the oil shock when per capita energy consumption fell by 5% in the member states of the Organization of Economic Cooperation and Development, while the per capita gross domestic product grew by a third. There has been a decrease in energy expenditure worldwide, and the scope for further energy savings is enormous, but governments need to recognize and seize the opportunity. PMID:12295818

  11. Type- and Subcomplex-Specific Neutralizing Antibodies against Domain III of Dengue Virus Type 2 Envelope Protein Recognize Adjacent Epitopes▿

    PubMed Central

    Sukupolvi-Petty, Soila; Austin, S. Kyle; Purtha, Whitney E.; Oliphant, Theodore; Nybakken, Grant E.; Schlesinger, Jacob J.; Roehrig, John T.; Gromowski, Gregory D.; Barrett, Alan D.; Fremont, Daved H.; Diamond, Michael S.

    2007-01-01

    Neutralization of flaviviruses in vivo correlates with the development of an antibody response against the viral envelope (E) protein. Previous studies demonstrated that monoclonal antibodies (MAbs) against an epitope on the lateral ridge of domain III (DIII) of the West Nile virus (WNV) E protein strongly protect against infection in animals. Based on X-ray crystallography and sequence analysis, an analogous type-specific neutralizing epitope for individual serotypes of the related flavivirus dengue virus (DENV) was hypothesized. Using yeast surface display of DIII variants, we defined contact residues of a panel of type-specific, subcomplex-specific, and cross-reactive MAbs that recognize DIII of DENV type 2 (DENV-2) and have different neutralizing potentials. Type-specific MAbs with neutralizing activity against DENV-2 localized to a sequence-unique epitope on the lateral ridge of DIII, centered at the FG loop near residues E383 and P384, analogous in position to that observed with WNV-specific strongly neutralizing MAbs. Subcomplex-specific MAbs that bound some but not all DENV serotypes and neutralized DENV-2 infection recognized an adjacent epitope centered on the connecting A strand of DIII at residues K305, K307, and K310. In contrast, several MAbs that had poor neutralizing activity against DENV-2 and cross-reacted with all DENV serotypes and other flaviviruses recognized an epitope with residues in the AB loop of DIII, a conserved region that is predicted to have limited accessibility on the mature virion. Overall, our experiments define adjacent and structurally distinct epitopes on DIII of DENV-2 which elicit type-specific, subcomplex-specific, and cross-reactive antibodies with different neutralizing potentials. PMID:17881453

  12. Type- and subcomplex-specific neutralizing antibodies against domain III of dengue virus type 2 envelope protein recognize adjacent epitopes.

    PubMed

    Sukupolvi-Petty, Soila; Austin, S Kyle; Purtha, Whitney E; Oliphant, Theodore; Nybakken, Grant E; Schlesinger, Jacob J; Roehrig, John T; Gromowski, Gregory D; Barrett, Alan D; Fremont, Daved H; Diamond, Michael S

    2007-12-01

    Neutralization of flaviviruses in vivo correlates with the development of an antibody response against the viral envelope (E) protein. Previous studies demonstrated that monoclonal antibodies (MAbs) against an epitope on the lateral ridge of domain III (DIII) of the West Nile virus (WNV) E protein strongly protect against infection in animals. Based on X-ray crystallography and sequence analysis, an analogous type-specific neutralizing epitope for individual serotypes of the related flavivirus dengue virus (DENV) was hypothesized. Using yeast surface display of DIII variants, we defined contact residues of a panel of type-specific, subcomplex-specific, and cross-reactive MAbs that recognize DIII of DENV type 2 (DENV-2) and have different neutralizing potentials. Type-specific MAbs with neutralizing activity against DENV-2 localized to a sequence-unique epitope on the lateral ridge of DIII, centered at the FG loop near residues E383 and P384, analogous in position to that observed with WNV-specific strongly neutralizing MAbs. Subcomplex-specific MAbs that bound some but not all DENV serotypes and neutralized DENV-2 infection recognized an adjacent epitope centered on the connecting A strand of DIII at residues K305, K307, and K310. In contrast, several MAbs that had poor neutralizing activity against DENV-2 and cross-reacted with all DENV serotypes and other flaviviruses recognized an epitope with residues in the AB loop of DIII, a conserved region that is predicted to have limited accessibility on the mature virion. Overall, our experiments define adjacent and structurally distinct epitopes on DIII of DENV-2 which elicit type-specific, subcomplex-specific, and cross-reactive antibodies with different neutralizing potentials.

  13. Calculations of the integral invariant coordinates I and L* in the magnetosphere and mapping of the regions where I is conserved

    NASA Astrophysics Data System (ADS)

    Konstantinidis, K.; Sarris, T.

    2014-09-01

    The integral invariant coordinate I and Roederer's L or L* are proxies for the second and third adiabatic invariants respectively, that characterize charged particle motion in a magnetic field. Their usefulness lies in the fact that they are expressed in more instructive ways than their counterparts: I is equivalent to the path length of the particle motion between two mirror points, whereas L*, although dimensionless, is roughly equivalent to the distance from the center of the Earth to the equatorial point of a given field line, in units of Earth radii, in the simplified case of a dipole magnetic field. However, care should be taken when calculating the above invariants, as the assumption of their adiabaticity is not valid everywhere in the Earth's magnetosphere. This is not clearly stated in state-of-the-art models that are widely used for the calculation of these invariants. In this paper, we compare the values of I and L* as calculated using LANLstar, an artificial neural network developed at the Los Alamos National Laboratory, SPENVIS, a space environment related online tool, IRBEM, a source code library dedicated to radiation belt modelling, and a 3-D particle tracing code that was developed for this purpose. We then attempt to quantify the variations between the calculations of I and L* of those models. The deviation between the results given by the models depends on particle starting position geocentric distance, pitch angle and magnetospheric conditions. Using the 3-D tracer we attempt to map the areas in the Earth's magnetosphere where I and L* can be assumed to be conserved by monitoring the constancy of I for energetic proton propagating forwards and backwards in time. These areas are found to be centered on the noon area and their size also depends on particle starting position geocentric distance, pitch angle and magnetospheric conditions.

  14. Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection

    PubMed Central

    Pagé Sabourin, Ariane; Nédélec, Yohann; Dumaine, Anne; Yotova, Vania; Johnson, Zachary P.; Lanford, Robert E.; Burge, Christopher B.

    2016-01-01

    The contribution of pre-mRNA processing mechanisms to the regulation of immune responses remains poorly studied despite emerging examples of their role as regulators of immune defenses. We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections. Here, we used mRNA sequencing to quantify gene expression and isoform abundances in primary macrophages from 60 individuals, before and after infection with Listeria monocytogenes and Salmonella typhimurium. In response to both bacteria we identified thousands of genes that significantly change isoform usage in response to infection, characterized by an overall increase in isoform diversity after infection. In response to both bacteria, we found global shifts towards (i) the inclusion of cassette exons and (ii) shorter 3’ UTRs, with near-universal shifts towards usage of more upstream polyadenylation sites. Using complementary data collected in non-human primates, we show that these features are evolutionarily conserved among primates. Following infection, we identify candidate RNA processing factors whose expression is associated with individual-specific variation in isoform abundance. Finally, by profiling microRNA levels, we show that 3’ UTRs with reduced abundance after infection are significantly enriched for target sites for particular miRNAs. These results suggest that the pervasive usage of shorter 3’ UTRs is a mechanism for particular genes to evade repression by immune-activated miRNAs. Collectively, our results suggest that dynamic changes in RNA processing may play key roles in the regulation of innate immune responses. PMID:27690314

  15. 76 FR 28954 - International Conservation and Management Measures Recognized by the United States

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-19

    ... Register in 1996 (61 FR 11751, March 22, 1996). Where applicable, the updated list of agreements is... Long Driftnets in the South Pacific Ocean; and International Convention for the Regulation of Whaling (Basic Instrument for the International Whaling Commission--IWC). Agreements To Which the United...

  16. Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and Ser250 phosphorylation in the conserved C-terminal regions.

    PubMed

    Iwashita, Shintaro; Suzuki, Takehiro; Yasuda, Takeshi; Nakashima, Kentaro; Sakamoto, Taiichi; Kohno, Toshiyuki; Takahashi, Ichiro; Kobayashi, Takayasu; Ohno-Iwashita, Yoshiko; Imajoh-Ohmi, Shinobu; Song, Si-Young; Dohmae, Naoshi

    2015-06-12

    The BCNT (Bucentaur) superfamily is classified by an uncharacteristic conserved sequence of ∼80 amino acids (aa) at the C-terminus, BCNT-C (the conserved C-terminal region of Bcnt/Cfdp1). Whereas the yeast Swc5 and Drosophila Yeti homologues play crucial roles in chromatin remodelling organization, mammalian Bcnt/Cfdp1 (craniofacial developmental protein 1) remains poorly understood. The protein, which lacks cysteine, is largely disordered and comprises an acidic N-terminal region, a lysine/glutamic acid/proline-rich 40 aa sequence and BCNT-C. It shows complex mobility on SDS/PAGE at ∼50 kDa, whereas its calculated molecular mass is ∼33 kDa. To characterize this mobility discrepancy and the effects of post-translational modifications (PTMs), we expressed various deleted His-Bcnt in E. coli and HEK cells and found that an acidic stretch in the N-terminal region is a main cause of the gel shift. Exogenous BCNT/CFDP1 constitutively expressed in HEK clones appears as a doublet at 49 and 47 kDa, slower than the protein expressed in Escherichia coli but faster than the endogenous protein on SDS/PAGE. Among seven in vivo phosphorylation sites, Ser(250), which resides in a region between disordered and ordered regions in BCNT-C, is heavily phosphorylated and detected predominantly in the 49 kDa band. Together with experiments involving treatment with phosphatases and Ser(250) substitutions, the results indicate that the complex behaviour of Bcnt/Cfdp1 on SDS/PAGE is caused mainly by an acidic stretch in the N-terminal region and Ser(250) phosphorylation in BCNT-C. Furthermore, Bcnt/Cfdp1 is acetylated in vitro by CREB-binding protein (CBP) and four lysine residues including Lys(268) in BCNT-C are also acetylated in vivo, revealing a protein regulated at multiple levels.

  17. Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and Ser250 phosphorylation in the conserved C-terminal regions

    PubMed Central

    Iwashita, Shintaro; Suzuki, Takehiro; Yasuda, Takeshi; Nakashima, Kentaro; Sakamoto, Taiichi; Kohno, Toshiyuki; Takahashi, Ichiro; Kobayashi, Takayasu; Ohno-Iwashita, Yoshiko; Imajoh-Ohmi, Shinobu; Song, Si-Young; Dohmae, Naoshi

    2015-01-01

    The BCNT (Bucentaur) superfamily is classified by an uncharacteristic conserved sequence of ∼80 amino acids (aa) at the C-terminus, BCNT-C (the conserved C-terminal region of Bcnt/Cfdp1). Whereas the yeast Swc5 and Drosophila Yeti homologues play crucial roles in chromatin remodelling organization, mammalian Bcnt/Cfdp1 (craniofacial developmental protein 1) remains poorly understood. The protein, which lacks cysteine, is largely disordered and comprises an acidic N-terminal region, a lysine/glutamic acid/proline-rich 40 aa sequence and BCNT-C. It shows complex mobility on SDS/PAGE at ∼50 kDa, whereas its calculated molecular mass is ∼33 kDa. To characterize this mobility discrepancy and the effects of post-translational modifications (PTMs), we expressed various deleted His–Bcnt in E. coli and HEK cells and found that an acidic stretch in the N-terminal region is a main cause of the gel shift. Exogenous BCNT/CFDP1 constitutively expressed in HEK clones appears as a doublet at 49 and 47 kDa, slower than the protein expressed in Escherichia coli but faster than the endogenous protein on SDS/PAGE. Among seven in vivo phosphorylation sites, Ser250, which resides in a region between disordered and ordered regions in BCNT-C, is heavily phosphorylated and detected predominantly in the 49 kDa band. Together with experiments involving treatment with phosphatases and Ser250 substitutions, the results indicate that the complex behaviour of Bcnt/Cfdp1 on SDS/PAGE is caused mainly by an acidic stretch in the N-terminal region and Ser250 phosphorylation in BCNT-C. Furthermore, Bcnt/Cfdp1 is acetylated in vitro by CREB-binding protein (CBP) and four lysine residues including Lys268 in BCNT-C are also acetylated in vivo, revealing a protein regulated at multiple levels. PMID:26182435

  18. Conservation genetics of North American freshwater mussels Amblema and Megalonaias

    USGS Publications Warehouse

    Mulvey, M.; Lydeard, C.; Pyer, D.L.; Hicks, K.M.; Brim-Box, J.; Williams, J.D.; Butler, R.S.

    1997-01-01

    Freshwater bivalves are among the most endangered groups of organisms in North America. Efforts to protect the declining mussel fauna are confounded by ambiguities associated with recognition of distinct evolutionary entities or species. This, in part, is due to the paucity of reliable morphological characters for differentiating taxa. We have employed allozymes and DNA sequence data to search for diagnosably distinct evolutionary entities within two problematic genera of unionid mussels, Amblema and Megalonaias. Within the genus Amblema three species are recognized based on our DNA sequence data for the mitochondrial 16S rRNA and allozyme data (Amblema neislerii, A. plicata, and A. elliotti). Only one taxonomically distinct entity is recognized within the genus Megalonaias—M. nervosa. Megalonaias boykiniana of the Apalachicolan Region is not diagnosable and does not warrant specific taxonomic status. Interestingly, Megalonaias from west of the Mississippi River, including the Mississippi, exhibited an allozyme and mtDNA haplotype frequency shift suggestive of an east-west dichotomy. The results of this study eliminate one subspecies of Amblema and increase the range of A. plicata. This should not affect the conservation status of “currently stable” assigned to A. plicata by Williams et al. (1993). The conservation status of A. elliotti needs to be reexamined because its distribution appears to be limited to the Coosa River System in Alabama and Georgia.

  19. Modeling opportunity costs of conservation in transitional landscapes.

    PubMed

    Naidoo, Robin; Adamowicz, Wiktor L

    2006-04-01

    Conservation scientists recognize the urgency of incorporating opportunity costs into conservation planning. Despite this, applications to date have been limited, perhaps partly because of the difficulty in determining costs in regions with limited data on land prices and ownership. We present methods for estimating opportunity costs of land preservation in landscapes or ecoregions that are a changing mix of agriculture and natural habitat. Our approach derives from the literature on estimating land values as opportunity costs of alternate land uses and takes advantage of general availability of necessary data, even in relatively data-poor regions. The methods integrate probabilities of habitat conversion with region-wide estimates of economic benefits from agricultural land uses and estimate land values with a discount rate to convert annual values into net present values. We applied our method in a landscape undergoing agricultural conversion in Paraguay. Our model of opportunity costs predicted an independent data set of land values and was consistent with implicit discount rates of 15-25%. Model-generated land values were strongly correlated with actual land values even after correcting for the effect of property size and proportion of property that was forested. We used the model to produce a map of opportunity costs and to estimate the costs of conserving forest within two proposed corridors in the landscape. This method can be applied to conservation planning in situations where natural habitat is currently being converted to market-oriented land uses. Incorporating not only biological attributes but also socioeconomic data can help in the design of efficient networks of protected areas that represent biodiversity at minimum costs.

  20. Formation and structure of a NAIP5-NLRC4 inflammasome induced by direct interactions with conserved N- and C-terminal regions of flagellin.

    PubMed

    Halff, Els F; Diebolder, Christoph A; Versteeg, Marian; Schouten, Arie; Brondijk, T Harma C; Huizinga, Eric G

    2012-11-01

    The NOD-like receptors NAIP5 and NLRC4 play an essential role in the innate immune response to the bacterial tail protein flagellin. Upon flagellin detection, NAIP5 and NLRC4 form a hetero-oligomeric inflammasome that induces caspase-1-dependent cell death. So far, both the mechanism of formation of the NAIP5-NLRC4 inflammasome and its structure are poorly understood. In this study we combine inflammasome reconstitution in HEK293 cells, purification of inflammasome components, and negative stain electron microscopy to address these issues. We find that a Salmonella typhimurium flagellin fragment comprising the D0 domain and the neighboring spoke region is able to co-precipitate NAIP5 and induce formation of the NAIP5-NLRC4 inflammasome. Comparison with smaller fragments indicates that flagellin recognition is mediated by its C-terminal residues as well as the spoke region. We reconstitute the inflammasome from purified flagellin, NAIP5, and NLRC4, thus proving that no other cellular components are required for its formation. Electron micrographs of the purified inflammasome provide unprecedented insight into its architecture, revealing disk-like complexes consisting of 11 or 12 protomers in which NAIP5 and NLRC4 appear to occupy equivalent positions. On the basis of our data, we propose a model for inflammasome formation wherein direct interaction of flagellin with a single NAIP5 induces the recruitment and progressive incorporation of NLRC4, resulting in the formation of a hetero-oligomeric inflammasome. PMID:23012363

  1. Conservation agriculture among small scale farmers in semi-arid region of Kenya does improve soil biological quality and soil organic carbon

    NASA Astrophysics Data System (ADS)

    Waweru, Geofrey; Okoba, Barrack; Cornelis, Wim

    2016-04-01

    The low food production in Sub-Saharan Africa (SSA) has been attributed to declining soil quality. This is due to soil degradation and fertility depletion resulting from unsustainable conventional farming practices such as continuous tillage, crop residue burning and mono cropping. To overcome these challenges, conservation agriculture (CA) is actively promoted. However, little has been done in evaluating the effect of each of the three principles of CA namely: minimum soil disturbance, maximum surface cover and diversified/crop rotation on soil quality in SSA. A study was conducted for three years from 2012 to 2015 in Laikipia East sub county in Kenya to evaluate the effect of tillage, surface cover and intercropping on a wide variety of physical, chemical and biological soil quality indicators, crop parameters and the field-water balance. This abstract reports on soil microbial biomass carbon (SMBC) and soil organic carbon (SOC). The experimental set up was a split plot design with tillage as main treatment (conventional till (CT), no-till (NT) and no-till with herbicide (NTH)), and intercropping and surface cover as sub treatment (intercropping maize with: beans, MB; beans and leucaena, MBL; beans and maize residues at 1.5 Mg ha-1 MBMu, and dolichos, MD). NT had significantly higher SMBC by 66 and 31% compared with CT and NTH respectively. SOC was significantly higher in NTH than CT and NT by 15 and 4%, respectively. Intercropping and mulching had significant effect on SMBC and SOC. MBMu resulted in higher SMBC by 31, 38 and 43%, and SOC by 9, 20 and 22% as compared with MBL, MD and MB, respectively. SMBC and SOC were significantly affected by the interaction between tillage, intercropping and soil cover with NTMBMu and NTHMBMu having the highest SMBC and SOC, respectively. We conclude that indeed tillage, intercropping and mulching substantially affect SMBC and SOC. On the individual components of CA, tillage and surface cover had the highest effect on SMBC and

  2. Attenuated Salmonella choleraesuis-mediated RNAi targeted to conserved regions against foot-and-mouth disease virus in guinea pigs and swine.

    PubMed

    Cong, Wei; Jin, Hong; Jiang, Chengda; Yan, Weiyao; Liu, Mingqiu; Chen, Jiulian; Zuo, Xiaoping; Zheng, Zhaoxin

    2010-01-01

    In this study, specific sequences within three genes (3D, VP4 and 2B) of the foot-and-mouth disease virus (FMDV) genome were determined to be effective RNAi targets. These sequences are highly conserved among different serotype viruses based on sequence analysis. Small interfering RNA (siRNA)-expressing plasmids (p3D-NT19, p3D-NT56, pVP4-NT19, pVP4-NT65 and p2B-NT25) were constructed to express siRNA targeting 3D, VP4 and 2B, respectively. The antiviral potential of these siRNA for various FMDV isolates was investigated in baby hamster kidney (BHK-21) cells and suckling mice. The results show that these siRNA inhibited virus yield 10- to 300-fold for different FMDV isolates of serotype O and serotype Asia I at 48 h post infection in BHK-21 cells compared to control cells. In suckling mice, p3D-NT56 and p2B-NT25 delayed the death of mice. Twenty percent to 40% of the animals that received a single siRNA dose survived 5 days post infection with serotype O or serotype Asia I. We used an attenuated Salmonella choleraesuis (C500) vaccine strain, to carry the plasmid that expresses siRNA directed against the polymerase gene 3D (p3D-NT56) of FMDV. We used guinea pigs to evaluate the inhibitory effects of recombinant S. cho (p3D-NT56/S. cho) on FMDV infection. The results show that 80% of guinea pigs inoculated with 10(9) CFU of p3D-NT56/S. cho and challenged 36 h later with 50 ID(50) of homologous FMDV were protected. We also measured the antiviral activity of p3D-NT56/S. cho in swine. The results indicate that 100% of the animals treated with 5 x 10(9) CFU of p3D-NT56/S. cho were protected in 9 days. PMID:20167192

  3. Perspective: Recognizing and rewarding clinical scholarship.

    PubMed

    Grigsby, R Kevin; Thorndyke, Luanne

    2011-01-01

    Faculty members in medical schools and academic medical centers are in a constant process of generating new knowledge. The cornerstone of academia--and academic medicine--is scholarship. Traditionally, tenure and/or academic promotion in the professorial ranks is awarded to those who meet institutional criteria in the missions of research, teaching, and service, including patient care. In the academic review process, priority is often placed on a record of demonstrated, consistent success in traditional laboratory research, also known as the scholarship of discovery. More recently, there has been greater recognition of other forms of scholarship: education, application, and integration. These forms of scholarship, although less recognized, also result in the generation of new knowledge. In an attempt to understand the breadth and scope of clinical scholarship, the authors searched the extant literature in academic medicine for a definition of clinical scholarship and expanded the search to disciplines outside of medicine. They found that succinct, discrete definitions of clinical scholarship have been published in other disciplines, but not in academic medicine. After reviewing definitions of clinical scholarship from other disciplines, adapting definitions of educational scholarship in academic medicine, and including qualities unique to clinical scholarship, the authors developed a framework for understanding clinical scholarship in academic medicine as a means for opening a dialogue within the academic medical community. This dialogue hopefully will lead to formulating a succinct, discrete definition of clinical scholarship that will allow greater recognition and reward for clinical scholars in the promotion and tenure process.

  4. Dogs recognize dog and human emotions.

    PubMed

    Albuquerque, Natalia; Guo, Kun; Wilkinson, Anna; Savalli, Carine; Otta, Emma; Mills, Daniel

    2016-01-01

    The perception of emotional expressions allows animals to evaluate the social intentions and motivations of each other. This usually takes place within species; however, in the case of domestic dogs, it might be advantageous to recognize the emotions of humans as well as other dogs. In this sense, the combination of visual and auditory cues to categorize others' emotions facilitates the information processing and indicates high-level cognitive representations. Using a cross-modal preferential looking paradigm, we presented dogs with either human or dog faces with different emotional valences (happy/playful versus angry/aggressive) paired with a single vocalization from the same individual with either a positive or negative valence or Brownian noise. Dogs looked significantly longer at the face whose expression was congruent to the valence of vocalization, for both conspecifics and heterospecifics, an ability previously known only in humans. These results demonstrate that dogs can extract and integrate bimodal sensory emotional information, and discriminate between positive and negative emotions from both humans and dogs. PMID:26763220

  5. Position, rotation, and intensity invariant recognizing method

    DOEpatents

    Ochoa, E.; Schils, G.F.; Sweeney, D.W.

    1987-09-15

    A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output plane to determine whether a particular target is present in the field of view. Preferably, a temporal pattern is imaged in the output plane with a optical detector having a plurality of pixels and a correlation coefficient for each pixel is determined by accumulating the intensity and intensity-square of each pixel. The orbiting of the constant response caused by the filter rotation is also preferably eliminated either by the use of two orthogonal mirrors pivoted correspondingly to the rotation of the filter or the attaching of a refracting wedge to the filter to remove the offset angle. Detection is preferably performed of the temporal pattern in the output plane at a plurality of different angles with angular separation sufficient to decorrelate successive frames. 1 fig.

  6. R